https://ohdsi.github.io/Achilles/articles/RunningAchilles.html
This repo contains the source code for edenceHealth's Docker image containing both OHDSI Achilles and OHDSI DataQualityDashboard. These two tools share some basic dependenices and have a similar use cases, so we bundle them together. The image adds a lightweight wrapper around these tools which simplifies the process of calling them without a separate R installation.
For more information about the tools, see the following links:
- OHDSI Achilles
- OHDSI DataQualityDashboard
The container can be used and configured via command-line arguments (for example passed to docker run) and with environment variables.
The following text is printed when invoking the container with the -h or --help arguments.
Achilles Wrapper
Usage:
achilles.R [options]
General options:
-h, --help Show this help message.
--num-threads=<n> The number of threads to use when running achilles [default: 1]
--optimize-atlas-cache Enables the optimizeAtlasCache option to the achilles function
--source-name=<name> The source name used by the achilles function and included as part of the output path [default: NA]
--timestamp=<time_str> The timestamp-style string to use when calculating some file output paths. Defaults to a string derived from the current date & time. [default: AUTO]
--skip-achilles This option prevents Achilles from running, which can be useful for running the other utilities like the DQD Shiny App
--output-base=<str> The output path used by achilles [default: /output]
--s3-target=<str> Optional AWS S3 bucket path to sync with the output_base directory (for uploading results to S3)
CDM Options:
--cdm-version=<semver> Which standard version of the CDM to use [default: 5]
Schema Options:
--cdm-schema=<name> DB schema name for CDM data [default: public]
--results-schema=<name> DB schema name for results data [default: results]
--vocab-schema=<name> DB schema name for vocabulary data [default: vocabulary]
CDM DB Options:
--db-dbms=<name> The database management system for the CDM database [default: postgresql]
--db-hostname=<name> The hostname the database server is listening on [default: db]
--db-port=<n> The port the database server is listening on [default: 5432]
--db-name=<name> The name of the database on the database server [default: cdm]
--db-username=<name> The username to connect to the database server with [default: pgadmin]
--db-password=<name> The password to connect to the database server with [default: postgres]
--db-extra-settings=<s> Optional additional settings for the database driver (in JDBC connection format)
--databaseconnector-jar-folder=<directory> The path to the driver jar files used by the DatabaseConnector to connect to various DBMS [default: /usr/local/lib/DatabaseConnectorJars]
JSON Export Options:
--json-export Whether to run the Achilles exportToJson function
--json-compress JSON files should be compressed into one zip file
--json-output-base=<DIRECTORY> The output path used by exportToJson [default: /output]
DataQualityDashboard Options:
--dqd Whether to run the DataQualityDashboard functions
--dqd-sql-only Return DQD queries but do not run them
--dqd-verbose Whether to write DataQualityDashboard info
--dqd-json-file Whether to write a JSON file to disk
--dqd-skip-db-write Skip writing results to the dqdashboard_results table in the results schema
--dqd-check-names=<list> Optional comma-separated list of check names to execute
--dqd-check-levels=<list> Comma-separated list of which DQ check levels to execute [default: TABLE,FIELD,CONCEPT]
--dqd-exclude-tables=<list> Comma-separated list of CDM tables to exclude from the checks
--dqd-output-base=<DIRECTORY> The output path used by the dqd functions [default: /output]
--dqd-table-threshold-file=<file> The optional location of the threshold file for evaluating the table checks; this is useful for overriding thresholds [default: default]
--dqd-field-threshold-file=<file> The optional location of the threshold file for evaluating the field checks; this is useful for overriding thresholds [default: default]
--dqd-concept-threshold-file=<file> The optional location of the threshold file for evaluating the concept checks; this is useful for overriding thresholds [default: default]
DQDWeb Options:
--dqd-web Whether to run the DataQualityDashboard Shiny App
--dqd-web-host=<hostname> The network host address the DataQualityDashboard Shiny App should listen on [default: 0.0.0.0]
--dqd-web-port=<n> The network port number the DataQualityDashboard Shiny App should listen on [default: 5641]
--dqd-web-display-mode=<mode> The Shiny App display.mode to use for the app, options include "showcase" or "normal" [default: normal]
--dqd-web-input-json=<PATH> Optionally override the input path used by the DataQualityDashboard Shiny App, by default this is derived from the output path by the DQD step [default: AUTO]
Running the container with the --version argument prints the version information:
edenceHealth Achilles/DQD Wrapper: 1.8 / Achilles: 1.7 / DataQualityDashboard: 1.4.1
Each command line argument has an equivalent environment variable, to determine name of the environment variable:
- start with the argument and remote the leading dashes
- convert to uppper-case
- replace dashes with underscores
- boolean, flag-style arguments like
--skip-achillesare assumed to be false, but they can be enabled by setting them with the values:1,TRUE,YES,Y, orON
For example:
--skip-achillesbecomesSKIP_ACHILLES=1--output-base=xyzbecomesOUTPUT_BASE=xyz