A command line interface for automatically extracting relevant metadata from code repositories (readme, configuration files, documentation, etc.).
-This repository is extracted from https://github.com/SciCodes/somef-core/issues
+This repository is extracted from https://github.com/SciCodes/somef-core/
+**Demo:** See a [demo running somef as a service](https://somef.linkeddata.es), through the [SOMEF-Vider tool](https://github.com/SoftwareUnderstanding/SOMEF-Vider/).
**Authors:** Daniel Garijo, Allen Mao, Miguel Ángel García Delgado, Haripriya Dharmala, Vedant Diwanji, Jiaying Wang, Aidan Kelley, Jenifer Tabita Ciuciu-Kiss, Luca Angheluta and Juanje Mendoza.
@@ -19,6 +18,13 @@ This repository is extracted from https://github.com/SciCodes/somef-core/issues
Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the following categories (if present), listed in alphabetical order:
- **Acknowledgement**: Text acknowledging funding sources or contributors
+- **Application domain**: The application domain of the repository. Current supported domains include: Astrophysics, Audio, Computer vision, Graphs, Natural language processing, Reinforcement learning, Semantc web, Sequential. Domains are not mutually exclusive. These domains have been extracted from [awesome lists](https://github.com/topics/awesome-list) and [Papers with code](https://paperswithcode.com/). Find more information in our [documentation](https://somef.readthedocs.io/en/latest/)
+- **Authors**: Person(s) or organization(s) responsible for the project. We recognize the following properties:
+ - Name: name of the author (including last name)
+ - Given name: First name of an author
+ - Family name: Last name of an author
+ - Email: email of author
+ - URL: website or ORCID associated with the author
- **Build file**: Build file(s) of the project. For example, files used to create a Docker image for the target software, package files, etc.
- **Citation**: Preferred citation as the authors have stated in their readme file. SOMEF recognizes Bibtex, Citation File Format files and other means by which authors cite their papers (e.g., by in-text citation). We aim to recognize the following properties:
- Title: Title of the publication
@@ -43,7 +49,7 @@ Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the follo
- **Forks url**: Links to forks made of the project
- **Full name**: Name + owner (owner/name)
- **Full title**: If the repository is a short name, we will attempt to extract the longer version of the repository name
-- **Identifier**: Identifier associated with the software (if any), such as Digital Object Identifiers. DOIs associated with publications will also be detected.
+- **Identifier**: Identifier associated with the software (if any), such as Digital Object Identifiers and Software Heritage identifiers (SWH). DOIs associated with publications will also be detected.
- **Images**: Images used to illustrate the software component
- **Installation instructions**: A set of instructions that indicate how to install a target repository
- **Invocation**: Execution command(s) needed to run a scientific software component
@@ -52,6 +58,7 @@ Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the follo
- **License**: License and usage terms of a software component
- **Logo**: Main logo used to represent the target software component
- **Name**: Name identifying a software component
+- **Ontologies**: URL and path to the ontology files present in the repository
- **Owner**: Name and type of the user or organization in charge of the repository
- **Package distribution**: Links to package sites like pypi in case the repository has a package available.
- **Package files**: Links to package files used to wrap the project in a package.
@@ -69,18 +76,23 @@ Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the follo
- Link to the tarball zip and code of the release
- **Repository status**: Repository status as it is described in [repostatus.org](https://www.repostatus.org/).
- **Requirements**: Pre-requisites and dependencies needed to execute a software component
+- **Run**: Running instructions of a software component. It may be wider than the `invocation` category, as it may include several steps and explanations.
+- **Runtime platform**: specifies runtime platform or script interpreter dependencies required to run the project..
+- **Script files**: Bash script files contained in the repository
- **Stargazers count**: Total number of stargazers of the project
- **Support**: Guidelines and links of where to obtain support for a software component
- **Support channels**: Help channels one can use to get support about the target software component
+- **Type**: type of software (command line application, notebook, ontology, scientific workflow, etc.)
- **Usage examples**: Assumptions and considerations recorded by the authors when executing a software component, or examples on how to use it
+- **Workflows**: URL and path to the computational workflow files present in the repository
We use different supervised classifiers, header analysis, regular expressions, the GitHub/Gitlab API to retrieve all these fields (more than one technique may be used for each field) and language specific metadata parsers (e.g., for package files). Each extraction records its provenance, with the confidence and technique used on each step. For more information check the [output format description](https://somef.readthedocs.io/en/latest/output/)
## Documentation
-The documentation for somef-core is available at [https://somef-core.readthedocs.io/en/latest/](https://somef-core.readthedocs.io/en/latest/)
+See full documentation for somef-core is available at [https://somef-core.readthedocs.io/en/latest/](https://somef-core.readthedocs.io/en/latest/)
-## Cite SOMEF and SOMEF-core:
+## Cite SOMEF-core:
Journal publication (preferred):
@@ -132,7 +144,7 @@ To run somef_core, please follow the next steps:
Clone this GitHub repository
```
-git clone https://github.com/KnowledgeCaptureAndDiscovery/somef-core.git
+git clone https://github.com/SciCodes/somef-core.git
```
We use [Poetry](https://python-poetry.org/) to ensure library compatibility. It can be installed as follows:
@@ -145,32 +157,36 @@ This option is recommended over installing Poetry with pip install.
Now Poetry will handle the installation of SOMEF-core and all its dependencies configured in the `toml` file.
-To test the correct installation of poetry run:
+To test the correct installation of poetry run (poetry version `> 2.0.0`):
```
poetry --version
```
-Install somef and all their dependencies.
+Install somef-core and all their dependencies.
```
cd /somef_core
poetry install
```
-Now we need to access our virtual environment, to do so you have to install the [poetry plugin shell](https://github.com/python-poetry/poetry-plugin-shell) and run the following command:
+Now we need to access our virtual environment, to do so you can run the following command:
+```bash
+poetry env activate
```
-pip install poetry-plugin-shell
-```
-After `shell` is set up, you can run the following comand to access the virtual environment
-```
-poetry shell
+If the environment is not active, paste the command shown when `poetry env activate` is run, typically something like the command below:
+
+```bash
+source /path_to_env/ENV_NAME/bin/activate
```
-Test SOMEF installation
+
+To learn more about poetry environment management, visit their official documentation [here](https://python-poetry.org/docs/managing-environments/).
+
+Test the SOMEF-core installation run:
```bash
-somef --help
+somef_core --help
```
If everything goes fine, you should see:
@@ -189,7 +205,31 @@ Commands:
## Installing through Docker
-We are working on this section
+We provide a Docker image with SOMEF already installed. To run through Docker, you may build the Dockerfile provided in the repository by running:
+
+```bash
+docker build -t somef .
+```
+
+Or just use the Docker image already built in [DockerHub](https://hub.docker.com/r/kcapd/somef):
+
+```bash
+docker pull kcapd/somef
+```
+
+Then, to run your image just type:
+
+```bash
+docker run --rm -it kcapd/somef
+```
+
+And you will be ready to use SOMEF (see section below). If you want to have access to the results we recommend [mounting a volume](https://docs.docker.com/storage/volumes/). For example, the following command will mount the current directory as the `out` folder in the Docker image:
+
+```bash
+docker run -it --rm -v $PWD/:/out kcapd/somef
+```
+
+If you move any files produced by somef into `/out`, then you will be able to see them in your current directory.
## Configure
@@ -228,6 +268,9 @@ Options:
-h, --help Show this message and exit.
```
+### Updating SOMEF
+
+If you update SOMEF to a newer version, we recommend you `configure` again the library (by running `somef configure`). The rationale is that different versions may rely on classifiers which may be stored in a different path.
## Usage
@@ -239,6 +282,7 @@ Usage: somef_core describe [OPTIONS]
Running the Command Line Interface
Options:
+ -t, --threshold FLOAT Threshold to classify the text [required]
Input: [mutually_exclusive, required]
-r, --repo_url URL Github/Gitlab Repository URL
-d, --doc_src PATH Path to the README file source
@@ -250,6 +294,15 @@ Options:
output will be in JSON
-c, --codemeta_out PATH Path to an output codemeta file
+ -g, --graph_out PATH Path to the output Knowledge Graph export
+ file. If supplied, the output will be a
+ Knowledge Graph, in the format given in the
+ --format option chosen (turtle, json-ld)
+
+ -f, --graph_format [turtle|json-ld]
+ If the --graph_out option is given, this is
+ the format that the graph will be stored in
+
-p, --pretty Pretty print the JSON output file so that it
is easy to compare to another JSON output
file.
@@ -264,6 +317,11 @@ Options:
will be stored at the
desired path
+ -all, --requirements_all Export all detected requirements, including
+ text and libraries (default).
+
+ -v, --requirements_v Export only requirements from structured
+ sources (pom.xml, requirements.txt, etc.)
-h, --help Show this message and exit.
```
@@ -273,9 +331,29 @@ Options:
The following command extracts all metadata available from [https://github.com/dgarijo/Widoco/](https://github.com/dgarijo/Widoco/).
```bash
-somef_core describe -r https://github.com/dgarijo/Widoco/ -o test.json
+somef_core describe -r https://github.com/dgarijo/Widoco/ -o test.json -t 0.8
```
+Try SOMEF in Binder with our sample notebook: [](https://mybinder.org/v2/gh/KnowledgeCaptureAndDiscovery/somef/HEAD?filepath=notebook%2FSOMEF%20Usage%20Example.ipynb)
+
## Contribute:
If you want to contribute with a pull request, please do so by submitting it to the `dev` branch.
+
+## Next features:
+
+To see upcoming features, please have a look at our [open issues](https://github.com/SciCodes/somef-core/issues) and [milestones](https://github.com/SciCodes/somef-core/milestones)
+
+## Extending SOMEF categories:
+
+To run a classifier with an additional category or remove an existing one, a corresponding path entry in the config.json should be provided and the category type should be added/removed in the category variable in `cli.py`.
+
+## Metadata Support
+
+SOMEF supports the extraction and analysis of metadata in package files of several programming languages. Current support includes: `setup.py` and `pyproject.toml` for Python, `pom.xml` for Java, `.gemspec` for Ruby, `DESCRIPTION` for R, `bower.json` for JavaScript, HTML or CSS, `.cabal` for Haskell, `cargo.toml` for RUST, `composer` for PHP, `.juliaProject.toml` for Julia , `AUTHORS`, `codemeta.json`, `publiccode.yml`, `dockerfile` and `citation.cff`
+This includes identifying dependencies, runtime requirements, and development tools specified in project configuration files.
+
+## Limitations
+
+SOMEF is designed to work primarily with repositories written in English.
+Repositories in other languages may not be processed as effectively, and results could be incomplete or less accurate.
diff --git a/docs/author 2.md b/docs/author 2.md
new file mode 100644
index 0000000..fd00768
--- /dev/null
+++ b/docs/author 2.md
@@ -0,0 +1,113 @@
+The following metadata fields can be extracted from a AUTHORS file.
+These fields are defined in the [Authors file specification](https://opensource.google/documentation/reference/releasing/authors/), and are mapped according to the [CodeMeta crosswalk for AUTHORS files](https://github.com/codemeta/codemeta/blob/master/crosswalks/codemeta-V2.csv).
+
+| Software metadata category | SOMEF metadata JSON path | AUTHORS metadata file field |
+|-------------------------------|---------------------------------------------|------------------------------|
+| authors - value | authors[i].result.value | *(1)* value |
+| authors - name | authors[i].result.name | *(2)* name |
+| authors - email | authors[i].result.email | *(3)* email |
+| authors - given name | authors[i].result.given_name | *(4)* if type person |
+| authors - last name | authors[i].result.last_name | *(5)* if type person |
+
+---
+
+*(1)*
+- Regex: line.strip()
+- Example: `Jane Doe [🔍](./author.md)
| [📄](https://opensource.google/documentation/reference/releasing/authors/)| |[Example](https://gist.github.com/juliengdt/91d80c812e41be891dcf) |
+| `pom.xml` | Java / Maven | Project configuration file containing metadata and dependencies | [🔍](./pom.md) | [📄](https://maven.apache.org/pom.html) | [4.0.0](https://maven.apache.org/xsd/maven-4.0.0.xsd) | [Example](https://github.com/apache/maven/blob/master/pom.xml) |
+| `bower.json` | JavaScript (Bower) | Package descriptor used for configuring packages that can be used as a dependency for Bower-managed front-end projects. |
[🔍](./bower.md)
| [📄](https://github.com/bower/spec/blob/master/json.md)| |[Example](https://github.com/juanjemdIos/somef/blob/master/src/somef/test/test_data/repositories/js-template/bower.json) |
+| `package.json` | JavaScript / Node.js | Defines metadata, scripts, and dependencies for Node.js projects | [🔍](./packagejson.md)| [📄](https://docs.npmjs.com/cli/v10/configuring-npm/package-json)| 10.9.4|[Example](https://github.com/npm/cli/blob/latest/package.json) |
+| `codemeta.json` | JSON-LD | Metadata file for research software using JSON-LD vocabulary |
+
+ org.apache.maven
+ maven-model
+ 3.9.0
+
+
+```
+
+
+The following Python code snippet show the logic used by the SOMEF parser to transform the XML elements to the JSON metadata structure:
+
+```
+ if project_data["dependencies"]:
+ for dependency in project_data["dependencies"]:
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": f'{dependency.get("groupId", "")}.{dependency.get("artifactId", "")}'.strip("."),
+ "name": dependency.get("artifactId", ""),
+ "version": dependency.get("version", ""),
+ "type": constants.SOFTWARE_APPLICATION
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+```
+
+
+After applying the mapping logic, the metadata for the dependency is stored under the requirements category (CAT_REQUIREMENTS in this case) with the following JSON structure:
+
+``` somef json
+
+ "requirements": [
+ {
+ "result": {
+ "value": "org.apache.maven.maven-model",
+ "name": "maven-model",
+ "version": "3.9.0",
+ "type": "Software_application"
+ },
+ "confidence": 1,
+ "technique": "code_parser",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/pom.xml"
+ },
+```
diff --git a/docs/supported_metadata_files.md b/docs/supported_metadata_files.md
new file mode 100644
index 0000000..36c8700
--- /dev/null
+++ b/docs/supported_metadata_files.md
@@ -0,0 +1,112 @@
+# Supported Metadata Files
+
+This project supports extracting metadata from specific types of files commonly used to declare authorship and contribution in open source repositories.
+
+
+## Supported Metadata Files in SOMEF
+
+SOMEF can extract metadata from a wide range of files commonly found in software repositories. Below is a list of supported file types, along with clickable examples from real projects:
+
+| File Name | Language | Description | Detail | Source Spec. | Version Spec.| Example |
+|--------------------|----------------|-------------|--------|--------------|--------------|---------|
+| `AUTHORS.md` | General | Lists contributors, authors, and affiliations relevant to the project |
[🔍](./codemetajson.md)
| [📄](https://github.com/codemeta/codemeta/blob/master/crosswalk.csv)| [v3.0](https://w3id.org/codemeta/3.0)|[Example](https://github.com/codemeta/codemeta/blob/master/codemeta.json) |
+| `readme.me` | Markdown | Main documentation file of repository | [🔍](./readmefile.md)
| | |[Example](https://github.com/KnowledgeCaptureAndDiscovery/somef/blob/master/README.md) |
+| `composer.json` | PHP | Manifest file serves as the package descriptor used in PHP projects. | [🔍](./composer.md)
| [📄](https://getcomposer.org/doc/04-schema.md)| [2.8.12](https://getcomposer.org/changelog/2.8.12)|[Example](https://github.com/composer/composer/blob/main/composer.json) |
+| `juliaProject.toml` | Python | Defines the package metadata and dependencies for Julia projects, used by the Pkg package manager.| [🔍](./julia.md)
| [📄](https://docs.julialang.org/en/v1/)| |[Example](https://github.com/JuliaLang/TOML.jl/blob/master/Project.toml) |
+| `pyproject.toml` | Python | Modern Python project configuration file used by tools like Poetry and Flit | [🔍](./pyprojecttoml.md)
| [📄](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/)| |[Example](https://github.com/KnowledgeCaptureAndDiscovery/somef/blob/master/pyproject.toml) |
+| `requirements.txt` | Python | Lists Python package dependencies | [🔍](./requirementstxt.md)
| [📄](https://pip.pypa.io/en/stable/reference/requirements-file-format/)| 25.2|[Example](https://github.com/oeg-upm/FAIR-Research-Object/blob/main/requirements.txt) |
+| `setup.py` | Python | Package file format used in python projects | [🔍](./setuppy.md)
| [📄](https://packaging.python.org/en/latest/guides/distributing-packages-using-setuptools/#setup-args)| |[Example](https://github.com/oeg-upm/soca/blob/main/setup.py) |
+| `DESCRIPTION` | R | Metadata file for R packages including title, author, and version | [🔍](./description.md)
| [📄](https://r-pkgs.org/description.html)| | [Example](https://github.com/cran/ggplot2/blob/master/DESCRIPTION) |
+| `*.gemspec` | Ruby | Manifest file serves as the package descriptor used in Ruby gem projects. | [🔍](./gemspec.md)
| [📄](https://guides.rubygems.org/specification-reference/)| |[Example](https://github.com/rubygems/rubygems/blob/master/bundler/bundler.gemspec) |
+| `cargo.toml` | Rust | Manifest file serves as the package descriptor used in Rust projects | [🔍](./cargo.md)
| [📄](https://doc.rust-lang.org/cargo/reference/manifest.html)| |[Example](https://github.com/rust-lang/cargo/blob/master/Cargo.toml) |
+| `*.cabal` | Haskell | Manifest file serving as the package descriptor for Haskell projects.| [🔍](./cabal.md)
| [📄](https://cabal.readthedocs.io/en/3.10/cabal-package.html)| |[Example](https://github.com/haskell/cabal/blob/master/Cabal/Cabal.cabal) |
+| `dockerfile` | Dockerfile | Build specification file for container images that can include software metadata via LABEL instructions (OCI specification).| [🔍](./dockerfiledoc.md)
| [📄](https://docs.docker.com/reference/dockerfile/)| |[Example](https://github.com/FairwindsOps/nova/blob/master/Dockerfile) |
+| `publiccode.yml` | YAML | YAML metadata file for public sector software projects| [🔍](./publiccode.md)
| [📄](https://yml.publiccode.tools//)| |[Example](https://github.com/maykinmedia/objects-api/blob/master/publiccode.yaml) |
+
+> **Note:** The general principles behind metadata mapping in SOMEF are based on the [CodeMeta crosswalk](https://github.com/codemeta/codemeta/blob/master/crosswalk.csv) and the [CodeMeta JSON-LD context](https://github.com/codemeta/codemeta/blob/master/codemeta.jsonld).
+> However, each supported file type may have specific characteristics and field interpretations.
+
+
+
+
+## Types of metadata in SOMEF
+
+| Type | Metadata Category |
+|----------------------|---------------------------|
+| Agent | authors |
+| Keywords | keywords |
+| License | license |
+| Release | version |
+| Software_application | requirements |
+| String | description |
+| String | name |
+| String | package_id |
+| String | runtime_platform |
+| Url | has_package_file |
+| Url | homepage |
+| Url | issue_tracker |
+| Url | package_distribution |
+
+
+## Example: Dependency Metadata Extraction from Configuration Files
+
+SOMEF parses configuration files like `pom.xml` to extract **structured metadata** about software dependencies and other requirements.
+
+---
+
+### Source File: Snippet from `Widoco/pom.xml`
+
+Below is the XML fragment for the Maven dependency that is being parsed:
+
+```xml
+[🔍](./author.md)
| [📄](https://opensource.google/documentation/reference/releasing/authors/)| |[Example](https://gist.github.com/juliengdt/91d80c812e41be891dcf) |
+| `pom.xml` | Java / Maven | Project configuration file containing metadata and dependencies | [🔍](./pom.md) | [📄](https://maven.apache.org/pom.html) | [4.0.0](https://maven.apache.org/xsd/maven-4.0.0.xsd) | [Example](https://github.com/apache/maven/blob/master/pom.xml) |
+| `bower.json` | JavaScript (Bower) | Package descriptor used for configuring packages that can be used as a dependency for Bower-managed front-end projects. |
[🔍](./bower.md)
| [📄](https://github.com/bower/spec/blob/master/json.md)| |[Example](https://github.com/juanjemdIos/somef/blob/master/src/somef/test/test_data/repositories/js-template/bower.json) |
+| `package.json` | JavaScript / Node.js | Defines metadata, scripts, and dependencies for Node.js projects | [🔍](./packagejson.md)| [📄](https://docs.npmjs.com/cli/v10/configuring-npm/package-json)| 10.9.4|[Example](https://github.com/npm/cli/blob/latest/package.json) |
+| `codemeta.json` | JSON-LD | Metadata file for research software using JSON-LD vocabulary |
+
+ org.apache.maven
+ maven-model
+ 3.9.0
+
+
+```
+
+
+The following Python code snippet show the logic used by the SOMEF parser to transform the XML elements to the JSON metadata structure:
+
+```
+ if project_data["dependencies"]:
+ for dependency in project_data["dependencies"]:
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": f'{dependency.get("groupId", "")}.{dependency.get("artifactId", "")}'.strip("."),
+ "name": dependency.get("artifactId", ""),
+ "version": dependency.get("version", ""),
+ "type": constants.SOFTWARE_APPLICATION
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+```
+
+
+After applying the mapping logic, the metadata for the dependency is stored under the requirements category (CAT_REQUIREMENTS in this case) with the following JSON structure:
+
+``` somef json
+
+ "requirements": [
+ {
+ "result": {
+ "value": "org.apache.maven.maven-model",
+ "name": "maven-model",
+ "version": "3.9.0",
+ "type": "Software_application"
+ },
+ "confidence": 1,
+ "technique": "code_parser",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/pom.xml"
+ },
+```
diff --git a/docs/usage.md b/docs/usage.md
index 7b51d73..89f3102 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -1,4 +1,4 @@
-To see the available options for SOMEF-core:
+To see the available options for SOMEF:
```bash
somef_core --help
@@ -52,7 +52,7 @@ Options:
file.
-m, --missing JSON report with the missing metadata fields
- SOMEF-core was not able to find. The report will
+ SOMEF was not able to find. The report will
be placed in $PATH_missing.json, where
$PATH is -o, -c or -g.
-kt, --keep_tmp PATH SOMEF will NOT delete the temporary folder
diff --git a/mkdocs.yml b/mkdocs.yml
index e3e2801..6000586 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -4,6 +4,23 @@ nav:
- Install: install.md
- Usage: usage.md
- Output: output.md
+ - Supported metadata files: supported_metadata_files.md
+ - Supported languages: supported_languages.md
+ # - Authors: author.md
+ # - Bower: bower.md
+ # - Cabal: cabal.md
+ # - Cargo: cargo.md
+ # - Codemeta: codemetajson.md
+ # - Composer: composer.md
+ # - Description: description.md
+ # - Gemespec: gemspec.md
+ # - Julia Projects: julia.md
+ # - Package JSON: packagejson.md
+ # - Pom: pom.md
+ # - Pyproject: pyprojecttoml.md
+ # - Requirements: requirementstxt.md
+ # - Setup: setuppy.md
+
theme:
name: material
diff --git a/output 2.json-ld b/output 2.json-ld
new file mode 100644
index 0000000..1944e63
--- /dev/null
+++ b/output 2.json-ld
@@ -0,0 +1,263 @@
+@prefix ns1: .
+@prefix ns2: .
+
+ a ns2:Person ;
+ ns2:name "tpronk" .
+
+ a ns2:CreativeWork ;
+ ns1:name "GNU Affero General Public License v3.0" ;
+ ns1:url "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/LICENSE"^^xsd:anyURI .
+
+ a ns1:Software ;
+ ns2:license ;
+ ns1:contactDetails """Contact person responsible for maintaining a software component
+""" ;
+ ns1:contributingGuidelines """These guidelines were copied from [PychoPy](https://github.com/psychopy/psychopy/edit/dev/CONTRIBUTING.md)
+
+# Have you ever contributed to an Open Source project?
+Your first contribution can be a bit intimidating, but feel free to give it a try. If you get stuck, don't hesitate to ask for help in our [developer forum](https://discourse.psychopy.org/c/dev). This is also a good place to pitch your idea. Next up:
+* **I won't program it myself.** Please file a [GitHub issue](https://github.com/psychopy/psychopy/issues).
+* **I'd like to take a shot.** Read on to find out how!
+
+# How to contribute
+Contributing to PsychoPy consists of four steps:
+1. Getting your own copy
+2. Making your changes
+3. Committing your changes
+4. Submitting a Pull Request
+
+## 1. Getting your own copy of the PsychoPy codebase
+To be sure your improvements can easily be integrated, follow these steps:
+1. **Make a [fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) of the [PsychoPy repo](https://github.com/psychopy/psychopy).** This provides you with your own copy of the PsychoPy source code.
+2. **Inside your fork, make a new [branch](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-branches) for the feature you've got in mind.** If you'd like to fix a bug, base your new branch on the *release* branch. If you'd like to add a new feature, base it on the *dev* branch. We tend to name branches after the feature we're building. For example `olfactory_component`.
+3. **Clone your fork to your hard drive.** Next, switch to the new branch and you're all set up!
+
+Look [here](https://www.psychopy.org/developers/repository.html) to see how the PsychoPy repo is organized.
+
+## 2. Making your changes
+To help you get started with modifying PsychoPy, we've got some [developer guides](https://www.psychopy.org/developers/index.html). To try out your modified PsychoPy, do a [developer's install](https://www.psychopy.org/download.html#developers-install).
+
+## 3. Committing your changes
+Once you're happy with your changes, commit them to your GitHub repo. Please use the tags below in your commit and add an informative message.
+ - **BF:** bug fix. For fixing bugs in the *release* branch.
+ - **FF:** ‘feature’ fix. For fixing bugs in the *dev* branch.
+ - **RF:** refactoring
+ - **NF:** new feature
+ - **ENH:** enhancement (to existing code, but don't worry too much about the difference between this and NF)
+ - **DOC:** for all kinds of documentation related commits
+ - **TEST:** for adding or changing tests
+
+## 4. File a Pull Request
+Once you're done, it's time to add it to the central PsychoPy source code. File a [Pull Request](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request) from your own fork and branch to the PsychoPy repo. Be sure to target the right branch in PsychoPy (*release* or *dev*). Thanks for contributing!
+""" ;
+ ns1:contributionInstructions """These guidelines were copied from [PychoPy](https://github.com/psychopy/psychopy/edit/dev/CONTRIBUTING.md)
+
+# Have you ever contributed to an Open Source project?
+Your first contribution can be a bit intimidating, but feel free to give it a try. If you get stuck, don't hesitate to ask for help in our [developer forum](https://discourse.psychopy.org/c/dev). This is also a good place to pitch your idea. Next up:
+* **I won't program it myself.** Please file a [GitHub issue](https://github.com/psychopy/psychopy/issues).
+* **I'd like to take a shot.** Read on to find out how!
+
+# How to contribute
+Contributing to PsychoPy consists of four steps:
+1. Getting your own copy
+2. Making your changes
+3. Committing your changes
+4. Submitting a Pull Request
+
+## 1. Getting your own copy of the PsychoPy codebase
+To be sure your improvements can easily be integrated, follow these steps:
+1. **Make a [fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) of the [PsychoPy repo](https://github.com/psychopy/psychopy).** This provides you with your own copy of the PsychoPy source code.
+2. **Inside your fork, make a new [branch](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-branches) for the feature you've got in mind.** If you'd like to fix a bug, base your new branch on the *release* branch. If you'd like to add a new feature, base it on the *dev* branch. We tend to name branches after the feature we're building. For example `olfactory_component`.
+3. **Clone your fork to your hard drive.** Next, switch to the new branch and you're all set up!
+
+Look [here](https://www.psychopy.org/developers/repository.html) to see how the PsychoPy repo is organized.
+
+## 2. Making your changes
+To help you get started with modifying PsychoPy, we've got some [developer guides](https://www.psychopy.org/developers/index.html). To try out your modified PsychoPy, do a [developer's install](https://www.psychopy.org/download.html#developers-install).
+
+## 3. Committing your changes
+Once you're happy with your changes, commit them to your GitHub repo. Please use the tags below in your commit and add an informative message.
+ - **BF:** bug fix. For fixing bugs in the *release* branch.
+ - **FF:** ‘feature’ fix. For fixing bugs in the *dev* branch.
+ - **RF:** refactoring
+ - **NF:** new feature
+ - **ENH:** enhancement (to existing code, but don't worry too much about the difference between this and NF)
+ - **DOC:** for all kinds of documentation related commits
+ - **TEST:** for adding or changing tests
+
+## 4. File a Pull Request
+Once you're done, it's time to add it to the central PsychoPy source code. File a [Pull Request](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request) from your own fork and branch to the PsychoPy repo. Be sure to target the right branch in PsychoPy (*release* or *dev*). Thanks for contributing!
+"""^^xsd:anyURI ;
+ ns1:dateCreated "2023-11-28T12:30:28+00:00"^^xsd:dateTime ;
+ ns1:dateModified "2023-12-12T15:35:54+00:00"^^xsd:dateTime ;
+ ns1:description "This repo aims to provide values for each metadata field that SOMEF (v0.9.4) can extract" ;
+ ns1:hasAcknowledgments """This demonstration repo was created during the maSMP hackathon at [ZB MED](https://www.zbmed.de/en) sponsored by [NFDI4DataScience](https://www.nfdi4datascience.de). NFDI4DataScience is a consortium funded by the German Research Foundation (DFG), project number 460234259.
+""" ;
+ ns1:hasBuildFile "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/Dockerfile"^^xsd:anyURI ;
+ ns1:hasCodeOfConduct """# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+ and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+ overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+ advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+ address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.
+""" ;
+ ns1:hasDownloadUrl "https://github.com/tpronk/somef-demo-repo/releases"^^xsd:anyURI ;
+ ns1:hasExample "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/executable_example.ipynb"^^xsd:anyURI ;
+ ns1:hasExecutableInstructions """There is no code in this repo that can be run.
+""" ;
+ ns1:hasExecutableNotebook "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/executable_example.ipynb" ;
+ ns1:hasFAQ """Frequently asked questions about a software component
+""" ;
+ ns1:hasInstallationInstructions """##Installation instructions
+A set of instructions that indicate how to install a target repository
+""" ;
+ ns1:hasLongName "somef-demo-repo" ;
+ ns1:hasSourceCode ;
+ ns1:hasSupportScriptLocation "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/script_file.sh"^^xsd:anyURI ;
+ ns1:hasUsageNotes """##Usage examples
+Assumptions and considerations recorded by the authors when executing a software component, or examples on how to use it.
+""" ;
+ ns1:hasVersion ;
+ ns1:identifier "https://zenodo.org/badge/latestdoi/450496579"^^xsd:anyURI ;
+ ns1:issueTracker "https://api.github.com/repos/tpronk/somef-demo-repo/issues"^^xsd:anyURI ;
+ ns1:keywords "topic1, topic2, topic3" ;
+ ns1:name "tpronk/somef-demo-repo" ;
+ ns1:readme "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/README.md"^^xsd:anyURI ;
+ ns1:softwareRequirements """Pre-requisites and dependencies needed to execute a software component.
+""" ;
+ ns1:supportDetails """Guidelines and links of where to obtain support for a software component
+""",
+ """[](https://gitter.im/OpenGeoscience/geonotebook)
+""" .
+
+ a ns2:SoftwareSourceCode ;
+ ns1:codeRepository "https://github.com/tpronk/somef-demo-repo"^^xsd:anyURI ;
+ ns1:name "tpronk/somef-demo-repo" ;
+ ns1:programmingLanguage "Common Workflow Language",
+ "Dockerfile",
+ "Jupyter Notebook",
+ "Shell" .
+
diff --git a/output.json-ld b/output.json-ld
new file mode 100644
index 0000000..1944e63
--- /dev/null
+++ b/output.json-ld
@@ -0,0 +1,263 @@
+@prefix ns1: .
+@prefix ns2: .
+
+ a ns2:Person ;
+ ns2:name "tpronk" .
+
+ a ns2:CreativeWork ;
+ ns1:name "GNU Affero General Public License v3.0" ;
+ ns1:url "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/LICENSE"^^xsd:anyURI .
+
+ a ns1:Software ;
+ ns2:license ;
+ ns1:contactDetails """Contact person responsible for maintaining a software component
+""" ;
+ ns1:contributingGuidelines """These guidelines were copied from [PychoPy](https://github.com/psychopy/psychopy/edit/dev/CONTRIBUTING.md)
+
+# Have you ever contributed to an Open Source project?
+Your first contribution can be a bit intimidating, but feel free to give it a try. If you get stuck, don't hesitate to ask for help in our [developer forum](https://discourse.psychopy.org/c/dev). This is also a good place to pitch your idea. Next up:
+* **I won't program it myself.** Please file a [GitHub issue](https://github.com/psychopy/psychopy/issues).
+* **I'd like to take a shot.** Read on to find out how!
+
+# How to contribute
+Contributing to PsychoPy consists of four steps:
+1. Getting your own copy
+2. Making your changes
+3. Committing your changes
+4. Submitting a Pull Request
+
+## 1. Getting your own copy of the PsychoPy codebase
+To be sure your improvements can easily be integrated, follow these steps:
+1. **Make a [fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) of the [PsychoPy repo](https://github.com/psychopy/psychopy).** This provides you with your own copy of the PsychoPy source code.
+2. **Inside your fork, make a new [branch](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-branches) for the feature you've got in mind.** If you'd like to fix a bug, base your new branch on the *release* branch. If you'd like to add a new feature, base it on the *dev* branch. We tend to name branches after the feature we're building. For example `olfactory_component`.
+3. **Clone your fork to your hard drive.** Next, switch to the new branch and you're all set up!
+
+Look [here](https://www.psychopy.org/developers/repository.html) to see how the PsychoPy repo is organized.
+
+## 2. Making your changes
+To help you get started with modifying PsychoPy, we've got some [developer guides](https://www.psychopy.org/developers/index.html). To try out your modified PsychoPy, do a [developer's install](https://www.psychopy.org/download.html#developers-install).
+
+## 3. Committing your changes
+Once you're happy with your changes, commit them to your GitHub repo. Please use the tags below in your commit and add an informative message.
+ - **BF:** bug fix. For fixing bugs in the *release* branch.
+ - **FF:** ‘feature’ fix. For fixing bugs in the *dev* branch.
+ - **RF:** refactoring
+ - **NF:** new feature
+ - **ENH:** enhancement (to existing code, but don't worry too much about the difference between this and NF)
+ - **DOC:** for all kinds of documentation related commits
+ - **TEST:** for adding or changing tests
+
+## 4. File a Pull Request
+Once you're done, it's time to add it to the central PsychoPy source code. File a [Pull Request](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request) from your own fork and branch to the PsychoPy repo. Be sure to target the right branch in PsychoPy (*release* or *dev*). Thanks for contributing!
+""" ;
+ ns1:contributionInstructions """These guidelines were copied from [PychoPy](https://github.com/psychopy/psychopy/edit/dev/CONTRIBUTING.md)
+
+# Have you ever contributed to an Open Source project?
+Your first contribution can be a bit intimidating, but feel free to give it a try. If you get stuck, don't hesitate to ask for help in our [developer forum](https://discourse.psychopy.org/c/dev). This is also a good place to pitch your idea. Next up:
+* **I won't program it myself.** Please file a [GitHub issue](https://github.com/psychopy/psychopy/issues).
+* **I'd like to take a shot.** Read on to find out how!
+
+# How to contribute
+Contributing to PsychoPy consists of four steps:
+1. Getting your own copy
+2. Making your changes
+3. Committing your changes
+4. Submitting a Pull Request
+
+## 1. Getting your own copy of the PsychoPy codebase
+To be sure your improvements can easily be integrated, follow these steps:
+1. **Make a [fork](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) of the [PsychoPy repo](https://github.com/psychopy/psychopy).** This provides you with your own copy of the PsychoPy source code.
+2. **Inside your fork, make a new [branch](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-branches) for the feature you've got in mind.** If you'd like to fix a bug, base your new branch on the *release* branch. If you'd like to add a new feature, base it on the *dev* branch. We tend to name branches after the feature we're building. For example `olfactory_component`.
+3. **Clone your fork to your hard drive.** Next, switch to the new branch and you're all set up!
+
+Look [here](https://www.psychopy.org/developers/repository.html) to see how the PsychoPy repo is organized.
+
+## 2. Making your changes
+To help you get started with modifying PsychoPy, we've got some [developer guides](https://www.psychopy.org/developers/index.html). To try out your modified PsychoPy, do a [developer's install](https://www.psychopy.org/download.html#developers-install).
+
+## 3. Committing your changes
+Once you're happy with your changes, commit them to your GitHub repo. Please use the tags below in your commit and add an informative message.
+ - **BF:** bug fix. For fixing bugs in the *release* branch.
+ - **FF:** ‘feature’ fix. For fixing bugs in the *dev* branch.
+ - **RF:** refactoring
+ - **NF:** new feature
+ - **ENH:** enhancement (to existing code, but don't worry too much about the difference between this and NF)
+ - **DOC:** for all kinds of documentation related commits
+ - **TEST:** for adding or changing tests
+
+## 4. File a Pull Request
+Once you're done, it's time to add it to the central PsychoPy source code. File a [Pull Request](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request) from your own fork and branch to the PsychoPy repo. Be sure to target the right branch in PsychoPy (*release* or *dev*). Thanks for contributing!
+"""^^xsd:anyURI ;
+ ns1:dateCreated "2023-11-28T12:30:28+00:00"^^xsd:dateTime ;
+ ns1:dateModified "2023-12-12T15:35:54+00:00"^^xsd:dateTime ;
+ ns1:description "This repo aims to provide values for each metadata field that SOMEF (v0.9.4) can extract" ;
+ ns1:hasAcknowledgments """This demonstration repo was created during the maSMP hackathon at [ZB MED](https://www.zbmed.de/en) sponsored by [NFDI4DataScience](https://www.nfdi4datascience.de). NFDI4DataScience is a consortium funded by the German Research Foundation (DFG), project number 460234259.
+""" ;
+ ns1:hasBuildFile "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/Dockerfile"^^xsd:anyURI ;
+ ns1:hasCodeOfConduct """# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+ and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+ overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+ advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+ address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.
+""" ;
+ ns1:hasDownloadUrl "https://github.com/tpronk/somef-demo-repo/releases"^^xsd:anyURI ;
+ ns1:hasExample "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/executable_example.ipynb"^^xsd:anyURI ;
+ ns1:hasExecutableInstructions """There is no code in this repo that can be run.
+""" ;
+ ns1:hasExecutableNotebook "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/executable_example.ipynb" ;
+ ns1:hasFAQ """Frequently asked questions about a software component
+""" ;
+ ns1:hasInstallationInstructions """##Installation instructions
+A set of instructions that indicate how to install a target repository
+""" ;
+ ns1:hasLongName "somef-demo-repo" ;
+ ns1:hasSourceCode ;
+ ns1:hasSupportScriptLocation "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/script_file.sh"^^xsd:anyURI ;
+ ns1:hasUsageNotes """##Usage examples
+Assumptions and considerations recorded by the authors when executing a software component, or examples on how to use it.
+""" ;
+ ns1:hasVersion ;
+ ns1:identifier "https://zenodo.org/badge/latestdoi/450496579"^^xsd:anyURI ;
+ ns1:issueTracker "https://api.github.com/repos/tpronk/somef-demo-repo/issues"^^xsd:anyURI ;
+ ns1:keywords "topic1, topic2, topic3" ;
+ ns1:name "tpronk/somef-demo-repo" ;
+ ns1:readme "https://raw.githubusercontent.com/tpronk/somef-demo-repo/main/README.md"^^xsd:anyURI ;
+ ns1:softwareRequirements """Pre-requisites and dependencies needed to execute a software component.
+""" ;
+ ns1:supportDetails """Guidelines and links of where to obtain support for a software component
+""",
+ """[](https://gitter.im/OpenGeoscience/geonotebook)
+""" .
+
+ a ns2:SoftwareSourceCode ;
+ ns1:codeRepository "https://github.com/tpronk/somef-demo-repo"^^xsd:anyURI ;
+ ns1:name "tpronk/somef-demo-repo" ;
+ ns1:programmingLanguage "Common Workflow Language",
+ "Dockerfile",
+ "Jupyter Notebook",
+ "Shell" .
+
diff --git a/poetry.lock b/poetry.lock
index 9bdb2f2..aa17c3d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,46 +2,38 @@
[[package]]
name = "anyascii"
-version = "0.3.2"
+version = "0.3.3"
description = "Unicode to ASCII transliteration"
optional = false
python-versions = ">=3.3"
groups = ["main"]
files = [
- {file = "anyascii-0.3.2-py3-none-any.whl", hash = "sha256:3b3beef6fc43d9036d3b0529050b0c48bfad8bc960e9e562d7223cfb94fe45d4"},
- {file = "anyascii-0.3.2.tar.gz", hash = "sha256:9d5d32ef844fe225b8bc7cba7f950534fae4da27a9bf3a6bea2cb0ea46ce4730"},
+ {file = "anyascii-0.3.3-py3-none-any.whl", hash = "sha256:f5ab5e53c8781a36b5a40e1296a0eeda2f48c649ef10c3921c1381b1d00dee7a"},
+ {file = "anyascii-0.3.3.tar.gz", hash = "sha256:c94e9dd9d47b3d9494eca305fef9447d00b4bf1a32aff85aa746fa3ec7fb95c3"},
]
[[package]]
name = "attrs"
-version = "25.3.0"
+version = "25.4.0"
description = "Classes Without Boilerplate"
optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
groups = ["main"]
files = [
- {file = "attrs-25.3.0-py3-none-any.whl", hash = "sha256:427318ce031701fea540783410126f03899a97ffc6f61596ad581ac2e40e3bc3"},
- {file = "attrs-25.3.0.tar.gz", hash = "sha256:75d7cefc7fb576747b2c81b4442d4d4a1ce0900973527c011d1030fd3bf4af1b"},
+ {file = "attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373"},
+ {file = "attrs-25.4.0.tar.gz", hash = "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11"},
]
-[package.extras]
-benchmark = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-cov = ["cloudpickle ; platform_python_implementation == \"CPython\"", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-dev = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pre-commit-uv", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier"]
-tests = ["cloudpickle ; platform_python_implementation == \"CPython\"", "hypothesis", "mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-xdist[psutil]"]
-tests-mypy = ["mypy (>=1.11.1) ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\"", "pytest-mypy-plugins ; platform_python_implementation == \"CPython\" and python_version >= \"3.10\""]
-
[[package]]
name = "beautifulsoup4"
-version = "4.13.4"
+version = "4.14.2"
description = "Screen-scraping library"
optional = false
python-versions = ">=3.7.0"
groups = ["main"]
files = [
- {file = "beautifulsoup4-4.13.4-py3-none-any.whl", hash = "sha256:9bbbb14bfde9d79f38b8cd5f8c7c85f4b8f2523190ebed90e950a8dea4cb1c4b"},
- {file = "beautifulsoup4-4.13.4.tar.gz", hash = "sha256:dbb3c4e1ceae6aefebdaf2423247260cd062430a410e38c66f2baa50a8437195"},
+ {file = "beautifulsoup4-4.14.2-py3-none-any.whl", hash = "sha256:5ef6fa3a8cbece8488d66985560f97ed091e22bbc4e9c2338508a9d5de6d4515"},
+ {file = "beautifulsoup4-4.14.2.tar.gz", hash = "sha256:2a98ab9f944a11acee9cc848508ec28d9228abfd522ef0fad6a02a72e0ded69e"},
]
[package.dependencies]
@@ -85,14 +77,14 @@ beautifulsoup4 = "*"
[[package]]
name = "certifi"
-version = "2025.6.15"
+version = "2025.10.5"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
python-versions = ">=3.7"
groups = ["main"]
files = [
- {file = "certifi-2025.6.15-py3-none-any.whl", hash = "sha256:2e0c7ce7cb5d8f8634ca55d2ba7e6ec2689a2fd6537d8dec1296a477a4910057"},
- {file = "certifi-2025.6.15.tar.gz", hash = "sha256:d747aa5a8b9bbbb1bb8c22bb13e22bd1f18e9796defa16bab421f7f7a317323b"},
+ {file = "certifi-2025.10.5-py3-none-any.whl", hash = "sha256:0f212c2744a9bb6de0c56639a6f68afe01ecd92d91f14ae897c4fe7bbeeef0de"},
+ {file = "certifi-2025.10.5.tar.gz", hash = "sha256:47c09d31ccf2acf0be3f701ea53595ee7e0b8fa08801c6624be771df09ae7b43"},
]
[[package]]
@@ -109,104 +101,91 @@ files = [
[[package]]
name = "charset-normalizer"
-version = "3.4.2"
+version = "3.4.3"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
optional = false
python-versions = ">=3.7"
groups = ["main"]
files = [
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[[package]]
name = "click-option-group"
-version = "0.5.7"
+version = "0.5.8"
description = "Option groups missing in Click"
optional = false
python-versions = ">=3.7"
groups = ["main"]
files = [
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[package.dependencies]
@@ -265,6 +244,7 @@ description = "Python library for calculating contours of 2D quadrilateral grids
optional = false
python-versions = ">=3.9"
groups = ["main"]
+markers = "python_version < \"3.11\""
files = [
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test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist", "wurlitzer"]
+[[package]]
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name = "contractions"
version = "0.1.73"
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[[package]]
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[[package]]
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+ {file = "rpds_py-0.27.1.tar.gz", hash = "sha256:26a1c73171d10b7acccbded82bf6a586ab8203601e565badc74bbbf8bc5a10f8"},
]
[[package]]
@@ -1860,14 +2219,14 @@ files = [
[[package]]
name = "soupsieve"
-version = "2.7"
+version = "2.8"
description = "A modern CSS selector implementation for Beautiful Soup."
optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
groups = ["main"]
files = [
- {file = "soupsieve-2.7-py3-none-any.whl", hash = "sha256:6e60cc5c1ffaf1cebcc12e8188320b72071e922c2e897f737cadce79ad5d30c4"},
- {file = "soupsieve-2.7.tar.gz", hash = "sha256:ad282f9b6926286d2ead4750552c8a6142bc4c783fd66b0293547c8fe6ae126a"},
+ {file = "soupsieve-2.8-py3-none-any.whl", hash = "sha256:0cc76456a30e20f5d7f2e14a98a4ae2ee4e5abdc7c5ea0aafe795f344bc7984c"},
+ {file = "soupsieve-2.8.tar.gz", hash = "sha256:e2dd4a40a628cb5f28f6d4b0db8800b8f581b65bb380b97de22ba5ca8d72572f"},
]
[[package]]
@@ -1999,14 +2358,14 @@ typing_extensions = ">=4.14.0"
[[package]]
name = "typing-extensions"
-version = "4.14.0"
+version = "4.15.0"
description = "Backported and Experimental Type Hints for Python 3.9+"
optional = false
python-versions = ">=3.9"
groups = ["main"]
files = [
- {file = "typing_extensions-4.14.0-py3-none-any.whl", hash = "sha256:a1514509136dd0b477638fc68d6a91497af5076466ad0fa6c338e44e359944af"},
- {file = "typing_extensions-4.14.0.tar.gz", hash = "sha256:8676b788e32f02ab42d9e7c61324048ae4c6d844a399eebace3d4979d75ceef4"},
+ {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
+ {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
]
[[package]]
@@ -2023,21 +2382,21 @@ files = [
[[package]]
name = "urllib3"
-version = "2.5.0"
+version = "2.6.0"
description = "HTTP library with thread-safe connection pooling, file post, and more."
optional = false
python-versions = ">=3.9"
groups = ["main"]
files = [
- {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"},
- {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"},
+ {file = "urllib3-2.6.0-py3-none-any.whl", hash = "sha256:c90f7a39f716c572c4e3e58509581ebd83f9b59cced005b7db7ad2d22b0db99f"},
+ {file = "urllib3-2.6.0.tar.gz", hash = "sha256:cb9bcef5a4b345d5da5d145dc3e30834f58e8018828cbc724d30b4cb7d4d49f1"},
]
[package.extras]
-brotli = ["brotli (>=1.0.9) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=0.8.0) ; platform_python_implementation != \"CPython\""]
+brotli = ["brotli (>=1.2.0) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=1.2.0.0) ; platform_python_implementation != \"CPython\""]
h2 = ["h2 (>=4,<5)"]
socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
-zstd = ["zstandard (>=0.18.0)"]
+zstd = ["backports-zstd (>=1.0.0) ; python_version < \"3.14\""]
[[package]]
name = "validators"
@@ -2086,4 +2445,4 @@ type = ["pytest-mypy"]
[metadata]
lock-version = "2.1"
python-versions = ">=3.9,<=3.13"
-content-hash = "c5239f0416a42725c120463e60fb2e556d90812da2d11c5615027f5b4be512bb"
+content-hash = "a9e23606801bb83f85f7d6c4a823adca5188d05fcf67cbf03e1496da67dba4a5"
diff --git a/pyproject.toml b/pyproject.toml
index bf4ea59..1bb5d2f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,49 +1,49 @@
-[project]
+[tool.poetry]
name = "somef_core"
version = "0.0.1"
-description = "SOftware Metadata Extraction Framework (CORE): A tool for automatically extracting relevant software metadata from readme files and package files."
-authors = [
- { name = "Daniel Garijo", email = "daniel.garijo@upm.es" }
-]
+description = "SOftware Metadata Extraction Framework (CORE): A tool for automatically extracting relevant software metadata from a source code repository (README, package files, etc)."
+authors = ["Daniel Garijo "]
+readme = "README.md"
packages = [
{ include = "somef_core", from = "src" }
]
-requires-python = ">=3.9,<=3.13"
classifiers = [
"Programming Language :: Python :: 3.10",
"Operating System :: OS Independent",
"License :: OSI Approved :: MIT License",
"Topic :: Software Development :: Libraries :: Python Modules"
]
-urls = { homepage = "https://github.com/SciCodes/somef-core" }
-
-readme = "README.md"
-
-dependencies = [
- "bs4 >=0.0.1",
- "click >=8.1.7",
- "click-option-group >=0.5.6",
- "matplotlib >=3.8.2",
- "nltk >=3.9.0",
- "numpy >=1.26.3",
- "pandas >=2.1.4",
- "textblob >=0.17.1",
- "validators >=0.22.0",
- "scipy >=1.11.4",
- "inflect >=7.0.0",
- "contractions >=0.1.73",
- "chardet >=5.2.0",
- "pytest >=7.4.4",
- "bibtexparser >=1.4.1",
- "nbformat >=5.9.2",
- "markdown >=3.5.2",
- "requests >=2.31.0",
- "pyyaml >=6.0.2",
- "lxml >=5.1.0",
- "tomli >=2.0.1"
-]
+
+[tool.poetry.urls]
+homepage = "https://github.com/SciCodes/somef-core"
-[project.scripts]
+[tool.poetry.dependencies]
+ python = ">=3.9,<=3.13"
+ bs4 = "^0.0.1"
+ click = "^8.1.7"
+ click-option-group = "^0.5.6"
+ matplotlib = "^3.8.2"
+ nltk = "^3.9.0"
+ numpy = "^1.26.3"
+ pandas = "^2.1.4"
+ textblob = "^0.17.1"
+ validators = "^0.22.0"
+ scipy = "^1.11.4"
+ inflect = "^7.0.0"
+ contractions = "^0.1.73"
+ chardet = "^5.2.0"
+ pytest = "^7.4.4"
+ bibtexparser = "^1.4.1"
+ nbformat = "^5.9.2"
+ markdown = "^3.5.2"
+ markdown-it-py = "^3.0"
+ requests = "^2.31.0"
+ pyyaml = "^6.0.2"
+ lxml = "^5.1.0"
+ tomli = "^2.0.1"
+
+
+[tool.poetry.scripts]
somef_core = "somef_core.__main__:cli"
[build-system]
diff --git a/pytest 2.ini b/pytest 2.ini
new file mode 100644
index 0000000..2f80c74
--- /dev/null
+++ b/pytest 2.ini
@@ -0,0 +1,7 @@
+[pytest]
+testpaths = somef/src/somef/test
+python_files = test_*.py
+python_classes = Test*
+python_functions = test_*
+
+norecursedirs = test_data .git .venv __pycache__ *.egg-info
diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 0000000..2f80c74
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,7 @@
+[pytest]
+testpaths = somef/src/somef/test
+python_files = test_*.py
+python_classes = Test*
+python_functions = test_*
+
+norecursedirs = test_data .git .venv __pycache__ *.egg-info
diff --git a/src/somef_core/__init__.py b/src/somef_core/__init__.py
index 5f1d2cc..3f3e589 100644
--- a/src/somef_core/__init__.py
+++ b/src/somef_core/__init__.py
@@ -1,3 +1,3 @@
# -*- coding: utf-8 -*-
-__version__ = "0.0.1"
+__version__ = "0.9.13"
diff --git a/src/somef_core/__main__.py b/src/somef_core/__main__.py
index 7e20e9b..9df797c 100644
--- a/src/somef_core/__main__.py
+++ b/src/somef_core/__main__.py
@@ -33,10 +33,10 @@ def configure(auto, base_uri):
configuration.update_base_uri(base_uri)
else:
authorization = click.prompt("Authorization", default="")
- description = None
- invocation = None
- installation = None
- citation = None
+ description = click.prompt("Documentation classifier model file", default=configuration.default_description)
+ invocation = click.prompt("Invocation classifier model file", default=configuration.default_invocation)
+ installation = click.prompt("Installation classifier model file", default=configuration.default_installation)
+ citation = click.prompt("Citation classifier model file", default=configuration.default_citation)
base_uri = click.prompt("Base URI for RDF generation", default=base_uri)
# configuration.configure()
configuration.configure(authorization, description, invocation, installation, citation, base_uri)
@@ -157,8 +157,30 @@ def configure(auto, base_uri):
default=True,
help="""SOMEF will ignore the contents of all files within folders named test (True by default)"""
)
-def describe(**kwargs):
+@click.option(
+ "--requirements_all",
+ "-all",
+ is_flag=True,
+ default=False,
+ help="Export all detected requirements, including text and libraries (default)."
+)
+@click.option(
+ "--requirements_v",
+ "-v",
+ is_flag=True,
+ default=False,
+ help="Export only requirements from structured sources (pom.xml, requirements.txt, etc.)"
+)
+def describe(requirements_v, requirements_all, **kwargs):
# import so missing packages get installed when appropriate
+ if requirements_v:
+ kwargs["requirements_mode"] = "v"
+ elif requirements_all:
+ kwargs["requirements_mode"] = "all"
+ else:
+ kwargs["requirements_mode"] = "all"
+
from . import somef_cli
somef_cli.run_cli(**kwargs)
- click.secho(f"Success", fg="green")
\ No newline at end of file
+ click.secho(f"Success", fg="green")
+
\ No newline at end of file
diff --git a/src/somef_core/configuration.py b/src/somef_core/configuration.py
index 177cf2e..d0d4004 100644
--- a/src/somef_core/configuration.py
+++ b/src/somef_core/configuration.py
@@ -3,8 +3,16 @@
import json
import sys
import logging
+
from .utils import constants
+path = Path(__file__).parent.absolute()
+default_description = os.path.join(str(path), "models", "description.p")
+default_invocation = os.path.join(str(path), "models", "invocation.p")
+default_installation = os.path.join(str(path), "models", "installation.p")
+default_citation = os.path.join(str(path), "models", "citation.p")
+
+
def get_configuration_file():
"""
Function that retrieves the configuration file
@@ -39,11 +47,12 @@ def update_base_uri(base_uri):
credentials_file.chmod(0o600)
json.dump(data, fh)
+
def configure(authorization="",
- description=None,
- invocation=None,
- installation=None,
- citation=None,
+ description=default_description,
+ invocation=default_invocation,
+ installation=default_installation,
+ citation=default_citation,
base_uri=constants.CONF_DEFAULT_BASE_URI):
""" Function to configure the main program"""
import nltk
diff --git a/src/somef_core/export/json_export.py b/src/somef_core/export/json_export.py
index 7fed51d..547344c 100644
--- a/src/somef_core/export/json_export.py
+++ b/src/somef_core/export/json_export.py
@@ -5,6 +5,7 @@
from dateutil import parser as date_parser
from ..utils import constants
from ..regular_expressions import detect_license_spdx,extract_scholarly_article_natural, extract_scholarly_article_properties
+from typing import List, Dict
def save_json_output(repo_data, out_path, missing, pretty=False):
"""
@@ -31,7 +32,7 @@ def save_json_output(repo_data, out_path, missing, pretty=False):
json.dump(repo_data, output)
-def save_codemeta_output(repo_data, outfile, pretty=False):
+def save_codemeta_output(repo_data, outfile, pretty=False, requirements_mode='all'):
"""
Function that saves a Codemeta JSONLD file with a summary of the results
@@ -40,6 +41,7 @@ def save_codemeta_output(repo_data, outfile, pretty=False):
@param repo_data: JSON with the results to translate to Codemeta
@param outfile: path where to save the codemeta file
@param pretty: option to show the JSON results in a nice format
+ @param requriments_mode: option to show all requriments or just machine readable
"""
def format_date(date_string):
date_object = date_parser.parse(date_string)
@@ -76,9 +78,40 @@ def format_date(date_string):
descriptions_text = []
if descriptions is not None:
- descriptions.sort(key=lambda x: (x[constants.PROP_CONFIDENCE] + (1 if x[constants.PROP_TECHNIQUE] == constants.GITHUB_API else 0)),
- reverse=True)
- descriptions_text = [x[constants.PROP_RESULT][constants.PROP_VALUE] for x in descriptions]
+
+ # priority descriptions: Codemeta, without codemeta but confidence 1, rest
+ codemeta_desc = [d for d in descriptions if d.get("technique") == "code_parser" and "codemeta.json" in d.get("source", "")]
+ github_desc = [d for d in descriptions if d.get("technique") == constants.GITHUB_API]
+ readme_desc = [d for d in descriptions if d.get("technique") not in ("code_parser", constants.GITHUB_API)]
+
+ if codemeta_desc:
+ # If codemeta just these
+ selected = codemeta_desc
+ elif github_desc:
+ # whitout codemeta, but we have descripciont with confidence 1
+ threshold_1 = [d for d in github_desc if d.get("confidence", 0) == 1]
+ selected = threshold_1 if threshold_1 else github_desc
+ else:
+ # Rest of descriptions
+ selected = sorted(readme_desc, key=lambda x: x.get("confidence", 0), reverse=True)[:1]
+
+ flat_descriptions = []
+ for d in selected:
+ value = d[constants.PROP_RESULT][constants.PROP_VALUE]
+ if isinstance(value, list):
+ for v in value:
+ if v not in flat_descriptions:
+ flat_descriptions.append(v)
+ else:
+ if value not in flat_descriptions:
+ flat_descriptions.append(value)
+
+ descriptions_text = flat_descriptions
+
+ # descriptions_text = [d[constants.PROP_RESULT][constants.PROP_VALUE] for d in selected]
+ # descriptions.sort(key=lambda x: (x[constants.PROP_CONFIDENCE] + (1 if x[constants.PROP_TECHNIQUE] == constants.GITHUB_API else 0)),
+ # reverse=True)
+ # descriptions_text = [x[constants.PROP_RESULT][constants.PROP_VALUE] for x in descriptions]
codemeta_output = {
@@ -123,25 +156,29 @@ def format_date(date_string):
l_result["identifier"] = constants.SPDX_BASE + l[constants.PROP_RESULT][constants.PROP_SPDX_ID]
l_result["spdx_id"] = l[constants.PROP_RESULT][constants.PROP_SPDX_ID]
- codemeta_output["license"] = l_result
+ codemeta_output[constants.CAT_CODEMETA_LICENSE] = l_result
if code_repository is not None:
- codemeta_output["codeRepository"] = code_repository
- codemeta_output["issueTracker"] = code_repository + "/issues"
+ codemeta_output[constants.CAT_CODEMETA_CODEREPOSITORY] = code_repository
+ codemeta_output[constants.CAT_CODEMETA_ISSUETRACKER] = code_repository + "/issues"
if constants.CAT_DATE_CREATED in repo_data:
- codemeta_output["dateCreated"] = format_date(repo_data[constants.CAT_DATE_CREATED][0][constants.PROP_RESULT][constants.PROP_VALUE])
+ value = repo_data[constants.CAT_DATE_CREATED][0][constants.PROP_RESULT][constants.PROP_VALUE]
+ if value:
+ codemeta_output[constants.CAT_CODEMETA_DATECREATED] = format_date(value)
if constants.CAT_DATE_UPDATED in repo_data:
- codemeta_output["dateModified"] = format_date(repo_data[constants.CAT_DATE_UPDATED][0][constants.PROP_RESULT][constants.PROP_VALUE])
+ value = repo_data[constants.CAT_DATE_UPDATED][0][constants.PROP_RESULT][constants.PROP_VALUE]
+ if value:
+ codemeta_output[constants.CAT_CODEMETA_DATEMODIFIED] = format_date(value)
if constants.CAT_DOWNLOAD_URL in repo_data:
- codemeta_output["downloadUrl"] = repo_data[constants.CAT_DOWNLOAD_URL][0][constants.PROP_RESULT][constants.PROP_VALUE]
+ codemeta_output[constants.CAT_CODEMETA_DOWNLOADURL] = repo_data[constants.CAT_DOWNLOAD_URL][0][constants.PROP_RESULT][constants.PROP_VALUE]
if constants.CAT_NAME in repo_data:
- codemeta_output["name"] = repo_data[constants.CAT_NAME][0][constants.PROP_RESULT][constants.PROP_VALUE]
+ codemeta_output[constants.CAT_CODEMETA_NAME] = repo_data[constants.CAT_NAME][0][constants.PROP_RESULT][constants.PROP_VALUE]
if constants.CAT_LOGO in repo_data:
- codemeta_output["logo"] = repo_data[constants.CAT_LOGO][0][constants.PROP_RESULT][constants.PROP_VALUE]
+ codemeta_output[constants.CAT_CODEMETA_LOGO] = repo_data[constants.CAT_LOGO][0][constants.PROP_RESULT][constants.PROP_VALUE]
if constants.CAT_KEYWORDS in repo_data:
- codemeta_output["keywords"] = repo_data[constants.CAT_KEYWORDS][0][constants.PROP_RESULT][constants.PROP_VALUE]
+ codemeta_output[constants.CAT_CODEMETA_KEYWORDS] = repo_data[constants.CAT_KEYWORDS][0][constants.PROP_RESULT][constants.PROP_VALUE]
if constants.CAT_PROGRAMMING_LANGUAGES in repo_data:
# Calculate the total code size of all the programming languages
- codemeta_output["programmingLanguage"] = []
+ codemeta_output[constants.CAT_CODEMETA_PROGRAMMINGLANGUAGE] = []
language_data = repo_data.get(constants.CAT_PROGRAMMING_LANGUAGES, [])
total_size = 0
for item in language_data:
@@ -154,38 +191,54 @@ def format_date(date_string):
result = item.get(constants.PROP_RESULT, {})
size = result.get(constants.PROP_SIZE)
value = result.get(constants.PROP_VALUE)
- if value not in codemeta_output["programmingLanguage"]:
+ if value not in codemeta_output[constants.CAT_CODEMETA_PROGRAMMINGLANGUAGE]:
if size is not None and value is not None and total_size > 0:
percentage = (size / total_size) * 100
if percentage > constants.MINIMUM_PERCENTAGE_LANGUAGE_PROGRAMMING:
- codemeta_output["programmingLanguage"].append(value)
+ codemeta_output[constants.CAT_CODEMETA_PROGRAMMINGLANGUAGE].append(value)
elif size is None: # when size is not available, it comes from the parsers
- codemeta_output["programmingLanguage"].append(value)
+ codemeta_output[constants.CAT_CODEMETA_PROGRAMMINGLANGUAGE].append(value)
if constants.CAT_REQUIREMENTS in repo_data:
- # codemeta_output["softwareRequirements"] = [x[constants.PROP_RESULT][constants.PROP_VALUE] for x in repo_data[constants.CAT_REQUIREMENTS]]
- code_parser_requirements = [
- {
- "name": x[constants.PROP_RESULT].get(constants.PROP_NAME)
- if x[constants.PROP_RESULT].get(constants.PROP_NAME)
- else x[constants.PROP_RESULT].get(constants.PROP_VALUE),
- "version": x[constants.PROP_RESULT].get(constants.PROP_VERSION)
- }
- for x in repo_data[constants.CAT_REQUIREMENTS]
- if x.get(constants.PROP_TECHNIQUE) == constants.TECHNIQUE_CODE_CONFIG_PARSER
- ]
+ structured_sources = ["pom.xml", "requirements.txt", "setup.py", "environment.yml"]
+
+ code_parser_requirements = []
+ seen_structured = set()
+ for x in repo_data[constants.CAT_REQUIREMENTS]:
+ if x.get(constants.PROP_TECHNIQUE) == constants.TECHNIQUE_CODE_CONFIG_PARSER:
+ source = x.get("source", "")
+ if any(src in source for src in structured_sources):
+ name = x[constants.PROP_RESULT].get(constants.PROP_NAME) or x[constants.PROP_RESULT].get(constants.PROP_VALUE)
+ version = x[constants.PROP_RESULT].get(constants.PROP_VERSION)
+ key = f"{name.strip()}|{version.strip() if version else ''}"
+ if key not in seen_structured:
+ entry = {"name": name.strip()}
+ if version:
+ entry["version"] = version.strip()
+ code_parser_requirements.append(entry)
+ seen_structured.add(key)
+
+ other_requirements = []
+ seen_text = set()
+ for x in repo_data[constants.CAT_REQUIREMENTS]:
+ if not (
+ x.get(constants.PROP_TECHNIQUE) == constants.TECHNIQUE_CODE_CONFIG_PARSER
+ and x.get("source") is not None
+ and any(src in x["source"] for src in structured_sources)
+ ):
+ value = x[constants.PROP_RESULT].get(constants.PROP_VALUE, "").strip().replace("\n", " ")
+ normalized = " ".join(value.split())
+ if normalized not in seen_text:
+ other_requirements.append(value)
+ seen_text.add(normalized)
+
+ if requirements_mode == "v":
+ codemeta_output[constants.CAT_CODEMETA_SOFTWAREREQUIREMENTS] = code_parser_requirements
+ else:
+ codemeta_output[constants.CAT_CODEMETA_SOFTWAREREQUIREMENTS] = code_parser_requirements + other_requirements
- other_requirements = [
- x[constants.PROP_RESULT][constants.PROP_VALUE]
- for x in repo_data[constants.CAT_REQUIREMENTS]
- if x.get(constants.PROP_TECHNIQUE) != constants.TECHNIQUE_CODE_CONFIG_PARSER
- ]
-
- codemeta_output["softwareRequirements"] = (
- code_parser_requirements if code_parser_requirements else other_requirements
- )
if constants.CAT_CONTINUOUS_INTEGRATION in repo_data:
- codemeta_output["continuousIntegration"] = repo_data[constants.CAT_CONTINUOUS_INTEGRATION][0][constants.PROP_RESULT][constants.PROP_VALUE]
+ codemeta_output[constants.CAT_CODEMETA_CONTINUOUSINTEGRATION] = repo_data[constants.CAT_CONTINUOUS_INTEGRATION][0][constants.PROP_RESULT][constants.PROP_VALUE]
# if constants.CAT_WORKFLOWS in repo_data:
# codemeta_output["workflows"] = repo_data[constants.CAT_WORKFLOWS][0][constants.PROP_RESULT][constants.PROP_VALUE]
if constants.CAT_RELEASES in repo_data:
@@ -212,11 +265,11 @@ def format_date(date_string):
oldest_version = l[constants.PROP_RESULT].get(constants.PROP_TAG)
if latest_description is not None:
- codemeta_output["releaseNotes"] = latest_description
+ codemeta_output[constants.CAT_CODEMETA_RELEASENOTES] = latest_description
if latest_version is not None:
- codemeta_output["softwareVersion"] = latest_version
+ codemeta_output[constants.CAT_CODEMETA_SOFTWAREVERSION] = latest_version
if oldest_date is not None:
- codemeta_output["datePublished"] = format_date(oldest_date.isoformat())
+ codemeta_output[constants.CAT_CODEMETA_DATEPUBLISHED] = format_date(oldest_date.isoformat())
install_links = []
if constants.CAT_INSTALLATION in repo_data:
@@ -237,22 +290,76 @@ def format_date(date_string):
if len(install_links) > 0:
# remove duplicates and generate codemeta
install_links = list(set(install_links))
- codemeta_output["buildInstructions"] = install_links
+ codemeta_output[constants.CAT_CODEMETA_BUILDINSTRUCTIONS] = install_links
if constants.CAT_OWNER in repo_data:
# if user then person, otherwise organization
type_aux = repo_data[constants.CAT_OWNER][0][constants.PROP_RESULT][constants.PROP_TYPE]
if type_aux == "User":
type_aux = "Person"
- codemeta_output["author"] = [
+ codemeta_output[constants.CAT_CODEMETA_AUTHOR] = [
{
"@type": type_aux,
"@id": "https://github.com/" + author_name
}
]
+ if constants.CAT_AUTHORS in repo_data:
+ if "author" not in codemeta_output:
+ codemeta_output[constants.CAT_CODEMETA_AUTHOR] = []
+
+ # print('-------AUTHORES')
+ # print(repo_data[constants.CAT_AUTHORS])
+ for author in repo_data[constants.CAT_AUTHORS]:
+ value_author = author[constants.PROP_RESULT].get(constants.PROP_VALUE)
+ name_author = author[constants.PROP_RESULT].get(constants.PROP_NAME)
+ if value_author and re.search(constants.REGEXP_LTD_INC, value_author, re.IGNORECASE):
+ type_author = "Organization"
+ else:
+ type_author = "Person"
+
+ author_l = {
+ "@type": type_author
+ }
+
+ if type_author == "Organization":
+ if name_author:
+ author_l['name'] = name_author
+ else:
+ family_name = None
+ given_name = None
+
+ if author[constants.PROP_RESULT].get('last_name'):
+ family_name = author[constants.PROP_RESULT].get('last_name')
+ author_l['familyName'] = family_name
+ if author[constants.PROP_RESULT].get('given_name'):
+ given_name = author[constants.PROP_RESULT].get('given_name')
+ author_l['givenName'] = given_name
+ if author[constants.PROP_RESULT].get('email'):
+ mail_author = author[constants.PROP_RESULT].get('email')
+ author_l['email'] = mail_author
+
+ if name_author:
+ author_l['name'] = name_author
+ else:
+ author_l['name'] = value_author
+
+ existing_authors = codemeta_output.get(constants.CAT_CODEMETA_AUTHOR, [])
+ existing = next((a for a in existing_authors if a.get("name") == author_l["name"]), None)
+
+ if existing:
+ for key, val in author_l.items():
+ if key not in existing or not existing[key]:
+ existing[key] = val
+ else:
+ codemeta_output[constants.CAT_CODEMETA_AUTHOR].append(author_l)
+ # if not any(a.get('name') == author_l['name'] for a in existing_authors):
+ # codemeta_output[constants.CAT_CODEMETA_AUTHOR].append(author_l)
+
+
if constants.CAT_CITATION in repo_data:
# url_cit = []
- codemeta_output["referencePublication"] = []
- scholarlyArticles = {}
+ codemeta_output[constants.CAT_CODEMETA_REFERENCEPUBLICATION] = []
+ all_reference_publications = []
+ # scholarlyArticles = {}
author_orcids = {}
for cit in repo_data[constants.CAT_CITATION]:
@@ -268,7 +375,6 @@ def format_date(date_string):
doi = yaml_content.get("doi") or preferred_citation.get("doi")
identifiers = yaml_content.get("identifiers", [])
url_citation = preferred_citation.get("url") or yaml_content.get("url")
-
identifier_url = next((id["value"] for id in identifiers if id["type"] == "url"), None)
identifier_doi = next((id["value"] for id in identifiers if id["type"] == "doi"), None)
@@ -329,14 +435,9 @@ def format_date(date_string):
if constants.PROP_DOI in cit[constants.PROP_RESULT].keys():
doi = cit[constants.PROP_RESULT][constants.PROP_DOI]
scholarlyArticle[constants.CAT_IDENTIFIER] = cit[constants.PROP_RESULT][constants.PROP_DOI]
- # elif constants.PROP_FORMAT in cit[constants.PROP_RESULT].keys() \
- # and cit[constants.PROP_RESULT][constants.PROP_FORMAT] == constants.FORMAT_CFF:
- # url_cit.append(cit[constants.PROP_SOURCE])
if constants.PROP_URL in cit[constants.PROP_RESULT].keys():
scholarlyArticle[constants.PROP_URL] = cit[constants.PROP_RESULT][constants.PROP_URL]
- # if constants.PROP_AUTHOR in cit[constants.PROP_RESULT].keys():
- # scholarlyArticle[constants.PROP_AUTHOR] = cit[constants.PROP_RESULT][constants.PROP_AUTHOR]
if constants.PROP_TITLE in cit[constants.PROP_RESULT].keys():
title = normalize_title(cit[constants.PROP_RESULT][constants.PROP_TITLE])
@@ -356,18 +457,12 @@ def format_date(date_string):
else:
scholarlyArticle = extract_scholarly_article_natural(cit[constants.PROP_RESULT][constants.PROP_VALUE], scholarlyArticle, 'CODEMETA')
- key = (doi, title)
+ all_reference_publications.append({
+ **scholarlyArticle,
+ "_source_format": "cff" if not is_bibtex else "bibtex"
+ })
- if key in scholarlyArticles:
- if is_bibtex:
- codemeta_output["referencePublication"].remove(scholarlyArticles[key])
- codemeta_output["referencePublication"].append(scholarlyArticle)
- scholarlyArticles[key] = scholarlyArticle
- else:
- codemeta_output["referencePublication"].append(scholarlyArticle)
- scholarlyArticles[key] = scholarlyArticle
-
- for article in codemeta_output["referencePublication"]:
+ for article in all_reference_publications:
if "author" in article:
for author in article["author"]:
family_name = author.get("familyName", "").strip()
@@ -376,21 +471,67 @@ def format_date(date_string):
if key and key in author_orcids:
author["@id"] = author_orcids[key]
+
+ codemeta_output[constants.CAT_CODEMETA_REFERENCEPUBLICATION] = deduplicate_publications(all_reference_publications)
if constants.CAT_STATUS in repo_data:
url_status = repo_data[constants.CAT_STATUS][0]['result'].get('value', '')
status = url_status.split('#')[-1] if '#' in url_status else None
if status:
- codemeta_output["developmentStatus"] = status
+ codemeta_output[constants.CAT_CODEMETA_DEVELOPMENTSTATUS] = status
+
if constants.CAT_IDENTIFIER in repo_data:
- codemeta_output["identifier"] = repo_data[constants.CAT_IDENTIFIER][0][constants.PROP_RESULT][constants.PROP_VALUE]
+ codemeta_output[constants.CAT_CODEMETA_IDENTIFIER] = []
+
+ for identifier in repo_data[constants.CAT_IDENTIFIER]:
+ value = identifier[constants.PROP_RESULT][constants.PROP_VALUE]
+ if value not in codemeta_output[constants.CAT_CODEMETA_IDENTIFIER]:
+ codemeta_output[constants.CAT_CODEMETA_IDENTIFIER].append(value)
+
+ if constants.CAT_HOMEPAGE in repo_data:
+
+ # example
+ # homepage_urls = {"http://foo.com", "https://foo.com", "http://bar.com"}
+ # Result--> filtered_urls = {"https://foo.com", "http://bar.com"}
+ # Prioritize https
+
+ homepage_urls = {hp[constants.PROP_RESULT][constants.PROP_VALUE].strip()
+ for hp in repo_data[constants.CAT_HOMEPAGE]}
+
+ filtered_urls = set()
+ roots_with_https = {url[len("https://"):] for url in homepage_urls if url.startswith("https://")}
+
+ for url in homepage_urls:
+ root = url.replace("http://", "").replace("https://", "")
+ if url.startswith("http://") and root in roots_with_https:
+ continue
+ filtered_urls.add(url)
+
+ codemeta_output[constants.CAT_CODEMETA_URL] = list(filtered_urls)
+
+ # codemeta_output["identifier"] = repo_data[constants.CAT_IDENTIFIER][0][constants.PROP_RESULT][constants.PROP_VALUE]
if constants.CAT_README_URL in repo_data:
- codemeta_output["readme"] = repo_data[constants.CAT_README_URL][0][constants.PROP_RESULT][constants.PROP_VALUE]
+ codemeta_output[constants.CAT_CODEMETA_README] = repo_data[constants.CAT_README_URL][0][constants.PROP_RESULT][constants.PROP_VALUE]
+
+ if constants.CAT_RUNTIME_PLATFORM in repo_data:
+ runtimes = []
+
+ for runtime_entry in repo_data[constants.CAT_RUNTIME_PLATFORM]:
+ result = runtime_entry.get("result", {})
+ # name = result.get("name")
+ value = result.get("value")
+ if value:
+ # runtimes.append(f"{name} {version}")
+ runtimes.append(value)
+
+ if runtimes:
+ codemeta_output[constants.CAT_CODEMETA_RUNTIMEPLATFORM] = ", ".join(runtimes)
+
# if "contributors" in repo_data:
# codemeta_output["contributor"] = data_path(["contributors", "excerpt"])
# A person is expected, and we extract text at the moment
if descriptions_text:
- codemeta_output["description"] = descriptions_text
+ codemeta_output[constants.CAT_CODEMETA_DESCRIPTION] = descriptions_text
# if published_date != "":
# commenting this out because we cannot assume the last published date to be the published date
# codemeta_output["datePublished"] = published_date
@@ -408,10 +549,70 @@ def create_missing_fields(result):
The categories are added to the JSON results. This won't be added if you export TTL or Codemeta"""
missing = []
repo_data = result
- for c in constants.categories_files_header:
+ # for c in constants.categories_files_header:
+ for c in constants.all_categories:
if c not in repo_data:
missing.append(c)
return missing
-def normalize_title(title):
- return re.sub(r"\s+", " ", title.strip().lower()) if title else None
+# def normalize_title(title):
+# return re.sub(r"\s+", " ", title.strip().lower()) if title else None
+
+def normalize_title(title: str) -> str:
+ if not title:
+ return None
+ title = re.sub(r'[{}]', '', title)
+ title = re.sub(r'\s+', ' ', title)
+ return title.strip().lower()
+
+
+def deduplicate_publications(publications: List[Dict]) -> List[Dict]:
+ seen = {}
+ for pub in publications:
+ # doi = pub.get("identifier", "").lower().strip()
+ # doi = (pub.get("identifier") or "").lower().strip()
+ doi = extract_doi(pub.get("identifier") or "")
+ title = normalize_title(pub.get("name", ""))
+ key = (doi, title)
+
+ if key not in seen:
+ seen[key] = pub
+ else:
+ existing = seen[key]
+ existing_format = existing.get("_source_format", "")
+ new_format = pub.get("_source_format", "")
+ existing_url = (existing.get("url") or "").lower()
+ new_url = (pub.get("url") or "").lower()
+
+ # is_doi_url_existing = existing_url.startswith("https://doi.org/")
+ # is_doi_url_new = new_url.startswith("https://doi.org/")
+ doi_existing = extract_doi(existing_url)
+ # print(f'-----> DOI existing: {doi_existing}')
+ doi_new = extract_doi(new_url)
+ # print(f'-----> DOI existing: {doi_new}')
+ is_doi_url_existing = bool(doi_existing)
+ is_doi_url_new = bool(doi_new)
+
+ # Priority CFF
+ if existing_format != "cff" and new_format == "cff":
+ seen[key] = pub
+
+ # Priority DOI URL
+ elif existing_format == new_format:
+ if not is_doi_url_existing and is_doi_url_new:
+ seen[key] = pub
+
+ result = []
+ for pub in seen.values():
+ pub.pop("_source_format", None)
+ result.append(pub)
+
+ return result
+
+
+def extract_doi(url: str) -> str:
+ if not url:
+ return ""
+
+ match = re.search(constants.REGEXP_ALL_DOIS, url, re.IGNORECASE)
+ return match.group(0).lower() if match else ""
diff --git a/src/somef_core/extract_software_type 2.py b/src/somef_core/extract_software_type 2.py
new file mode 100644
index 0000000..27aebea
--- /dev/null
+++ b/src/somef_core/extract_software_type 2.py
@@ -0,0 +1,329 @@
+import os
+from pathlib import Path
+import nbformat
+from nbformat.reader import NotJSONError
+from chardet import detect
+import re
+from .extract_workflows import is_file_workflow
+from .process_results import Result
+from .utils import constants
+# from .extract_ontologies import is_file_ontology
+
+import pdb
+
+
+def check_repository_type(path_repo, title, metadata_result: Result):
+ """ Function that adds the metadata result in the JSON
+ output depending on the software type or if the repository is not considered software"""
+
+ if check_static_websites(path_repo, metadata_result):
+ metadata_result.add_result(constants.CAT_TYPE,
+ {
+ constants.PROP_VALUE: 'static-website',
+ constants.PROP_TYPE: constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_HEURISTICS)
+ # elif check_ontologies(path_repo):
+ # metadata_result.add_result(constants.CAT_TYPE,
+ # {
+ # constants.PROP_VALUE: 'ontology',
+ # constants.PROP_TYPE: constants.STRING
+ # },
+ # 1,
+ # constants.TECHNIQUE_HEURISTICS)
+ elif check_notebooks(path_repo):
+ metadata_result.add_result(constants.CAT_TYPE,
+ {
+ constants.PROP_VALUE: 'notebook-application',
+ constants.PROP_TYPE: constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_HEURISTICS)
+ # commenting out this heuristic, as if a repository contains other files apart from workflows, it may not be a wf
+ # elif check_workflow(path_repo, title):
+ # metadata_result.add_result(constants.CAT_TYPE,
+ # {
+ # constants.PROP_VALUE: 'workflow',
+ # constants.PROP_TYPE: constants.STRING
+ # },
+ # 1,
+ # constants.TECHNIQUE_HEURISTICS)
+ elif check_command_line(path_repo):
+ """The 0.82 confidence result is from running the analysis on 300 repos and showing the precision
+ of the heuristic"""
+ metadata_result.add_result(constants.CAT_TYPE,
+ {
+ constants.PROP_VALUE: 'commandline-application',
+ constants.PROP_TYPE: constants.STRING
+ },
+ 0.82,
+ constants.TECHNIQUE_HEURISTICS)
+
+ elif check_extras(path_repo):
+ metadata_result.add_result(constants.CAT_TYPE,
+ {
+ constants.PROP_VALUE: 'non-software',
+ constants.PROP_TYPE: constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_HEURISTICS)
+ return metadata_result
+
+
+def check_notebooks(path_repo):
+ """Function which checks if the specified repository is a Notebook Application
+ depending on the extensions present and number of notebooks which contain code
+
+ The function checks for presence of more than one code_notebook inside the repo and checks against code
+ extensions present returning true if both conditions are fulfilled ."""
