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cli.md

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CLI commands

  • Options:

    command help
    -h, --help Show help message and exit
    -v, --verbose Verbose logging (logs are also writen to a log file in the systems tmp folder)
    -V, --version The current installed version
    --config Optional path to the ini config file that holds the database engine configuration. Alternatively set the RIAB_CONFIG environment variable, pointing to the ini file. Or place a riab.ini file in the current directory.

  • ETL Commands:

    command help
    -tdc, --test-db-connection Test the database connection
    -cd, --create-db Create the OMOP CDM tables
    -cf, --create-folders [PATH] Create the ETL folder structure that will hold your queries, Usagi CSV's an custom concept CSV's.
    -i, --import-vocabularies [VOCABULARIES_ZIP_FILE] Extracts the vocabulary zip file (downloaded from the Athena website) and imports it into the OMOP CDM database.
    -r [PATH], --run-etl [PATH] Runs the ETL, pass the path to ETL folder structure that holds your queries, Usagi CSV's an custom concept CSV's.
    -c, --cleanup [TABLE] Cleanup of the all Work tables, and all the OMOP clinical tables. If you pass a table name as argument, then that table and all the work and clinical tables in the ETL flow (in the levels comming after that table) will be cleaned up.
    -dq, --data-quality Check the data quality and store the results.
    -dqd, --data-quality-dashboard View the results of the data quality checks.
    --print-etl-flow Print the sequence in which the ETL tables that will be processed

  • Run ETL specific command options (-r [PATH], --run-etl [PATH]):

    command help
    -t [TABLE], --table [TABLE] Do only ETL on this specific OMOP CDM table (this argument can be used multiple times). (ex: --run-etl ~/git/omop-cdm/ -t cdm_source -t metadata -t vocabulary -t location). This option is only usefull while developing the ETL queries or testing Usagi mappings, to speed up the ETL process. Do not use in production.
    -q [PATH], --only-query [PATH] Do ETL for a specified sql file in the CDM folder structure (this argument can be used multiple times). (ex: measurement/lab_measurements.sql). This option is only usefull while developing a specific ETL query, to speed up the ETL process. Do not use in production.
    -s, --skip-usagi-and-custom-concept-upload Skips the parsing and uploading of the Usagi and custom concept CSV's. Skipping results in a significant speed boost.
    -sa, --process-semi-approved-mappings In addition to 'APPROVED' as mapping status, 'SEMI-APPROVED' will be processed as valid Usagi concept mappings.
    -se, --skip-event-fks-step Skip the event foreign keys ETL step.

  • Cleanup specific command options (-c [TABLE], --cleanup [TABLE]):

    command help
    --clear-auto-generated-custom-concept-ids Cleanup the auto generated custom concept ID's (above 2 million). Without this argument, the cleanup command will not clear the mapping table (that maps the custom concept with the auto generated id above 2 million), so that you can use those above 2 million concept id's in your cohort builder, without the fear that those id's will change.

  • Data quality specific command options (-dq, --data-quality):

    command help
    --json [PATH] Save the data quality result as JSON file for use in the OHDSI Data Quality Dashboard.

  • Data quality dashboard specific command options (-dqd, --data-quality-check):

    command help
    --port [PORT] The port the dashboard schould listen on.

CLI Examples

Create the OMOP CDM database:

riab --create-db

Import your downloaded vocabularies (from Athena) zip file:

riab --import-vocabularies ./vocabulary_20240329.zip

Create the ETL folder structure:

riab --create-folders ./OMOP_CDM

Run full ETL:

riab --run-etl ./OMOP_CDM

Run ETL on one table:

riab --run-etl ./OMOP_CDM \
  --table provider

Run ETL without re-upload of Usagi CSV's and custom concept CSV's:

riab --run-etl ./OMOP_CDM \
  --skip-usagi-and-custom-concept-upload

Run ETL for a specified sql file in the CDM folder structure. (ex: measurement/lab_measurements.sql)

riab --run-etl ./OMOP_CDM \
  --skip-usagi-and-custom-concept-upload \
  --skip-event-fks-step \
  --only-query measurement/lab_measurements.sql

Run ETL with SEMI-APPROVED concepts during ETL testing in dev branch

riab --run-etl ./OMOP_CDM \
  --process-semi-approved-mappings

Cleanup all tables:

riab --cleanup

Cleanup one table (example provider table):

riab --cleanup provider

Data quality check:

riab --data-quality

Data quality check (export result to JSON):

riab --data-quality --json dqd_result.json

Data quality dashboard (default port = 8050):

riab --data-quality-dashboard --port 8888

Linux requires a port exceeding 1024