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TASK-6780 - Port Patch 3.2.1 -> 4.0.0 - Xetabase 2.2.1 -> 3.0.0 #2513

Merged
merged 224 commits into from
Oct 14, 2024
Merged

TASK-6780 - Port Patch 3.2.1 -> 4.0.0 - Xetabase 2.2.1 -> 3.0.0 #2513

merged 224 commits into from
Oct 14, 2024

Commits on Jan 25, 2024

  1. catalog: fix clinical analysis creation, #TASK-5538, #TASK-5516

    @jtarraga
    jtarraga committed Jan 25, 2024
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  2. pom: workaround for SonarCloud issue on CI/CD, #TASK-5516

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    jtarraga committed Jan 25, 2024
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Commits on Feb 8, 2024

  1. Resolve conflicts, #TASK-5516

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Commits on Mar 8, 2024

  1. Prepare cicd release

    @juanfeSanahuja
    juanfeSanahuja committed Mar 8, 2024
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Commits on Mar 12, 2024

  1. Resolve conflicts, #TASK-5516

    @jtarraga
    jtarraga committed Mar 12, 2024
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Commits on Apr 15, 2024

  1. Merge branch 'develop' into TASK-5516

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Commits on Apr 19, 2024

  1. storage: Implement HBase table autoscale #TASK-5448

    @j-coll
    j-coll committed Apr 19, 2024
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Commits on May 14, 2024

  1. Merge branch 'develop' into TASK-5448

    @j-coll
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Commits on May 16, 2024

  1. storage: Fix hbase compatibility for table autoscale. #TASK-5448

    @j-coll
    j-coll committed May 16, 2024
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  2. storage: Add variant-setup operation. #TASK-5861, #TASK-5448

    @j-coll
    j-coll committed May 16, 2024
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  3. storage: Make variant-setup mandatory for any operation. #TASK-5861, … 

    …#TASK-5448
    @j-coll
    j-coll committed May 16, 2024
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Commits on May 17, 2024

  1. storage: Change some default variant-setup values. #TASK-5861, #TASK-… 

    …5448
    @j-coll
    j-coll committed May 17, 2024
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Commits on May 20, 2024

  1. Merge branch 'release-3.1.x'

    @juanfeSanahuja
    juanfeSanahuja committed May 20, 2024
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  2. Merge branch 'release-3.1.x'

    @juanfeSanahuja
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  3. pom: Release 3.1.0

    @juanfeSanahuja
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  4. Merge branch 'develop'

    @juanfeSanahuja
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  5. Merge branch 'release-3.1.x'

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Commits on May 21, 2024

  1. Merge branch 'release-3.1.x'

    @juanfeSanahuja
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  2. Merge branch 'release-3.1.x'

    @juanfeSanahuja
    juanfeSanahuja committed May 21, 2024
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  3. Merge branch 'release-3.1.x'

    @juanfeSanahuja
    juanfeSanahuja committed May 21, 2024
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  4. Merge branch 'release-3.1.x'

    @juanfeSanahuja
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Commits on May 22, 2024

  1. app: Add migration VariantSetupMigration. Add migration test. #TASK-5… 

    …861, #TASK-5448
    @j-coll
    j-coll committed May 22, 2024
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  2. storage: Change param names from VariantSetupParams #TASK-5861, #TASK… 

    …-5448
    @j-coll
    j-coll committed May 22, 2024
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  3. app: Fix compilation issue. #TASK-5861, #TASK-5448

    @j-coll
    j-coll committed May 22, 2024
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Commits on May 23, 2024

  1. analysis: update Exomiser analysis in order to use the Docker version… 

    … 14.0.0 by taking it from the configuration file, #TASK-6297, #TASK-6255
    @jtarraga
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  2. app: add Exomiser version as paremeter for the Exomiser interpretatio… 

    …n analysis, #TASK-6297, #TASK-6255
    @jtarraga
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  3. app: add parameter descriptions, #TASK-6297, #TASK-6255

    @jtarraga
    jtarraga committed May 23, 2024
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  4. client: generate clients, #TASK-6297, #TASK-6255

    @jtarraga
    jtarraga committed May 23, 2024
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  5. storage: Fix tests. #TASK-5861, #TASK-5448

    @j-coll
    j-coll committed May 23, 2024
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  6. core: Add data field descriptions to VariantSetupPatams. #TASK-5861, … 

    …#TASK-5448
    @j-coll
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  7. core: fix configuration file, #TASK-6297, #TASK-6255

    @jtarraga
    jtarraga committed May 23, 2024
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  8. storage: Add normalization extensions to setup params. #TASK-5861, #T… 

    …ASK-5448
    @j-coll
    j-coll committed May 23, 2024
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Commits on May 27, 2024

