OHDSI Glue is a container designed specifically to facilitate the setup and ongoing maintenance of OHDSI & EHDEN tool deployments, including Atlas, WebAPI, Achilles, DataQualityDashboard, CDMInspection, CatalogueExport, among others. The primary function of OHDSI Glue is to simplify the configuration process for WebAPI. It serves as a practical tool for users of the OHDSI & EHDEN suite, aiming to streamline operations and reduce manual intervention in maintaining the deployments.
- GitHub Repo: https://github.com/edencehealth/ohdsi-glue
- Docker Hub Repo: https://hub.docker.com/r/edence/ohdsi-glue
The container produces the following help text when invoked with the -h or --help arguments:
usage: glue [-h] [--version] [--log-level {DEBUG,INFO,WARNING,ERROR}]
[--log-dir LOG_DIR] [--input-dir INPUT_DIR]
[--batch-size BATCH_SIZE] [--atlas-username ATLAS_USERNAME]
[--atlas-password ATLAS_PASSWORD]
[--db-dialect {postgresql,sql server}] [--db-server DB_SERVER]
[--db-username DB_USERNAME] [--db-password DB_PASSWORD]
[--db-database DB_DATABASE]
[--cdm-db-dialect {postgresql,sql server}]
[--cdm-db-server CDM_DB_SERVER]
[--cdm-db-username CDM_DB_USERNAME]
[--cdm-db-password CDM_DB_PASSWORD]
[--cdm-db-database CDM_DB_DATABASE]
[--security-db-dialect {postgresql,sql server}]
[--security-db-server SECURITY_DB_SERVER]
[--security-db-username SECURITY_DB_USERNAME]
[--security-db-password SECURITY_DB_PASSWORD]
[--security-db-database SECURITY_DB_DATABASE]
[--webapi-addr WEBAPI_ADDR] [--webapi-tls | --no-webapi-tls]
[--webapi-base-path WEBAPI_BASE_PATH]
[--init-concept-hierarchy | --no-init-concept-hierarchy]
[--ohdsi-schema OHDSI_SCHEMA] [--security-schema SECURITY_SCHEMA]
[--cdm-schema CDM_SCHEMA] [--cem-schema CEM_SCHEMA]
[--results-schema RESULTS_SCHEMA] [--temp-schema TEMP_SCHEMA]
[--vocab-schema VOCAB_SCHEMA] [--source-name SOURCE_NAME]
[--source-cache | --no-source-cache] [--source-key SOURCE_KEY]
[--enable-cem-results-init | --no-enable-cem-results-init]
[--enable-concept-count-init | --no-enable-concept-count-init]
[--enable-result-init | --no-enable-result-init]
[--enable-source-setup | --no-enable-source-setup]
[--enable-basic-security | --no-enable-basic-security]
[--update-passwords | --no-update-passwords]
[--bulk-user-file BULK_USER_FILE]
Utility for working with OHDSI WebAPI and related apps
options:
-h, --help show this help message and exit
--version show program's version number and exit
--log-level {DEBUG,INFO,WARNING,ERROR}
how verbosely to log (one of: DEBUG, INFO, WARNING,
ERROR) (default: 'DEBUG')
--log-dir LOG_DIR directory in which to create run logs (default:
'logs')
--input-dir INPUT_DIR
directory from which to load CSV-format input data
files (default: 'input')
--batch-size BATCH_SIZE
batch size to use during bulk insert, see
https://zillow.github.io/ctds/bulk_insert.html#batch-
size (default: None)
--atlas-username ATLAS_USERNAME
an admin user which will be created in the basic
security database (default: 'admin')
--atlas-password ATLAS_PASSWORD
the password associated the atlas_username account
(default: '')
--db-dialect {postgresql,sql server}
the sql database dialect (default: 'postgresql')
--db-server DB_SERVER
host address of the database to load data into
(default: 'db:1433')
--db-username DB_USERNAME
username to use when connecting to the database
(default: 'postgres')
--db-password DB_PASSWORD
password associated with the given db_username
(default: '')
--db-database DB_DATABASE
name of database on the server to write to (default:
'cdm')
--cdm-db-dialect {postgresql,sql server}
sql database dialect of the OMOP CDM database to
connect to WebAPI (default: 'postgresql')
--cdm-db-server CDM_DB_SERVER
host address of the OMOP CDM database to connect to
WebAPI (default: 'sourcedb:1433')
--cdm-db-username CDM_DB_USERNAME
username of the OMOP CDM database to connect to WebAPI
