examples: refactor a bit the examples

- moved the common storage code to vdk-storage library
- refactored confluence-reader to directly use it instead of using file

Author: antoniivanov

examples/confluence-reader/README.md

@@ -13,9 +13,9 @@ The `ConfluenceDataSource` class is the heart of this data job. It provides a se
 
 These methods make use of the last_modification.txt file to determine the last modification date and track changes in the Confluence space, allowing for efficient data retrieval and management.
 
-## JSON Data Format
+## Output Data Format
 
-The resulting JSON data (confluence_data.json) is generated using the `ConfluenceDocument` class (see confluence_document.py).
+The resulting data is generated using the `ConfluenceDocument` class (see confluence_document.py).
 It follows this structured format:
 
 ```json

examples/confluence-reader/confluence_document.py

@@ -3,7 +3,7 @@
 
 
 class ConfluenceDocument:
-    def __init__(self, metadata, data, deleted=False):
+    def __init__(self, metadata: dict, data: str, deleted=False):
         """
         Initializes a ConfluenceDocument instance.
 

examples/confluence-reader/fetch_confluence_space.py

@@ -1,76 +1,33 @@
 # Copyright 2023-2024 Broadcom
 # SPDX-License-Identifier: Apache-2.0
-import json
 import logging
 import os
-import pathlib
 from datetime import datetime
 
-from common.database_storage import DatabaseStorage
 from confluence_document import ConfluenceDocument
 from langchain_community.document_loaders import ConfluenceLoader
 from vdk.api.job_input import IJobInput
-
+from vdk.plugin.storage.database_storage import DatabaseStorage
 
 log = logging.getLogger(__name__)
 
 
-def read_json_file(file_path):
-    try:
-        with open(file_path) as file:
-            return json.load(file)
-    except (FileNotFoundError, json.JSONDecodeError) as e:
-        log.error(f"Error reading JSON file: {e}")
-        return None
-
-
-def write_json_file(file_path, data):
-    try:
-        with open(file_path, "w") as file:
-            json.dump(data, file, indent=4)
-    except OSError as e:
-        log.error(f"Error writing JSON file: {e}")
-
-
-def update_saved_documents(file_path, new_docs):
-    existing_docs = read_json_file(file_path) or []
-
-    if (
-        isinstance(existing_docs, list)
-        and existing_docs
-        and isinstance(existing_docs[0], dict)
-    ):
-        existing_docs = [
-            ConfluenceDocument(
-                doc["metadata"], doc["data"], doc["metadata"].get("deleted", False)
-            )
-            for doc in existing_docs
-        ]
-
-    existing_docs_dict = {doc.metadata["id"]: doc for doc in existing_docs}
-
-    for doc in new_docs:
-        existing_docs_dict[doc.metadata["id"]] = doc
+def merge_docs(existing_docs, new_docs) -> list:
+    if existing_docs:
+        existing_docs_dict = {doc.metadata["id"]: doc for doc in existing_docs}
 
-    updated_docs_list = list(existing_docs_dict.values())
+        for doc in new_docs:
+            existing_docs_dict[doc.metadata["id"]] = doc
+        return list(existing_docs_dict.values())
+    else:
+        return new_docs
 
-    serialized_docs = [doc.serialize() for doc in updated_docs_list]
-    write_json_file(file_path, serialized_docs)
 
-
-def flag_deleted_pages(file_path, current_confluence_documents):
-    existing_docs = read_json_file(file_path)
+def flag_deleted_pages(existing_docs, current_confluence_documents):
     if existing_docs is None:
         log.error("Existing documents not found. Exiting.")
         return
 
-    existing_docs = [
-        ConfluenceDocument(
