ohdsi-aresindexer

This image is a Dockerization of the OHDSI/AresIndexer R package's development branch. This image also incorporates the core elements of the suggested run script used to generate the proper data files for the OHDSI/Ares web application.

See the included docker-compose.example.yml for the configuration necessary to deploy the image with docker compose.

NOTE In the assets directory you will find two header-only CSV files:

• netwtork-unmapped-source-codes.csv
• temporal-characterization.csv

If you have no unmapped codes in your source, you may need to place the network...csv file in the data root directory for the application to function properly. If your data source does not allow for temporal characterization, you will need to place the temporal...csv file in the source release directory for that given source

Functionality

Within the ares.R script the following OHDSI R functions are used. Documentation for these functions can help understand what the options in the Configuration section do.

• https://ohdsi.github.io/Achilles/reference/achilles.html
• https://ohdsi.github.io/Achilles/reference/exportToAres.html
• https://ohdsi.github.io/Achilles/reference/performTemporalCharacterization.html
• https://ohdsi.github.io/AresIndexer/reference/augmentConceptFiles.html
• https://ohdsi.github.io/AresIndexer/reference/buildDataQualityIndex.html
• https://ohdsi.github.io/AresIndexer/reference/buildNetworkIndex.html
• https://ohdsi.github.io/AresIndexer/reference/buildNetworkUnmappedSourceCodeIndex.html
• https://ohdsi.github.io/DataQualityDashboard/reference/executeDqChecks.html
• https://ohdsi.github.io/DatabaseConnector/reference/createConnectionDetails.html

Configuration

The following environment variables can be used to control the operation of the container at run time.

Environment Variable	Default Value	Description
ACHILLES_ANALYSIS_IDS	NULL	optional comma-separated list of Achilles analysisIds for which results will be generated (defaults to all)
ACHILLES_EXCLUDE_ANALYSIS_IDS	NULL	optional comma-separated list containing the set of Achilles analyses to exclude
ACHILLES_NUM_THREADS	1	The number of threads to use to run Achilles in parallel. Default is 1 thread.
ACHILLES_OUTPUT_FOLDER	output	Path to store logs and SQL files
ACHILLES_SMALL_CELL_COUNT	5	To avoid patient identification, cells with small counts (<= smallCellCount) are deleted. Set to 0 for complete summary without small cell count restrictions. (defaults to 5)
ARES_CONCEPT_FORMAT	json	Storage format of concept data: 'json' or 'duckdb'; defaults to JSON
ARES_DATA_ROOT	/output/ares	base directory for ares data
CDM_SCHEMA	omopcdm	name of database schema where CDM data is located
CDM_SOURCE	cdm	name of the CDM data source (used by DataQualityDashboard)
CDM_VERSION	5.4	OMOP CDM version number; use only major and minor version e.g. '5.3' or '5.4'
DB_DBMS	postgresql	type of DBMS running on the server
DB_HOSTNAME	db	the DNS hostname or address of the server to connect to
DB_NAME	cdm	the name of the database to connect to on the database server
DB_PASSWORD	postgres	the password to use when authenticating to the datbase server
DB_PORT	5432	the TCP port number to use when connecting to the database server
DB_USERNAME	postgres	the username to use when authenticating to the database server
DQD_CHECK_LEVELS	TABLE,FIELD,CONCEPT	comma-separated list of DQ check levels to execute. Default is all 3: TABLE,FIELD,CONCEPT)
DQD_CHECK_NAMES	NULL	(OPTIONAL) comma-separated list of check names to execute
DQD_CONCEPT_CHECK_THRESHOLD_LOC	default	location of the threshold file for evaluating the concept checks. If not specified the default thresholds will be applied
DQD_FIELD_CHECK_THRESHOLD_LOC	default	location of the threshold file for evaluating the field checks. If not specified the default thresholds will be applied
DQD_NUM_THREADS	1	The number of concurrent threads to use to execute the queries Default is 1 thread.
DQD_OUTPUT_FILE	dq-result.json	File to write DQD results JSON object
DQD_TABLES_TO_EXCLUDE	(see note below this table)	CDM tables to exclude from the execution
DQD_TABLE_CHECK_THRESHOLD_LOC	default	location of the threshold file for evaluating the table checks. If not specified the default thresholds will be applied
DQD_VERBOSE_MODE	FALSE	determines if the console will show all DQD execution steps
PATH_TO_DRIVER	/usr/local/lib/DatabaseConnectorJars	the path to the DatabaseConnectorJars directory
RESULTS_SCHEMA	results	name of schema to write results into
RUN_MODE	SOURCE	mode of operation; possible values: SOURCE, NETWORK
SCRATCH_DATABASE_SCHEMA	resultsDatabaseSchema	see achilles docs linked above
TEMP_EMULATION_DATABASE_SCHEMA	resultsDatabaseSchema	see achilles docs linked above
VOCAB_DATABASE_SCHEMA	cdmDatabaseSchema	schema where the vocab tables are located

• The default value for the DQD_TABLES_TO_EXCLUDE environment variable is CONCEPT,VOCABULARY,CONCEPT_ANCESTOR,CONCEPT_RELATIONSHIP,CONCEPT_CLASS,CONCEPT_SYNONYM,RELATIONSHIP,DOMAIN