ocl_omrs

This django project has scripts that make it easier to work with OCL and OpenMRS:

• extract_db generates JSON files from an OpenMRS v1.11 concept dictionary formatted for import into OCL
• validate_export validates an OCL export file against an OpenMRS v1.11 concept dictionary

Before running any of these commands, you must first set the MySQL database settings in omrs/settings.py.

validate_export: OCL Export Validation

This command compares OCL export files to an OpenMRS concept dictionary stored in MySql.

Usage:

./manage.py validate_export --export=EXPORT_FILE_NAME [--ignore_retired_mappings] [-v[2]]

extract_db: OpenMRS Database JSON Export

This command produces OCL JSON import files for concepts and mappings stored in an OpenMRS v1.11 concept dictionary saved in MySql. Typically you run this on a local machine with MySQL installed.

See the OpenMRS Website/wiki for download of the raw SQL and data dictionary.

Separate files should be created for concepts and mappings, for example:

manage.py extract_db --org_id=CIEL --source_id=CIEL --raw -v0 --concepts > concepts.json
manage.py extract_db --org_id=CIEL --source_id=CIEL --raw -v0 --mappings > mappings.json

By default JSON is outputted in a human-readable format. Use the raw option to indicate that JSON should be formatted one record per line (JSON lines file), which is the required format for OCL import files.

Set verbosity to 0 (e.g. -v0) to suppress the results summary output, which is required for the OCL import files. Set verbosity to 3 (-v3) to see all debug output.

To create a smaller test dataset, use the concept_limit option (e.g. --concept_limit=2000):

manage.py extract_db --org_id=CIEL --source_id=CIEL --raw -v0 --concept_limit=2000 --concepts > c2k.json
manage.py extract_db --org_id=CIEL --source_id=CIEL --raw -v0 --concept_limit=2000 --mappings > m2k.json

Note that the concept_limit parameter simply sets a maximum value for the OpenMRS concept_id. It is not a count of concepts, which means it current only works well for sequential numeric ID systems.

You should validate reference sources before generating the export with the check_sources option:

manage.py extract_db --check_sources --env=... --token=...

It is also possible to create a list of retired concept IDs (this is not used during import):

manage.py extract_db --org_id=CIEL --source_id=CIEL --raw -v0 --retired > retired_concepts.json

NOTES:

• OCL does not handle the OpenMRS drug table -- it is ignored for now

Design Notes

The models.py file was created partially by scanning the mySQL schema, and the fixed up by hand. Not all classes are fully mapped yet, as not all are imported into OCL.