+ code_notebooks = 0
+ total_files = 0
+
+ bad_extensions = False
+ for root, dirs, files in os.walk(path_repo):
+ for file in files:
+ if file.endswith((".ipynb", ".rmd", '.Rmd')):
+ notebook_path = os.path.join(root, file)
+ try:
+ if file.endswith(".ipynb"):
+ if is_notebook_code(notebook_path):
+ code_notebooks += 1
+ elif file.endswith(".rmd") or file.endswith('.Rmd'):
+ if has_code_in_rmd(notebook_path):
+ code_notebooks += 1
+ except Exception as e:
+ print(f"Error reading notebook file {notebook_path}: {str(e)}")
+ pass
+ if file.endswith(constants.code_extensions):
+ bad_extensions = True
+ if code_notebooks > 1:
+ return not bad_extensions
+ return False
+
+
+# def check_ontologies(path_repo):
+# """Function which detects if repository is an Ontology based on files present
+# and the non-existence of code files"""
+# ontology = False
+# for root, dirs, files in os.walk(path_repo):
+# repo_relative_path = os.path.relpath(root, path_repo)
+# for file in files:
+# file_path = os.path.join(repo_relative_path, file)
+# # print(os.path.join(repo_relative_path,file_path))
+# if file.endswith(constants.code_extensions):
+# return False
+# elif file.endswith(constants.ontology_extensions):
+# if not ontology:
+# ontology = is_file_ontology(os.path.join(path_repo, file_path))
+# return ontology
+
+
+def check_command_line(path_repo):
+ """Function which detects if repository is a Commandline Application
+ based on README analysis of commandline arguments and implementations"""
+ pattern_commandline = r"(?i)command[-\s]?line"
+ pattern_cmd_arg = r"(?i)(explanation\s+of\s+)?arguments\b"
+ pattern_cmd_arg2 = r"(?i)-\w+:"
+ for dir_path, dir_names, filenames in os.walk(path_repo):
+ repo_relative_path = os.path.relpath(dir_path, path_repo)
+ for filename in filenames:
+ file_path = os.path.join(repo_relative_path, filename)
+ filename_no_ext = os.path.splitext(filename)[0]
+ if "README" == filename_no_ext.upper():
+ if repo_relative_path == ".":
+ try:
+ # print(os.path.join(dir_path, filename))
+ with open(os.path.join(dir_path, filename), "r", encoding="utf-8") as data_file:
+ data_file_text = data_file.read()
+ try:
+ cmd_match2 = re.search(pattern_commandline, data_file_text)
+ cmd_match3 = re.search(pattern_cmd_arg, data_file_text)
+ cmd_match4 = re.search(pattern_cmd_arg2, data_file_text)
+ if cmd_match2 or (cmd_match3 and cmd_match4):
+ return True
+ except:
+ return False
+ except:
+ pass
+
+ return False
+
+
+def check_extras(path_repo):
+ """Function which detects if a repository is non-software by checking against
+ software related files"""
+ for root, dirs, files in os.walk(path_repo):
+ for file in files:
+ notebook_path = os.path.join(root, file)
+ if file.endswith(constants.code_extensions) or file.endswith(constants.ontology_extensions):
+ return False
+ elif file.endswith(".ipynb"):
+ if is_notebook_code(notebook_path):
+ return False
+ elif file.endswith(".rmd") or file.endswith('.Rmd'):
+ if has_code_in_rmd(notebook_path):
+ return False
+ return True
+
+
+def check_static_websites(path_repo, repo_metadata: Result):
+ """Function that analyzes byte size of js,css,html languages and checks if
+ repository contains files not associated with static websites
+
+ The evaluation numbers were extracted from the analysis of 997 css repositories representing libraries nad 998 js repos containing libraries
+ with control repositories .
+
+ """
+ # print(path_repo)
+ nr_files = 0
+ web_files = 0
+ total_size = 0
+ js_size = 0
+ css_size = 0
+ html_file = 0
+ for root, dirs, files in os.walk(path_repo):
+ for file in files:
+ file_path = os.path.join(root, file)
+ if file.endswith(constants.code_extensions) or file.endswith(
+ constants.ontology_extensions) or file.lower() in (('bower.json', 'package.json')):
+ return False
+ elif file.endswith((".js", ".css", ".scss")):
+ web_files += 1
+ elif file.endswith(".html"):
+ html_file += 1
+ elif file.endswith(".ipynb"):
+ if is_notebook_code(file_path):
+ return False
+ elif file.endswith(".rmd") or file.endswith('.Rmd'):
+ if has_code_in_rmd(file_path):
+ return False
+ try:
+ languages = repo_metadata[constants.CAT_PROGRAMMING_LANGUAGES]
+ print(languages)
+ for language in languages:
+ language_name = language[constants.PROP_RESULT][constants.PROP_NAME]
+ print(language_name)
+ if language_name.lower() == "javascript":
+ js_size += language[constants.PROP_RESULT][constants.PROP_SIZE]
+ print(js_size)
+ elif language_name.lower() == "scss" or language_name.lower() == "css":
+ css_size += language[constants.PROP_RESULT][constants.PROP_SIZE]
+ total_size += language[constants.PROP_RESULT][constants.PROP_SIZE]
+ except Exception as e:
+ print(e)
+ if html_file > 0:
+ if js_size > 0 and css_size == 0:
+ if js_size / total_size < 0.91:
+ return True
+ elif js_size == 0 and css_size > 0:
+ if css_size / total_size < 0.798:
+ return True
+ return True
+
+ return False
+
+
+def check_workflow(repo_path, title):
+ """Function which checks inside text for presence of repository being a workflow and analysis of the
+ files inside to check if they are correct workflow files. Also checks for repositories with no information
+ the name of the files which might point to it being a workflow.
+ PARAMETERS:
+ @repo_path(path to the repository directory)
+ @title(title of the repository)
+ """
+ list = []
+ total_workflows = 0
+ good_workflows = 0
+ for root, dirs, files in os.walk(repo_path):
+ repo_relative_path = os.path.relpath(root, repo_path)
+ for file in files:
+ filename_no_ext = os.path.splitext(file)[0]
+ if "README" == filename_no_ext.upper():
+ if repo_relative_path == ".":
+ try:
+ with open(os.path.join(root, file), "r") as readme_file:
+ readme_contents = readme_file.read()
+
+ title_words = title.split()
+
+ pattern = r'([^.?!]*(?:\b|\W){}(?:\b|\W)[^.?!]*[.?!])'.format(
+ '|'.join(map(re.escape, title_words)))
+ sentences = re.findall(pattern, readme_contents, flags=re.IGNORECASE)
+ for sentence in sentences:
+ if re.search(rf'\b{title}\b', sentence, flags=re.IGNORECASE) and re.search(
+ r'\b(pipeline|workflow)\b', sentence, flags=re.IGNORECASE):
+ return True
+
+ pattern_md = r'##.*\b(workflow|pipeline)\b'
+ pattern_rst = r'^([^=\n]+(?:\n(?![-=]).*)*\b(workflow|pipeline)\b(?:\n(?![-=]).*)*)\n=+'
+
+ match_md = re.findall(pattern_md, readme_contents, re.IGNORECASE)
+ match_rst = re.findall(pattern_rst, readme_contents, re.MULTILINE | re.IGNORECASE)
+
+ if match_md or match_rst:
+ return True
+
+ except:
+ continue
+
+ if file.endswith(constants.workflow_extensions) or file == "Snakefile":
+ total_workflows += 1
+ file_path = os.path.join(root, file)
+ if is_file_workflow(file_path):
+ list.append(file_path)
+ good_workflows += 1
+ else:
+ continue
+ if check_name(file):
+ return True
+ if list != []:
+ return True
+ else:
+ return False
+
+
+def check_name(filename):
+ """Assisting function for check_workflow to look for specific named files"""
+ pattern1 = re.compile(r"pipeline", re.IGNORECASE)
+ pattern2 = re.compile(r"(model|example)", re.IGNORECASE)
+ programming_language_extensions = (
+ ".py", ".java", ".cpp", ".c", ".php", ".rb", ".js", ".html", ".css", ".go", ".swift", ".scala", ".pl", ".ipynb")
+ if pattern1.search(filename) and pattern2.search(filename):
+ if filename.endswith(programming_language_extensions):
+ return True
+ elif pattern1.search(filename) and not pattern2.search(filename):
+ return False
+ elif (not pattern1.search(filename) and not pattern2.search(filename)) or (
+ not pattern1.search(filename) and pattern2.search(filename)):
+ return False
+
+
+def is_notebook_code(file_path):
+ has_code = False
+ num_code_cells = 0
+ num_total_cells = 0
+ try:
+ nb = nbformat.read(file_path, as_version=4)
+
+ for cell in nb['cells']:
+ if cell['cell_type'] == 'code':
+ num_total_cells += 1
+ if cell['source'].strip():
+ num_code_cells += 1
+ has_code = True
+ return has_code
+ except NotJSONError:
+ return False
+ except Exception:
+ return False
+
+
+def has_code_in_rmd(file_path):
+ try:
+ with open(file_path, 'r') as file:
+ content = file.read()
+ if "```{r" in content or "```{python" in content or "```{bash" in content:
+ return True
+ except:
+ return False
diff --git a/src/somef_core/extract_software_type.py b/src/somef_core/extract_software_type.py
new file mode 100644
index 0000000..27aebea
--- /dev/null
+++ b/src/somef_core/extract_software_type.py
@@ -0,0 +1,329 @@
+import os
+from pathlib import Path
+import nbformat
+from nbformat.reader import NotJSONError
+from chardet import detect
+import re
+from .extract_workflows import is_file_workflow
+from .process_results import Result
+from .utils import constants
+# from .extract_ontologies import is_file_ontology
+
+import pdb
+
+
+def check_repository_type(path_repo, title, metadata_result: Result):
+ """ Function that adds the metadata result in the JSON
+ output depending on the software type or if the repository is not considered software"""
+
+ if check_static_websites(path_repo, metadata_result):
+ metadata_result.add_result(constants.CAT_TYPE,
+ {
+ constants.PROP_VALUE: 'static-website',
+ constants.PROP_TYPE: constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_HEURISTICS)
+ # elif check_ontologies(path_repo):
+ # metadata_result.add_result(constants.CAT_TYPE,
+ # {
+ # constants.PROP_VALUE: 'ontology',
+ # constants.PROP_TYPE: constants.STRING
+ # },
+ # 1,
+ # constants.TECHNIQUE_HEURISTICS)
+ elif check_notebooks(path_repo):
+ metadata_result.add_result(constants.CAT_TYPE,
+ {
+ constants.PROP_VALUE: 'notebook-application',
+ constants.PROP_TYPE: constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_HEURISTICS)
+ # commenting out this heuristic, as if a repository contains other files apart from workflows, it may not be a wf
+ # elif check_workflow(path_repo, title):
+ # metadata_result.add_result(constants.CAT_TYPE,
+ # {
+ # constants.PROP_VALUE: 'workflow',
+ # constants.PROP_TYPE: constants.STRING
+ # },
+ # 1,
+ # constants.TECHNIQUE_HEURISTICS)
+ elif check_command_line(path_repo):
+ """The 0.82 confidence result is from running the analysis on 300 repos and showing the precision
+ of the heuristic"""
+ metadata_result.add_result(constants.CAT_TYPE,
+ {
+ constants.PROP_VALUE: 'commandline-application',
+ constants.PROP_TYPE: constants.STRING
+ },
+ 0.82,
+ constants.TECHNIQUE_HEURISTICS)
+
+ elif check_extras(path_repo):
+ metadata_result.add_result(constants.CAT_TYPE,
+ {
+ constants.PROP_VALUE: 'non-software',
+ constants.PROP_TYPE: constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_HEURISTICS)
+ return metadata_result
+
+
+def check_notebooks(path_repo):
+ """Function which checks if the specified repository is a Notebook Application
+ depending on the extensions present and number of notebooks which contain code
+
+ The function checks for presence of more than one code_notebook inside the repo and checks against code
+ extensions present returning true if both conditions are fulfilled ."""
+ code_notebooks = 0
+ total_files = 0
+
+ bad_extensions = False
+ for root, dirs, files in os.walk(path_repo):
+ for file in files:
+ if file.endswith((".ipynb", ".rmd", '.Rmd')):
+ notebook_path = os.path.join(root, file)
+ try:
+ if file.endswith(".ipynb"):
+ if is_notebook_code(notebook_path):
+ code_notebooks += 1
+ elif file.endswith(".rmd") or file.endswith('.Rmd'):
+ if has_code_in_rmd(notebook_path):
+ code_notebooks += 1
+ except Exception as e:
+ print(f"Error reading notebook file {notebook_path}: {str(e)}")
+ pass
+ if file.endswith(constants.code_extensions):
+ bad_extensions = True
+ if code_notebooks > 1:
+ return not bad_extensions
+ return False
+
+
+# def check_ontologies(path_repo):
+# """Function which detects if repository is an Ontology based on files present
+# and the non-existence of code files"""
+# ontology = False
+# for root, dirs, files in os.walk(path_repo):
+# repo_relative_path = os.path.relpath(root, path_repo)
+# for file in files:
+# file_path = os.path.join(repo_relative_path, file)
+# # print(os.path.join(repo_relative_path,file_path))
+# if file.endswith(constants.code_extensions):
+# return False
+# elif file.endswith(constants.ontology_extensions):
+# if not ontology:
+# ontology = is_file_ontology(os.path.join(path_repo, file_path))
+# return ontology
+
+
+def check_command_line(path_repo):
+ """Function which detects if repository is a Commandline Application
+ based on README analysis of commandline arguments and implementations"""
+ pattern_commandline = r"(?i)command[-\s]?line"
+ pattern_cmd_arg = r"(?i)(explanation\s+of\s+)?arguments\b"
+ pattern_cmd_arg2 = r"(?i)-\w+:"
+ for dir_path, dir_names, filenames in os.walk(path_repo):
+ repo_relative_path = os.path.relpath(dir_path, path_repo)
+ for filename in filenames:
+ file_path = os.path.join(repo_relative_path, filename)
+ filename_no_ext = os.path.splitext(filename)[0]
+ if "README" == filename_no_ext.upper():
+ if repo_relative_path == ".":
+ try:
+ # print(os.path.join(dir_path, filename))
+ with open(os.path.join(dir_path, filename), "r", encoding="utf-8") as data_file:
+ data_file_text = data_file.read()
+ try:
+ cmd_match2 = re.search(pattern_commandline, data_file_text)
+ cmd_match3 = re.search(pattern_cmd_arg, data_file_text)
+ cmd_match4 = re.search(pattern_cmd_arg2, data_file_text)
+ if cmd_match2 or (cmd_match3 and cmd_match4):
+ return True
+ except:
+ return False
+ except:
+ pass
+
+ return False
+
+
+def check_extras(path_repo):
+ """Function which detects if a repository is non-software by checking against
+ software related files"""
+ for root, dirs, files in os.walk(path_repo):
+ for file in files:
+ notebook_path = os.path.join(root, file)
+ if file.endswith(constants.code_extensions) or file.endswith(constants.ontology_extensions):
+ return False
+ elif file.endswith(".ipynb"):
+ if is_notebook_code(notebook_path):
+ return False
+ elif file.endswith(".rmd") or file.endswith('.Rmd'):
+ if has_code_in_rmd(notebook_path):
+ return False
+ return True
+
+
+def check_static_websites(path_repo, repo_metadata: Result):
+ """Function that analyzes byte size of js,css,html languages and checks if
+ repository contains files not associated with static websites
+
+ The evaluation numbers were extracted from the analysis of 997 css repositories representing libraries nad 998 js repos containing libraries
+ with control repositories .
+
+ """
+ # print(path_repo)
+ nr_files = 0
+ web_files = 0
+ total_size = 0
+ js_size = 0
+ css_size = 0
+ html_file = 0
+ for root, dirs, files in os.walk(path_repo):
+ for file in files:
+ file_path = os.path.join(root, file)
+ if file.endswith(constants.code_extensions) or file.endswith(
+ constants.ontology_extensions) or file.lower() in (('bower.json', 'package.json')):
+ return False
+ elif file.endswith((".js", ".css", ".scss")):
+ web_files += 1
+ elif file.endswith(".html"):
+ html_file += 1
+ elif file.endswith(".ipynb"):
+ if is_notebook_code(file_path):
+ return False
+ elif file.endswith(".rmd") or file.endswith('.Rmd'):
+ if has_code_in_rmd(file_path):
+ return False
+ try:
+ languages = repo_metadata[constants.CAT_PROGRAMMING_LANGUAGES]
+ print(languages)
+ for language in languages:
+ language_name = language[constants.PROP_RESULT][constants.PROP_NAME]
+ print(language_name)
+ if language_name.lower() == "javascript":
+ js_size += language[constants.PROP_RESULT][constants.PROP_SIZE]
+ print(js_size)
+ elif language_name.lower() == "scss" or language_name.lower() == "css":
+ css_size += language[constants.PROP_RESULT][constants.PROP_SIZE]
+ total_size += language[constants.PROP_RESULT][constants.PROP_SIZE]
+ except Exception as e:
+ print(e)
+ if html_file > 0:
+ if js_size > 0 and css_size == 0:
+ if js_size / total_size < 0.91:
+ return True
+ elif js_size == 0 and css_size > 0:
+ if css_size / total_size < 0.798:
+ return True
+ return True
+
+ return False
+
+
+def check_workflow(repo_path, title):
+ """Function which checks inside text for presence of repository being a workflow and analysis of the
+ files inside to check if they are correct workflow files. Also checks for repositories with no information
+ the name of the files which might point to it being a workflow.
+ PARAMETERS:
+ @repo_path(path to the repository directory)
+ @title(title of the repository)
+ """
+ list = []
+ total_workflows = 0
+ good_workflows = 0
+ for root, dirs, files in os.walk(repo_path):
+ repo_relative_path = os.path.relpath(root, repo_path)
+ for file in files:
+ filename_no_ext = os.path.splitext(file)[0]
+ if "README" == filename_no_ext.upper():
+ if repo_relative_path == ".":
+ try:
+ with open(os.path.join(root, file), "r") as readme_file:
+ readme_contents = readme_file.read()
+
+ title_words = title.split()
+
+ pattern = r'([^.?!]*(?:\b|\W){}(?:\b|\W)[^.?!]*[.?!])'.format(
+ '|'.join(map(re.escape, title_words)))
+ sentences = re.findall(pattern, readme_contents, flags=re.IGNORECASE)
+ for sentence in sentences:
+ if re.search(rf'\b{title}\b', sentence, flags=re.IGNORECASE) and re.search(
+ r'\b(pipeline|workflow)\b', sentence, flags=re.IGNORECASE):
+ return True
+
+ pattern_md = r'##.*\b(workflow|pipeline)\b'
+ pattern_rst = r'^([^=\n]+(?:\n(?![-=]).*)*\b(workflow|pipeline)\b(?:\n(?![-=]).*)*)\n=+'
+
+ match_md = re.findall(pattern_md, readme_contents, re.IGNORECASE)
+ match_rst = re.findall(pattern_rst, readme_contents, re.MULTILINE | re.IGNORECASE)
+
+ if match_md or match_rst:
+ return True
+
+ except:
+ continue
+
+ if file.endswith(constants.workflow_extensions) or file == "Snakefile":
+ total_workflows += 1
+ file_path = os.path.join(root, file)
+ if is_file_workflow(file_path):
+ list.append(file_path)
+ good_workflows += 1
+ else:
+ continue
+ if check_name(file):
+ return True
+ if list != []:
+ return True
+ else:
+ return False
+
+
+def check_name(filename):
+ """Assisting function for check_workflow to look for specific named files"""
+ pattern1 = re.compile(r"pipeline", re.IGNORECASE)
+ pattern2 = re.compile(r"(model|example)", re.IGNORECASE)
+ programming_language_extensions = (
+ ".py", ".java", ".cpp", ".c", ".php", ".rb", ".js", ".html", ".css", ".go", ".swift", ".scala", ".pl", ".ipynb")
+ if pattern1.search(filename) and pattern2.search(filename):
+ if filename.endswith(programming_language_extensions):
+ return True
+ elif pattern1.search(filename) and not pattern2.search(filename):
+ return False
+ elif (not pattern1.search(filename) and not pattern2.search(filename)) or (
+ not pattern1.search(filename) and pattern2.search(filename)):
+ return False
+
+
+def is_notebook_code(file_path):
+ has_code = False
+ num_code_cells = 0
+ num_total_cells = 0
+ try:
+ nb = nbformat.read(file_path, as_version=4)
+
+ for cell in nb['cells']:
+ if cell['cell_type'] == 'code':
+ num_total_cells += 1
+ if cell['source'].strip():
+ num_code_cells += 1
+ has_code = True
+ return has_code
+ except NotJSONError:
+ return False
+ except Exception:
+ return False
+
+
+def has_code_in_rmd(file_path):
+ try:
+ with open(file_path, 'r') as file:
+ content = file.read()
+ if "```{r" in content or "```{python" in content or "```{bash" in content:
+ return True
+ except:
+ return False
diff --git a/src/somef_core/extract_workflows.py b/src/somef_core/extract_workflows.py
index a1426e9..f07037d 100644
--- a/src/somef_core/extract_workflows.py
+++ b/src/somef_core/extract_workflows.py
@@ -1,4 +1,5 @@
import re
+import logging
Galaxy_pattern = r"(?i)a[_\s-]?galaxy[_\s-]?workflow"
CWL_pattern = r"\bclass:\s*[Ww]orkflow\b"
@@ -9,6 +10,32 @@
GitLab_ContinuosIntegration_keywords = [r"script:", r"rules:", r"variables:", r"before_script:", r"after_script:", r"image:"]
+def is_file_workflow(file_path):
+ try:
+ with open(file_path, "rb") as file:
+ raw_data = file.read()
+
+ try:
+ content = raw_data.decode("utf-8")
+ except UnicodeDecodeError:
+ logging.warning(f"File {file_path} is not UTF-8 decodable. Skipping.")
+ return False
+
+ Galaxy_match = re.search(Galaxy_pattern, content)
+ CWL_match = re.search(CWL_pattern, content)
+ Workflow_match = re.search(Workflow_content_pattern, content)
+ Workflow_match_2 = re.search(workflow_pattern, content, re.IGNORECASE)
+ Nextflow_match = re.search(Nextflow_pattern, content)
+
+ if Galaxy_match or CWL_match or Workflow_match or Workflow_match_2 or Nextflow_match:
+ return True
+ else:
+ return False
+
+ except Exception as e:
+ logging.warning(f"Error reading file {file_path}: {e}")
+ return False
+
def is_file_continuous_integration_gitlab(file_path):
"""Detects if a file is a GitLab CI/CD pipeline."""
with open(file_path, 'r') as file:
diff --git a/src/somef_core/header_analysis.py b/src/somef_core/header_analysis.py
index 1545fdb..4a4088d 100644
--- a/src/somef_core/header_analysis.py
+++ b/src/somef_core/header_analysis.py
@@ -9,9 +9,14 @@
from .process_results import Result
from .parser import mardown_parser
from .utils import constants
-
+from typing import Dict, Iterable, List, Tuple
+from functools import lru_cache
pd.options.mode.chained_assignment = None # default='warn'
+
+SIMILARITY_THRESHOLD = 0.8
+
+
# Define wordnet groups
group = dict()
@@ -81,36 +86,69 @@
Word("report").synsets[6]]
group.update({constants.CAT_SUPPORT: support})
-
-def extract_bash_code(text):
- """Function to detect code blocks"""
- split = text.split("```")
- output = []
- if len(split) >= 3:
- for index, value in enumerate(split):
- if index % 2 == 1:
- output.append(split[index])
- return output
-
-
-def extract_header_content(text):
- """Function designed to extract headers and contents of text and place it in a dataframe"""
- header = []
+@lru_cache(maxsize=4096)
+def get_synsets(word: str):
+ """Cached access to WordNet synsets."""
+ return Word(word).synsets
+
+
+@lru_cache(maxsize=16384)
+def path_similarity_cached(sense1, sense2) -> float:
+ """Cached path similarity lookup."""
+ sim = sense1.path_similarity(sense2)
+ return sim if sim is not None else 0.0
+
+# def extract_bash_code(text):
+# """Function to detect code blocks"""
+# split = text.split("```")
+# output = []
+# if len(split) >= 3:
+# for index, value in enumerate(split):
+# if index % 2 == 1:
+# output.append(split[index])
+# return output
+def extract_bash_code(text: str) -> List[str]:
+ blocks = text.split("```")
+ return [blocks[i] for i in range(1, len(blocks), 2)]
+
+# def extract_header_content(text):
+# """Function designed to extract headers and contents of text and place it in a dataframe"""
+# header = []
+# headers = mardown_parser.extract_headers(text)
+# for key in headers.keys():
+# if headers[key]:
+# header.append(key)
+# content, none_header_content = mardown_parser.extract_content_per_header(text, headers)
+# parent_headers = mardown_parser.extract_headers_parents(text)
+# # into dataframe
+# df = pd.DataFrame(columns=['Header', 'Content', 'ParentHeader'])
+# dfs = [pd.DataFrame({'Header': [i], 'Content': [j], 'ParentHeader': [parent_headers.get(i, None)]}) for i, j in
+# zip(header, content)]
+# df = pd.concat(dfs, ignore_index=True)
+# # for i, j in zip(header, content):
+# # df = df.append({'Header': i, 'Content': j, 'ParentHeader': parent_headers[i]}, ignore_index=True)
+# # df['Content'].replace('', np.nan, inplace=True)
+# df['Content'] = df['Content'].replace('', np.nan)
+
+# df.dropna(subset=['Content'], inplace=True)
+# return df, none_header_content
+def extract_header_content(text: str) -> Tuple[pd.DataFrame, str | None]:
headers = mardown_parser.extract_headers(text)
- for key in headers.keys():
- if headers[key]:
- header.append(key)
+ header_list = [h for h, v in headers.items() if v]
+
content, none_header_content = mardown_parser.extract_content_per_header(text, headers)
- parent_headers = mardown_parser.extract_headers_parents(text)
- # into dataframe
- df = pd.DataFrame(columns=['Header', 'Content', 'ParentHeader'])
- dfs = [pd.DataFrame({'Header': [i], 'Content': [j], 'ParentHeader': [parent_headers.get(i, None)]}) for i, j in
- zip(header, content)]
- df = pd.concat(dfs, ignore_index=True)
- # for i, j in zip(header, content):
- # df = df.append({'Header': i, 'Content': j, 'ParentHeader': parent_headers[i]}, ignore_index=True)
- df['Content'].replace('', np.nan, inplace=True)
+ parents = mardown_parser.extract_headers_parents(text)
+
+ df = pd.DataFrame({
+ 'Header': header_list,
+ 'Content': content,
+ 'ParentHeader': [parents.get(h) for h in header_list],
+ })
+
+ # df['Content'].replace('', np.nan, inplace=True)
+ df['Content'] = df['Content'].replace('', np.nan)
df.dropna(subset=['Content'], inplace=True)
+
return df, none_header_content
@@ -136,21 +174,21 @@ def find_sim(wordlist, wd):
return 0
-def match_group(word_syn, group, threshold):
- """Function designed to match a word with a subgroup"""
- currmax = 0
- maxgroup = ""
- simvalues = dict()
- for sense in word_syn: # for a given sense of a word
- similarities = []
- for key, value in group.items(): # value has all the similar words
- path_sim = find_sim(value, sense)
- # print("Similarity is:",path_sim)
- if path_sim > threshold: # then append to the list
- if path_sim > currmax:
- maxgroup = key
- currmax = path_sim
- return maxgroup
+# def match_group(word_syn, group, threshold):
+# """Function designed to match a word with a subgroup"""
+# currmax = 0
+# maxgroup = ""
+# simvalues = dict()
+# for sense in word_syn: # for a given sense of a word
+# similarities = []
+# for key, value in group.items(): # value has all the similar words
+# path_sim = find_sim(value, sense)
+# # print("Similarity is:",path_sim)
+# if path_sim > threshold: # then append to the list
+# if path_sim > currmax:
+# maxgroup = key
+# currmax = path_sim
+# return maxgroup
def label_header(header):
@@ -160,11 +198,12 @@ def label_header(header):
sentence = header_clean.strip().split(" ")
label = []
for s in sentence:
- synn = Word(s).synsets
+ synn = Word(s).synsets
if len(synn) > 0:
- bestgroup = match_group(synn, group, 0.8)
+ # bestgroup = match_group(synn, group, 0.8)
+ bestgroup = match_group(synn)
if bestgroup != "" and bestgroup not in label:
- label.append(bestgroup)
+ label.append(bestgroup)
return label
@@ -180,7 +219,8 @@ def label_parent_headers(parentHeaders):
for s in sentence:
synn = Word(s).synsets
if len(synn) > 0:
- bestgroup = match_group(synn, group, 0.8)
+ # bestgroup = match_group(synn, group, 0.8)
+ bestgroup = match_group(synn)
if bestgroup != "" and bestgroup not in label:
label.append(bestgroup)
return label
@@ -193,75 +233,285 @@ def clean_html(text):
return cleantext
-def extract_categories(repo_data, repository_metadata: Result):
- """
- Function that adds category information extracted using header information
- Parameters
- ----------
- @param repo_data: data to use the header analysis
- @param repository_metadata: Result object with the results found so far in the repo
-
- Returns
- -------
- @return Result with the information added.
- """
+def max_similarity(word_synsets, group_synsets) -> float:
+ return max(
+ (path_similarity_cached(ws, gs) for ws in word_synsets for gs in group_synsets),
+ default=0.0,
+ )
+
+
+WORDNET_GROUPS: Dict[str, List] | None = None
+
+
+def get_groups() -> Dict[str, List]:
+ global WORDNET_GROUPS
+ if WORDNET_GROUPS is None:
+ WORDNET_GROUPS = build_wordnet_groups()
+ return WORDNET_GROUPS
+
+def match_group(word_synsets) -> str:
+ best_group = ""
+ best_score = 0.0
+
+ for key, synsets in get_groups().items():
+ score = max_similarity(word_synsets, synsets)
+ if score > SIMILARITY_THRESHOLD and score > best_score:
+ best_score = score
+ best_group = key
+
+ return best_group
+
+
+# def tokenize_header(text: str) -> Iterable[str]:
+# clean = text.translate(str.maketrans('', '', string.punctuation))
+# return clean.strip().split()
+def tokenize_header(text) -> Iterable[str]:
+ # if list transform to string
+ if isinstance(text, list):
+ text = " ".join(map(str, text))
+ elif text is None:
+ text = ""
+ clean = text.translate(str.maketrans('', '', string.punctuation))
+ return clean.strip().split()
+
+def label_text(text: str) -> List[str]:
+ labels: List[str] = []
+ for token in tokenize_header(text):
+ synsets = get_synsets(token)
+ if synsets:
+ grp = match_group(synsets)
+ if grp and grp not in labels:
+ labels.append(grp)
+ return labels
+# def extract_categories(repo_data, repository_metadata: Result):
+# """
+# Function that adds category information extracted using header information
+# Parameters
+# ----------
+# @param repo_data: data to use the header analysis
+# @param repository_metadata: Result object with the results found so far in the repo
+
+# Returns
+# -------
+# @return Result with the information added.
+# """
+# logging.info("Extracting information using headers")
+# if repo_data is None or repo_data == "" or len(repo_data) == 0:
+# return repository_metadata, []
+# try:
+# data, none_header_content = extract_header_content(repo_data)
+# logging.info('Labeling headers.')
+# if data.empty:
+# logging.warning("File to analyze has no headers")
+# return repository_metadata, [repo_data]
+# data['Group'] = data['Header'].apply(lambda row: label_header(row))
+# data['GroupParent'] = data['ParentHeader'].apply(lambda row: label_parent_headers(row))
+# for i in data.index:
+# if len(data['Group'][i]) == 0 and len(data['GroupParent'][i]) > 0:
+# data.at[i, 'Group'] = data['GroupParent'][i]
+# data = data.drop(columns=['GroupParent'])
+# if len(data['Group'].iloc[0]) == 0:
+# # data['Group'].iloc[0] = ['unknown']
+# data.loc[0, 'Group'] = ['unknown']
+# groups = data.apply(lambda x: pd.Series(x['Group']), axis=1).stack().reset_index(level=1, drop=True)
+
+# groups.name = 'Group'
+# data = data.drop('Group', axis=1).join(groups)
+# if data['Group'].iloc[0] == 'unknown':
+# # data['Group'].iloc[0] = np.NaN
+# data.loc[0, 'Group'] = np.nan
+
+# # to json
+# group = data.loc[(data['Group'] != 'None') & pd.notna(data['Group'])]
+# group.rename(columns={'Content': constants.PROP_VALUE}, inplace=True)
+# group.rename(columns={'Header': constants.PROP_ORIGINAL_HEADER}, inplace=True)
+# group.rename(columns={'ParentHeader': constants.PROP_PARENT_HEADER}, inplace=True)
+# for index, row in group.iterrows():
+# source = ""
+# if constants.CAT_README_URL in repository_metadata.results.keys():
+# source = repository_metadata.results[constants.CAT_README_URL][0]
+# source = source[constants.PROP_RESULT][constants.PROP_VALUE]
+# parent_header = ""
+# if row[constants.PROP_PARENT_HEADER] != "":
+# parent_header = row.loc[constants.PROP_PARENT_HEADER]
+# result = {
+# constants.PROP_VALUE: row.loc[constants.PROP_VALUE],
+# constants.PROP_TYPE: constants.TEXT_EXCERPT,
+# constants.PROP_ORIGINAL_HEADER: row.loc[constants.PROP_ORIGINAL_HEADER]
+# }
+# if parent_header != "" and len(parent_header) > 0:
+# result[constants.PROP_PARENT_HEADER] = parent_header
+# if source != "":
+# repository_metadata.add_result(row.Group, result, 1, constants.TECHNIQUE_HEADER_ANALYSIS, source)
+# else:
+# repository_metadata.add_result(row.Group, result, 1, constants.TECHNIQUE_HEADER_ANALYSIS)
+
+# # strings without tag (they will be classified)
+# string_list = data.loc[data['Group'].isna(), ['Content']].values.squeeze().tolist()
+# if type(string_list) != list:
+# string_list = [string_list]
+# if none_header_content is not None and none_header_content != "":
+# string_list.append(none_header_content.strip())
+# logging.info("Header information extracted.")
+# return repository_metadata, string_list
+# except Exception as e:
+# logging.error("Error while extracting headers: ", str(e))
+# return repository_metadata, [repo_data]
+
+def extract_categories(repo_data: str, repository_metadata: Result) -> Tuple[Result, List[str]]:
logging.info("Extracting information using headers")
- if repo_data is None or repo_data == "" or len(repo_data) == 0:
+
+ if not repo_data:
return repository_metadata, []
+
try:
- data, none_header_content = extract_header_content(repo_data)
- logging.info('Labeling headers.')
- if data.empty:
+ df, none_header_content = extract_header_content(repo_data)
+
+ if df.empty:
logging.warning("File to analyze has no headers")
return repository_metadata, [repo_data]
- data['Group'] = data['Header'].apply(lambda row: label_header(row))
- data['GroupParent'] = data['ParentHeader'].apply(lambda row: label_parent_headers(row))
- for i in data.index:
- if len(data['Group'][i]) == 0 and len(data['GroupParent'][i]) > 0:
- data.at[i, 'Group'] = data['GroupParent'][i]
- data = data.drop(columns=['GroupParent'])
- if len(data['Group'].iloc[0]) == 0:
- data['Group'].iloc[0] = ['unknown']
- groups = data.apply(lambda x: pd.Series(x['Group']), axis=1).stack().reset_index(level=1, drop=True)
-
- groups.name = 'Group'
- data = data.drop('Group', axis=1).join(groups)
- if data['Group'].iloc[0] == 'unknown':
- data['Group'].iloc[0] = np.NaN
-
- # to json
- group = data.loc[(data['Group'] != 'None') & pd.notna(data['Group'])]
- group.rename(columns={'Content': constants.PROP_VALUE}, inplace=True)
- group.rename(columns={'Header': constants.PROP_ORIGINAL_HEADER}, inplace=True)
- group.rename(columns={'ParentHeader': constants.PROP_PARENT_HEADER}, inplace=True)
- for index, row in group.iterrows():
- source = ""
- if constants.CAT_README_URL in repository_metadata.results.keys():
- source = repository_metadata.results[constants.CAT_README_URL][0]
- source = source[constants.PROP_RESULT][constants.PROP_VALUE]
- parent_header = ""
- if row[constants.PROP_PARENT_HEADER] != "":
- parent_header = row.loc[constants.PROP_PARENT_HEADER]
+
+ df['Group'] = df['Header'].map(label_text)
+ df['ParentGroup'] = df['ParentHeader'].fillna('').map(label_text)
+
+ df.loc[df['Group'].str.len() == 0, 'Group'] = df['ParentGroup']
+ df.drop(columns=['ParentGroup'], inplace=True)
+
+ if not df.iloc[0]['Group']:
+ df.loc[df.index[0], 'Group'] = ['unknown']
+
+ df = df.explode('Group')
+ df.loc[df['Group'] == 'unknown', 'Group'] = np.nan
+
+ valid = df[df['Group'].notna()].copy()
+ valid.rename(columns={
+ 'Content': constants.PROP_VALUE,
+ 'Header': constants.PROP_ORIGINAL_HEADER,
+ 'ParentHeader': constants.PROP_PARENT_HEADER,
+ }, inplace=True)
+
+ source = None
+ if constants.CAT_README_URL in repository_metadata.results:
+ source = repository_metadata.results[constants.CAT_README_URL][0]
+ source = source[constants.PROP_RESULT][constants.PROP_VALUE]
+
+ logging.info("Extracting information using headers - iterating over valid entries")
+ logging.info("Valid rows: %s", len(valid))
+
+ for _, row in valid.iterrows():
result = {
- constants.PROP_VALUE: row.loc[constants.PROP_VALUE],
+ constants.PROP_VALUE: row[constants.PROP_VALUE],
constants.PROP_TYPE: constants.TEXT_EXCERPT,
- constants.PROP_ORIGINAL_HEADER: row.loc[constants.PROP_ORIGINAL_HEADER]
+ constants.PROP_ORIGINAL_HEADER: row[constants.PROP_ORIGINAL_HEADER],
}
- if parent_header != "" and len(parent_header) > 0:
- result[constants.PROP_PARENT_HEADER] = parent_header
- if source != "":
- repository_metadata.add_result(row.Group, result, 1, constants.TECHNIQUE_HEADER_ANALYSIS, source)
- else:
- repository_metadata.add_result(row.Group, result, 1, constants.TECHNIQUE_HEADER_ANALYSIS)
-
- # strings without tag (they will be classified)
- string_list = data.loc[data['Group'].isna(), ['Content']].values.squeeze().tolist()
- if type(string_list) != list:
- string_list = [string_list]
- if none_header_content is not None and none_header_content != "":
- string_list.append(none_header_content.strip())
- logging.info("Header information extracted.")
- return repository_metadata, string_list
- except Exception as e:
- logging.error("Error while extracting headers: ", str(e))
+
+ if row[constants.PROP_PARENT_HEADER]:
+ result[constants.PROP_PARENT_HEADER] = row[constants.PROP_PARENT_HEADER]
+
+ repository_metadata.add_result(
+ row['Group'],
+ result,
+ 1,
+ constants.TECHNIQUE_HEADER_ANALYSIS,
+ source,
+ )
+
+ leftovers = df[df['Group'].isna()]['Content'].tolist()
+ if none_header_content:
+ leftovers.append(none_header_content.strip())
+
+ return repository_metadata, leftovers
+
+ except Exception:
+ logging.exception("Error while extracting headers")
return repository_metadata, [repo_data]
+
+
+def build_wordnet_groups() -> Dict[str, List]:
+ """Build WordNet groups lazily."""
+ g: Dict[str, List] = {}
+
+ g[constants.CAT_CITATION] = [
+ Word("citation").synsets[3],
+ Word("reference").synsets[1],
+ Word("cite").synsets[3],
+ ]
+
+ g[constants.CAT_ACKNOWLEDGEMENT] = [Word("acknowledgement").synsets[0]]
+
+ g[constants.CAT_RUN] = [
+ Word("run").synsets[9],
+ Word("run").synsets[34],
+ Word("execute").synsets[4],
+ ]
+
+ g[constants.CAT_INSTALLATION] = [
+ Word("installation").synsets[0],
+ Word("install").synsets[0],
+ Word("setup").synsets[1],
+ Word("prepare").synsets[0],
+ Word("preparation").synsets[0],
+ Word("manual").synsets[0],
+ Word("guide").synsets[2],
+ Word("guide").synsets[9],
+ ]
+
+ g[constants.CAT_DOWNLOAD] = [Word("download").synsets[0]]
+
+ g[constants.CAT_REQUIREMENTS] = [
+ Word("requirement").synsets[2],
+ Word("prerequisite").synsets[0],
+ Word("prerequisite").synsets[1],
+ Word("dependency").synsets[0],
+ Word("dependent").synsets[0],
+ ]
+
+ g[constants.CAT_CONTACT] = [Word("contact").synsets[9]]
+
+ g[constants.CAT_DESCRIPTION] = [
+ Word("description").synsets[0],
+ Word("description").synsets[1],
+ Word("introduction").synsets[3],
+ Word("introduction").synsets[6],
+ Word("basics").synsets[0],
+ Word("initiation").synsets[1],
+ Word("summary").synsets[0],
+ Word("summary").synsets[2],
+ ]
+
+ g[constants.CAT_CONTRIBUTORS] = [Word("contributor").synsets[0]]
+ g[constants.CAT_CONTRIBUTING_GUIDELINES] = [Word("contributing").synsets[1]]
+ g[constants.CAT_DOCUMENTATION] = [Word("documentation").synsets[1]]
+ g[constants.CAT_LICENSE] = [Word("license").synsets[3], Word("license").synsets[0]]
+
+ g[constants.CAT_USAGE] = [
+ Word("usage").synsets[0],
+ Word("example").synsets[0],
+ Word("example").synsets[5],
+ Word("demo").synsets[1],
+ Word("tutorial").synsets[0],
+ Word("tutorial").synsets[1],
+ Word("start").synsets[0],
+ Word("start").synsets[4],
+ Word("started").synsets[0],
+ Word("started").synsets[1],
+ Word("started").synsets[7],
+ Word("started").synsets[8],
+ ]
+
+ g[constants.CAT_FAQ] = [
+ Word("errors").synsets[5],
+ Word("problems").synsets[0],
+ Word("problems").synsets[2],
+ Word("faq").synsets[0],
+ ]
+
+ g[constants.CAT_SUPPORT] = [
+ Word("support").synsets[7],
+ Word("help").synsets[0],
+ Word("help").synsets[9],
+ Word("report").synsets[0],
+ Word("report").synsets[6],
+ ]
+
+ return g
diff --git a/src/somef_core/parser/authors_parser 2.py b/src/somef_core/parser/authors_parser 2.py
new file mode 100644
index 0000000..0a8a2f1
--- /dev/null
+++ b/src/somef_core/parser/authors_parser 2.py
@@ -0,0 +1,81 @@
+import re
+from ..utils import constants
+
+def parse_author_file(author_str):
+ """
+ Process a text with possible authors from markdown-style AUTHORS files.
+ Filters and extracts only lines that match expected person or organization patterns.
+ """
+ if not author_str:
+ return []
+
+ author_str = re.sub(r'\{[^}]*\}', '', author_str, flags=re.DOTALL)
+
+ authors = []
+ lines = author_str.splitlines()
+
+ for i, line in enumerate(lines):
+ line = line.replace("\t", " ").strip()
+ next_line = lines[i + 1].strip() if i + 1 < len(lines) else ""
+ email_match = re.search(r'<[^<>@ ]+@[^<>@ ]+\.[^<>@ ]+>', line)
+
+ if (
+ not line or
+ line.startswith("#") or
+ line.startswith("*") or
+ line.startswith("=") or
+ (line[0].islower() and not email_match) or
+ re.match(r'^\s*\{.*\}\s*$', line) or
+ re.match(r'^https?://', line) or
+ len(re.findall(r'[A-Za-z]', line)) < 2 or
+ (
+ line.endswith(".")
+ and not re.match(r'^([A-Z][a-zA-Z0-9&\-\.]+(?:\s+[A-Z][a-zA-Z0-9&\-\.]+){0,3})\.$', line)
+ and not re.search(constants.REGEXP_LTD_INC, line, re.IGNORECASE)
+ ) or
+ line.endswith(",") or
+ line.endswith(":") or
+ re.match(r'^[A-Z][a-z]+ *:$', line) or
+ re.match(r"^[=\-*]{2,}$", next_line)
+ ):
+ continue
+
+ email_match = re.search(r'<(.*?)>', line)
+ email = email_match.group(1) if email_match else None
+ name_part = line[:email_match.start()].strip() if email_match else line
+
+ name_part = re.sub(r'\(.*?\)', '', name_part)
+
+ parts = name_part.split('-')
+ if len(parts) > 1 and parts[0].strip() == "":
+ name_part = parts[1].strip()
+ else:
+ name_part = parts[0].strip()
+
+ name_words = name_part.split()
+
+ if re.search(constants.REGEXP_LTD_INC, name_part, re.IGNORECASE):
+ raw_author = {
+ "type": "Organization",
+ "name": name_part,
+ "value": name_part
+ }
+ if email:
+ raw_author["email"] = email
+ authors.append(raw_author)
+ continue
+
+ if email or len(name_words) >= 2 and len(name_words) <= 4:
+ raw_author = {
+ "type": "Person",
+ "name": name_part,
+ "value": name_part,
+ "given_name": name_words[0]
+ }
+ if len(name_words) > 1:
+ raw_author["last_name"] = " ".join(name_words[1:])
+ if email:
+ raw_author["email"] = email
+ authors.append(raw_author)
+
+ return authors
\ No newline at end of file
diff --git a/src/somef_core/parser/authors_parser.py b/src/somef_core/parser/authors_parser.py
new file mode 100644
index 0000000..0a8a2f1
--- /dev/null
+++ b/src/somef_core/parser/authors_parser.py
@@ -0,0 +1,81 @@
+import re
+from ..utils import constants
+
+def parse_author_file(author_str):
+ """
+ Process a text with possible authors from markdown-style AUTHORS files.
+ Filters and extracts only lines that match expected person or organization patterns.
+ """
+ if not author_str:
+ return []
+
+ author_str = re.sub(r'\{[^}]*\}', '', author_str, flags=re.DOTALL)
+
+ authors = []
+ lines = author_str.splitlines()
+
+ for i, line in enumerate(lines):
+ line = line.replace("\t", " ").strip()
+ next_line = lines[i + 1].strip() if i + 1 < len(lines) else ""
+ email_match = re.search(r'<[^<>@ ]+@[^<>@ ]+\.[^<>@ ]+>', line)
+
+ if (
+ not line or
+ line.startswith("#") or
+ line.startswith("*") or
+ line.startswith("=") or
+ (line[0].islower() and not email_match) or
+ re.match(r'^\s*\{.*\}\s*$', line) or
+ re.match(r'^https?://', line) or
+ len(re.findall(r'[A-Za-z]', line)) < 2 or
+ (
+ line.endswith(".")
+ and not re.match(r'^([A-Z][a-zA-Z0-9&\-\.]+(?:\s+[A-Z][a-zA-Z0-9&\-\.]+){0,3})\.$', line)
+ and not re.search(constants.REGEXP_LTD_INC, line, re.IGNORECASE)
+ ) or
+ line.endswith(",") or
+ line.endswith(":") or
+ re.match(r'^[A-Z][a-z]+ *:$', line) or
+ re.match(r"^[=\-*]{2,}$", next_line)
+ ):
+ continue
+
+ email_match = re.search(r'<(.*?)>', line)
+ email = email_match.group(1) if email_match else None
+ name_part = line[:email_match.start()].strip() if email_match else line
+
+ name_part = re.sub(r'\(.*?\)', '', name_part)
+
+ parts = name_part.split('-')
+ if len(parts) > 1 and parts[0].strip() == "":
+ name_part = parts[1].strip()
+ else:
+ name_part = parts[0].strip()
+
+ name_words = name_part.split()
+
+ if re.search(constants.REGEXP_LTD_INC, name_part, re.IGNORECASE):
+ raw_author = {
+ "type": "Organization",
+ "name": name_part,
+ "value": name_part
+ }
+ if email:
+ raw_author["email"] = email
+ authors.append(raw_author)
+ continue
+
+ if email or len(name_words) >= 2 and len(name_words) <= 4:
+ raw_author = {
+ "type": "Person",
+ "name": name_part,
+ "value": name_part,
+ "given_name": name_words[0]
+ }
+ if len(name_words) > 1:
+ raw_author["last_name"] = " ".join(name_words[1:])
+ if email:
+ raw_author["email"] = email
+ authors.append(raw_author)
+
+ return authors
\ No newline at end of file
diff --git a/src/somef_core/parser/bower_parser 2.py b/src/somef_core/parser/bower_parser 2.py
new file mode 100644
index 0000000..1479388
--- /dev/null
+++ b/src/somef_core/parser/bower_parser 2.py
@@ -0,0 +1,183 @@
+import json
+import logging
+import os
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+from ..regular_expressions import detect_license_spdx
+
+def parse_bower_json_file(file_path, metadata_result: Result, source):
+ """
+
+ Parameters
+ ----------
+ file_path: path of the bower file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the package file (URL)
+
+ Returns
+ -------
+
+ """
+ try:
+ if Path(file_path).name.lower() in ["bower.json"]:
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": "bower.json",
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, 'r', encoding='utf-8') as file:
+ data = json.load(file)
+
+ if "name" in data:
+ metadata_result.add_result(
+ constants.CAT_NAME,
+ {
+ "value": data["name"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "description" in data:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": data["description"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "homepage" in data:
+ home = data["homepage"]
+ if home and home.strip():
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": data["homepage"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "version" in data:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": data["version"],
+ "type": constants.RELEASE,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "authors" in data:
+ authors_data = data["authors"]
+ if isinstance(authors_data, str):
+ authors_list = [a.strip() for a in authors_data.split(",") if a.strip()]
+ elif isinstance(authors_data, list):
+ authors_list = []
+ for a in authors_data:
+ if isinstance(a, str):
+ authors_list.extend([s.strip() for s in a.split(",") if s.strip()])
+ elif isinstance(a, dict):
+ name = a.get("name", "")
+ email = f" <{a['email']}>" if "email" in a else ""
+ authors_list.append(f"{name}{email}".strip())
+ else:
+ authors_list = []
+
+ for aut in authors_list:
+ # "value": data["authors"],
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ {
+ "value": aut,
+ "type": constants.AGENT
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "license" in data:
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ {
+ "value": data["license"],
+ "type": constants.LICENSE
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ if "dependencies" in data and isinstance(data["dependencies"], dict):
+ for name, version in data["dependencies"].items():
+ req = f"{name}: {version}"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "runtime"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "devDependencies" in data and isinstance(data["devDependencies"], dict):
+ for name, version in data["devDependencies"].items():
+ req = f"{name}: {version}"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "dev"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "keywords" in data:
+ for keyword in data["keywords"]:
+ metadata_result.add_result(
+ constants.CAT_KEYWORDS,
+ {
+ "value": keyword,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ except Exception as e:
+ logging.error(f"Error parsing bower.json from {file_path}: {str(e)}")
+
+ return metadata_result
\ No newline at end of file
diff --git a/src/somef_core/parser/bower_parser.py b/src/somef_core/parser/bower_parser.py
new file mode 100644
index 0000000..1479388
--- /dev/null
+++ b/src/somef_core/parser/bower_parser.py
@@ -0,0 +1,183 @@
+import json
+import logging
+import os
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+from ..regular_expressions import detect_license_spdx
+
+def parse_bower_json_file(file_path, metadata_result: Result, source):
+ """
+
+ Parameters
+ ----------
+ file_path: path of the bower file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the package file (URL)
+
+ Returns
+ -------
+
+ """
+ try:
+ if Path(file_path).name.lower() in ["bower.json"]:
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": "bower.json",
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, 'r', encoding='utf-8') as file:
+ data = json.load(file)
+
+ if "name" in data:
+ metadata_result.add_result(
+ constants.CAT_NAME,
+ {
+ "value": data["name"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "description" in data:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": data["description"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "homepage" in data:
+ home = data["homepage"]
+ if home and home.strip():
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": data["homepage"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "version" in data:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": data["version"],
+ "type": constants.RELEASE,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "authors" in data:
+ authors_data = data["authors"]
+ if isinstance(authors_data, str):
+ authors_list = [a.strip() for a in authors_data.split(",") if a.strip()]
+ elif isinstance(authors_data, list):
+ authors_list = []
+ for a in authors_data:
+ if isinstance(a, str):
+ authors_list.extend([s.strip() for s in a.split(",") if s.strip()])
+ elif isinstance(a, dict):
+ name = a.get("name", "")
+ email = f" <{a['email']}>" if "email" in a else ""
+ authors_list.append(f"{name}{email}".strip())
+ else:
+ authors_list = []
+
+ for aut in authors_list:
+ # "value": data["authors"],
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ {
+ "value": aut,
+ "type": constants.AGENT
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "license" in data:
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ {
+ "value": data["license"],
+ "type": constants.LICENSE
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ if "dependencies" in data and isinstance(data["dependencies"], dict):
+ for name, version in data["dependencies"].items():
+ req = f"{name}: {version}"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "runtime"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "devDependencies" in data and isinstance(data["devDependencies"], dict):
+ for name, version in data["devDependencies"].items():
+ req = f"{name}: {version}"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "dev"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "keywords" in data:
+ for keyword in data["keywords"]:
+ metadata_result.add_result(
+ constants.CAT_KEYWORDS,
+ {
+ "value": keyword,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ except Exception as e:
+ logging.error(f"Error parsing bower.json from {file_path}: {str(e)}")
+
+ return metadata_result
\ No newline at end of file
diff --git a/src/somef_core/parser/cabal_parser 2.py b/src/somef_core/parser/cabal_parser 2.py
new file mode 100644
index 0000000..74ed7bd
--- /dev/null
+++ b/src/somef_core/parser/cabal_parser 2.py
@@ -0,0 +1,221 @@
+import os
+import re
+import logging
+from pathlib import Path
+from ..process_results import Result
+from ..regular_expressions import detect_license_spdx
+from ..utils import constants
+
+def parse_cabal_file(file_path, metadata_result: Result, source):
+ """
+ Parse a .cabal file and extract relevant metadata.
+
+ Parameters
+ ----------
+ file_path: path of the cabal file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the package file (URL)
+
+ Returns
+ """
+
+ try:
+ if file_path.endswith('.cabal'):
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": Path(file_path).name,
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, 'r', encoding='utf-8') as file:
+ content = file.read()
+
+ name_match = re.search(r'name:\s*(.*)', content, re.IGNORECASE)
+ if name_match:
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_ID,
+ {
+ "value": name_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ version_match = re.search(r'version:\s*(.*)', content, re.IGNORECASE)
+ if version_match:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": version_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ # description_match = re.search(r'description:\s*(.*)', content, re.IGNORECASE)
+ cleaned_content = content.replace('\r\n', '\n').replace('\r', '\n')
+ description_regex = re.compile(
+ r'description:\s*(.*?)(?=\n\S|\Z)',
+ re.IGNORECASE | re.DOTALL
+ )
+
+ description_match = description_regex.search(cleaned_content)
+ synopsis_match = re.search(r'synopsis:\s*(.*)', content, re.IGNORECASE)
+ if description_match:
+
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": description_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ if synopsis_match:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": synopsis_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ homepage_match = re.search(r'homepage:\s*(.*)', content, re.IGNORECASE)
+ if homepage_match:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": homepage_match.group(1),
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ stability_match = re.search(r'stability:\s*(.*)', content, re.IGNORECASE)
+ if stability_match:
+ metadata_result.add_result(
+ constants.CAT_DEV_STATUS,
+ {
+ "value": stability_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ bug_reports_match = re.search(r'bug-reports:\s*(.*)', content, re.IGNORECASE)
+ if bug_reports_match:
+ metadata_result.add_result(
+ constants.CAT_ISSUE_TRACKER,
+ {
+ "value": bug_reports_match.group(1),
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ license_match = re.search(r'license:\s*(.*)', content, re.IGNORECASE)
+ if license_match:
+ license_value = license_match.group(1)
+ license_text = ""
+
+ dir_path = os.path.dirname(file_path)
+ license_paths = [
+ os.path.join(dir_path, "LICENSE"),
+ os.path.join(dir_path, "LICENSE.txt"),
+ os.path.join(dir_path, "LICENSE.md")
+ ]
+
+ for license_path in license_paths:
+ if os.path.exists(license_path):
+ with open(license_path, "r", encoding="utf-8") as lf:
+ license_text = lf.read()
+ break
+
+ license_info_spdx = detect_license_spdx(license_text, 'Ruby')
+
+ if license_info_spdx:
+ license_data = {
+ "value": license_value,
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": license_value,
+ "type": constants.LICENSE
+ }
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ library_section_match = re.search(r'library\s*\n(.*?)(?=\n\S|\Z)', content, re.DOTALL | re.IGNORECASE)
+ if library_section_match:
+ library_content = library_section_match.group(1)
+
+ build_depends_match = re.search(
+ r'build-depends:\s*(.*?)(?=\n\s*(?:[A-Za-z0-9_-]+\s*:|if\s|\Z))',
+ library_content,
+ re.DOTALL
+ )
+ # build_depends_match = re.search(r'build-depends:\s*(.*?)(?=\n\s*\w+:|\Z)', library_content, re.DOTALL)
+ if build_depends_match:
+ build_depends_content = build_depends_match.group(1)
+
+ dependencies = re.split(r'[,\n]', build_depends_content)
+
+ for dep_line in dependencies:
+ dep_line = dep_line.strip()
+ if dep_line and not dep_line.startswith(','):
+
+ dep_match = re.match(r'^([a-zA-Z0-9-_]+)\s*(.*?)$', dep_line)
+ if dep_match:
+ name = dep_match.group(1)
+ version_constraint = dep_match.group(2).strip() if dep_match.group(2) else "any"
+ req = f"{name}: {version_constraint}" if version_constraint != "any" else name
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version_constraint,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "runtime"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ except Exception as e:
+ logging.error(f"Error parsing gemspec file from {file_path}: {str(e)}")
+
+ return metadata_result
\ No newline at end of file
diff --git a/src/somef_core/parser/cabal_parser.py b/src/somef_core/parser/cabal_parser.py
new file mode 100644
index 0000000..74ed7bd
--- /dev/null
+++ b/src/somef_core/parser/cabal_parser.py
@@ -0,0 +1,221 @@
+import os
+import re
+import logging
+from pathlib import Path
+from ..process_results import Result
+from ..regular_expressions import detect_license_spdx
+from ..utils import constants
+
+def parse_cabal_file(file_path, metadata_result: Result, source):
+ """
+ Parse a .cabal file and extract relevant metadata.