-            doc["metadata"], doc["data"], doc["metadata"].get("deleted", False)
-        )
-        for doc in existing_docs
-    ]
-
     current_page_ids = {doc.metadata["id"] for doc in current_confluence_documents}
 
     num_deleted = 0
@@ -80,9 +37,6 @@ def flag_deleted_pages(file_path, current_confluence_documents):
             num_deleted += 1
     log.info(f"Found {num_deleted} deleted pages.")
 
-    serialized_docs = [doc.serialize() for doc in existing_docs]
-    write_json_file(file_path, serialized_docs)
-
 
 class ConfluenceDataSource:
     """
@@ -170,34 +124,33 @@ def run(job_input: IJobInput):
         .setdefault(parent_page_id, {})
         .get("last_date", "1900-01-01 12:00")
     )
-    data_file = os.path.join(
-        job_input.get_temporary_write_directory(), "confluence_data.json"
-    )
     storage_name = get_value(job_input, "storage_name", "confluence_data")
     storage = DatabaseStorage(get_value(job_input, "storage_connection_string"))
     # TODO: this is not optimal . We just care about the IDs, we should not need to retrieve everything
-    data = storage.retrieve(storage_name)
-    pathlib.Path(data_file).write_text(data if data else "[]")
+    existing_docs = storage.retrieve(storage_name)
+    if existing_docs:
+        existing_docs = [ConfluenceDocument(**doc) for doc in existing_docs]
 
     confluence_reader = ConfluenceDataSource(confluence_url, token, space_key)
-
     updated_docs = confluence_reader.fetch_updated_pages_in_confluence_space(
         last_date, parent_page_id
     )
     log.info(f"Found {len(updated_docs)} updated pages")
-    update_saved_documents(data_file, updated_docs)
+    all_docs = merge_docs(existing_docs, updated_docs)
 
     # This is buggy , it doesn't account for server timezone and local timezone
     # But also assumes that server clock and local clock are synchronized (which they are likely not)
     # The ts should be the one of the latest processed page.
     set_property(job_input, "last_date", datetime.now().strftime("%Y-%m-%d %H:%M"))
 
     flag_deleted_pages(
-        data_file,
+        all_docs,
         confluence_reader.fetch_all_pages_in_confluence_space(parent_page_id),
     )
 
     # TODO: it would be better to save each page in separate row.
     # But that's quick solution for now to pass the data to the next job
 
-    storage.store(storage_name, pathlib.Path(data_file).read_text())
+    log.info(f"Store {len(all_docs)} documents in {storage_name}")
+    # TODO: why not use job_input.send_object_for_ingestion ... it's our ingestion interface
+    storage.store(storage_name, [doc.serialize() for doc in all_docs])

examples/confluence-reader/requirements.txt

@@ -3,7 +3,8 @@
 # The file is optional and can be deleted if no extra library dependencies are necessary.
 
 atlassian-python-api
-langchain_community
+langchain-community
 lxml
 psycopg2-binary
 sqlalchemy
+vdk-storage

examples/pgvector-embedder/00_properties.py

@@ -20,3 +20,7 @@ def run(job_input: IJobInput):
         )
     )
     job_input.set_all_properties(properties)
+
+    hf_home = job_input.get_temporary_write_directory() / "hf"
+    hf_home.mkdir(parents=True, exist_ok=True)
+    os.environ["HF_HOME"] = str(hf_home)

examples/pgvector-embedder/01_local_properties.py

@@ -0,0 +1,29 @@
+# Copyright 2021-2024 VMware, Inc.
+# SPDX-License-Identifier: Apache-2.0
+import os
+
+from vdk.api.job_input import IJobInput
+
+
+def set_property(job_input: IJobInput, key, value):
+    props = job_input.get_all_properties()
+    props[key] = value
+    job_input.set_all_properties(props)
+
+
+def run(job_input: IJobInput):
+    set_property(
+        job_input,
+        "storage_connection_string",
