[ALS-5979] AIM-AHEAD PIC-SURE: Downloaded dataset seems incorrect #161
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Different fields for queryTemplateText are set based on the idp_provider in FENCEAuthenticationService. The "?fields" parameter of the query is now conditionally filled, with it being set to the parentAccessionField if idp_provider equals "fence", and empty otherwise. This change provides more flexibility for FENCE authentication depending on the provider setting.
Luke-Sikina
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Mar 26, 2024
...rc/main/java/edu/harvard/hms/dbmi/avillach/auth/service/auth/FENCEAuthenticationService.java
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* Update release with Fence-Integration (#153) * [HOT-FIX] Add maven war plugin version to fix production build [HOT-FIX] Add maven war plugin version to fix production build * [ALS-5514] AIM-AHEAD PIC-SURE AuthN (#150) [ALS-5332] BDC PIC-SURE: Support PSAMA persist admin roles fix compile issue Add manual roles check if roles are empty Add StudyAccessService Better error code; clean up Bump swagger version? Added jersey-server for tests Add guava to pom Adds method to look for accounts missing a subject Check if subject is empty * [ALS-5514] Add OktaOAuthAuthenticationService for user authentication The new class, OktaOAuthAuthenticationService, has been added to manage user authentication via Okta. This involves the process of code-token exchange, token introspection, and user initialization. It also contains utility methods for making requests to Okta API and processing the responses. * [ALS-5514] Add Okta authentication support in PIC-SURE This commit includes the addition of an OktaAuthenticationController which is responsible for handling Okta-based authentication requests. It also restructures the JAXRSConfiguration class's startup sequence and adds more flexibility in handling different Identity Provider (IDP) setups; specifically, it enhances the class's ability to properly configure and handle Okta IDP. * [ALS-5514] Remove unused import in AuthService.java * [ALS-5514] The 'standalone.xml' file has been updated to include OTKA parameters configuration. * [ALS-5514] Update maven war plugin * [ALS-5514] Use unauthorizedError in place of less specific error * [ALS-5514] Refactor UserRepository and improve user metadata generation Updated UserRepository.java to streamline the user data querying and creation process, and added explicit save(user) method for better clarity. In OktaOAuthAuthenticationService.java, a refactoring was done to simplify the process of updating user metadata. A unit test for generating user metadata was also added in a new OktaOAuthAuthenticationServiceTest.java file for improved code coverage and reliability. *[ALS-5514] Remove mapped clientId, refactor beanConfig scheme The commit eliminates mapped clientId resource in JAXRSConfiguration.java, instead retrieving it through ctx.lookup. This resolves issues in the cases where client_id may be empty. --------- Co-authored-by: James <Jamestp19@gmail.com> --------- Co-authored-by: James <Jamestp19@gmail.com> * [ALS-5858] AIM-AHEAD PIC-SURE: Landing page shows 0 studies (#156) * [ALS-5858] In order to upsert user studies we needed many of the same configuration values depended on by FENCE. I have refactored common JAXRSConfigurations to methods. They are now reused across different idp provider configurations. * ALS-6142: Update apache httpclient version (#160) * [ALS-5979] AIM-AHEAD PIC-SURE: Downloaded dataset seems incorrect (#161) * Refactor FENCEAuthenticationService to customize query fields Different fields for queryTemplateText are set based on the idp_provider in FENCEAuthenticationService. The "?fields" parameter of the query is now conditionally filled, with it being set to the parentAccessionField if idp_provider equals "fence", and empty otherwise. This change provides more flexibility for FENCE authentication depending on the provider setting. * Remove empty string for fields * Flip equals to avoid npe --------- Co-authored-by: James <Jamestp19@gmail.com> Co-authored-by: ramari16 <ramari16@gmail.com>
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When a study is added for AIM-AHEAD or any non-fence environment we no longer include the
parentAccessionField.