+
+ Parameters
+ ----------
+ file_path: path of the cabal file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the package file (URL)
+
+ Returns
+ """
+
+ try:
+ if file_path.endswith('.cabal'):
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": Path(file_path).name,
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, 'r', encoding='utf-8') as file:
+ content = file.read()
+
+ name_match = re.search(r'name:\s*(.*)', content, re.IGNORECASE)
+ if name_match:
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_ID,
+ {
+ "value": name_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ version_match = re.search(r'version:\s*(.*)', content, re.IGNORECASE)
+ if version_match:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": version_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ # description_match = re.search(r'description:\s*(.*)', content, re.IGNORECASE)
+ cleaned_content = content.replace('\r\n', '\n').replace('\r', '\n')
+ description_regex = re.compile(
+ r'description:\s*(.*?)(?=\n\S|\Z)',
+ re.IGNORECASE | re.DOTALL
+ )
+
+ description_match = description_regex.search(cleaned_content)
+ synopsis_match = re.search(r'synopsis:\s*(.*)', content, re.IGNORECASE)
+ if description_match:
+
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": description_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ if synopsis_match:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": synopsis_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ homepage_match = re.search(r'homepage:\s*(.*)', content, re.IGNORECASE)
+ if homepage_match:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": homepage_match.group(1),
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ stability_match = re.search(r'stability:\s*(.*)', content, re.IGNORECASE)
+ if stability_match:
+ metadata_result.add_result(
+ constants.CAT_DEV_STATUS,
+ {
+ "value": stability_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ bug_reports_match = re.search(r'bug-reports:\s*(.*)', content, re.IGNORECASE)
+ if bug_reports_match:
+ metadata_result.add_result(
+ constants.CAT_ISSUE_TRACKER,
+ {
+ "value": bug_reports_match.group(1),
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ license_match = re.search(r'license:\s*(.*)', content, re.IGNORECASE)
+ if license_match:
+ license_value = license_match.group(1)
+ license_text = ""
+
+ dir_path = os.path.dirname(file_path)
+ license_paths = [
+ os.path.join(dir_path, "LICENSE"),
+ os.path.join(dir_path, "LICENSE.txt"),
+ os.path.join(dir_path, "LICENSE.md")
+ ]
+
+ for license_path in license_paths:
+ if os.path.exists(license_path):
+ with open(license_path, "r", encoding="utf-8") as lf:
+ license_text = lf.read()
+ break
+
+ license_info_spdx = detect_license_spdx(license_text, 'Ruby')
+
+ if license_info_spdx:
+ license_data = {
+ "value": license_value,
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": license_value,
+ "type": constants.LICENSE
+ }
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ library_section_match = re.search(r'library\s*\n(.*?)(?=\n\S|\Z)', content, re.DOTALL | re.IGNORECASE)
+ if library_section_match:
+ library_content = library_section_match.group(1)
+
+ build_depends_match = re.search(
+ r'build-depends:\s*(.*?)(?=\n\s*(?:[A-Za-z0-9_-]+\s*:|if\s|\Z))',
+ library_content,
+ re.DOTALL
+ )
+ # build_depends_match = re.search(r'build-depends:\s*(.*?)(?=\n\s*\w+:|\Z)', library_content, re.DOTALL)
+ if build_depends_match:
+ build_depends_content = build_depends_match.group(1)
+
+ dependencies = re.split(r'[,\n]', build_depends_content)
+
+ for dep_line in dependencies:
+ dep_line = dep_line.strip()
+ if dep_line and not dep_line.startswith(','):
+
+ dep_match = re.match(r'^([a-zA-Z0-9-_]+)\s*(.*?)$', dep_line)
+ if dep_match:
+ name = dep_match.group(1)
+ version_constraint = dep_match.group(2).strip() if dep_match.group(2) else "any"
+ req = f"{name}: {version_constraint}" if version_constraint != "any" else name
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version_constraint,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "runtime"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ except Exception as e:
+ logging.error(f"Error parsing gemspec file from {file_path}: {str(e)}")
+
+ return metadata_result
\ No newline at end of file
diff --git a/src/somef_core/parser/codemeta_parser 2.py b/src/somef_core/parser/codemeta_parser 2.py
new file mode 100644
index 0000000..6c6098a
--- /dev/null
+++ b/src/somef_core/parser/codemeta_parser 2.py
@@ -0,0 +1,695 @@
+import json
+import logging
+from ..process_results import Result
+from ..utils import constants
+import re
+
+
+def parse_keywords(keywords_data):
+ """
+ Parse keywords from codemeta.json file
+
+ Parameters
+ ----------
+ keywords_data: str or list
+ The keywords data from codemeta.json, can be a comma-separated string or a list
+
+ Returns
+ -------
+ list
+ List of processed keywords
+ """
+ processed_keywords = []
+ if isinstance(keywords_data, str):
+ for k in keywords_data.split(","):
+ k = k.strip()
+ if k:
+ processed_keywords.append(k)
+ return processed_keywords
+ elif isinstance(keywords_data, list):
+ for item in keywords_data:
+ if isinstance(item, str):
+ sub_parts = item.split(",")
+ for sub_part in sub_parts:
+ processed_keywords.append(sub_part.strip())
+ else:
+ processed_keywords.append(str(item).strip())
+ return processed_keywords
+ return processed_keywords
+
+
+def parse_license(license_data):
+ """
+ Parse license information from codemeta.json
+
+ Parameters
+ ----------
+ license_data: dict or str
+ The license data from codemeta.json
+
+ Returns
+ -------
+ dict or None
+ Processed license information with keys: name, url, identifier, spdx_id
+ """
+ license_info = {}
+ if isinstance(license_data, dict):
+ license_info["name"] = license_data.get("name")
+ license_info["url"] = license_data.get("url")
+ license_info["identifier"] = license_data.get("identifier")
+
+ identifier = license_info.get("identifier", "")
+ if "spdx.org/licenses/" in identifier:
+ spdx_id = identifier.split("spdx.org/licenses/")[-1].split("/")[0]
+ license_info["spdx_id"] = spdx_id
+ elif isinstance(license_data, str):
+ license_info["name"] = license_data
+ license_info["identifier"] = f"https://spdx.org/licenses/{license_data}"
+ license_info["spdx_id"] = license_data
+ else:
+ return None
+ return license_info
+
+
+def parse_software_requirements(requirements_data):
+ """
+ Parse software requirements information from codemeta.json
+
+ Parameters
+ ----------
+ requirements_data: list or str
+ The software requirements data from codemeta.json
+
+ Returns
+ -------
+ list
+ """
+ requirements = []
+
+ if isinstance(requirements_data, str):
+ requirements_data = [requirements_data]
+
+ if isinstance(requirements_data, list):
+ for req in requirements_data:
+ if isinstance(req, str):
+ original = req.strip()
+
+ match = re.match(r'^([a-zA-Z0-9_.\-]+)([<>=!~].*)?$', original)
+ if match:
+ name = match.group(1)
+ version = match.group(2).strip() if match.group(2) else None
+ requirements.append({
+ "value": original,
+ # "name": name,
+ # "version": version
+ **({"name": name} if name else {}),
+ **({"version": version} if version else {})
+ })
+ else:
+ requirements.append({
+ "value": original
+ })
+ elif isinstance(req, dict):
+ # Handle structured object format
+ name = req.get("name") or req.get("identifier")
+ version = req.get("version")
+ identifier = req.get("identifier")
+
+ if name:
+ requirement_dict = {
+ "value": name,
+ "name": name
+ }
+
+ if version:
+ requirement_dict["version"] = version
+ requirement_dict["value"] = f"{name}=={version}" if version else name
+
+ if identifier and identifier != name:
+ requirement_dict["identifier"] = identifier
+
+ requirements.append(requirement_dict)
+
+ return requirements
+
+
+def parse_referenced_publication(reference_data):
+ """
+ Parse referenced publication information from codemeta.json
+
+ Parameters
+ ----------
+ reference_data: dict
+ The reference publication data from codemeta.json
+
+ Returns
+ -------
+ dict or None
+ """
+ if isinstance(reference_data, dict):
+ return {
+ "title": reference_data.get("name") or reference_data.get("title"),
+ "author": reference_data.get("author"),
+ "url": reference_data.get("url"),
+ "date_published": reference_data.get("datePublished"),
+ "identifier": reference_data.get("identifier")
+ }
+ return None
+
+
+def parse_funding(funding_data):
+ """
+ Parse funding information from codemeta.json
+
+ Parameters
+ ----------
+ funding_data: dict, str
+ The funding data from codemeta.json
+
+ Returns
+ -------
+ dict or None
+ """
+ if isinstance(funding_data, dict):
+ funder_name = None
+ if "funder" in funding_data:
+ funder = funding_data["funder"]
+ if isinstance(funder, dict):
+ funder_name = funder.get("name")
+
+ return {
+ "funder": funder_name,
+ "funding": funding_data.get("fundingIdentifier")
+ }
+ elif isinstance(funding_data, str):
+ return {
+ "funder": None,
+ "funding": funding_data
+ }
+
+ return None
+
+def parse_programming_language(language_data):
+ """
+ Parse programming language information from codemeta.json
+
+ Parameters
+ ----------
+ language_data: dict or str
+ The programming language data from codemeta.json
+
+ Returns
+ -------
+ dict or None
+ Processed programming language information
+ """
+ if isinstance(language_data, dict):
+ name = language_data.get("name")
+ version = language_data.get("version")
+ url = language_data.get("url")
+
+ if name:
+ lang_info = {
+ "name": name,
+ "value": name,
+ "type": constants.LANGUAGE
+ # "version": version if version is not None else None
+ }
+ if version:
+ lang_info["version"] = version
+
+ if url:
+ lang_info["url"] = url
+
+ return lang_info
+
+ elif isinstance(language_data, str):
+ return {
+ "name": language_data,
+ "value": language_data,
+ "type": constants.LANGUAGE
+ # ,
+ # "version": None
+ }
+
+ return None
+
+def parse_codemeta_json_file(file_path, metadata_result: Result, source):
+ """
+
+ Parameters
+ ----------
+ file_path: path of the package file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the codemeta file (URL)
+
+ Returns
+ -------
+
+ """
+ print(f"CODEMETA PARSER - Processing file: {file_path}")
+ print(f"CODEMETA PARSER - Source: {source}")
+
+ try:
+ with open(file_path, 'r', encoding='utf-8') as file:
+ data = json.load(file)
+
+ if "applicationCategory" in data:
+ metadata_result.add_result(
+ constants.CAT_APPLICATION_DOMAIN,
+ {
+ "value": data["applicationCategory"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "softwareVersion" in data:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": data["softwareVersion"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "codeRepository" in data:
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": data["codeRepository"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "issueTracker" in data:
+ metadata_result.add_result(
+ constants.CAT_ISSUE_TRACKER,
+ {
+ "value": data["issueTracker"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "dateCreated" in data:
+ date_created = data["dateCreated"]
+ if date_created:
+ metadata_result.add_result(
+ constants.CAT_DATE_CREATED,
+ {
+ "value": date_created,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "dateModified" in data:
+ date_modified = data["dateModified"]
+ if date_modified:
+ metadata_result.add_result(
+ constants.CAT_DATE_UPDATED,
+ {
+ "value": date_modified,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "datePublished" in data:
+ date_published = data["datePublished"]
+ if date_published:
+ metadata_result.add_result(
+ constants.CAT_DATE_PUBLISHED,
+ {
+ "value": date_published,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "downloadUrl" in data:
+ metadata_result.add_result(
+ constants.CAT_DOWNLOAD_URL,
+ {
+ "value": data["downloadUrl"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "name" in data:
+ metadata_result.add_result(
+ constants.CAT_NAME,
+ {
+ "value": data["name"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "contIntegration" in data:
+ metadata_result.add_result(
+ constants.CAT_CONTINUOUS_INTEGRATION,
+ {
+ "value": data["contIntegration"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "keywords" in data:
+ keywords = parse_keywords(data['keywords'])
+ metadata_result.add_result(
+ constants.CAT_KEYWORDS,
+ {
+ "value": keywords,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "referencePublication" in data:
+ ref_publications = data["referencePublication"]
+ if isinstance(ref_publications, list):
+
+ for pub in ref_publications:
+ pub_data = parse_referenced_publication(pub)
+ if pub_data:
+
+ result_dict = {
+ "value": pub_data.get("title", ""),
+ "title": pub_data.get("title", ""),
+ "type": constants.SCHOLARLY_ARTICLE
+ }
+
+ if pub_data.get("url"):
+ result_dict["url"] = pub_data.get("url")
+
+ if pub_data.get("date_published"):
+ result_dict["date_published"] = pub_data.get("date_published")
+
+ if pub_data.get("identifier"):
+ result_dict["doi"] = pub_data.get("identifier")
+
+ metadata_result.add_result(
+ # constants.CAT_REF_PUBLICATION,
+ constants.CAT_CITATION,
+ result_dict,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ elif isinstance(ref_publications, dict):
+
+ pub_data = parse_referenced_publication(ref_publications)
+ if pub_data:
+ result_dict = {
+ "value": pub_data.get("title", ""),
+ "title": pub_data.get("title", ""),
+ "type": constants.SCHOLARLY_ARTICLE
+ }
+
+ if pub_data.get("url"):
+ result_dict["url"] = pub_data.get("url")
+
+ if pub_data.get("date_published"):
+ result_dict["date_published"] = pub_data.get("date_published")
+
+ if pub_data.get("identifier"):
+ result_dict["doi"] = pub_data.get("identifier")
+
+ metadata_result.add_result(
+ # constants.CAT_REF_PUBLICATION,
+ constants.CAT_CITATION,
+ result_dict,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ else:
+ metadata_result.add_result(
+ # constants.CAT_REF_PUBLICATION,
+ constants.CAT_CITATION,
+ {
+ "value": data["referencePublication"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "funding" in data:
+ funding_data = data["funding"]
+ if isinstance(funding_data, list):
+ for fund in funding_data:
+ fund_info = parse_funding(fund)
+ if fund_info:
+ metadata_result.add_result(
+ constants.CAT_FUNDING,
+ {
+ "funder": fund_info.get("funder", ""),
+ "funding": fund_info.get("funding", ""),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ elif isinstance(funding_data, dict):
+ fund_info = parse_funding(funding_data)
+ if fund_info:
+ metadata_result.add_result(
+ constants.CAT_FUNDING,
+ {
+ "funder": fund_info.get("funder", ""),
+ "funding": fund_info.get("funding", ""),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "developmentStatus" in data:
+ metadata_result.add_result(
+ constants.CAT_DEV_STATUS,
+ {
+ "value": data["developmentStatus"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "identifier" in data:
+ metadata_result.add_result(
+ constants.CAT_IDENTIFIER,
+ {
+ "value": data["identifier"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "readme" in data:
+ metadata_result.add_result(
+ constants.CAT_README_URL,
+ {
+ "value": data["readme"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "description" in data:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": data["description"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "version" in data:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": data["version"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "author" in data:
+ authors = data["author"]
+ if isinstance(authors, list):
+ for author in authors:
+ if isinstance(author, dict):
+ author_name = ""
+ if "givenName" in author and "familyName" in author:
+ author_name = f"{author['givenName']} {author['familyName']}"
+ elif "name" in author:
+ author_name = author["name"]
+
+ if author_name:
+ author_info = {
+ "value": author_name,
+ "type": constants.STRING
+ }
+
+ if "email" in author:
+ author_info["email"] = author["email"]
+
+ if "affiliation" in author:
+ if isinstance(author["affiliation"], dict) and "name" in author["affiliation"]:
+ author_info["affiliation"] = author["affiliation"]["name"]
+ elif isinstance(author["affiliation"], str):
+ author_info["affiliation"] = author["affiliation"]
+
+ identifier = author.get("identifier") or author.get("@id")
+ if identifier:
+ author_info["identifier"] = identifier
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author_info,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ elif isinstance(authors, dict):
+ author = authors
+ author_name = ""
+ if "givenName" in author and "familyName" in author:
+ author_name = f"{author['givenName']} {author['familyName']}"
+ elif "name" in author:
+ author_name = author["name"]
+
+ if author_name:
+ author_info = {
+ "value": author_name,
+ "type": constants.STRING
+ }
+
+ if "email" in author:
+ author_info["email"] = author["email"]
+
+ if "affiliation" in author and "name" in author["affiliation"]:
+ author_info["affiliation"] = author["affiliation"]["name"]
+
+ if "identifier" in author:
+ author_info["identifier"] = author["identifier"]
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author_info,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "license" in data:
+ license_info = parse_license(data["license"])
+ if license_info:
+ result_dict = {
+ "value": license_info.get("name", ""),
+ "type": constants.LICENSE
+ }
+
+ if license_info.get("url"):
+ result_dict["url"] = license_info["url"]
+ if license_info.get("identifier"):
+ result_dict["identifier"] = license_info["identifier"]
+ if license_info.get("spdx_id"):
+ result_dict["spdx_id"] = license_info["spdx_id"]
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ result_dict,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "softwareRequirements" in data:
+ requirements = parse_software_requirements(data["softwareRequirements"])
+ for requirement in requirements:
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": requirement.get("value"),
+ # "name": requirement.get("name"),
+ # "version": requirement.get("version"),
+ **({"name": requirement["name"]} if "name" in requirement else {}),
+ **({"version": requirement["version"]} if "version" in requirement else {}),
+ "type": constants.SOFTWARE_APPLICATION
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ if "programmingLanguage" in data:
+ programming_language = data["programmingLanguage"]
+ if isinstance(programming_language, list):
+ for lang in programming_language:
+ lang_info = parse_programming_language(lang)
+ if lang_info:
+ metadata_result.add_result(
+ constants.CAT_PROGRAMMING_LANGUAGES,
+ lang_info,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ else:
+ lang_info = parse_programming_language(programming_language)
+ if lang_info:
+ metadata_result.add_result(
+ constants.CAT_PROGRAMMING_LANGUAGES,
+ lang_info,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ except Exception as e:
+ logging.error(f"Error parsing codemeta JSON file {file_path}: {str(e)}")
+
+ return metadata_result
+
diff --git a/src/somef_core/parser/codemeta_parser.py b/src/somef_core/parser/codemeta_parser.py
new file mode 100644
index 0000000..6c6098a
--- /dev/null
+++ b/src/somef_core/parser/codemeta_parser.py
@@ -0,0 +1,695 @@
+import json
+import logging
+from ..process_results import Result
+from ..utils import constants
+import re
+
+
+def parse_keywords(keywords_data):
+ """
+ Parse keywords from codemeta.json file
+
+ Parameters
+ ----------
+ keywords_data: str or list
+ The keywords data from codemeta.json, can be a comma-separated string or a list
+
+ Returns
+ -------
+ list
+ List of processed keywords
+ """
+ processed_keywords = []
+ if isinstance(keywords_data, str):
+ for k in keywords_data.split(","):
+ k = k.strip()
+ if k:
+ processed_keywords.append(k)
+ return processed_keywords
+ elif isinstance(keywords_data, list):
+ for item in keywords_data:
+ if isinstance(item, str):
+ sub_parts = item.split(",")
+ for sub_part in sub_parts:
+ processed_keywords.append(sub_part.strip())
+ else:
+ processed_keywords.append(str(item).strip())
+ return processed_keywords
+ return processed_keywords
+
+
+def parse_license(license_data):
+ """
+ Parse license information from codemeta.json
+
+ Parameters
+ ----------
+ license_data: dict or str
+ The license data from codemeta.json
+
+ Returns
+ -------
+ dict or None
+ Processed license information with keys: name, url, identifier, spdx_id
+ """
+ license_info = {}
+ if isinstance(license_data, dict):
+ license_info["name"] = license_data.get("name")
+ license_info["url"] = license_data.get("url")
+ license_info["identifier"] = license_data.get("identifier")
+
+ identifier = license_info.get("identifier", "")
+ if "spdx.org/licenses/" in identifier:
+ spdx_id = identifier.split("spdx.org/licenses/")[-1].split("/")[0]
+ license_info["spdx_id"] = spdx_id
+ elif isinstance(license_data, str):
+ license_info["name"] = license_data
+ license_info["identifier"] = f"https://spdx.org/licenses/{license_data}"
+ license_info["spdx_id"] = license_data
+ else:
+ return None
+ return license_info
+
+
+def parse_software_requirements(requirements_data):
+ """
+ Parse software requirements information from codemeta.json
+
+ Parameters
+ ----------
+ requirements_data: list or str
+ The software requirements data from codemeta.json
+
+ Returns
+ -------
+ list
+ """
+ requirements = []
+
+ if isinstance(requirements_data, str):
+ requirements_data = [requirements_data]
+
+ if isinstance(requirements_data, list):
+ for req in requirements_data:
+ if isinstance(req, str):
+ original = req.strip()
+
+ match = re.match(r'^([a-zA-Z0-9_.\-]+)([<>=!~].*)?$', original)
+ if match:
+ name = match.group(1)
+ version = match.group(2).strip() if match.group(2) else None
+ requirements.append({
+ "value": original,
+ # "name": name,
+ # "version": version
+ **({"name": name} if name else {}),
+ **({"version": version} if version else {})
+ })
+ else:
+ requirements.append({
+ "value": original
+ })
+ elif isinstance(req, dict):
+ # Handle structured object format
+ name = req.get("name") or req.get("identifier")
+ version = req.get("version")
+ identifier = req.get("identifier")
+
+ if name:
+ requirement_dict = {
+ "value": name,
+ "name": name
+ }
+
+ if version:
+ requirement_dict["version"] = version
+ requirement_dict["value"] = f"{name}=={version}" if version else name
+
+ if identifier and identifier != name:
+ requirement_dict["identifier"] = identifier
+
+ requirements.append(requirement_dict)
+
+ return requirements
+
+
+def parse_referenced_publication(reference_data):
+ """
+ Parse referenced publication information from codemeta.json
+
+ Parameters
+ ----------
+ reference_data: dict
+ The reference publication data from codemeta.json
+
+ Returns
+ -------
+ dict or None
+ """
+ if isinstance(reference_data, dict):
+ return {
+ "title": reference_data.get("name") or reference_data.get("title"),
+ "author": reference_data.get("author"),
+ "url": reference_data.get("url"),
+ "date_published": reference_data.get("datePublished"),
+ "identifier": reference_data.get("identifier")
+ }
+ return None
+
+
+def parse_funding(funding_data):
+ """
+ Parse funding information from codemeta.json
+
+ Parameters
+ ----------
+ funding_data: dict, str
+ The funding data from codemeta.json
+
+ Returns
+ -------
+ dict or None
+ """
+ if isinstance(funding_data, dict):
+ funder_name = None
+ if "funder" in funding_data:
+ funder = funding_data["funder"]
+ if isinstance(funder, dict):
+ funder_name = funder.get("name")
+
+ return {
+ "funder": funder_name,
+ "funding": funding_data.get("fundingIdentifier")
+ }
+ elif isinstance(funding_data, str):
+ return {
+ "funder": None,
+ "funding": funding_data
+ }
+
+ return None
+
+def parse_programming_language(language_data):
+ """
+ Parse programming language information from codemeta.json
+
+ Parameters
+ ----------
+ language_data: dict or str
+ The programming language data from codemeta.json
+
+ Returns
+ -------
+ dict or None
+ Processed programming language information
+ """
+ if isinstance(language_data, dict):
+ name = language_data.get("name")
+ version = language_data.get("version")
+ url = language_data.get("url")
+
+ if name:
+ lang_info = {
+ "name": name,
+ "value": name,
+ "type": constants.LANGUAGE
+ # "version": version if version is not None else None
+ }
+ if version:
+ lang_info["version"] = version
+
+ if url:
+ lang_info["url"] = url
+
+ return lang_info
+
+ elif isinstance(language_data, str):
+ return {
+ "name": language_data,
+ "value": language_data,
+ "type": constants.LANGUAGE
+ # ,
+ # "version": None
+ }
+
+ return None
+
+def parse_codemeta_json_file(file_path, metadata_result: Result, source):
+ """
+
+ Parameters
+ ----------
+ file_path: path of the package file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the codemeta file (URL)
+
+ Returns
+ -------
+
+ """
+ print(f"CODEMETA PARSER - Processing file: {file_path}")
+ print(f"CODEMETA PARSER - Source: {source}")
+
+ try:
+ with open(file_path, 'r', encoding='utf-8') as file:
+ data = json.load(file)
+
+ if "applicationCategory" in data:
+ metadata_result.add_result(
+ constants.CAT_APPLICATION_DOMAIN,
+ {
+ "value": data["applicationCategory"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "softwareVersion" in data:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": data["softwareVersion"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "codeRepository" in data:
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": data["codeRepository"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "issueTracker" in data:
+ metadata_result.add_result(
+ constants.CAT_ISSUE_TRACKER,
+ {
+ "value": data["issueTracker"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "dateCreated" in data:
+ date_created = data["dateCreated"]
+ if date_created:
+ metadata_result.add_result(
+ constants.CAT_DATE_CREATED,
+ {
+ "value": date_created,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "dateModified" in data:
+ date_modified = data["dateModified"]
+ if date_modified:
+ metadata_result.add_result(
+ constants.CAT_DATE_UPDATED,
+ {
+ "value": date_modified,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "datePublished" in data:
+ date_published = data["datePublished"]
+ if date_published:
+ metadata_result.add_result(
+ constants.CAT_DATE_PUBLISHED,
+ {
+ "value": date_published,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "downloadUrl" in data:
+ metadata_result.add_result(
+ constants.CAT_DOWNLOAD_URL,
+ {
+ "value": data["downloadUrl"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "name" in data:
+ metadata_result.add_result(
+ constants.CAT_NAME,
+ {
+ "value": data["name"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "contIntegration" in data:
+ metadata_result.add_result(
+ constants.CAT_CONTINUOUS_INTEGRATION,
+ {
+ "value": data["contIntegration"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "keywords" in data:
+ keywords = parse_keywords(data['keywords'])
+ metadata_result.add_result(
+ constants.CAT_KEYWORDS,
+ {
+ "value": keywords,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "referencePublication" in data:
+ ref_publications = data["referencePublication"]
+ if isinstance(ref_publications, list):
+
+ for pub in ref_publications:
+ pub_data = parse_referenced_publication(pub)
+ if pub_data:
+
+ result_dict = {
+ "value": pub_data.get("title", ""),
+ "title": pub_data.get("title", ""),
+ "type": constants.SCHOLARLY_ARTICLE
+ }
+
+ if pub_data.get("url"):
+ result_dict["url"] = pub_data.get("url")
+
+ if pub_data.get("date_published"):
+ result_dict["date_published"] = pub_data.get("date_published")
+
+ if pub_data.get("identifier"):
+ result_dict["doi"] = pub_data.get("identifier")
+
+ metadata_result.add_result(
+ # constants.CAT_REF_PUBLICATION,
+ constants.CAT_CITATION,
+ result_dict,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ elif isinstance(ref_publications, dict):
+
+ pub_data = parse_referenced_publication(ref_publications)
+ if pub_data:
+ result_dict = {
+ "value": pub_data.get("title", ""),
+ "title": pub_data.get("title", ""),
+ "type": constants.SCHOLARLY_ARTICLE
+ }
+
+ if pub_data.get("url"):
+ result_dict["url"] = pub_data.get("url")
+
+ if pub_data.get("date_published"):
+ result_dict["date_published"] = pub_data.get("date_published")
+
+ if pub_data.get("identifier"):
+ result_dict["doi"] = pub_data.get("identifier")
+
+ metadata_result.add_result(
+ # constants.CAT_REF_PUBLICATION,
+ constants.CAT_CITATION,
+ result_dict,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ else:
+ metadata_result.add_result(
+ # constants.CAT_REF_PUBLICATION,
+ constants.CAT_CITATION,
+ {
+ "value": data["referencePublication"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "funding" in data:
+ funding_data = data["funding"]
+ if isinstance(funding_data, list):
+ for fund in funding_data:
+ fund_info = parse_funding(fund)
+ if fund_info:
+ metadata_result.add_result(
+ constants.CAT_FUNDING,
+ {
+ "funder": fund_info.get("funder", ""),
+ "funding": fund_info.get("funding", ""),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ elif isinstance(funding_data, dict):
+ fund_info = parse_funding(funding_data)
+ if fund_info:
+ metadata_result.add_result(
+ constants.CAT_FUNDING,
+ {
+ "funder": fund_info.get("funder", ""),
+ "funding": fund_info.get("funding", ""),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "developmentStatus" in data:
+ metadata_result.add_result(
+ constants.CAT_DEV_STATUS,
+ {
+ "value": data["developmentStatus"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "identifier" in data:
+ metadata_result.add_result(
+ constants.CAT_IDENTIFIER,
+ {
+ "value": data["identifier"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "readme" in data:
+ metadata_result.add_result(
+ constants.CAT_README_URL,
+ {
+ "value": data["readme"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "description" in data:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": data["description"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "version" in data:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": data["version"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "author" in data:
+ authors = data["author"]
+ if isinstance(authors, list):
+ for author in authors:
+ if isinstance(author, dict):
+ author_name = ""
+ if "givenName" in author and "familyName" in author:
+ author_name = f"{author['givenName']} {author['familyName']}"
+ elif "name" in author:
+ author_name = author["name"]
+
+ if author_name:
+ author_info = {
+ "value": author_name,
+ "type": constants.STRING
+ }
+
+ if "email" in author:
+ author_info["email"] = author["email"]
+
+ if "affiliation" in author:
+ if isinstance(author["affiliation"], dict) and "name" in author["affiliation"]:
+ author_info["affiliation"] = author["affiliation"]["name"]
+ elif isinstance(author["affiliation"], str):
+ author_info["affiliation"] = author["affiliation"]
+
+ identifier = author.get("identifier") or author.get("@id")
+ if identifier:
+ author_info["identifier"] = identifier
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author_info,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ elif isinstance(authors, dict):
+ author = authors
+ author_name = ""
+ if "givenName" in author and "familyName" in author:
+ author_name = f"{author['givenName']} {author['familyName']}"
+ elif "name" in author:
+ author_name = author["name"]
+
+ if author_name:
+ author_info = {
+ "value": author_name,
+ "type": constants.STRING
+ }
+
+ if "email" in author:
+ author_info["email"] = author["email"]
+
+ if "affiliation" in author and "name" in author["affiliation"]:
+ author_info["affiliation"] = author["affiliation"]["name"]
+
+ if "identifier" in author:
+ author_info["identifier"] = author["identifier"]
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author_info,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "license" in data:
+ license_info = parse_license(data["license"])
+ if license_info:
+ result_dict = {
+ "value": license_info.get("name", ""),
+ "type": constants.LICENSE
+ }
+
+ if license_info.get("url"):
+ result_dict["url"] = license_info["url"]
+ if license_info.get("identifier"):
+ result_dict["identifier"] = license_info["identifier"]
+ if license_info.get("spdx_id"):
+ result_dict["spdx_id"] = license_info["spdx_id"]
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ result_dict,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "softwareRequirements" in data:
+ requirements = parse_software_requirements(data["softwareRequirements"])
+ for requirement in requirements:
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": requirement.get("value"),
+ # "name": requirement.get("name"),
+ # "version": requirement.get("version"),
+ **({"name": requirement["name"]} if "name" in requirement else {}),
+ **({"version": requirement["version"]} if "version" in requirement else {}),
+ "type": constants.SOFTWARE_APPLICATION
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ if "programmingLanguage" in data:
+ programming_language = data["programmingLanguage"]
+ if isinstance(programming_language, list):
+ for lang in programming_language:
+ lang_info = parse_programming_language(lang)
+ if lang_info:
+ metadata_result.add_result(
+ constants.CAT_PROGRAMMING_LANGUAGES,
+ lang_info,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ else:
+ lang_info = parse_programming_language(programming_language)
+ if lang_info:
+ metadata_result.add_result(
+ constants.CAT_PROGRAMMING_LANGUAGES,
+ lang_info,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ except Exception as e:
+ logging.error(f"Error parsing codemeta JSON file {file_path}: {str(e)}")
+
+ return metadata_result
+
diff --git a/src/somef_core/parser/composer_parser 2.py b/src/somef_core/parser/composer_parser 2.py
new file mode 100644
index 0000000..d1b0794
--- /dev/null
+++ b/src/somef_core/parser/composer_parser 2.py
@@ -0,0 +1,217 @@
+import json
+import logging
+import os
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+from ..regular_expressions import detect_license_spdx
+
+def parse_composer_json(file_path, metadata_result: Result, source):
+ """
+ Parse a composer.json file to extract metadata.
+
+ Parameters
+ ----------
+ file_path: path to the composer.json file being analyzed
+ metadata_result: Metadata object dictionary
+ source: source of the package file (URL)
+
+ Returns
+ -------
+ """
+ try:
+
+ if Path(file_path).name.lower() in ["composer.json"]:
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": "composer.json",
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, "r", encoding="utf-8") as f:
+ data = json.load(f)
+
+ if "name" in data:
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_ID,
+ {
+ "value": data["name"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "description" in data:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": data["description"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "homepage" in data:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": data["homepage"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "version" in data:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": data["version"],
+ "type": constants.RELEASE,
+ "tag": data["version"]
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "authors" in data:
+ for author in data["authors"]:
+ author_data = {
+ "type": constants.AGENT,
+ "value": author.get("name", "")
+ }
+
+ if "name" in author:
+ author_data["name"] = author["name"]
+
+ if "email" in author:
+ author_data["email"] = author["email"]
+
+ if "homepage" in author:
+ author_data["url"] = author["homepage"]
+
+ if "role" in author:
+ author_data["role"] = author["role"]
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "license" in data:
+ license_value = data["license"]
+ license_text = ""
+
+ dir_path = os.path.dirname(file_path)
+ license_paths = [
+ os.path.join(dir_path, "LICENSE"),
+ os.path.join(dir_path, "LICENSE.txt"),
+ os.path.join(dir_path, "LICENSE.md")
+ ]
+
+ for license_path in license_paths:
+ if os.path.exists(license_path):
+ with open(license_path, "r", encoding="utf-8") as lf:
+ license_text = lf.read()
+ break
+
+ license_info_spdx = detect_license_spdx(license_text, 'JSON')
+
+ if license_info_spdx:
+ license_data = {
+ "value": license_value,
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": license_value,
+ "type": constants.LICENSE
+ }
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ dependency_sections = ["require", "require-dev"]
+ for section in dependency_sections:
+ if section in data:
+ for name, version in data[section].items():
+ req = f"{name}: {version}"
+ if section == "require-dev":
+ dep_type = "dev"
+ else:
+ dep_type = "runtime"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": dep_type
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "repository" in data:
+ repo_data = data["repository"]
+ if isinstance(repo_data, str):
+ repo_url = repo_data
+ elif isinstance(repo_data, dict) and "url" in repo_data:
+ repo_url = repo_data["url"]
+ else:
+ repo_url = None
+
+ if repo_url:
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": repo_url,
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "keywords" in data:
+ for keyword in data["keywords"]:
+ metadata_result.add_result(
+ constants.CAT_KEYWORDS,
+ {
+ "value": keyword,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ except Exception as e:
+ logging.error(f"Error parsing composer.json from {file_path}: {str(e)}")
+
+ return metadata_result
\ No newline at end of file
diff --git a/src/somef_core/parser/composer_parser.py b/src/somef_core/parser/composer_parser.py
new file mode 100644
index 0000000..d1b0794
--- /dev/null
+++ b/src/somef_core/parser/composer_parser.py
@@ -0,0 +1,217 @@
+import json
+import logging
+import os
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+from ..regular_expressions import detect_license_spdx
+
+def parse_composer_json(file_path, metadata_result: Result, source):
+ """
+ Parse a composer.json file to extract metadata.
+
+ Parameters
+ ----------
+ file_path: path to the composer.json file being analyzed
+ metadata_result: Metadata object dictionary
+ source: source of the package file (URL)
+
+ Returns
+ -------
+ """
+ try:
+
+ if Path(file_path).name.lower() in ["composer.json"]:
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": "composer.json",
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, "r", encoding="utf-8") as f:
+ data = json.load(f)
+
+ if "name" in data:
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_ID,
+ {
+ "value": data["name"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "description" in data:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": data["description"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "homepage" in data:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": data["homepage"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "version" in data:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": data["version"],
+ "type": constants.RELEASE,
+ "tag": data["version"]
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "authors" in data:
+ for author in data["authors"]:
+ author_data = {
+ "type": constants.AGENT,
+ "value": author.get("name", "")
+ }
+
+ if "name" in author:
+ author_data["name"] = author["name"]
+
+ if "email" in author:
+ author_data["email"] = author["email"]
+
+ if "homepage" in author:
+ author_data["url"] = author["homepage"]
+
+ if "role" in author:
+ author_data["role"] = author["role"]
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "license" in data:
+ license_value = data["license"]
+ license_text = ""
+
+ dir_path = os.path.dirname(file_path)
+ license_paths = [
+ os.path.join(dir_path, "LICENSE"),
+ os.path.join(dir_path, "LICENSE.txt"),
+ os.path.join(dir_path, "LICENSE.md")
+ ]
+
+ for license_path in license_paths:
+ if os.path.exists(license_path):
+ with open(license_path, "r", encoding="utf-8") as lf:
+ license_text = lf.read()
+ break
+
+ license_info_spdx = detect_license_spdx(license_text, 'JSON')
+
+ if license_info_spdx:
+ license_data = {
+ "value": license_value,
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": license_value,
+ "type": constants.LICENSE
+ }
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ dependency_sections = ["require", "require-dev"]
+ for section in dependency_sections:
+ if section in data:
+ for name, version in data[section].items():
+ req = f"{name}: {version}"
+ if section == "require-dev":
+ dep_type = "dev"
+ else:
+ dep_type = "runtime"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": dep_type
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "repository" in data:
+ repo_data = data["repository"]
+ if isinstance(repo_data, str):
+ repo_url = repo_data
+ elif isinstance(repo_data, dict) and "url" in repo_data:
+ repo_url = repo_data["url"]
+ else:
+ repo_url = None
+
+ if repo_url:
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": repo_url,
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "keywords" in data:
+ for keyword in data["keywords"]:
+ metadata_result.add_result(
+ constants.CAT_KEYWORDS,
+ {
+ "value": keyword,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ except Exception as e:
+ logging.error(f"Error parsing composer.json from {file_path}: {str(e)}")
+
+ return metadata_result
\ No newline at end of file
diff --git a/src/somef_core/parser/create_excerpts.py b/src/somef_core/parser/create_excerpts.py
index c4ef97b..bf0f4a2 100644
--- a/src/somef_core/parser/create_excerpts.py
+++ b/src/somef_core/parser/create_excerpts.py
@@ -28,43 +28,44 @@ def unmark_element(element, stream=None):
__md.stripTopLevelTags = False
-def split_into_excerpts(string_list):
- """
- ## Function takes readme text as input and divides it into excerpts
- Parameters
- ----------
- string_list: input text
+# def split_into_excerpts(string_list):
+# """
+# ## Function takes readme text as input and divides it into excerpts
+# Parameters
+# ----------
+# string_list: input text
- Returns
- -------
- Returns the extracted excerpts
- """
- divisions = []
- for text in string_list:
- if text:
- divisions = divisions + markdown_utils.unmark(text).splitlines()
- divisions = [i for i in divisions if i]
- return divisions
+# Returns
+# -------
+# Returns the extracted excerpts
+# """
+# divisions = []
+# for text in string_list:
+# if text:
+# divisions = divisions + markdown_utils.unmark(text).splitlines()
+# divisions = [i for i in divisions if i]
+# return divisions
-def create_excerpts(string_list):
- """
- Function takes readme text as input and divides it into excerpts
- Parameters
- ----------
- string_list: Markdown text passed as input
- Returns
- -------
- Extracted excerpts
- """
- logging.info("Splitting text into valid excerpts for classification")
- string_list = markdown_utils.remove_bibtex(string_list)
- divisions = mardown_parser.extract_blocks_excerpts(string_list)
- logging.info("Text Successfully split.")
- output = {}
- for division in divisions:
- original = division
- division = regular_expressions.remove_links_images(division)
- if len(division) > 0:
- output[division] = original
- return output
+# def create_excerpts(string_list):
+# """
+# Function takes readme text as input and divides it into excerpts
+# Parameters
+# ----------
+# string_list: Markdown text passed as input
+# Returns
+# -------
+# Extracted excerpts
+# """
+# logging.info("Splitting text into valid excerpts for classification")
+# string_list = markdown_utils.remove_bibtex(string_list)
+# logging.info("Extracting excerpts for classification")
+# divisions = mardown_parser.extract_blocks_excerpts(string_list)
+# logging.info("Text Successfully split.")
+# output = {}
+# for division in divisions:
+# original = division
+# division = regular_expressions.remove_links_images(division)
+# if len(division) > 0:
+# output[division] = original
+# return output
diff --git a/src/somef_core/parser/description_parser 2.py b/src/somef_core/parser/description_parser 2.py
new file mode 100644
index 0000000..0da8f8f
--- /dev/null
+++ b/src/somef_core/parser/description_parser 2.py
@@ -0,0 +1,204 @@
+import re
+import logging
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+
+def parse_description_file(file_path, metadata_result: Result, source):
+
+ """
+ Parse a DESCRIPTION file to extract metadata.
+
+ Parameters
+ ----------
+ file_path: path of the DESCRIPTION file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the package file (URL)
+
+ Returns
+ -------
+ """
+
+ try:
+ if Path(file_path).name.upper() == "DESCRIPTION":
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": "DESCRIPTION",
+ "value": source,
+ "type": constants.URL,
+ "source": source
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, "r", encoding="utf-8") as f:
+ content = f.read()
+
+ package_match = re.search(r'Package:\s*([^\n]+)', content)
+ if package_match:
+ print("FOUND PACKAGE NAME")
+ package_name = package_match.group(1).strip()
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_ID,
+ {
+ "value": package_name,
+ "type": constants.STRING,
+ "source": source
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ else:
+ print("NO PACKAGE NAME FOUND")
+
+ desc_match = re.search(r'Description:\s*([^\n]+(?:\n\s+[^\n]+)*)', content)
+ if desc_match:
+ description = desc_match.group(1).strip()
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": description,
+ "type": constants.STRING,
+ "source": source
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ version_match = re.search(r'Version:\s*([^\n]+)', content)
+ if version_match:
+ version = version_match.group(1).strip()
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": version,
+ "type": constants.STRING,
+ "source": source
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ authors_section = re.search(r'Authors@R:\s*c\(([\s\S]*?)\)\s*$', content, re.MULTILINE)
+ # authors_section = re.search(r'Authors@R:\s*c\(([^)]+)\)', content, re.DOTALL)
+ if authors_section:
+ authors_text = authors_section.group(1)
+
+ pattern = re.compile(
+ r'''person\(
+ \s*"([^"]+)"
+ (?:\s*,\s*"([^"]*)")?
+ (?:\s*,\s*)*
+ (?:
+ "(?P[^"]+@[^"]+)"
+ |
+ .*?email\s*=\s*"(?P[^"]+)"
+ )?
+ [^)]*
+ \)''',
+ re.VERBOSE
+ )
+ # person_entries = re.findall(r'person\(\s*"([^"]+)"\s*,\s*"([^"]+)"(?:\s*,\s*)?(?:"[^"]*")?(?:\s*,\s*)?(?:"([^"]+)")?', authors_text)
+ person_entries = []
+ for match in pattern.finditer(authors_text):
+ given = match.group(1)
+ family = match.group(2) or ""
+ email = match.group("email1") or match.group("email2") or ""
+ person_entries.append((given, family, email))
+
+ for given, family, email in person_entries:
+ name = given.strip()
+ if family:
+ name += " " + family.strip()
+ author = {
+ "value": name,
+ "type": constants.AGENT,
+ }
+
+ if email:
+ author["email"] = email.strip()
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ license_match = re.search(r'License:\s*([^\n]+)', content)
+ if license_match:
+ license_text = license_match.group(1).strip()
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ {
+ "value": license_text,
+ "type": constants.STRING,
+ "source": source
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ url_section = re.search(r'URL:\s*([^\n]+(?:\n\s+[^\n]+)*)', content)
+ if url_section:
+ url_text = url_section.group(1).strip()
+ urls = []
+ for url in re.split(r',\s*', url_text):
+ stripped = url.strip()
+ if stripped:
+ urls.append(stripped)
+
+ for url in urls:
+ if 'github.com' in url.lower() or 'gitlab.com' in url.lower():
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": url,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ else:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": url,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ issue_tracker_match = re.search(r'BugReports:\s*([^\n]+)', content)
+ if issue_tracker_match:
+ issue_tracker_url = issue_tracker_match.group(1).strip()
+ metadata_result.add_result(
+ constants.CAT_ISSUE_TRACKER,
+ {
+ "value": issue_tracker_url,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ except Exception as e:
+ logging.error(f"Error parsing gemspec file from {file_path}: {str(e)}")
+
+ return metadata_result
+
+
diff --git a/src/somef_core/parser/description_parser.py b/src/somef_core/parser/description_parser.py
new file mode 100644
index 0000000..0da8f8f
--- /dev/null
+++ b/src/somef_core/parser/description_parser.py
@@ -0,0 +1,204 @@
+import re
+import logging
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+
+def parse_description_file(file_path, metadata_result: Result, source):
+
+ """
+ Parse a DESCRIPTION file to extract metadata.
+
+ Parameters
+ ----------
+ file_path: path of the DESCRIPTION file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the package file (URL)
+
+ Returns
+ -------
+ """
+
+ try:
+ if Path(file_path).name.upper() == "DESCRIPTION":
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": "DESCRIPTION",
+ "value": source,
+ "type": constants.URL,
+ "source": source
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, "r", encoding="utf-8") as f:
+ content = f.read()
+
+ package_match = re.search(r'Package:\s*([^\n]+)', content)
+ if package_match:
+ print("FOUND PACKAGE NAME")
+ package_name = package_match.group(1).strip()
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_ID,
+ {
+ "value": package_name,
+ "type": constants.STRING,
+ "source": source
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ else:
+ print("NO PACKAGE NAME FOUND")
+
+ desc_match = re.search(r'Description:\s*([^\n]+(?:\n\s+[^\n]+)*)', content)
+ if desc_match:
+ description = desc_match.group(1).strip()
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": description,
+ "type": constants.STRING,
+ "source": source
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ version_match = re.search(r'Version:\s*([^\n]+)', content)
+ if version_match:
+ version = version_match.group(1).strip()
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": version,
+ "type": constants.STRING,
+ "source": source
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ authors_section = re.search(r'Authors@R:\s*c\(([\s\S]*?)\)\s*$', content, re.MULTILINE)
+ # authors_section = re.search(r'Authors@R:\s*c\(([^)]+)\)', content, re.DOTALL)
+ if authors_section:
+ authors_text = authors_section.group(1)
+
+ pattern = re.compile(
+ r'''person\(
+ \s*"([^"]+)"
+ (?:\s*,\s*"([^"]*)")?
+ (?:\s*,\s*)*
+ (?:
+ "(?P[^"]+@[^"]+)"
+ |
+ .*?email\s*=\s*"(?P[^"]+)"
+ )?
+ [^)]*
+ \)''',
+ re.VERBOSE
+ )
+ # person_entries = re.findall(r'person\(\s*"([^"]+)"\s*,\s*"([^"]+)"(?:\s*,\s*)?(?:"[^"]*")?(?:\s*,\s*)?(?:"([^"]+)")?', authors_text)
+ person_entries = []
+ for match in pattern.finditer(authors_text):
+ given = match.group(1)
+ family = match.group(2) or ""
+ email = match.group("email1") or match.group("email2") or ""
+ person_entries.append((given, family, email))
+
+ for given, family, email in person_entries:
+ name = given.strip()
+ if family:
+ name += " " + family.strip()
+ author = {
+ "value": name,
+ "type": constants.AGENT,
+ }
+
+ if email:
+ author["email"] = email.strip()
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ license_match = re.search(r'License:\s*([^\n]+)', content)
+ if license_match:
+ license_text = license_match.group(1).strip()
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ {
+ "value": license_text,
+ "type": constants.STRING,
+ "source": source
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ url_section = re.search(r'URL:\s*([^\n]+(?:\n\s+[^\n]+)*)', content)
+ if url_section:
+ url_text = url_section.group(1).strip()
+ urls = []
+ for url in re.split(r',\s*', url_text):
+ stripped = url.strip()
+ if stripped:
+ urls.append(stripped)
+
+ for url in urls:
+ if 'github.com' in url.lower() or 'gitlab.com' in url.lower():
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": url,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ else:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": url,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ issue_tracker_match = re.search(r'BugReports:\s*([^\n]+)', content)
+ if issue_tracker_match:
+ issue_tracker_url = issue_tracker_match.group(1).strip()
+ metadata_result.add_result(
+ constants.CAT_ISSUE_TRACKER,
+ {
+ "value": issue_tracker_url,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ except Exception as e:
+ logging.error(f"Error parsing gemspec file from {file_path}: {str(e)}")
+
+ return metadata_result
+
+
diff --git a/src/somef_core/parser/dockerfile_parser 2.py b/src/somef_core/parser/dockerfile_parser 2.py
new file mode 100644
index 0000000..d47cd44
--- /dev/null
+++ b/src/somef_core/parser/dockerfile_parser 2.py
@@ -0,0 +1,227 @@
+import logging
+import os
+import re
+from ..utils import constants
+from ..process_results import Result
+
+def parse_dockerfile(file_path, metadata_result: Result, source):
+
+ print(f"Extracting properties from Dockerfile: {file_path}")
+
+ try:
+ with open(file_path, "rb") as file:
+ raw_data = file.read()
+
+ content = raw_data.decode("utf-8")
+ except (OSError, UnicodeDecodeError) as e:
+ logging.warning(f"Could not process Dockerfile {file_path}: {e}")
+ return None
+
+ # print(content)
+ title_match = re.search(
+ constants.REGEXP_DOCKER_TITLE,
+ content,
+ re.IGNORECASE
+ )
+
+ if title_match:
+ title = title_match.group(1).strip()
+ if title:
+ metadata_result.add_result(
+ constants.CAT_NAME,
+ {
+ "value": title,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ description_match = re.search(
+ constants.REGEXP_DOCKER_DESCRIPTION,
+ content,
+ re.IGNORECASE
+ )
+
+ if description_match:
+ description = description_match.group(1).strip()
+ if description:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": description,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ licenses_match = re.search(constants.REGEXP_DOCKER_LICENSES, content, re.IGNORECASE)
+ if licenses_match:
+ license_info_spdx = detect_license_spdx(licenses_match.group(1).strip())
+
+ if license_info_spdx:
+ license_data = {
+ "value": licenses_match.group(1).strip(),
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": licenses_match.group(1).strip(),
+ "type": constants.LICENSE
+ }
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ # source_match = re.search(constants.REGEXP_DOCKER_SOURCE, content, re.IGNORECASE)
+ # if source_match:
+ # properties[constants.PROP_SOURCE] = source_match.group(1).strip()
+
+ url_match = re.search(constants.REGEXP_DOCKER_URL, content, re.IGNORECASE)
+ if url_match:
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": url_match.group(1).strip(),
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ version_match = re.search(constants.REGEXP_DOCKER_VERSION, content, re.IGNORECASE)
+ if version_match:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": version_match.group(1).strip(),
+ "type": constants.RELEASE,
+ "tag": version_match.group(1).strip()
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ documentation_match = re.search(constants.REGEXP_DOCKER_DOCUMENTATION, content, re.IGNORECASE)
+ if documentation_match:
+ metadata_result.add_result(
+ constants.CAT_DOCUMENTATION,
+ {
+ "value": documentation_match.group(1).strip(),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ vendor_match = re.search(
+ constants.REGEXP_DOCKER_VENDOR,
+ content,
+ re.IGNORECASE
+ )
+
+ if vendor_match:
+ vendor = vendor_match.group(1).strip()
+ if vendor:
+ if vendor and re.search(constants.REGEXP_LTD_INC, vendor, re.IGNORECASE):
+ type_vendor = "Organization"
+ else:
+ type_vendor = "Person"
+
+ metadata_result.add_result(
+ constants.CAT_OWNER,
+ {
+ "value": vendor,
+ "type": type_vendor
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ # Extract maintainers
+ maintainers = []
+ unique_maintainers = []
+
+ maintainer_oci_match = re.findall(
+ constants.REGEXP_MAINTAINER_LABEL_OCI,
+ content,
+ re.IGNORECASE | re.MULTILINE
+ )
+ # LABEL maintainer free
+ maintanainer_label_match = re.findall(
+ constants.REGEXP_MAINTAINER_LABEL_FREE,
+ content,
+ re.IGNORECASE | re.MULTILINE
+ )
+ # Deprecated maintainer
+ maintainer_match = re.findall(
+ constants.REGEXP_MAINTAINER,
+ content,
+ re.IGNORECASE | re.MULTILINE
+ )
+ maintainers.extend(maintainer_oci_match)
+ maintainers.extend(maintanainer_label_match)
+ maintainers.extend(maintainer_match)
+
+ unique_maintainers = list({m.strip() for m in maintainers if m.strip()})
+
+ for maintainer in unique_maintainers:
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ {
+ "type": constants.AGENT,
+ "value": maintainer
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ return metadata_result
+
+def detect_license_spdx(license_text):
+ """
+ Function that given a license text, infers the name and spdx id in a dockerfile
+ Parameters
+ ----------
+ license_text
+
+ Returns
+ -------
+ A JSON dictionary with name and spdx id
+ """
+ print("Detecting license from text:", license_text)
+ for license_name, license_info in constants.LICENSES_DICT.items():
+ if re.search(license_info["regex"], license_text, re.IGNORECASE):
+ return {
+ "name": license_name,
+ "spdx_id": f"{license_info['spdx_id']}",
+ "@id": f"https://spdx.org/licenses/{license_info['spdx_id']}"
+ }
+
+ for license_name, license_info in constants.LICENSES_DICT.items():
+ spdx_id = license_info["spdx_id"]
+ if re.search(rf'\b{re.escape(spdx_id)}\b', license_text, re.IGNORECASE):
+ return {
+ "name": license_name,
+ "spdx_id": spdx_id,
+ "@id": f"https://spdx.org/licenses/{spdx_id}"
+ }
+ return None
+
+
\ No newline at end of file
diff --git a/src/somef_core/parser/dockerfile_parser.py b/src/somef_core/parser/dockerfile_parser.py
new file mode 100644
index 0000000..d47cd44
--- /dev/null
+++ b/src/somef_core/parser/dockerfile_parser.py
@@ -0,0 +1,227 @@
+import logging
+import os
+import re
+from ..utils import constants
+from ..process_results import Result
+
+def parse_dockerfile(file_path, metadata_result: Result, source):
+
+ print(f"Extracting properties from Dockerfile: {file_path}")
+
+ try:
+ with open(file_path, "rb") as file:
+ raw_data = file.read()
+
+ content = raw_data.decode("utf-8")
+ except (OSError, UnicodeDecodeError) as e:
+ logging.warning(f"Could not process Dockerfile {file_path}: {e}")
+ return None
+
+ # print(content)
+ title_match = re.search(
+ constants.REGEXP_DOCKER_TITLE,
+ content,
+ re.IGNORECASE
+ )
+
+ if title_match:
+ title = title_match.group(1).strip()
+ if title:
+ metadata_result.add_result(
+ constants.CAT_NAME,
+ {
+ "value": title,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ description_match = re.search(
+ constants.REGEXP_DOCKER_DESCRIPTION,
+ content,
+ re.IGNORECASE
+ )
+
+ if description_match:
+ description = description_match.group(1).strip()
+ if description:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": description,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ licenses_match = re.search(constants.REGEXP_DOCKER_LICENSES, content, re.IGNORECASE)
+ if licenses_match:
+ license_info_spdx = detect_license_spdx(licenses_match.group(1).strip())
+
+ if license_info_spdx:
+ license_data = {
+ "value": licenses_match.group(1).strip(),
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": licenses_match.group(1).strip(),
+ "type": constants.LICENSE
+ }
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ # source_match = re.search(constants.REGEXP_DOCKER_SOURCE, content, re.IGNORECASE)
+ # if source_match:
+ # properties[constants.PROP_SOURCE] = source_match.group(1).strip()
+
+ url_match = re.search(constants.REGEXP_DOCKER_URL, content, re.IGNORECASE)
+ if url_match:
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": url_match.group(1).strip(),
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ version_match = re.search(constants.REGEXP_DOCKER_VERSION, content, re.IGNORECASE)
+ if version_match:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": version_match.group(1).strip(),
+ "type": constants.RELEASE,
+ "tag": version_match.group(1).strip()
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ documentation_match = re.search(constants.REGEXP_DOCKER_DOCUMENTATION, content, re.IGNORECASE)
+ if documentation_match:
+ metadata_result.add_result(
+ constants.CAT_DOCUMENTATION,
+ {
+ "value": documentation_match.group(1).strip(),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ vendor_match = re.search(
+ constants.REGEXP_DOCKER_VENDOR,
+ content,
+ re.IGNORECASE
+ )
+
+ if vendor_match:
+ vendor = vendor_match.group(1).strip()
+ if vendor:
+ if vendor and re.search(constants.REGEXP_LTD_INC, vendor, re.IGNORECASE):
+ type_vendor = "Organization"
+ else:
+ type_vendor = "Person"
+
+ metadata_result.add_result(
+ constants.CAT_OWNER,
+ {
+ "value": vendor,
+ "type": type_vendor
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ # Extract maintainers
+ maintainers = []
+ unique_maintainers = []
+
+ maintainer_oci_match = re.findall(
+ constants.REGEXP_MAINTAINER_LABEL_OCI,
+ content,
+ re.IGNORECASE | re.MULTILINE
+ )
+ # LABEL maintainer free
+ maintanainer_label_match = re.findall(
+ constants.REGEXP_MAINTAINER_LABEL_FREE,
+ content,
+ re.IGNORECASE | re.MULTILINE
+ )
+ # Deprecated maintainer
+ maintainer_match = re.findall(
+ constants.REGEXP_MAINTAINER,
+ content,
+ re.IGNORECASE | re.MULTILINE
+ )
+ maintainers.extend(maintainer_oci_match)
+ maintainers.extend(maintanainer_label_match)
+ maintainers.extend(maintainer_match)
+
+ unique_maintainers = list({m.strip() for m in maintainers if m.strip()})
+
+ for maintainer in unique_maintainers:
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ {
+ "type": constants.AGENT,
+ "value": maintainer
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ return metadata_result
+
+def detect_license_spdx(license_text):
+ """
+ Function that given a license text, infers the name and spdx id in a dockerfile
+ Parameters
+ ----------
+ license_text
+
+ Returns
+ -------
+ A JSON dictionary with name and spdx id
+ """
+ print("Detecting license from text:", license_text)
+ for license_name, license_info in constants.LICENSES_DICT.items():
+ if re.search(license_info["regex"], license_text, re.IGNORECASE):
+ return {
+ "name": license_name,
+ "spdx_id": f"{license_info['spdx_id']}",
+ "@id": f"https://spdx.org/licenses/{license_info['spdx_id']}"
+ }
+
+ for license_name, license_info in constants.LICENSES_DICT.items():
+ spdx_id = license_info["spdx_id"]
+ if re.search(rf'\b{re.escape(spdx_id)}\b', license_text, re.IGNORECASE):
+ return {
+ "name": license_name,
+ "spdx_id": spdx_id,
+ "@id": f"https://spdx.org/licenses/{spdx_id}"
+ }
+ return None
+
+
\ No newline at end of file
diff --git a/src/somef_core/parser/gemspec_parser 2.py b/src/somef_core/parser/gemspec_parser 2.py
new file mode 100644
index 0000000..6714b01
--- /dev/null
+++ b/src/somef_core/parser/gemspec_parser 2.py
@@ -0,0 +1,222 @@
+import os
+import re
+import logging
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+from ..regular_expressions import detect_license_spdx
+
+def parse_gemspec_file(file_path, metadata_result: Result, source):
+ # To do Version
+ # To do Email
+ """
+ Parse a Ruby gemspec file to extract metadata.
+
+ Parameters
+ ----------
+ file_path: path of the gemspec file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the package file (URL)
+
+ Returns
+ -------
+ metadata_result: Updated metadata result object
+ """
+ try:
+ if file_path.endswith('.gemspec'):
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": Path(file_path).name,
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, 'r', encoding='utf-8') as file:
+ content = file.read()
+
+ name_match = re.search(r'gem\.name\s*=\s*["\']([^"\']+)["\']', content)
+ if name_match:
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_ID,
+ {
+ "value": name_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ desc_match = re.search(r'gem\.description\s*=\s*%q{([^}]+)}|gem\.description\s*=\s*["\']([^"\']+)["\']', content)
+ if desc_match:
+ description = desc_match.group(1) if desc_match.group(1) else desc_match.group(2)
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": description,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ homepage_match = re.search(r'gem\.homepage\s*=\s*["\']([^"\']+)["\']', content)
+ if homepage_match:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": homepage_match.group(1),
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ authors_match = re.findall(r'gem\.author[s]?\s*=\s*(?P"[^"]*"|\[[^\]]*\])', content)
+
+ for match in authors_match:
+ if match.startswith('['):
+ author_list = re.findall(r'["\']([^"\']+)["\']', match)
+ else:
+ author_list = [re.sub(r'["\']', '', match).strip()]
+
+ for author in author_list:
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ {
+ "type": constants.AGENT,
+ "value": author
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ # authors_str = authors_match.group(1)
+ # author_list = re.findall(r'["\']([^"\']+)["\']', authors_str)
+
+ # for author in author_list:
+ # metadata_result.add_result(
+ # constants.CAT_AUTHORS,
+ # {
+ # "type": constants.AGENT,
+ # "value": author
+ # },
+ # 1,
+ # constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ # source
+ # )
+
+ # license_match = re.search(r'gem\.license\s*=\s*["\']([^"\']+)["\']', content)
+ license_match = re.search(r'gem\.license[s]?\s*=\s*["\']([^"\']+)["\']', content)
+ if license_match:
+ license_value = license_match.group(1)
+ license_text = ""
+
+ dir_path = os.path.dirname(file_path)
+ license_paths = [
+ os.path.join(dir_path, "LICENSE"),
+ os.path.join(dir_path, "LICENSE.txt"),
+ os.path.join(dir_path, "LICENSE.md")
+ ]
+
+ for license_path in license_paths:
+ if os.path.exists(license_path):
+ with open(license_path, "r", encoding="utf-8") as lf:
+ license_text = lf.read()
+ break
+
+ license_info_spdx = detect_license_spdx(license_text, 'Ruby')
+
+ if license_info_spdx:
+ license_data = {
+ "value": license_value,
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": license_value,
+ "type": constants.LICENSE
+ }
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ dependency_matches = re.search(r'gem\.requirements\s*=\s*(\[.*?\])', content, re.DOTALL)
+
+ if dependency_matches:
+ array_requirements = dependency_matches.group(1)
+ dependencies = re.findall(r'["\']([^"\']+)["\']', array_requirements)
+
+ if dependencies:
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": dependencies,
+ "type": constants.SOFTWARE_APPLICATION,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ dependency_matches = re.findall(r'gem\.add_dependency\s*["\']([^"\']+)["\'](?:\s*,\s*["\']([^"\']+)["\'])?', content)
+ for dep in dependency_matches:
+ name = dep[0]
+ version = dep[1] if len(dep) > 1 and dep[1] else "any"
+ req = f"{name}: {version}"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "runtime"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ dev_dependency_matches = re.findall(r'gem\.add_development_dependency\s*["\']([^"\']+)["\'](?:\s*,\s*["\']([^"\']+)["\'])?', content)
+ for dep in dev_dependency_matches:
+ name = dep[0]
+ version = dep[1] if len(dep) > 1 and dep[1] else "any"
+ req = f"{name}: {version}"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "dev"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ except Exception as e:
+ logging.error(f"Error parsing gemspec file from {file_path}: {str(e)}")
+
+ return metadata_result
\ No newline at end of file
diff --git a/src/somef_core/parser/gemspec_parser.py b/src/somef_core/parser/gemspec_parser.py
new file mode 100644
index 0000000..6714b01
--- /dev/null
+++ b/src/somef_core/parser/gemspec_parser.py
@@ -0,0 +1,222 @@
+import os
+import re
+import logging
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+from ..regular_expressions import detect_license_spdx
+
+def parse_gemspec_file(file_path, metadata_result: Result, source):
+ # To do Version
+ # To do Email
+ """
+ Parse a Ruby gemspec file to extract metadata.
+
+ Parameters
+ ----------
+ file_path: path of the gemspec file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the package file (URL)
+
+ Returns
+ -------
+ metadata_result: Updated metadata result object
+ """
+ try:
+ if file_path.endswith('.gemspec'):
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": Path(file_path).name,
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, 'r', encoding='utf-8') as file:
+ content = file.read()
+
+ name_match = re.search(r'gem\.name\s*=\s*["\']([^"\']+)["\']', content)
+ if name_match:
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_ID,
+ {
+ "value": name_match.group(1),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ desc_match = re.search(r'gem\.description\s*=\s*%q{([^}]+)}|gem\.description\s*=\s*["\']([^"\']+)["\']', content)
+ if desc_match:
+ description = desc_match.group(1) if desc_match.group(1) else desc_match.group(2)
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": description,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ homepage_match = re.search(r'gem\.homepage\s*=\s*["\']([^"\']+)["\']', content)
+ if homepage_match:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": homepage_match.group(1),
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ authors_match = re.findall(r'gem\.author[s]?\s*=\s*(?P"[^"]*"|\[[^\]]*\])', content)
+
+ for match in authors_match:
+ if match.startswith('['):
+ author_list = re.findall(r'["\']([^"\']+)["\']', match)
+ else:
+ author_list = [re.sub(r'["\']', '', match).strip()]
+
+ for author in author_list:
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ {
+ "type": constants.AGENT,
+ "value": author
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ # authors_str = authors_match.group(1)
+ # author_list = re.findall(r'["\']([^"\']+)["\']', authors_str)
+
+ # for author in author_list:
+ # metadata_result.add_result(
+ # constants.CAT_AUTHORS,
+ # {
+ # "type": constants.AGENT,
+ # "value": author
+ # },
+ # 1,
+ # constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ # source
+ # )
+
+ # license_match = re.search(r'gem\.license\s*=\s*["\']([^"\']+)["\']', content)
+ license_match = re.search(r'gem\.license[s]?\s*=\s*["\']([^"\']+)["\']', content)
+ if license_match:
+ license_value = license_match.group(1)
+ license_text = ""
+
+ dir_path = os.path.dirname(file_path)
+ license_paths = [
+ os.path.join(dir_path, "LICENSE"),
+ os.path.join(dir_path, "LICENSE.txt"),
+ os.path.join(dir_path, "LICENSE.md")
+ ]
+
+ for license_path in license_paths:
+ if os.path.exists(license_path):
+ with open(license_path, "r", encoding="utf-8") as lf:
+ license_text = lf.read()
+ break
+
+ license_info_spdx = detect_license_spdx(license_text, 'Ruby')
+
+ if license_info_spdx:
+ license_data = {
+ "value": license_value,
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": license_value,
+ "type": constants.LICENSE
+ }
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ dependency_matches = re.search(r'gem\.requirements\s*=\s*(\[.*?\])', content, re.DOTALL)
+
+ if dependency_matches:
+ array_requirements = dependency_matches.group(1)
+ dependencies = re.findall(r'["\']([^"\']+)["\']', array_requirements)
+
+ if dependencies:
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": dependencies,
+ "type": constants.SOFTWARE_APPLICATION,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ dependency_matches = re.findall(r'gem\.add_dependency\s*["\']([^"\']+)["\'](?:\s*,\s*["\']([^"\']+)["\'])?', content)
+ for dep in dependency_matches:
+ name = dep[0]
+ version = dep[1] if len(dep) > 1 and dep[1] else "any"
+ req = f"{name}: {version}"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "runtime"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ dev_dependency_matches = re.findall(r'gem\.add_development_dependency\s*["\']([^"\']+)["\'](?:\s*,\s*["\']([^"\']+)["\'])?', content)
+ for dep in dev_dependency_matches:
+ name = dep[0]
+ version = dep[1] if len(dep) > 1 and dep[1] else "any"
+ req = f"{name}: {version}"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "dev"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ except Exception as e:
+ logging.error(f"Error parsing gemspec file from {file_path}: {str(e)}")
+
+ return metadata_result
\ No newline at end of file
diff --git a/src/somef_core/parser/package_json_parser.py b/src/somef_core/parser/package_json_parser.py
index 83ba1eb..a0884c5 100644
--- a/src/somef_core/parser/package_json_parser.py
+++ b/src/somef_core/parser/package_json_parser.py
@@ -46,7 +46,18 @@ def parse_package_json_file(file_path, metadata_result: Result, source):
constants.TECHNIQUE_CODE_CONFIG_PARSER,
source
)
-
+
+ if "homepage" in data:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": data["homepage"],
+ "type": constants.URL},
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
if "version" in data:
metadata_result.add_result(
constants.CAT_VERSION,
@@ -137,7 +148,24 @@ def parse_package_json_file(file_path, metadata_result: Result, source):
constants.TECHNIQUE_CODE_CONFIG_PARSER,
source
)
-
+
+ runtimes = parse_runtime_platform_from_package_json(data)
+ if runtimes:
+ for runtime in runtimes:
+ metadata_result.add_result(
+ constants.CAT_RUNTIME_PLATFORM,
+ runtime,
+ # {
+ # "value": runtime["version"],
+ # "version": runtime["version"],
+ # "name": runtime["name"],
+ # "type": constants.STRING
+ # },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
deps = {}
deps.update(data.get("dependencies", {}))
deps.update(data.get("devDependencies", {}))
@@ -160,7 +188,8 @@ def parse_package_json_file(file_path, metadata_result: Result, source):
metadata_result.add_result(
constants.CAT_HAS_PACKAGE_FILE,
{
- "value": "package.json",
+ # "value": "package.json",
+ "value": source,
"type": constants.URL,
},
1,
@@ -199,4 +228,40 @@ def parse_bugs(bugs_data):
return bugs_data["url"]
if isinstance(bugs_data, str):
return bugs_data
- return None
\ No newline at end of file
+ return None
+
+def parse_runtime_platform_from_package_json(data):
+ """
+ Extract runtime information from a package.json dict.
+ Returns a list of dicts with 'name' and 'version', e.g.:
+ [{'name': 'Node.js', 'version': '18.x'}]
+ """
+ runtimes = []
+
+ engines = data.get("engines", {})
+ if isinstance(engines, dict):
+ for runtime_name, version_value in engines.items():
+
+ if version_value:
+ value_str = f"{runtime_name}: {version_value}".strip()
+ else:
+ value_str = runtime_name
+
+ run = {
+ "value": value_str,
+ "name": runtime_name.capitalize(),
+ "type": constants.STRING
+ }
+ if version_value:
+ run["version"] = version_value.strip()
+
+ # if version_value:
+ # # runtimes.append({
+ # # "name": runtime_name.capitalize(),
+ # # "version": version_value.strip()
+ # # })
+ # run["version"]= version_value.strip()
+
+ runtimes.append(run)
+
+ return runtimes
\ No newline at end of file
diff --git a/src/somef_core/parser/pom_xml_parser.py b/src/somef_core/parser/pom_xml_parser.py
index b9a799e..dfb9c1c 100644
--- a/src/somef_core/parser/pom_xml_parser.py
+++ b/src/somef_core/parser/pom_xml_parser.py
@@ -40,6 +40,7 @@ def parse_pom_file(file_path, metadata_result: Result, source):
data = lxml.etree.parse(file)
root = data.getroot()
+
if root.tag != "{" + POM_NAMESPACE + "}project":
logging.warning(f"Expected root tag 'project' in {POM_NAMESPACE} namespace, got {root.tag} instead")
return metadata_result
@@ -59,7 +60,9 @@ def parse_pom_file(file_path, metadata_result: Result, source):
"dependencies": [],
"developers": [],
"issue_tracker": None,
- "scm_url": None
+ "scm_url": None,
+ "homepage": [],
+ "runtime_platform": []
}
for key, node in parse_node(root):
@@ -81,9 +84,17 @@ def parse_pom_file(file_path, metadata_result: Result, source):
project_data["scm_url"] = parse_scm(node)
elif key == "developers":
project_data["developers"] = parse_developers(node)
+ # elif key == "dependencies" or key == "dependencyManagement":
+ # project_data["dependencies"] = parse_dependencies(node)
elif key == "dependencies":
- project_data["dependencies"] = parse_dependencies(node)
-
+ project_data["dependencies"].extend(parse_dependencies(node))
+ elif key == "dependencyManagement":
+ for k, n in parse_node(node):
+ if k == "dependencies":
+ project_data["dependencies"].extend(parse_dependencies(n))
+ elif key == "properties":
+ project_data["runtime_platform"] = parse_runtime_platform(node)
+
if group_id or artifact_id:
identifier_value = f"{group_id or ''}.{artifact_id or ''}".strip(':')
metadata_result.add_result(
@@ -120,7 +131,18 @@ def parse_pom_file(file_path, metadata_result: Result, source):
constants.TECHNIQUE_CODE_CONFIG_PARSER,
source
)
-
+
+ if project_data["homepage"]:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": project_data["homepage"],
+ "type": constants.URL},
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
if project_data["scm_url"]:
metadata_result.add_result(
constants.CAT_PACKAGE_DISTRIBUTION,
@@ -132,7 +154,7 @@ def parse_pom_file(file_path, metadata_result: Result, source):
constants.TECHNIQUE_CODE_CONFIG_PARSER,
source
)
-
+
if project_data["dependencies"]:
for dependency in project_data["dependencies"]:
metadata_result.add_result(
@@ -148,29 +170,60 @@ def parse_pom_file(file_path, metadata_result: Result, source):
source
)
- if project_data["developers"] :
- metadata_result.add_result(
- constants.CAT_AUTHORS ,
- {
- "value": project_data["developers"],
- "type": constants.URL
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
+
+ if project_data["developers"]:
+ for author in project_data["developers"]:
+
+ if "type" not in author:
+ author["type"] = constants.AGENT
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
if repositories:
- metadata_result.add_result(
- constants.CAT_PACKAGE_DISTRIBUTION,
- {
- "value": repositories,
- "type": constants.URL
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
+
+ for rep in repositories:
+ rep["type"] = constants.URL
+
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_DISTRIBUTION,
+ rep,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ # constants.CAT_PACKAGE_DISTRIBUTION,
+ # {
+ # # "value": repositories,
+ # rep,
+ # "type": constants.URL
+ # },
+ # 1,
+ # constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ # source
+ # )
+
+ if project_data["runtime_platform"]:
+
+ for runtime in project_data["runtime_platform"]:
+ metadata_result.add_result(
+ constants.CAT_RUNTIME_PLATFORM,
+ {
+ "value": runtime["value"],
+ "version": runtime["version"],
+ "name": runtime["name"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
metadata = {}
for k, v in project_data.items():
@@ -180,7 +233,8 @@ def parse_pom_file(file_path, metadata_result: Result, source):
metadata_result.add_result(
constants.CAT_HAS_PACKAGE_FILE,
{
- "value": "pom.xml",
+ # "value": "pom.xml",
+ "value": source,
"type": constants.URL
},
1,
@@ -189,7 +243,6 @@ def parse_pom_file(file_path, metadata_result: Result, source):
)
processed_pom = True
-
return metadata_result
def parse_licenses(licenses_node):
@@ -204,16 +257,27 @@ def parse_licenses(licenses_node):
licenses.append(license_data)
return licenses
-def parse_dependencies(dependencies_node):
+def parse_dependencies(node):
dependencies = []
- for key, node in parse_node(dependencies_node):
- if key == "dependency":
+
+ for child in node:
+ if not isinstance(child.tag, str):
+ continue
+
+ tag = child.tag.split("}")[-1]
+ if tag == "dependencies":
+ dependencies.extend(parse_dependencies(child))
+ elif tag == "dependency":
dep_data = {}
- for key2, node2 in parse_node(node):
- if key2 in ["groupId", "artifactId", "version"] and node2.text:
- dep_data[key2] = node2.text
+ for sub in child:
+ if not isinstance(sub.tag, str):
+ continue
+ sub_tag = sub.tag.split("}")[-1]
+ if sub_tag in ["groupId", "artifactId", "version"] and sub.text:
+ dep_data[sub_tag] = sub.text.strip()
if dep_data:
dependencies.append(dep_data)
+
return dependencies
def parse_developers(developers_node):
@@ -222,10 +286,10 @@ def parse_developers(developers_node):
if key == "developer":
dev_data = {}
author_data = {
- "name": None,
- "email": None,
- "url": None,
- "organization": None,
+ # "name": None,
+ # "email": None,
+ # "url": None,
+ # "affiliation": None,
"type": constants.AGENT
}
for key2, node2 in parse_node(node):
@@ -237,10 +301,10 @@ def parse_developers(developers_node):
elif key2 == "url" and node2.text:
author_data["url"] = node2.text
elif key2 == "organization" and node2.text:
- author_data["organization"] = node2.text
+ author_data["affiliation"] = node2.text
- if not author_data["value"]:
- author_data["value"] = author_data["email"] or author_data["organization"]
+ if "value" not in author_data:
+ author_data["value"] = author_data["email"] or author_data["affiliation"]
dev_data.update({k: v for k, v in author_data.items() if k != "type"})
developers.append(dev_data)
return developers
@@ -264,7 +328,65 @@ def parse_repositories(repo_node):
repo_data = {}
for key2, node2 in parse_node(node):
if key2 in ["id", "name", "url"] and node2.text:
- repo_data[key2] = node2.text
+ if key2 == "id":
+ repo_data["value"] = node2.text
+ else:
+ repo_data[key2] = node2.text
if repo_data:
repos.append(repo_data)
- return repos
\ No newline at end of file
+ return repos
+
+def parse_runtime_platform(properties_node):
+ """
+ Extracts runtime platform information from a node in a pom.xml.
+ Returns a list of dictionaries with runtime names and versions, or an empty list if none are found.
+
+ Parameters
+ ----------
+ properties_node : lxml.etree.Element
+ The node from the POM file.
+
+ Returns
+ -------
+ list of dict
+ Each dict has the keys 'name' and 'version', e.g. [{'name': 'Java', 'version': '1.8'}, {'name': 'Python', 'version': '3.11'}].
+ Returns an empty list if no runtime information is present.
+ """
+ runtimes = []
+
+ if properties_node is None:
+ return runtimes
+
+ for child in properties_node:
+ if not isinstance(child.tag, str):
+ continue
+ tag = child.tag.split("}")[-1].lower()
+ text = (child.text or "").strip()
+
+ if not text:
+ continue
+ # if tag.startswith(f"{{{POM_NAMESPACE}}}") and tag.endswith(".version") and child.text:
+ # print('entramos')
+ # runtime_name = tag.split("}")[-1].split(".")[0].capitalize()
+ # version_value = child.text.strip()
+ # runtimes.append({"value": f'{runtime_name} {version_value}',"name": runtime_name, "version": version_value})
+ if any(x in tag for x in ["java.version", "javaversion", "java_version"]):
+ runtimes.append({
+ "name": "Java",
+ "version": text,
+ "value": f"Java: {text}"
+ })
+ elif any(x in tag for x in ["kotlin.version", "kotlinversion", "kotlin_version"]):
+ runtimes.append({
+ "name": "Kotlin",
+ "version": text,
+ "value": f"Kotlin: {text}"
+ })
+ elif any(x in tag for x in ["scala.version", "scalaversion", "scala_version"]):
+ runtimes.append({
+ "name": "Scala",
+ "version": text,
+ "value": f"Scala: {text}"
+ })
+
+ return runtimes
\ No newline at end of file
diff --git a/src/somef_core/parser/publiccode_parser 2.py b/src/somef_core/parser/publiccode_parser 2.py
new file mode 100644
index 0000000..d51651b
--- /dev/null
+++ b/src/somef_core/parser/publiccode_parser 2.py
@@ -0,0 +1,384 @@
+
+import json
+import yaml
+import logging
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+import re
+
+def parse_publiccode_file(file_path, metadata_result: Result, source):
+ """
+ Parse a publiccode.yml file and extract relevant metadata.
+
+ Parameters
+ ----------
+ file_path: path of the publiccode.yml file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the package file (URL)
+
+ Returns
+ """
+ print("file_path publiccode:", file_path)
+ try:
+ with open(file_path, 'r', encoding='utf-8') as file:
+ content = yaml.safe_load(file)
+
+ except Exception as e:
+ logging.warning(f"Could not parse publiccode.yml {file_path}: {e}")
+ return metadata_result
+
+ if not isinstance(content, dict):
+ return metadata_result
+
+ if Path(file_path).name.lower() in {"publiccode.yml", "publiccode.yaml"}:
+ print("Detected publiccode.yml file.")