  1. storage: Fix VariantSearchTest. #TASK-6136

    @j-coll
    j-coll committed May 27, 2024
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  2. catalog: add 'version' to ClinicalAnalysis, #TASK-5964 #TASK-6289

    @pfurio
    pfurio committed May 27, 2024
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Commits on May 28, 2024

  1. catalog: add new test for versioning, #TASK-5964 #TASK-6289

    @pfurio
    pfurio committed May 28, 2024
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  2. catalog: fix issue in installIndexes, #TASK-5964

    @pfurio
    pfurio committed May 28, 2024
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  3. catalog: add new ADMIN permission for ClinicalAnalysis, #TASK-6288 

    - #TASK-5964
    @pfurio
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  4. storage: Fix tests from HadoopVariantStorageEngineSplitDataTest #TASK… 

    …-6136
    @j-coll
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Commits on May 29, 2024

  1. catalog: test new ADMIN permission, #TASK-6288 #TASK-5964

    @pfurio
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Commits on May 31, 2024

  1. storage: Avoid unnecesary sample metadata updates updating cohorts #T… 

    …ASK-5895
    @j-coll
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  2. storage: Improve HBaseLockManager errors and warn messages. #TASK-5895

    @j-coll
    j-coll committed May 31, 2024
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  3. storage: Increase metadata lock duration and timeout. #TASK-5895

    @j-coll
    j-coll committed May 31, 2024
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  4. storage: Improve testing SampleIndexAggregation of intergenic queries… 

    …. #TASK-6136
    @j-coll
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Commits on Jun 3, 2024

  1. Merge branch 'release-2.12.x' into TASK-6136

    @j-coll
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  2. analysis: use the FileUtils.copyFile and rename Tool to AnalysisTool,… 

    … #TASK-6297, #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/config/Analysis.java
	renamed:    opencga-core/src/main/java/org/opencb/opencga/core/config/Tool.java -> opencga-core/src/main/java/org/opencb/opencga/core/config/AnalysisTool.java
    @jtarraga
    jtarraga committed Jun 3, 2024
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Commits on Jun 4, 2024

  1. Prepare next release 2.12.6-SNAPSHOT

    @juanfeSanahuja
    juanfeSanahuja committed Jun 4, 2024
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Commits on Jun 5, 2024

  1. Merge branch 'develop' into TASK-5964

    @pfurio
    pfurio committed Jun 5, 2024
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  2. analysis: use a list of tools instead of a map in the configuration f… 

    …ile and update code according to that, #TASK-6297, #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/ConfigurationUtils.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysis.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/ClinicalCommandOptions.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/VariantCommandOptions.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java
	modified:   opencga-catalog/src/test/resources/configuration-test.yml
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/config/Analysis.java
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/config/AnalysisTool.java
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ExomiserInterpretationAnalysisParams.java
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ExomiserWrapperParams.java
	modified:   opencga-core/src/main/resources/configuration.yml
    @jtarraga
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Commits on Jun 6, 2024

  1. analysis: use the resource version instead of the exomiser version to… 

    … identify the Exomiser files to download, #TASK-6297, #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java
    @jtarraga
    jtarraga committed Jun 6, 2024
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  2. Merge branch 'develop' into TASK-5448

    @j-coll
    j-coll committed Jun 6, 2024
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  3. storage: Change default enabled normalization extensions. From NONE t… 

    …o ALL. #TASK-5861, #TASK-5448
    @j-coll
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  4. server: Add variant/setup operation. #TASK-5861, #TASK-5448

    @j-coll
    j-coll committed Jun 6, 2024
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  5. Merge pull request #2457 from opencb/TASK-6136 

    TASK-6136 - OpenCGA-Storage tests failed on OpenCGA 2.12.x
    @j-coll
    j-coll authored Jun 6, 2024
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  6. Merge branch 'release-2.12.x' into TASK-5895

    @j-coll
    j-coll committed Jun 6, 2024
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  7. analysis: set dinamically the ClinVar white list depending on the fil… 

    …e exists in the Exomiser data, #TASK-6297, TASK-6255

In addition:
 - the user is set in the docker command line according to the user/group of the job dir.
 - the assembly is checked (a little step to support GRCh37)

On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysis.java
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java
	modified:   opencga-analysis/src/test/resources/exomiser/application.properties
	modified:   opencga-app/app/analysis/exomiser/application.properties
	modified:   opencga-core/src/main/resources/configuration.yml
    @jtarraga
    jtarraga committed Jun 6, 2024
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Commits on Jun 7, 2024

  1. analysis: improve log messages, #TASK-6297, #TASK-6255 

    On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
    @jtarraga
    jtarraga committed Jun 7, 2024
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  2. core: improve description of the Exomiser version parameter, #TASK-62… 