(default: 'postgres')
--cdm-db-password CDM_DB_PASSWORD
password of the OMOP CDM database to connect to WebAPI
(default: '')
--cdm-db-database CDM_DB_DATABASE
name of of the OMOP CDM database to connect to WebAPI
(default: 'cdm')
--security-db-dialect {postgresql,sql server}
sql database dialect of the WebAPI basic security
database (default: 'postgresql')
--security-db-server SECURITY_DB_SERVER
host address of the WebAPI basic security database
(default: 'sourcedb:1433')
--security-db-username SECURITY_DB_USERNAME
username of the WebAPI basic security database
(default: 'postgres')
--security-db-password SECURITY_DB_PASSWORD
password of the WebAPI basic security database
(default: '')
--security-db-database SECURITY_DB_DATABASE
name of of the WebAPI basic security database
(default: 'basic_security')
--webapi-addr WEBAPI_ADDR
the hostname (and optional port) of the webapi
instance (default: 'webapi')
--webapi-tls, --no-webapi-tls
boolean that determines if http or https should be
used to communicate with webapi (default: True)
--webapi-base-path WEBAPI_BASE_PATH
the path to WebAPI on its host, this is almost always
/WebAPI (default: '/WebAPI')
--init-concept-hierarchy, --no-init-concept-hierarchy
whether to establish the concept_hierarchy (a cached
version of the OMOP vocabulary specific to the
concepts found in your CDM) (default: True)
--ohdsi-schema OHDSI_SCHEMA
the schema used by webapi to manage its own
configuration and other state (default: 'ohdsi')
--security-schema SECURITY_SCHEMA
(default: 'basic_security')
--cdm-schema CDM_SCHEMA
(default: 'cdm')
--cem-schema CEM_SCHEMA
Common Evidence Model ("CEM") results schema (default:
'cemresults')
--results-schema RESULTS_SCHEMA
(default: 'results')
--temp-schema TEMP_SCHEMA
(default: 'temp')
--vocab-schema VOCAB_SCHEMA
(default: 'vocabulary')
--source-name SOURCE_NAME
the name of the data source, used by webapi to refer
to the data source (default: 'My Cdm')
--source-cache, --no-source-cache
determines is_cache_enabled when adding a CDM source
to WebAPI (default: True)
--source-key SOURCE_KEY
a key identifying the data source, used by webapi, if
not given it will be derived from source_name
(default: None)
--enable-cem-results-init, --no-enable-cem-results-init
enable creating the Common Evidence Model results
schema (default: False)
--enable-concept-count-init, --no-enable-concept-count-init
enable creating the concept count table(s) (see:
https://github.com/OHDSI/WebAPI/wiki/CDM-
Configuration#concept-count-tables)NOTE: this assumes
you have already run achilles (default: False)
--enable-result-init, --no-enable-result-init
enable setting up the results tables (see:
https://github.com/OHDSI/WebAPI/wiki/CDM-
Configuration#results-schema-setup) (default: True)
--enable-source-setup, --no-enable-source-setup
enable setting up the WebAPI source & source_daimon
tables (see: https://github.com/OHDSI/WebAPI/wiki/CDM-
Configuration#source-and-source_daimon-table-setup)
(default: True)
--enable-basic-security, --no-enable-basic-security
enable setting up the basic security schema & table
(see: https://github.com/OHDSI/WebAPI/wiki/Basic-
Security-Configuration) (default: True)
--update-passwords, --no-update-passwords
enable glue to update the password for existing atlas
users when verifying the basic security configuration
(default: False)
--bulk-user-file BULK_USER_FILE
create/update user accounts from a csv file; requires
these headings:
username,password,firstname,middlename,lastname
(default: None)
- WebAPI CDM configuration docs - documentation for most of the tasks we're trying to accomplish
- WebAPI git trunk's pom.xml - useful resource to find settings that need setting
- cTDS documentation - docs for our SQL Server database library
- psycopg documentation - docs for our PostgreSQL database library
- PEP 249 -- Python Database API Specification v2.0