ohdsi/webapi repository overview

⁠OHDSI WebAPI

OHDSI WebAPI contains all OHDSI RESTful services that can be called from OHDSI applications.

⁠Features

• Provides a centralized API for working with 1 or more databases converted to the Common Data Model⁠ (CDM) v5.
• Searching the OMOP standardized vocabularies for medical concepts and constructing concept sets.
• Defining cohort definitions for use in identifying patient populations.
• Characterizing cohorts
• Computing incidence rates
• Retrieve patient profiles
• Design population level estimation and patient level prediction studies

⁠Technology

OHDSI WebAPI is a Java 8 web application that utilizes a PostgreSQL database for storage.

⁠API Documentation

The API Documentation is found at http://webapidoc.ohdsi.org/⁠

⁠System Requirements & Installation

Documentation can be found a the Web API Installation Guide⁠ which covers the system requirements and installation instructions.

⁠SAML Auth support

The following parameters are used:

• security.saml.idpMetadataLocation=classpath:saml/dev/idp-metadata.xml - path to metadata used by identity provider
• security.saml.metadataLocation=saml/dev/sp-metadata.xml - service provider metadata path
• security.saml.keyManager.keyStoreFile=classpath:saml/samlKeystore.jks - path to keystore
• security.saml.keyManager.storePassword=nalle123 - keystore password
• security.saml.keyManager.passwords.arachnenetwork=nalle123 - private key password
• security.saml.keyManager.defaultKey=apollo - keystore alias
• security.saml.sloUrl=https://localhost:8443/cas/logout - identity provider logout URL
• security.saml.callbackUrl=http://localhost:8080/WebAPI/user/saml/callback - URL called from identity provider after login

Sample idp metadata and sp metadata config files for okta:

• saml/dev/idp-metadata-okta.xml
• saml/dev/sp-metadata-okta.xml

⁠Managing auth providers

The following parameters are used to enable/disable certain provider:

• security.auth.windows.enabled
• security.auth.kerberos.enabled
• security.auth.openid.enabled
• security.auth.facebook.enabled
• security.auth.github.enabled
• security.auth.google.enabled
• security.auth.jdbc.enabled
• security.auth.ldap.enabled
• security.auth.ad.enabled
• security.auth.cas.enabled

Acceptable values are true and false

⁠Geospatial support

Instructions can be found at webapi-component-geospatial⁠

⁠Testing

It was chosen to use embedded PG instead of H2 for unit tests since H2 doesn't support window functions, md5 function, HEX to BIT conversion, setval, set datestyle, CTAS + CTE.

⁠Support

• Developer questions/comments/feedback: OHDSI forum⁠
• We use the GitHub issue tracker⁠ for all bugs/issues/enhancements.

⁠Versioning

• WebAPI follows Semantic versioning⁠;
• Only Non-SNAPSHOT dependencies should be presented in POM.xml on release branches/tags.

⁠GitHub Repo

https://github.com/OHDSI/WebAPI⁠

⁠License

OHDSI WebAPI is licensed under Apache License 2.0