Redcap2omop

Short description and motivation.

Usage

How to use my plugin.

Installation

Add this line to your application's Gemfile:

gem 'redcap2omop'

And then execute:

$ bundle

Or install it yourself as:

$ gem install redcap2omop

Contributing

Contribution directions go here.

License

The gem is available as open source under the terms of the MIT License.

Initial setup

Do not forget to create secrets.yaml or add to existing one the following keys:

development:
  redcap:
    api_url:
    verify_ssl: true

$ bundle exec rake db:create
$ rails g redcap2omop:install

Download the latest OMOP vocabulary distribution from http://athena.ohdsi.org Unzip and copy the vocabulary to /db/migrate/CommonDataModel-5.3.1/PostgreSQL/VocabImport

$ bundle exec rake redcap2omop:data:truncate_omop_vocabulary_tables
$ bundle exec rake redcap2omop:data:load_omop_vocabulary_tables
$ bundle exec rake redcap2omop:data:drop_omop_vocabulary_indexes
$ bundle exec rake redcap2omop:data:compile_omop_vocabulary_indexes

CCC19 workflow

$ bundle exec rake app:redcap2omop:setup:ccc19:project

$ bundle exec rake app:redcap2omop:ingest:data_dictionary:cleanup
$ bundle exec rake app:redcap2omop:ingest:data_dictionary:from_csv PROJECT_ID=0 FILE=lib/setup/data/data_dictionaries/CCC19_DataDictionary_clean.csv
$ bundle exec rake app:redcap2omop:setup:omop_tables
$ bundle exec rake app:redcap2omop:setup:ccc19:maps
$ bundle exec rake redcap2omop:ingest:data
$ bundle exec rake redcap2omop:ingest:redcap2omop

Compile indexes after loading data

$ bundle exec rake redcap2omop:data:compile_omop_indexes
$ bundle exec rake redcap2omop:data:compile_omop_constraints

Drop stuff

$ bundle exec rake redcap2omop:data:truncate_omop_clinical_data_tables
$ bundle exec rake redcap2omop:data:drop_omop_constraints
$ bundle exec rake redcap2omop:data:drop_omop_indexes
$ bundle exec rake redcap2omop:data:drop_omop_vocabulary_indexes
$ bundle exec rake redcap2omop:data:drop_all_tables

Install and configure Redis

brew install redis
brew services start redis

Testing

Download the latest OMOP vocabulary distribution from http://athena.ohdsi.org

Unzip and copy the vocabulary to spec/dummy/db/migrate/CommonDataModel-5.3.1/PostgreSQL/VocabImport

Run the following rake tasks to prepare the testing environment.

RAILS_ENV=test bundle exec rake db:create
rails g redcap2omop:install --migrations=false

Download the latest OMOP vocabulary distribution from http://athena.ohdsi.org Unzip and copy the vocabulary to spec/dummy/db/migrate/CommonDataModel-5.3.1/PostgreSQL/VocabImport

RAILS_ENV=test bundle exec rake db:migrate
RAILS_ENV=test bundle exec rake app:redcap2omop:data:load_omop_vocabulary_tables
RAILS_ENV=test bundle exec rake app:redcap2omop:data:compile_omop_vocabulary_indexes
bundle exec rspec