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "url" in content:
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": content["url"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ #application domain: Categories and description.[lang].genericName
+ if "categories" in content:
+ for category in content["categories"]:
+ metadata_result.add_result(
+ constants.CAT_APPLICATION_DOMAIN,
+ {
+ "value": category,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "name" in content:
+ metadata_result.add_result(
+ constants.CAT_NAME,
+ {
+ "value": content["name"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "description" in content:
+ # this is the structure. But we don't need the language
+ # description:
+ # en:
+ # genericName: Registry
+ # es:
+ # genericName: Registro
+ description = content.get("description", {})
+
+ generic_names = {
+ lang_block["genericName"]
+ for lang_block in description.values()
+ if isinstance(lang_block, dict) and "genericName" in lang_block
+ }
+ for generic_name in generic_names:
+ metadata_result.add_result(
+ constants.CAT_APPLICATION_DOMAIN,
+ {
+ "value": generic_name,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ short_descriptions = [
+ lang_block.get("shortDescription")
+ for lang_block in description.values()
+ if isinstance(lang_block, dict)
+ ]
+ for short_desc in filter(None, short_descriptions):
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": short_desc.strip(),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ long_descriptions = [
+ lang_block.get("longDescription")
+ for lang_block in description.values()
+ if isinstance(lang_block, dict)
+ ]
+ for long_desc in filter(None, long_descriptions):
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": long_desc.strip(),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ names = {
+ lang_block.get("localisedName")
+ for lang_block in description.values()
+ if isinstance(lang_block, dict)
+ }
+ for name in filter(None, names):
+ metadata_result.add_result(
+ constants.CAT_NAME,
+ {
+ "value": name.strip(),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ keywords = []
+ for lang_block in description.values():
+ if not isinstance(lang_block, dict):
+ continue
+
+ features = lang_block.get("features", [])
+ if isinstance(features, list):
+ for feature in features:
+ if isinstance(feature, str):
+ keywords.append(feature)
+
+ if keywords:
+ metadata_result.add_result(
+ constants.CAT_KEYWORDS,
+ {
+ "value": keywords,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "platforms" in content:
+ for platform in content["platforms"]:
+ metadata_result.add_result(
+ constants.CAT_RUNTIME_PLATFORM,
+ {
+ "value": platform,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ depends_on = content.get("dependsOn", {})
+# dependsOn:
+# open: or propietary or hardware
+# - name: MySQL
+# versionMin: "1.1"
+# versionMax: "1.3"
+# optional: true
+ for dep_type, dep_list in depends_on.items(): # dep_type = "open", "proprietary", "hardware"
+ for dep in dep_list:
+ name = dep.get("name")
+ version = None
+ version_str = None
+
+ # complex version handling because sometimes is version and sometimes versionMin/versionMax
+ if "version" in dep:
+ version = dep["version"]
+ version_str = f"=={version}"
+ else:
+ version_min = dep.get("versionMin")
+ version_max = dep.get("versionMax")
+ if version_min and version_max:
+ version = f">={version_min},<{version_max}"
+ version_str = version
+ elif version_min:
+ version = f">={version_min}"
+ version_str = version
+ elif version_max:
+ version = f"<{version_max}"
+ version_str = version
+
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": f"{name}{version_str}" if version_str else name,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "runtime"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "softwareVersion" in content:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": content["softwareVersion"],
+ "type": constants.RELEASE,
+ "tag": content["softwareVersion"]
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "developmentStatus" in content:
+ metadata_result.add_result(
+ constants.CAT_DEV_STATUS,
+ {
+ "value": content["developmentStatus"],
+ "type": constants.RELEASE,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "legal" in content:
+ legal = content["legal"]
+ if "license" in legal:
+ license_info_spdx = detect_license_spdx(legal["license"])
+
+ if license_info_spdx:
+ license_data = {
+ "value": legal["license"],
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": legal["license"],
+ "type": constants.LICENSE
+ }
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "releaseDate" in content:
+ date_published = content["releaseDate"]
+ # Add both date published and date updated with the same value
+ if date_published:
+ metadata_result.add_result(
+ constants.CAT_DATE_PUBLISHED,
+ {
+ "value": date_published,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ metadata_result.add_result(
+ constants.CAT_DATE_UPDATED,
+ {
+ "value": date_published,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "maintenance" in content:
+ maintenance = content.get("maintenance", {})
+ # maintenance_type = maintenance.get("type")
+
+ # if maintenance_type == "contract":
+ role_map = [
+ ("contractors", "maintenance_contractor"),
+ ("contacts", "maintenance_contact"),
+ ]
+
+ for key, role in role_map:
+ for person in maintenance.get(key, []):
+ author_data = {
+ "type": constants.AGENT,
+ "value": person.get("name", ""),
+ "name": person.get("name", ""),
+ "role": role
+ }
+
+ if "email" in person:
+ author_data["email"] = person["email"]
+
+ if "website" in person:
+ author_data["url"] = person["website"]
+
+ if "affiliation" in person:
+ author_data["affiliation"] = person["affiliation"]
+
+ metadata_result.add_result(
+ constants.CAT_OWNER,
+ author_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ return metadata_result
+
+
+def detect_license_spdx(license_text):
+ """
+ Function that given a license text, infers the name and spdx id in a dockerfile
+ Parameters
+ ----------
+ license_text
+
+ Returns
+ -------
+ A JSON dictionary with name and spdx id
+ """
+
+ for license_name, license_info in constants.LICENSES_DICT.items():
+ if re.search(license_info["regex"], license_text, re.IGNORECASE):
+ return {
+ "name": license_name,
+ "spdx_id": f"{license_info['spdx_id']}",
+ "@id": f"https://spdx.org/licenses/{license_info['spdx_id']}"
+ }
+
+ for license_name, license_info in constants.LICENSES_DICT.items():
+ spdx_id = license_info["spdx_id"]
+ if re.search(rf'\b{re.escape(spdx_id)}\b', license_text, re.IGNORECASE):
+ return {
+ "name": license_name,
+ "spdx_id": spdx_id,
+ "@id": f"https://spdx.org/licenses/{spdx_id}"
+ }
+ return None
diff --git a/src/somef_core/parser/publiccode_parser.py b/src/somef_core/parser/publiccode_parser.py
new file mode 100644
index 0000000..d51651b
--- /dev/null
+++ b/src/somef_core/parser/publiccode_parser.py
@@ -0,0 +1,384 @@
+
+import json
+import yaml
+import logging
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+import re
+
+def parse_publiccode_file(file_path, metadata_result: Result, source):
+ """
+ Parse a publiccode.yml file and extract relevant metadata.
+
+ Parameters
+ ----------
+ file_path: path of the publiccode.yml file being analysed
+ metadata_result: metadata object where the metadata dictionary is kept
+ source: source of the package file (URL)
+
+ Returns
+ """
+ print("file_path publiccode:", file_path)
+ try:
+ with open(file_path, 'r', encoding='utf-8') as file:
+ content = yaml.safe_load(file)
+
+ except Exception as e:
+ logging.warning(f"Could not parse publiccode.yml {file_path}: {e}")
+ return metadata_result
+
+ if not isinstance(content, dict):
+ return metadata_result
+
+ if Path(file_path).name.lower() in {"publiccode.yml", "publiccode.yaml"}:
+ print("Detected publiccode.yml file.")
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "url" in content:
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": content["url"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ #application domain: Categories and description.[lang].genericName
+ if "categories" in content:
+ for category in content["categories"]:
+ metadata_result.add_result(
+ constants.CAT_APPLICATION_DOMAIN,
+ {
+ "value": category,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "name" in content:
+ metadata_result.add_result(
+ constants.CAT_NAME,
+ {
+ "value": content["name"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "description" in content:
+ # this is the structure. But we don't need the language
+ # description:
+ # en:
+ # genericName: Registry
+ # es:
+ # genericName: Registro
+ description = content.get("description", {})
+
+ generic_names = {
+ lang_block["genericName"]
+ for lang_block in description.values()
+ if isinstance(lang_block, dict) and "genericName" in lang_block
+ }
+ for generic_name in generic_names:
+ metadata_result.add_result(
+ constants.CAT_APPLICATION_DOMAIN,
+ {
+ "value": generic_name,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ short_descriptions = [
+ lang_block.get("shortDescription")
+ for lang_block in description.values()
+ if isinstance(lang_block, dict)
+ ]
+ for short_desc in filter(None, short_descriptions):
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": short_desc.strip(),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ long_descriptions = [
+ lang_block.get("longDescription")
+ for lang_block in description.values()
+ if isinstance(lang_block, dict)
+ ]
+ for long_desc in filter(None, long_descriptions):
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": long_desc.strip(),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ names = {
+ lang_block.get("localisedName")
+ for lang_block in description.values()
+ if isinstance(lang_block, dict)
+ }
+ for name in filter(None, names):
+ metadata_result.add_result(
+ constants.CAT_NAME,
+ {
+ "value": name.strip(),
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ keywords = []
+ for lang_block in description.values():
+ if not isinstance(lang_block, dict):
+ continue
+
+ features = lang_block.get("features", [])
+ if isinstance(features, list):
+ for feature in features:
+ if isinstance(feature, str):
+ keywords.append(feature)
+
+ if keywords:
+ metadata_result.add_result(
+ constants.CAT_KEYWORDS,
+ {
+ "value": keywords,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "platforms" in content:
+ for platform in content["platforms"]:
+ metadata_result.add_result(
+ constants.CAT_RUNTIME_PLATFORM,
+ {
+ "value": platform,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ depends_on = content.get("dependsOn", {})
+# dependsOn:
+# open: or propietary or hardware
+# - name: MySQL
+# versionMin: "1.1"
+# versionMax: "1.3"
+# optional: true
+ for dep_type, dep_list in depends_on.items(): # dep_type = "open", "proprietary", "hardware"
+ for dep in dep_list:
+ name = dep.get("name")
+ version = None
+ version_str = None
+
+ # complex version handling because sometimes is version and sometimes versionMin/versionMax
+ if "version" in dep:
+ version = dep["version"]
+ version_str = f"=={version}"
+ else:
+ version_min = dep.get("versionMin")
+ version_max = dep.get("versionMax")
+ if version_min and version_max:
+ version = f">={version_min},<{version_max}"
+ version_str = version
+ elif version_min:
+ version = f">={version_min}"
+ version_str = version
+ elif version_max:
+ version = f"<{version_max}"
+ version_str = version
+
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": f"{name}{version_str}" if version_str else name,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": "runtime"
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "softwareVersion" in content:
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ {
+ "value": content["softwareVersion"],
+ "type": constants.RELEASE,
+ "tag": content["softwareVersion"]
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "developmentStatus" in content:
+ metadata_result.add_result(
+ constants.CAT_DEV_STATUS,
+ {
+ "value": content["developmentStatus"],
+ "type": constants.RELEASE,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "legal" in content:
+ legal = content["legal"]
+ if "license" in legal:
+ license_info_spdx = detect_license_spdx(legal["license"])
+
+ if license_info_spdx:
+ license_data = {
+ "value": legal["license"],
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": legal["license"],
+ "type": constants.LICENSE
+ }
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "releaseDate" in content:
+ date_published = content["releaseDate"]
+ # Add both date published and date updated with the same value
+ if date_published:
+ metadata_result.add_result(
+ constants.CAT_DATE_PUBLISHED,
+ {
+ "value": date_published,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ metadata_result.add_result(
+ constants.CAT_DATE_UPDATED,
+ {
+ "value": date_published,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "maintenance" in content:
+ maintenance = content.get("maintenance", {})
+ # maintenance_type = maintenance.get("type")
+
+ # if maintenance_type == "contract":
+ role_map = [
+ ("contractors", "maintenance_contractor"),
+ ("contacts", "maintenance_contact"),
+ ]
+
+ for key, role in role_map:
+ for person in maintenance.get(key, []):
+ author_data = {
+ "type": constants.AGENT,
+ "value": person.get("name", ""),
+ "name": person.get("name", ""),
+ "role": role
+ }
+
+ if "email" in person:
+ author_data["email"] = person["email"]
+
+ if "website" in person:
+ author_data["url"] = person["website"]
+
+ if "affiliation" in person:
+ author_data["affiliation"] = person["affiliation"]
+
+ metadata_result.add_result(
+ constants.CAT_OWNER,
+ author_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ return metadata_result
+
+
+def detect_license_spdx(license_text):
+ """
+ Function that given a license text, infers the name and spdx id in a dockerfile
+ Parameters
+ ----------
+ license_text
+
+ Returns
+ -------
+ A JSON dictionary with name and spdx id
+ """
+
+ for license_name, license_info in constants.LICENSES_DICT.items():
+ if re.search(license_info["regex"], license_text, re.IGNORECASE):
+ return {
+ "name": license_name,
+ "spdx_id": f"{license_info['spdx_id']}",
+ "@id": f"https://spdx.org/licenses/{license_info['spdx_id']}"
+ }
+
+ for license_name, license_info in constants.LICENSES_DICT.items():
+ spdx_id = license_info["spdx_id"]
+ if re.search(rf'\b{re.escape(spdx_id)}\b', license_text, re.IGNORECASE):
+ return {
+ "name": license_name,
+ "spdx_id": spdx_id,
+ "@id": f"https://spdx.org/licenses/{spdx_id}"
+ }
+ return None
diff --git a/src/somef_core/parser/python_parser.py b/src/somef_core/parser/python_parser.py
index f0f02e1..63a3f3a 100644
--- a/src/somef_core/parser/python_parser.py
+++ b/src/somef_core/parser/python_parser.py
@@ -13,17 +13,20 @@
"""
def parse_dependency(dependency_str):
+
if not dependency_str:
return None, None
- parts = re.split(r'(>=|<=|==|!=|>|<|~=|\[)', dependency_str, 1)
+ # parts = re.split(r'(>=|<=|==|!=|>|<|~=|\[)', dependency_str, 1)
+ parts = re.split(r'(>=|<=|==|!=|>|<|~=)', dependency_str, 1)
name = parts[0].strip()
if len(parts) > 1:
version = ''.join(parts[1:])
else:
version = ""
- version = version.strip("[]() -.,:")
-
+ # version = version.strip("[]() -.,:")
+ version = re.sub(r'[\[\]\(\)]', '', version)
+
return name, version
def parse_url_type(url_label):
@@ -39,6 +42,8 @@ def parse_url_type(url_label):
return constants.CAT_README_URL
elif "download" in label:
return constants.CAT_DOWNLOAD_URL
+ elif "homepage" in label:
+ return constants.CAT_HOMEPAGE
else:
return constants.CAT_RELATED_DOCUMENTATION
@@ -60,246 +65,6 @@ def get_project_data(data):
project = data["tool"]["poetry"]
return project
-def parse_pyproject_toml(file_path, metadata_result: Result, source):
- """
-
- Parameters
- ----------
- file_path: path to the package file being analysed
- metadata_result: Metadata object dictionary
- source: source of the package file (URL)
-
- Returns
- -------
-
- """
- try:
- if Path(file_path).name == "pyproject.toml":
- metadata_result.add_result(
- constants.CAT_HAS_PACKAGE_FILE,
- {
- "value": "pyproject.toml",
- "type": constants.URL,
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
- with open(file_path, "rb") as f:
- data = tomli.load(f)
-
- project = get_project_data(data)
-
- if "name" in project:
- metadata_result.add_result(
- constants.CAT_PACKAGE_ID,
- {
- "value": project["name"],
- "type": constants.STRING
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
-
- if "description" in project:
- metadata_result.add_result(
- constants.CAT_DESCRIPTION,
- {
- "value": project["description"],
- "type": constants.STRING
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
-
- if "version" in project:
- metadata_result.add_result(
- constants.CAT_VERSION,
- {
- "value": project["version"],
- "type": constants.RELEASE,
- "tag": project["version"]
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
-
- dependencies = project.get("dependencies", [])
- if isinstance(dependencies, list):
- for req in dependencies:
- name, version = parse_dependency(req)
- if name:
- metadata_result.add_result(
- constants.CAT_REQUIREMENTS,
- {
- "value": req,
- "name": name,
- "version": version,
- "type": constants.SOFTWARE_APPLICATION
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
- elif isinstance(dependencies, dict):
- for name, version in dependencies.items():
- req = f"{name}{version}" if version else name
- metadata_result.add_result(
- constants.CAT_REQUIREMENTS,
- {
- "value": req,
- "name": name,
- "version": version,
- "type": constants.SOFTWARE_APPLICATION
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
-
- # This is for detecting the "requires" section in a pyrpoject.toml file
- if "build-system" in data and "requires" in data["build-system"]:
- build_requires = data["build-system"]["requires"]
- if isinstance(build_requires, list):
- for req in build_requires:
- name, version = parse_dependency(req)
- if name:
- metadata_result.add_result(
- constants.CAT_REQUIREMENTS,
- {
- "value": req,
- "name": name,
- "version": version,
- "type": constants.SOFTWARE_APPLICATION
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
-
- urls = project.get("urls", {})
- if not urls and "tool" in data and "poetry" in data["tool"]:
-
- poetry = data["tool"]["poetry"]
- if "repository" in poetry:
- urls["repository"] = poetry["repository"]
- if "homepage" in poetry:
- urls["homepage"] = poetry["homepage"]
- if "documentation" in poetry:
- urls["documentation"] = poetry["documentation"]
-
- for url_type, url in urls.items():
- category = parse_url_type(url_type)
- metadata_result.add_result(
- category,
- {
- "value": url,
- "type": constants.URL
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
-
- authors = project.get("authors", [])
- if isinstance(authors, list):
- for author in authors:
- if isinstance(author, dict):
- author_data = {
- "name": author.get("name"),
- "email": author.get("email"),
- "type": constants.AGENT,
- "value": author.get("name")
- }
- if author.get("url") is not None:
- author_data["url"] = author.get("url")
- else:
-
- parsed = parse_author_string(author)
- author_data = {
- "name": parsed["name"],
- "email": parsed["email"],
- "type": constants.AGENT,
- "value": parsed["name"]
- }
-
- metadata_result.add_result(
- constants.CAT_AUTHORS,
- author_data,
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
-
- if "license" in project:
- license_info = project["license"]
- license_text = ""
-
- if isinstance(license_info, dict):
- # Check if license is specified as a file
- license_path_file = license_info["file"]
- dir_path_license = os.path.dirname(file_path)
- license_path = os.path.join(dir_path_license, license_path_file)
-
- if os.path.exists(license_path):
- with open(license_path, "r", encoding="utf-8") as f:
- license_text = f.read()
-
- if "file" in license_info:
- license_value = f"License file: {license_info['file']}"
- else:
- license_text = license_info.get("text", "")
- license_value = license_info.get("type", "")
- else:
- license_text = ""
- license_value = license_info
-
- license_info_spdx = detect_license_spdx(license_text, 'JSON')
- spdx_id = ""
- spdx_name = ""
-
- if license_info_spdx:
- license_data = {
- "value": license_value,
- "spdx_id": license_info_spdx.get('spdx_id'),
- "name": license_info_spdx.get('name'),
- "type": constants.LICENSE
- }
- else:
- license_data = {
- "value": license_value,
- "type": constants.LICENSE
- }
-
- metadata_result.add_result(
- constants.CAT_LICENSE,
- license_data,
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
-
- if "keywords" in project:
- for keyword in project["keywords"]:
- metadata_result.add_result(
- constants.CAT_KEYWORDS,
- {
- "value": keyword,
- "type": constants.STRING
- },
- 1,
- constants.TECHNIQUE_CODE_CONFIG_PARSER,
- source
- )
-
- except Exception as e:
- logging.error(f"Error parsing pyproject.toml from {file_path}: {str(e)}")
-
- return metadata_result
-
def parse_requirements_txt(file_path, metadata_result: Result, source):
"""
Parameters
@@ -314,22 +79,43 @@ def parse_requirements_txt(file_path, metadata_result: Result, source):
"""
try:
if Path(file_path).name.lower() in ["requirements.txt", "requirement.txt"]:
-
-
+
with open(file_path, "r", encoding="utf-8") as f:
- for line in f:
+ lines = f.readlines()
+
+ for line in lines:
line = line.strip()
if not line or line.startswith('#'):
continue
name, version = parse_dependency(line)
if name:
- metadata_result.add_result(
- constants.CAT_REQUIREMENTS,
- {
+ req = {
"value": line,
"name": name,
- "version": version,
"type": constants.SOFTWARE_APPLICATION
+ }
+ if version:
+ req['version'] = version
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ req,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+ runtimes = parse_runtime_platform_from_requirements(lines)
+ if runtimes:
+ for runtime in runtimes:
+ metadata_result.add_result(
+ constants.CAT_RUNTIME_PLATFORM,
+ {
+ "value": runtime["value"],
+ "version": runtime["version"],
+ "name": runtime["name"],
+ "type": constants.STRING
},
1,
constants.TECHNIQUE_CODE_CONFIG_PARSER,
@@ -404,7 +190,7 @@ def parse_setup_py(file_path, metadata_result: Result, source):
constants.CAT_AUTHORS,
{
"name": value,
- "email": None,
+ # "email": None,
"type": constants.AGENT,
},
1,
@@ -420,8 +206,12 @@ def parse_setup_py(file_path, metadata_result: Result, source):
value = module_vars[keyword.value.id]
else:
value = ast.literal_eval(keyword.value)
-
- author_results = metadata_result.results.get(constants.CAT_AUTHORS, [])
+
+ # author_results = metadata_result.results.get(constants.CAT_AUTHORS, [])
+ author_results = [
+ a for a in metadata_result.results.get(constants.CAT_AUTHORS, [])
+ if a.get("technique") == constants.TECHNIQUE_CODE_CONFIG_PARSER
+ ]
if author_results:
for result in author_results:
result["result"]["email"] = value
@@ -429,7 +219,7 @@ def parse_setup_py(file_path, metadata_result: Result, source):
metadata_result.add_result(
constants.CAT_AUTHORS,
{
- "name": None,
+ # "name": None,
"email": value,
"type": constants.AGENT,
"value": value
@@ -564,4 +354,72 @@ def parse_setup_py(file_path, metadata_result: Result, source):
except Exception as e:
logging.error(f"Error parsing setup.py from {file_path}: {str(e)}")
- return metadata_result
\ No newline at end of file
+ return metadata_result
+
+def parse_runtime_platform_from_pyproject(project_section):
+ """
+ Given the `[tool.poetry]` section from pyproject.toml,
+ this method extracts the runtime platform(s) declared (e.g. Python version). Return a list of dicts.
+
+ """
+ runtimes = []
+
+ deps = project_section.get("dependencies", {})
+ if isinstance(deps, dict):
+ python_spec = deps.get("python")
+ if python_spec:
+ runtimes.append({"name": "Python", "version": python_spec, "value": f'Python {python_spec}'})
+
+ req_python = project_section.get("requires-python")
+ if req_python:
+ runtimes.append({"name": "Python", "version": req_python, "value": f'Python {python_spec}'})
+
+ return runtimes
+
+def parse_runtime_platform_from_requirements(requirements_lines):
+ """
+ Extracts runtime information (e.g., Python) from a requirements.txt file.
+ Only returns an entry if the runtime is explicitly mentioned with a version.
+
+ Parameters
+ ----------
+ requirements_lines :
+ Lines from the requirements.txt file.
+
+ Returns
+ -------
+ list of dict
+ Each dictionary has the keys 'name' and 'version', e.g.:
+ [{'name': 'Python', 'version': '3.11'}]
+ Returns an empty list if no explicit runtime information is found.
+ """
+ runtimes = []
+
+ if not requirements_lines:
+ return runtimes
+
+ for line in requirements_lines:
+ clean_line = line.strip()
+ if not clean_line or clean_line.startswith('#'):
+ continue
+
+ if clean_line.lower().startswith('python'):
+ version = None
+
+ for sep in ['==', '>=', '<=', '~=', '>', '<']:
+ if sep in clean_line:
+ version = clean_line.split(sep)[1].strip()
+ break
+
+ if version is None:
+ match = re.search(r'python\s*([0-9.]+)', clean_line, re.IGNORECASE)
+ if not match:
+ match = re.search(r'python([0-9.]+)', clean_line, re.IGNORECASE)
+ if match:
+ version = match.group(1)
+
+ if version:
+ runtimes.append({'name': 'Python', 'version': version, 'value': f'Python: {version}'})
+ break
+
+ return runtimes
\ No newline at end of file
diff --git a/src/somef_core/parser/toml_parser 2.py b/src/somef_core/parser/toml_parser 2.py
new file mode 100644
index 0000000..fb33080
--- /dev/null
+++ b/src/somef_core/parser/toml_parser 2.py
@@ -0,0 +1,675 @@
+# -*- coding: utf-8 -*-
+import tomli
+import re
+import os
+import logging
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+from ..regular_expressions import detect_license_spdx, detect_spdx_from_declared
+
+
+def parse_toml_file(file_path, metadata_result: Result, source):
+ """
+ Unified TOML parser that handles Cargo.toml, pyproject.toml, and Project.toml files.
+
+ Parameters
+ ----------
+ file_path: path to the TOML file being analyzed
+ metadata_result: Metadata object dictionary
+ source: source of the package file (URL)
+
+ Returns
+ -------
+ metadata_result: Updated metadata result object
+ """
+ try:
+ filename = Path(file_path).name.lower()
+
+ if filename == "cargo.toml":
+ file_type = "cargo"
+ display_name = "Cargo.toml"
+
+ elif filename == "pyproject.toml":
+ file_type = "pyproject"
+ display_name = "pyproject.toml"
+
+ elif filename == "project.toml":
+ file_type = "julia_project"
+ display_name = "Project.toml"
+
+ else:
+ logging.warning(f"Unknown TOML file type: {filename}")
+ return metadata_result
+
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": display_name,
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, "rb") as f:
+ data = tomli.load(f)
+
+ if file_type == "cargo":
+ parse_cargo_metadata(data, metadata_result, source, file_path)
+ elif file_type == "pyproject":
+ parse_pyproject_metadata(data, metadata_result, source, file_path)
+ elif file_type == "julia_project":
+ parse_julia_project_metadata(data, metadata_result, source)
+
+ except Exception as e:
+ logging.error(f"Error parsing TOML file {file_path}: {str(e)}")
+
+ return metadata_result
+
+
+def extract_common_name_field(data, metadata_result, source, file_type):
+ """
+ Extract 'name' field that's common across Cargo.toml, pyproject.toml, and Project.toml.
+
+ For Cargo.toml: data["package"]["name"]
+ For pyproject.toml: data["project"]["name"] or data["tool"]["poetry"]["name"]
+ For Project.toml: data["name"]
+ """
+ name_value = None
+
+ if file_type == "cargo" and "package" in data and "name" in data["package"]:
+ name_value = data["package"]["name"]
+
+ elif file_type == "pyproject":
+ project = get_project_data(data)
+ if "name" in project:
+ name_value = project["name"]
+
+ elif file_type == "julia_project" and "name" in data:
+ name_value = data["name"]
+
+ if name_value:
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_ID,
+ {
+ "value": name_value,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def extract_common_version_field(data, metadata_result, source, file_type):
+ """
+ Extract 'version' field that's common across all three TOML types.
+
+ For Cargo.toml: data["package"]["version"]
+ For pyproject.toml: data["project"]["version"] or data["tool"]["poetry"]["version"]
+ For Project.toml: data["version"]
+ """
+ version_value = None
+
+ if file_type == "cargo" and "package" in data and "version" in data["package"]:
+ version_value = data["package"]["version"]
+ version_type = constants.RELEASE
+
+ elif file_type == "pyproject":
+ project = get_project_data(data)
+ if "version" in project:
+ version_value = project["version"]
+ version_type = constants.RELEASE
+
+ elif file_type == "julia_project" and "version" in data:
+ version_value = data["version"]
+ version_type = constants.STRING
+
+ if version_value:
+ result_dict = {
+ "value": version_value,
+ "type": version_type
+ }
+ if file_type in ["cargo", "pyproject"]:
+ result_dict["tag"] = version_value
+
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ result_dict,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def extract_common_description_field(data, metadata_result, source, file_type):
+ """
+ Extract 'description' field common to Cargo.toml and pyproject.toml.
+
+ For Cargo.toml: data["package"]["description"]
+ For pyproject.toml: data["project"]["description"] or data["tool"]["poetry"]["description"]
+ """
+ description_value = None
+
+ if file_type == "cargo" and "package" in data and "description" in data["package"]:
+ description_value = data["package"]["description"]
+
+ elif file_type == "pyproject":
+ project = get_project_data(data)
+ if "description" in project:
+ description_value = project["description"]
+
+ if description_value:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": description_value,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def extract_common_authors_field(data, metadata_result, source, file_type):
+ """
+ Extract 'authors' field common across all three TOML types.
+
+ All three formats can have authors with name and email.
+ """
+ authors = None
+
+ if file_type == "cargo" and "package" in data and "authors" in data["package"]:
+ authors = data["package"]["authors"]
+
+ elif file_type == "pyproject":
+ project = get_project_data(data)
+ if "authors" in project:
+ authors = project["authors"]
+
+ elif file_type == "julia_project" and "authors" in data:
+ authors = data["authors"]
+
+ if authors:
+ for author in authors:
+ if isinstance(author, dict):
+ # pyproject.toml format: {name: "...", email: "..."}
+ author_data = {
+ "name": author.get("name"),
+ "email": author.get("email"),
+ "type": constants.AGENT,
+ "value": author.get("name")
+ }
+ if author.get("url"):
+ author_data["url"] = author.get("url")
+ else:
+ # String format "Name " or just "Name"
+ match = re.match(r'^(.+?)\s*<(.+?)>$', str(author).strip())
+ if match:
+ author_name = match.group(1).strip()
+ author_email = match.group(2).strip()
+ author_data = {
+ "name": author_name,
+ "email": author_email,
+ "type": constants.AGENT,
+ "value": author_name
+ }
+ else:
+ author_data = {
+ "name": str(author).strip(),
+ "email": None,
+ "type": constants.AGENT,
+ "value": str(author).strip()
+ }
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def extract_common_keywords_field(data, metadata_result, source, file_type):
+ """
+ Extract 'keywords' field common to Cargo.toml and pyproject.toml.
+ """
+ keywords = None
+
+ if file_type == "cargo" and "package" in data and "keywords" in data["package"]:
+ keywords = data["package"]["keywords"]
+ elif file_type == "pyproject":
+ project = get_project_data(data)
+ if "keywords" in project:
+ keywords = project["keywords"]
+
+ if keywords:
+ for keyword in keywords:
+ metadata_result.add_result(
+ constants.CAT_KEYWORDS,
+ {
+ "value": keyword,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def parse_cargo_metadata(data, metadata_result, source, file_path):
+ """Parse Cargo.toml specific metadata."""
+
+ extract_common_name_field(data, metadata_result, source, "cargo")
+ extract_common_version_field(data, metadata_result, source, "cargo")
+ extract_common_description_field(data, metadata_result, source, "cargo")
+ extract_common_authors_field(data, metadata_result, source, "cargo")
+ extract_common_keywords_field(data, metadata_result, source, "cargo")
+
+ if "package" in data and "repository" in data["package"]:
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": data["package"]["repository"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "package" in data and "license" in data["package"]:
+ license_value = data["package"]["license"]
+ license_text = ""
+
+ dir_path = os.path.dirname(file_path)
+ license_paths = [
+ os.path.join(dir_path, "LICENSE"),
+ os.path.join(dir_path, "LICENSE.txt"),
+ os.path.join(dir_path, "LICENSE.md")
+ ]
+
+ for license_path in license_paths:
+ if os.path.exists(license_path):
+ with open(license_path, "r", encoding="utf-8") as lf:
+ license_text = lf.read()
+ break
+
+ license_info_spdx = detect_license_spdx(license_text, 'JSON')
+
+ if license_info_spdx:
+ license_data = {
+ "value": license_value,
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": license_value,
+ "type": constants.LICENSE
+ }
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "dependencies" in data:
+ dependencies = data["dependencies"]
+ for name, info in dependencies.items():
+ version, dep_type, req_details = determine_dependency_type(info)
+ req = f"{name} = {{ {req_details} }}"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": dep_type
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ # target-specific dependencies
+ for key in data:
+ if key.startswith("target.") and isinstance(data[key], dict) and "dependencies" in data[key]:
+ target_deps = data[key]["dependencies"]
+ for name, info in target_deps.items():
+ version, dep_type, req_details = determine_dependency_type(info)
+ req = f"{name} = {{ {req_details} }} (target-specific)"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": dep_type
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def parse_pyproject_metadata(data, metadata_result, source, file_path):
+ """Parse pyproject.toml specific metadata."""
+ project = get_project_data(data)
+
+ extract_common_name_field(data, metadata_result, source, "pyproject")
+ extract_common_version_field(data, metadata_result, source, "pyproject")
+ extract_common_description_field(data, metadata_result, source, "pyproject")
+ extract_common_authors_field(data, metadata_result, source, "pyproject")
+ extract_common_keywords_field(data, metadata_result, source, "pyproject")
+
+ if "homepage" in project:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": project["homepage"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ dependencies = project.get("dependencies", [])
+ if isinstance(dependencies, list):
+ for req in dependencies:
+ name, version = parse_dependency(req)
+ if name:
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ elif isinstance(dependencies, dict):
+ for name, version in dependencies.items():
+ req = f"{name}{version}" if version else name
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ # build-system requires
+ if "build-system" in data and "requires" in data["build-system"]:
+ build_requires = data["build-system"]["requires"]
+ if isinstance(build_requires, list):
+ for req in build_requires:
+ name, version = parse_dependency(req)
+ if name:
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ urls = project.get("urls", {})
+
+ if not urls and "tool" in data and "poetry" in data["tool"]:
+ poetry = data["tool"]["poetry"]
+ if "repository" in poetry:
+ urls["repository"] = poetry["repository"]
+ if "homepage" in poetry:
+ urls["homepage"] = poetry["homepage"]
+ if "documentation" in poetry:
+ urls["documentation"] = poetry["documentation"]
+
+ for url_type, url in urls.items():
+ category = parse_url_type(url_type)
+ metadata_result.add_result(
+ category,
+ {
+ "value": url,
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "license" in project:
+ license_info = project["license"]
+ license_text = ""
+
+ if isinstance(license_info, dict):
+ license_path_file = license_info.get("file")
+ if license_path_file:
+ dir_path_license = os.path.dirname(file_path)
+ license_path = os.path.join(dir_path_license, license_path_file)
+
+ if os.path.exists(license_path):
+ with open(license_path, "r", encoding="utf-8") as f:
+ license_text = f.read()
+
+ license_value = f"License file: {license_path_file}"
+ else:
+ license_text = license_info.get("text", "")
+ license_value = license_info.get("type", "")
+ else:
+ license_text = ""
+ license_value = license_info
+
+
+ licence_info_spdx = None
+
+ if license_text:
+ license_info_spdx = detect_license_spdx(license_text, 'JSON')
+ else:
+ # there is no text in licence and we cant detect license in the text as usual,
+ # so we check if the declared license matches an SPDX ID from our dictionary of licences
+ license_info_spdx = detect_spdx_from_declared(license_value)
+
+ if license_info_spdx:
+ license_data = {
+ "value": license_value,
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": license_value,
+ "type": constants.LICENSE
+ }
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ runtimes = parse_runtime_platform_from_pyproject(project)
+ if runtimes:
+ for runtime in runtimes:
+ metadata_result.add_result(
+ constants.CAT_RUNTIME_PLATFORM,
+ {
+ "value": f'{runtime["name"]}{runtime["version"]}',
+ "name": runtime["name"],
+ "version": runtime["version"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def parse_julia_project_metadata(data, metadata_result, source):
+ """Parse Project.toml (Julia) specific metadata."""
+ extract_common_name_field(data, metadata_result, source, "julia_project")
+ extract_common_version_field(data, metadata_result, source, "julia_project")
+ extract_common_authors_field(data, metadata_result, source, "julia_project")
+
+ if "uuid" in data:
+ metadata_result.add_result(
+ constants.CAT_IDENTIFIER,
+ {
+ "value": data["uuid"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "deps" in data:
+ deps = data["deps"]
+ for req in deps.keys():
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "compat" in data:
+ compat = data["compat"]
+ for package_name, version in compat.items():
+ metadata_result.add_result(
+ constants.CAT_RUNTIME_PLATFORM,
+ {
+ "value": f"{package_name}",
+ "package": package_name,
+ "version": version,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+# Helper functions
+
+def get_project_data(data):
+ """Get project section from pyproject.toml (handles both standard and Poetry formats)."""
+ project = data.get("project", {})
+ if not project and "tool" in data and "poetry" in data["tool"]:
+ project = data["tool"]["poetry"]
+ return project
+
+
+def parse_dependency(dependency_str):
+ """Parse a dependency string to extract name and version."""
+ if not dependency_str:
+ return None, None
+
+ parts = re.split(r'(>=|<=|==|!=|>|<|~=)', dependency_str, 1)
+ name = parts[0].strip()
+ if len(parts) > 1:
+ version = ''.join(parts[1:])
+ else:
+ version = ""
+
+ version = re.sub(r'[\[\]]', '', version)
+
+ return name, version
+
+
+def parse_url_type(url_label):
+ """Determine the category for a URL based on its label."""
+ label = url_label.lower()
+
+ if "repository" in label or label in ("git", "github", "code", "sourcecode", "source"):
+ return constants.CAT_CODE_REPOSITORY
+ elif "issue" in label or label in ("bug tracker", "tracker", "issues"):
+ return constants.CAT_ISSUE_TRACKER
+ elif "doc" in label or label in ("documentation", "api reference", "reference"):
+ return constants.CAT_DOCUMENTATION
+ elif label == "readme":
+ return constants.CAT_README_URL
+ elif "download" in label:
+ return constants.CAT_DOWNLOAD_URL
+ elif "homepage" in label:
+ return constants.CAT_HOMEPAGE
+ else:
+ return constants.CAT_RELATED_DOCUMENTATION
+
+
+def determine_dependency_type(info):
+ """Determine the type of dependency for Cargo.toml."""
+ if isinstance(info, dict):
+ if "version" in info:
+ version = info["version"]
+ req = f"version = {version}"
+ dep_type = "version"
+ elif "git" in info:
+ version = info["git"]
+ req = f"git = \"{version}\""
+ dep_type = "url"
+ elif "path" in info:
+ version = info["path"]
+ req = f"path = \"{version}\""
+ dep_type = "path"
+ else:
+ version = str(info)
+ req = f"other = {version}"
+ dep_type = "other"
+ else:
+ version = info
+ req = f"version = {version}"
+ dep_type = "version"
+
+ return version, dep_type, req
+
+
+def parse_runtime_platform_from_pyproject(project_section):
+ """Extract runtime platform from pyproject.toml."""
+ runtimes = []
+
+ deps = project_section.get("dependencies", {})
+ if isinstance(deps, dict):
+ python_spec = deps.get("python")
+ if python_spec:
+ runtimes.append({"name": "Python", "version": python_spec})
+
+ req_python = project_section.get("requires-python")
+ if req_python:
+ runtimes.append({"name": "Python", "version": req_python})
+
+ return runtimes
diff --git a/src/somef_core/parser/toml_parser.py b/src/somef_core/parser/toml_parser.py
new file mode 100644
index 0000000..fb33080
--- /dev/null
+++ b/src/somef_core/parser/toml_parser.py
@@ -0,0 +1,675 @@
+# -*- coding: utf-8 -*-
+import tomli
+import re
+import os
+import logging
+from pathlib import Path
+from ..process_results import Result
+from ..utils import constants
+from ..regular_expressions import detect_license_spdx, detect_spdx_from_declared
+
+
+def parse_toml_file(file_path, metadata_result: Result, source):
+ """
+ Unified TOML parser that handles Cargo.toml, pyproject.toml, and Project.toml files.
+
+ Parameters
+ ----------
+ file_path: path to the TOML file being analyzed
+ metadata_result: Metadata object dictionary
+ source: source of the package file (URL)
+
+ Returns
+ -------
+ metadata_result: Updated metadata result object
+ """
+ try:
+ filename = Path(file_path).name.lower()
+
+ if filename == "cargo.toml":
+ file_type = "cargo"
+ display_name = "Cargo.toml"
+
+ elif filename == "pyproject.toml":
+ file_type = "pyproject"
+ display_name = "pyproject.toml"
+
+ elif filename == "project.toml":
+ file_type = "julia_project"
+ display_name = "Project.toml"
+
+ else:
+ logging.warning(f"Unknown TOML file type: {filename}")
+ return metadata_result
+
+ metadata_result.add_result(
+ constants.CAT_HAS_PACKAGE_FILE,
+ {
+ # "value": display_name,
+ "value": source,
+ "type": constants.URL,
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ with open(file_path, "rb") as f:
+ data = tomli.load(f)
+
+ if file_type == "cargo":
+ parse_cargo_metadata(data, metadata_result, source, file_path)
+ elif file_type == "pyproject":
+ parse_pyproject_metadata(data, metadata_result, source, file_path)
+ elif file_type == "julia_project":
+ parse_julia_project_metadata(data, metadata_result, source)
+
+ except Exception as e:
+ logging.error(f"Error parsing TOML file {file_path}: {str(e)}")
+
+ return metadata_result
+
+
+def extract_common_name_field(data, metadata_result, source, file_type):
+ """
+ Extract 'name' field that's common across Cargo.toml, pyproject.toml, and Project.toml.
+
+ For Cargo.toml: data["package"]["name"]
+ For pyproject.toml: data["project"]["name"] or data["tool"]["poetry"]["name"]
+ For Project.toml: data["name"]
+ """
+ name_value = None
+
+ if file_type == "cargo" and "package" in data and "name" in data["package"]:
+ name_value = data["package"]["name"]
+
+ elif file_type == "pyproject":
+ project = get_project_data(data)
+ if "name" in project:
+ name_value = project["name"]
+
+ elif file_type == "julia_project" and "name" in data:
+ name_value = data["name"]
+
+ if name_value:
+ metadata_result.add_result(
+ constants.CAT_PACKAGE_ID,
+ {
+ "value": name_value,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def extract_common_version_field(data, metadata_result, source, file_type):
+ """
+ Extract 'version' field that's common across all three TOML types.
+
+ For Cargo.toml: data["package"]["version"]
+ For pyproject.toml: data["project"]["version"] or data["tool"]["poetry"]["version"]
+ For Project.toml: data["version"]
+ """
+ version_value = None
+
+ if file_type == "cargo" and "package" in data and "version" in data["package"]:
+ version_value = data["package"]["version"]
+ version_type = constants.RELEASE
+
+ elif file_type == "pyproject":
+ project = get_project_data(data)
+ if "version" in project:
+ version_value = project["version"]
+ version_type = constants.RELEASE
+
+ elif file_type == "julia_project" and "version" in data:
+ version_value = data["version"]
+ version_type = constants.STRING
+
+ if version_value:
+ result_dict = {
+ "value": version_value,
+ "type": version_type
+ }
+ if file_type in ["cargo", "pyproject"]:
+ result_dict["tag"] = version_value
+
+ metadata_result.add_result(
+ constants.CAT_VERSION,
+ result_dict,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def extract_common_description_field(data, metadata_result, source, file_type):
+ """
+ Extract 'description' field common to Cargo.toml and pyproject.toml.
+
+ For Cargo.toml: data["package"]["description"]
+ For pyproject.toml: data["project"]["description"] or data["tool"]["poetry"]["description"]
+ """
+ description_value = None
+
+ if file_type == "cargo" and "package" in data and "description" in data["package"]:
+ description_value = data["package"]["description"]
+
+ elif file_type == "pyproject":
+ project = get_project_data(data)
+ if "description" in project:
+ description_value = project["description"]
+
+ if description_value:
+ metadata_result.add_result(
+ constants.CAT_DESCRIPTION,
+ {
+ "value": description_value,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def extract_common_authors_field(data, metadata_result, source, file_type):
+ """
+ Extract 'authors' field common across all three TOML types.
+
+ All three formats can have authors with name and email.
+ """
+ authors = None
+
+ if file_type == "cargo" and "package" in data and "authors" in data["package"]:
+ authors = data["package"]["authors"]
+
+ elif file_type == "pyproject":
+ project = get_project_data(data)
+ if "authors" in project:
+ authors = project["authors"]
+
+ elif file_type == "julia_project" and "authors" in data:
+ authors = data["authors"]
+
+ if authors:
+ for author in authors:
+ if isinstance(author, dict):
+ # pyproject.toml format: {name: "...", email: "..."}
+ author_data = {
+ "name": author.get("name"),
+ "email": author.get("email"),
+ "type": constants.AGENT,
+ "value": author.get("name")
+ }
+ if author.get("url"):
+ author_data["url"] = author.get("url")
+ else:
+ # String format "Name " or just "Name"
+ match = re.match(r'^(.+?)\s*<(.+?)>$', str(author).strip())
+ if match:
+ author_name = match.group(1).strip()
+ author_email = match.group(2).strip()
+ author_data = {
+ "name": author_name,
+ "email": author_email,
+ "type": constants.AGENT,
+ "value": author_name
+ }
+ else:
+ author_data = {
+ "name": str(author).strip(),
+ "email": None,
+ "type": constants.AGENT,
+ "value": str(author).strip()
+ }
+
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def extract_common_keywords_field(data, metadata_result, source, file_type):
+ """
+ Extract 'keywords' field common to Cargo.toml and pyproject.toml.
+ """
+ keywords = None
+
+ if file_type == "cargo" and "package" in data and "keywords" in data["package"]:
+ keywords = data["package"]["keywords"]
+ elif file_type == "pyproject":
+ project = get_project_data(data)
+ if "keywords" in project:
+ keywords = project["keywords"]
+
+ if keywords:
+ for keyword in keywords:
+ metadata_result.add_result(
+ constants.CAT_KEYWORDS,
+ {
+ "value": keyword,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def parse_cargo_metadata(data, metadata_result, source, file_path):
+ """Parse Cargo.toml specific metadata."""
+
+ extract_common_name_field(data, metadata_result, source, "cargo")
+ extract_common_version_field(data, metadata_result, source, "cargo")
+ extract_common_description_field(data, metadata_result, source, "cargo")
+ extract_common_authors_field(data, metadata_result, source, "cargo")
+ extract_common_keywords_field(data, metadata_result, source, "cargo")
+
+ if "package" in data and "repository" in data["package"]:
+ metadata_result.add_result(
+ constants.CAT_CODE_REPOSITORY,
+ {
+ "value": data["package"]["repository"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "package" in data and "license" in data["package"]:
+ license_value = data["package"]["license"]
+ license_text = ""
+
+ dir_path = os.path.dirname(file_path)
+ license_paths = [
+ os.path.join(dir_path, "LICENSE"),
+ os.path.join(dir_path, "LICENSE.txt"),
+ os.path.join(dir_path, "LICENSE.md")
+ ]
+
+ for license_path in license_paths:
+ if os.path.exists(license_path):
+ with open(license_path, "r", encoding="utf-8") as lf:
+ license_text = lf.read()
+ break
+
+ license_info_spdx = detect_license_spdx(license_text, 'JSON')
+
+ if license_info_spdx:
+ license_data = {
+ "value": license_value,
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": license_value,
+ "type": constants.LICENSE
+ }
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "dependencies" in data:
+ dependencies = data["dependencies"]
+ for name, info in dependencies.items():
+ version, dep_type, req_details = determine_dependency_type(info)
+ req = f"{name} = {{ {req_details} }}"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": dep_type
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ # target-specific dependencies
+ for key in data:
+ if key.startswith("target.") and isinstance(data[key], dict) and "dependencies" in data[key]:
+ target_deps = data[key]["dependencies"]
+ for name, info in target_deps.items():
+ version, dep_type, req_details = determine_dependency_type(info)
+ req = f"{name} = {{ {req_details} }} (target-specific)"
+
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION,
+ "dependency_type": dep_type
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def parse_pyproject_metadata(data, metadata_result, source, file_path):
+ """Parse pyproject.toml specific metadata."""
+ project = get_project_data(data)
+
+ extract_common_name_field(data, metadata_result, source, "pyproject")
+ extract_common_version_field(data, metadata_result, source, "pyproject")
+ extract_common_description_field(data, metadata_result, source, "pyproject")
+ extract_common_authors_field(data, metadata_result, source, "pyproject")
+ extract_common_keywords_field(data, metadata_result, source, "pyproject")
+
+ if "homepage" in project:
+ metadata_result.add_result(
+ constants.CAT_HOMEPAGE,
+ {
+ "value": project["homepage"],
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ dependencies = project.get("dependencies", [])
+ if isinstance(dependencies, list):
+ for req in dependencies:
+ name, version = parse_dependency(req)
+ if name:
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+ elif isinstance(dependencies, dict):
+ for name, version in dependencies.items():
+ req = f"{name}{version}" if version else name
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ # build-system requires
+ if "build-system" in data and "requires" in data["build-system"]:
+ build_requires = data["build-system"]["requires"]
+ if isinstance(build_requires, list):
+ for req in build_requires:
+ name, version = parse_dependency(req)
+ if name:
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "name": name,
+ "version": version,
+ "type": constants.SOFTWARE_APPLICATION
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ urls = project.get("urls", {})
+
+ if not urls and "tool" in data and "poetry" in data["tool"]:
+ poetry = data["tool"]["poetry"]
+ if "repository" in poetry:
+ urls["repository"] = poetry["repository"]
+ if "homepage" in poetry:
+ urls["homepage"] = poetry["homepage"]
+ if "documentation" in poetry:
+ urls["documentation"] = poetry["documentation"]
+
+ for url_type, url in urls.items():
+ category = parse_url_type(url_type)
+ metadata_result.add_result(
+ category,
+ {
+ "value": url,
+ "type": constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "license" in project:
+ license_info = project["license"]
+ license_text = ""
+
+ if isinstance(license_info, dict):
+ license_path_file = license_info.get("file")
+ if license_path_file:
+ dir_path_license = os.path.dirname(file_path)
+ license_path = os.path.join(dir_path_license, license_path_file)
+
+ if os.path.exists(license_path):
+ with open(license_path, "r", encoding="utf-8") as f:
+ license_text = f.read()
+
+ license_value = f"License file: {license_path_file}"
+ else:
+ license_text = license_info.get("text", "")
+ license_value = license_info.get("type", "")
+ else:
+ license_text = ""
+ license_value = license_info
+
+
+ licence_info_spdx = None
+
+ if license_text:
+ license_info_spdx = detect_license_spdx(license_text, 'JSON')
+ else:
+ # there is no text in licence and we cant detect license in the text as usual,
+ # so we check if the declared license matches an SPDX ID from our dictionary of licences
+ license_info_spdx = detect_spdx_from_declared(license_value)
+
+ if license_info_spdx:
+ license_data = {
+ "value": license_value,
+ "spdx_id": license_info_spdx.get('spdx_id'),
+ "name": license_info_spdx.get('name'),
+ "type": constants.LICENSE
+ }
+ else:
+ license_data = {
+ "value": license_value,
+ "type": constants.LICENSE
+ }
+
+ metadata_result.add_result(
+ constants.CAT_LICENSE,
+ license_data,
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ runtimes = parse_runtime_platform_from_pyproject(project)
+ if runtimes:
+ for runtime in runtimes:
+ metadata_result.add_result(
+ constants.CAT_RUNTIME_PLATFORM,
+ {
+ "value": f'{runtime["name"]}{runtime["version"]}',
+ "name": runtime["name"],
+ "version": runtime["version"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+def parse_julia_project_metadata(data, metadata_result, source):
+ """Parse Project.toml (Julia) specific metadata."""
+ extract_common_name_field(data, metadata_result, source, "julia_project")
+ extract_common_version_field(data, metadata_result, source, "julia_project")
+ extract_common_authors_field(data, metadata_result, source, "julia_project")
+
+ if "uuid" in data:
+ metadata_result.add_result(
+ constants.CAT_IDENTIFIER,
+ {
+ "value": data["uuid"],
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "deps" in data:
+ deps = data["deps"]
+ for req in deps.keys():
+ metadata_result.add_result(
+ constants.CAT_REQUIREMENTS,
+ {
+ "value": req,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+ if "compat" in data:
+ compat = data["compat"]
+ for package_name, version in compat.items():
+ metadata_result.add_result(
+ constants.CAT_RUNTIME_PLATFORM,
+ {
+ "value": f"{package_name}",
+ "package": package_name,
+ "version": version,
+ "type": constants.STRING
+ },
+ 1,
+ constants.TECHNIQUE_CODE_CONFIG_PARSER,
+ source
+ )
+
+
+# Helper functions
+
+def get_project_data(data):
+ """Get project section from pyproject.toml (handles both standard and Poetry formats)."""
+ project = data.get("project", {})
+ if not project and "tool" in data and "poetry" in data["tool"]:
+ project = data["tool"]["poetry"]
+ return project
+
+
+def parse_dependency(dependency_str):
+ """Parse a dependency string to extract name and version."""
+ if not dependency_str:
+ return None, None
+
+ parts = re.split(r'(>=|<=|==|!=|>|<|~=)', dependency_str, 1)
+ name = parts[0].strip()
+ if len(parts) > 1:
+ version = ''.join(parts[1:])
+ else:
+ version = ""
+
+ version = re.sub(r'[\[\]]', '', version)
+
+ return name, version
+
+
+def parse_url_type(url_label):
+ """Determine the category for a URL based on its label."""
+ label = url_label.lower()
+
+ if "repository" in label or label in ("git", "github", "code", "sourcecode", "source"):
+ return constants.CAT_CODE_REPOSITORY
+ elif "issue" in label or label in ("bug tracker", "tracker", "issues"):
+ return constants.CAT_ISSUE_TRACKER
+ elif "doc" in label or label in ("documentation", "api reference", "reference"):
+ return constants.CAT_DOCUMENTATION
+ elif label == "readme":
+ return constants.CAT_README_URL
+ elif "download" in label:
+ return constants.CAT_DOWNLOAD_URL
+ elif "homepage" in label:
+ return constants.CAT_HOMEPAGE
+ else:
+ return constants.CAT_RELATED_DOCUMENTATION
+
+
+def determine_dependency_type(info):
+ """Determine the type of dependency for Cargo.toml."""
+ if isinstance(info, dict):
+ if "version" in info:
+ version = info["version"]
+ req = f"version = {version}"
+ dep_type = "version"
+ elif "git" in info:
+ version = info["git"]
+ req = f"git = \"{version}\""
+ dep_type = "url"
+ elif "path" in info:
+ version = info["path"]
+ req = f"path = \"{version}\""
+ dep_type = "path"
+ else:
+ version = str(info)
+ req = f"other = {version}"
+ dep_type = "other"
+ else:
+ version = info
+ req = f"version = {version}"
+ dep_type = "version"
+
+ return version, dep_type, req
+
+
+def parse_runtime_platform_from_pyproject(project_section):
+ """Extract runtime platform from pyproject.toml."""
+ runtimes = []
+
+ deps = project_section.get("dependencies", {})
+ if isinstance(deps, dict):
+ python_spec = deps.get("python")
+ if python_spec:
+ runtimes.append({"name": "Python", "version": python_spec})
+
+ req_python = project_section.get("requires-python")
+ if req_python:
+ runtimes.append({"name": "Python", "version": req_python})
+
+ return runtimes
diff --git a/src/somef_core/process_files.py b/src/somef_core/process_files.py
index 548bb39..95ad611 100644
--- a/src/somef_core/process_files.py
+++ b/src/somef_core/process_files.py
@@ -3,18 +3,30 @@
import re
import urllib
import yaml
+import string
from urllib.parse import urlparse
-from .utils import constants, markdown_utils
+from .utils import constants
+# from . import extract_workflows, extract_ontologies
from . import extract_workflows
from .process_results import Result
from .regular_expressions import detect_license_spdx, extract_scholarly_article_natural, extract_scholarly_article_properties
from .parser.pom_xml_parser import parse_pom_file
from .parser.package_json_parser import parse_package_json_file
-from .parser.python_parser import parse_pyproject_toml
from .parser.python_parser import parse_setup_py
-from.parser.python_parser import parse_requirements_txt
+from .parser.codemeta_parser import parse_codemeta_json_file
+from .parser.composer_parser import parse_composer_json
+from .parser.python_parser import parse_requirements_txt
+from .parser.authors_parser import parse_author_file
+from .parser.bower_parser import parse_bower_json_file
+from .parser.gemspec_parser import parse_gemspec_file
+from .parser.description_parser import parse_description_file
+from .parser.toml_parser import parse_toml_file
+from .parser.cabal_parser import parse_cabal_file
+from .parser.dockerfile_parser import parse_dockerfile
+from .parser.publiccode_parser import parse_publiccode_file
from chardet import detect
+
domain_gitlab = ''
def process_repository_files(repo_dir, metadata_result: Result, repo_type, owner="", repo_name="",
@@ -41,12 +53,20 @@ def process_repository_files(repo_dir, metadata_result: Result, repo_type, owner
domain_gitlab = extract_gitlab_domain(metadata_result, repo_type)
text = ""
+ readmeMD_proccesed = False
+
try:
+ parsed_build_files = set()
+
for dir_path, dir_names, filenames in os.walk(repo_dir):
+
+ dir_names[:] = [d for d in dir_names if d.lower() not in constants.IGNORED_DIRS]
repo_relative_path = os.path.relpath(dir_path, repo_dir)
+ current_dir = os.path.basename(repo_relative_path).lower()
# if this is a test folder, we ignore it (except for the root repo)
- if ignore_test_folder and repo_relative_path != "." and "test" in repo_relative_path.lower():
- # skip this file if it's in a test folder, or inside one
+ # if ignore_test_folder and repo_relative_path != "." and "test" in repo_relative_path.lower():
+ if ignore_test_folder and repo_relative_path != "." and current_dir in constants.IGNORED_DIRS:
+ # skip this file if it's in a test folder, ignored dire, or inside one
continue
for filename in filenames:
file_path = os.path.join(repo_relative_path, filename)
@@ -58,18 +78,31 @@ def process_repository_files(repo_dir, metadata_result: Result, repo_type, owner
if filename == "Dockerfile" or filename.lower() == "docker-compose.yml":
docker_url = get_file_link(repo_type, file_path, owner, repo_name, repo_default_branch, repo_dir,
repo_relative_path, filename)
+
+ # full_path = os.path.join(repo_dir, file_path)
+
+ result_value = {
+ constants.PROP_VALUE: docker_url,
+ constants.PROP_TYPE: constants.URL,
+ }
+
if filename == "Dockerfile":
format_file = constants.FORMAT_DOCKERFILE
+ result_value[constants.PROP_FORMAT] = format_file
+ metadata_result = parse_dockerfile(os.path.join(dir_path, filename), metadata_result, docker_url)
else:
format_file = constants.FORMAT_DOCKER_COMPOSE
- metadata_result.add_result(constants.CAT_HAS_BUILD_FILE,
- {
- constants.PROP_VALUE: docker_url,
- constants.PROP_TYPE: constants.URL,
- constants.PROP_FORMAT: format_file
- },
- 1,
- constants.TECHNIQUE_FILE_EXPLORATION, docker_url)
+
+ result_value[constants.PROP_FORMAT] = format_file
+
+ metadata_result.add_result(
+ constants.CAT_HAS_BUILD_FILE,
+ result_value,
+ 1,
+ constants.TECHNIQUE_FILE_EXPLORATION,
+ docker_url
+ )
+
if filename.lower().endswith(".ipynb"):
notebook_url = get_file_link(repo_type, file_path, owner, repo_name, repo_default_branch, repo_dir,
repo_relative_path, filename)
@@ -84,29 +117,51 @@ def process_repository_files(repo_dir, metadata_result: Result, repo_type, owner
filename_no_ext = os.path.splitext(filename)[0]
# this will take into account README, README.MD, README.TXT, README.RST
if "README" == filename_no_ext.upper():
- if repo_relative_path == ".":
- try:
- with open(os.path.join(dir_path, filename), "rb") as data_file:
- data_file_text = data_file.read()
- try:
- text = data_file_text.decode("utf-8")
- except UnicodeError as err:
- logging.error(f"{type(err).__name__} was raised: {err} Trying other encodings...")
- text = data_file_text.decode(detect(data_file_text)["encoding"])
- if repo_type == constants.RepositoryType.GITHUB:
- readme_url = convert_to_raw_user_content_github(filename, owner,
- repo_name,
- repo_default_branch)
- metadata_result.add_result(constants.CAT_README_URL,
- {
- constants.PROP_VALUE: readme_url,
- constants.PROP_TYPE: constants.URL
- },
- 1,
- constants.TECHNIQUE_FILE_EXPLORATION)
- except ValueError:
- logging.error("README Error: error while reading file content")
- logging.error(f"{type(err).__name__} was raised: {err}")
+ # There is unexpected behavior when the README is available in multiple formats.
+ # We prioritize the .md format as it is more readable than pdf and others
+ if not readmeMD_proccesed:
+ if repo_relative_path == ".":
+ try:
+
+ with open(os.path.join(dir_path, filename), "rb") as data_file:
+ data_file_text = data_file.read()
+
+ try:
+ text = data_file_text.decode("utf-8")
+ except UnicodeError as err:
+ logging.error(f"{type(err).__name__} was raised: {err} Trying other encodings...")
+ # text = data_file_text.decode(detect(data_file_text)["encoding"])
+ result_detect = detect(data_file_text)
+ encoding = result_detect.get("encoding")
+ if encoding:
+ try:
+ text = data_file_text.decode(encoding)
+ except UnicodeError as err:
+ logging.warning(f"Detected encoding '{encoding}' failed: {err}. Using utf-8 with replacement.")
+ text = data_file_text.decode("utf-8", errors="replace")
+ else:
+ logging.warning("Could not detect encoding. Using utf-8 with replacement.")
+ text = data_file_text.decode("utf-8", errors="replace")
+ text = clean_text(text)
+
+ if repo_type == constants.RepositoryType.GITHUB:
+ readme_url = convert_to_raw_user_content_github(filename, owner,
+ repo_name,
+ repo_default_branch)
+ metadata_result.add_result(constants.CAT_README_URL,
+ {
+ constants.PROP_VALUE: readme_url,
+ constants.PROP_TYPE: constants.URL
+ },
+ 1,
+ constants.TECHNIQUE_FILE_EXPLORATION)
+
+ if filename.upper() == "README.MD":
+ readmeMD_proccesed = True
+
+ except ValueError:
+ logging.error("README Error: error while reading file content")
+ logging.error(f"{type(err).__name__} was raised: {err}")
if ("LICENCE" == filename.upper() or "LICENSE" == filename.upper() or "LICENSE.MD"== filename.upper()
or "LICENSE.RST"== filename.upper()):
metadata_result = get_file_content_or_link(repo_type, file_path, owner, repo_name,
@@ -133,7 +188,13 @@ def process_repository_files(repo_dir, metadata_result: Result, repo_type, owner
metadata_result = get_file_content_or_link(repo_type, file_path, owner, repo_name,
repo_default_branch,
repo_dir, repo_relative_path, filename, dir_path,
- metadata_result, constants.CAT_CONTRIBUTORS)
+ metadata_result, constants.CAT_CONTRIBUTORS)
+ if "AUTHORS" == filename.upper() or "AUTHORS.MD" == filename.upper() or "AUTHORS.TXT" == filename.upper():
+ metadata_result = get_file_content_or_link(repo_type, file_path, owner, repo_name,
+ repo_default_branch,
+ repo_dir, repo_relative_path, filename, dir_path,
+ metadata_result, constants.CAT_AUTHORS)
+
if "INSTALL" in filename.upper() and filename.upper().endswith("MD"):
metadata_result = get_file_content_or_link(repo_type, file_path, owner, repo_name,
repo_default_branch,
@@ -162,15 +223,33 @@ def process_repository_files(repo_dir, metadata_result: Result, repo_type, owner
constants.PROP_TYPE: constants.URL
}, 1, constants.TECHNIQUE_FILE_EXPLORATION
)
+
if filename.upper() == constants.CODEOWNERS_FILE:
codeowners_json = parse_codeowners_structured(dir_path,filename)
+ if filename.lower() == "codemeta.json":
+ if filename.lower() in parsed_build_files and repo_relative_path != ".":
+ logging.info(f"Ignoring secondary {filename} in {dir_path}")
+ continue
+
+ codemeta_file_url = get_file_link(repo_type, file_path, owner, repo_name, repo_default_branch, repo_dir, repo_relative_path, filename)
+ metadata_result = parse_codemeta_json_file(os.path.join(dir_path, filename), metadata_result, codemeta_file_url)
+ parsed_build_files.add(filename.lower())
# TO DO: Code owners not fully implemented yet
+
if filename.lower() == "pom.xml" or filename.lower() == "package.json" or \
- filename.lower() == "pyproject.toml" or filename.lower() == "setup.py" or filename.lower() == "requirements.txt":
+ filename.lower() == "pyproject.toml" or filename.lower() == "setup.py" or filename.endswith(".gemspec") or \
+ filename.lower() == "requirements.txt" or filename.lower() == "bower.json" or filename == "DESCRIPTION" or \
+ (filename.lower() == "cargo.toml" and repo_relative_path == ".") or (filename.lower() == "composer.json" and repo_relative_path == ".") or \
+ (filename == "Project.toml" or (filename.lower()== "publiccode.yml" or filename.lower()== "publiccode.yaml") and repo_relative_path == "."):
+ if filename.lower() in parsed_build_files and repo_relative_path != ".":
+ logging.info(f"Ignoring secondary {filename} in {dir_path}")
+ continue
+
build_file_url = get_file_link(repo_type, file_path, owner, repo_name, repo_default_branch,
repo_dir,
repo_relative_path, filename)
+
metadata_result.add_result(constants.CAT_HAS_BUILD_FILE,
{
constants.PROP_VALUE: build_file_url,
@@ -179,18 +258,31 @@ def process_repository_files(repo_dir, metadata_result: Result, repo_type, owner
},
1,
constants.TECHNIQUE_FILE_EXPLORATION, build_file_url)
- logging.info(f"############### Processing package file: {filename} ############### ")
+ logging.info(f"############### (NEW UPDATE) Processing package file: {filename} ############### ")
if filename.lower() == "pom.xml":
metadata_result = parse_pom_file(os.path.join(dir_path, filename), metadata_result, build_file_url)
if filename.lower() == "package.json":
metadata_result = parse_package_json_file(os.path.join(dir_path, filename), metadata_result, build_file_url)
- if filename.lower() == "pyproject.toml":
- metadata_result = parse_pyproject_toml(os.path.join(dir_path, filename), metadata_result, build_file_url)
if filename.lower() == "setup.py":
metadata_result = parse_setup_py(os.path.join(dir_path, filename), metadata_result, build_file_url)
if filename.lower() == "requirements.txt":
metadata_result = parse_requirements_txt(os.path.join(dir_path, filename), metadata_result, build_file_url)
-
+ if filename.lower() == "bower.json":
+ metadata_result = parse_bower_json_file(os.path.join(dir_path, filename), metadata_result, build_file_url)
+ if filename.lower() == "composer.json":
+ metadata_result = parse_composer_json(os.path.join(dir_path, filename), metadata_result, build_file_url)
+ if filename.endswith(".gemspec"):
+ metadata_result = parse_gemspec_file(os.path.join(dir_path, filename), metadata_result, build_file_url)
+ if filename == "DESCRIPTION":
+ metadata_result = parse_description_file(os.path.join(dir_path, filename), metadata_result, build_file_url)
+ if filename.lower() == "pyproject.toml" or filename.lower() == "cargo.toml" or filename == "Project.toml":
+ metadata_result = parse_toml_file(os.path.join(dir_path, filename), metadata_result, build_file_url)
+ if filename.endswith == ".cabal":
+ metadata_result = parse_cabal_file(os.path.join(dir_path, filename), metadata_result, build_file_url)
+ if filename.lower() == "publiccode.yml" or filename.lower() == "publiccode.yaml":
+ metadata_result = parse_publiccode_file(os.path.join(dir_path, filename), metadata_result, build_file_url)
+ parsed_build_files.add(filename.lower())
+
# if repo_type == constants.RepositoryType.GITLAB:
if filename.endswith(".yml"):
if repo_type == constants.RepositoryType.GITLAB:
@@ -202,7 +294,15 @@ def process_repository_files(repo_dir, metadata_result: Result, repo_type, owner
{
constants.PROP_VALUE: workflow_url_gitlab,
constants.PROP_TYPE: constants.URL
- }, 1, constants.TECHNIQUE_FILE_EXPLORATION)
+ }, 1, constants.TECHNIQUE_FILE_EXPLORATION)
+ elif extract_workflows.is_file_workflow(os.path.join(repo_dir, file_path)):
+ workflow_url = get_file_link(repo_type, file_path, owner, repo_name, repo_default_branch,
+ repo_dir, repo_relative_path, filename)
+ metadata_result.add_result(constants.CAT_WORKFLOWS,
+ {
+ constants.PROP_VALUE: workflow_url,
+ constants.PROP_TYPE: constants.URL
+ }, 1, constants.TECHNIQUE_FILE_EXPLORATION)
elif repo_type == constants.RepositoryType.GITHUB:
# if file_path.startswith(".github/workflows/"):
# category = constants.CAT_WORKFLOWS
@@ -220,7 +320,23 @@ def process_repository_files(repo_dir, metadata_result: Result, repo_type, owner
repo_dir, repo_relative_path, filename)
metadata_result.add_result(category,
{constants.PROP_VALUE: workflow_url, constants.PROP_TYPE: constants.URL},
- 1, constants.TECHNIQUE_FILE_EXPLORATION)
+ 1, constants.TECHNIQUE_FILE_EXPLORATION)
+
+ if filename.endswith(".ga") or filename.endswith(".cwl") or filename.endswith(".nf") or (
+ filename.endswith(".snake") or filename.endswith(
+ ".smk") or "Snakefile" == filename_no_ext) or filename.endswith(".knwf") or filename.endswith(
+ ".t2flow") or filename.endswith(".dag") or filename.endswith(".kar") or filename.endswith(
+ ".wdl"):
+ analysis = extract_workflows.is_file_workflow(os.path.join(repo_dir, file_path))
+ if analysis:
+ workflow_url = get_file_link(repo_type, file_path, owner, repo_name, repo_default_branch,
+ repo_dir, repo_relative_path, filename)
+ metadata_result.add_result(constants.CAT_WORKFLOWS,
+ {
+ constants.PROP_VALUE: workflow_url,
+ constants.PROP_TYPE: constants.URL
+ }, 1, constants.TECHNIQUE_FILE_EXPLORATION)
+
if 'citation' in metadata_result.results:
for cit in metadata_result.results['citation']:
scholarly_article = {}
@@ -356,6 +472,33 @@ def get_file_content_or_link(repo_type, file_path, owner, repo_name, repo_defaul
if license_info:
result[constants.PROP_NAME] = license_info['name']
result[constants.PROP_SPDX_ID] = license_info['spdx_id']
+
+ if category is constants.CAT_AUTHORS:
+ result = {}
+ authors_list = parse_author_file(file_text)
+ for author_l in authors_list:
+
+ author_data = {
+ "name": author_l.get("name"),
+ "type": constants.AGENT,
+ "value": author_l.get("name")
+ }
+
+ if author_l.get("url") is not None:
+ author_data["url"] = author_l.get("url")
+ if author_l.get("email") is not None:
+ author_data["email"] = author_l.get("email")
+ if author_l["type"] == "Person":
+ if author_l.get("last_name") is not None:
+ author_data["last_name"] = author_l.get("last_name")
+ if author_l.get("given_name") is not None:
+ author_data["given_name"] = author_l.get("given_name")
+ metadata_result.add_result(
+ constants.CAT_AUTHORS,
+ author_data,
+ 1,
+ constants.TECHNIQUE_FILE_EXPLORATION, url
+ )
# Properties extraction from cff
if format_result == 'cff':
yaml_content = yaml.safe_load(file_text)
@@ -364,13 +507,13 @@ def get_file_content_or_link(repo_type, file_path, owner, repo_name, repo_defaul
identifiers = yaml_content.get("identifiers", [])
url_citation = preferred_citation.get("url") or yaml_content.get("url")
+ if identifiers:
+ result[constants.CAT_IDENTIFIER] = identifiers
+
identifier_url = next((id["value"] for id in identifiers if id["type"] == "url"), None)
identifier_doi = next((id["value"] for id in identifiers if id["type"] == "doi"), None)
-
+
title = yaml_content.get("title") or preferred_citation.get("title", None)
- # doi = preferred_citation.get("doi", None)
- # url_citation = preferred_citation.get("url", None)
- # authors = preferred_citation.get("authors", [])
authors = yaml_content.get("authors", [])
if identifier_doi:
@@ -415,16 +558,8 @@ def get_file_content_or_link(repo_type, file_path, owner, repo_name, repo_defaul
if author_list:
result[constants.PROP_AUTHOR] = author_list
-
-
- # author_names = ", ".join(
- # f"{a.get('given-names', '').strip()} {a.get('family-names', '').strip()}".strip()
- # for a in authors if a.get('given-names') and a.get('family-names')
- # ) or None
if title:
result[constants.PROP_TITLE] = title
- # if author_names:
- # result[constants.PROP_AUTHOR] = author_names
if final_url:
result[constants.PROP_URL] = final_url
if doi:
@@ -510,9 +645,17 @@ def parse_codeowners_structured(dir_path, filename):
line = line.strip()
if line and not line.startswith("#"):
parts = line.split()
- path = parts[0] # Primera parte es el path o patrón
- owners = parts[1:] # Lo demás son los propietarios
+ path = parts[0]
+ owners = parts[1:]
codeowners.append({"path": path, "owners": owners})
return {"codeowners": codeowners}
+def clean_text(text):
+ cleaned_lines = []
+ for line in text.splitlines():
+ printable_chars = sum(1 for c in line if c in string.printable)
+ if len(line) == 0 or (printable_chars / len(line)) > 0.9:
+ cleaned_lines.append(line)
+ return "\n".join(cleaned_lines)
+
diff --git a/src/somef_core/process_repository.py b/src/somef_core/process_repository.py
index 280fc5e..2258e00 100644
--- a/src/somef_core/process_repository.py
+++ b/src/somef_core/process_repository.py
@@ -30,7 +30,6 @@ def is_gitlab(gitlab_server):
api_url = f"https://{gitlab_server}/api/v4/projects"
try:
response = requests.get(api_url, timeout=5)
- print(response.status_code)
if response.status_code in [200, 401, 403]:
return True
except requests.RequestException:
@@ -38,14 +37,51 @@ def is_gitlab(gitlab_server):
return False
# the same as requests.get(args).json(), but protects against rate limiting
-def rate_limit_get(*args, backoff_rate=2, initial_backoff=1, **kwargs):
+def rate_limit_get(*args, backoff_rate=2, initial_backoff=1, size_limit_mb=constants.SIZE_DOWNLOAD_LIMIT_MB, **kwargs):
+# def rate_limit_get(*args, backoff_rate=2, initial_backoff=1, **kwargs):
"""Function to obtain how many requests we have pending with the GitHub API"""
+
+ """GET request that handles rate limiting and prevents downloading excessively large files"""
+ size_limit_bytes = size_limit_mb * 1024 * 1024
+ url = args[0] if args else kwargs.get("url")
+ if not url:
+ raise ValueError("Missing URL in rate_limit_get")
+
+ parsed = urlparse(url)
+ is_api_request = "api.github.com" in parsed.netloc
+ content_length = None
+ # just verify size if NOT is a request to api.github.com
+ if not is_api_request:
+ try:
+ head_response = requests.get(url, stream=True, allow_redirects=True, **kwargs)
+ content_length = head_response.headers.get("Content-Length")
+ if content_length is not None:
+ size_bytes = int(content_length)
+ print(f"HEAD Content-Length: {size_bytes}")
+ if size_bytes > size_limit_bytes:
+ logging.warning(
+ f"Download size {size_bytes} bytes exceeds limit of {size_limit_bytes} bytes. Skipping download."
