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JREastonMarks wants to merge 157 commits intoFIX-10702---Fix-SAML-Documentationfrom
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Update branch with master#2JREastonMarks wants to merge 157 commits intoFIX-10702---Fix-SAML-Documentationfrom
JREastonMarks wants to merge 157 commits intoFIX-10702---Fix-SAML-Documentationfrom
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Sprint Issues Rollover script will roll over issue sprint on every Monday night
…ated all templates title
Some small information added for better understanding. Especially for Windows users.
Fixed paths for files in commands accourding to current repository
- tables pdb_uniprot_alignment and pdb_uniprot_residue_mapping were removed at db version 2.12.12 - whitespace standardization in migration.sql
Add generic assay profiles checking in study view page
…nly implementation (cBioPortal#11368) * ♻️ Refactor legacy code to be in legacy package and start clean arch project structure * Move PortalApplication to root * Create CancerStudy Domain and getCancerStudiesMetadata api * Update Interceptor to use legacy package structure * Update to support projection for cancerstudy endpoint * Add Tests for GetCancerStudyUseCase * Update return of getAllStudies * ;dd Sort Feature to cancerStudy endpoint * Add Code Style Guides roughdraft * Add Profiles enable (new) clickhouse components * Update tests and mappers in legacy * Add legacy prefix to StudyviewFilterMapper for mutationOption
…r-build-version Update docker build and push action to latest version
* update localdb tests to use new setup * push both images * push both images * fix paths * use spec file pattern variable
* Add reference to spring security * remove skin.user_display_name
…c-assay-patient-categorical Generic Assay categorical patient level filtering - legacy
Label new issues automatically
…late Remove default assignees from template
* add database migration guide for v6.3.0 * update docs
- Remove unneccesary cgds.sql copy in integration test to avoid seed database importing issue
…n-test Fix integration test after database migration
* Use off_panel flag to rule out not-profiled genes * Unit tests and comments * Spotless * Skip api tests relating to off panel discrepancies --------- Co-authored-by: alisman <lisman.aaron@gmail.com>
* Fix Study DTO to adhere to what frontend expects * Update DTO fields
- add sql to "fix" sample_profile table with missing samples (in mutated case list but not represented in sample_profile) - add MUTATION_UNCALLED to excluded profiles (this profile type should not be included in genetic_alteration_derived) - include protein-encoding events (drop the filtering of off-panel genes from profiles) - whitespace in pom.xml standardized to two space indenting - add correction code for clickhouse import tests Co-authored-by: alisman <lisman.aaron@gmail.com>
…tal#11586) * automate master deployment to blue/green portals * sync blue/green master deployments with argocd cli
Co-authored-by: Vicky398 <89054315+Vicky398@users.noreply.github.com>
Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>
* Added numberOfAlteredCasesOffPanel property to allow frontend to disregard offpanel events
* Refactor SessionServiceController to have all low-level http calls in SessionServiceHandler * Fix sonarqube regex vulnerability for user-controlled data in SessionServiceRequestHandler * Remov wildcard imports
…al#11604) Co-authored-by: Bryan Lai <laib1@mskcc.org>
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