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[RFC72] Spring Boot Upgrade#10425

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JREastonMarks merged 116 commits intomastercBioPortal/cbioportal:masterfrom demo-rfc72cBioPortal/cbioportal:demo-rfc72Copy head branch name to clipboardDec 18, 2023

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Commits

Commits on Aug 22, 2023

• Initial Commit Updating CbioPortal Backend to spring-boot

  

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Commits on Aug 24, 2023

• Merge branch 'master' into demo-rfc72

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Commits on Aug 25, 2023

• 🚧 Updated cbioportal project to get a successfull build

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• 🐛 Use correct annotation to set prefix

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• Hotfix remove use of PatientMapper.select from SampleMapper.xml

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• Remove ReadPermissionService

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• Fixes for Deployment

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Commits on Sep 4, 2023

• 🚨 Update peristence module tests to pass within spring… (#10363)

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• Remove ReadPermissionService IF and update test (#10364)

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Commits on Sep 5, 2023

• fix api path in InvolvedCancerStudyExtractorInterceptor

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Commits on Sep 7, 2023

• Fix Unit Tests in Web Module (#10371)

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• Fix Github Action Core tests (#10369)

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Commits on Sep 8, 2023

• Use simpler web docker image (#10377)

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  inodb

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• Spring Boot Upgrade: Fix CircleCI build_backend step (#10379)

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Commits on Sep 13, 2023

• Fix Api prefix for ProxyController (#10383)

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Commits on Sep 14, 2023

• Update postData to set undefined when map is empty

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• Add SampleTypeHandler to sessionFactory for mybatis

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• Update redirect url for patient and results pages

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Commits on Sep 19, 2023

• Update redirect urls for login and results

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Commits on Sep 20, 2023

• Fix /Comparison url redirect

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• Fix index.do redirect

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Commits on Sep 22, 2023

• Fix oncoprinter redirect

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Commits on Sep 25, 2023

• Update FrontendPropertiesService to handle boolean values

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Commits on Sep 26, 2023

• Add ability to decompress gzip request body

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• Update gzip stream request wrapper to use legacy code

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Commits on Sep 27, 2023

• Add mutation_mapper to redirect ruleset

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• support for /study? as well as /study/ redirect

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• Update to support encodedRedirect

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Commits on Sep 28, 2023

• Add enable_cross_study_expression frontend property

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• in docker action login first

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• upgrade docker image actions

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Commits on Sep 29, 2023

• Add properties to show download study button

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• Merge branch 'master' into demo-rfc72

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Commits on Oct 4, 2023

• Feature/rfc72/fix integration tests (#10418)

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• Merge remote-tracking branch 'origin/master' into demo-rfc72

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Commits on Oct 6, 2023

• Add instructions for local dev

  inodb

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• fix typo in README

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• make a few changes to debugging section

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Commits on Oct 9, 2023

• Delete SAML BootStrapRSA256 fails build

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• Revert "Delete SAML BootStrapRSA256 fails build"

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• Fix Deps for SamlBootStrap

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Commits on Oct 10, 2023

• Delete un-needed portal.properties and renamed jar to cBioPortal.jar

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• Update jar to cbioportal.jar

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Commits on Oct 11, 2023

• Add dependency for SAML2 integration (#10431)

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Commits on Oct 16, 2023

• Update to Java 21

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• Update Docker Images for openJdk 21 and Spring boot 3

  

  inodb

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• Fix token integration tests

  

  pvannierop

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• Merge branch 'feature/rfc72/Springboot-Upgrade' into demo-rfc72

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Commits on Nov 13, 2023

• Demo rfc72 squash (#10466)

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• Remove heroku

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• Update web/dockerfile to use -exec jar

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Commits on Nov 14, 2023

• Update docker-entrypoint to run when jar or running via exploded jar

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• Update docker-entrypoint.sh

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• Update migrate.sql path

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• 🔒 Allow /api/health endpoint regardless of authentication

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• Update action to always run

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• Update integration test

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Commits on Nov 15, 2023

• Fix build backend circleci action

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• Update ProxyController to grab oncokb properties from spring boot

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Commits on Nov 16, 2023

• 🔧 Add all missing frontend configs

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Commits on Nov 22, 2023

• fix thymeleaf deprecation warning

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Commits on Nov 27, 2023

• Update oauth config to check before grabbing claims from userinfo

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• Add spring-session-data-redis dep

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Commits on Nov 28, 2023

• Update to support Post for /study/summary endpoint

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• Add dep for spring boot http Redis session

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Commits on Nov 30, 2023

• Update to remove social_auth

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• Fix bugs with /summary/study

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Commits on Dec 1, 2023

• add to migration guide

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• Add some more clarification to migration guide

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• Enable Compression on responses

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Commits on Dec 4, 2023

• Update to allow datasets and posts to /results

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• force session service to use type Settings if type is null

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Commits on Dec 5, 2023

• update to v5.4.8 frontend

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• Bump frontend to v5.4.9

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• Add new line for application.properties.Example

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Commits on Dec 7, 2023

• Update SwaggerConfig to add HttpAction to end of operationId

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• Fix Swagger Type Names by forcing CustomObjectMapper

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Commits on Dec 8, 2023

• Force Api Response for each endpoint to remove ResponseEntity prefix

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• Update to fix pValue property in Swagger

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• Add GenericAssayEnrichMentController to endpoints

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• Update Mutation object to pass Object for annotationJSON

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• Update String type to return Object

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• add some comments on saml to migration gudie

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• add some more notes on saml migration

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• in saml migration mention jks change

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Commits on Dec 10, 2023

• Add fix for swagger docs to fix frontend code generation

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Commits on Dec 11, 2023

• add trailing line for gene-panel api

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• Update to use Enable Method Security

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• Add static fields to method security config

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• Update to fix AOP proxy issue with cacheable and GlobalWebSecurityConfi

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• Fix GenPanelController Test

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Commits on Dec 12, 2023

• Add support for both api/gene-panels/ api/gene-panels apis

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• Add ReadPermissionService

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• Fix failing tests

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• Update redirect logout url for optional_oauth2

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• 🔧 Add Config for Study View Help Button

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Commits on Dec 13, 2023

• Add EOL and Character return to application.properties

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Commits on Dec 14, 2023

• Merge branch 'master' into demo-rfc72

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• Revert frontend version to v5.4.9

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• Update Login Page

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• Fix login url

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• SonarCube

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• Update Java Version to 21

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• Create LoginController to handle /login endpoint for authentication

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• SonarCube Fixes

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• Fix bug in jwt correction and molecular data service

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Commits on Dec 15, 2023

• Remove Pattern.compile

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• Fix Logout Page for SAML2

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• Fix SessionServiceController

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• New Regex for Session Service

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• Set logout/login page for authenticate=oauth2 with more than one client setup

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• Revert REGEX for session service

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• Fix compilation error

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• Update docs for migration guide to v6

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• Fix login page with oauth

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Commits on Dec 18, 2023

• Fix redirect issue when requesting api endpoint... should be 401

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