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 database (PostgreSQL, SQL Server or Oracle) for storage.

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.

Contribution

Versioning

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

License

OHDSI WebAPI is licensed under Apache License 2.0

stefpiatek/WebAPI