+ )
+ return None, None
+ else:
+ # logging.warning(f"Could not determine file size for {url}. Skipping download.")
+ # return None, None
+ logging.warning(f"No Content-Length header for {url}. Proceeding with download anyway (unable to estimate size).")
+ except Exception as e:
+ logging.warning(f"HEAD/stream request failed: {e}. Continuing with GET...")
+
rate_limited = True
- response = {}
date = ""
+ response = {}
while rate_limited:
- response = requests.get(*args, **kwargs)
- date = response.headers["Date"]
+ use_stream = not is_api_request and (content_length is None or int(content_length) > 10 * 1024 * 1024)
+ response = requests.get(
+ *args,
+ timeout=(constants.DOWNLOAD_TIMEOUT_SECONDS, constants.DOWNLOAD_TIMEOUT_SECONDS),
+ stream=use_stream,
+ **kwargs
+ )
+ date = response.headers.get("Date", "")
# Show rate limit information if available
if "X-RateLimit-Remaining" in response.headers:
rate_limit_remaining = response.headers["X-RateLimit-Remaining"]
@@ -54,14 +90,54 @@ def rate_limit_get(*args, backoff_rate=2, initial_backoff=1, **kwargs):
logging.info(
"Remaining GitHub API requests: " + rate_limit_remaining + " ### Next rate limit reset at: " + str(
date_reset))
- if 'message' in response and 'API rate limit exceeded' in response['message']:
- rate_limited = True
- logging.warning(f"rate limited. Backing off for {initial_backoff} seconds")
- time.sleep(initial_backoff)
- # increase the backoff for next time
- initial_backoff *= backoff_rate
- else:
- rate_limited = False
+
+ if not use_stream:
+ try:
+ json_data = response.json()
+ msg = json_data.get("message", "")
+ if "API rate limit exceeded" in msg:
+ rate_limited = True
+ logging.warning(f"Rate limited. Backing off for {initial_backoff} seconds")
+ time.sleep(initial_backoff)
+ initial_backoff *= backoff_rate
+ continue
+ except Exception:
+ pass
+
+ rate_limited = False
+
+ if not is_api_request and use_stream:
+ content = bytearray()
+ total_read = 0
+ chunk_size = 1024 * 1024 # 1 MB
+ start_time = time.monotonic()
+
+ try:
+ for i, chunk in enumerate(response.iter_content(chunk_size=chunk_size)):
+ if not chunk:
+ # logging.debug(f"Chunk {i} empty, continue...")
+ continue
+
+ # logging.debug(f"Chunk read {i}: {len(chunk)} bytes")
+ content.extend(chunk)
+ total_read += len(chunk)
+
+ # Comprobar límite de tamaño
+ if total_read > size_limit_bytes:
+ logging.warning(f"Downloaded content exceeded {size_limit_bytes} bytes. Aborting.")
+ return None, None
+
+ # Comprobar límite de tiempo
+ elapsed = time.monotonic() - start_time
+ if elapsed > constants.DOWNLOAD_TIMEOUT_SECONDS:
+ logging.warning(f"Download exceeded time limit ({elapsed:.2f}s). Aborting.")
+ return None, None
+
+ except Exception as e:
+ logging.warning(f"Error while streaming: {e}")
+ return None, None
+
+ response._content = bytes(content)
return response, date
@@ -148,6 +224,26 @@ def load_gitlab_repository_metadata(repo_metadata: Result, repository_url):
elif zip_gz_entry:
value = zip_gz_entry["url"]
+ if category == constants.CAT_ASSETS:
+ assets_release_list_filtered = []
+ for source in release[constants.CAT_ASSETS]['sources']:
+ source_asset = {
+ constants.PROP_ENCODING_FORMAT: source[constants.PROP_FORMAT],
+ constants.PROP_CONTENT_URL: source[constants.PROP_URL]
+ }
+ assets_release_list_filtered.append(source_asset)
+
+ for link in release[constants.CAT_ASSETS]['links']:
+ link_asset = {
+ constants.PROP_NAME: link[constants.PROP_NAME],
+ constants.PROP_ENCODING_FORMAT: link["link_type"],
+ constants.PROP_URL: constants.PROP_URL,
+ constants.PROP_CONTENT_URL: link["direct_asset_url"],
+ }
+ assets_release_list_filtered.append(link_asset)
+
+ value = assets_release_list_filtered
+
if value:
release_obj[category] = value
else:
@@ -362,10 +458,17 @@ def download_readme(owner, repo_name, default_branch, repo_type, authorization):
logging.info(f"Downloading {primary_url}")
repo_download, date = rate_limit_get(primary_url, headers=header_template(authorization))
+
+ if repo_download is None:
+ logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or content-lenght none")
+ return None
if repo_download.status_code == 404:
logging.error(f"Error: Archive request failed with HTTP {repo_download.status_code}")
logging.info(f"Trying to download {secondary_url}")
repo_download, date = rate_limit_get(secondary_url, headers=header_template(authorization))
+ if repo_download is None:
+ logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or content-lenght none")
+ return None
if repo_download.status_code != 200:
logging.error(f"Error: Archive request failed with HTTP {repo_download.status_code}")
return None
@@ -440,7 +543,12 @@ def load_online_repository_metadata(repository_metadata: Result, repository_url,
date = ""
if not ignore_api_metadata:
general_resp_raw, date = rate_limit_get(repo_api_base_url, headers=header)
+ if general_resp_raw is None:
+ logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or content-lenght none")
+ return repository_metadata, "", "", ""
+
general_resp = general_resp_raw.json()
+
if 'message' in general_resp:
if general_resp['message'] == "Not Found":
logging.error("Error: Repository name is private or incorrect")
@@ -474,7 +582,7 @@ def load_online_repository_metadata(repository_metadata: Result, repository_url,
value = '%s,' % (', '.join(value))
value = value.rstrip(',')
if category in [constants.CAT_CODE_REPOSITORY, constants.CAT_ISSUE_TRACKER,
- constants.CAT_DOWNLOAD_URL, constants.CAT_FORKS_URLS]:
+ constants.CAT_DOWNLOAD_URL, constants.CAT_FORKS_URLS, constants.CAT_HOMEPAGE]:
value_type = constants.URL
if category in [constants.CAT_DATE_CREATED, constants.CAT_DATE_UPDATED]:
value_type = constants.DATE
@@ -494,12 +602,13 @@ def load_online_repository_metadata(repository_metadata: Result, repository_url,
constants.PROP_VALUE: value,
constants.PROP_TYPE: value_type
}
-
+
if (result['value']):
repository_metadata.add_result(category, result, 1, constants.TECHNIQUE_GITHUB_API)
# get languages
if not ignore_api_metadata:
languages_raw, date = rate_limit_get(filtered_resp['languages_url'], headers=header)
+
languages = languages_raw.json()
if "message" in languages:
logging.error("Error while retrieving languages: " + languages["message"])
@@ -537,7 +646,6 @@ def load_online_repository_metadata(repository_metadata: Result, repository_url,
value = {
constants.PROP_NAME: value,
constants.PROP_TYPE: release[constants.AGENT_TYPE]
-
}
if value != "":
release_obj[category] = value
@@ -582,8 +690,7 @@ def get_path(obj, path):
def do_crosswalk(data, crosswalk_table):
output = {}
- # print('------------data realeases')
- # print(data)
+
for somef_key, path in crosswalk_table.items():
value = get_path(data, path)
if value is not None:
@@ -641,12 +748,20 @@ def download_github_files(directory, owner, repo_name, repo_ref, authorization):
repo_archive_url = f"https://github.com/{owner}/{repo_name}/archive/{repo_ref}.zip"
logging.info(f"Downloading {repo_archive_url}")
repo_download, date = rate_limit_get(repo_archive_url, headers=header_template(authorization))
+
+ if repo_download is None:
+ logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or not content lenght.")
+ return None
+
if repo_download.status_code == 404:
logging.error(f"Error: Archive request failed with HTTP {repo_download.status_code}")
repo_archive_url = f"https://github.com/{owner}/{repo_name}/archive/main.zip"
logging.info(f"Trying to download {repo_archive_url}")
repo_download, date = rate_limit_get(repo_archive_url, headers=header_template(authorization))
-
+ if repo_download is None:
+ logging.warning(f"Repository archive skipped due to size limit: {constants.SIZE_DOWNLOAD_LIMIT_MB} MB or not content lenght.")
+ return None
+
if repo_download.status_code != 200:
sys.exit(f"Error: Archive request failed with HTTP {repo_download.status_code}")
@@ -659,13 +774,19 @@ def download_github_files(directory, owner, repo_name, repo_ref, authorization):
with open(repo_zip_file, "wb") as f:
f.write(repo_zip)
- with zipfile.ZipFile(repo_zip_file, "r") as zip_ref:
- zip_ref.extractall(repo_extract_dir)
-
+ try:
+ with zipfile.ZipFile(repo_zip_file, "r") as zip_ref:
+ zip_ref.extractall(repo_extract_dir)
+ except zipfile.BadZipFile:
+ logging.error("Downloaded archive is not a valid zip (repo may be empty)")
+ return None
+
repo_folders = os.listdir(repo_extract_dir)
+ if not repo_folders:
+ logging.warning("Repository archive is empty")
+ return None
repo_dir = os.path.join(repo_extract_dir, repo_folders[0])
-
return repo_dir
@@ -715,34 +836,34 @@ def get_all_gitlab_releases(repo_api_base_url):
while True:
url = f"{repo_api_base_url}/releases?page={page}&per_page=100"
- logging.info(f"Obteniendo releases desde: {url}")
+ logging.info(f"Getting releases from: {url}")
response = requests.get(url)
- logging.info(f"Respuesta: {response.status_code}")
+ logging.info(f"Response: {response.status_code}")
content_type = response.headers.get("Content-Type", "")
if response.status_code != 200 or "application/json" not in content_type:
- logging.error(f"Error en la respuesta o no es JSON: {response.text}")
- break # Termina el bucle si la respuesta no es válida
+ logging.error(f"Error in response or not JSON: {response.text}")
+ break
try:
releases = response.json()
except requests.exceptions.JSONDecodeError as e:
- logging.error(f"Error al decodificar JSON: {e}. Respuesta: {response.text}")
+ logging.error(f"Error decoding JSON: {e}. Response: {response.text}")
break
if not releases:
- break # Si ya no hay releases, termina el bucle
+ break
all_releases.extend(releases)
- # Verifica si hay más páginas
+ # check if more pages
next_page = response.headers.get("X-Next-Page")
if not next_page:
- break # Si no hay más páginas, termina el bucle
+ break # No more pages
page = int(next_page)
if not all_releases:
- logging.warning("No se encontraron releases.")
+ logging.warning("Not releseases found.")
return []
@@ -760,25 +881,24 @@ def get_all_gitlab_releases(repo_api_base_url):
def get_gitlab_releases(project_id, base_url):
"""
- Obtiene las releases de un repositorio en GitLab sin autenticación.
-
- :param project_id: ID del proyecto en GitLab
- :param base_url: URL base del GitLab donde está alojado el proyecto (ej: https://gitlab.in2p3.fr)
- :return: Lista de releases con información relevante
+ Retrieves the releases of a GitLab repository without authentication.
+
+ :param project_id: ID of the project in GitLab
+ :param base_url: Base URL of the GitLab where the project is hosted (e.g., https://gitlab.in2p3.fr)
+ :return: List of releases with relevant information
"""
releases_url = f"{base_url}/api/v4/projects/{project_id}/releases"
- logging.info(f"Obteniendo releases desde: {releases_url}")
+ logging.info(f"Getting releases from: {releases_url}")
response = requests.get(releases_url)
if response.status_code != 200:
- logging.error(f"Error obteniendo releases: {response.text}")
+ logging.error(f"Error getting releases: {response.text}")
return []
releases_list = response.json()
- # Filtrar información relevante
release_list_filtered = [
{
"url": release.get("description"),
@@ -793,7 +913,6 @@ def get_gitlab_releases(project_id, base_url):
# error when github url is wrong
class GithubUrlError(Exception):
- # print("The URL provided seems to be incorrect")
pass
@@ -821,7 +940,6 @@ def get_all_paginated_results(base_url, headers, per_page=100):
while True:
url = f"{base_url}?per_page={per_page}&page={page}"
- print(url)
response, _ = rate_limit_get(url, headers=headers)
if response.status_code != 200:
@@ -835,4 +953,4 @@ def get_all_paginated_results(base_url, headers, per_page=100):
all_results.extend(page_data)
page += 1
- return all_results
\ No newline at end of file
+ return all_results
diff --git a/src/somef_core/regular_expressions.py b/src/somef_core/regular_expressions.py
index 27da864..6bfe346 100644
--- a/src/somef_core/regular_expressions.py
+++ b/src/somef_core/regular_expressions.py
@@ -3,40 +3,49 @@
import re
import markdown
import requests
+import json
import validators
from .utils import constants
from .process_results import Result
from urllib.parse import urlparse
+
import bibtexparser
def extract_title(unfiltered_text, repository_metadata: Result, readme_source) -> Result:
+ from .header_analysis import label_header
"""
- Regexp to extract title (first header) from a repository
- Parameters
- ----------
- @param unfiltered_text: repo text
- @param repository_metadata: Result with the extractions so far
- @param readme_source: url to the file used (for provenance)
-
- Returns
- -------
- @returns a Result including the title (if found)
-
+ Regexp to extract title (first header) from a repository
+ Parameters
+ ----------
+ @param unfiltered_text: repo text
+ @param repository_metadata: Result with the extractions so far
+ @param readme_source: url to the file used (for provenance)
+
+ Returns
+ -------
+ @returns a Result including the title (if found)
"""
+
html_text = markdown.markdown(unfiltered_text)
splitted = html_text.split("\n")
index = 0
limit = len(splitted)
output = ""
regex = r'<[^<>]+>'
+
while index < limit:
line = splitted[index]
if line.startswith(""):
- output = re.sub(regex, '', line)
+ title = re.sub(regex, '', line).strip()
+ header_labels = label_header(title.lower())
+ if not header_labels and title.lower() != "overview":
+ output = title
break
index += 1
+
+
# If the output is empty or none, the category doesn't make sense and shouldn't be displayed in the final result
if has_valid_output(output):
repository_metadata.add_result(constants.CAT_FULL_TITLE,
@@ -63,7 +72,7 @@ def extract_title_old(unfiltered_text):
# header declared with ====
title = ""
if len(underline_header) != 0:
- title = re.split('.+[=]+[\n]+', unfiltered_text)[0].strip()
+ title = re.split(r'.+[=]+[\n]+', unfiltered_text)[0].strip()
else:
# The first occurrence is assumed to be the title.
title = re.findall(r'# .+', unfiltered_text)[0]
@@ -72,7 +81,7 @@ def extract_title_old(unfiltered_text):
title = title[1:].strip()
# Remove other markup (links, etc.)
if "[!" in title:
- title = re.split('\[\!', title)[0].strip()
+ title = re.split(r'\[\!', title)[0].strip()
return title
@@ -111,7 +120,8 @@ def extract_readthedocs(readme_text, repository_metadata: Result, readme_source)
}
try:
# if name of the repo is known then compare against the readthedocs one. Only add it if it's similar/same
- name_in_link = re.findall('https://([^.]+)\.readthedocs\.io', link)
+ # name_in_link = re.findall('https://([^.]+)\.readthedocs\.io', link)
+ name_in_link = re.findall(r'https://([^.]+)\.readthedocs\.io', link)
name_in_link = name_in_link[0]
if name == "" or name_in_link.lower() == name.lower():
repository_metadata.add_result(constants.CAT_DOCUMENTATION, result, 1,
@@ -424,6 +434,30 @@ def extract_package_distributions(unfiltered_text, repository_metadata: Result,
constants.PROP_TYPE: constants.URL,
constants.PROP_VALUE: output
}, 1, constants.TECHNIQUE_REGULAR_EXPRESSION, readme_source)
+
+ matches = re.findall(constants.REGEXP_PACKAGE_MANAGER, unfiltered_text, re.VERBOSE)
+ found_urls = set()
+
+ for match in matches:
+ try:
+ response = requests.get(match, timeout=5)
+ final_url = response.url
+ except requests.RequestException:
+ final_url = match
+
+ if final_url not in found_urls and has_valid_output(final_url):
+ found_urls.add(final_url)
+ repository_metadata.add_result(
+ constants.CAT_PACKAGE_DISTRIBUTION,
+ {
+ constants.PROP_TYPE: constants.URL,
+ constants.PROP_VALUE: final_url
+ },
+ 1,
+ constants.TECHNIQUE_REGULAR_EXPRESSION,
+ readme_source
+ )
+
return repository_metadata
@@ -541,17 +575,232 @@ def extract_doi_badges(readme_text, repository_metadata: Result, source) -> Resu
"""
# regex = r'\[\!\[DOI\]([^\]]+)\]\(([^)]+)\)'
# regex = r'\[\!\[DOI\]\(.+\)\]\(([^)]+)\)'
+
doi_badges = re.findall(constants.REGEXP_DOI, readme_text)
# The identifier is in position 1. Position 0 is the badge id, which we don't want to export
- for doi in doi_badges:
- repository_metadata.add_result(constants.CAT_IDENTIFIER,
+ if not doi_badges:
+ match = re.search(constants.REGEXP_ZENODO_LATEST_DOI, readme_text)
+ badge_url = None
+ if match:
+ badge_url = match.group(1)
+ else:
+ match = re.search(constants.REGEXP_ZENODO_DOI, readme_text)
+ if match:
+ badge_url = match.group(0)
+ try:
+ if badge_url is not None:
+ response = requests.get(badge_url, allow_redirects=True, timeout=10)
+ match = re.search(constants.REGEXP_ZENODO_JSON_LD,
+ response.text,
+ re.DOTALL | re.IGNORECASE
+ )
+ if match:
+ json_ld_text = match.group(1).strip()
+ try:
+ json_ld_data = json.loads(json_ld_text)
+ identifier = json_ld_data.get('identifier')
+ repository_metadata.add_result(constants.CAT_IDENTIFIER,
+ {
+ constants.PROP_TYPE: constants.URL,
+ constants.PROP_VALUE: identifier,
+ }, 1, constants.TECHNIQUE_REGULAR_EXPRESSION, source)
+ except json.JSONDecodeError:
+ logging.warning("Error parsing Zenodo JSON-LD")
+ except requests.RequestException as e:
+ logging.warning(f"Error fetching DOI from Zenodo badge: {e}")
+ else:
+
+ for doi in doi_badges:
+ repository_metadata.add_result(constants.CAT_IDENTIFIER,
+ {
+ constants.PROP_TYPE: constants.URL,
+ constants.PROP_VALUE: doi[1]
+ }, 1, constants.TECHNIQUE_REGULAR_EXPRESSION, source)
+
+ return repository_metadata
+
+def extract_project_homepage_badges(readme_text, repository_metadata: Result, source) -> Result:
+ """
+ Function that takes the text of a readme file and searches if there are any project homepages.
+ Parameters
+ ----------
+ @param readme_text: Text of the readme
+ @param repository_metadata: Result with all the findings in the repo
+ @param source: source file on top of which the extraction is performed (provenance)
+ Returns
+ -------
+ @returns Result with the Sofware heritage badges found
+ """
+ homepage_badges = re.findall(constants.REGEXP_PROJECT_HOMEPAGE, readme_text)
+ # The identifier is in position 1. Position 0 is the badge id, which we don't want to export
+
+ for homepage in homepage_badges:
+ repository_metadata.add_result(constants.CAT_HOMEPAGE,
{
constants.PROP_TYPE: constants.URL,
- constants.PROP_VALUE: doi[1]
+ constants.PROP_VALUE: homepage[1]
}, 1, constants.TECHNIQUE_REGULAR_EXPRESSION, source)
+
return repository_metadata
+# def extract_readthedocs_badgeds(readme_text, repository_metadata: Result, source) -> Result:
+# """
+# Function that takes the text of a readme file and searches if there are readthedocs badges.
+# Parameters
+# ----------
+# @param readme_text: Text of the readme
+# @param repository_metadata: Result with all the findings in the repo
+# @param source: source file on top of which the extraction is performed (provenance)
+# Returns
+# -------
+# @returns Result with the readthedocs badges found
+# """
+# print("--------------------------> Extracting readthedocs badges")
+# readthedocs_badges = re.findall(constants.REGEXP_READTHEDOCS_BADGES, readme_text, re.DOTALL)
+# print(readthedocs_badges)
+# for doc in readthedocs_badges:
+# print(f'Doc found: {doc}')
+# url = doc[0] or doc[1]
+# if url:
+# repository_metadata.add_result(constants.CAT_DOCUMENTATION,
+# {
+# constants.PROP_TYPE: constants.URL,
+# constants.PROP_VALUE: url
+# }, 1, constants.TECHNIQUE_REGULAR_EXPRESSION, source)
+
+# return repository_metadata
+
+
+def extract_readthedocs_badgeds(readme_text, repository_metadata: Result, source) -> Result:
+ """
+ Function that takes the text of a readme file and searches if there are readthedocs badges.
+ Parameters
+ ----------
+ @param readme_text: Text of the readme
+ @param repository_metadata: Result with all the findings in the repo
+ @param source: source file on top of which the extraction is performed (provenance)
+ Returns
+ -------
+ @returns Result with the readthedocs badges found
+ """
+
+ urls = set()
+
+ # RST
+ for match in re.findall(constants.REGEXP_READTHEDOCS_RST, readme_text):
+ print(match)
+ if isinstance(match, tuple):
+ urls.update([u for u in match if u])
+ elif match:
+ urls.add(match)
+
+ # Markdown
+ for match in re.findall(constants.REGEXP_READTHEDOCS_MD, readme_text):
+ if isinstance(match, tuple):
+ urls.update([u for u in match if u])
+ elif match:
+ urls.add(match)
+
+ # HTML
+ pattern_html = re.compile(constants.REGEXP_READTHEDOCS_HTML, flags=re.VERBOSE |re.DOTALL | re.IGNORECASE)
+ for match in pattern_html.findall(readme_text):
+ if isinstance(match, tuple):
+ urls.update([u for u in match if u])
+ elif match:
+ urls.add(match)
+
+ for url in urls:
+ if "pypi.org/project" in url:
+ category = constants.CAT_PACKAGE_DISTRIBUTION
+ else:
+ category = constants.CAT_DOCUMENTATION
+
+ repository_metadata.add_result(
+ category,
+ {
+ constants.PROP_TYPE: constants.URL,
+ constants.PROP_VALUE: url
+ },
+ 1,
+ constants.TECHNIQUE_REGULAR_EXPRESSION,
+ source
+ )
+
+ return repository_metadata
+
+# def extract_package_manager_badgeds(readme_text, repository_metadata: Result, source) -> Result:
+# """
+# Function that takes the text of a readme file and searches if there are package manager badges.
+# Parameters
+# ----------
+# @param readme_text: Text of the readme
+# @param repository_metadata: Result with all the findings in the repo
+# @param source: source file on top of which the extraction is performed (provenance)
+# Returns
+# -------
+# @returns Result with the package badges found
+# """
+# package_manager_badges = re.findall(constants.REGEXP_READTHEDOCS_BADGES, readme_text, re.DOTALL)
+# for package in package_manager_badges:
+# repository_metadata.add_result(constants.CAT_DOCUMENTATION,
+# {
+# constants.PROP_TYPE: constants.URL,
+# constants.PROP_VALUE: package
+# }, 1, constants.TECHNIQUE_REGULAR_EXPRESSION, source)
+
+
+# return repository_metadata
+
+
+def extract_swh_badges(readme_text, repository_metadata: Result, source) -> Result:
+ """
+ Function that takes the text of a readme file and searches if there are any Software Heritage (swh) badges.
+ Parameters
+ ----------
+ @param readme_text: Text of the readme
+ @param repository_metadata: Result with all the findings in the repo
+ @param source: source file on top of which the extraction is performed (provenance)
+ Returns
+ -------
+ @returns Result with the Sofware heritage badges found
+ """
+ swh_badges = re.findall(constants.REGEXP_SWH, readme_text)
+ # The identifier is in position 1. Position 0 is the badge id, which we don't want to export
+
+ for swh in swh_badges:
+
+ identifier = extract_swh_identifier_from_url(swh[1])
+ if identifier:
+ url_identifier = constants.SWH_ROOT + identifier
+ repository_metadata.add_result(constants.CAT_IDENTIFIER,
+ {
+ constants.PROP_TYPE: constants.URL,
+ constants.PROP_VALUE: url_identifier
+ }, 1, constants.TECHNIQUE_REGULAR_EXPRESSION, source)
+
+ return repository_metadata
+
+def extract_swh_identifier_from_url(url: str) -> str | None:
+ """
+ Function that look for a correct identifier en the swh url
+ """
+
+ # If anchor look for identifier
+ anchor_match = re.search(constants.REGEXP_SWH_ANCHOR, url)
+ if anchor_match:
+ return anchor_match.group(1)
+
+ # If no anchor look for all identifiers
+ all_matches = re.findall(constants.REGEXP_SWH_ALL_IDENTIFIERS, url)
+ if all_matches:
+ for preferred_type in ['rev', 'snp', 'dir', 'cnt']:
+ for match in all_matches:
+ if f"swh:1:{preferred_type}:" in match:
+ return match
+
+ return None
+
def extract_binder_links(readme_text, repository_metadata: Result, source) -> Result:
"""
Function that does a regex to extract binder and colab links used as reference in the readme.
@@ -654,6 +903,7 @@ def detect_license_spdx(license_text, type):
-------
A JSON dictionary with name and spdx id
"""
+
for license_name, license_info in constants.LICENSES_DICT.items():
if re.search(license_info["regex"], license_text, re.IGNORECASE):
if type == 'JSON':
@@ -667,16 +917,28 @@ def detect_license_spdx(license_text, type):
"name": license_name,
"identifier": f"https://spdx.org/licenses/{license_info['spdx_id']}"
}
+ for license_name, license_info in constants.LICENSES_DICT.items():
+ spdx_id = license_info["spdx_id"]
+ if re.search(rf'\b{re.escape(spdx_id)}\b', license_text, re.IGNORECASE):
+ return {
+ "name": license_name,
+ "spdx_id": spdx_id,
+ "@id": f"https://spdx.org/licenses/{spdx_id}"
+ }
return None
-# def detect_license(license_text):
-# for license_name, license_info in constants.LICENSES_DICT.items():
-# if re.search(license_info["regex"], license_text, re.IGNORECASE):
-# return {
-# "name": license_name,
-# "identifier": f"https://spdx.org/licenses/{license_info['spdx_id']}"
-# }
-# return None
+def detect_spdx_from_declared(value: str):
+ """
+ Check if declared license matches an SPDX ID in LICENSES_DICT.
+ """
+ for name, info in constants.LICENSES_DICT.items():
+ if value == info["spdx_id"]:
+ return {
+ "name": name,
+ "spdx_id": info["spdx_id"],
+ "@id": f"https://spdx.org/licenses/{info['spdx_id']}"
+ }
+ return None
def extract_scholarly_article_properties(bibtex_entry, scholarlyArticle, type):
"""
diff --git a/src/somef_core/somef_cli.py b/src/somef_core/somef_cli.py
index 0188d3b..1f4fea0 100644
--- a/src/somef_core/somef_cli.py
+++ b/src/somef_core/somef_cli.py
@@ -1,5 +1,5 @@
import sys
-from uu import encode
+# from uu import encode
import validators
import logging
@@ -13,11 +13,12 @@
from .utils import constants, markdown_utils
from .parser import mardown_parser, create_excerpts
from .export import json_export
+from .extract_software_type import check_repository_type
from urllib.parse import urlparse, quote
def cli_get_data(threshold, ignore_classifiers, repo_url=None, doc_src=None, local_repo=None,
ignore_github_metadata=False, readme_only=False, keep_tmp=None, authorization=None,
- ignore_test_folder=True) -> Result:
+ ignore_test_folder=True,requirements_mode='all') -> Result:
"""
Main function to get the data through the command line
Parameters
@@ -32,6 +33,7 @@ def cli_get_data(threshold, ignore_classifiers, repo_url=None, doc_src=None, loc
@param keep_tmp: path where to store TMP files in case SOMEF is instructed to keep them
@param authorization: GitHub authorization token
@param ignore_test_folder: Ignore contents of test folders
+ @param requiriments_mode: flag to indicate what requirements show in codemeta
Returns
-------
@@ -67,6 +69,7 @@ def cli_get_data(threshold, ignore_classifiers, repo_url=None, doc_src=None, loc
logging.info(f"{servidor} is GitLab.")
bGitLab = True
+ print(f"DEBUG: {servidor} is_gitlab = {bGitLab}")
if bGitLab:
repo_type = constants.RepositoryType.GITLAB
repository_metadata, owner, repo_name, def_branch = process_repository.load_online_repository_metadata(
@@ -86,22 +89,35 @@ def cli_get_data(threshold, ignore_classifiers, repo_url=None, doc_src=None, loc
os.makedirs(keep_tmp, exist_ok=True)
local_folder = process_repository.download_repository_files(owner, repo_name, def_branch, repo_type,
keep_tmp, repo_url, authorization)
- readme_text, full_repository_metadata = process_files.process_repository_files(local_folder,
+ if local_folder is not None:
+ readme_text, full_repository_metadata = process_files.process_repository_files(local_folder,
repository_metadata,
repo_type, owner,
repo_name,
def_branch,
- ignore_test_folder)
+ ignore_test_folder)
+ repository_metadata = check_repository_type(local_folder, repo_name, full_repository_metadata)
+ else:
+ logging.error("Error processing the target repository")
+ return repository_metadata
else: # Use a temp directory
+
with tempfile.TemporaryDirectory() as temp_dir:
local_folder = process_repository.download_repository_files(owner, repo_name, def_branch, repo_type,
temp_dir, repo_url, authorization)
- readme_text, full_repository_metadata = process_files.process_repository_files(local_folder,
- repository_metadata,
- repo_type, owner,
- repo_name,
- def_branch,
+ if local_folder is not None:
+ readme_text, full_repository_metadata = process_files.process_repository_files(local_folder,
+ repository_metadata,
+ repo_type, owner,
+ repo_name,
+ def_branch,
ignore_test_folder)
+
+ repository_metadata = check_repository_type(local_folder, repo_name, full_repository_metadata)
+ else:
+ logging.error("Error processing the target repository")
+ return repository_metadata
+
if readme_text == "":
logging.warning("README document does not exist in the target repository")
except process_repository.GithubUrlError:
@@ -130,7 +146,11 @@ def cli_get_data(threshold, ignore_classifiers, repo_url=None, doc_src=None, loc
readme_unfiltered_text = markdown_utils.remove_comments(readme_unfiltered_text)
repository_metadata, string_list = header_analysis.extract_categories(readme_unfiltered_text,
repository_metadata)
+
+ logging.info("Extracted categories from headers successfully.")
readme_text_unmarked = markdown_utils.unmark(readme_text)
+ logging.info("readme text unmarked successfully.")
+
if readme_text_unmarked != "":
try:
readme_source = repository_metadata.results[constants.CAT_README_URL][0]
@@ -141,12 +161,18 @@ def cli_get_data(threshold, ignore_classifiers, repo_url=None, doc_src=None, loc
readme_source)
repository_metadata = regular_expressions.extract_doi_badges(readme_unfiltered_text, repository_metadata,
readme_source)
+ repository_metadata = regular_expressions.extract_swh_badges(readme_unfiltered_text, repository_metadata,
+ readme_source)
+ repository_metadata = regular_expressions.extract_project_homepage_badges(readme_unfiltered_text, repository_metadata,
+ readme_source)
repository_metadata = regular_expressions.extract_title(readme_unfiltered_text, repository_metadata,
readme_source)
repository_metadata = regular_expressions.extract_binder_links(readme_unfiltered_text, repository_metadata,
readme_source)
repository_metadata = regular_expressions.extract_readthedocs(readme_unfiltered_text, repository_metadata,
readme_source)
+ repository_metadata = regular_expressions.extract_readthedocs_badgeds(readme_unfiltered_text, repository_metadata,
+ readme_source)
repository_metadata = regular_expressions.extract_repo_status(readme_unfiltered_text, repository_metadata,
readme_source)
repository_metadata = regular_expressions.extract_wiki_links(readme_unfiltered_text, repo_url,
@@ -191,7 +217,8 @@ def run_cli(*,
pretty=False,
missing=False,
keep_tmp=None,
- ignore_test_folder=True
+ ignore_test_folder=True,
+ requirements_mode="all"
):
"""Function to run all the required components of the cli for a repository"""
# check if it is a valid url
@@ -225,7 +252,7 @@ def run_cli(*,
encoded_url = encoded_url.replace(".","") #removing dots just in case
repo_data = cli_get_data(threshold=threshold, ignore_classifiers=ignore_classifiers, repo_url=repo_url,
ignore_github_metadata=ignore_github_metadata, readme_only=readme_only,
- keep_tmp=keep_tmp, ignore_test_folder=ignore_test_folder)
+ keep_tmp=keep_tmp, ignore_test_folder=ignore_test_folder, requirements_mode=requirements_mode)
if output is not None:
output = output.replace(".json","")
@@ -234,7 +261,7 @@ def run_cli(*,
if codemeta_out is not None:
codemeta_out = codemeta_out.replace(".json", "")
codemeta_out = codemeta_out + "_" + encoded_url + ".json"
- json_export.save_codemeta_output(repo_data.results, codemeta_out, pretty=pretty)
+ json_export.save_codemeta_output(repo_data.results, codemeta_out, pretty=pretty, requirements_mode= requirements_mode)
except:
logging.error("Error when processing repo: " + repo_url)
else:
@@ -255,7 +282,7 @@ def run_cli(*,
if output is not None:
json_export.save_json_output(repo_data.results, output, missing, pretty=pretty)
if codemeta_out is not None:
- json_export.save_codemeta_output(repo_data.results, codemeta_out, pretty=pretty)
+ json_export.save_codemeta_output(repo_data.results, codemeta_out, pretty=pretty, requirements_mode=requirements_mode)
diff --git a/src/somef_core/test/test_JSON_export.py b/src/somef_core/test/test_JSON_export.py
index 27dc464..befc47f 100644
--- a/src/somef_core/test/test_JSON_export.py
+++ b/src/somef_core/test/test_JSON_export.py
@@ -7,65 +7,70 @@
test_data_path = str(Path(__file__).parent / "test_data") + os.path.sep
test_data_repositories = str(Path(__file__).parent / "test_data" / "repositories") + os.path.sep
-
+test_data_api_json = str(Path(__file__).parent / "test_data" / "api_responses") + os.path.sep
class TestJSONExport(unittest.TestCase):
@classmethod
def setUpClass(cls):
"""Runs somef_cli once and saves the JSON"""
- cls.json_file = test_data_path + "test_json_widoco_export.json"
-
- somef_cli.run_cli(threshold=0.8,
- ignore_classifiers=False,
- repo_url="https://github.com/dgarijo/Widoco",
- local_repo=None,
- doc_src=None,
- in_file=None,
- output=cls.json_file,
- graph_out=None,
- graph_format="turtle",
- codemeta_out=None,
- pretty=True,
- missing=False,
- readme_only=False)
+ # cls.json_file = test_data_path + "test_json_widoco_export.json"
+ cls.api_results_file = test_data_api_json + "widoco_api_response.json"
+ with open(cls.api_results_file, "r", encoding="utf-8") as f:
+ cls.json_content= json.load(f)
+
+ # somef_cli.run_cli(threshold=0.8,
+ # ignore_classifiers=False,
+ # repo_url="https://github.com/dgarijo/Widoco",
+ # local_repo=None,
+ # doc_src=None,
+ # in_file=None,
+ # output=cls.json_file,
+ # graph_out=None,
+ # graph_format="turtle",
+ # codemeta_out=None,
+ # pretty=True,
+ # missing=False,
+ # readme_only=False)
- with open(cls.json_file, "r") as f:
- cls.json_content = json.load(f)
+ # with open(cls.json_file, "r") as f:
+ # cls.json_content = json.load(f)
- def test_issue_417(self):
- """Checks whether a repository correctly extracts to Codemeta"""
- somef_cli.run_cli(threshold=0.8,
- ignore_classifiers=False,
- repo_url="https://github.com/dgarijo/Widoco",
- local_repo=None,
- doc_src=None,
- in_file=None,
- output=None,
- graph_out=None,
- graph_format="turtle",
- codemeta_out=test_data_path + "test-417.json-ld",
- pretty=True,
- missing=False,
- readme_only=False)
-
- text_file = open(test_data_path + "test-417.json-ld", "r")
- data = text_file.read()
- text_file.close()
- json_content = json.loads(data)
- issue_tracker = json_content["issueTracker"] # JSON is in Codemeta format
+ # def test_issue_417(self):
+ # """Checks whether a repository correctly extracts to Codemeta"""
+
+
+ # somef_cli.run_cli(threshold=0.8,
+ # ignore_classifiers=False,
+ # repo_url="https://github.com/dgarijo/Widoco",
+ # local_repo=None,
+ # doc_src=None,
+ # in_file=None,
+ # output=None,
+ # graph_out=None,
+ # graph_format="turtle",
+ # codemeta_out=test_data_path + "test-417.json-ld",
+ # pretty=True,
+ # missing=False,
+ # readme_only=False)
- #len(json_content["citation"])
- #codemeta category citation is now referencePublication
- assert issue_tracker == 'https://github.com/dgarijo/Widoco/issues' and len(json_content["referencePublication"]) > 0 and \
- len(json_content["name"]) > 0 and len(json_content["identifier"]) > 0 and \
- len(json_content["description"]) > 0 and len(json_content["readme"]) > 0 and \
- len(json_content["author"]) > 0 and len(json_content["buildInstructions"]) > 0 and \
- len(json_content["softwareRequirements"]) > 0 and len(json_content["programmingLanguage"]) > 0 and \
- len(json_content["keywords"]) > 0 and len(json_content["logo"]) > 0 and \
- len(json_content["license"]) > 0 and len(json_content["dateCreated"]) > 0
+ # text_file = open(test_data_path + "test-417.json-ld", "r")
+ # data = text_file.read()
+ # text_file.close()
+ # json_content = json.loads(data)
+ # issue_tracker = json_content["issueTracker"] # JSON is in Codemeta format
+
+ # #len(json_content["citation"])
+ # #codemeta category citation is now referencePublication
+ # assert issue_tracker == 'https://github.com/dgarijo/Widoco/issues' and len(json_content["referencePublication"]) > 0 and \
+ # len(json_content["name"]) > 0 and len(json_content["identifier"]) > 0 and \
+ # len(json_content["description"]) > 0 and len(json_content["readme"]) > 0 and \
+ # len(json_content["author"]) > 0 and len(json_content["buildInstructions"]) > 0 and \
+ # len(json_content["softwareRequirements"]) > 0 and len(json_content["programmingLanguage"]) > 0 and \
+ # len(json_content["keywords"]) > 0 and len(json_content["logo"]) > 0 and \
+ # len(json_content["license"]) > 0 and len(json_content["dateCreated"]) > 0
- os.remove(test_data_path + "test-417.json-ld")
+ # os.remove(test_data_path + "test-417.json-ld")
def test_issue_311(self):
"""Checks if Codemeta export has labels defined outside Codemeta"""
@@ -155,6 +160,8 @@ def test_issue_629(self):
# os.remove(test_data_path + "test_issue_629.json")
+
+
def test_issue_651(self):
"""Checks if keywords is in the missing categories because is empty"""
somef_cli.run_cli(threshold=0.8,
@@ -179,8 +186,9 @@ def test_issue_745(self):
"""Checks whether all the items in license has a spdx_id"""
somef_cli.run_cli(threshold=0.8,
ignore_classifiers=False,
- repo_url="https://github.com/sunpy/sunpy",
- local_repo=None,
+ # repo_url="https://github.com/sunpy/sunpy",
+ repo_url=None,
+ local_repo=test_data_repositories + "sunpy",
doc_src=None,
in_file=None,
output=test_data_path + "test_issue_745.json",
@@ -197,25 +205,269 @@ def test_issue_745(self):
json_content = json.loads(data)
licenses = json_content["license"]
+ # print('---------------------------')
+ # print(licenses)
+
for i, license_entry in enumerate(licenses):
assert "spdx_id" in license_entry["result"], f"Missing 'spdx_id' in license{i}"
assert license_entry["result"]["spdx_id"], f"'spdx_id' empty in license {i}"
os.remove(test_data_path + "test_issue_745.json")
+ def test_issue_499(self):
+ """Checks whether a repository correctly extracts assets from release"""
+
+ # somef_cli.run_cli(threshold=0.8,
+ # ignore_classifiers=False,
+ # repo_url="https://github.com/dgarijo/Widoco",
+ # local_repo=None,
+ # doc_src=None,
+ # in_file=None,
+ # output=test_data_path + "test-499.json-ld",
+ # graph_out=None,
+ # graph_format="turtle",
+ # codemeta_out= None,
+ # pretty=True,
+ # missing=False,
+ # readme_only=False)
+
+ # text_file = open(test_data_path + "test-499.json-ld", "r")
+ # data = text_file.read()
+ # text_file.close()
+ # json_content = json.loads(data)
+
+ assert "releases" in self.json_content, "Missing 'releases' key in JSON content"
+ assert isinstance(self.json_content["releases"], list), "'releases' should be a list"
+
+ release_1425 = None
+ for release in self.json_content["releases"]:
+ if release.get("result", {}).get("tag") == "v1.4.25":
+ release_1425 = release
+ break
+
+ assert release_1425 is not None, "No release with tag 'v1.4.25' found"
+
+ assets = release_1425.get("result", {}).get("assets", [])
+ assert any(asset.get("name") == "widoco-1.4.25-jar-with-dependencies_JDK-11.jar" for asset in assets), \
+ "Asset 'widoco-1.4.25-jar-with-dependencies_JDK-11.jar' not found in release v1.4.25"
+
+ # os.remove(test_data_path + "test-499.json-ld")
+
+ def test_issue_577(self):
+ """Checks if there are idenfiers from Software Heritage in the README file"""
+ somef_cli.run_cli(threshold=0.8,
+ ignore_classifiers=False,
+ repo_url=None,
+ doc_src=test_data_path + "README-widoco-swh.md",
+ in_file=None,
+ output=test_data_path + "test-577.json",
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out=None,
+ pretty=True,
+ missing=True)
+
+ with open(test_data_path + "test-577.json", "r") as text_file:
+ data = json.load(text_file)
+
+ expected_values = {
+ "https://doi.org/10.5281/zenodo.11093793",
+ "https://archive.softwareheritage.org/swh:1:rev:fec66b89a4f4acb015a44c7f8cb671d49bec626a"
+ }
+ identifiers = data.get("identifier", [])
+ found_values = set()
+
+ for item in identifiers:
+ value = item["result"]["value"]
+ found_values.add(value)
+
+ for expected in expected_values:
+ assert expected in found_values, f"Expected identifier not found: {expected}"
+
+ os.remove(test_data_path + "test-577.json")
+
+
+ def test_issue_580(self):
+ """Checks if there are Project homepage in the readme file"""
+ somef_cli.run_cli(threshold=0.8,
+ ignore_classifiers=False,
+ repo_url=None,
+ doc_src=test_data_path + "README-citation-file-format.md",
+ in_file=None,
+ output=test_data_path + "test-580.json",
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out=None,
+ pretty=True,
+ missing=True)
+
+ with open(test_data_path + "test-580.json", "r") as text_file:
+ data = json.load(text_file)
+
+ found = False
+ homepage_entries = data.get("homepage", [])
+ print('---------------------------')
+ print(homepage_entries)
+ for item in homepage_entries:
+ technique = item.get("technique")
+ result = item.get("result", {})
+ value = result.get("value")
+
+ if technique == "regular_expression" and value == "https://citation-file-format.github.io":
+ found = True
+ break
+
+ assert found, "Expected homepage not found"
+
+ os.remove(test_data_path + "test-580.json")
+
def test_issue_653(self):
"""Checks if json from widoco repo has more than 30 releases"""
assert len(self.json_content["releases"]) > 30, f"Expected more than 30 releases, found {len(self.json_content['release'])}"
- @classmethod
- def tearDownClass(cls):
- """delete temp file JSON just if all the test pass"""
- if os.path.exists(cls.json_file):
- try:
- os.remove(cls.json_file)
- print(f"Deleted {cls.json_file}")
- except Exception as e:
- print(f"Failed to delete {cls.json_file}: {e}")
-
-if __name__ == '__main__':
- unittest.main()
+ def test_not_recursive_folders(self):
+ """
+ Checks that build files in subfolders are ignored if they already exist in the root,
+ and that duplicates do not appear in the results.
+ pom.xml has been duplicated in docs/pom.xml
+ """
+
+ output_path = test_data_path + 'test_widoco_not_recursive_folders.json'
+
+ somef_cli.run_cli( threshold=0.8,
+ local_repo=test_data_repositories + "Widoco",
+ doc_src=None,
+ in_file=None,
+ output=output_path,
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out=None,
+ pretty=True,
+ missing=False,
+ readme_only=False)
+
+
+ with open(output_path, "r") as f:
+ json_content = json.load(f)
+
+ build_files = [
+ entry[constants.PROP_RESULT][constants.PROP_VALUE]
+ for key in json_content
+ for entry in json_content[key]
+ if key == constants.CAT_HAS_BUILD_FILE
+ ]
+
+ # root
+ assert any("pom.xml" in bf for bf in build_files), "The root pom.xml should be present"
+ # No docs/pom.xml
+ assert not any("docs/pom.xml" in bf for bf in build_files), "The pom.xml in docs/ should not be processed"
+ assert len(build_files) == len(set(build_files)), "There should be no duplicate build files"
+
+
+ def test_runtime_platform(self):
+ """
+ Checks that the runtime_platform information is correctly extracted from the project.
+ """
+
+ runtime_entries = [
+ entry[constants.PROP_RESULT]
+ for key in self.json_content
+ for entry in self.json_content[key]
+ if key == constants.CAT_RUNTIME_PLATFORM
+ ]
+
+ assert len(runtime_entries) > 0, "There should be at least one runtime_platform entry"
+
+ found_java = any(
+ entry.get("name") == "Java" and entry.get("value") == "Java: 1.8"
+ for entry in runtime_entries
+ )
+ assert found_java, "Java runtime with value Java: 1.8 should be present"
+
+
+ def test_issue_830(self):
+ """Checks if citattion have identifiers """
+ citation = self.json_content.get("citation", [])
+ assert citation, "No 'citation' found in JSON"
+ assert any(
+ entry.get("result", {}).get("format") == "cff"
+ and any(id.get("value") == "10.5281/zenodo.591294"
+ for id in entry.get("result", {}).get("identifier", [])
+ )
+ for entry in citation
+ ), "Citation.cff must have identifier id 10.5281/zenodo.591294"
+
+ # @classmethod
+ # def tearDownClass(cls):
+ # """delete temp file JSON just if all the test pass"""
+ # if os.path.exists(cls.json_file):
+ # try:
+ # os.remove(cls.json_file)
+ # print(f"Deleted {cls.json_file}")
+ # except Exception as e:
+ # print(f"Failed to delete {cls.json_file}: {e}")
+
+ def test_issue_862(self):
+ """Checks if this repository does not gets stuck when labeling headers"""
+ somef_cli.run_cli(threshold=0.8,
+ ignore_classifiers=False,
+ repo_url=None,
+ local_repo=test_data_repositories + "componentInstaller",
+ doc_src=None,
+ in_file=None,
+ output=test_data_path + "test_issue_862.json",
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out=None,
+ pretty=True,
+ missing=False,
+ readme_only=False)
+
+ text_file = open(test_data_path + "test_issue_862.json", "r")
+ data = text_file.read()
+ text_file.close()
+ json_content = json.loads(data)
+
+ assert "description" in json_content, "Missing 'description' property"
+
+ assert len(json_content["description"]) > 0, "Description list is empty"
+
+ first_desc = json_content["description"][0]["result"]
+ assert "value" in first_desc, "Missing 'value' in description result"
+ assert first_desc["value"], "Description 'value' is empty"
+
+ os.remove(test_data_path + "test_issue_862.json")
+
+ def test_issue_859(self):
+ """Checks whether a repository without content works fine. Must have just some results from the API."""
+
+ somef_cli.run_cli(threshold=0.8,
+ ignore_classifiers=False,
+ repo_url="https://github.com/shiningZZ/GU-CAFF",
+ local_repo=None,
+ doc_src=None,
+ in_file=None,
+ output=test_data_path + "test-859.json",
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out= None,
+ pretty=True,
+ missing=False,
+ readme_only=False)
+
+ with open(test_data_path + "test-859.json", "r") as text_file:
+ json_content = json.load(text_file)
+
+ assert "code_repository" in json_content
+ assert len(json_content["code_repository"]) > 0
+
+ for key, entries in json_content.items():
+ if isinstance(entries, list):
+ for entry in entries:
+ assert entry.get("technique") == "GitHub_API", \
+ f"Unexpected technique {entry.get('technique')} in key {key}"
+
+ os.remove(test_data_path + "test-859.json")
+
+
+
\ No newline at end of file
diff --git a/src/somef_core/test/test_bower_parser 2.py b/src/somef_core/test/test_bower_parser 2.py
new file mode 100644
index 0000000..9a2ad9d
--- /dev/null
+++ b/src/somef_core/test/test_bower_parser 2.py
@@ -0,0 +1,111 @@
+import unittest
+import os
+from pathlib import Path
+
+from somef_core.parser.bower_parser import parse_bower_json_file
+from somef_core.process_results import Result
+from somef_core.utils import constants
+
+test_data_path = str(Path(__file__).parent / "test_data") + os.path.sep
+test_data_repositories = str(Path(__file__).parent / "test_data" / "repositories") + os.path.sep
+
+class TestBowerParser(unittest.TestCase):
+
+ def test_parse_bower_json(self):
+ bower_file_path = test_data_repositories + os.path.sep + "js-template" + os.path.sep + "bower.json"
+
+ result = Result()
+
+ # metadata_result = parse_bower_json_file(bower_file_path, result, "https://example.org/bower.json")
+ metadata_result = parse_bower_json_file(bower_file_path, result, bower_file_path)
+ package_results = metadata_result.results.get(constants.CAT_HAS_PACKAGE_FILE, [])
+ self.assertTrue(len(package_results) > 0, "No package file info found")
+ # self.assertEqual(package_results[0]["result"]["value"], "bower.json")
+ self.assertEqual(package_results[0]["result"]["value"], bower_file_path)
+ self.assertEqual(package_results[0]["result"]["type"], constants.URL)
+
+ name_results = metadata_result.results.get(constants.CAT_NAME, [])
+ self.assertTrue(len(name_results) > 0, "No name found")
+ self.assertEqual(name_results[0]["result"]["value"], "alarm")
+ self.assertEqual(name_results[0]["result"]["type"], constants.STRING)
+
+ description_results = metadata_result.results.get(constants.CAT_DESCRIPTION, [])
+ self.assertTrue(len(description_results) > 0, "No description found")
+ self.assertEqual(description_results[0]["result"]["value"], "Alarm clock project during week1 day2 JS at Epicodus.")
+ self.assertEqual(description_results[0]["result"]["type"], constants.STRING)
+
+ # there is a homepage with "" in the bower. None, null and "" must not show in metadatos
+
+ # homepage_results = metadata_result.results.get(constants.CAT_HOMEPAGE, [])
+ # self.assertTrue(len(homepage_results) > 0, "No homepage found")
+ # self.assertEqual(homepage_results[0]["result"]["value"], "")
+ # self.assertEqual(homepage_results[0]["result"]["type"], constants.URL)
+
+ homepage_results = metadata_result.results.get(constants.CAT_HOMEPAGE, [])
+ self.assertEqual(len(homepage_results), 0, "Expected no homepage for this bower.json")
+
+ license_results = metadata_result.results.get(constants.CAT_LICENSE, [])
+ self.assertTrue(len(license_results) > 0, "No license found")
+ self.assertEqual(license_results[0]["result"]["value"], "ISC")
+ self.assertEqual(license_results[0]["result"]["type"], constants.LICENSE)
+
+ requirements_results = metadata_result.results.get(constants.CAT_REQUIREMENTS, [])
+ self.assertTrue(len(requirements_results) > 0, "No dependencies found")
+
+ authors_results = metadata_result.results.get(constants.CAT_AUTHORS, [])
+ self.assertTrue(len(authors_results) > 0, "No authors found")
+ self.assertEqual(len(authors_results), 2, "Expected two authors")
+
+ self.assertEqual(authors_results[0]["result"]["value"], "Andrew Accuardi ")
+ self.assertEqual(authors_results[1]["result"]["value"], "Another Author ")
+
+ found_jquery = False
+ found_bootstrap = False
+ for req_result in requirements_results:
+ dependency = req_result["result"]
+ if dependency.get("name") == "jquery" and dependency.get("dependency_type") == "runtime":
+ found_jquery = True
+ self.assertTrue(found_jquery, "jQuery dependency not found")
+
+ def test_parse_2_bower_json(self):
+ bower_file_path = test_data_repositories + os.path.sep + "chosen" + os.path.sep + "bower.json"
+
+ result = Result()
+
+ # metadata_result = parse_bower_json_file(bower_file_path, result, "https://example.org/bower.json")
+ metadata_result = parse_bower_json_file(bower_file_path, result, bower_file_path)
+ package_results = metadata_result.results.get(constants.CAT_HAS_PACKAGE_FILE, [])
+ self.assertTrue(len(package_results) > 0, "No package file info found")
+ # self.assertEqual(package_results[0]["result"]["value"], "bower.json")
+ self.assertEqual(package_results[0]["result"]["value"], bower_file_path)
+ self.assertEqual(package_results[0]["result"]["type"], constants.URL)
+
+ name_results = metadata_result.results.get(constants.CAT_NAME, [])
+ self.assertTrue(len(name_results) > 0, "No name found")
+ self.assertEqual(name_results[0]["result"]["value"], "chosen")
+ self.assertEqual(name_results[0]["result"]["type"], constants.STRING)
+
+ description_results = metadata_result.results.get(constants.CAT_DESCRIPTION, [])
+ self.assertTrue(len(description_results) > 0, "No description found")
+ self.assertEqual(description_results[0]["result"]["value"], "Chosen is a JavaScript plugin that makes select boxes user-friendly. It is currently available in both jQuery and Prototype flavors.")
+ self.assertEqual(description_results[0]["result"]["type"], constants.STRING)
+
+
+ homepage_results = metadata_result.results.get(constants.CAT_HOMEPAGE, [])
+ self.assertEqual(homepage_results[0]["result"]["value"], "https://harvesthq.github.io/chosen/")
+
+ license_results = metadata_result.results.get(constants.CAT_LICENSE, [])
+ self.assertTrue(len(license_results) > 0, "No license found")
+ self.assertEqual(license_results[0]["result"]["value"], "https://github.com/harvesthq/chosen/blob/master/LICENSE.md")
+ self.assertEqual(license_results[0]["result"]["type"], constants.LICENSE)
+
+
+ authors_results = metadata_result.results.get(constants.CAT_AUTHORS, [])
+ self.assertTrue(len(authors_results) > 0, "No authors found")
+ self.assertEqual(len(authors_results), 4, "Expected two authors")
+
+ self.assertEqual(authors_results[0]["result"]["value"], "Patrick Filler")
+
+
+if __name__ == "__main__":
+ unittest.main()
\ No newline at end of file
diff --git a/src/somef_core/test/test_bower_parser.py b/src/somef_core/test/test_bower_parser.py
new file mode 100644
index 0000000..9a2ad9d
--- /dev/null
+++ b/src/somef_core/test/test_bower_parser.py
@@ -0,0 +1,111 @@
+import unittest
+import os
+from pathlib import Path
+
+from somef_core.parser.bower_parser import parse_bower_json_file
+from somef_core.process_results import Result
+from somef_core.utils import constants
+
+test_data_path = str(Path(__file__).parent / "test_data") + os.path.sep
+test_data_repositories = str(Path(__file__).parent / "test_data" / "repositories") + os.path.sep
+
+class TestBowerParser(unittest.TestCase):
+
+ def test_parse_bower_json(self):
+ bower_file_path = test_data_repositories + os.path.sep + "js-template" + os.path.sep + "bower.json"
+
+ result = Result()
+
+ # metadata_result = parse_bower_json_file(bower_file_path, result, "https://example.org/bower.json")
+ metadata_result = parse_bower_json_file(bower_file_path, result, bower_file_path)
+ package_results = metadata_result.results.get(constants.CAT_HAS_PACKAGE_FILE, [])
+ self.assertTrue(len(package_results) > 0, "No package file info found")
+ # self.assertEqual(package_results[0]["result"]["value"], "bower.json")
+ self.assertEqual(package_results[0]["result"]["value"], bower_file_path)
+ self.assertEqual(package_results[0]["result"]["type"], constants.URL)
+
+ name_results = metadata_result.results.get(constants.CAT_NAME, [])
+ self.assertTrue(len(name_results) > 0, "No name found")
+ self.assertEqual(name_results[0]["result"]["value"], "alarm")
+ self.assertEqual(name_results[0]["result"]["type"], constants.STRING)
+
+ description_results = metadata_result.results.get(constants.CAT_DESCRIPTION, [])
+ self.assertTrue(len(description_results) > 0, "No description found")
+ self.assertEqual(description_results[0]["result"]["value"], "Alarm clock project during week1 day2 JS at Epicodus.")
+ self.assertEqual(description_results[0]["result"]["type"], constants.STRING)
+
+ # there is a homepage with "" in the bower. None, null and "" must not show in metadatos
+
+ # homepage_results = metadata_result.results.get(constants.CAT_HOMEPAGE, [])
+ # self.assertTrue(len(homepage_results) > 0, "No homepage found")
+ # self.assertEqual(homepage_results[0]["result"]["value"], "")
+ # self.assertEqual(homepage_results[0]["result"]["type"], constants.URL)
+
+ homepage_results = metadata_result.results.get(constants.CAT_HOMEPAGE, [])
+ self.assertEqual(len(homepage_results), 0, "Expected no homepage for this bower.json")
+
+ license_results = metadata_result.results.get(constants.CAT_LICENSE, [])
+ self.assertTrue(len(license_results) > 0, "No license found")
+ self.assertEqual(license_results[0]["result"]["value"], "ISC")
+ self.assertEqual(license_results[0]["result"]["type"], constants.LICENSE)
+
+ requirements_results = metadata_result.results.get(constants.CAT_REQUIREMENTS, [])
+ self.assertTrue(len(requirements_results) > 0, "No dependencies found")
+
+ authors_results = metadata_result.results.get(constants.CAT_AUTHORS, [])
+ self.assertTrue(len(authors_results) > 0, "No authors found")
+ self.assertEqual(len(authors_results), 2, "Expected two authors")
+
+ self.assertEqual(authors_results[0]["result"]["value"], "Andrew Accuardi ")
+ self.assertEqual(authors_results[1]["result"]["value"], "Another Author ")
+
+ found_jquery = False
+ found_bootstrap = False
+ for req_result in requirements_results:
+ dependency = req_result["result"]
+ if dependency.get("name") == "jquery" and dependency.get("dependency_type") == "runtime":
+ found_jquery = True
+ self.assertTrue(found_jquery, "jQuery dependency not found")
+
+ def test_parse_2_bower_json(self):
+ bower_file_path = test_data_repositories + os.path.sep + "chosen" + os.path.sep + "bower.json"
+
+ result = Result()
+
+ # metadata_result = parse_bower_json_file(bower_file_path, result, "https://example.org/bower.json")
+ metadata_result = parse_bower_json_file(bower_file_path, result, bower_file_path)
+ package_results = metadata_result.results.get(constants.CAT_HAS_PACKAGE_FILE, [])
+ self.assertTrue(len(package_results) > 0, "No package file info found")
+ # self.assertEqual(package_results[0]["result"]["value"], "bower.json")
+ self.assertEqual(package_results[0]["result"]["value"], bower_file_path)
+ self.assertEqual(package_results[0]["result"]["type"], constants.URL)
+
+ name_results = metadata_result.results.get(constants.CAT_NAME, [])
+ self.assertTrue(len(name_results) > 0, "No name found")
+ self.assertEqual(name_results[0]["result"]["value"], "chosen")
+ self.assertEqual(name_results[0]["result"]["type"], constants.STRING)
+
+ description_results = metadata_result.results.get(constants.CAT_DESCRIPTION, [])
+ self.assertTrue(len(description_results) > 0, "No description found")
+ self.assertEqual(description_results[0]["result"]["value"], "Chosen is a JavaScript plugin that makes select boxes user-friendly. It is currently available in both jQuery and Prototype flavors.")
+ self.assertEqual(description_results[0]["result"]["type"], constants.STRING)
+
+
+ homepage_results = metadata_result.results.get(constants.CAT_HOMEPAGE, [])
+ self.assertEqual(homepage_results[0]["result"]["value"], "https://harvesthq.github.io/chosen/")
+
+ license_results = metadata_result.results.get(constants.CAT_LICENSE, [])
+ self.assertTrue(len(license_results) > 0, "No license found")
+ self.assertEqual(license_results[0]["result"]["value"], "https://github.com/harvesthq/chosen/blob/master/LICENSE.md")
+ self.assertEqual(license_results[0]["result"]["type"], constants.LICENSE)
+
+
+ authors_results = metadata_result.results.get(constants.CAT_AUTHORS, [])
+ self.assertTrue(len(authors_results) > 0, "No authors found")
+ self.assertEqual(len(authors_results), 4, "Expected two authors")
+
+ self.assertEqual(authors_results[0]["result"]["value"], "Patrick Filler")
+
+
+if __name__ == "__main__":
+ unittest.main()
\ No newline at end of file
diff --git a/src/somef_core/test/test_cabal_parser 2.py b/src/somef_core/test/test_cabal_parser 2.py
new file mode 100644
index 0000000..3efddc2
--- /dev/null
+++ b/src/somef_core/test/test_cabal_parser 2.py
@@ -0,0 +1,94 @@
+import unittest
+import os
+from pathlib import Path
+
+from somef_core.parser.cabal_parser import parse_cabal_file
+from somef_core.process_results import Result
+from somef_core.utils import constants
+
+test_data_path = str(Path(__file__).parent / "test_data") + os.path.sep
+test_data_repositories = str(Path(__file__).parent / "test_data" / "repositories") + os.path.sep
+
+class TestCabalParser(unittest.TestCase):
+
+ def test_parse_cabal(self):
+ cabal_file_path = test_data_repositories + os.path.sep + "unused" + os.path.sep + "unused.cabal"
+ result = Result()
+
+ # metadata_result = parse_cabal_file(cabal_file_path, result, "https://example.org/unused.cabal")
+ metadata_result = parse_cabal_file(cabal_file_path, result, cabal_file_path)
+ package_results = metadata_result.results.get(constants.CAT_HAS_PACKAGE_FILE, [])
+ self.assertTrue(len(package_results) > 0, "No package file info found")
+ # self.assertEqual(package_results[0]["result"]["value"], "unused.cabal")
+ self.assertEqual(package_results[0]["result"]["value"], cabal_file_path)
+ self.assertEqual(package_results[0]["result"]["type"], constants.URL)
+
+ id_results = metadata_result.results.get(constants.CAT_PACKAGE_ID, [])
+ self.assertTrue(len(id_results) > 0, "No identifier found")
+ self.assertEqual(id_results[0]["result"]["value"], "unused")
+ self.assertEqual(id_results[0]["result"]["type"], constants.STRING)
+
+ description_results = metadata_result.results.get(constants.CAT_DESCRIPTION, [])
+ self.assertTrue(len(description_results) > 0, "No description found")
+ self.assertEqual(description_results[0]["result"]["value"], "Please see README.md")
+ self.assertEqual(description_results[0]["result"]["type"], constants.STRING)
+
+ homepage_results = metadata_result.results.get(constants.CAT_HOMEPAGE, [])
+ self.assertTrue(len(homepage_results) > 0, "No homepage found")
+ self.assertEqual(homepage_results[0]["result"]["value"], "https://github.com/joshuaclayton/unused#readme")
+ self.assertEqual(homepage_results[0]["result"]["type"], constants.URL)
+
+ license_results = metadata_result.results.get(constants.CAT_LICENSE, [])
+ self.assertTrue(len(license_results) > 0, "No license found")
+ self.assertEqual(license_results[0]["result"]["value"], "MIT")
+ self.assertEqual(license_results[0]["result"]["type"], constants.LICENSE)
+
+ requirements_results = metadata_result.results.get(constants.CAT_REQUIREMENTS, [])
+ self.assertTrue(len(requirements_results) > 0, "No dependencies found")
+
+ found_dep = False
+ for req_result in requirements_results:
+ dependency = req_result["result"]
+ if dependency.get("name") == "terminal-progress-bar" and dependency.get("dependency_type") == "runtime":
+ found_dep = True
+ self.assertTrue(found_dep, "Dependency not found")
+
+ def test_parse_2_cabal(self):
+ cabal_file_path = test_data_repositories + os.path.sep + "haskell" + os.path.sep + "cabal.cabal"
+ result = Result()
+
+ # metadata_result = parse_cabal_file(cabal_file_path, result, "https://example.org/cabal.cabal")
+ metadata_result = parse_cabal_file(cabal_file_path, result, cabal_file_path)
+ package_results = metadata_result.results.get(constants.CAT_HAS_PACKAGE_FILE, [])
+ self.assertTrue(len(package_results) > 0, "No package file info found")
+ # self.assertEqual(package_results[0]["result"]["value"], "cabal.cabal")
+ self.assertEqual(package_results[0]["result"]["value"], cabal_file_path)
+ self.assertEqual(package_results[0]["result"]["type"], constants.URL)
+ description_results = metadata_result.results.get(constants.CAT_DESCRIPTION, [])
+ self.assertTrue(len(description_results) > 0, "No description found")
+ expected_start = "The Haskell Common Architecture"
+
+ self.assertTrue(
+ description_results[0]["result"]["value"].strip().startswith(expected_start)
+ )
+
+ homepage_results = metadata_result.results.get(constants.CAT_HOMEPAGE, [])
+ self.assertTrue(len(homepage_results) > 0, "No homepage found")
+ self.assertEqual(homepage_results[0]["result"]["value"], "http://www.haskell.org/cabal/")
+ self.assertEqual(homepage_results[0]["result"]["type"], constants.URL)
+
+ license_results = metadata_result.results.get(constants.CAT_LICENSE, [])
+ self.assertTrue(len(license_results) > 0, "No license found")
+ self.assertEqual(license_results[0]["result"]["value"], "BSD-3-Clause")
+ self.assertEqual(license_results[0]["result"]["type"], constants.LICENSE)
+
+ requirements_results = metadata_result.results.get(constants.CAT_REQUIREMENTS, [])
+ self.assertEqual(requirements_results[0]["result"]["name"], "Cabal-syntax")
+ self.assertEqual(requirements_results[1]["result"]["version"], ">= 0.4.0.1 && < 0.6")
+
+ issue_tracker_results = metadata_result.results.get(constants.CAT_ISSUE_TRACKER, [])
+ self.assertEqual(issue_tracker_results[0]["result"]["value"], "https://github.com/haskell/cabal/issues")
+
+
+if __name__ == "__main__":
+ unittest.main()
\ No newline at end of file
diff --git a/src/somef_core/test/test_cabal_parser.py b/src/somef_core/test/test_cabal_parser.py
new file mode 100644
index 0000000..3efddc2
--- /dev/null
+++ b/src/somef_core/test/test_cabal_parser.py
@@ -0,0 +1,94 @@
+import unittest
+import os
+from pathlib import Path
+
+from somef_core.parser.cabal_parser import parse_cabal_file
+from somef_core.process_results import Result
+from somef_core.utils import constants
+
+test_data_path = str(Path(__file__).parent / "test_data") + os.path.sep
+test_data_repositories = str(Path(__file__).parent / "test_data" / "repositories") + os.path.sep
+
+class TestCabalParser(unittest.TestCase):
+
+ def test_parse_cabal(self):
+ cabal_file_path = test_data_repositories + os.path.sep + "unused" + os.path.sep + "unused.cabal"
+ result = Result()
+
+ # metadata_result = parse_cabal_file(cabal_file_path, result, "https://example.org/unused.cabal")
+ metadata_result = parse_cabal_file(cabal_file_path, result, cabal_file_path)
+ package_results = metadata_result.results.get(constants.CAT_HAS_PACKAGE_FILE, [])
+ self.assertTrue(len(package_results) > 0, "No package file info found")
+ # self.assertEqual(package_results[0]["result"]["value"], "unused.cabal")
+ self.assertEqual(package_results[0]["result"]["value"], cabal_file_path)
+ self.assertEqual(package_results[0]["result"]["type"], constants.URL)
+
+ id_results = metadata_result.results.get(constants.CAT_PACKAGE_ID, [])
+ self.assertTrue(len(id_results) > 0, "No identifier found")
+ self.assertEqual(id_results[0]["result"]["value"], "unused")
+ self.assertEqual(id_results[0]["result"]["type"], constants.STRING)
+
+ description_results = metadata_result.results.get(constants.CAT_DESCRIPTION, [])
+ self.assertTrue(len(description_results) > 0, "No description found")
+ self.assertEqual(description_results[0]["result"]["value"], "Please see README.md")
+ self.assertEqual(description_results[0]["result"]["type"], constants.STRING)
+
+ homepage_results = metadata_result.results.get(constants.CAT_HOMEPAGE, [])
+ self.assertTrue(len(homepage_results) > 0, "No homepage found")
+ self.assertEqual(homepage_results[0]["result"]["value"], "https://github.com/joshuaclayton/unused#readme")
+ self.assertEqual(homepage_results[0]["result"]["type"], constants.URL)
+
+ license_results = metadata_result.results.get(constants.CAT_LICENSE, [])
+ self.assertTrue(len(license_results) > 0, "No license found")
+ self.assertEqual(license_results[0]["result"]["value"], "MIT")
+ self.assertEqual(license_results[0]["result"]["type"], constants.LICENSE)
+
+ requirements_results = metadata_result.results.get(constants.CAT_REQUIREMENTS, [])
+ self.assertTrue(len(requirements_results) > 0, "No dependencies found")
+
+ found_dep = False
+ for req_result in requirements_results:
+ dependency = req_result["result"]
+ if dependency.get("name") == "terminal-progress-bar" and dependency.get("dependency_type") == "runtime":
+ found_dep = True
+ self.assertTrue(found_dep, "Dependency not found")
+
+ def test_parse_2_cabal(self):
+ cabal_file_path = test_data_repositories + os.path.sep + "haskell" + os.path.sep + "cabal.cabal"
+ result = Result()
+
+ # metadata_result = parse_cabal_file(cabal_file_path, result, "https://example.org/cabal.cabal")
+ metadata_result = parse_cabal_file(cabal_file_path, result, cabal_file_path)
+ package_results = metadata_result.results.get(constants.CAT_HAS_PACKAGE_FILE, [])
+ self.assertTrue(len(package_results) > 0, "No package file info found")
+ # self.assertEqual(package_results[0]["result"]["value"], "cabal.cabal")
+ self.assertEqual(package_results[0]["result"]["value"], cabal_file_path)
+ self.assertEqual(package_results[0]["result"]["type"], constants.URL)
+ description_results = metadata_result.results.get(constants.CAT_DESCRIPTION, [])
+ self.assertTrue(len(description_results) > 0, "No description found")
+ expected_start = "The Haskell Common Architecture"
+
+ self.assertTrue(
+ description_results[0]["result"]["value"].strip().startswith(expected_start)
+ )
+
+ homepage_results = metadata_result.results.get(constants.CAT_HOMEPAGE, [])
+ self.assertTrue(len(homepage_results) > 0, "No homepage found")
+ self.assertEqual(homepage_results[0]["result"]["value"], "http://www.haskell.org/cabal/")
+ self.assertEqual(homepage_results[0]["result"]["type"], constants.URL)
+
+ license_results = metadata_result.results.get(constants.CAT_LICENSE, [])
+ self.assertTrue(len(license_results) > 0, "No license found")
+ self.assertEqual(license_results[0]["result"]["value"], "BSD-3-Clause")
+ self.assertEqual(license_results[0]["result"]["type"], constants.LICENSE)
+
+ requirements_results = metadata_result.results.get(constants.CAT_REQUIREMENTS, [])
+ self.assertEqual(requirements_results[0]["result"]["name"], "Cabal-syntax")
+ self.assertEqual(requirements_results[1]["result"]["version"], ">= 0.4.0.1 && < 0.6")
+
+ issue_tracker_results = metadata_result.results.get(constants.CAT_ISSUE_TRACKER, [])
+ self.assertEqual(issue_tracker_results[0]["result"]["value"], "https://github.com/haskell/cabal/issues")
+
+
+if __name__ == "__main__":
+ unittest.main()
\ No newline at end of file
diff --git a/src/somef_core/test/test_cli.py b/src/somef_core/test/test_cli.py
index fa548e5..fc27ed5 100644
--- a/src/somef_core/test/test_cli.py
+++ b/src/somef_core/test/test_cli.py
@@ -296,6 +296,7 @@ def test_issue_319_1(self):
assert data.find(constants.FORMAT_CFF) > 0
os.remove(test_data_path + "test-319-1.json")
+
def test_issue_319_2(self):
"""Test checks that the output format of citation files is specified in the output"""
somef_cli.run_cli(threshold=0.8,
@@ -406,17 +407,19 @@ def test_issue_314(self):
def test_issue_314_1(self):
"""Checks that the program can be run using only a single readme. GitHub"""
somef_cli.run_cli(threshold=0.8,
- ignore_classifiers=False,
- repo_url="https://github.com/tensorflow/tensorflow/tree/v2.6.0",
- doc_src=None,
- in_file=None,
- output=test_data_path + "test-314-1.json",
- graph_out=None,
- graph_format="turtle",
- codemeta_out=None,
- pretty=True,
- missing=True,
- readme_only=True)
+ ignore_classifiers=False,
+ # repo_url="https://github.com/tensorflow/tensorflow/tree/v2.6.0",
+ repo_url=None,
+ # doc_src=None,
+ doc_src= test_data_path + "README-tensorflow-2.6.0.md",
+ in_file=None,
+ output=test_data_path + "test-314-1.json",
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out=None,
+ pretty=True,
+ missing=True,
+ readme_only=True)
text_file = open(test_data_path + "test-314-1.json", "r")
data = text_file.read()
text_file.close()
@@ -425,11 +428,14 @@ def test_issue_314_1(self):
assert image is not None
os.remove(test_data_path + "test-314-1.json")
+
def test_issue_403(self):
"""Checks that the readme link returned by somef is correct"""
somef_cli.run_cli(threshold=0.8,
ignore_classifiers=False,
repo_url="https://github.com/oeg-upm/wot-hive",
+ # repo_url=None,
+ # local_repo=test_data_repositories + "wot-hive",
doc_src=None,
in_file=None,
output=test_data_path + "test-403.json",
@@ -489,7 +495,6 @@ def test_issue_225_406(self):
text_file = open(test_data_path + "test-225.json", "r")
data = text_file.read()
text_file.close()
- print(data)
assert data.find("\"" + constants.PROP_FORMAT + "\": \"" + constants.FORMAT_WIKI + "\"")
os.remove(test_data_path + "test-225.json")
@@ -517,18 +522,20 @@ def test_issue_406(self):
def test_issue_255(self):
"""Tests if somef can detect wiki articles"""
somef_cli.run_cli(threshold=0.8,
- ignore_classifiers=False,
- repo_url="https://github.com/mbloch/mapshaper/",
- local_repo=None,
- doc_src=None,
- in_file=None,
- output=test_data_path + "test-255.json",
- graph_out=None,
- graph_format="turtle",
- codemeta_out=None,
- pretty=True,
- missing=True,
- readme_only=False)
+ ignore_classifiers=False,
+ # repo_url="https://github.com/mbloch/mapshaper/",
+ repo_url=None,
+ local_repo=None,
+ # doc_src=None,
+ doc_src=test_data_path + "README-mapshaper.md",
+ in_file=None,
+ output=test_data_path + "test-255.json",
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out=None,
+ pretty=True,
+ missing=True,
+ readme_only=False)
text_file = open(test_data_path + "test-255.json", "r")
data = text_file.read()
text_file.close()
@@ -661,6 +668,7 @@ def test_issue_366(self):
assert data.find(constants.FORMAT_DOCKERFILE) >= 0
os.remove(test_data_path + "test-366.json")
+
def test_issue_443(self):
somef_cli.run_cli(threshold=0.8,
ignore_classifiers=False,
@@ -705,6 +713,7 @@ def test_issue_443_3(self):
assert description is not None
os.remove(test_data_path + "test-443.json")
+
def test_issue_556(self):
"""
This test assesses whether documentation links that have been commented in the readme out are ignored.