+        "postgresql://pgadmin:ePgqsEQ2823S8J7L2w4gVziNz7IWm0@10.148.186.71:5432/spulov-test",
+    )
+
+    props = job_input.get_all_properties()
+    props.update(
+        dict(
+            destination_metadata_table="vdk_confluence_sc_metadata",
+            destination_embeddings_table="vdk_confluence_sc_embeddings",
+            storage_name="supercollider_chunked",
+        )
+    )
+    job_input.set_all_properties(props)

examples/pgvector-embedder/01_setup_huggingface.py

@@ -0,0 +1,14 @@
+# Copyright 2021-2024 VMware, Inc.
+# SPDX-License-Identifier: Apache-2.0
+import os.path
+import pathlib
+
+from vdk.api.job_input import IJobInput
+
+
+def run(job_input: IJobInput):
+    # HF uses temporary directories in the process of its work
+    # So make sure to use only allowed ones
+    hf_home = job_input.get_temporary_write_directory() / "hf"
+    hf_home.mkdir(parents=True, exist_ok=True)
+    os.environ["HF_HOME"] = str(hf_home)

examples/pgvector-embedder/20_embed_data.py

@@ -5,19 +5,14 @@
 import json
 import logging
 
-from common.database_storage import DatabaseStorage
 from config import get_value
 from sentence_transformers import SentenceTransformer
 from vdk.api.job_input import IJobInput
+from vdk.plugin.storage.database_storage import DatabaseStorage
 
 log = logging.getLogger(__name__)
 
 
-def load_documents(json_file_path):
-    with open(json_file_path, encoding="utf-8") as file:
-        return json.load(file)
-
-
 def embed_documents_in_batches(documents):
     # the model card: https://huggingface.co/sentence-transformers/all-mpnet-base-v2
     model = SentenceTransformer("all-mpnet-base-v2")
@@ -41,7 +36,7 @@ def run(job_input: IJobInput):
     storage = DatabaseStorage(get_value(job_input, "storage_connection_string"))
     storage_name = get_value(job_input, "storage_name", "confluence_data")
 
-    documents = load_documents(storage.retrieve(storage_name))
+    documents = storage.retrieve(storage_name)
     if documents:
         log.info(f"{len(documents)} chunks loaded and cleaned for embedding.")
         embeddings = embed_documents_in_batches(documents)

examples/pgvector-embedder/30_create_schema.sql

@@ -4,9 +4,15 @@ DROP TABLE IF EXISTS public.{destination_metadata_table} CASCADE;
 DROP TABLE IF EXISTS public.{destination_embeddings_table} CASCADE;
 
 -- TODO (missing vdk feature): we need to create the tables as the postgres plugin doesn't support automatic schema inference
+CREATE TABLE IF NOT EXISTS public.{destination_embeddings_table}
+(
+    id TEXT PRIMARY KEY,
+    embedding public.vector
+);
+
 CREATE TABLE IF NOT EXISTS public.{destination_metadata_table}
 (
-    id VARCHAR PRIMARY KEY,
+    id TEXT PRIMARY KEY,
     title TEXT,
     source TEXT,
     data TEXT,

examples/pgvector-embedder/40_ingest_embeddings.py

@@ -1,13 +1,12 @@
 # Copyright 2023-2024 Broadcom
 # SPDX-License-Identifier: Apache-2.0
-import json
 import logging
 import pickle
 
 import numpy as np
-from common.database_storage import DatabaseStorage
 from config import get_value
 from vdk.api.job_input import IJobInput
+from vdk.plugin.storage.database_storage import DatabaseStorage
 
 log = logging.getLogger(__name__)
 
@@ -21,7 +20,7 @@ def run(job_input: IJobInput):
         embeddings = pickle.load(file)
     storage = DatabaseStorage(get_value(job_input, "storage_connection_string"))
     storage_name = get_value(job_input, "storage_name", "confluence_data")
-    documents = json.loads(storage.retrieve(storage_name))
+    documents = storage.retrieve(storage_name)
 
     # TODO: our postgres plugin doesn't support updates (upserts) so updating with same ID fails.