@@ -778,3 +787,5 @@ def test_issue_567(self):
text_file.close()
assert constants.CAT_ACKNOWLEDGEMENT not in json_content
os.remove(test_data_path + "repositories/software_catalog/test-567.json")
+
+
diff --git a/src/somef_core/test/test_codemeta_export.py b/src/somef_core/test/test_codemeta_export.py
index e40b261..2277aca 100644
--- a/src/somef_core/test/test_codemeta_export.py
+++ b/src/somef_core/test/test_codemeta_export.py
@@ -3,34 +3,57 @@
import json
from pathlib import Path
from .. import somef_cli
+from ..parser import pom_xml_parser
+from ..export import json_export
test_data_path = str(Path(__file__).parent / "test_data") + os.path.sep
+test_data_repositories = str(Path(__file__).parent / "test_data" / "repositories") + os.path.sep
+test_data_api_json = str(Path(__file__).parent / "test_data" / "api_responses") + os.path.sep
class TestCodemetaExport(unittest.TestCase):
-
+
+
@classmethod
def setUpClass(cls):
"""Runs somef_cli once and saves the JSON"""
cls.json_file = test_data_path + "test_json_codemeta_export.json"
- somef_cli.run_cli(
- threshold=0.8,
- ignore_classifiers=False,
- repo_url="https://github.com/tpronk/somef-demo-repo/",
- doc_src=None,
- in_file=None,
- output=None,
- graph_out=None,
- graph_format="turtle",
- codemeta_out=cls.json_file,
+ cls.api_results_file = test_data_api_json + "somef-demo.json"
+ with open(cls.api_results_file, "r", encoding="utf-8") as f:
+ cls.api_results = json.load(f)
+
+ json_export.save_codemeta_output(
+ cls.api_results,
+ cls.json_file,
pretty=True,
- missing=True,
- readme_only=False
+ requirements_mode=False
)
- with open(cls.json_file, "r") as f:
+ with open(cls.json_file, "r", encoding="utf-8") as f:
cls.json_content = json.load(f)
+ # somef_cli.run_cli(
+ # threshold=0.8,
+ # ignore_classifiers=False,
+ # repo_url="https://github.com/juanjemdIos/somef-demo-repo/",
+ # # repo_url=None,
+ # # local_repo= test_data_repositories + "somef-demo",
+ # doc_src=None,
+ # in_file=None,
+ # output=None,
+ # graph_out=None,
+ # graph_format="turtle",
+ # codemeta_out=cls.json_file,
+ # pretty=True,
+ # missing=True,
+ # readme_only=False
+ # )
+
+ # with open(cls.json_file, "r") as f:
+ # cls.json_content = json.load(f)
+
+ # print(cls.json_content)
+
def test_codemeta_version(self):
"""Checks if codemeta version is v3"""
@@ -210,18 +233,302 @@ def test_codemeta_relevants_programming_languages(self):
expected_languages = ["Jupyter Notebook"]
assert set(self.json_content["programmingLanguage"]) == set(expected_languages), f"Mismatch: {self.json_content['programmingLanguage']}"
+ def test_codemeta_author_file(self):
+ """Checks if codemeta file has extracted the authors in the author file"""
+ authors = [author.get("name") for author in self.json_content["author"] if author["@type"] == "Person"]
+ expected_authors = {"Daniel Garijo", "Juanje Mendoza"}
+ assert set(authors) >= expected_authors, f"Mismatch in authors: {authors}"
+
+ def test_issue_763(self):
+ """
+ Checks that several citations of same item in json become in one in codemeta
+
+ Export to codemeta: Reconcile Bibtex and CFF exports
+ """
+
+ somef_cli.run_cli(threshold=0.9,
+ ignore_classifiers=False,
+ repo_url=None,
+ doc_src=None,
+ local_repo=test_data_repositories + "inspect4py",
+ in_file=None,
+ output=None,
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out= test_data_path + 'test_codemeta_several_citations.json',
+ pretty=True,
+ missing=False)
+
+ json_file_path = test_data_path + "test_codemeta_several_citations.json"
+ text_file = open(json_file_path, "r")
+ data = text_file.read()
+ json_content = json.loads(data)
+ text_file.close()
+
+ reference_publications = json_content.get("referencePublication", [])
+
+ # just one reference
+ assert len(reference_publications) == 1, f"Expected 1 referencePublication, found {len(reference_publications)}"
+
+ # reference with doi expected
+ assert reference_publications[0].get("identifier") == "10.1145/3524842.3528497", \
+ f"Expected identifier '10.1145/3524842.3528497', found '{reference_publications[0].get('identifier')}'"
+ os.remove(json_file_path)
+
+ def test_codemeta_duplicate_dois(self):
+ """Checks if codemeta duplicates dois whith diferent format: doi.org, dx.doi...."""
+ somef_cli.run_cli(threshold=0.8,
+ ignore_classifiers=False,
+ repo_url=None,
+ doc_src=test_data_path + "README-widoco-duplicate-dois.md",
+ in_file=None,
+ output=None,
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out=test_data_path + 'test_codemeta_dup_dois.json',
+ pretty=True,
+ missing=True)
+
+ json_file_path = test_data_path + "test_codemeta_dup_dois.json"
+ # check if the file has been created in the correct path
+ assert os.path.exists(json_file_path), f"File {json_file_path} doesn't exist."
+
+ with open(json_file_path, "r") as f:
+ codemeta = json.load(f)
+
+ ref_pubs = codemeta.get("referencePublication", [])
+
+ dois = set()
+ for pub in ref_pubs:
+ if isinstance(pub, dict) and "identifier" in pub:
+ dois.add(pub["identifier"])
+ assert len(dois) == 1, f"Expected 1 DOI, got {len(dois)}: {dois}"
+
+ os.remove(json_file_path)
+
+ def test_requirements_mode(self):
+
+ """
+ Checks that when requirements_mode='v', only structured requirements from code parsers are exported,
+ and textual requirements (e.g. from README or codemeta.json) are excluded.
+ """
+ output_path = test_data_path + 'test_codemeta_widoco_requirements_v.json'
+
+ somef_cli.run_cli(threshold=0.9,
+ ignore_classifiers=False,
+ repo_url=None,
+ doc_src=None,
+ local_repo=test_data_repositories + "Widoco",
+ in_file=None,
+ output=None,
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out= output_path,
+ pretty=True,
+ missing=False,
+ requirements_mode="v")
+
+ with open(output_path, "r") as f:
+ json_content = json.load(f)
+
+ requirements = json_content.get("softwareRequirements", [])
+
+ assert all(isinstance(req, dict) and "name" in req for req in requirements), \
+ f"Expected only structured requirements, found: {requirements}"
+
+ assert all(not isinstance(req, str) for req in requirements), \
+ f"Found unexpected textual requirement entries: {[r for r in requirements if isinstance(r, str)]}"
+
+ os.remove(output_path)
+
+ def test_requirements_not_duplicate(self):
+
+ """
+ Checks that when requirements_mode='all', the exported softwareRequirements list contains no duplicates,
+ even if the same requirement appears from multiple sources or techniques.
+ """
+ output_path = test_data_path + 'test_codemeta_widoco_requirements_not_duplicate.json'
+
+ somef_cli.run_cli(threshold=0.9,
+ ignore_classifiers=False,
+ repo_url=None,
+ doc_src=None,
+ local_repo=test_data_repositories + "Widoco",
+ in_file=None,
+ output=None,
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out= output_path,
+ pretty=True,
+ missing=False,
+ requirements_mode="all")
+
+ with open(output_path, "r") as f:
+ json_content = json.load(f)
+
+ requirements = json_content.get("softwareRequirements", [])
+
+ seen = set()
+ for req in requirements:
+ if isinstance(req, dict):
+ key = f"{req['name'].strip()}|{req.get('version', '').strip()}"
+ else:
+ key = " ".join(req.strip().replace("\n", " ").split())
+ assert key not in seen, f"Duplicate requirement found: {key}"
+ seen.add(key)
+
+ os.remove(output_path)
+
+
+ def test_description_not_duplicate(self):
+ """
+ Checks that the 'description' field in the exported codemeta contains no duplicate entries,
+ even if the same description appears from multiple sources or techniques.
+ """
+
+ output_path = test_data_path + 'test_codemeta_widoco_description_not_duplicate.json'
+
+ somef_cli.run_cli(
+ threshold=0.9,
+ ignore_classifiers=False,
+ repo_url=None,
+ doc_src=None,
+ local_repo=test_data_repositories + "Widoco",
+ in_file=None,
+ output=None,
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out=output_path,
+ pretty=True,
+ missing=False,
+ requirements_mode="all"
+ )
+
+ with open(output_path, "r") as f:
+ json_content = json.load(f)
+
+ descriptions = json_content.get("description", [])
+ os.remove(output_path)
+
+ seen = set()
+ for desc in descriptions:
+ normalized = " ".join(desc.strip().replace("\n", " ").split())
+ assert normalized not in seen, f"Duplicate description found: {normalized}"
+ seen.add(normalized)
+
+
+ def test_codemeta_runtime(self):
+
+ """
+ Checks runtime in codemeta file
+ """
+
+ pom_xml_parser.processed_pom = False
+
+ output_path = test_data_path + 'test_codemeta_widoco_runtime_platform.json'
+ if os.path.exists(output_path):
+ os.remove(output_path)
+
+ somef_cli.run_cli(threshold=0.9,
+ ignore_classifiers=False,
+ repo_url=None,
+ doc_src=None,
+ local_repo=test_data_repositories + "Widoco",
+ in_file=None,
+ output=None,
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out= output_path,
+ pretty=True,
+ missing=False,
+ requirements_mode="v")
+
+ with open(output_path, "r") as f:
+ json_content = json.load(f)
+
+ runtime = json_content.get("runtimePlatform", [])
+ assert runtime == "Java: 1.8", f"It was expected 'Java: 1.8' but it was '{runtime}'"
+ os.remove(output_path)
+
+ def test_issue_832_join_authors(self):
+ """
+ Check that an author who appears multiple times in the JSON appears only once in the Codemeta output, merging their properties.
+ """
+
+ somef_cli.run_cli(threshold=0.9,
+ ignore_classifiers=False,
+ repo_url=None,
+ doc_src=None,
+ local_repo=test_data_repositories + "fuji",
+ in_file=None,
+ output=None,
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out= test_data_path + 'test_codemeta_join_authors.json',
+ pretty=True,
+ missing=False)
+
+ json_file_path = test_data_path + "test_codemeta_join_authors.json"
+ text_file = open(json_file_path, "r")
+ data = text_file.read()
+ json_content = json.loads(data)
+ text_file.close()
+
+ authors = json_content.get("author", [])
+ assert len(authors) == 9, f"Expected 9 author, found {len(authors)}"
+ assert authors[0].get("name") == "Robert Huber", "Second author must be Robert Huber"
+ assert authors[1].get("email") == "anusuriya.devaraju@googlemail.com", \
+ "Third author must have email anusuriya.devaraju@googlemail.com"
+
+ os.remove(json_file_path)
+
+ def test_issue_417(self):
+ """Checks whether a repository correctly extracts to Codemeta"""
+
+
+ somef_cli.run_cli(threshold=0.8,
+ ignore_classifiers=False,
+ repo_url=None,
+ local_repo=test_data_repositories + "Widoco",
+ doc_src=None,
+ in_file=None,
+ output=None,
+ graph_out=None,
+ graph_format="turtle",
+ codemeta_out=test_data_path + "test-417.json-ld",
+ pretty=True,
+ missing=False,
+ readme_only=False)
+
+ text_file = open(test_data_path + "test-417.json-ld", "r")
+ data = text_file.read()
+ text_file.close()
+ json_content = json.loads(data)
+ issue_tracker = json_content["issueTracker"] # JSON is in Codemeta format
+
+ #len(json_content["citation"])
+ #codemeta category citation is now referencePublication
+ assert issue_tracker == 'https://github.com/dgarijo/Widoco/issues' and len(json_content["referencePublication"]) > 0 and \
+ len(json_content["name"]) > 0 and len(json_content["identifier"]) > 0 and \
+ len(json_content["description"]) > 0 and len(json_content["readme"]) > 0 and \
+ len(json_content["buildInstructions"]) > 0 and \
+ len(json_content["softwareRequirements"]) > 0 and len(json_content["programmingLanguage"]) > 0 and \
+ len(json_content["keywords"]) > 0 and len(json_content["logo"]) > 0 and \
+ len(json_content["license"]) > 0 and len(json_content["dateCreated"]) > 0
+
+ os.remove(test_data_path + "test-417.json-ld")
@classmethod
def tearDownClass(cls):
"""delete temp file JSON just if all the test pass"""
- if os.path.exists(cls.json_file): # Verifica que el archivo exista
+ if os.path.exists(cls.json_file):
try:
os.remove(cls.json_file)
- print(f"Deleted {cls.json_file}") # Mensaje para confirmar la eliminación
+ print(f"Deleted {cls.json_file}")
except Exception as e:
- print(f"Failed to delete {cls.json_file}: {e}") # Captura errores de eliminación
-
+ print(f"Failed to delete {cls.json_file}: {e}")
+
if __name__ == "__main__":
unittest.main()
diff --git a/src/somef_core/test/test_codemeta_parser 2.py b/src/somef_core/test/test_codemeta_parser 2.py
new file mode 100644
index 0000000..880cb0f
--- /dev/null
+++ b/src/somef_core/test/test_codemeta_parser 2.py
@@ -0,0 +1,66 @@
+import unittest
+import os
+import yaml
+from pathlib import Path
+
+from somef_core.parser.codemeta_parser import parse_codemeta_json_file
+from somef_core.process_results import Result
+from somef_core.utils import constants
+
+TEST_ROOT = Path(__file__).parent
+REPOS_DIR = TEST_ROOT / "test_data" / "repositories"
+EXPECT_DIR = TEST_ROOT / "test_data" / "expected"
+
+class TestCodemetaParser(unittest.TestCase):
+
+ def load_expected(self, repo_name):
+ """Load expected YAML for a given repo."""
+ yaml_path = EXPECT_DIR / f"{repo_name}.yaml"
+ if not yaml_path.exists():
+ self.skipTest(f"No expected YAML for repository '{repo_name}'")
+ with open(yaml_path, "r", encoding="utf-8") as f:
+ return yaml.safe_load(f)
+
+ def test_parse_multiple_codemeta_files(self):
+ for repo_folder in os.listdir(REPOS_DIR):
+ print(f"################# Testing {repo_folder} #################")
+ repo_path = REPOS_DIR / repo_folder
+ codemeta_path = repo_path / "codemeta.json"
+ if not codemeta_path.is_file():
+ continue
+
+ expected = self.load_expected(repo_folder)
+ result = Result()
+ metadata_result = parse_codemeta_json_file(
+ str(codemeta_path),
+ result,
+ "https://example.org/codemeta.json"
+ )
+
+ with self.subTest(repo=repo_folder):
+ # In order for us to check every test, we need every file in "expected" directory to be of .yaml,
+ # and make sure the name is the same as the repo folder
+ print(f"################# Processing expectation of {repo_folder} #################")
+ for cat_name, expected_val in expected.items():
+ cat_const = getattr(constants, cat_name)
+ actual_list = metadata_result.results.get(cat_const, [])
+ self.assertTrue(
+ actual_list,
+ f"[{repo_folder}] No results for {cat_name}"
+ )
+
+ first = actual_list[0]["result"]
+ if isinstance(expected_val, dict):
+ for key, val in expected_val.items():
+ self.assertEqual(
+ first.get(key), val,
+ f"[{repo_folder}] Mismatch in {cat_name}.{key}"
+ )
+ else:
+ self.assertEqual(
+ first.get("value"), expected_val,
+ f"[{repo_folder}] Mismatch in {cat_name}"
+ )
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/src/somef_core/test/test_codemeta_parser.py b/src/somef_core/test/test_codemeta_parser.py
new file mode 100644
index 0000000..880cb0f
--- /dev/null
+++ b/src/somef_core/test/test_codemeta_parser.py
@@ -0,0 +1,66 @@
+import unittest
+import os
+import yaml
+from pathlib import Path
+
+from somef_core.parser.codemeta_parser import parse_codemeta_json_file
+from somef_core.process_results import Result
+from somef_core.utils import constants
+
+TEST_ROOT = Path(__file__).parent
+REPOS_DIR = TEST_ROOT / "test_data" / "repositories"
+EXPECT_DIR = TEST_ROOT / "test_data" / "expected"
+
+class TestCodemetaParser(unittest.TestCase):
+
+ def load_expected(self, repo_name):
+ """Load expected YAML for a given repo."""
+ yaml_path = EXPECT_DIR / f"{repo_name}.yaml"
+ if not yaml_path.exists():
+ self.skipTest(f"No expected YAML for repository '{repo_name}'")
+ with open(yaml_path, "r", encoding="utf-8") as f:
+ return yaml.safe_load(f)
+
+ def test_parse_multiple_codemeta_files(self):
+ for repo_folder in os.listdir(REPOS_DIR):
+ print(f"################# Testing {repo_folder} #################")
+ repo_path = REPOS_DIR / repo_folder
+ codemeta_path = repo_path / "codemeta.json"
+ if not codemeta_path.is_file():
+ continue
+
+ expected = self.load_expected(repo_folder)
+ result = Result()
+ metadata_result = parse_codemeta_json_file(
+ str(codemeta_path),
+ result,
+ "https://example.org/codemeta.json"
+ )
+
+ with self.subTest(repo=repo_folder):
+ # In order for us to check every test, we need every file in "expected" directory to be of .yaml,
+ # and make sure the name is the same as the repo folder
+ print(f"################# Processing expectation of {repo_folder} #################")
+ for cat_name, expected_val in expected.items():
+ cat_const = getattr(constants, cat_name)
+ actual_list = metadata_result.results.get(cat_const, [])
+ self.assertTrue(
+ actual_list,
+ f"[{repo_folder}] No results for {cat_name}"
+ )
+
+ first = actual_list[0]["result"]
+ if isinstance(expected_val, dict):
+ for key, val in expected_val.items():
+ self.assertEqual(
+ first.get(key), val,
+ f"[{repo_folder}] Mismatch in {cat_name}.{key}"
+ )
+ else:
+ self.assertEqual(
+ first.get("value"), expected_val,
+ f"[{repo_folder}] Mismatch in {cat_name}"
+ )
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/src/somef_core/test/test_composer_parser 2.py b/src/somef_core/test/test_composer_parser 2.py
new file mode 100644
index 0000000..e525e58
--- /dev/null
+++ b/src/somef_core/test/test_composer_parser 2.py
@@ -0,0 +1,59 @@
+import unittest
+import os
+import sys
+import json
+from pathlib import Path
+from somef_core.process_results import Result
+from somef_core.parser.composer_parser import parse_composer_json
+from somef_core.utils import constants
+
+test_data_path = str(Path(__file__).parent / "test_data") + os.path.sep
+test_data_repositories = str(Path(__file__).parent / "test_data" / "repositories") + os.path.sep
+
+class TestComposerParser(unittest.TestCase):
+ def test_parse_composer_json(self):
+ composer_path = test_data_repositories + os.path.sep+ "composer"+ os.path.sep+ "composer.json"
+ result = Result()
+
+ metadata_result = parse_composer_json(composer_path, result, "https://example.org/composer.json")
+
+ self.assertIn(constants.CAT_PACKAGE_ID, metadata_result.results)
+ package_id = result.results[constants.CAT_PACKAGE_ID][0]["result"]["value"]
+ self.assertEqual(package_id, "composer/composer")
+
+ self.assertIn(constants.CAT_DESCRIPTION, metadata_result.results)
+ description = result.results[constants.CAT_DESCRIPTION][0]["result"]["value"]
+ self.assertEqual(description, "Composer helps you declare, manage and install dependencies of PHP projects. It ensures you have the right stack everywhere.")
+
+ self.assertIn(constants.CAT_LICENSE, metadata_result.results)
+ license_value = result.results[constants.CAT_LICENSE][0]["result"]["value"]
+ self.assertEqual(license_value, "MIT")
+
+ self.assertIn(constants.CAT_REQUIREMENTS, metadata_result.results)
+ dependencies = result.results[constants.CAT_REQUIREMENTS]
+ dep_names = [d["result"]["name"] for d in dependencies]
+ self.assertIn("php", dep_names)
+
+
+ def test_parse_composer_json_2(self):
+ composer_path = test_data_repositories + os.path.sep+ "codecov"+ os.path.sep+ "composer.json"
+ result = Result()
+
+ metadata_result = parse_composer_json(composer_path, result, "https://example.org/composer_2.json")
+
+ self.assertIn(constants.CAT_DESCRIPTION, metadata_result.results)
+ description = result.results[constants.CAT_DESCRIPTION][0]["result"]["value"]
+ self.assertEqual(description, "Codecov Example PHP")
+
+ self.assertIn(constants.CAT_PACKAGE_ID, metadata_result.results)
+ package_id = result.results[constants.CAT_PACKAGE_ID][0]["result"]["value"]
+ self.assertEqual(package_id, "codecov/codecov-php")
+
+ self.assertIn(constants.CAT_REQUIREMENTS, metadata_result.results)
+ dependencies = result.results[constants.CAT_REQUIREMENTS]
+ self.assertEqual(dependencies[0]["result"]["name"], "php")
+ self.assertEqual(dependencies[0]["result"]["dependency_type"], "runtime")
+ self.assertEqual(dependencies[1]["result"]["dependency_type"], "dev")
+
+if __name__ == "__main__":
+ unittest.main()
\ No newline at end of file
diff --git a/src/somef_core/test/test_composer_parser.py b/src/somef_core/test/test_composer_parser.py
new file mode 100644
index 0000000..e525e58
--- /dev/null
+++ b/src/somef_core/test/test_composer_parser.py
@@ -0,0 +1,59 @@
+import unittest
+import os
+import sys
+import json
+from pathlib import Path
+from somef_core.process_results import Result
+from somef_core.parser.composer_parser import parse_composer_json
+from somef_core.utils import constants
+
+test_data_path = str(Path(__file__).parent / "test_data") + os.path.sep
+test_data_repositories = str(Path(__file__).parent / "test_data" / "repositories") + os.path.sep
+
+class TestComposerParser(unittest.TestCase):
+ def test_parse_composer_json(self):
+ composer_path = test_data_repositories + os.path.sep+ "composer"+ os.path.sep+ "composer.json"
+ result = Result()
+
+ metadata_result = parse_composer_json(composer_path, result, "https://example.org/composer.json")
+
+ self.assertIn(constants.CAT_PACKAGE_ID, metadata_result.results)
+ package_id = result.results[constants.CAT_PACKAGE_ID][0]["result"]["value"]
+ self.assertEqual(package_id, "composer/composer")
+
+ self.assertIn(constants.CAT_DESCRIPTION, metadata_result.results)
+ description = result.results[constants.CAT_DESCRIPTION][0]["result"]["value"]
+ self.assertEqual(description, "Composer helps you declare, manage and install dependencies of PHP projects. It ensures you have the right stack everywhere.")
+
+ self.assertIn(constants.CAT_LICENSE, metadata_result.results)
+ license_value = result.results[constants.CAT_LICENSE][0]["result"]["value"]
+ self.assertEqual(license_value, "MIT")
+
+ self.assertIn(constants.CAT_REQUIREMENTS, metadata_result.results)
+ dependencies = result.results[constants.CAT_REQUIREMENTS]
+ dep_names = [d["result"]["name"] for d in dependencies]
+ self.assertIn("php", dep_names)
+
+
+ def test_parse_composer_json_2(self):
+ composer_path = test_data_repositories + os.path.sep+ "codecov"+ os.path.sep+ "composer.json"
+ result = Result()
+
+ metadata_result = parse_composer_json(composer_path, result, "https://example.org/composer_2.json")
+
+ self.assertIn(constants.CAT_DESCRIPTION, metadata_result.results)
+ description = result.results[constants.CAT_DESCRIPTION][0]["result"]["value"]
+ self.assertEqual(description, "Codecov Example PHP")
+
+ self.assertIn(constants.CAT_PACKAGE_ID, metadata_result.results)
+ package_id = result.results[constants.CAT_PACKAGE_ID][0]["result"]["value"]
+ self.assertEqual(package_id, "codecov/codecov-php")
+
+ self.assertIn(constants.CAT_REQUIREMENTS, metadata_result.results)
+ dependencies = result.results[constants.CAT_REQUIREMENTS]
+ self.assertEqual(dependencies[0]["result"]["name"], "php")
+ self.assertEqual(dependencies[0]["result"]["dependency_type"], "runtime")
+ self.assertEqual(dependencies[1]["result"]["dependency_type"], "dev")
+
+if __name__ == "__main__":
+ unittest.main()
\ No newline at end of file
diff --git a/src/somef_core/test/test_configuration.py b/src/somef_core/test/test_configuration.py
index c8bf9f9..6097a3f 100644
--- a/src/somef_core/test/test_configuration.py
+++ b/src/somef_core/test/test_configuration.py
@@ -1,6 +1,6 @@
import unittest
from ..configuration import get_configuration_file
-from somef.utils import constants
+from somef_core.utils import constants
class TestConfiguration(unittest.TestCase):
diff --git a/src/somef_core/test/test_data/README-EUVpy 2.md b/src/somef_core/test/test_data/README-EUVpy 2.md
new file mode 100644
index 0000000..26c2756
--- /dev/null
+++ b/src/somef_core/test/test_data/README-EUVpy 2.md
@@ -0,0 +1,166 @@
+
+
+
+[_(EUV imagery of the solar disk, taken by NASA SDO)_](https://www.nist.gov/image/1280px-sun-august12010jpg)
+
+# Overview
+`EUVpy` is a Python module that contains the NEUVAC empirical model of solar EUV irradiance for use primarily in thermosphere-ionosphere models.
+Conceptual development was carried out by Dr. Aaron J. Ridley and analysis and contributions were made by Dr. Daniel A. Brandt and Dr. Joseph Paki.
+
+`EUVpy` also contains code for running, comparing, and analyzing the performance of NEUVAC in comparison to other
+empirical models such as EUVAC, HEUVAC, HFG, and FISM2. As such, the package includes access to EUVAC, HEUVAC, and HFG,
+and allows the user to download the F10.7 index at will.
+
+# Installation
+
+You can obtain `EUVpy` with a simple git clone command. In the terminal, execute the following command:
+
+> git clone https://github.com/DanBrandt/EUVpy.git
+
+The EUVpy package provides access to the HEUVAC model, which is written in Fortran and requires gfortran to be installed. To
+install gfortran (if you don't already have it), open a terminal and execute the following command:
+
+> sudo apt-get install gfortran
+
+Now, enter into the package folder and run the following command in order to compile the Fortran code that HEUVAC
+alone depends upon:
+
+> cd EUVpy\
+> . install_heuvac.sh
+
+If this step gives you trouble, try executing the following code **first**, and then retry the above commands.
+
+> git submodule update --init --recursive --remote
+
+After HEUVAC is compiled once, you should never have to compile it again.
+
+Now you are in a position to install the rest of the EUVpy package. Before doing this, you will first want to initialize a Python virtual environment.
+
+> cd ~/.virtualenvs\
+> python**3.x** -m venv myVenv\
+> pip install --upgrade pip\
+> pip install wheel\
+> source myVenv/bin/activate
+
+Above, 'python**3.x**' refers to whatever version of Python 3 you have installed. EUVpy works with any version of Python 3.
+You may now use one of two ways to install EUVpy. You can install from the cloned repo directly, or you can install from PyPI.
+
+## Installing from the Cloned Repository
+
+Navigate back to the package folder:
+
+> cd\
+> cd myDirectory/EUVpy
+
+After this is done, simply execute the following command:
+
+> pip install .
+
+## Installing from PyPI
+
+A simpler way to install also involves just entering the following in the terminal:
+
+> pip install EUVpy
+
+**Note:** If you choose this route, you'll have to install HEUVAC differently than described above. You will have to
+navigate the directory containing the HEUVAC files, and execute the following command, as follows:
+
+> cd src/EUVpy/empiricalModels/models/HEUVAC/srcHEUVAC
+> . compile.sh
+
+You can then return to the top package directory. This should only have to be done once.
+This approach will be replaced with a user-friendly console script in the next release of this package.
+
+### Unit Testing
+
+**Note: this section only applies if you installed from the cloned repo.**
+
+Just to make sure everything installed correctly, while in the package folder, run the following command in the terminal.
+
+> pytest
+
+If all of the tests pass, you should be good to go! If you find an issue at this step (or any other) please don't hesitate
+to reach out!
+
+# Usage
+EUVpy contains modules for **4** different EUV irradiance models. These models include:
+* NEUVAC
+* EUVAC
+* HEUVAC
+* HFG (SOLOMON)
+
+We note that SOLOMON in the literature can either refer to the empirical model between F10.7 and 81 day-averaged F10.7
+centered on the current day (hereafter F10.7A) and EUV irradiance in 22 overlapping bands as described by Solomon and
+Qian 2005, or it can refer to _any_ EUV irradiance data summed into those 22 overlapping bins (referred to as the STAN
+BANDS). In this package, SOLOMON only refers to the former, though functionality does exist to run all other models in
+the STAN BANDS.
+
+## Finding your way around
+
+There are few folders in this package:
+* **empiricalModels**: Contains code and data for EUVAC, HEUVAC, and SOLOMON, as well as FISM:
+* **experiments**: Contains code and figures related to the publication associated with NEUVAC. In this folder, the file
+_fitNeuvac.py_ s used for actually performing the NEUVAC fits between F10.7, F10.7A, and FISM2, while _uncNeuvac.py_
+contains code for computing the correlation matrix used to enable running NEUVAC ensembles, as well as generating plots
+of the squared difference between NEUVAC and FISM2 in different bands.
+* **NEUVAC**: Contains the code for running NEUVAC.
+* **solarIndices**: Contains F10.7 solar index data, from both OMNIWeb and Penticton.
+* **tools**: Contains code for miscellaneous helper functions. In this folder appears the following:
+ * _EUV_: Contains numerous functions within fism2_process.py for reading in and rebinning FISM2 data.
+ * _processIndices.py_: Contains functions for reading in, downloading, and cleaning OMNIWeb data.
+ * _processIrradiances.py_: Contains functions for reading in data from TIMED/SEE, SDO/EVE, and FISM.
+ * _spectralAnalysis.py_: Contains functions for converting between solar spectral irradiance and solar spectral flux.
+ * _toolbox.py_: Contains miscellaneous helper functions that mainly focus on directory management, loading and saving data, statistics, and fitting.
+
+Each of the models in EUVpy requires F10.7 as an input. To grab F10.7 between any two dates, simply do the following:
+
+> from EUVpy.tools import processIndices
+>
+> f107times, f107, f107a, f107b = processIndices.getCLSF107('YYYY-MM-DD', 'YYYY-MM-DD', truncate=False)
+
+To import any of the models, simply do as follows:
+
+NEUVAC
+> from EUVpy.NEUVAC import neuvac
+>
+> neuvacIrr, _, _, _ = neuvac.neuvacEUV(f107, f107b, bands='EUVAC')
+
+EUVAC
+> from EUVpy.empiricalModels.models.EUVAC import euvac
+>
+> euvacFlux, euvacIrr, _, _, _ = euvac.euvac(f107, f107a)
+
+HEUVAC
+> from EUVpy.empiricalModels.models.HEUVAC import heuvac
+>
+> heuvac_wav, heuvacFlux, heuvacIrr, _, _, _ = heuvac.heuvac(f107, f107a, torr=True)
+
+SOLOMON
+> from EUVpy.empiricalModels.models.SOLOMON import solomon
+>
+> solomonFluxHFG, solomonIrrHFG = SOLOMON.solomon.solomon(f107, f107a, model='HFG')
+>
+> solomonFluxEUVAC, solomonIrrEUVAC = SOLOMON.solomon.solomon(f107, f107a, model='EUVAC')
+
+# Examples
+
+There is a [Python notebook](https://github.com/DanBrandt/EUVpy/blob/main/examples/euvpy_examples.ipynb) you can walk through in order to get familiar with the basic functionality of EUVpy.
+
+We encourage you to peruse [more examples](https://github.com/DanBrandt/EUVpy/blob/main/docs/source/examples.rst) in the documentation for guidelines on how to run each of the models.
+
+Due to the unique construction of NEUVAC, at present, we only recommend running ensembles for NEUVAC, and not any of the
+other models.
+
+# Code of Conduct
+In using this code, depending on the module used, proper citations should be given to the original authors responsible
+for developing each model or dataset:
+
+NEUVAC: [Brandt and Ridley, 2024](https://agupubs.onlinelibrary.wiley.com/doi/pdfdirect/10.1029/2024SW004043)
+
+EUVAC: [Richards, et al. 1994](https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/94ja00518)
+
+HEUVAC [Richards, et al. 2006](https://www.sciencedirect.com/science/article/pii/S0273117705008288?casa_token=zEhwbyXrC8MAAAAA:qHFmKe0ZDE4gMsAX9qAHESvPyoEDFLBlhHuLaEsIwYFykhFXN79--XttCW-QDg1sA4wgD54ysFc)
+
+SOLOMON [Solomon and Qian, 2005](https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2005JA011160)
+
+FISM2: [Chamberlin, et al. 2020](https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020SW002588)
diff --git a/src/somef_core/test/test_data/README-EUVpy.md b/src/somef_core/test/test_data/README-EUVpy.md
new file mode 100644
index 0000000..26c2756
--- /dev/null
+++ b/src/somef_core/test/test_data/README-EUVpy.md
@@ -0,0 +1,166 @@
+
+
+
+[_(EUV imagery of the solar disk, taken by NASA SDO)_](https://www.nist.gov/image/1280px-sun-august12010jpg)
+
+# Overview
+`EUVpy` is a Python module that contains the NEUVAC empirical model of solar EUV irradiance for use primarily in thermosphere-ionosphere models.
+Conceptual development was carried out by Dr. Aaron J. Ridley and analysis and contributions were made by Dr. Daniel A. Brandt and Dr. Joseph Paki.
+
+`EUVpy` also contains code for running, comparing, and analyzing the performance of NEUVAC in comparison to other
+empirical models such as EUVAC, HEUVAC, HFG, and FISM2. As such, the package includes access to EUVAC, HEUVAC, and HFG,
+and allows the user to download the F10.7 index at will.
+
+# Installation
+
+You can obtain `EUVpy` with a simple git clone command. In the terminal, execute the following command:
+
+> git clone https://github.com/DanBrandt/EUVpy.git
+
+The EUVpy package provides access to the HEUVAC model, which is written in Fortran and requires gfortran to be installed. To
+install gfortran (if you don't already have it), open a terminal and execute the following command:
+
+> sudo apt-get install gfortran
+
+Now, enter into the package folder and run the following command in order to compile the Fortran code that HEUVAC
+alone depends upon:
+
+> cd EUVpy\
+> . install_heuvac.sh
+
+If this step gives you trouble, try executing the following code **first**, and then retry the above commands.
+
+> git submodule update --init --recursive --remote
+
+After HEUVAC is compiled once, you should never have to compile it again.
+
+Now you are in a position to install the rest of the EUVpy package. Before doing this, you will first want to initialize a Python virtual environment.
+
+> cd ~/.virtualenvs\
+> python**3.x** -m venv myVenv\
+> pip install --upgrade pip\
+> pip install wheel\
+> source myVenv/bin/activate
+
+Above, 'python**3.x**' refers to whatever version of Python 3 you have installed. EUVpy works with any version of Python 3.
+You may now use one of two ways to install EUVpy. You can install from the cloned repo directly, or you can install from PyPI.
+
+## Installing from the Cloned Repository
+
+Navigate back to the package folder:
+
+> cd\
+> cd myDirectory/EUVpy
+
+After this is done, simply execute the following command:
+
+> pip install .
+
+## Installing from PyPI
+
+A simpler way to install also involves just entering the following in the terminal:
+
+> pip install EUVpy
+
+**Note:** If you choose this route, you'll have to install HEUVAC differently than described above. You will have to
+navigate the directory containing the HEUVAC files, and execute the following command, as follows:
+
+> cd src/EUVpy/empiricalModels/models/HEUVAC/srcHEUVAC
+> . compile.sh
+
+You can then return to the top package directory. This should only have to be done once.
+This approach will be replaced with a user-friendly console script in the next release of this package.
+
+### Unit Testing
+
+**Note: this section only applies if you installed from the cloned repo.**
+
+Just to make sure everything installed correctly, while in the package folder, run the following command in the terminal.
+
+> pytest
+
+If all of the tests pass, you should be good to go! If you find an issue at this step (or any other) please don't hesitate
+to reach out!
+
+# Usage
+EUVpy contains modules for **4** different EUV irradiance models. These models include:
+* NEUVAC
+* EUVAC
+* HEUVAC
+* HFG (SOLOMON)
+
+We note that SOLOMON in the literature can either refer to the empirical model between F10.7 and 81 day-averaged F10.7
+centered on the current day (hereafter F10.7A) and EUV irradiance in 22 overlapping bands as described by Solomon and
+Qian 2005, or it can refer to _any_ EUV irradiance data summed into those 22 overlapping bins (referred to as the STAN
+BANDS). In this package, SOLOMON only refers to the former, though functionality does exist to run all other models in
+the STAN BANDS.
+
+## Finding your way around
+
+There are few folders in this package:
+* **empiricalModels**: Contains code and data for EUVAC, HEUVAC, and SOLOMON, as well as FISM:
+* **experiments**: Contains code and figures related to the publication associated with NEUVAC. In this folder, the file
+_fitNeuvac.py_ s used for actually performing the NEUVAC fits between F10.7, F10.7A, and FISM2, while _uncNeuvac.py_
+contains code for computing the correlation matrix used to enable running NEUVAC ensembles, as well as generating plots
+of the squared difference between NEUVAC and FISM2 in different bands.
+* **NEUVAC**: Contains the code for running NEUVAC.
+* **solarIndices**: Contains F10.7 solar index data, from both OMNIWeb and Penticton.
+* **tools**: Contains code for miscellaneous helper functions. In this folder appears the following:
+ * _EUV_: Contains numerous functions within fism2_process.py for reading in and rebinning FISM2 data.
+ * _processIndices.py_: Contains functions for reading in, downloading, and cleaning OMNIWeb data.
+ * _processIrradiances.py_: Contains functions for reading in data from TIMED/SEE, SDO/EVE, and FISM.
+ * _spectralAnalysis.py_: Contains functions for converting between solar spectral irradiance and solar spectral flux.
+ * _toolbox.py_: Contains miscellaneous helper functions that mainly focus on directory management, loading and saving data, statistics, and fitting.
+
+Each of the models in EUVpy requires F10.7 as an input. To grab F10.7 between any two dates, simply do the following:
+
+> from EUVpy.tools import processIndices
+>
+> f107times, f107, f107a, f107b = processIndices.getCLSF107('YYYY-MM-DD', 'YYYY-MM-DD', truncate=False)
+
+To import any of the models, simply do as follows:
+
+NEUVAC
+> from EUVpy.NEUVAC import neuvac
+>
+> neuvacIrr, _, _, _ = neuvac.neuvacEUV(f107, f107b, bands='EUVAC')
+
+EUVAC
+> from EUVpy.empiricalModels.models.EUVAC import euvac
+>
+> euvacFlux, euvacIrr, _, _, _ = euvac.euvac(f107, f107a)
+
+HEUVAC
+> from EUVpy.empiricalModels.models.HEUVAC import heuvac
+>
+> heuvac_wav, heuvacFlux, heuvacIrr, _, _, _ = heuvac.heuvac(f107, f107a, torr=True)
+
+SOLOMON
+> from EUVpy.empiricalModels.models.SOLOMON import solomon
+>
+> solomonFluxHFG, solomonIrrHFG = SOLOMON.solomon.solomon(f107, f107a, model='HFG')
+>
+> solomonFluxEUVAC, solomonIrrEUVAC = SOLOMON.solomon.solomon(f107, f107a, model='EUVAC')
+
+# Examples
+
+There is a [Python notebook](https://github.com/DanBrandt/EUVpy/blob/main/examples/euvpy_examples.ipynb) you can walk through in order to get familiar with the basic functionality of EUVpy.
+
+We encourage you to peruse [more examples](https://github.com/DanBrandt/EUVpy/blob/main/docs/source/examples.rst) in the documentation for guidelines on how to run each of the models.
+
+Due to the unique construction of NEUVAC, at present, we only recommend running ensembles for NEUVAC, and not any of the
+other models.
+
+# Code of Conduct
+In using this code, depending on the module used, proper citations should be given to the original authors responsible
+for developing each model or dataset:
+
+NEUVAC: [Brandt and Ridley, 2024](https://agupubs.onlinelibrary.wiley.com/doi/pdfdirect/10.1029/2024SW004043)
+
+EUVAC: [Richards, et al. 1994](https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/94ja00518)
+
+HEUVAC [Richards, et al. 2006](https://www.sciencedirect.com/science/article/pii/S0273117705008288?casa_token=zEhwbyXrC8MAAAAA:qHFmKe0ZDE4gMsAX9qAHESvPyoEDFLBlhHuLaEsIwYFykhFXN79--XttCW-QDg1sA4wgD54ysFc)
+
+SOLOMON [Solomon and Qian, 2005](https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2005JA011160)
+
+FISM2: [Chamberlin, et al. 2020](https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020SW002588)
diff --git a/src/somef_core/test/test_data/README-citation-file-format 2.md b/src/somef_core/test/test_data/README-citation-file-format 2.md
new file mode 100644
index 0000000..1f5e486
--- /dev/null
+++ b/src/somef_core/test/test_data/README-citation-file-format 2.md
@@ -0,0 +1,158 @@
+# Citation File Format
+
+[](https://github.com/citation-file-format/citation-file-format/actions/workflows/testing.yml?query=branch%3Amain)
+[](https://doi.org/10.5281/zenodo.1003149)
+[](https://creativecommons.org/licenses/by/4.0/)
+[](https://citation-file-format.github.io)
+
+The Citation File Format lets you provide citation metadata for software or datasets
+in plaintext files that are easy to read by both humans and machines.
+
+## Structure
+
+You can specify citation metadata for your software (or dataset) in a file named `CITATION.cff`.
+This is what a typical `CITATION.cff` file may look like for research software:
+
+```yaml
+cff-version: 1.2.0
+message: If you use this software, please cite it using these metadata.
+title: My Research Software
+abstract: This is my awesome research software. It does many things.
+authors:
+ - family-names: Druskat
+ given-names: Stephan
+ orcid: "https://orcid.org/1234-5678-9101-1121"
+ - name: "The Research Software project"
+version: 0.11.2
+date-released: "2021-07-18"
+identifiers:
+ - description: This is the collection of archived snapshots of all versions of My Research Software
+ type: doi
+ value: "10.5281/zenodo.123456"
+ - description: This is the archived snapshot of version 0.11.2 of My Research Software
+ type: doi
+ value: "10.5281/zenodo.123457"
+license: Apache-2.0
+repository-code: "https://github.com/citation-file-format/my-research-software"
+```
+
+In addition, the Citation File Format allows you to
+
+- provide references to works that your software or dataset builds on ([see here for more info](schema-guide.md#referencing-other-work));
+- ask people to cite a different, related work instead of the software or dataset itself ([see here for more info](schema-guide.md#credit-redirection)).
+
+## Format specifications :books:
+
+**You can find the complete format specifications in the [Guide to the Citation File Format schema](schema-guide.md).**
+
+## Why should I add a `CITATION.cff` file to my repository? :bulb:
+
+When you do this, great things may happen:
+
+1. Users of your software can easily cite it using the metadata from `CITATION.cff`!
+2. If your repository is hosted on GitHub, they will [show the citation information in the sidebar](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files), which makes it easy for visitors to cite your software or dataset correctly.
+3. When you publish your software on Zenodo via the [GitHub-Zenodo integration](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content), they will use the metadata from your `CITATION.cff` file.
+4. People can import the correct reference to your software into the [Zotero](https://www.zotero.org) reference manager via a [browser plugin](https://www.zotero.org/download/).
+
+## Creation :heavy_plus_sign:
+
+To create a `CITATION.cff` file, you can
+
+- use the [**cffinit** website](https://citation-file-format.github.io/cff-initializer-javascript/#/),
+- copy and paste the [example snippet](#structure), and adapt it to your needs, or
+- create a new file called `CITATION.cff` using the *Add file* button on GitHub, and use the template they provide.
+
+## Validation :heavy_check_mark:
+
+You can validate your `CITATION.cff` file on the command line with the [`cffconvert` Python package](https://pypi.org/project/cffconvert/):
+
+```shell
+# Install cffconvert with pip in user space
+python3 -m pip install --user cffconvert
+
+# Validate your CFF file
+cffconvert --validate
+```
+
+If you get a Traceback with error messages, look for the relevant validation error and fix it.
+If the output is very long, it may help if you search it for lines starting with `jsonschema.exceptions.ValidationError`.
+
+If you prefer to use Docker, you can use the [`cffconvert` Docker image](https://hub.docker.com/r/citationcff/cffconvert):
+
+```bash
+cd
+docker run --rm -v ${PWD}:/app citationcff/cffconvert --validate
+```
+
+
+
+## Tools to work with `CITATION.cff` files :wrench:
+
+There is tooling available to work with `CITATION.cff` files to do different things:
+create new files, edit existing files, validate existing files, convert files from the Citation File Format into another format.
+The following table gives an overview of the tools that we know about. If there is a tool missing from this table, please [open a new issue](https://github.com/citation-file-format/citation-file-format/issues/new/choose) and let us know.
+
+| | Creation | Editing/Updating | Validation | Conversion |
+| -------------- | ------------------------------------------------------------------------------- | ------------------------------------------------------------------- | ------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| Command line | | | • [cffconvert](#validation-heavy_check_mark) | • [cffconvert](https://pypi.org/project/cffconvert/)
• [bibtex-to-cff](https://github.com/monperrus/bibtexbrowser/)
• [cff-from-621](https://pypi.org/project/cff-from-621/)
• [openCARP-CI](https://git.opencarp.org/openCARP/openCARP-CI/-/tree/master/#create_cff) | +| GitHub Actions | | | [cff-validator](https://github.com/marketplace/actions/cff-validator) | • [cffconvert](https://github.com/marketplace/actions/cffconvert)
• [codemeta2cff](https://github.com/caltechlibrary/codemeta2cff) | +| GitHub Bot | | | [#238](https://github.com/citation-file-format/citation-file-format/issues/238) | | +| Docker | | | [cffconvert Docker image](#validation-heavy_check_mark) | [cffconvert Docker image](https://hub.docker.com/r/citationcff/cffconvert) | +| Go | | | | • [datatools/codemeta2cff](https://github.com/caltechlibrary/datatools/) | +| Haskell | | • [cffreference](https://github.com/kevinmatthes/cffreference) | | | +| Java | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | +| JavaScript | | | | • [Citation.js](https://citation.js.org/) [plugin](https://www.npmjs.com/package/@citation-js/plugin-software-formats) | +| Julia | | | • [Bibliography.jl](https://github.com/Humans-of-Julia/Bibliography.jl) | • [Bibliography.jl](https://github.com/Humans-of-Julia/Bibliography.jl) | +| PHP | | | | • [bibtex-to-cff](https://github.com/monperrus/bibtexbrowser/) | +| Python | | • [cff2toml](https://github.com/willynilly/cff2toml)
• [doi2cff](https://github.com/citation-file-format/doi2cff)
• [updateCitation](https://github.com/hunterhogan/updateCitation) | • [cffconvert](#validation-heavy_check_mark) | • [cff-from-621](https://pypi.org/project/cff-from-621/)
• [cff2toml](https://github.com/willynilly/cff2toml)
• [cffconvert](https://github.com/citation-file-format/cff-converter-python)
• [doi2cff](https://github.com/citation-file-format/doi2cff)
• [openCARP-CI](https://git.opencarp.org/openCARP/openCARP-CI/-/tree/master/#create_cff)
• [py_bibtex_to_cff_converter](https://github.com/vdplasthijs/py_bibtex_to_cff_converter) | +| R | | | • [cffr](https://CRAN.R-project.org/package=cffr) | • [citation](https://cran.r-project.org/web/packages/citation/)
• [r2cff](https://github.com/ocbe-uio/RCFF)
• [handlr](https://github.com/ropensci/handlr)
• [cffr](https://CRAN.R-project.org/package=cffr) | +| Ruby | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | +| Rust | • [Aeruginous](https://github.com/kevinmatthes/aeruginous-rs) | • [Aeruginous](https://github.com/kevinmatthes/aeruginous-rs) | | • [citeworks](https://github.com/passcod/citeworks) | +| TypeScript | | | | [#28](https://github.com/citation-file-format/citation-file-format/issues/28#issuecomment-892105342) | +| Website | • [cffinit](https://citation-file-format.github.io/cff-initializer-javascript/) | | | | + +## Maintainers :nerd_face: + +The Citation File Format schema is maintained by + +- Stephan Druskat ([@sdruskat](https://github.com/sdruskat/)) +- Jurriaan H. Spaaks ([@jspaaks](https://github.com/jspaaks/)) + +## Contributing :handshake: + +The Citation File Format is a collaborative project and we welcome suggestions and contributions. We hope one of the invitations below works for you, but if not, please let us know! + +:running: **I'm busy, I only have 1 minute** +- Tell a friend about the Citation File Format, or tweet about it! +- Give the project a star :star:! + +:hourglass_flowing_sand: **I've got 10 minutes - tell me what I should do** +- Create a `CITATION.cff` file for your repository. +- Suggest ideas for how you would like to use the Citation File Format, or for an improvement to the format or its tooling. +- If you know how to validate `CITATION.cff` files, help someone with a validation problem and look at the [issues labeled ](https://github.com/citation-file-format/citation-file-format/issues?q=is%3Aopen+is%3Aissue+label%3A%22help+wanted%22+label%3Avalidation) + +:computer: **I've got a few hours to work on this** +- Help create tooling for the community by looking at the [issues labeled ](https://github.com/citation-file-format/citation-file-format/issues?q=is%3Aopen+is%3Aissue+label%3A%22help+wanted%22+label%3Atooling) + +:tada: **I want to help grow the community** +- Write a blog post or news item for your own community. +- Organise a hack event or workshop to help others use or improve the Citation File Format. + +Please read the more detailed [contributing guidelines](CONTRIBUTING.md) and [open a GitHub issue](https://github.com/citation-file-format/citation-file-format/issues) to suggest a new idea or let us know about bugs. Please put up pull requests for changes to the format and schema against the `develop` branch! + +## License :balance_scale: + +Copyright © 2016 - 2023. The Citation File Format Contributors + +This work is licensed under a [Creative Commons Attribution 4.0 International (CC-BY-4.0)](https://creativecommons.org/licenses/by/4.0/legalcode) license. + +## Acknowledgments :pray: + +**We'd like to thank everyone who has contributed to the Citation File Format!** +They are listed in the [`CITATION.cff`](CITATION.cff) file for this repository. Please open an issue if you find that you are missing from the file. + +We gratefully acknowledge support from: + +- The [Institute for Software Technology](https://www.dlr.de/en/sc) of the [German Aerospace Center (DLR)](https://www.dlr.de/en/) +- The [Netherlands eScience Center](https://www.esciencecenter.nl) +- The [Software Sustainability Institute](https://software.ac.uk/) \ No newline at end of file diff --git a/src/somef_core/test/test_data/README-citation-file-format.md b/src/somef_core/test/test_data/README-citation-file-format.md new file mode 100644 index 0000000..1f5e486 --- /dev/null +++ b/src/somef_core/test/test_data/README-citation-file-format.md @@ -0,0 +1,158 @@ +# Citation File Format + +[](https://github.com/citation-file-format/citation-file-format/actions/workflows/testing.yml?query=branch%3Amain) +[](https://doi.org/10.5281/zenodo.1003149) +[](https://creativecommons.org/licenses/by/4.0/) +[](https://citation-file-format.github.io) + +The Citation File Format lets you provide citation metadata for software or datasets +in plaintext files that are easy to read by both humans and machines. + +## Structure + +You can specify citation metadata for your software (or dataset) in a file named `CITATION.cff`. +This is what a typical `CITATION.cff` file may look like for research software: + +```yaml +cff-version: 1.2.0 +message: If you use this software, please cite it using these metadata. +title: My Research Software +abstract: This is my awesome research software. It does many things. +authors: + - family-names: Druskat + given-names: Stephan + orcid: "https://orcid.org/1234-5678-9101-1121" + - name: "The Research Software project" +version: 0.11.2 +date-released: "2021-07-18" +identifiers: + - description: This is the collection of archived snapshots of all versions of My Research Software + type: doi + value: "10.5281/zenodo.123456" + - description: This is the archived snapshot of version 0.11.2 of My Research Software + type: doi + value: "10.5281/zenodo.123457" +license: Apache-2.0 +repository-code: "https://github.com/citation-file-format/my-research-software" +``` + +In addition, the Citation File Format allows you to + +- provide references to works that your software or dataset builds on ([see here for more info](schema-guide.md#referencing-other-work)); +- ask people to cite a different, related work instead of the software or dataset itself ([see here for more info](schema-guide.md#credit-redirection)). + +## Format specifications :books: + +**You can find the complete format specifications in the [Guide to the Citation File Format schema](schema-guide.md).** + +## Why should I add a `CITATION.cff` file to my repository? :bulb: + +When you do this, great things may happen: + +1. Users of your software can easily cite it using the metadata from `CITATION.cff`! +2. If your repository is hosted on GitHub, they will [show the citation information in the sidebar](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files), which makes it easy for visitors to cite your software or dataset correctly. +3. When you publish your software on Zenodo via the [GitHub-Zenodo integration](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content), they will use the metadata from your `CITATION.cff` file. +4. People can import the correct reference to your software into the [Zotero](https://www.zotero.org) reference manager via a [browser plugin](https://www.zotero.org/download/). + +## Creation :heavy_plus_sign: + +To create a `CITATION.cff` file, you can + +- use the [**cffinit** website](https://citation-file-format.github.io/cff-initializer-javascript/#/), +- copy and paste the [example snippet](#structure), and adapt it to your needs, or +- create a new file called `CITATION.cff` using the *Add file* button on GitHub, and use the template they provide. + +## Validation :heavy_check_mark: + +You can validate your `CITATION.cff` file on the command line with the [`cffconvert` Python package](https://pypi.org/project/cffconvert/): + +```shell +# Install cffconvert with pip in user space +python3 -m pip install --user cffconvert + +# Validate your CFF file +cffconvert --validate +``` + +If you get a Traceback with error messages, look for the relevant validation error and fix it. +If the output is very long, it may help if you search it for lines starting with `jsonschema.exceptions.ValidationError`. + +If you prefer to use Docker, you can use the [`cffconvert` Docker image](https://hub.docker.com/r/citationcff/cffconvert): + +```bash +cd
+docker run --rm -v ${PWD}:/app citationcff/cffconvert --validate
+```
+
+
+
+## Tools to work with `CITATION.cff` files :wrench:
+
+There is tooling available to work with `CITATION.cff` files to do different things:
+create new files, edit existing files, validate existing files, convert files from the Citation File Format into another format.
+The following table gives an overview of the tools that we know about. If there is a tool missing from this table, please [open a new issue](https://github.com/citation-file-format/citation-file-format/issues/new/choose) and let us know.
+
+| | Creation | Editing/Updating | Validation | Conversion |
+| -------------- | ------------------------------------------------------------------------------- | ------------------------------------------------------------------- | ------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| Command line | | | • [cffconvert](#validation-heavy_check_mark) | • [cffconvert](https://pypi.org/project/cffconvert/)
• [bibtex-to-cff](https://github.com/monperrus/bibtexbrowser/)
• [cff-from-621](https://pypi.org/project/cff-from-621/)
• [openCARP-CI](https://git.opencarp.org/openCARP/openCARP-CI/-/tree/master/#create_cff) | +| GitHub Actions | | | [cff-validator](https://github.com/marketplace/actions/cff-validator) | • [cffconvert](https://github.com/marketplace/actions/cffconvert)
• [codemeta2cff](https://github.com/caltechlibrary/codemeta2cff) | +| GitHub Bot | | | [#238](https://github.com/citation-file-format/citation-file-format/issues/238) | | +| Docker | | | [cffconvert Docker image](#validation-heavy_check_mark) | [cffconvert Docker image](https://hub.docker.com/r/citationcff/cffconvert) | +| Go | | | | • [datatools/codemeta2cff](https://github.com/caltechlibrary/datatools/) | +| Haskell | | • [cffreference](https://github.com/kevinmatthes/cffreference) | | | +| Java | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | +| JavaScript | | | | • [Citation.js](https://citation.js.org/) [plugin](https://www.npmjs.com/package/@citation-js/plugin-software-formats) | +| Julia | | | • [Bibliography.jl](https://github.com/Humans-of-Julia/Bibliography.jl) | • [Bibliography.jl](https://github.com/Humans-of-Julia/Bibliography.jl) | +| PHP | | | | • [bibtex-to-cff](https://github.com/monperrus/bibtexbrowser/) | +| Python | | • [cff2toml](https://github.com/willynilly/cff2toml)
• [doi2cff](https://github.com/citation-file-format/doi2cff)
• [updateCitation](https://github.com/hunterhogan/updateCitation) | • [cffconvert](#validation-heavy_check_mark) | • [cff-from-621](https://pypi.org/project/cff-from-621/)
• [cff2toml](https://github.com/willynilly/cff2toml)
• [cffconvert](https://github.com/citation-file-format/cff-converter-python)
• [doi2cff](https://github.com/citation-file-format/doi2cff)
• [openCARP-CI](https://git.opencarp.org/openCARP/openCARP-CI/-/tree/master/#create_cff)
• [py_bibtex_to_cff_converter](https://github.com/vdplasthijs/py_bibtex_to_cff_converter) | +| R | | | • [cffr](https://CRAN.R-project.org/package=cffr) | • [citation](https://cran.r-project.org/web/packages/citation/)
• [r2cff](https://github.com/ocbe-uio/RCFF)
• [handlr](https://github.com/ropensci/handlr)
• [cffr](https://CRAN.R-project.org/package=cffr) | +| Ruby | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | +| Rust | • [Aeruginous](https://github.com/kevinmatthes/aeruginous-rs) | • [Aeruginous](https://github.com/kevinmatthes/aeruginous-rs) | | • [citeworks](https://github.com/passcod/citeworks) | +| TypeScript | | | | [#28](https://github.com/citation-file-format/citation-file-format/issues/28#issuecomment-892105342) | +| Website | • [cffinit](https://citation-file-format.github.io/cff-initializer-javascript/) | | | | + +## Maintainers :nerd_face: + +The Citation File Format schema is maintained by + +- Stephan Druskat ([@sdruskat](https://github.com/sdruskat/)) +- Jurriaan H. Spaaks ([@jspaaks](https://github.com/jspaaks/)) + +## Contributing :handshake: + +The Citation File Format is a collaborative project and we welcome suggestions and contributions. We hope one of the invitations below works for you, but if not, please let us know! + +:running: **I'm busy, I only have 1 minute** +- Tell a friend about the Citation File Format, or tweet about it! +- Give the project a star :star:! + +:hourglass_flowing_sand: **I've got 10 minutes - tell me what I should do** +- Create a `CITATION.cff` file for your repository. +- Suggest ideas for how you would like to use the Citation File Format, or for an improvement to the format or its tooling. +- If you know how to validate `CITATION.cff` files, help someone with a validation problem and look at the [issues labeled ](https://github.com/citation-file-format/citation-file-format/issues?q=is%3Aopen+is%3Aissue+label%3A%22help+wanted%22+label%3Avalidation) + +:computer: **I've got a few hours to work on this** +- Help create tooling for the community by looking at the [issues labeled ](https://github.com/citation-file-format/citation-file-format/issues?q=is%3Aopen+is%3Aissue+label%3A%22help+wanted%22+label%3Atooling) + +:tada: **I want to help grow the community** +- Write a blog post or news item for your own community. +- Organise a hack event or workshop to help others use or improve the Citation File Format. + +Please read the more detailed [contributing guidelines](CONTRIBUTING.md) and [open a GitHub issue](https://github.com/citation-file-format/citation-file-format/issues) to suggest a new idea or let us know about bugs. Please put up pull requests for changes to the format and schema against the `develop` branch! + +## License :balance_scale: + +Copyright © 2016 - 2023. The Citation File Format Contributors + +This work is licensed under a [Creative Commons Attribution 4.0 International (CC-BY-4.0)](https://creativecommons.org/licenses/by/4.0/legalcode) license. + +## Acknowledgments :pray: + +**We'd like to thank everyone who has contributed to the Citation File Format!** +They are listed in the [`CITATION.cff`](CITATION.cff) file for this repository. Please open an issue if you find that you are missing from the file. + +We gratefully acknowledge support from: + +- The [Institute for Software Technology](https://www.dlr.de/en/sc) of the [German Aerospace Center (DLR)](https://www.dlr.de/en/) +- The [Netherlands eScience Center](https://www.esciencecenter.nl) +- The [Software Sustainability Institute](https://software.ac.uk/) \ No newline at end of file diff --git a/src/somef_core/test/test_data/README-componentinstaller 2.md b/src/somef_core/test/test_data/README-componentinstaller 2.md new file mode 100644 index 0000000..376776d --- /dev/null +++ b/src/somef_core/test/test_data/README-componentinstaller 2.md @@ -0,0 +1,139 @@ + +# Component Installer for deploying PySSA +[](http://www.gnu.org/licenses/gpl-3.0) +[](https://GitHub.com/urban233/ComponentInstaller/graphs/commit-activity) +[](https://GitHub.com/urban233/ComponentInstaller/issues/) +[](https://GitHub.com/urban233/ComponentInstaller/graphs/contributors/) +[](https://github.com/urban233/ComponentInstaller/releases/) + +## Contents of this document +* [Description](#Description) +* [Contents of this repository](#Contents-of-this-repository) + * [Sources](#Sources) + * [Documentation](#Documentation) + * [Assets](#Assets) +* [Build](#Build) + * [Windows](#Windows) + * [Source code](#Source-code) +* [Dependencies](#Dependencies) +* [Citation](#Citation) +* [References and useful links](#References-and-useful-links) +* [Acknowledgements](#Acknowledgements) + +## Description +The Component Installer is a software tool designed for use as a component-based installer. +It is capable of addressing a range of deployment contexts that typically necessitate more +intricate configuration than is typically required in other scenarios. +The PySSA Installer serves as a case study demonstrating +the potential utility of the component-based installation methodology. + + +## Contents of this repository +### Sources +The repository comprises four distinct source code units. + +- _src/main/java_ + - The package contains the communicator class, which is utilized for communication with WindowsTasks.exe. +- _src/main/kotlin_ + - The package contains the main source code, including gui and model. +- _WindowsWrapper/WindowsCmdElevator_ + - The package contains the class to elevate a normal cmd shell with admin privileges. +- _WindowsWrapper/WindowsTasks_ + - The package contains the communicator, which facilitates communication with the Kotlin application, as well as a number of useful classes for the management of the MS Windows operating system. + +### Documentation +The "deployment" folder +contains a user guide as PDF file. +This [PDF file](https://github.com/urban233/ComponentInstaller/blob/v1.0.1/deployment/inno_setup/PySSA-Component-Installer-User-Guide.pdf) is also available through the help menu item within the PySSA Component Installer. +The user guide explains the installation and uninstallation of every component +as well as the update procedure for ColabFold and PySSA. Furthermore, +it contains a troubleshooting section for WSL2 and ColabFold. + +### Assets +The "assets" folder contains +all logos including the WSL2, ColabFold and PySSA logo, as well as the PySSA Component Installer logo. +If you are using PySSA Component Installer for your own projects, you are welcome to give credit to PySSA Component Installer by using the logo in your presentations, etc. + +## Build +The Component Installer consists of a Kotlin/Java project and a C# solution with two projects. + +### Windows +To deploy the installer on a Microsoft Windows OS (10 or 11), use the provided +inno setup script as a starting point. +Be aware that the inno setup compiler needs to be pre-installed! + +### Source code +The Kotlin/Java project is a Gradle project. +In order to use the source code for your own software or do your own Component Installer build, +download or clone the repository and open it in a Gradle-supporting IDE (e.g. IntelliJ) +as a Gradle project and execute the build.gradle file. +Gradle will then take care of installing all dependencies. +A Java Development Kit (JDK) of version 17 must also be pre-installed and +set as project JDK / project compiler. + +The C# solution contains the C# project WindowsCmdElevator and WindowsTasks. Both can be compiled to +an .exe file using the provided FolderProfile.pubxml files. + +## Dependencies +**Needs to be pre-installed:** +* Java Development Kit (JDK) version 17 + * [Adoptium Open JDK](https://adoptium.net/temurin/archive/?version=17) (as one possible source of the JDK) +* .NET 8.0 + * [Microsoft .NET 8.0](https://dotnet.microsoft.com/en-us/download/dotnet/8.0) + +**Managed by Gradle:** +* Java Native Access (JNA) version 5.8.0 + * [Java Native Access GitHub repository](https://github.com/java-native-access) + * [LGPL, version 2.1 or later, or (from version 4.0 onward) the Apache License, version 2.0](https://github.com/java-native-access/jna?tab=License-1-ov-file) +* JeroMQ version 0.6.0 + * [JeroMQ GitHub repository](https://github.com/zeromq/jeromq) + * Mozilla Public License Version 2.0 + +**Managed by NuGet:** +* NLog version 5.3.2 + * [NLog GitHub repository](https://github.com/NLog/NLog) + * BSD-3-Clause license +* NetMQ version 4.0.1.13 + * [NetMQ GitHub repository](https://github.com/zeromq/netmq/) + * GNU Lesser General Public License 3 + +## Citation +You can cite this software or this repository as it is defined in the CITATION.cff file. + +## References and useful links +**Windows Subsystem for Linux** +* [What is the Windows Subsystem for Linux? (Article)](https://learn.microsoft.com/en-us/windows/wsl/about) +* [How to install Linux on Windows with WSL (Article)](https://learn.microsoft.com/en-us/windows/wsl/install) + +**ZeroMQ** +* [ZeroMQ Homepage](https://zeromq.org/) + * [Java implementation (JeroMQ)](https://github.com/zeromq/jeromq) + * [C# implementation (NetMQ)](https://github.com/zeromq/netmq/) + +## Acknowledgements +**Developers:** +* Martin Urban +* Hannah Kullik + +**End-user testers:** +* Jonas Schaub +* Achim Zielesny + +**Logo:** +* Martin Urban +* Hannah Kullik + +**Initialization, conceptualization, and supervision:** +* Achim Zielesny and Angelika Loidl-Stahlhofen + +**The ComponentInstaller project team would like to thank +the communities behind the open software libraries for their amazing work.** + + diff --git a/src/somef_core/test/test_data/README-componentinstaller.md b/src/somef_core/test/test_data/README-componentinstaller.md new file mode 100644 index 0000000..376776d --- /dev/null +++ b/src/somef_core/test/test_data/README-componentinstaller.md @@ -0,0 +1,139 @@ + +# Component Installer for deploying PySSA +[](http://www.gnu.org/licenses/gpl-3.0) +[](https://GitHub.com/urban233/ComponentInstaller/graphs/commit-activity) +[](https://GitHub.com/urban233/ComponentInstaller/issues/) +[](https://GitHub.com/urban233/ComponentInstaller/graphs/contributors/) +[](https://github.com/urban233/ComponentInstaller/releases/) + +## Contents of this document +* [Description](#Description) +* [Contents of this repository](#Contents-of-this-repository) + * [Sources](#Sources) + * [Documentation](#Documentation) + * [Assets](#Assets) +* [Build](#Build) + * [Windows](#Windows) + * [Source code](#Source-code) +* [Dependencies](#Dependencies) +* [Citation](#Citation) +* [References and useful links](#References-and-useful-links) +* [Acknowledgements](#Acknowledgements) + +## Description +The Component Installer is a software tool designed for use as a component-based installer. +It is capable of addressing a range of deployment contexts that typically necessitate more +intricate configuration than is typically required in other scenarios. +The PySSA Installer serves as a case study demonstrating +the potential utility of the component-based installation methodology. + + +## Contents of this repository +### Sources +The repository comprises four distinct source code units. + +- _src/main/java_ + - The package contains the communicator class, which is utilized for communication with WindowsTasks.exe. +- _src/main/kotlin_ + - The package contains the main source code, including gui and model. +- _WindowsWrapper/WindowsCmdElevator_ + - The package contains the class to elevate a normal cmd shell with admin privileges. +- _WindowsWrapper/WindowsTasks_ + - The package contains the communicator, which facilitates communication with the Kotlin application, as well as a number of useful classes for the management of the MS Windows operating system. + +### Documentation +The "deployment" folder +contains a user guide as PDF file. +This [PDF file](https://github.com/urban233/ComponentInstaller/blob/v1.0.1/deployment/inno_setup/PySSA-Component-Installer-User-Guide.pdf) is also available through the help menu item within the PySSA Component Installer. +The user guide explains the installation and uninstallation of every component +as well as the update procedure for ColabFold and PySSA. Furthermore, +it contains a troubleshooting section for WSL2 and ColabFold. + +### Assets +The "assets" folder contains +all logos including the WSL2, ColabFold and PySSA logo, as well as the PySSA Component Installer logo. +If you are using PySSA Component Installer for your own projects, you are welcome to give credit to PySSA Component Installer by using the logo in your presentations, etc. + +## Build +The Component Installer consists of a Kotlin/Java project and a C# solution with two projects. + +### Windows +To deploy the installer on a Microsoft Windows OS (10 or 11), use the provided +inno setup script as a starting point. +Be aware that the inno setup compiler needs to be pre-installed! + +### Source code +The Kotlin/Java project is a Gradle project. +In order to use the source code for your own software or do your own Component Installer build, +download or clone the repository and open it in a Gradle-supporting IDE (e.g. IntelliJ) +as a Gradle project and execute the build.gradle file. +Gradle will then take care of installing all dependencies. +A Java Development Kit (JDK) of version 17 must also be pre-installed and +set as project JDK / project compiler. + +The C# solution contains the C# project WindowsCmdElevator and WindowsTasks. Both can be compiled to +an .exe file using the provided FolderProfile.pubxml files. + +## Dependencies +**Needs to be pre-installed:** +* Java Development Kit (JDK) version 17 + * [Adoptium Open JDK](https://adoptium.net/temurin/archive/?version=17) (as one possible source of the JDK) +* .NET 8.0 + * [Microsoft .NET 8.0](https://dotnet.microsoft.com/en-us/download/dotnet/8.0) + +**Managed by Gradle:** +* Java Native Access (JNA) version 5.8.0 + * [Java Native Access GitHub repository](https://github.com/java-native-access) + * [LGPL, version 2.1 or later, or (from version 4.0 onward) the Apache License, version 2.0](https://github.com/java-native-access/jna?tab=License-1-ov-file) +* JeroMQ version 0.6.0 + * [JeroMQ GitHub repository](https://github.com/zeromq/jeromq) + * Mozilla Public License Version 2.0 + +**Managed by NuGet:** +* NLog version 5.3.2 + * [NLog GitHub repository](https://github.com/NLog/NLog) + * BSD-3-Clause license +* NetMQ version 4.0.1.13 + * [NetMQ GitHub repository](https://github.com/zeromq/netmq/) + * GNU Lesser General Public License 3 + +## Citation +You can cite this software or this repository as it is defined in the CITATION.cff file. + +## References and useful links +**Windows Subsystem for Linux** +* [What is the Windows Subsystem for Linux? (Article)](https://learn.microsoft.com/en-us/windows/wsl/about) +* [How to install Linux on Windows with WSL (Article)](https://learn.microsoft.com/en-us/windows/wsl/install) + +**ZeroMQ** +* [ZeroMQ Homepage](https://zeromq.org/) + * [Java implementation (JeroMQ)](https://github.com/zeromq/jeromq) + * [C# implementation (NetMQ)](https://github.com/zeromq/netmq/) + +## Acknowledgements +**Developers:** +* Martin Urban +* Hannah Kullik + +**End-user testers:** +* Jonas Schaub +* Achim Zielesny + +**Logo:** +* Martin Urban +* Hannah Kullik + +**Initialization, conceptualization, and supervision:** +* Achim Zielesny and Angelika Loidl-Stahlhofen + +**The ComponentInstaller project team would like to thank +the communities behind the open software libraries for their amazing work.** + + diff --git a/src/somef_core/test/test_data/README-menty 2.md b/src/somef_core/test/test_data/README-menty 2.md new file mode 100644 index 0000000..8ac3d87 --- /dev/null +++ b/src/somef_core/test/test_data/README-menty 2.md @@ -0,0 +1,94 @@ +`__ in the ``sunpy`` documentation.
+This will walk you through installing ``sunpy`` and all of its dependencies.
+
+Usage
+=====
+
+If you are new to ``sunpy``, the best place to start is the `tutorial `__.
+the `example gallery `__ also includes a collection of shorter and more specific examples of using ``sunpy``.
+
+Changes
+=======
+
+See our `changelog `__. for the latest changes in ``sunpy``.
+
+Getting Help
+============
+
+For more information or to ask questions about ``sunpy`` or any other SunPy Project package, please check out:
+
+- `sunpy documentation `__
+- `SunPy Chat`_
+- `SunPy mailing list `__
+- `SunPy Community forum `__
+
+Acknowledging or Citing ``sunpy``
+=================================
+
+If you use ``sunpy`` in your scientific work, we would appreciate your `citing it in your publications `__.
+The continued growth and development of ``sunpy`` is dependent on the community being aware of ``sunpy``.
+
+Contributing
+============
+
+The SunPy Project is a community-driven open-source project that welcomes any and all contributions.
+Whether you are a developer, student, or user, you can help by contributing code, documentation, or community support.
+
+If you would like to get involved, the `Newcomers Guide`_ guide explains the many different ways to contribute to the SunPy Project and also shows how to get set up with a development workflow.
+
+Help is always welcome, so come and say hello by joining the `SunPy Chat`_ and look over the `Good First Issues list`_ for the ideal places to start.
+
+.. _Newcomers Guide: https://docs.sunpy.org/en/latest/dev_guide/contents/newcomers.html
+.. _Good First Issues list: https://github.com/sunpy/sunpy/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc+label%3A%22Good+First+Issue%22
+
+Usage of Generative AI
+======================
+
+We expect authentic engagement in our community.
+Be wary of posting output from Large Language Models or similar generative AI as comments on GitHub or any other platform, as such comments tend to be formulaic and low quality content.
+If you use generative AI tools as an aid in developing code or documentation changes, ensure that you fully understand the proposed changes and can explain why they are the correct approach and an improvement to the current state.
+
+Code of Conduct
+===============
+
+When you are interacting with the SunPy Community you are asked to follow our `Code of Conduct `__.
+
+.. _SunPy Chat: https://app.element.io/#/room/#sunpy:openastronomy.org
\ No newline at end of file
diff --git a/src/somef_core/test/test_data/README-sunpy.rst b/src/somef_core/test/test_data/README-sunpy.rst
new file mode 100644
index 0000000..75c6d1a
--- /dev/null
+++ b/src/somef_core/test/test_data/README-sunpy.rst
@@ -0,0 +1,115 @@
+*********
+``sunpy``
+*********
+|SunPy Logo|
+
++-----------------------------------+-----------------------------------+-----------------------------------+
+| Release | Development | Community |
++===================================+===================================+===================================+
+| |Latest PyPi Version| | |Python Versions| | |Matrix Chat Room| |
++-----------------------------------+-----------------------------------+-----------------------------------+
+| |Latest Conda Version| | |Project Status: Active| | |OpenAstronomy Discourse| |
++-----------------------------------+-----------------------------------+-----------------------------------+
+| |Zenodo - Latest DOI| | |Continuous Integration Status| | |Google Groups Mailing List| |
++-----------------------------------+-----------------------------------+-----------------------------------+
+| |sunpy stable documentation| | |CodeCov Code Coverage| | |Powered by NumFOCUS| |
++-----------------------------------+-----------------------------------+-----------------------------------+
+| |sunpy citation| | | |pyOpenSci| |
++-----------------------------------+-----------------------------------+-----------------------------------+
+
+.. |SunPy Logo| image:: https://raw.githubusercontent.com/sunpy/sunpy-logo/master/generated/sunpy_logo_landscape.png
+ :width: 200px
+.. |Latest PyPi Version| image:: https://img.shields.io/pypi/v/sunpy.svg
+ :target: https://pypi.python.org/pypi/sunpy/
+.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/sunpy
+ :target: https://pypi.python.org/pypi/sunpy/
+.. |Matrix Chat Room| image:: https://img.shields.io/matrix/sunpy:openastronomy.org.svg?colorB=%23FE7900&label=Chat&logo=matrix&server_fqdn=matrix.org
+ :target: https://app.element.io/#/room/#sunpy:openastronomy.org
+.. |Latest Conda Version| image:: https://anaconda.org/conda-forge/sunpy/badges/version.svg
+ :target: https://anaconda.org/conda-forge/sunpy
+.. |Project Status: Active| image:: https://www.repostatus.org/badges/latest/active.svg
+ :target: https://www.repostatus.org/#active
+.. |OpenAstronomy Discourse| image:: https://cdck-file-uploads-global.s3.dualstack.us-west-2.amazonaws.com/try2/original/1X/5e1e3b3cada2d7fbae4734d4bc53999933d71c95.svg
+ :height: 20px
+ :target: https://community.openastronomy.org/
+.. |Zenodo - Latest DOI| image:: https://zenodo.org/badge/2165383.svg
+ :target: https://zenodo.org/badge/latestdoi/2165383
+.. |Continuous Integration Status| image:: https://github.com/sunpy/sunpy/actions/workflows/ci.yml/badge.svg?branch=main
+ :target: https://github.com/sunpy/sunpy/actions/workflows/ci.yml
+.. |Google Groups Mailing List| image:: https://upload.wikimedia.org/wikipedia/commons/2/27/Google_Groups_logo.gif
+ :height: 20px
+ :target: https://groups.google.com/g/sunpy
+.. |sunpy stable documentation| image:: https://readthedocs.org/projects/sunpy/badge/?version=stable
+ :target: https://docs.sunpy.org/
+.. |CodeCov Code Coverage| image:: https://codecov.io/gh/sunpy/sunpy/branch/main/graph/badge.svg
+ :target: https://codecov.io/gh/sunpy/sunpy
+.. |Powered by NumFOCUS| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A
+ :target: https://numfocus.org
+.. |sunpy citation| image:: https://img.shields.io/badge/cite-sunpy-orange
+ :target: https://docs.sunpy.org/en/stable/citation.html
+.. |pyOpenSci| image:: https://tinyurl.com/y22nb8up
+ :target: https://github.com/pyOpenSci/software-submission/issues/147
+
+``sunpy`` is a Python software package that provides fundamental tools for accessing, loading and interacting with solar physics data in Python.
+It includes an interface for searching and downloading data from multiple data providers, data containers for image and time series data, commonly used solar coordinate frames and associated transformations, as well as other functionality needed for solar data analysis.
+
+Installation
+============
+
+We recommended following the `installation guide `__ in the ``sunpy`` documentation.
+This will walk you through installing ``sunpy`` and all of its dependencies.
+
+Usage
+=====
+
+If you are new to ``sunpy``, the best place to start is the `tutorial `__.
+the `example gallery `__ also includes a collection of shorter and more specific examples of using ``sunpy``.
+
+Changes
+=======
+
+See our `changelog `__. for the latest changes in ``sunpy``.
+
+Getting Help
+============
+
+For more information or to ask questions about ``sunpy`` or any other SunPy Project package, please check out:
+
+- `sunpy documentation `__
+- `SunPy Chat`_
+- `SunPy mailing list `__
+- `SunPy Community forum `__
+
+Acknowledging or Citing ``sunpy``
+=================================
+
+If you use ``sunpy`` in your scientific work, we would appreciate your `citing it in your publications `__.
+The continued growth and development of ``sunpy`` is dependent on the community being aware of ``sunpy``.
+
+Contributing
+============
+
+The SunPy Project is a community-driven open-source project that welcomes any and all contributions.
+Whether you are a developer, student, or user, you can help by contributing code, documentation, or community support.
+
+If you would like to get involved, the `Newcomers Guide`_ guide explains the many different ways to contribute to the SunPy Project and also shows how to get set up with a development workflow.
+
+Help is always welcome, so come and say hello by joining the `SunPy Chat`_ and look over the `Good First Issues list`_ for the ideal places to start.
+
+.. _Newcomers Guide: https://docs.sunpy.org/en/latest/dev_guide/contents/newcomers.html
+.. _Good First Issues list: https://github.com/sunpy/sunpy/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc+label%3A%22Good+First+Issue%22
+
+Usage of Generative AI
+======================
+
+We expect authentic engagement in our community.
+Be wary of posting output from Large Language Models or similar generative AI as comments on GitHub or any other platform, as such comments tend to be formulaic and low quality content.
+If you use generative AI tools as an aid in developing code or documentation changes, ensure that you fully understand the proposed changes and can explain why they are the correct approach and an improvement to the current state.
+
+Code of Conduct
+===============
+
+When you are interacting with the SunPy Community you are asked to follow our `Code of Conduct `__.
+
+.. _SunPy Chat: https://app.element.io/#/room/#sunpy:openastronomy.org
\ No newline at end of file
diff --git a/src/somef_core/test/test_data/README-unboundedsystems 2.md b/src/somef_core/test/test_data/README-unboundedsystems 2.md
new file mode 100644
index 0000000..7183625
--- /dev/null
+++ b/src/somef_core/test/test_data/README-unboundedsystems 2.md
@@ -0,0 +1,86 @@
+[](https://adaptjs.org)
+
+[](https://www.npmjs.com/package/@adpt/cli)
+[](https://gitter.im/UnboundedSystems/Adapt)
+[](https://opensource.org/licenses/Apache-2.0)
+
+# Adapt - ReactJS for your infrastructure.
+
+AdaptJS is a system to easily, reliably, and repeatably deploy your full-stack applications. Adapt specifications look like [React](https://reactjs.org) apps, but instead of rendering browser DOM elements like ``, or `
[🔍](./codemetajson.md)
| [📄](https://github.com/codemeta/codemeta/blob/master/crosswalk.csv)| [v3.0](https://w3id.org/codemeta/3.0)|[Example](https://github.com/codemeta/codemeta/blob/master/codemeta.json) |
+| `readme.me` | Markdown | Main documentation file of repository | [🔍](./readmefile.md)
| | |[Example](https://github.com/KnowledgeCaptureAndDiscovery/somef/blob/master/README.md) |
+| `composer.json` | PHP | Manifest file serves as the package descriptor used in PHP projects. | [🔍](./composer.md)
| [📄](https://getcomposer.org/doc/04-schema.md)| [2.8.12](https://getcomposer.org/changelog/2.8.12)|[Example](https://github.com/composer/composer/blob/main/composer.json) |
+| `juliaProject.toml` | Python | Defines the package metadata and dependencies for Julia projects, used by the Pkg package manager.| [🔍](./julia.md)
| [📄](https://docs.julialang.org/en/v1/)| |[Example](https://github.com/JuliaLang/TOML.jl/blob/master/Project.toml) |
+| `pyproject.toml` | Python | Modern Python project configuration file used by tools like Poetry and Flit | [🔍](./pyprojecttoml.md)
| [📄](https://packaging.python.org/en/latest/guides/writing-pyproject-toml/)| |[Example](https://github.com/KnowledgeCaptureAndDiscovery/somef/blob/master/pyproject.toml) |
+| `requirements.txt` | Python | Lists Python package dependencies | [🔍](./requirementstxt.md)
| [📄](https://pip.pypa.io/en/stable/reference/requirements-file-format/)| 25.2|[Example](https://github.com/oeg-upm/FAIR-Research-Object/blob/main/requirements.txt) |
+| `setup.py` | Python | Package file format used in python projects | [🔍](./setuppy.md)
| [📄](https://packaging.python.org/en/latest/guides/distributing-packages-using-setuptools/#setup-args)| |[Example](https://github.com/oeg-upm/soca/blob/main/setup.py) |
+| `DESCRIPTION` | R | Metadata file for R packages including title, author, and version | [🔍](./description.md)
| [📄](https://r-pkgs.org/description.html)| | [Example](https://github.com/cran/ggplot2/blob/master/DESCRIPTION) |
+| `*.gemspec` | Ruby | Manifest file serves as the package descriptor used in Ruby gem projects. | [🔍](./gemspec.md)
| [📄](https://guides.rubygems.org/specification-reference/)| |[Example](https://github.com/rubygems/rubygems/blob/master/bundler/bundler.gemspec) |
+| `cargo.toml` | Rust | Manifest file serves as the package descriptor used in Rust projects | [🔍](./cargo.md)
| [📄](https://doc.rust-lang.org/cargo/reference/manifest.html)| |[Example](https://github.com/rust-lang/cargo/blob/master/Cargo.toml) |
+| `*.cabal` | Haskell | Manifest file serving as the package descriptor for Haskell projects.| [🔍](./cabal.md)
| [📄](https://cabal.readthedocs.io/en/3.10/cabal-package.html)| |[Example](https://github.com/haskell/cabal/blob/master/Cabal/Cabal.cabal) |
+| `dockerfile` | Dockerfile | Build specification file for container images that can include software metadata via LABEL instructions (OCI specification).| [🔍](./dockerfiledoc.md)
| [📄](https://docs.docker.com/reference/dockerfile/)| |[Example](https://github.com/FairwindsOps/nova/blob/master/Dockerfile) |
+| `publiccode.yml` | YAML | YAML metadata file for public sector software projects| [🔍](./publiccode.md)
| [📄](https://yml.publiccode.tools//)| |[Example](https://github.com/maykinmedia/objects-api/blob/master/publiccode.yaml) |
+
+> **Note:** The general principles behind metadata mapping in SOMEF are based on the [CodeMeta crosswalk](https://github.com/codemeta/codemeta/blob/master/crosswalk.csv) and the [CodeMeta JSON-LD context](https://github.com/codemeta/codemeta/blob/master/codemeta.jsonld).
+> However, each supported file type may have specific characteristics and field interpretations.
+
+
+
+
+## Types of metadata in SOMEF
+
+| Type | Metadata Category |
+|----------------------|---------------------------|
+| Agent | authors |
+| Keywords | keywords |
+| License | license |
+| Release | version |
+| Software_application | requirements |
+| String | description |
+| String | name |
+| String | package_id |
+| String | runtime_platform |
+| Url | has_package_file |
+| Url | homepage |
+| Url | issue_tracker |
+| Url | package_distribution |
+
+
+## Example: Dependency Metadata Extraction from Configuration Files
+
+SOMEF parses configuration files like `pom.xml` to extract **structured metadata** about software dependencies and other requirements.
+
+---
+
+### Source File: Snippet from `Widoco/pom.xml`
+
+Below is the XML fragment for the Maven dependency that is being parsed:
+
+```xml
+
+
+[_(EUV imagery of the solar disk, taken by NASA SDO)_](https://www.nist.gov/image/1280px-sun-august12010jpg)
+
+# Overview
+`EUVpy` is a Python module that contains the NEUVAC empirical model of solar EUV irradiance for use primarily in thermosphere-ionosphere models.
+Conceptual development was carried out by Dr. Aaron J. Ridley and analysis and contributions were made by Dr. Daniel A. Brandt and Dr. Joseph Paki.
+
+`EUVpy` also contains code for running, comparing, and analyzing the performance of NEUVAC in comparison to other
+empirical models such as EUVAC, HEUVAC, HFG, and FISM2. As such, the package includes access to EUVAC, HEUVAC, and HFG,
+and allows the user to download the F10.7 index at will.
+
+# Installation
+
+You can obtain `EUVpy` with a simple git clone command. In the terminal, execute the following command:
+
+> git clone https://github.com/DanBrandt/EUVpy.git
+
+The EUVpy package provides access to the HEUVAC model, which is written in Fortran and requires gfortran to be installed. To
+install gfortran (if you don't already have it), open a terminal and execute the following command:
+
+> sudo apt-get install gfortran
+
+Now, enter into the package folder and run the following command in order to compile the Fortran code that HEUVAC
+alone depends upon:
+
+> cd EUVpy\
+> . install_heuvac.sh
+
+If this step gives you trouble, try executing the following code **first**, and then retry the above commands.
+
+> git submodule update --init --recursive --remote
+
+After HEUVAC is compiled once, you should never have to compile it again.
+
+Now you are in a position to install the rest of the EUVpy package. Before doing this, you will first want to initialize a Python virtual environment.
+
+> cd ~/.virtualenvs\
+> python**3.x** -m venv myVenv\
+> pip install --upgrade pip\
+> pip install wheel\
+> source myVenv/bin/activate
+
+Above, 'python**3.x**' refers to whatever version of Python 3 you have installed. EUVpy works with any version of Python 3.
+You may now use one of two ways to install EUVpy. You can install from the cloned repo directly, or you can install from PyPI.
+
+## Installing from the Cloned Repository
+
+Navigate back to the package folder:
+
+> cd\
+> cd myDirectory/EUVpy
+
+After this is done, simply execute the following command:
+
+> pip install .
+
+## Installing from PyPI
+
+A simpler way to install also involves just entering the following in the terminal:
+
+> pip install EUVpy
+
+**Note:** If you choose this route, you'll have to install HEUVAC differently than described above. You will have to
+navigate the directory containing the HEUVAC files, and execute the following command, as follows:
+
+> cd src/EUVpy/empiricalModels/models/HEUVAC/srcHEUVAC
+> . compile.sh
+
+You can then return to the top package directory. This should only have to be done once.
+This approach will be replaced with a user-friendly console script in the next release of this package.
+
+### Unit Testing
+
+**Note: this section only applies if you installed from the cloned repo.**
+
+Just to make sure everything installed correctly, while in the package folder, run the following command in the terminal.
+
+> pytest
+
+If all of the tests pass, you should be good to go! If you find an issue at this step (or any other) please don't hesitate
+to reach out!
+
+# Usage
+EUVpy contains modules for **4** different EUV irradiance models. These models include:
+* NEUVAC
+* EUVAC
+* HEUVAC
+* HFG (SOLOMON)
+
+We note that SOLOMON in the literature can either refer to the empirical model between F10.7 and 81 day-averaged F10.7
+centered on the current day (hereafter F10.7A) and EUV irradiance in 22 overlapping bands as described by Solomon and
+Qian 2005, or it can refer to _any_ EUV irradiance data summed into those 22 overlapping bins (referred to as the STAN
+BANDS). In this package, SOLOMON only refers to the former, though functionality does exist to run all other models in
+the STAN BANDS.
+
+## Finding your way around
+
+There are few folders in this package:
+* **empiricalModels**: Contains code and data for EUVAC, HEUVAC, and SOLOMON, as well as FISM:
+* **experiments**: Contains code and figures related to the publication associated with NEUVAC. In this folder, the file
+_fitNeuvac.py_ s used for actually performing the NEUVAC fits between F10.7, F10.7A, and FISM2, while _uncNeuvac.py_
+contains code for computing the correlation matrix used to enable running NEUVAC ensembles, as well as generating plots
+of the squared difference between NEUVAC and FISM2 in different bands.
+* **NEUVAC**: Contains the code for running NEUVAC.
+* **solarIndices**: Contains F10.7 solar index data, from both OMNIWeb and Penticton.
+* **tools**: Contains code for miscellaneous helper functions. In this folder appears the following:
+ * _EUV_: Contains numerous functions within fism2_process.py for reading in and rebinning FISM2 data.
+ * _processIndices.py_: Contains functions for reading in, downloading, and cleaning OMNIWeb data.
+ * _processIrradiances.py_: Contains functions for reading in data from TIMED/SEE, SDO/EVE, and FISM.
+ * _spectralAnalysis.py_: Contains functions for converting between solar spectral irradiance and solar spectral flux.
+ * _toolbox.py_: Contains miscellaneous helper functions that mainly focus on directory management, loading and saving data, statistics, and fitting.
+
+Each of the models in EUVpy requires F10.7 as an input. To grab F10.7 between any two dates, simply do the following:
+
+> from EUVpy.tools import processIndices
+>
+> f107times, f107, f107a, f107b = processIndices.getCLSF107('YYYY-MM-DD', 'YYYY-MM-DD', truncate=False)
+
+To import any of the models, simply do as follows:
+
+NEUVAC
+> from EUVpy.NEUVAC import neuvac
+>
+> neuvacIrr, _, _, _ = neuvac.neuvacEUV(f107, f107b, bands='EUVAC')
+
+EUVAC
+> from EUVpy.empiricalModels.models.EUVAC import euvac
+>
+> euvacFlux, euvacIrr, _, _, _ = euvac.euvac(f107, f107a)
+
+HEUVAC
+> from EUVpy.empiricalModels.models.HEUVAC import heuvac
+>
+> heuvac_wav, heuvacFlux, heuvacIrr, _, _, _ = heuvac.heuvac(f107, f107a, torr=True)
+
+SOLOMON
+> from EUVpy.empiricalModels.models.SOLOMON import solomon
+>
+> solomonFluxHFG, solomonIrrHFG = SOLOMON.solomon.solomon(f107, f107a, model='HFG')
+>
+> solomonFluxEUVAC, solomonIrrEUVAC = SOLOMON.solomon.solomon(f107, f107a, model='EUVAC')
+
+# Examples
+
+There is a [Python notebook](https://github.com/DanBrandt/EUVpy/blob/main/examples/euvpy_examples.ipynb) you can walk through in order to get familiar with the basic functionality of EUVpy.
+
+We encourage you to peruse [more examples](https://github.com/DanBrandt/EUVpy/blob/main/docs/source/examples.rst) in the documentation for guidelines on how to run each of the models.
+
+Due to the unique construction of NEUVAC, at present, we only recommend running ensembles for NEUVAC, and not any of the
+other models.
+
+# Code of Conduct
+In using this code, depending on the module used, proper citations should be given to the original authors responsible
+for developing each model or dataset:
+
+NEUVAC: [Brandt and Ridley, 2024](https://agupubs.onlinelibrary.wiley.com/doi/pdfdirect/10.1029/2024SW004043)
+
+EUVAC: [Richards, et al. 1994](https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/94ja00518)
+
+HEUVAC [Richards, et al. 2006](https://www.sciencedirect.com/science/article/pii/S0273117705008288?casa_token=zEhwbyXrC8MAAAAA:qHFmKe0ZDE4gMsAX9qAHESvPyoEDFLBlhHuLaEsIwYFykhFXN79--XttCW-QDg1sA4wgD54ysFc)
+
+SOLOMON [Solomon and Qian, 2005](https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2005JA011160)
+
+FISM2: [Chamberlin, et al. 2020](https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020SW002588)
diff --git a/src/somef_core/test/test_data/README-EUVpy.md b/src/somef_core/test/test_data/README-EUVpy.md
new file mode 100644
index 0000000..26c2756
--- /dev/null
+++ b/src/somef_core/test/test_data/README-EUVpy.md
@@ -0,0 +1,166 @@
+
+
+
+[_(EUV imagery of the solar disk, taken by NASA SDO)_](https://www.nist.gov/image/1280px-sun-august12010jpg)
+
+# Overview
+`EUVpy` is a Python module that contains the NEUVAC empirical model of solar EUV irradiance for use primarily in thermosphere-ionosphere models.
+Conceptual development was carried out by Dr. Aaron J. Ridley and analysis and contributions were made by Dr. Daniel A. Brandt and Dr. Joseph Paki.
+
+`EUVpy` also contains code for running, comparing, and analyzing the performance of NEUVAC in comparison to other
+empirical models such as EUVAC, HEUVAC, HFG, and FISM2. As such, the package includes access to EUVAC, HEUVAC, and HFG,
+and allows the user to download the F10.7 index at will.
+
+# Installation
+
+You can obtain `EUVpy` with a simple git clone command. In the terminal, execute the following command:
+
+> git clone https://github.com/DanBrandt/EUVpy.git
+
+The EUVpy package provides access to the HEUVAC model, which is written in Fortran and requires gfortran to be installed. To
+install gfortran (if you don't already have it), open a terminal and execute the following command:
+
+> sudo apt-get install gfortran
+
+Now, enter into the package folder and run the following command in order to compile the Fortran code that HEUVAC
+alone depends upon:
+
+> cd EUVpy\
+> . install_heuvac.sh
+
+If this step gives you trouble, try executing the following code **first**, and then retry the above commands.
+
+> git submodule update --init --recursive --remote
+
+After HEUVAC is compiled once, you should never have to compile it again.
+
+Now you are in a position to install the rest of the EUVpy package. Before doing this, you will first want to initialize a Python virtual environment.
+
+> cd ~/.virtualenvs\
+> python**3.x** -m venv myVenv\
+> pip install --upgrade pip\
+> pip install wheel\
+> source myVenv/bin/activate
+
+Above, 'python**3.x**' refers to whatever version of Python 3 you have installed. EUVpy works with any version of Python 3.
+You may now use one of two ways to install EUVpy. You can install from the cloned repo directly, or you can install from PyPI.
+
+## Installing from the Cloned Repository
+
+Navigate back to the package folder:
+
+> cd\
+> cd myDirectory/EUVpy
+
+After this is done, simply execute the following command:
+
+> pip install .
+
+## Installing from PyPI
+
+A simpler way to install also involves just entering the following in the terminal:
+
+> pip install EUVpy
+
+**Note:** If you choose this route, you'll have to install HEUVAC differently than described above. You will have to
+navigate the directory containing the HEUVAC files, and execute the following command, as follows:
+
+> cd src/EUVpy/empiricalModels/models/HEUVAC/srcHEUVAC
+> . compile.sh
+
+You can then return to the top package directory. This should only have to be done once.
+This approach will be replaced with a user-friendly console script in the next release of this package.
+
+### Unit Testing
+
+**Note: this section only applies if you installed from the cloned repo.**
+
+Just to make sure everything installed correctly, while in the package folder, run the following command in the terminal.
+
+> pytest
+
+If all of the tests pass, you should be good to go! If you find an issue at this step (or any other) please don't hesitate
+to reach out!
+
+# Usage
+EUVpy contains modules for **4** different EUV irradiance models. These models include:
+* NEUVAC
+* EUVAC
+* HEUVAC
+* HFG (SOLOMON)
+
+We note that SOLOMON in the literature can either refer to the empirical model between F10.7 and 81 day-averaged F10.7
+centered on the current day (hereafter F10.7A) and EUV irradiance in 22 overlapping bands as described by Solomon and
+Qian 2005, or it can refer to _any_ EUV irradiance data summed into those 22 overlapping bins (referred to as the STAN
+BANDS). In this package, SOLOMON only refers to the former, though functionality does exist to run all other models in
+the STAN BANDS.
+
+## Finding your way around
+
+There are few folders in this package:
+* **empiricalModels**: Contains code and data for EUVAC, HEUVAC, and SOLOMON, as well as FISM:
+* **experiments**: Contains code and figures related to the publication associated with NEUVAC. In this folder, the file
+_fitNeuvac.py_ s used for actually performing the NEUVAC fits between F10.7, F10.7A, and FISM2, while _uncNeuvac.py_
+contains code for computing the correlation matrix used to enable running NEUVAC ensembles, as well as generating plots
+of the squared difference between NEUVAC and FISM2 in different bands.
+* **NEUVAC**: Contains the code for running NEUVAC.
+* **solarIndices**: Contains F10.7 solar index data, from both OMNIWeb and Penticton.
+* **tools**: Contains code for miscellaneous helper functions. In this folder appears the following:
+ * _EUV_: Contains numerous functions within fism2_process.py for reading in and rebinning FISM2 data.
+ * _processIndices.py_: Contains functions for reading in, downloading, and cleaning OMNIWeb data.
+ * _processIrradiances.py_: Contains functions for reading in data from TIMED/SEE, SDO/EVE, and FISM.
+ * _spectralAnalysis.py_: Contains functions for converting between solar spectral irradiance and solar spectral flux.
+ * _toolbox.py_: Contains miscellaneous helper functions that mainly focus on directory management, loading and saving data, statistics, and fitting.
+
+Each of the models in EUVpy requires F10.7 as an input. To grab F10.7 between any two dates, simply do the following:
+
+> from EUVpy.tools import processIndices
+>
+> f107times, f107, f107a, f107b = processIndices.getCLSF107('YYYY-MM-DD', 'YYYY-MM-DD', truncate=False)
+
+To import any of the models, simply do as follows:
+
+NEUVAC
+> from EUVpy.NEUVAC import neuvac
+>
+> neuvacIrr, _, _, _ = neuvac.neuvacEUV(f107, f107b, bands='EUVAC')
+
+EUVAC
+> from EUVpy.empiricalModels.models.EUVAC import euvac
+>
+> euvacFlux, euvacIrr, _, _, _ = euvac.euvac(f107, f107a)
+
+HEUVAC
+> from EUVpy.empiricalModels.models.HEUVAC import heuvac
+>
+> heuvac_wav, heuvacFlux, heuvacIrr, _, _, _ = heuvac.heuvac(f107, f107a, torr=True)
+
+SOLOMON
+> from EUVpy.empiricalModels.models.SOLOMON import solomon
+>
+> solomonFluxHFG, solomonIrrHFG = SOLOMON.solomon.solomon(f107, f107a, model='HFG')
+>
+> solomonFluxEUVAC, solomonIrrEUVAC = SOLOMON.solomon.solomon(f107, f107a, model='EUVAC')
+
+# Examples
+
+There is a [Python notebook](https://github.com/DanBrandt/EUVpy/blob/main/examples/euvpy_examples.ipynb) you can walk through in order to get familiar with the basic functionality of EUVpy.
+
+We encourage you to peruse [more examples](https://github.com/DanBrandt/EUVpy/blob/main/docs/source/examples.rst) in the documentation for guidelines on how to run each of the models.
+
+Due to the unique construction of NEUVAC, at present, we only recommend running ensembles for NEUVAC, and not any of the
+other models.
+
+# Code of Conduct
+In using this code, depending on the module used, proper citations should be given to the original authors responsible
+for developing each model or dataset:
+
+NEUVAC: [Brandt and Ridley, 2024](https://agupubs.onlinelibrary.wiley.com/doi/pdfdirect/10.1029/2024SW004043)
+
+EUVAC: [Richards, et al. 1994](https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/94ja00518)
+
+HEUVAC [Richards, et al. 2006](https://www.sciencedirect.com/science/article/pii/S0273117705008288?casa_token=zEhwbyXrC8MAAAAA:qHFmKe0ZDE4gMsAX9qAHESvPyoEDFLBlhHuLaEsIwYFykhFXN79--XttCW-QDg1sA4wgD54ysFc)
+
+SOLOMON [Solomon and Qian, 2005](https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2005JA011160)
+
+FISM2: [Chamberlin, et al. 2020](https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020SW002588)
diff --git a/src/somef_core/test/test_data/README-citation-file-format 2.md b/src/somef_core/test/test_data/README-citation-file-format 2.md
new file mode 100644
index 0000000..1f5e486
--- /dev/null
+++ b/src/somef_core/test/test_data/README-citation-file-format 2.md
@@ -0,0 +1,158 @@
+# Citation File Format
+
+[](https://github.com/citation-file-format/citation-file-format/actions/workflows/testing.yml?query=branch%3Amain)
+[](https://doi.org/10.5281/zenodo.1003149)
+[](https://creativecommons.org/licenses/by/4.0/)
+[](https://citation-file-format.github.io)
+
+The Citation File Format lets you provide citation metadata for software or datasets
+in plaintext files that are easy to read by both humans and machines.
+
+## Structure
+
+You can specify citation metadata for your software (or dataset) in a file named `CITATION.cff`.
+This is what a typical `CITATION.cff` file may look like for research software:
+
+```yaml
+cff-version: 1.2.0
+message: If you use this software, please cite it using these metadata.
+title: My Research Software
+abstract: This is my awesome research software. It does many things.
+authors:
+ - family-names: Druskat
+ given-names: Stephan
+ orcid: "https://orcid.org/1234-5678-9101-1121"
+ - name: "The Research Software project"
+version: 0.11.2
+date-released: "2021-07-18"
+identifiers:
+ - description: This is the collection of archived snapshots of all versions of My Research Software
+ type: doi
+ value: "10.5281/zenodo.123456"
+ - description: This is the archived snapshot of version 0.11.2 of My Research Software
+ type: doi
+ value: "10.5281/zenodo.123457"
+license: Apache-2.0
+repository-code: "https://github.com/citation-file-format/my-research-software"
+```
+
+In addition, the Citation File Format allows you to
+
+- provide references to works that your software or dataset builds on ([see here for more info](schema-guide.md#referencing-other-work));
+- ask people to cite a different, related work instead of the software or dataset itself ([see here for more info](schema-guide.md#credit-redirection)).
+
+## Format specifications :books:
+
+**You can find the complete format specifications in the [Guide to the Citation File Format schema](schema-guide.md).**
+
+## Why should I add a `CITATION.cff` file to my repository? :bulb:
+
+When you do this, great things may happen:
+
+1. Users of your software can easily cite it using the metadata from `CITATION.cff`!
+2. If your repository is hosted on GitHub, they will [show the citation information in the sidebar](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files), which makes it easy for visitors to cite your software or dataset correctly.
+3. When you publish your software on Zenodo via the [GitHub-Zenodo integration](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content), they will use the metadata from your `CITATION.cff` file.
+4. People can import the correct reference to your software into the [Zotero](https://www.zotero.org) reference manager via a [browser plugin](https://www.zotero.org/download/).
+
+## Creation :heavy_plus_sign:
+
+To create a `CITATION.cff` file, you can
+
+- use the [**cffinit** website](https://citation-file-format.github.io/cff-initializer-javascript/#/),
+- copy and paste the [example snippet](#structure), and adapt it to your needs, or
+- create a new file called `CITATION.cff` using the *Add file* button on GitHub, and use the template they provide.
+
+## Validation :heavy_check_mark:
+
+You can validate your `CITATION.cff` file on the command line with the [`cffconvert` Python package](https://pypi.org/project/cffconvert/):
+
+```shell
+# Install cffconvert with pip in user space
+python3 -m pip install --user cffconvert
+
+# Validate your CFF file
+cffconvert --validate
+```
+
+If you get a Traceback with error messages, look for the relevant validation error and fix it.
+If the output is very long, it may help if you search it for lines starting with `jsonschema.exceptions.ValidationError`.
+
+If you prefer to use Docker, you can use the [`cffconvert` Docker image](https://hub.docker.com/r/citationcff/cffconvert):
+
+```bash
+cd • [bibtex-to-cff](https://github.com/monperrus/bibtexbrowser/)
• [cff-from-621](https://pypi.org/project/cff-from-621/)
• [openCARP-CI](https://git.opencarp.org/openCARP/openCARP-CI/-/tree/master/#create_cff) | +| GitHub Actions | | | [cff-validator](https://github.com/marketplace/actions/cff-validator) | • [cffconvert](https://github.com/marketplace/actions/cffconvert)
• [codemeta2cff](https://github.com/caltechlibrary/codemeta2cff) | +| GitHub Bot | | | [#238](https://github.com/citation-file-format/citation-file-format/issues/238) | | +| Docker | | | [cffconvert Docker image](#validation-heavy_check_mark) | [cffconvert Docker image](https://hub.docker.com/r/citationcff/cffconvert) | +| Go | | | | • [datatools/codemeta2cff](https://github.com/caltechlibrary/datatools/) | +| Haskell | | • [cffreference](https://github.com/kevinmatthes/cffreference) | | | +| Java | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | +| JavaScript | | | | • [Citation.js](https://citation.js.org/) [plugin](https://www.npmjs.com/package/@citation-js/plugin-software-formats) | +| Julia | | | • [Bibliography.jl](https://github.com/Humans-of-Julia/Bibliography.jl) | • [Bibliography.jl](https://github.com/Humans-of-Julia/Bibliography.jl) | +| PHP | | | | • [bibtex-to-cff](https://github.com/monperrus/bibtexbrowser/) | +| Python | | • [cff2toml](https://github.com/willynilly/cff2toml)
• [doi2cff](https://github.com/citation-file-format/doi2cff)
• [updateCitation](https://github.com/hunterhogan/updateCitation) | • [cffconvert](#validation-heavy_check_mark) | • [cff-from-621](https://pypi.org/project/cff-from-621/)
• [cff2toml](https://github.com/willynilly/cff2toml)
• [cffconvert](https://github.com/citation-file-format/cff-converter-python)
• [doi2cff](https://github.com/citation-file-format/doi2cff)
• [openCARP-CI](https://git.opencarp.org/openCARP/openCARP-CI/-/tree/master/#create_cff)
• [py_bibtex_to_cff_converter](https://github.com/vdplasthijs/py_bibtex_to_cff_converter) | +| R | | | • [cffr](https://CRAN.R-project.org/package=cffr) | • [citation](https://cran.r-project.org/web/packages/citation/)
• [r2cff](https://github.com/ocbe-uio/RCFF)
• [handlr](https://github.com/ropensci/handlr)
• [cffr](https://CRAN.R-project.org/package=cffr) | +| Ruby | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | +| Rust | • [Aeruginous](https://github.com/kevinmatthes/aeruginous-rs) | • [Aeruginous](https://github.com/kevinmatthes/aeruginous-rs) | | • [citeworks](https://github.com/passcod/citeworks) | +| TypeScript | | | | [#28](https://github.com/citation-file-format/citation-file-format/issues/28#issuecomment-892105342) | +| Website | • [cffinit](https://citation-file-format.github.io/cff-initializer-javascript/) | | | | + +## Maintainers :nerd_face: + +The Citation File Format schema is maintained by + +- Stephan Druskat ([@sdruskat](https://github.com/sdruskat/)) +- Jurriaan H. Spaaks ([@jspaaks](https://github.com/jspaaks/)) + +## Contributing :handshake: + +The Citation File Format is a collaborative project and we welcome suggestions and contributions. We hope one of the invitations below works for you, but if not, please let us know! + +:running: **I'm busy, I only have 1 minute** +- Tell a friend about the Citation File Format, or tweet about it! +- Give the project a star :star:! + +:hourglass_flowing_sand: **I've got 10 minutes - tell me what I should do** +- Create a `CITATION.cff` file for your repository. +- Suggest ideas for how you would like to use the Citation File Format, or for an improvement to the format or its tooling. +- If you know how to validate `CITATION.cff` files, help someone with a validation problem and look at the [issues labeled ](https://github.com/citation-file-format/citation-file-format/issues?q=is%3Aopen+is%3Aissue+label%3A%22help+wanted%22+label%3Avalidation) + +:computer: **I've got a few hours to work on this** +- Help create tooling for the community by looking at the [issues labeled ](https://github.com/citation-file-format/citation-file-format/issues?q=is%3Aopen+is%3Aissue+label%3A%22help+wanted%22+label%3Atooling) + +:tada: **I want to help grow the community** +- Write a blog post or news item for your own community. +- Organise a hack event or workshop to help others use or improve the Citation File Format. + +Please read the more detailed [contributing guidelines](CONTRIBUTING.md) and [open a GitHub issue](https://github.com/citation-file-format/citation-file-format/issues) to suggest a new idea or let us know about bugs. Please put up pull requests for changes to the format and schema against the `develop` branch! + +## License :balance_scale: + +Copyright © 2016 - 2023. The Citation File Format Contributors + +This work is licensed under a [Creative Commons Attribution 4.0 International (CC-BY-4.0)](https://creativecommons.org/licenses/by/4.0/legalcode) license. + +## Acknowledgments :pray: + +**We'd like to thank everyone who has contributed to the Citation File Format!** +They are listed in the [`CITATION.cff`](CITATION.cff) file for this repository. Please open an issue if you find that you are missing from the file. + +We gratefully acknowledge support from: + +- The [Institute for Software Technology](https://www.dlr.de/en/sc) of the [German Aerospace Center (DLR)](https://www.dlr.de/en/) +- The [Netherlands eScience Center](https://www.esciencecenter.nl) +- The [Software Sustainability Institute](https://software.ac.uk/) \ No newline at end of file diff --git a/src/somef_core/test/test_data/README-citation-file-format.md b/src/somef_core/test/test_data/README-citation-file-format.md new file mode 100644 index 0000000..1f5e486 --- /dev/null +++ b/src/somef_core/test/test_data/README-citation-file-format.md @@ -0,0 +1,158 @@ +# Citation File Format + +[](https://github.com/citation-file-format/citation-file-format/actions/workflows/testing.yml?query=branch%3Amain) +[](https://doi.org/10.5281/zenodo.1003149) +[](https://creativecommons.org/licenses/by/4.0/) +[](https://citation-file-format.github.io) + +The Citation File Format lets you provide citation metadata for software or datasets +in plaintext files that are easy to read by both humans and machines. + +## Structure + +You can specify citation metadata for your software (or dataset) in a file named `CITATION.cff`. +This is what a typical `CITATION.cff` file may look like for research software: + +```yaml +cff-version: 1.2.0 +message: If you use this software, please cite it using these metadata. +title: My Research Software +abstract: This is my awesome research software. It does many things. +authors: + - family-names: Druskat + given-names: Stephan + orcid: "https://orcid.org/1234-5678-9101-1121" + - name: "The Research Software project" +version: 0.11.2 +date-released: "2021-07-18" +identifiers: + - description: This is the collection of archived snapshots of all versions of My Research Software + type: doi + value: "10.5281/zenodo.123456" + - description: This is the archived snapshot of version 0.11.2 of My Research Software + type: doi + value: "10.5281/zenodo.123457" +license: Apache-2.0 +repository-code: "https://github.com/citation-file-format/my-research-software" +``` + +In addition, the Citation File Format allows you to + +- provide references to works that your software or dataset builds on ([see here for more info](schema-guide.md#referencing-other-work)); +- ask people to cite a different, related work instead of the software or dataset itself ([see here for more info](schema-guide.md#credit-redirection)). + +## Format specifications :books: + +**You can find the complete format specifications in the [Guide to the Citation File Format schema](schema-guide.md).** + +## Why should I add a `CITATION.cff` file to my repository? :bulb: + +When you do this, great things may happen: + +1. Users of your software can easily cite it using the metadata from `CITATION.cff`! +2. If your repository is hosted on GitHub, they will [show the citation information in the sidebar](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files), which makes it easy for visitors to cite your software or dataset correctly. +3. When you publish your software on Zenodo via the [GitHub-Zenodo integration](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content), they will use the metadata from your `CITATION.cff` file. +4. People can import the correct reference to your software into the [Zotero](https://www.zotero.org) reference manager via a [browser plugin](https://www.zotero.org/download/). + +## Creation :heavy_plus_sign: + +To create a `CITATION.cff` file, you can + +- use the [**cffinit** website](https://citation-file-format.github.io/cff-initializer-javascript/#/), +- copy and paste the [example snippet](#structure), and adapt it to your needs, or +- create a new file called `CITATION.cff` using the *Add file* button on GitHub, and use the template they provide. + +## Validation :heavy_check_mark: + +You can validate your `CITATION.cff` file on the command line with the [`cffconvert` Python package](https://pypi.org/project/cffconvert/): + +```shell +# Install cffconvert with pip in user space +python3 -m pip install --user cffconvert + +# Validate your CFF file +cffconvert --validate +``` + +If you get a Traceback with error messages, look for the relevant validation error and fix it. +If the output is very long, it may help if you search it for lines starting with `jsonschema.exceptions.ValidationError`. + +If you prefer to use Docker, you can use the [`cffconvert` Docker image](https://hub.docker.com/r/citationcff/cffconvert): + +```bash +cd
• [bibtex-to-cff](https://github.com/monperrus/bibtexbrowser/)
• [cff-from-621](https://pypi.org/project/cff-from-621/)
• [openCARP-CI](https://git.opencarp.org/openCARP/openCARP-CI/-/tree/master/#create_cff) | +| GitHub Actions | | | [cff-validator](https://github.com/marketplace/actions/cff-validator) | • [cffconvert](https://github.com/marketplace/actions/cffconvert)
• [codemeta2cff](https://github.com/caltechlibrary/codemeta2cff) | +| GitHub Bot | | | [#238](https://github.com/citation-file-format/citation-file-format/issues/238) | | +| Docker | | | [cffconvert Docker image](#validation-heavy_check_mark) | [cffconvert Docker image](https://hub.docker.com/r/citationcff/cffconvert) | +| Go | | | | • [datatools/codemeta2cff](https://github.com/caltechlibrary/datatools/) | +| Haskell | | • [cffreference](https://github.com/kevinmatthes/cffreference) | | | +| Java | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | | • [CFF Maven plugin](https://github.com/hexatomic/cff-maven-plugin) | +| JavaScript | | | | • [Citation.js](https://citation.js.org/) [plugin](https://www.npmjs.com/package/@citation-js/plugin-software-formats) | +| Julia | | | • [Bibliography.jl](https://github.com/Humans-of-Julia/Bibliography.jl) | • [Bibliography.jl](https://github.com/Humans-of-Julia/Bibliography.jl) | +| PHP | | | | • [bibtex-to-cff](https://github.com/monperrus/bibtexbrowser/) | +| Python | | • [cff2toml](https://github.com/willynilly/cff2toml)
• [doi2cff](https://github.com/citation-file-format/doi2cff)
• [updateCitation](https://github.com/hunterhogan/updateCitation) | • [cffconvert](#validation-heavy_check_mark) | • [cff-from-621](https://pypi.org/project/cff-from-621/)
• [cff2toml](https://github.com/willynilly/cff2toml)
• [cffconvert](https://github.com/citation-file-format/cff-converter-python)
• [doi2cff](https://github.com/citation-file-format/doi2cff)
• [openCARP-CI](https://git.opencarp.org/openCARP/openCARP-CI/-/tree/master/#create_cff)
• [py_bibtex_to_cff_converter](https://github.com/vdplasthijs/py_bibtex_to_cff_converter) | +| R | | | • [cffr](https://CRAN.R-project.org/package=cffr) | • [citation](https://cran.r-project.org/web/packages/citation/)
• [r2cff](https://github.com/ocbe-uio/RCFF)
• [handlr](https://github.com/ropensci/handlr)
• [cffr](https://CRAN.R-project.org/package=cffr) | +| Ruby | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | • [ruby-cff](https://github.com/citation-file-format/ruby-cff) | +| Rust | • [Aeruginous](https://github.com/kevinmatthes/aeruginous-rs) | • [Aeruginous](https://github.com/kevinmatthes/aeruginous-rs) | | • [citeworks](https://github.com/passcod/citeworks) | +| TypeScript | | | | [#28](https://github.com/citation-file-format/citation-file-format/issues/28#issuecomment-892105342) | +| Website | • [cffinit](https://citation-file-format.github.io/cff-initializer-javascript/) | | | | + +## Maintainers :nerd_face: + +The Citation File Format schema is maintained by + +- Stephan Druskat ([@sdruskat](https://github.com/sdruskat/)) +- Jurriaan H. Spaaks ([@jspaaks](https://github.com/jspaaks/)) + +## Contributing :handshake: + +The Citation File Format is a collaborative project and we welcome suggestions and contributions. We hope one of the invitations below works for you, but if not, please let us know! + +:running: **I'm busy, I only have 1 minute** +- Tell a friend about the Citation File Format, or tweet about it! +- Give the project a star :star:! + +:hourglass_flowing_sand: **I've got 10 minutes - tell me what I should do** +- Create a `CITATION.cff` file for your repository. +- Suggest ideas for how you would like to use the Citation File Format, or for an improvement to the format or its tooling. +- If you know how to validate `CITATION.cff` files, help someone with a validation problem and look at the [issues labeled ](https://github.com/citation-file-format/citation-file-format/issues?q=is%3Aopen+is%3Aissue+label%3A%22help+wanted%22+label%3Avalidation) + +:computer: **I've got a few hours to work on this** +- Help create tooling for the community by looking at the [issues labeled ](https://github.com/citation-file-format/citation-file-format/issues?q=is%3Aopen+is%3Aissue+label%3A%22help+wanted%22+label%3Atooling) + +:tada: **I want to help grow the community** +- Write a blog post or news item for your own community. +- Organise a hack event or workshop to help others use or improve the Citation File Format. + +Please read the more detailed [contributing guidelines](CONTRIBUTING.md) and [open a GitHub issue](https://github.com/citation-file-format/citation-file-format/issues) to suggest a new idea or let us know about bugs. Please put up pull requests for changes to the format and schema against the `develop` branch! + +## License :balance_scale: + +Copyright © 2016 - 2023. The Citation File Format Contributors + +This work is licensed under a [Creative Commons Attribution 4.0 International (CC-BY-4.0)](https://creativecommons.org/licenses/by/4.0/legalcode) license. + +## Acknowledgments :pray: + +**We'd like to thank everyone who has contributed to the Citation File Format!** +They are listed in the [`CITATION.cff`](CITATION.cff) file for this repository. Please open an issue if you find that you are missing from the file. + +We gratefully acknowledge support from: + +- The [Institute for Software Technology](https://www.dlr.de/en/sc) of the [German Aerospace Center (DLR)](https://www.dlr.de/en/) +- The [Netherlands eScience Center](https://www.esciencecenter.nl) +- The [Software Sustainability Institute](https://software.ac.uk/) \ No newline at end of file diff --git a/src/somef_core/test/test_data/README-componentinstaller 2.md b/src/somef_core/test/test_data/README-componentinstaller 2.md new file mode 100644 index 0000000..376776d --- /dev/null +++ b/src/somef_core/test/test_data/README-componentinstaller 2.md @@ -0,0 +1,139 @@ + +# Component Installer for deploying PySSA +[](http://www.gnu.org/licenses/gpl-3.0) +[](https://GitHub.com/urban233/ComponentInstaller/graphs/commit-activity) +[](https://GitHub.com/urban233/ComponentInstaller/issues/) +[](https://GitHub.com/urban233/ComponentInstaller/graphs/contributors/) +[](https://github.com/urban233/ComponentInstaller/releases/) + +## Contents of this document +* [Description](#Description) +* [Contents of this repository](#Contents-of-this-repository) + * [Sources](#Sources) + * [Documentation](#Documentation) + * [Assets](#Assets) +* [Build](#Build) + * [Windows](#Windows) + * [Source code](#Source-code) +* [Dependencies](#Dependencies) +* [Citation](#Citation) +* [References and useful links](#References-and-useful-links) +* [Acknowledgements](#Acknowledgements) + +## Description +The Component Installer is a software tool designed for use as a component-based installer. +It is capable of addressing a range of deployment contexts that typically necessitate more +intricate configuration than is typically required in other scenarios. +The PySSA Installer serves as a case study demonstrating +the potential utility of the component-based installation methodology. + + +## Contents of this repository +### Sources +The repository comprises four distinct source code units. + +- _src/main/java_ + - The package contains the communicator class, which is utilized for communication with WindowsTasks.exe. +- _src/main/kotlin_ + - The package contains the main source code, including gui and model. +- _WindowsWrapper/WindowsCmdElevator_ + - The package contains the class to elevate a normal cmd shell with admin privileges. +- _WindowsWrapper/WindowsTasks_ + - The package contains the communicator, which facilitates communication with the Kotlin application, as well as a number of useful classes for the management of the MS Windows operating system. + +### Documentation +The "deployment" folder +contains a user guide as PDF file. +This [PDF file](https://github.com/urban233/ComponentInstaller/blob/v1.0.1/deployment/inno_setup/PySSA-Component-Installer-User-Guide.pdf) is also available through the help menu item within the PySSA Component Installer. +The user guide explains the installation and uninstallation of every component +as well as the update procedure for ColabFold and PySSA. Furthermore, +it contains a troubleshooting section for WSL2 and ColabFold. + +### Assets +The "assets" folder contains +all logos including the WSL2, ColabFold and PySSA logo, as well as the PySSA Component Installer logo. +If you are using PySSA Component Installer for your own projects, you are welcome to give credit to PySSA Component Installer by using the logo in your presentations, etc. + +## Build +The Component Installer consists of a Kotlin/Java project and a C# solution with two projects. + +### Windows +To deploy the installer on a Microsoft Windows OS (10 or 11), use the provided +inno setup script as a starting point. +Be aware that the inno setup compiler needs to be pre-installed! + +### Source code +The Kotlin/Java project is a Gradle project. +In order to use the source code for your own software or do your own Component Installer build, +download or clone the repository and open it in a Gradle-supporting IDE (e.g. IntelliJ) +as a Gradle project and execute the build.gradle file. +Gradle will then take care of installing all dependencies. +A Java Development Kit (JDK) of version 17 must also be pre-installed and +set as project JDK / project compiler. + +The C# solution contains the C# project WindowsCmdElevator and WindowsTasks. Both can be compiled to +an .exe file using the provided FolderProfile.pubxml files. + +## Dependencies +**Needs to be pre-installed:** +* Java Development Kit (JDK) version 17 + * [Adoptium Open JDK](https://adoptium.net/temurin/archive/?version=17) (as one possible source of the JDK) +* .NET 8.0 + * [Microsoft .NET 8.0](https://dotnet.microsoft.com/en-us/download/dotnet/8.0) + +**Managed by Gradle:** +* Java Native Access (JNA) version 5.8.0 + * [Java Native Access GitHub repository](https://github.com/java-native-access) + * [LGPL, version 2.1 or later, or (from version 4.0 onward) the Apache License, version 2.0](https://github.com/java-native-access/jna?tab=License-1-ov-file) +* JeroMQ version 0.6.0 + * [JeroMQ GitHub repository](https://github.com/zeromq/jeromq) + * Mozilla Public License Version 2.0 + +**Managed by NuGet:** +* NLog version 5.3.2 + * [NLog GitHub repository](https://github.com/NLog/NLog) + * BSD-3-Clause license +* NetMQ version 4.0.1.13 + * [NetMQ GitHub repository](https://github.com/zeromq/netmq/) + * GNU Lesser General Public License 3 + +## Citation +You can cite this software or this repository as it is defined in the CITATION.cff file. + +## References and useful links +**Windows Subsystem for Linux** +* [What is the Windows Subsystem for Linux? (Article)](https://learn.microsoft.com/en-us/windows/wsl/about) +* [How to install Linux on Windows with WSL (Article)](https://learn.microsoft.com/en-us/windows/wsl/install) + +**ZeroMQ** +* [ZeroMQ Homepage](https://zeromq.org/) + * [Java implementation (JeroMQ)](https://github.com/zeromq/jeromq) + * [C# implementation (NetMQ)](https://github.com/zeromq/netmq/) + +## Acknowledgements +**Developers:** +* Martin Urban +* Hannah Kullik + +**End-user testers:** +* Jonas Schaub +* Achim Zielesny + +**Logo:** +* Martin Urban +* Hannah Kullik + +**Initialization, conceptualization, and supervision:** +* Achim Zielesny and Angelika Loidl-Stahlhofen + +**The ComponentInstaller project team would like to thank +the communities behind the open software libraries for their amazing work.** + + diff --git a/src/somef_core/test/test_data/README-componentinstaller.md b/src/somef_core/test/test_data/README-componentinstaller.md new file mode 100644 index 0000000..376776d --- /dev/null +++ b/src/somef_core/test/test_data/README-componentinstaller.md @@ -0,0 +1,139 @@ + +# Component Installer for deploying PySSA +[](http://www.gnu.org/licenses/gpl-3.0) +[](https://GitHub.com/urban233/ComponentInstaller/graphs/commit-activity) +[](https://GitHub.com/urban233/ComponentInstaller/issues/) +[](https://GitHub.com/urban233/ComponentInstaller/graphs/contributors/) +[](https://github.com/urban233/ComponentInstaller/releases/) + +## Contents of this document +* [Description](#Description) +* [Contents of this repository](#Contents-of-this-repository) + * [Sources](#Sources) + * [Documentation](#Documentation) + * [Assets](#Assets) +* [Build](#Build) + * [Windows](#Windows) + * [Source code](#Source-code) +* [Dependencies](#Dependencies) +* [Citation](#Citation) +* [References and useful links](#References-and-useful-links) +* [Acknowledgements](#Acknowledgements) + +## Description +The Component Installer is a software tool designed for use as a component-based installer. +It is capable of addressing a range of deployment contexts that typically necessitate more +intricate configuration than is typically required in other scenarios. +The PySSA Installer serves as a case study demonstrating +the potential utility of the component-based installation methodology. + + +## Contents of this repository +### Sources +The repository comprises four distinct source code units. + +- _src/main/java_ + - The package contains the communicator class, which is utilized for communication with WindowsTasks.exe. +- _src/main/kotlin_ + - The package contains the main source code, including gui and model. +- _WindowsWrapper/WindowsCmdElevator_ + - The package contains the class to elevate a normal cmd shell with admin privileges. +- _WindowsWrapper/WindowsTasks_ + - The package contains the communicator, which facilitates communication with the Kotlin application, as well as a number of useful classes for the management of the MS Windows operating system. + +### Documentation +The "deployment" folder +contains a user guide as PDF file. +This [PDF file](https://github.com/urban233/ComponentInstaller/blob/v1.0.1/deployment/inno_setup/PySSA-Component-Installer-User-Guide.pdf) is also available through the help menu item within the PySSA Component Installer. +The user guide explains the installation and uninstallation of every component +as well as the update procedure for ColabFold and PySSA. Furthermore, +it contains a troubleshooting section for WSL2 and ColabFold. + +### Assets +The "assets" folder contains +all logos including the WSL2, ColabFold and PySSA logo, as well as the PySSA Component Installer logo. +If you are using PySSA Component Installer for your own projects, you are welcome to give credit to PySSA Component Installer by using the logo in your presentations, etc. + +## Build +The Component Installer consists of a Kotlin/Java project and a C# solution with two projects. + +### Windows +To deploy the installer on a Microsoft Windows OS (10 or 11), use the provided +inno setup script as a starting point. +Be aware that the inno setup compiler needs to be pre-installed! + +### Source code +The Kotlin/Java project is a Gradle project. +In order to use the source code for your own software or do your own Component Installer build, +download or clone the repository and open it in a Gradle-supporting IDE (e.g. IntelliJ) +as a Gradle project and execute the build.gradle file. +Gradle will then take care of installing all dependencies. +A Java Development Kit (JDK) of version 17 must also be pre-installed and +set as project JDK / project compiler. + +The C# solution contains the C# project WindowsCmdElevator and WindowsTasks. Both can be compiled to +an .exe file using the provided FolderProfile.pubxml files. + +## Dependencies +**Needs to be pre-installed:** +* Java Development Kit (JDK) version 17 + * [Adoptium Open JDK](https://adoptium.net/temurin/archive/?version=17) (as one possible source of the JDK) +* .NET 8.0 + * [Microsoft .NET 8.0](https://dotnet.microsoft.com/en-us/download/dotnet/8.0) + +**Managed by Gradle:** +* Java Native Access (JNA) version 5.8.0 + * [Java Native Access GitHub repository](https://github.com/java-native-access) + * [LGPL, version 2.1 or later, or (from version 4.0 onward) the Apache License, version 2.0](https://github.com/java-native-access/jna?tab=License-1-ov-file) +* JeroMQ version 0.6.0 + * [JeroMQ GitHub repository](https://github.com/zeromq/jeromq) + * Mozilla Public License Version 2.0 + +**Managed by NuGet:** +* NLog version 5.3.2 + * [NLog GitHub repository](https://github.com/NLog/NLog) + * BSD-3-Clause license +* NetMQ version 4.0.1.13 + * [NetMQ GitHub repository](https://github.com/zeromq/netmq/) + * GNU Lesser General Public License 3 + +## Citation +You can cite this software or this repository as it is defined in the CITATION.cff file. + +## References and useful links +**Windows Subsystem for Linux** +* [What is the Windows Subsystem for Linux? (Article)](https://learn.microsoft.com/en-us/windows/wsl/about) +* [How to install Linux on Windows with WSL (Article)](https://learn.microsoft.com/en-us/windows/wsl/install) + +**ZeroMQ** +* [ZeroMQ Homepage](https://zeromq.org/) + * [Java implementation (JeroMQ)](https://github.com/zeromq/jeromq) + * [C# implementation (NetMQ)](https://github.com/zeromq/netmq/) + +## Acknowledgements +**Developers:** +* Martin Urban +* Hannah Kullik + +**End-user testers:** +* Jonas Schaub +* Achim Zielesny + +**Logo:** +* Martin Urban +* Hannah Kullik + +**Initialization, conceptualization, and supervision:** +* Achim Zielesny and Angelika Loidl-Stahlhofen + +**The ComponentInstaller project team would like to thank +the communities behind the open software libraries for their amazing work.** + + diff --git a/src/somef_core/test/test_data/README-menty 2.md b/src/somef_core/test/test_data/README-menty 2.md new file mode 100644 index 0000000..8ac3d87 --- /dev/null +++ b/src/somef_core/test/test_data/README-menty 2.md @@ -0,0 +1,94 @@ +
+ 
+
+ 
+ 
+ 
+ 
+
+
+
`, Adapt specifications use elements like AWS ``, Kubernetes ``, or `` database.
+
+If you're already familiar with React, you'll feel right at home with Adapt.
+But if not, don't worry, knowledge of React isn't required to start using Adapt.
+
+## Getting Started
+
+For a new project, it's easy to get started with Adapt by using a starter template.
+The [Getting Started Guide](https://adaptjs.org/docs/getting_started) will walk through installing Adapt and deploying your first starter app.
+
+## Creating and deploying an app
+
+This example creates a new full-stack app from a starter template.
+It has a [React](https://reactjs.org) UI, an [Nginx](https://nginx.org) web server, a [Node.js](https://nodejs.org) API server, and a [Postgres](https://postgresql.org) database, then deploys it to [Kubernetes](https://kubernetes.io/):
+
+```bash
+# Install adapt
+npm install -g @adpt/cli
+
+# Create a new app from a starter template
+adapt new hello-react-node-postgres ./myapp
+cd myapp/deploy
+
+# Deploy full stack locally using Docker
+adapt run laptop
+
+# Or just as easily deploy everything to Kubernetes
+adapt run k8s-test
+```
+
+An Adapt description for a complete front end and back end app stack looks like this:
+
+```jsx
+import Adapt from "@adpt/core";
+import { NodeService, ReactApp } from "@adpt/cloud/nodejs";
+import { Postgres } from "@adpt/cloud/postgres";
+
+function MyApp() {
+ const pg = Adapt.handle();
+
+ return (
+
+
+ );
+}
+```
+
+## Adapt in action
+
+This demo shows using Adapt to create and deploy a simple app called MovieDB that has a [React](https://reactjs.org) UI, an [Nginx](https://nginx.org) web server, an Nginx URL router, a [Node.js](https://nodejs.org) API server, and a [Postgres](https://postgresql.org) database, then deploys it to [Kubernetes](https://kubernetes.io/):
+
+
+
+## More info
+
+* [Adaptjs.org](https://adaptjs.org)
+
+ Learn more about Adapt.
+
+* [Getting Started Guide](https://adaptjs.org/docs/getting_started)
+
+ This guide will walk you through setting up Adapt and then deploying an example MovieDB app.
+
+* [Adapt Documentation](https://adaptjs.org/docs)
+
+ Adapt tutorials, API References, and more.
+
+## Getting Help
+
+[](https://gitter.im/UnboundedSystems/Adapt)
+
+We'd love to hear about your experience with Adapt!
+Join us on our [Gitter channel](https://gitter.im/UnboundedSystems/Adapt) to ask questions or to give us your feedback and suggestions.
+
+If you've found a bug, you can also [file an issue](https://gitlab.com/unboundedsystems/adapt/issues).
diff --git a/src/somef_core/test/test_data/README-unboundedsystems.md b/src/somef_core/test/test_data/README-unboundedsystems.md
new file mode 100644
index 0000000..7183625
--- /dev/null
+++ b/src/somef_core/test/test_data/README-unboundedsystems.md
@@ -0,0 +1,86 @@
+[](https://adaptjs.org)
+
+[](https://www.npmjs.com/package/@adpt/cli)
+[](https://gitter.im/UnboundedSystems/Adapt)
+[](https://opensource.org/licenses/Apache-2.0)
+
+# Adapt - ReactJS for your infrastructure.
+
+AdaptJS is a system to easily, reliably, and repeatably deploy your full-stack applications. Adapt specifications look like [React](https://reactjs.org) apps, but instead of rendering browser DOM elements like ``, or `
`, Adapt specifications use elements like AWS ``, Kubernetes ``, or `` database.
+
+If you're already familiar with React, you'll feel right at home with Adapt.
+But if not, don't worry, knowledge of React isn't required to start using Adapt.
+
+## Getting Started
+
+For a new project, it's easy to get started with Adapt by using a starter template.
+The [Getting Started Guide](https://adaptjs.org/docs/getting_started) will walk through installing Adapt and deploying your first starter app.
+
+## Creating and deploying an app
+
+This example creates a new full-stack app from a starter template.
+It has a [React](https://reactjs.org) UI, an [Nginx](https://nginx.org) web server, a [Node.js](https://nodejs.org) API server, and a [Postgres](https://postgresql.org) database, then deploys it to [Kubernetes](https://kubernetes.io/):
+
+```bash
+# Install adapt
+npm install -g @adpt/cli
+
+# Create a new app from a starter template
+adapt new hello-react-node-postgres ./myapp
+cd myapp/deploy
+
+# Deploy full stack locally using Docker
+adapt run laptop
+
+# Or just as easily deploy everything to Kubernetes
+adapt run k8s-test
+```
+
+An Adapt description for a complete front end and back end app stack looks like this:
+
+```jsx
+import Adapt from "@adpt/core";
+import { NodeService, ReactApp } from "@adpt/cloud/nodejs";
+import { Postgres } from "@adpt/cloud/postgres";
+
+function MyApp() {
+ const pg = Adapt.handle();
+
+ return (
+
+
+ );
+}
+```
+
+## Adapt in action
+
+This demo shows using Adapt to create and deploy a simple app called MovieDB that has a [React](https://reactjs.org) UI, an [Nginx](https://nginx.org) web server, an Nginx URL router, a [Node.js](https://nodejs.org) API server, and a [Postgres](https://postgresql.org) database, then deploys it to [Kubernetes](https://kubernetes.io/):
+
+
+
+## More info
+
+* [Adaptjs.org](https://adaptjs.org)
+
+ Learn more about Adapt.
+
+* [Getting Started Guide](https://adaptjs.org/docs/getting_started)
+
+ This guide will walk you through setting up Adapt and then deploying an example MovieDB app.
+
+* [Adapt Documentation](https://adaptjs.org/docs)
+
+ Adapt tutorials, API References, and more.
+
+## Getting Help
+
+[](https://gitter.im/UnboundedSystems/Adapt)
+
+We'd love to hear about your experience with Adapt!
+Join us on our [Gitter channel](https://gitter.im/UnboundedSystems/Adapt) to ask questions or to give us your feedback and suggestions.
+
+If you've found a bug, you can also [file an issue](https://gitlab.com/unboundedsystems/adapt/issues).
diff --git a/src/somef_core/test/test_data/README-uncbiag 2.md b/src/somef_core/test/test_data/README-uncbiag 2.md
new file mode 100644
index 0000000..49a45ef
--- /dev/null
+++ b/src/somef_core/test/test_data/README-uncbiag 2.md
@@ -0,0 +1,91 @@
+
+
+
+# ICON: Learning Regular Maps through Inverse Consistency
+
+[
](https://github.com/uncbiag/ICON/actions)
+[
](https://pypi.org/project/icon-registration)
+[
](https://icon.readthedocs.io/en/master/)
+
+
+This is the official repository for
+
+**ICON: Learning Regular Maps through Inverse Consistency.**
+Hastings Greer, Roland Kwitt, Francois-Xavier Vialard, Marc Niethammer.
+_ICCV 2021_ https://arxiv.org/abs/2105.04459
+
+**GradICON: Approximate Diffeomorphisms via Gradient Inverse Consistency.**
+Lin Tian, Hastings Greer, Francois-Xavier Vialard, Roland Kwitt, Raúl San José Estépar, Marc Niethammer.
+_CVPR 2023_ https://arxiv.org/abs/2206.05897
+
+**Inverse Consistency by Construction for Multistep Deep Registration.**
+Hastings Greer, Lin Tian, Francois-Xavier Vialard, Roland Kwitt, Sylvain Bouix, Raul San Jose Estepar, Richard Rushmore and Marc Niethammer.
+_MICCAI 2023_ https://arxiv.org/abs/2305.00087
+
+## Cite this work
+```
+@InProceedings{Greer_2021_ICCV,
+ author = {Greer, Hastings and Kwitt, Roland and Vialard, Francois-Xavier and Niethammer, Marc},
+ title = {ICON: Learning Regular Maps Through Inverse Consistency},
+ booktitle = {Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV)},
+ month = {October},
+ year = {2021},
+ pages = {3396-3405}
+}
+```
+
+```
+@article{Tian_2022_arXiv,
+ title={GradICON: Approximate Diffeomorphisms via Gradient Inverse Consistency},
+ author={Tian, Lin and Greer, Hastings and Vialard, Fran{\c{c}}ois-Xavier and Kwitt, Roland and Est{\'e}par, Ra{\'u}l San Jos{\'e} and Niethammer, Marc},
+ journal={arXiv preprint arXiv:2206.05897},
+ year={2022}
+}
+```
+```
+@misc{greer2023inverseconsistencyconstructionmultistep,
+ title={Inverse Consistency by Construction for Multistep Deep Registration},
+ author={Hastings Greer and Lin Tian and Francois-Xavier Vialard and Roland Kwitt and Sylvain Bouix and Raul San Jose Estepar and Richard Rushmore and Marc Niethammer},
+ year={2023},
+ eprint={2305.00087},
+ archivePrefix={arXiv},
+ primaryClass={cs.CV},
+ url={https://arxiv.org/abs/2305.00087},
+}
+```
+
+
+## uniGradICON and multiGradICON
+
+If you are interested in general purpose deep learning registration approaches check out [uniGradICON and multiGradICON](https://github.com/uncbiag/uniGradICON). These networks were trained using the GradICON technology but over many different datasets allowing them to generalize to different unimodal and multimodal registration tasks.
+
+## Video Presentation
+
+[
](https://youtu.be/7kZsJ3zWDCA)
+
+
+## Running our code
+
+We are available on PyPI!
+```bash
+pip install icon-registration
+```
+
+
+To run our pretrained model in the cloud on sample images from OAI knees, visit [our knee google colab notebook](https://colab.research.google.com/drive/1svftgw-vYWnLp9lSf3UkrG547atjbIrg?usp=sharing)
+
+To run our pretrained model for lung CT scans on an example from COPDgene, visit [our lung google colab notebook](https://colab.research.google.com/github/uncbiag/ICON/blob/master/notebooks/ICON_lung_demo.ipynb)
+
+----------------
+
+To train from scratch on the synthetic triangles and circles dataset:
+
+```bash
+git clone https://github.com/uncbiag/ICON
+cd ICON
+
+pip install -e .
+
+python training_scripts/2d_triangles_example.py
+```
+
diff --git a/src/somef_core/test/test_data/README-uncbiag.md b/src/somef_core/test/test_data/README-uncbiag.md
new file mode 100644
index 0000000..49a45ef
--- /dev/null
+++ b/src/somef_core/test/test_data/README-uncbiag.md
@@ -0,0 +1,91 @@
+
+
+
+# ICON: Learning Regular Maps through Inverse Consistency
+
+[](https://github.com/uncbiag/ICON/actions)
+[](https://pypi.org/project/icon-registration)
+[](https://icon.readthedocs.io/en/master/)
+
+
+This is the official repository for
+
+**ICON: Learning Regular Maps through Inverse Consistency.**
+Hastings Greer, Roland Kwitt, Francois-Xavier Vialard, Marc Niethammer.
+_ICCV 2021_ https://arxiv.org/abs/2105.04459
+
+**GradICON: Approximate Diffeomorphisms via Gradient Inverse Consistency.**
+Lin Tian, Hastings Greer, Francois-Xavier Vialard, Roland Kwitt, Raúl San José Estépar, Marc Niethammer.
+_CVPR 2023_ https://arxiv.org/abs/2206.05897
+
+**Inverse Consistency by Construction for Multistep Deep Registration.**
+Hastings Greer, Lin Tian, Francois-Xavier Vialard, Roland Kwitt, Sylvain Bouix, Raul San Jose Estepar, Richard Rushmore and Marc Niethammer.
+_MICCAI 2023_ https://arxiv.org/abs/2305.00087
+
+## Cite this work
+```
+@InProceedings{Greer_2021_ICCV,
+ author = {Greer, Hastings and Kwitt, Roland and Vialard, Francois-Xavier and Niethammer, Marc},
+ title = {ICON: Learning Regular Maps Through Inverse Consistency},
+ booktitle = {Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV)},
+ month = {October},
+ year = {2021},
+ pages = {3396-3405}
+}
+```
+
+```
+@article{Tian_2022_arXiv,
+ title={GradICON: Approximate Diffeomorphisms via Gradient Inverse Consistency},
+ author={Tian, Lin and Greer, Hastings and Vialard, Fran{\c{c}}ois-Xavier and Kwitt, Roland and Est{\'e}par, Ra{\'u}l San Jos{\'e} and Niethammer, Marc},
+ journal={arXiv preprint arXiv:2206.05897},
+ year={2022}
+}
+```
+```
+@misc{greer2023inverseconsistencyconstructionmultistep,
+ title={Inverse Consistency by Construction for Multistep Deep Registration},
+ author={Hastings Greer and Lin Tian and Francois-Xavier Vialard and Roland Kwitt and Sylvain Bouix and Raul San Jose Estepar and Richard Rushmore and Marc Niethammer},
+ year={2023},
+ eprint={2305.00087},
+ archivePrefix={arXiv},
+ primaryClass={cs.CV},
+ url={https://arxiv.org/abs/2305.00087},
+}
+```
+
+
+## uniGradICON and multiGradICON
+
+If you are interested in general purpose deep learning registration approaches check out [uniGradICON and multiGradICON](https://github.com/uncbiag/uniGradICON). These networks were trained using the GradICON technology but over many different datasets allowing them to generalize to different unimodal and multimodal registration tasks.
+
+## Video Presentation
+
+[](https://youtu.be/7kZsJ3zWDCA)
+
+
+## Running our code
+
+We are available on PyPI!
+```bash
+pip install icon-registration
+```
+
+
+To run our pretrained model in the cloud on sample images from OAI knees, visit [our knee google colab notebook](https://colab.research.google.com/drive/1svftgw-vYWnLp9lSf3UkrG547atjbIrg?usp=sharing)
+
+To run our pretrained model for lung CT scans on an example from COPDgene, visit [our lung google colab notebook](https://colab.research.google.com/github/uncbiag/ICON/blob/master/notebooks/ICON_lung_demo.ipynb)
+
+----------------
+
+To train from scratch on the synthetic triangles and circles dataset:
+
+```bash
+git clone https://github.com/uncbiag/ICON
+cd ICON
+
+pip install -e .
+
+python training_scripts/2d_triangles_example.py
+```
+
diff --git a/src/somef_core/test/test_data/README-widoco-duplicate-dois 2.md b/src/somef_core/test/test_data/README-widoco-duplicate-dois 2.md
new file mode 100644
index 0000000..85fb4f0
--- /dev/null
+++ b/src/somef_core/test/test_data/README-widoco-duplicate-dois 2.md
@@ -0,0 +1,198 @@
+# WIzard for DOCumenting Ontologies (WIDOCO)
+[](https://zenodo.org/badge/latestdoi/11427075) [](https://jitpack.io/#dgarijo/Widoco)
+
+
+
+WIDOCO helps you to publish and create an enriched and customized documentation of your ontology automatically, by following a series of steps in a GUI.
+
+**Author**: Daniel Garijo Verdejo (@dgarijo)
+
+**Contributors**: María Poveda, Idafen Santana, Almudena Ruiz, Miguel Angel García, Oscar Corcho, Daniel Vila, Sergio Barrio, Martin Scharm, Maxime Lefrancois, Alfredo Serafini, @kartgk, Pat Mc Bennett, Christophe Camel, Jacobus Geluk, Martin Scharm, @rpietzsch, Jonathan Leitschuh, Jodi Schneider, Giacomo Lanza, Alejandra Gonzalez-Beltran, Mario Scrocca, Miguel Angel García and Flores Bakker.
+
+**Citing WIDOCO**: If you used WIDOCO in your work, please cite the ISWC 2017 paper: https://iswc2017.semanticweb.org/paper-138
+
+```bib
+@inproceedings{garijo2017widoco,
+ title={WIDOCO: a wizard for documenting ontologies},
+ author={Garijo, Daniel},
+ booktitle={International Semantic Web Conference},
+ pages={94--102},
+ year={2017},
+ organization={Springer, Cham},
+ doi = {10.1007/978-3-319-68204-4_9},
+ funding = {USNSF ICER-1541029, NIH 1R01GM117097-01},
+ url={http://dgarijo.com/papers/widoco-iswc2017.pdf}
+}
+
+@inproceedings{garijo2017widoco_duplicate,
+ title={WIDOCO: a wizard for documenting ontologies},
+ author={Garijo, Daniel},
+ booktitle={International Semantic Web Conference},
+ pages={94--102},
+ year={2017},
+ organization={Springer, Cham},
+ doi = {https://dx.doi.org/10.1007/978-3-319-68204-4_9},
+ url={http://dgarijo.com/papers/widoco-iswc2017.pdf}
+}
+```
+If you want to cite the latest version of the software, you can do so by using: https://zenodo.org/badge/latestdoi/11427075.
+
+## Downloading the executable
+
+To download WIDOCO, you need to download a JAR executable file. Check the latest release for more details: (https://github.com/dgarijo/WIDOCO/releases/latest).
+
+## Importing WIDOCO as a dependency
+Just add the dependency and repository to your `pom.xml` file as follows. See the [WIDOCO JitPack](https://jitpack.io/#dgarijo/Widoco) page to find alternative means to incorporate WIDOCO to your project.
+
+```xml
+
+
+ com.github.dgarijo
+ Widoco
+ v1.4.15
+
+
+
+[ ... ]
+
+
+
+ jitpack.io
+ https://jitpack.io
+
+
+```
+
+## Description
+WIDOCO helps you to publish and create an enriched and customized documentation of your ontology, by following a series of steps in a wizard. We extend the LODE framework by Silvio Peroni to describe the classes, properties and data properties of the ontology, the OOPS! webservice by María Poveda to print an evaluation and the Licensius service by Victor Rodriguez Doncel to determine the license URI and title being used. In addition, we use WebVowl to visualize the ontology and have extended Bubastis to show a complete changelog between different versions of your ontology.
+
+Features of WIDOCO:
+* Automatic documentation of the terms in your ontology (based on [LODE](http://www.essepuntato.it/lode/)). Now you can use Markdown on your class descriptions (see [example](doc/gallery/index.html))
+* Automatic annotation in JSON-LD snippets of the html produced.
+* Association of a provenance page which includes the history of your vocabulary (W3C PROV-O compliant).
+* Metadata extraction from the ontology plus the means to complete it on the fly when generating your ontology. Check the [best practice document](http://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html) to know more about the terms recognized by WIDOCO.
+* Guidelines on the main sections that your document should have and how to complete them.
+* Integration with diagram creators ([WebVOWL](http://vowl.visualdataweb.org/webvowl/)).
+* Automatic changelog of differences between the actual and the previous version of the ontology (based on [Bubastis](http://www.ebi.ac.uk/efo/bubastis/)).
+* Separation of the sections of your html page so you can write them independently and replace only those needed.
+* Content negotiation and serialization of your ontology according to [W3C best practices](https://www.w3.org/TR/swbp-vocab-pub/)
+* Evaluation reports of your ontology (using the [OOPS! web service](http://oops.linkeddata.es/))
+* Integration with license metadata services ([Licensius](http://licensius.com/)) to automatically describe the license used in your ontology.
+
+## Examples
+Examples of the features of WIDOCO can be seen on [the gallery](http://dgarijo.github.io/Widoco/doc/gallery/)
+
+## GUI Tutorial
+A tutorial explaining the main features of the GUI can be found [here](http://dgarijo.github.io/Widoco/doc/tutorial/)
+
+## How to use WIDOCO
+
+### JAR execution
+
+Download the latest `.jar` [WIDOCO available release](https://github.com/dgarijo/WIDOCO/releases/latest) (it will be something like `widoco-VERSION-jar-with-dependencies.jar`). Then just double click the `.jar` file.
+
+You may also execute WIDOCO through the command line. Usage:
+```bash
+java -jar widoco-VERSION-jar-with-dependencies.jar [OPTIONS]
+```
+
+### Docker execution
+
+First build the image using the `Dockerfile` in project folder:
+
+```bash
+docker build -t dgarijo/widoco .
+```
+
+You can now execute WIDOCO through the command line. Usage:
+
+```bash
+docker run -ti --rm dgarijo/widoco [OPTIONS]
+```
+
+If you want to share data between the Docker Container and your Host, for instance to load a local ontology file (from PATH), you will need to mount the container
+with host directories. For instance:
+
+```bash
+docker run -ti --rm \
+ -v `pwd`/test:/usr/local/widoco/in \
+ -v `pwd`/target/generated-doc:/usr/local/widoco/out \
+ dgarijo/widoco -ontFile in/bne.ttl -outFolder out -rewriteAll
+```
+
+### Options
+
+`-ontFile PATH` [required (unless -ontURI is used)]: Load a local ontology file (from PATH) to document. This option is incompatible with -ontURI
+
+`-ontURI URI` [required (unless -ontFile is used)]: Load an ontology to document from its URI. This option is incompatible with -ontFile
+
+`-outFolder folderName`: Specifies the name of the folder where to save the documentation. By default is 'myDocumentation'
+
+`-confFile PATH`: Load your own configuration file for the ontology metadata. Incompatible with -getOntologyMetadata
+
+`-getOntologyMetadata`: Extract ontology metadata from the given ontology
+
+`-oops`: Create an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/)
+
+`-rewriteAll`: Replace any existing files when documenting an ontology (e.g., from a previous execution)
+
+`-crossRef`: ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag is intended to be used only after a first version of the documentation exists.
+
+`-saveConfig PATH`: Save a configuration file on PATH with the properties of a given ontology
+
+`-useCustomStyle`: Export the documentation using alternate css files (by Daniel Vila).
+
+`-lang LANG1-LANG2`: Generate documentation in multiple languages (separated by "-"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es
+
+`-includeImportedOntologies`: Indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not.
+
+`-htaccess`: Create a bundle for publication ready to be deployed on your Apache server.
+
+`-webVowl`: Create a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#) in the documentation.
+
+`-licensius`: Use the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata flag is enabled.
+
+`-ignoreIndividuals`: Individuals will not be included in the documentation.
+
+`-includeAnnotationProperties`: Include annotation properties defined in your ontology in the documentation (by default they are not included)
+
+`-analytics CODE`: Add a code snippet for Google analytics to track your HTML documentation. You need to add your CODE next to the flag. For example: UA-1234
+
+`-doNotDisplaySerializations`: The serializations of the ontology will not be displayed.
+
+`-displayDirectImportsOnly`: Only those imported ontologies that are directly imported in the ontology being documented.
+
+`-rewriteBase PATH`: Change the default rewrite base path. The default value is "/". This flag can only be used with the htaccess option.
+
+`-excludeIntroduction`: Skip the introduction section in the documentation.
+
+`-uniteSections`: Write all HTML sections into a single HTML document.
+
+`-noPlaceHolderText`: Do not add any placeholder text (this will remove intro, abstract (if empty) and description sections).
+
+`--help`: Shows a help message and exits.
+
+
+## How can I make WIDOCO automatically recognize my vocabulary annotations?
+There are two alternative ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology.
+
+* The recommended way: add them in your OWL file. For guidelines on which ones to include, follow our [best practices document](https://w3id.org/widoco/bestPractices), which indicates which ones we recommend.
+* Alternatively, edit the project properties of /config/config.properties. This is a key-value pair file with metadata properties. Some people consider it easier than adding the property annotations to the OWL file, although I recommend doing the former option. Note that the character ";" is used for lists (for instance first author; second author; third author).
+
+## Browser issues (Why can't I see the generated documentation / visualization?)
+WIDOCO separates the contents of different sections in HTML files, which are then loaded in the `index.html` file. WIDOCO was designed this way because it's easier to edit your introduction or description sections independently without being all aggregated together in a huge HTML document. **When all the contents generated by WIDOCO are stored in a server, you will be able to see the documentation of your ontology using any browser**. However, if you open the `index.html` file **on your local browser**, you may see a document missing most of the sections in your documentation. This happens because browsers don't allow loading separate content when opening a file locally for security reasons. If you want to explore how your ontology would look locally, you have two options:
+
+* a) Execute WIDOCO with the `-uniteSections` flag; or select the option `add al sections in a single document` in the "load sections" step in the WIDOCO GUI. This will make all the sections of WIDOCO to be in the `index.html`; and you will be able to see it in your browser. Note that the **LODE visualization will not be available** when exploring your ontology locally.
+* b) Create a local server: Set up a local server (e.g., using XAMPP or Tomcat) and serve the files WIDOCO generates (in the `htdocs` folder for Apache servers).
+
+If you place the files generated by WIDOCO in a server and access them via its URL (for example, a Github page), you should be able to see your documentation appropriately.
+
+## Current improvements
+For a complete list of the current improvements and next features, check the [project open issues](https://github.com/dgarijo/Widoco/issues) and [milestones](https://github.com/dgarijo/Widoco/milestones) in the repository.
+
+## Requirements
+You will need Java 1.8 or higher (SDK 1.8 or JRE 8) for WIDOCO to work
+Otherwise, you will probably experience an "Unsupported major.minor version 52.0" exception when executing the JAR file.
+
+## Contribution guidelines
+Contributions to address any of the current issues are welcome. In order to push your contribution, just **push your pull request to the develop branch**. The master branch has only the code associated to the latest release.
diff --git a/src/somef_core/test/test_data/README-widoco-duplicate-dois.md b/src/somef_core/test/test_data/README-widoco-duplicate-dois.md
new file mode 100644
index 0000000..85fb4f0
--- /dev/null
+++ b/src/somef_core/test/test_data/README-widoco-duplicate-dois.md
@@ -0,0 +1,198 @@
+# WIzard for DOCumenting Ontologies (WIDOCO)
+[](https://zenodo.org/badge/latestdoi/11427075) [](https://jitpack.io/#dgarijo/Widoco)
+
+
+
+WIDOCO helps you to publish and create an enriched and customized documentation of your ontology automatically, by following a series of steps in a GUI.
+
+**Author**: Daniel Garijo Verdejo (@dgarijo)
+
+**Contributors**: María Poveda, Idafen Santana, Almudena Ruiz, Miguel Angel García, Oscar Corcho, Daniel Vila, Sergio Barrio, Martin Scharm, Maxime Lefrancois, Alfredo Serafini, @kartgk, Pat Mc Bennett, Christophe Camel, Jacobus Geluk, Martin Scharm, @rpietzsch, Jonathan Leitschuh, Jodi Schneider, Giacomo Lanza, Alejandra Gonzalez-Beltran, Mario Scrocca, Miguel Angel García and Flores Bakker.
+
+**Citing WIDOCO**: If you used WIDOCO in your work, please cite the ISWC 2017 paper: https://iswc2017.semanticweb.org/paper-138
+
+```bib
+@inproceedings{garijo2017widoco,
+ title={WIDOCO: a wizard for documenting ontologies},
+ author={Garijo, Daniel},
+ booktitle={International Semantic Web Conference},
+ pages={94--102},
+ year={2017},
+ organization={Springer, Cham},
+ doi = {10.1007/978-3-319-68204-4_9},
+ funding = {USNSF ICER-1541029, NIH 1R01GM117097-01},
+ url={http://dgarijo.com/papers/widoco-iswc2017.pdf}
+}
+
+@inproceedings{garijo2017widoco_duplicate,
+ title={WIDOCO: a wizard for documenting ontologies},
+ author={Garijo, Daniel},
+ booktitle={International Semantic Web Conference},
+ pages={94--102},
+ year={2017},
+ organization={Springer, Cham},
+ doi = {https://dx.doi.org/10.1007/978-3-319-68204-4_9},
+ url={http://dgarijo.com/papers/widoco-iswc2017.pdf}
+}
+```
+If you want to cite the latest version of the software, you can do so by using: https://zenodo.org/badge/latestdoi/11427075.
+
+## Downloading the executable
+
+To download WIDOCO, you need to download a JAR executable file. Check the latest release for more details: (https://github.com/dgarijo/WIDOCO/releases/latest).
+
+## Importing WIDOCO as a dependency
+Just add the dependency and repository to your `pom.xml` file as follows. See the [WIDOCO JitPack](https://jitpack.io/#dgarijo/Widoco) page to find alternative means to incorporate WIDOCO to your project.
+
+```xml
+
+
+ com.github.dgarijo
+ Widoco
+ v1.4.15
+
+
+
+[ ... ]
+
+
+
+ jitpack.io
+ https://jitpack.io
+
+
+```
+
+## Description
+WIDOCO helps you to publish and create an enriched and customized documentation of your ontology, by following a series of steps in a wizard. We extend the LODE framework by Silvio Peroni to describe the classes, properties and data properties of the ontology, the OOPS! webservice by María Poveda to print an evaluation and the Licensius service by Victor Rodriguez Doncel to determine the license URI and title being used. In addition, we use WebVowl to visualize the ontology and have extended Bubastis to show a complete changelog between different versions of your ontology.
+
+Features of WIDOCO:
+* Automatic documentation of the terms in your ontology (based on [LODE](http://www.essepuntato.it/lode/)). Now you can use Markdown on your class descriptions (see [example](doc/gallery/index.html))
+* Automatic annotation in JSON-LD snippets of the html produced.
+* Association of a provenance page which includes the history of your vocabulary (W3C PROV-O compliant).
+* Metadata extraction from the ontology plus the means to complete it on the fly when generating your ontology. Check the [best practice document](http://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html) to know more about the terms recognized by WIDOCO.
+* Guidelines on the main sections that your document should have and how to complete them.
+* Integration with diagram creators ([WebVOWL](http://vowl.visualdataweb.org/webvowl/)).
+* Automatic changelog of differences between the actual and the previous version of the ontology (based on [Bubastis](http://www.ebi.ac.uk/efo/bubastis/)).
+* Separation of the sections of your html page so you can write them independently and replace only those needed.
+* Content negotiation and serialization of your ontology according to [W3C best practices](https://www.w3.org/TR/swbp-vocab-pub/)
+* Evaluation reports of your ontology (using the [OOPS! web service](http://oops.linkeddata.es/))
+* Integration with license metadata services ([Licensius](http://licensius.com/)) to automatically describe the license used in your ontology.
+
+## Examples
+Examples of the features of WIDOCO can be seen on [the gallery](http://dgarijo.github.io/Widoco/doc/gallery/)
+
+## GUI Tutorial
+A tutorial explaining the main features of the GUI can be found [here](http://dgarijo.github.io/Widoco/doc/tutorial/)
+
+## How to use WIDOCO
+
+### JAR execution
+
+Download the latest `.jar` [WIDOCO available release](https://github.com/dgarijo/WIDOCO/releases/latest) (it will be something like `widoco-VERSION-jar-with-dependencies.jar`). Then just double click the `.jar` file.
+
+You may also execute WIDOCO through the command line. Usage:
+```bash
+java -jar widoco-VERSION-jar-with-dependencies.jar [OPTIONS]
+```
+
+### Docker execution
+
+First build the image using the `Dockerfile` in project folder:
+
+```bash
+docker build -t dgarijo/widoco .
+```
+
+You can now execute WIDOCO through the command line. Usage:
+
+```bash
+docker run -ti --rm dgarijo/widoco [OPTIONS]
+```
+
+If you want to share data between the Docker Container and your Host, for instance to load a local ontology file (from PATH), you will need to mount the container
+with host directories. For instance:
+
+```bash
+docker run -ti --rm \
+ -v `pwd`/test:/usr/local/widoco/in \
+ -v `pwd`/target/generated-doc:/usr/local/widoco/out \
+ dgarijo/widoco -ontFile in/bne.ttl -outFolder out -rewriteAll
+```
+
+### Options
+
+`-ontFile PATH` [required (unless -ontURI is used)]: Load a local ontology file (from PATH) to document. This option is incompatible with -ontURI
+
+`-ontURI URI` [required (unless -ontFile is used)]: Load an ontology to document from its URI. This option is incompatible with -ontFile
+
+`-outFolder folderName`: Specifies the name of the folder where to save the documentation. By default is 'myDocumentation'
+
+`-confFile PATH`: Load your own configuration file for the ontology metadata. Incompatible with -getOntologyMetadata
+
+`-getOntologyMetadata`: Extract ontology metadata from the given ontology
+
+`-oops`: Create an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/)
+
+`-rewriteAll`: Replace any existing files when documenting an ontology (e.g., from a previous execution)
+
+`-crossRef`: ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag is intended to be used only after a first version of the documentation exists.
+
+`-saveConfig PATH`: Save a configuration file on PATH with the properties of a given ontology
+
+`-useCustomStyle`: Export the documentation using alternate css files (by Daniel Vila).
+
+`-lang LANG1-LANG2`: Generate documentation in multiple languages (separated by "-"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es
+
+`-includeImportedOntologies`: Indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not.
+
+`-htaccess`: Create a bundle for publication ready to be deployed on your Apache server.
+
+`-webVowl`: Create a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#) in the documentation.
+
+`-licensius`: Use the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata flag is enabled.
+
+`-ignoreIndividuals`: Individuals will not be included in the documentation.
+
+`-includeAnnotationProperties`: Include annotation properties defined in your ontology in the documentation (by default they are not included)
+
+`-analytics CODE`: Add a code snippet for Google analytics to track your HTML documentation. You need to add your CODE next to the flag. For example: UA-1234
+
+`-doNotDisplaySerializations`: The serializations of the ontology will not be displayed.
+
+`-displayDirectImportsOnly`: Only those imported ontologies that are directly imported in the ontology being documented.
+
+`-rewriteBase PATH`: Change the default rewrite base path. The default value is "/". This flag can only be used with the htaccess option.
+
+`-excludeIntroduction`: Skip the introduction section in the documentation.
+
+`-uniteSections`: Write all HTML sections into a single HTML document.
+
+`-noPlaceHolderText`: Do not add any placeholder text (this will remove intro, abstract (if empty) and description sections).
+
+`--help`: Shows a help message and exits.
+
+
+## How can I make WIDOCO automatically recognize my vocabulary annotations?
+There are two alternative ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology.
+
+* The recommended way: add them in your OWL file. For guidelines on which ones to include, follow our [best practices document](https://w3id.org/widoco/bestPractices), which indicates which ones we recommend.
+* Alternatively, edit the project properties of /config/config.properties. This is a key-value pair file with metadata properties. Some people consider it easier than adding the property annotations to the OWL file, although I recommend doing the former option. Note that the character ";" is used for lists (for instance first author; second author; third author).
+
+## Browser issues (Why can't I see the generated documentation / visualization?)
+WIDOCO separates the contents of different sections in HTML files, which are then loaded in the `index.html` file. WIDOCO was designed this way because it's easier to edit your introduction or description sections independently without being all aggregated together in a huge HTML document. **When all the contents generated by WIDOCO are stored in a server, you will be able to see the documentation of your ontology using any browser**. However, if you open the `index.html` file **on your local browser**, you may see a document missing most of the sections in your documentation. This happens because browsers don't allow loading separate content when opening a file locally for security reasons. If you want to explore how your ontology would look locally, you have two options:
+
+* a) Execute WIDOCO with the `-uniteSections` flag; or select the option `add al sections in a single document` in the "load sections" step in the WIDOCO GUI. This will make all the sections of WIDOCO to be in the `index.html`; and you will be able to see it in your browser. Note that the **LODE visualization will not be available** when exploring your ontology locally.
+* b) Create a local server: Set up a local server (e.g., using XAMPP or Tomcat) and serve the files WIDOCO generates (in the `htdocs` folder for Apache servers).
+
+If you place the files generated by WIDOCO in a server and access them via its URL (for example, a Github page), you should be able to see your documentation appropriately.
+
+## Current improvements
+For a complete list of the current improvements and next features, check the [project open issues](https://github.com/dgarijo/Widoco/issues) and [milestones](https://github.com/dgarijo/Widoco/milestones) in the repository.
+
+## Requirements
+You will need Java 1.8 or higher (SDK 1.8 or JRE 8) for WIDOCO to work
+Otherwise, you will probably experience an "Unsupported major.minor version 52.0" exception when executing the JAR file.
+
+## Contribution guidelines
+Contributions to address any of the current issues are welcome. In order to push your contribution, just **push your pull request to the develop branch**. The master branch has only the code associated to the latest release.
diff --git a/src/somef_core/test/test_data/README-widoco-swh 2.md b/src/somef_core/test/test_data/README-widoco-swh 2.md
new file mode 100644
index 0000000..0f72c58
--- /dev/null
+++ b/src/somef_core/test/test_data/README-widoco-swh 2.md
@@ -0,0 +1,233 @@
+# WIzard for DOCumenting Ontologies (WIDOCO)
+[](https://doi.org/10.5281/zenodo.11093793) [](https://jitpack.io/#dgarijo/Widoco) [](https://www.repostatus.org/#active) [](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/dgarijo/Widoco) [](https://archive.softwareheritage.org/swh:1:dir:40d462bbecefc3a9c3e810567d1f0d7606e0fae7;origin=https://github.com/dgarijo/Widoco;visit=swh:1:snp:4d8570d390a18fee1d37f262ad79b36c021c611a;anchor=swh:1:rev:fec66b89a4f4acb015a44c7f8cb671d49bec626a)
+
+
+
+WIDOCO helps you to publish and create an enriched and customized documentation of your ontology automatically, by following a series of steps in a GUI.
+
+**Author**: Daniel Garijo Verdejo (@dgarijo)
+
+**Contributors**: María Poveda, Idafen Santana, Almudena Ruiz, Miguel Angel García, Oscar Corcho, Daniel Vila, Sergio Barrio, Martin Scharm, Maxime Lefrancois, Alfredo Serafini, @kartgk, Pat Mc Bennett, Christophe Camel, Jacobus Geluk, Martin Scharm, @rpietzsch, Jonathan Leitschuh, Jodi Schneider, Giacomo Lanza, Alejandra Gonzalez-Beltran, Mario Scrocca, Miguel Angel García, Flores Bakker, @JohnnyMoonlight, René Fritze, @telecsur, Jan Vlug, Han Kruiger, Johannes Theissen-Lipp, Roberto Polli, Victor Chavez, Sirko Schindler and Michaël Dierick.
+
+**Citing WIDOCO**: If you used WIDOCO in your work, please cite the ISWC 2017 paper: https://iswc2017.semanticweb.org/paper-138
+
+```bib
+@inproceedings{garijo2017widoco,
+ title={WIDOCO: a wizard for documenting ontologies},
+ author={Garijo, Daniel},
+ booktitle={International Semantic Web Conference},
+ pages={94--102},
+ year={2017},
+ organization={Springer, Cham},
+ doi = {10.1007/978-3-319-68204-4_9},
+ funding = {USNSF ICER-1541029, NIH 1R01GM117097-01},
+ url={http://dgarijo.com/papers/widoco-iswc2017.pdf}
+}
+```
+If you want to cite the latest version of the software, you can do so by using: https://zenodo.org/badge/latestdoi/11427075.
+
+## Downloading the executable
+
+To download WIDOCO, you need to download a JAR executable file. Check the latest release for more details: (https://github.com/dgarijo/WIDOCO/releases/latest).
+
+## Importing WIDOCO as a dependency
+Just add the dependency and repository to your `pom.xml` file as follows. See the [WIDOCO JitPack](https://jitpack.io/#dgarijo/Widoco) page to find alternative means to incorporate WIDOCO to your project.
+
+```xml
+
+
+ com.github.dgarijo
+ Widoco
+ v1.4.24
+
+
+
+[ ... ]
+
+
+
+ jitpack.io
+ https://jitpack.io
+
+
+```
+
+## Description
+WIDOCO helps you to publish and create an enriched and customized documentation of your ontology, by following a series of steps in a wizard. We extend the LODE framework by Silvio Peroni to describe the classes, properties and data properties of the ontology, the OOPS! webservice by María Poveda to print an evaluation and the Licensius service by Victor Rodriguez Doncel to determine the license URI and title being used. In addition, we use WebVowl to visualize the ontology and have extended Bubastis to show a complete changelog between different versions of your ontology.
+
+Features of WIDOCO:
+* Automatic documentation of the terms in your ontology (based on [LODE](http://www.essepuntato.it/lode/)). Now **you can use Markdown on your class descriptions** (see [example](https://dgarijo.github.io/Widoco/doc/gallery/index.html))
+* Massive metadata extraction and support: WIDOCO will enhance your ontology documentation based on your ontology annotations. Now you can add custom logos and images, edit the content of your sections, etc. by just editing metadata. See our [supported metadata](doc/metadataGuide/guide.md) and [recommendations](https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html) for more information.
+* Automatic annotation in JSON-LD snippets of the html produced.
+* Association of a provenance page which includes the history of your vocabulary (W3C PROV-O compliant).
+* Guidelines on the main sections that your document should have and how to complete them.
+* Integration with diagram creators ([WebVOWL](http://vowl.visualdataweb.org/webvowl/)).
+* Automatic changelog of differences between the actual and the previous version of the ontology (based on [Bubastis](http://www.ebi.ac.uk/efo/bubastis/)).
+* Separation of the sections of your html page so you can write them independently and replace only those needed.
+* Content negotiation and serialization of your ontology according to [W3C best practices](https://www.w3.org/TR/swbp-vocab-pub/)
+* Evaluation reports of your ontology (using the [OOPS! web service](https://oops.linkeddata.es/))
+* Integration with license metadata services ([Licensius](http://licensius.com/)) to automatically describe the license used in your ontology.
+
+## Examples
+Examples of the features of WIDOCO can be seen on [the gallery](https://dgarijo.github.io/Widoco/doc/gallery/)
+
+## GUI Tutorial
+A tutorial explaining the main features of the GUI can be found [here](https://dgarijo.github.io/Widoco/doc/tutorial/)
+
+## Metadata usage
+To see how WIDOCO recognizes metadata annotations in your ontology to create the documentation files, see [the WIDOCO metadata documentation](doc/metadataGuide/guide.md). To learn which metadata properties we recommend adding to your ontology for producing a nice-looking documentation, have a look at our [best practices guide](https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html).
+
+For example, in order to show your logo in your documentation you just need to use `foaf:logo` as an annotation, as follows:
+```
+@prefix owl: .
+@prefix foaf: a owl:Ontology ;
+ foaf:logo .
+```
+
+and it will show right next to the title. The [WIDOCO metadata documentation](doc/metadataGuide/guide.md) shows all supported metadata fields.
+
+## How to use WIDOCO
+
+### Building the JAR executable
+We provide JAR files for each release (see the [releases](https://github.com/dgarijo/Widoco/releases) page). However, if you want to build WIDOCO from scratch, just cd into the project folder and run:
+
+```bash
+mvn install
+```
+The JAR will be generated in a "JAR" folder. The name will follow the pattern: `widoco-{VERSION_ID}-jar-with-dependencies.jar`, where {VERSION_ID} is the version number of the tool.
+
+### JAR execution
+
+Download the latest `.jar` [WIDOCO available release](https://github.com/dgarijo/WIDOCO/releases/latest) (it will be something like `widoco-VERSION-jar-with-dependencies.jar`). Then just double click the `.jar` file.
+
+You may also execute WIDOCO through the command line. Usage:
+```bash
+java -jar widoco-VERSION-jar-with-dependencies.jar [OPTIONS]
+```
+
+### Docker execution
+If you don't want to use the JAR directly, you may run the project using a [Docker container](https://www.docker.com/). First you will need to download or build the image, and then run it.
+
+#### Reusing a pre-existing image
+We build containers in the [GitHub image registry](https://github.com/dgarijo/Widoco/pkgs/container/widoco) for all latest releases. In order to import one, just run the following command, stating the version of Widoco you prefer (e.g., for v1.4.23):
+
+```
+docker pull ghcr.io/dgarijo/widoco:v1.4.23
+```
+
+To browse all available images, see the [GitHub image registry](https://github.com/dgarijo/Widoco/pkgs/container/widoco).
+
+#### Building the image yourself
+
+Build the image using the `Dockerfile` in project folder:
+
+```bash
+docker build -t dgarijo/widoco .
+```
+
+#### Running WIDOCO's image
+
+You can now execute WIDOCO through the command line. Usage:
+
+```bash
+docker run -ti --rm dgarijo/widoco [OPTIONS]
+```
+
+**Note:** If you downloaded the image from the GitHub registry, you will have to change `dgarijo/widoco` with the name of the image you downloaded. For example `ghcr.io/dgarijo/widoco:v1.4.23`.
+
+If you want to share data between the Docker Container and your Host, for instance to load a local ontology file (from PATH), you will need to mount the container
+with host directories. For instance:
+
+```bash
+docker run -ti --rm \
+ -v `pwd`/test:/usr/local/widoco/in:Z \
+ -v `pwd`/target/generated-doc:/usr/local/widoco/out:Z \
+ dgarijo/widoco -ontFile in/bne.ttl -outFolder out -rewriteAll
+```
+
+### Execution options
+
+`-analytics CODE`: Add a code snippet for Google analytics to track your HTML documentation. You need to add your CODE next to the flag. For example: UA-1234
+
+`-confFile PATH`: Load your own configuration file for the ontology metadata. Use this option if you want to load your own HTML sections as well. Incompatible with -getOntologyMetadata. See [the configuration documentation](doc/configuration/configuration_doc.md) for more information about the accepted fields.
+
+`-crossRef`: ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag is intended to be used only after a first version of the documentation exists.
+
+`-displayDirectImportsOnly`: Only those imported ontologies that are directly imported in the ontology being documented.
+
+`-doNotDisplaySerializations`: The serializations of the ontology will not be displayed.
+
+`-excludeIntroduction`: Skip the introduction section in the documentation.
+
+`-excludeProvenance`: Do not add the link "Provenance of this page" in the metadata header section
+
+`-getOntologyMetadata`: Extract ontology metadata from the given ontology
+
+`--help`: Shows a help message and exits.
+
+`-htaccess`: Create a bundle for publication ready to be deployed on your Apache server.
+
+
+`-ignoreIndividuals`: Individuals will not be included in the documentation.
+
+`-includeAnnotationProperties`: Include annotation properties defined in your ontology in the documentation (by default they are not included)
+
+`-includeImportedOntologies`: Indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not.
+
+`-import`: imports a local ontology (e.g., if you don't want to load an online ontology, you may load its local version)
+
+`-lang LANG1-LANG2`: Generate documentation in multiple languages (separated by "-"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es
+
+`-licensius`: Use the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata flag is enabled.
+
+`-noPlaceHolderText`: Do not add any placeholder text (this will remove intro, abstract (if empty) and description sections).
+
+`-ontFile PATH` [required (unless -ontURI is used)]: Load a local ontology file (from PATH) to document. This option is incompatible with -ontURI
+
+`-outFolder folderName`: Specifies the name of the folder where to save the documentation. By default is 'myDocumentation'
+
+`-ontURI URI` [required (unless -ontFile is used)]: Load an ontology to document from its URI. This option is incompatible with -ontFile
+
+`-oops`: Create an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/)
+
+`-rewriteAll`: Replace any existing files when documenting an ontology (e.g., from a previous execution)
+
+`-rewriteBase PATH`: Change the default rewrite base path. The default value is "/". This flag can only be used with the htaccess option.
+
+`-saveConfig PATH`: Save a configuration file on PATH with the properties of a given ontology
+
+`-uniteSections`: Write all HTML sections into a single HTML document.
+
+`-useCustomStyle`: Export the documentation using alternate css files (by Daniel Vila).
+
+`--version`: Shows the current version of WIDOCO.
+
+`-webVowl`: Create a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#) in the documentation.
+
+
+## How can I make WIDOCO automatically recognize my vocabulary annotations?
+There are two alternative ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology.
+
+* The recommended way: add them in your OWL file. For guidelines on which ones to include, follow our [best practices document](https://w3id.org/widoco/bestPractices), which indicates which ones we recommend.
+* Alternatively, edit the project properties of /config/config.properties. This is a key-value pair file with metadata properties. Some people consider it easier than adding the property annotations to the OWL file, although I recommend doing the former option. Note that the character ";" is used for lists (for instance first author; second author; third author).
+
+For more information, see the [Widoco metadata guide](doc/metadataGuide/guide.md)
+
+## Browser issues (Why can't I see the generated documentation / visualization?)
+WIDOCO separates the contents of different sections in HTML files, which are then loaded in the `index.html` file. WIDOCO was designed this way because it's easier to edit your introduction or description sections independently without being all aggregated together in a huge HTML document. **When all the contents generated by WIDOCO are stored in a server, you will be able to see the documentation of your ontology using any browser**. However, if you open the `index.html` file **on your local browser**, you may see a document missing most of the sections in your documentation. This happens because browsers don't allow loading separate content when opening a file locally for security reasons. If you want to explore how your ontology would look locally, you have two options:
+
+* a) Execute WIDOCO with the `-uniteSections` flag; or select the option `add al sections in a single document` in the "load sections" step in the WIDOCO GUI. This will make all the sections of WIDOCO to be in the `index.html`; and you will be able to see it in your browser. Note that the **LODE visualization will not be available** when exploring your ontology locally.
+* b) Create a local server: Set up a local server (e.g., using XAMPP or Tomcat) and serve the files WIDOCO generates (in the `htdocs` folder for Apache servers).
+
+If you place the files generated by WIDOCO in a server and access them via its URL (for example, a Github page), you should be able to see your documentation appropriately.
+
+## Current improvements
+For a complete list of the current improvements and next features, check the [project open issues](https://github.com/dgarijo/Widoco/issues) and [milestones](https://github.com/dgarijo/Widoco/milestones) in the repository.
+
+## Requirements
+You will need Java 1.8 or higher (SDK 1.8 or JRE 8) for WIDOCO to work
+Otherwise, you will probably experience an "Unsupported major.minor version 52.0" exception when executing the JAR file.
+
+## Contribution guidelines
+Contributions to address any of the current issues are welcome. In order to push your contribution, just **push your pull request to the develop branch**. The master branch has only the code associated to the latest release.
\ No newline at end of file
diff --git a/src/somef_core/test/test_data/README-widoco-swh.md b/src/somef_core/test/test_data/README-widoco-swh.md
new file mode 100644
index 0000000..0f72c58
--- /dev/null
+++ b/src/somef_core/test/test_data/README-widoco-swh.md
@@ -0,0 +1,233 @@
+# WIzard for DOCumenting Ontologies (WIDOCO)
+[](https://doi.org/10.5281/zenodo.11093793) [](https://jitpack.io/#dgarijo/Widoco) [](https://www.repostatus.org/#active) [](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/dgarijo/Widoco) [](https://archive.softwareheritage.org/swh:1:dir:40d462bbecefc3a9c3e810567d1f0d7606e0fae7;origin=https://github.com/dgarijo/Widoco;visit=swh:1:snp:4d8570d390a18fee1d37f262ad79b36c021c611a;anchor=swh:1:rev:fec66b89a4f4acb015a44c7f8cb671d49bec626a)
+
+
+
+WIDOCO helps you to publish and create an enriched and customized documentation of your ontology automatically, by following a series of steps in a GUI.
+
+**Author**: Daniel Garijo Verdejo (@dgarijo)
+
+**Contributors**: María Poveda, Idafen Santana, Almudena Ruiz, Miguel Angel García, Oscar Corcho, Daniel Vila, Sergio Barrio, Martin Scharm, Maxime Lefrancois, Alfredo Serafini, @kartgk, Pat Mc Bennett, Christophe Camel, Jacobus Geluk, Martin Scharm, @rpietzsch, Jonathan Leitschuh, Jodi Schneider, Giacomo Lanza, Alejandra Gonzalez-Beltran, Mario Scrocca, Miguel Angel García, Flores Bakker, @JohnnyMoonlight, René Fritze, @telecsur, Jan Vlug, Han Kruiger, Johannes Theissen-Lipp, Roberto Polli, Victor Chavez, Sirko Schindler and Michaël Dierick.
+
+**Citing WIDOCO**: If you used WIDOCO in your work, please cite the ISWC 2017 paper: https://iswc2017.semanticweb.org/paper-138
+
+```bib
+@inproceedings{garijo2017widoco,
+ title={WIDOCO: a wizard for documenting ontologies},
+ author={Garijo, Daniel},
+ booktitle={International Semantic Web Conference},
+ pages={94--102},
+ year={2017},
+ organization={Springer, Cham},
+ doi = {10.1007/978-3-319-68204-4_9},
+ funding = {USNSF ICER-1541029, NIH 1R01GM117097-01},
+ url={http://dgarijo.com/papers/widoco-iswc2017.pdf}
+}
+```
+If you want to cite the latest version of the software, you can do so by using: https://zenodo.org/badge/latestdoi/11427075.
+
+## Downloading the executable
+
+To download WIDOCO, you need to download a JAR executable file. Check the latest release for more details: (https://github.com/dgarijo/WIDOCO/releases/latest).
+
+## Importing WIDOCO as a dependency
+Just add the dependency and repository to your `pom.xml` file as follows. See the [WIDOCO JitPack](https://jitpack.io/#dgarijo/Widoco) page to find alternative means to incorporate WIDOCO to your project.
+
+```xml
+
+
+ com.github.dgarijo
+ Widoco
+ v1.4.24
+
+
+
+[ ... ]
+
+
+
+ jitpack.io
+ https://jitpack.io
+
+
+```
+
+## Description
+WIDOCO helps you to publish and create an enriched and customized documentation of your ontology, by following a series of steps in a wizard. We extend the LODE framework by Silvio Peroni to describe the classes, properties and data properties of the ontology, the OOPS! webservice by María Poveda to print an evaluation and the Licensius service by Victor Rodriguez Doncel to determine the license URI and title being used. In addition, we use WebVowl to visualize the ontology and have extended Bubastis to show a complete changelog between different versions of your ontology.
+
+Features of WIDOCO:
+* Automatic documentation of the terms in your ontology (based on [LODE](http://www.essepuntato.it/lode/)). Now **you can use Markdown on your class descriptions** (see [example](https://dgarijo.github.io/Widoco/doc/gallery/index.html))
+* Massive metadata extraction and support: WIDOCO will enhance your ontology documentation based on your ontology annotations. Now you can add custom logos and images, edit the content of your sections, etc. by just editing metadata. See our [supported metadata](doc/metadataGuide/guide.md) and [recommendations](https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html) for more information.
+* Automatic annotation in JSON-LD snippets of the html produced.
+* Association of a provenance page which includes the history of your vocabulary (W3C PROV-O compliant).
+* Guidelines on the main sections that your document should have and how to complete them.
+* Integration with diagram creators ([WebVOWL](http://vowl.visualdataweb.org/webvowl/)).
+* Automatic changelog of differences between the actual and the previous version of the ontology (based on [Bubastis](http://www.ebi.ac.uk/efo/bubastis/)).
+* Separation of the sections of your html page so you can write them independently and replace only those needed.
+* Content negotiation and serialization of your ontology according to [W3C best practices](https://www.w3.org/TR/swbp-vocab-pub/)
+* Evaluation reports of your ontology (using the [OOPS! web service](https://oops.linkeddata.es/))
+* Integration with license metadata services ([Licensius](http://licensius.com/)) to automatically describe the license used in your ontology.
+
+## Examples
+Examples of the features of WIDOCO can be seen on [the gallery](https://dgarijo.github.io/Widoco/doc/gallery/)
+
+## GUI Tutorial
+A tutorial explaining the main features of the GUI can be found [here](https://dgarijo.github.io/Widoco/doc/tutorial/)
+
+## Metadata usage
+To see how WIDOCO recognizes metadata annotations in your ontology to create the documentation files, see [the WIDOCO metadata documentation](doc/metadataGuide/guide.md). To learn which metadata properties we recommend adding to your ontology for producing a nice-looking documentation, have a look at our [best practices guide](https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html).
+
+For example, in order to show your logo in your documentation you just need to use `foaf:logo` as an annotation, as follows:
+```
+@prefix owl: .
+@prefix foaf: a owl:Ontology ;
+ foaf:logo .
+```
+
+and it will show right next to the title. The [WIDOCO metadata documentation](doc/metadataGuide/guide.md) shows all supported metadata fields.
+
+## How to use WIDOCO
+
+### Building the JAR executable
+We provide JAR files for each release (see the [releases](https://github.com/dgarijo/Widoco/releases) page). However, if you want to build WIDOCO from scratch, just cd into the project folder and run:
+
+```bash
+mvn install
+```
+The JAR will be generated in a "JAR" folder. The name will follow the pattern: `widoco-{VERSION_ID}-jar-with-dependencies.jar`, where {VERSION_ID} is the version number of the tool.
+
+### JAR execution
+
+Download the latest `.jar` [WIDOCO available release](https://github.com/dgarijo/WIDOCO/releases/latest) (it will be something like `widoco-VERSION-jar-with-dependencies.jar`). Then just double click the `.jar` file.
+
+You may also execute WIDOCO through the command line. Usage:
+```bash
+java -jar widoco-VERSION-jar-with-dependencies.jar [OPTIONS]
+```
+
+### Docker execution
+If you don't want to use the JAR directly, you may run the project using a [Docker container](https://www.docker.com/). First you will need to download or build the image, and then run it.
+
+#### Reusing a pre-existing image
+We build containers in the [GitHub image registry](https://github.com/dgarijo/Widoco/pkgs/container/widoco) for all latest releases. In order to import one, just run the following command, stating the version of Widoco you prefer (e.g., for v1.4.23):
+
+```
+docker pull ghcr.io/dgarijo/widoco:v1.4.23
+```
+
+To browse all available images, see the [GitHub image registry](https://github.com/dgarijo/Widoco/pkgs/container/widoco).
+
+#### Building the image yourself
+
+Build the image using the `Dockerfile` in project folder:
+
+```bash
+docker build -t dgarijo/widoco .
+```
+
+#### Running WIDOCO's image
+
+You can now execute WIDOCO through the command line. Usage:
+
+```bash
+docker run -ti --rm dgarijo/widoco [OPTIONS]
+```
+
+**Note:** If you downloaded the image from the GitHub registry, you will have to change `dgarijo/widoco` with the name of the image you downloaded. For example `ghcr.io/dgarijo/widoco:v1.4.23`.
+
+If you want to share data between the Docker Container and your Host, for instance to load a local ontology file (from PATH), you will need to mount the container
+with host directories. For instance:
+
+```bash
+docker run -ti --rm \
+ -v `pwd`/test:/usr/local/widoco/in:Z \
+ -v `pwd`/target/generated-doc:/usr/local/widoco/out:Z \
+ dgarijo/widoco -ontFile in/bne.ttl -outFolder out -rewriteAll
+```
+
+### Execution options
+
+`-analytics CODE`: Add a code snippet for Google analytics to track your HTML documentation. You need to add your CODE next to the flag. For example: UA-1234
+
+`-confFile PATH`: Load your own configuration file for the ontology metadata. Use this option if you want to load your own HTML sections as well. Incompatible with -getOntologyMetadata. See [the configuration documentation](doc/configuration/configuration_doc.md) for more information about the accepted fields.
+
+`-crossRef`: ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag is intended to be used only after a first version of the documentation exists.
+
+`-displayDirectImportsOnly`: Only those imported ontologies that are directly imported in the ontology being documented.
+
+`-doNotDisplaySerializations`: The serializations of the ontology will not be displayed.
+
+`-excludeIntroduction`: Skip the introduction section in the documentation.
+
+`-excludeProvenance`: Do not add the link "Provenance of this page" in the metadata header section
+
+`-getOntologyMetadata`: Extract ontology metadata from the given ontology
+
+`--help`: Shows a help message and exits.
+
+`-htaccess`: Create a bundle for publication ready to be deployed on your Apache server.
+
+
+`-ignoreIndividuals`: Individuals will not be included in the documentation.
+
+`-includeAnnotationProperties`: Include annotation properties defined in your ontology in the documentation (by default they are not included)
+
+`-includeImportedOntologies`: Indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not.
+
+`-import`: imports a local ontology (e.g., if you don't want to load an online ontology, you may load its local version)
+
+`-lang LANG1-LANG2`: Generate documentation in multiple languages (separated by "-"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es
+
+`-licensius`: Use the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata flag is enabled.
+
+`-noPlaceHolderText`: Do not add any placeholder text (this will remove intro, abstract (if empty) and description sections).
+
+`-ontFile PATH` [required (unless -ontURI is used)]: Load a local ontology file (from PATH) to document. This option is incompatible with -ontURI
+
+`-outFolder folderName`: Specifies the name of the folder where to save the documentation. By default is 'myDocumentation'
+
+`-ontURI URI` [required (unless -ontFile is used)]: Load an ontology to document from its URI. This option is incompatible with -ontFile
+
+`-oops`: Create an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/)
+
+`-rewriteAll`: Replace any existing files when documenting an ontology (e.g., from a previous execution)
+
+`-rewriteBase PATH`: Change the default rewrite base path. The default value is "/". This flag can only be used with the htaccess option.
+
+`-saveConfig PATH`: Save a configuration file on PATH with the properties of a given ontology
+
+`-uniteSections`: Write all HTML sections into a single HTML document.
+
+`-useCustomStyle`: Export the documentation using alternate css files (by Daniel Vila).
+
+`--version`: Shows the current version of WIDOCO.
+
+`-webVowl`: Create a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#) in the documentation.
+
+
+## How can I make WIDOCO automatically recognize my vocabulary annotations?
+There are two alternative ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology.
+
+* The recommended way: add them in your OWL file. For guidelines on which ones to include, follow our [best practices document](https://w3id.org/widoco/bestPractices), which indicates which ones we recommend.
+* Alternatively, edit the project properties of /config/config.properties. This is a key-value pair file with metadata properties. Some people consider it easier than adding the property annotations to the OWL file, although I recommend doing the former option. Note that the character ";" is used for lists (for instance first author; second author; third author).
+
+For more information, see the [Widoco metadata guide](doc/metadataGuide/guide.md)
+
+## Browser issues (Why can't I see the generated documentation / visualization?)
+WIDOCO separates the contents of different sections in HTML files, which are then loaded in the `index.html` file. WIDOCO was designed this way because it's easier to edit your introduction or description sections independently without being all aggregated together in a huge HTML document. **When all the contents generated by WIDOCO are stored in a server, you will be able to see the documentation of your ontology using any browser**. However, if you open the `index.html` file **on your local browser**, you may see a document missing most of the sections in your documentation. This happens because browsers don't allow loading separate content when opening a file locally for security reasons. If you want to explore how your ontology would look locally, you have two options:
+
+* a) Execute WIDOCO with the `-uniteSections` flag; or select the option `add al sections in a single document` in the "load sections" step in the WIDOCO GUI. This will make all the sections of WIDOCO to be in the `index.html`; and you will be able to see it in your browser. Note that the **LODE visualization will not be available** when exploring your ontology locally.
+* b) Create a local server: Set up a local server (e.g., using XAMPP or Tomcat) and serve the files WIDOCO generates (in the `htdocs` folder for Apache servers).
+
+If you place the files generated by WIDOCO in a server and access them via its URL (for example, a Github page), you should be able to see your documentation appropriately.
+
+## Current improvements
+For a complete list of the current improvements and next features, check the [project open issues](https://github.com/dgarijo/Widoco/issues) and [milestones](https://github.com/dgarijo/Widoco/milestones) in the repository.
+
+## Requirements
+You will need Java 1.8 or higher (SDK 1.8 or JRE 8) for WIDOCO to work
+Otherwise, you will probably experience an "Unsupported major.minor version 52.0" exception when executing the JAR file.
+
+## Contribution guidelines
+Contributions to address any of the current issues are welcome. In order to push your contribution, just **push your pull request to the develop branch**. The master branch has only the code associated to the latest release.
\ No newline at end of file
diff --git a/src/somef_core/test/test_data/api_responses/somef-demo.json b/src/somef_core/test/test_data/api_responses/somef-demo.json
new file mode 100644
index 0000000..15434bb
--- /dev/null
+++ b/src/somef_core/test/test_data/api_responses/somef-demo.json
@@ -0,0 +1,648 @@
+{
+ "somef_provenance": {
+ "somef_version": "0.9.12",
+ "somef_schema_version": "1.0.0",
+ "date": "2025-12-10 11:21:43"
+ },
+ "code_repository": [
+ {
+ "result": {
+ "value": "https://github.com/juanjemdIos/somef-demo-repo",
+ "type": "Url"
+ },
+ "confidence": 1,
+ "technique": "GitHub_API"
+ }
+ ],
+ "owner": [
+ {
+ "result": {
+ "value": "juanjemdIos",
+ "type": "User"
+ },
+ "confidence": 1,
+ "technique": "GitHub_API"
+ }
+ ],
+ "date_created": [
+ {
+ "result": {
+ "value": "2025-04-23T13:26:06Z",
+ "type": "Date"
+ },
+ "confidence": 1,
+ "technique": "GitHub_API"
+ }
+ ],
+ "date_updated": [
+ {
+ "result": {
+ "value": "2025-05-05T06:57:47Z",
+ "type": "Date"
+ },
+ "confidence": 1,
+ "technique": "GitHub_API"
+ }
+ ],
+ "license": [
+ {
+ "result": {
+ "value": "https://api.github.com/licenses/agpl-3.0",
+ "type": "License",
+ "name": "GNU Affero General Public License v3.0",
+ "url": "https://api.github.com/licenses/agpl-3.0",
+ "spdx_id": "AGPL-3.0"
+ },
+ "confidence": 1,
+ "technique": "GitHub_API"
+ },
+ {
+ "result": {
+ "value": " GNU AFFERO GENERAL PUBLIC LICENSE\n Version 3, 19 November 2007\n\n Copyright (C) 2007 Free Software Foundation, Inc. \n Copyright (C) \n\n This program is free software: you can redistribute it and/or modify\n it under the terms of the GNU Affero General Public License as published\n by the Free Software Foundation, either version 3 of the License, or\n (at your option) any later version.\n\n This program is distributed in the hope that it will be useful,\n but WITHOUT ANY WARRANTY; without even the implied warranty of\n MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n GNU Affero General Public License for more details.\n\n You should have received a copy of the GNU Affero General Public License\n along with this program. If not, see \n \n com.github.dgarijo \n Widoco \n v1.4.24 \n \n \n\n[ ... ]\n\n\n\t\n\t jitpack.io \n\t https://jitpack.io \n\t \n \n```",
+ "type": "Software_application"
+ },
+ "confidence": 1,
+ "technique": "code_parser",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/codemeta.json"
+ },
+ {
+ "result": {
+ "value": "You will need Java 1.8 or higher (SDK 1.8 or JRE 8) for WIDOCO to work\nOtherwise, you will probably experience an \"Unsupported major.minor version 52.0\" exception when executing the JAR file.",
+ "type": "Software_application"
+ },
+ "confidence": 1,
+ "technique": "code_parser",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/codemeta.json"
+ },
+ {
+ "result": {
+ "value": "Just add the dependency and repository to your `pom.xml` file as follows. See the [WIDOCO JitPack](https://jitpack.io/#dgarijo/Widoco) page to find alternative means to incorporate WIDOCO to your project.\n\n```xml\n\n \n com.github.dgarijo \n Widoco \n v1.4.24 \n \n \n\n[ ... ]\n\n\n\t\n\t jitpack.io \n\t https://jitpack.io \n\t \n \n```\n",
+ "type": "Text_excerpt",
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+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)"
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+ "technique": "header_analysis",
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+ "type": "Text_excerpt",
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+ "parent_header": [
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+ "result": {
+ "value": "https://raw.githubusercontent.com/dgarijo/Widoco/master/doc/vocabulary/1.0.0/ontology.nt",
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+ },
+ "confidence": 1,
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+ },
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+ "result": {
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+ },
+ "confidence": 1,
+ "technique": "file_exploration"
+ },
+ {
+ "result": {
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+ "type": [
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+ "download": [
+ {
+ "result": {
+ "value": "To download WIDOCO, you need to download a JAR executable file. Check the latest release for more details: (https://github.com/dgarijo/WIDOCO/releases/latest).\n",
+ "type": "Text_excerpt",
+ "original_header": "Downloading the executable",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ }
+ ],
+ "usage": [
+ {
+ "result": {
+ "value": "Examples of the features of WIDOCO can be seen on [the gallery](https://dgarijo.github.io/Widoco/doc/gallery/)\n",
+ "type": "Text_excerpt",
+ "original_header": "Examples",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ },
+ {
+ "result": {
+ "value": "A tutorial explaining the main features of the GUI can be found [here](https://dgarijo.github.io/Widoco/doc/tutorial/) \n",
+ "type": "Text_excerpt",
+ "original_header": "GUI Tutorial",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ },
+ {
+ "result": {
+ "value": "To see how WIDOCO recognizes metadata annotations in your ontology to create the documentation files, see [the WIDOCO metadata documentation](doc/metadataGuide/guide.md). To learn which metadata properties we recommend adding to your ontology for producing a nice-looking documentation, have a look at our [best practices guide](https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html).\n\nFor example, in order to show your logo in your documentation you just need to use `foaf:logo` as an annotation, as follows:\n```\n@prefix owl: .\n@prefix foaf: a owl:Ontology ;\n foaf:logo .\n```\n\nand it will show right next to the title. The [WIDOCO metadata documentation](doc/metadataGuide/guide.md) shows all supported metadata fields.\n",
+ "type": "Text_excerpt",
+ "original_header": "Metadata usage",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)"
+ ]
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+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ },
+ {
+ "result": {
+ "value": "We provide JAR files for each release (see the [releases](https://github.com/dgarijo/Widoco/releases) page). However, if you want to build WIDOCO from scratch, just cd into the project folder and run:\n\n```bash\nmvn install\n```\nThe JAR will be generated in a \"JAR\" folder. The name will follow the pattern: `widoco-{VERSION_ID}-jar-with-dependencies.jar`, where {VERSION_ID} is the version number of the tool.\n",
+ "type": "Text_excerpt",
+ "original_header": "Building the JAR executable",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)",
+ "How to use WIDOCO"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ },
+ {
+ "result": {
+ "value": "Download the latest `.jar` [WIDOCO available release](https://github.com/dgarijo/WIDOCO/releases/latest) (it will be something like `widoco-VERSION-jar-with-dependencies.jar`). Then just double click the `.jar` file.\n\nYou may also execute WIDOCO through the command line. Usage:\n```bash\njava -jar widoco-VERSION-jar-with-dependencies.jar [OPTIONS]\n```\n",
+ "type": "Text_excerpt",
+ "original_header": "JAR execution",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)",
+ "How to use WIDOCO"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ },
+ {
+ "result": {
+ "value": "If you don't want to use the JAR directly, you may run the project using a [Docker container](https://www.docker.com/). First you will need to download or build the image, and then run it.\n",
+ "type": "Text_excerpt",
+ "original_header": "Docker execution",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)",
+ "How to use WIDOCO"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ },
+ {
+ "result": {
+ "value": "We build containers in the [GitHub image registry](https://github.com/dgarijo/Widoco/pkgs/container/widoco) for all latest releases. In order to import one, just run the following command, stating the version of Widoco you prefer (e.g., for v1.4.23):\n\n```\ndocker pull ghcr.io/dgarijo/widoco:v1.4.23\n```\n\nTo browse all available images, see the [GitHub image registry](https://github.com/dgarijo/Widoco/pkgs/container/widoco).\n",
+ "type": "Text_excerpt",
+ "original_header": "Reusing a pre-existing image",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)",
+ "How to use WIDOCO",
+ "Docker execution"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ },
+ {
+ "result": {
+ "value": "Build the image using the `Dockerfile` in project folder:\n\n```bash\ndocker build -t dgarijo/widoco .\n```\n",
+ "type": "Text_excerpt",
+ "original_header": "Building the image yourself",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)",
+ "How to use WIDOCO",
+ "Docker execution"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ },
+ {
+ "result": {
+ "value": "`-analytics CODE`: Add a code snippet for Google analytics to track your HTML documentation. You need to add your CODE next to the flag. For example: UA-1234\n\n`-confFile PATH`: Load your own configuration file for the ontology metadata. Use this option if you want to load your own HTML sections as well. Incompatible with -getOntologyMetadata. See [the configuration documentation](doc/configuration/configuration_doc.md) for more information about the accepted fields.\n\n`-crossRef`: ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag is intended to be used only after a first version of the documentation exists.\n\n`-displayDirectImportsOnly`: Only those imported ontologies that are directly imported in the ontology being documented.\n\n`-doNotDisplaySerializations`: The serializations of the ontology will not be displayed.\n\n`-excludeIntroduction`: Skip the introduction section in the documentation.\n\n`-excludeProvenance`: Do not add the link \"Provenance of this page\" in the metadata header section\n\n`-getOntologyMetadata`: Extract ontology metadata from the given ontology\n\n`--help`: Shows a help message and exits.\n\n`-htaccess`: Create a bundle for publication ready to be deployed on your Apache server.\n\n\n`-ignoreIndividuals`: Individuals will not be included in the documentation.\n\n`-includeAnnotationProperties`: Include annotation properties defined in your ontology in the documentation (by default they are not included)\n\n`-includeImportedOntologies`: Indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not.\n\n`-import`: imports a local ontology (e.g., if you don't want to load an online ontology, you may load its local version)\n\n`-lang LANG1-LANG2`: Generate documentation in multiple languages (separated by \"-\"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es\n\n`-licensius`: Use the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata flag is enabled.\n\n`-noPlaceHolderText`: Do not add any placeholder text (this will remove intro, abstract (if empty) and description sections).\n\n`-ontFile PATH` [required (unless -ontURI is used)]: Load a local ontology file (from PATH) to document. This option is incompatible with -ontURI\n\n`-outFolder folderName`: Specifies the name of the folder where to save the documentation. By default is 'myDocumentation'\n\n`-ontURI URI` [required (unless -ontFile is used)]: Load an ontology to document from its URI. This option is incompatible with -ontFile\n\n`-oops`: Create an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/)\n\n`-rewriteAll`: Replace any existing files when documenting an ontology (e.g., from a previous execution)\n\n`-rewriteBase PATH`: Change the default rewrite base path. The default value is \"/\". This flag can only be used with the htaccess option.\n\n`-saveConfig PATH`: Save a configuration file on PATH with the properties of a given ontology\n\n`-uniteSections`: Write all HTML sections into a single HTML document.\n\n`-useCustomStyle`: Export the documentation using alternate css files (by Daniel Vila).\n\n`--version`: Shows the current version of WIDOCO.\n\n`-webVowl`: Create a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#) in the documentation.\n\n",
+ "type": "Text_excerpt",
+ "original_header": "Execution options",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)",
+ "How to use WIDOCO"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ }
+ ],
+ "run": [
+ {
+ "result": {
+ "value": "You can now execute WIDOCO through the command line. Usage:\n\n```bash\ndocker run -ti --rm dgarijo/widoco [OPTIONS]\n```\n\n**Note:** If you downloaded the image from the GitHub registry, you will have to change `dgarijo/widoco` with the name of the image you downloaded. For example `ghcr.io/dgarijo/widoco:v1.4.23`.\n\nIf you want to share data between the Docker Container and your Host, for instance to load a local ontology file (from PATH), you will need to mount the container\nwith host directories. For instance:\n\n```bash\ndocker run -ti --rm \\\n -v `pwd`/test:/usr/local/widoco/in:Z \\\n -v `pwd`/target/generated-doc:/usr/local/widoco/out:Z \\\n dgarijo/widoco -ontFile in/bne.ttl -outFolder out -rewriteAll\n```\n",
+ "type": "Text_excerpt",
+ "original_header": "Running WIDOCO's image",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)",
+ "How to use WIDOCO",
+ "Docker execution"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ }
+ ],
+ "documentation": [
+ {
+ "result": {
+ "value": "WIDOCO separates the contents of different sections in HTML files, which are then loaded in the `index.html` file. WIDOCO was designed this way because it's easier to edit your introduction or description sections independently without being all aggregated together in a huge HTML document. **When all the contents generated by WIDOCO are stored in a server, you will be able to see the documentation of your ontology using any browser**. However, if you open the `index.html` file **on your local browser**, you may see a document missing most of the sections in your documentation. This happens because browsers don't allow loading separate content when opening a file locally for security reasons. If you want to explore how your ontology would look locally, you have two options:\n\n* a) Execute WIDOCO with the `-uniteSections` flag; or select the option `add al sections in a single document` in the \"load sections\" step in the WIDOCO GUI. This will make all the sections of WIDOCO to be in the `index.html`; and you will be able to see it in your browser. Note that the **LODE visualization will not be available** when exploring your ontology locally.\n* b) Create a local server: Set up a local server (e.g., using XAMPP or Tomcat) and serve the files WIDOCO generates (in the `htdocs` folder for Apache servers).\n\nIf you place the files generated by WIDOCO in a server and access them via its URL (for example, a Github page), you should be able to see your documentation appropriately.\n",
+ "type": "Text_excerpt",
+ "original_header": "Browser issues (Why can't I see the generated documentation / visualization?)",
+ "parent_header": [
+ "WIzard for DOCumenting Ontologies (WIDOCO)"
+ ]
+ },
+ "confidence": 1,
+ "technique": "header_analysis",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ }
+ ],
+ "application_domain": [
+ {
+ "result": {
+ "type": "String",
+ "value": "Semantic web"
+ },
+ "confidence": 0.921888526958785,
+ "technique": "supervised_classification"
+ }
+ ],
+ "full_title": [
+ {
+ "result": {
+ "type": "String",
+ "value": "WIzard for DOCumenting Ontologies (WIDOCO)"
+ },
+ "confidence": 1,
+ "technique": "regular_expression",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ }
+ ],
+ "repository_status": [
+ {
+ "result": {
+ "type": "Url",
+ "value": "https://www.repostatus.org/#active",
+ "description": "Active \u2013 The project has reached a stable, usable state and is being actively developed."
+ },
+ "confidence": 1,
+ "technique": "regular_expression",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ }
+ ],
+ "logo": [
+ {
+ "result": {
+ "type": "Url",
+ "value": "https://raw.githubusercontent.com/dgarijo/Widoco/master/src/main/resources/logo/logo2.png"
+ },
+ "confidence": 1,
+ "technique": "regular_expression",
+ "source": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+ }
+ ]
+}
\ No newline at end of file
diff --git a/src/somef_core/test/test_data/authors_files/docker_AUTHORS 2.txt b/src/somef_core/test/test_data/authors_files/docker_AUTHORS 2.txt
new file mode 100644
index 0000000..3d3fe3c
--- /dev/null
+++ b/src/somef_core/test/test_data/authors_files/docker_AUTHORS 2.txt
@@ -0,0 +1,718 @@
+# This file lists all individuals having contributed content to the repository.
+# For how it is generated, see `project/generate-authors.sh`.
+
+Aanand Prasad
+Aaron Feng
+Aaron Huslage
+Abel Muiño
+Abhinav Ajgaonkar
+Abin Shahab
+Adam Miller
+Adam Singer
+Aditya
+Adrian Mouat
+Adrien Folie
+Ahmet Alp Balkan
+AJ Bowen
+alambike
+Alan Thompson
+Albert Callarisa
+Albert Zhang
+Aleksa Sarai
+Alexander Larsson
+Alexander Shopov
+Alexandr Morozov
+Alexey Kotlyarov
+Alexey Shamrin
+Alex Gaynor
+Alexis THOMAS
+Alex Warhawk
+almoehi
+Al Tobey
+Álvaro Lázaro
+amangoel
+Amit Bakshi
+AnandkumarPatel
+Anand Patil
+Andrea Luzzardi
+Andreas Köhler
+Andreas Savvides
+Andreas Tiefenthaler
+Andrea Turli
+Andre Dublin <81dublin@gmail.com>
+Andrew Duckworth
+Andrew France
+Andrew Macgregor
+Andrew Munsell
+Andrews Medina
+Andrew Weiss
+Andrew Williams
+Andrey Petrov
+Andrey Stolbovsky
+Andy Chambers
+andy diller
+Andy Goldstein
+Andy Kipp
+Andy Rothfusz
+Andy Smith
+Andy Wilson
+Anthony Bishopric
+Anton Löfgren
+Anton Nikitin
+Antony Messerli
+apocas
+ArikaChen
+Arnaud Porterie
+Arthur Gautier
+Asbjørn Enge
+averagehuman
+Avi Miller
+Barnaby Gray
+Barry Allard
+Bartłomiej Piotrowski
+bdevloed
+Ben Firshman
+Benjamin Atkin
+Benoit Chesneau
+Ben Sargent
+Ben Toews
+Ben Wiklund
+Bernerd Schaefer
+Bert Goethals
+Bhiraj Butala
+bin liu
+Blake Geno
+Bouke Haarsma
+Boyd Hemphill
+Brandon Liu
+Brandon Philips
+Brandon Rhodes
+Brett Kochendorfer
+Brian (bex) Exelbierd
+Brian Dorsey
+Brian Flad
+Brian Goff
+Brian McCallister
+Brian Olsen
+Brian Shumate
+Brice Jaglin
+Briehan Lombaard
+Bruno Bigras
+Bruno Binet
+Bruno Renié
+Bryan Bess
+Bryan Matsuo
+Bryan Murphy
+Burke Libbey
+Byung Kang
+Caleb Spare
+Calen Pennington
+Cameron Boehmer
+Carl X. Su
+Charles Hooper
+Charles Lindsay
+Charles Merriam
+Charlie Lewis
+Chewey
+Chia-liang Kao
+Chris Alfonso
+Chris Armstrong
+chrismckinnel
+Chris Snow
+Chris St. Pierre
+Christian Berendt
+ChristoperBiscardi
+Christopher Currie
+Christopher Rigor
+Christophe Troestler
+Ciro S. Costa
+Clayton Coleman
+Colin Dunklau
+Colin Rice
+Colin Walters
+Cory Forsyth
+cressie176
+Cruceru Calin-Cristian
+Daan van Berkel
+Daehyeok.Mun
+Dafydd Crosby
+Dan Buch
+Dan Cotora
+Dan Griffin
+Dan Hirsch
+Daniel, Dao Quang Minh
+Daniel Exner
+Daniel Farrell
+Daniel Garcia
+Daniel Gasienica
+Daniel Menet
+Daniel Mizyrycki
+Daniel Norberg
+Daniel Nordberg
](https://github.com/uncbiag/ICON/actions)
+[](https://pypi.org/project/icon-registration)
+[](https://youtu.be/7kZsJ3zWDCA)
+
+
+## Running our code
+
+We are available on PyPI!
+```bash
+pip install icon-registration
+```
+
+
+To run our pretrained model in the cloud on sample images from OAI knees, visit [our knee google colab notebook](https://colab.research.google.com/drive/1svftgw-vYWnLp9lSf3UkrG547atjbIrg?usp=sharing)
+
+To run our pretrained model for lung CT scans on an example from COPDgene, visit [our lung google colab notebook](https://colab.research.google.com/github/uncbiag/ICON/blob/master/notebooks/ICON_lung_demo.ipynb)
+
+----------------
+
+To train from scratch on the synthetic triangles and circles dataset:
+
+```bash
+git clone https://github.com/uncbiag/ICON
+cd ICON
+
+pip install -e .
+
+python training_scripts/2d_triangles_example.py
+```
+
diff --git a/src/somef_core/test/test_data/README-uncbiag.md b/src/somef_core/test/test_data/README-uncbiag.md
new file mode 100644
index 0000000..49a45ef
--- /dev/null
+++ b/src/somef_core/test/test_data/README-uncbiag.md
@@ -0,0 +1,91 @@
+
+
+
+# ICON: Learning Regular Maps through Inverse Consistency
+
+[](https://github.com/uncbiag/ICON/actions)
+[](https://pypi.org/project/icon-registration)
+[](https://youtu.be/7kZsJ3zWDCA)
+
+
+## Running our code
+
+We are available on PyPI!
+```bash
+pip install icon-registration
+```
+
+
+To run our pretrained model in the cloud on sample images from OAI knees, visit [our knee google colab notebook](https://colab.research.google.com/drive/1svftgw-vYWnLp9lSf3UkrG547atjbIrg?usp=sharing)
+
+To run our pretrained model for lung CT scans on an example from COPDgene, visit [our lung google colab notebook](https://colab.research.google.com/github/uncbiag/ICON/blob/master/notebooks/ICON_lung_demo.ipynb)
+
+----------------
+
+To train from scratch on the synthetic triangles and circles dataset:
+
+```bash
+git clone https://github.com/uncbiag/ICON
+cd ICON
+
+pip install -e .
+
+python training_scripts/2d_triangles_example.py
+```
+
diff --git a/src/somef_core/test/test_data/README-widoco-duplicate-dois 2.md b/src/somef_core/test/test_data/README-widoco-duplicate-dois 2.md
new file mode 100644
index 0000000..85fb4f0
--- /dev/null
+++ b/src/somef_core/test/test_data/README-widoco-duplicate-dois 2.md
@@ -0,0 +1,198 @@
+# WIzard for DOCumenting Ontologies (WIDOCO)
+[](https://zenodo.org/badge/latestdoi/11427075) [](https://jitpack.io/#dgarijo/Widoco)
+
+
+
+WIDOCO helps you to publish and create an enriched and customized documentation of your ontology automatically, by following a series of steps in a GUI.
+
+**Author**: Daniel Garijo Verdejo (@dgarijo)
+
+**Contributors**: María Poveda, Idafen Santana, Almudena Ruiz, Miguel Angel García, Oscar Corcho, Daniel Vila, Sergio Barrio, Martin Scharm, Maxime Lefrancois, Alfredo Serafini, @kartgk, Pat Mc Bennett, Christophe Camel, Jacobus Geluk, Martin Scharm, @rpietzsch, Jonathan Leitschuh, Jodi Schneider, Giacomo Lanza, Alejandra Gonzalez-Beltran, Mario Scrocca, Miguel Angel García and Flores Bakker.
+
+**Citing WIDOCO**: If you used WIDOCO in your work, please cite the ISWC 2017 paper: https://iswc2017.semanticweb.org/paper-138
+
+```bib
+@inproceedings{garijo2017widoco,
+ title={WIDOCO: a wizard for documenting ontologies},
+ author={Garijo, Daniel},
+ booktitle={International Semantic Web Conference},
+ pages={94--102},
+ year={2017},
+ organization={Springer, Cham},
+ doi = {10.1007/978-3-319-68204-4_9},
+ funding = {USNSF ICER-1541029, NIH 1R01GM117097-01},
+ url={http://dgarijo.com/papers/widoco-iswc2017.pdf}
+}
+
+@inproceedings{garijo2017widoco_duplicate,
+ title={WIDOCO: a wizard for documenting ontologies},
+ author={Garijo, Daniel},
+ booktitle={International Semantic Web Conference},
+ pages={94--102},
+ year={2017},
+ organization={Springer, Cham},
+ doi = {https://dx.doi.org/10.1007/978-3-319-68204-4_9},
+ url={http://dgarijo.com/papers/widoco-iswc2017.pdf}
+}
+```
+If you want to cite the latest version of the software, you can do so by using: https://zenodo.org/badge/latestdoi/11427075.
+
+## Downloading the executable
+
+To download WIDOCO, you need to download a JAR executable file. Check the latest release for more details: (https://github.com/dgarijo/WIDOCO/releases/latest).
+
+## Importing WIDOCO as a dependency
+Just add the dependency and repository to your `pom.xml` file as follows. See the [WIDOCO JitPack](https://jitpack.io/#dgarijo/Widoco) page to find alternative means to incorporate WIDOCO to your project.
+
+```xml
+