    …97, #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java
    @jtarraga
    jtarraga committed Jun 7, 2024
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  3. client: generate clients, #TASK-6297, #TASK-6255 

    On branch TASK-6255
Changes to be committed:
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
	modified:   opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java
	modified:   opencga-client/src/main/R/R/Admin-methods.R
	modified:   opencga-client/src/main/R/R/Alignment-methods.R
	modified:   opencga-client/src/main/R/R/AllGenerics.R
	modified:   opencga-client/src/main/R/R/Clinical-methods.R
	modified:   opencga-client/src/main/R/R/Cohort-methods.R
	modified:   opencga-client/src/main/R/R/Family-methods.R
	modified:   opencga-client/src/main/R/R/File-methods.R
	modified:   opencga-client/src/main/R/R/GA4GH-methods.R
	modified:   opencga-client/src/main/R/R/Individual-methods.R
	modified:   opencga-client/src/main/R/R/Job-methods.R
	modified:   opencga-client/src/main/R/R/Meta-methods.R
	modified:   opencga-client/src/main/R/R/Operation-methods.R
	modified:   opencga-client/src/main/R/R/Organization-methods.R
	modified:   opencga-client/src/main/R/R/Panel-methods.R
	modified:   opencga-client/src/main/R/R/Project-methods.R
	modified:   opencga-client/src/main/R/R/Sample-methods.R
	modified:   opencga-client/src/main/R/R/Study-methods.R
	modified:   opencga-client/src/main/R/R/User-methods.R
	modified:   opencga-client/src/main/R/R/Variant-methods.R
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java
	modified:   opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java
	modified:   opencga-client/src/main/javascript/Admin.js
	modified:   opencga-client/src/main/javascript/Alignment.js
	modified:   opencga-client/src/main/javascript/ClinicalAnalysis.js
	modified:   opencga-client/src/main/javascript/Cohort.js
	modified:   opencga-client/src/main/javascript/DiseasePanel.js
	modified:   opencga-client/src/main/javascript/Family.js
	modified:   opencga-client/src/main/javascript/File.js
	modified:   opencga-client/src/main/javascript/GA4GH.js
	modified:   opencga-client/src/main/javascript/Individual.js
	modified:   opencga-client/src/main/javascript/Job.js
	modified:   opencga-client/src/main/javascript/Meta.js
	modified:   opencga-client/src/main/javascript/Organization.js
	modified:   opencga-client/src/main/javascript/Project.js
	modified:   opencga-client/src/main/javascript/Sample.js
	modified:   opencga-client/src/main/javascript/Study.js
	modified:   opencga-client/src/main/javascript/User.js
	modified:   opencga-client/src/main/javascript/Variant.js
	modified:   opencga-client/src/main/javascript/VariantOperation.js
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/family_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/file_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/job_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/project_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/study_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/user_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py
	modified:   opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py
    @jtarraga
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  4. Merge branch 'develop' into TASK-6255 

    Resolve conflicts by generating clients:
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
	opencga-client/src/main/R/R/Admin-methods.R
	opencga-client/src/main/R/R/Alignment-methods.R
	opencga-client/src/main/R/R/AllGenerics.R
	opencga-client/src/main/R/R/Clinical-methods.R
	opencga-client/src/main/R/R/Cohort-methods.R
	opencga-client/src/main/R/R/Family-methods.R
	opencga-client/src/main/R/R/File-methods.R
	opencga-client/src/main/R/R/GA4GH-methods.R
	opencga-client/src/main/R/R/Individual-methods.R
	opencga-client/src/main/R/R/Job-methods.R
	opencga-client/src/main/R/R/Meta-methods.R
	opencga-client/src/main/R/R/Operation-methods.R
	opencga-client/src/main/R/R/Organization-methods.R
	opencga-client/src/main/R/R/Panel-methods.R
	opencga-client/src/main/R/R/Project-methods.R
	opencga-client/src/main/R/R/Sample-methods.R
	opencga-client/src/main/R/R/Study-methods.R
	opencga-client/src/main/R/R/User-methods.R
	opencga-client/src/main/R/R/Variant-methods.R
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/OrganizationClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java
	opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java
	opencga-client/src/main/javascript/Admin.js
	opencga-client/src/main/javascript/Alignment.js
	opencga-client/src/main/javascript/ClinicalAnalysis.js
	opencga-client/src/main/javascript/Cohort.js
	opencga-client/src/main/javascript/DiseasePanel.js
	opencga-client/src/main/javascript/Family.js
	opencga-client/src/main/javascript/File.js
	opencga-client/src/main/javascript/GA4GH.js
	opencga-client/src/main/javascript/Individual.js
	opencga-client/src/main/javascript/Job.js
	opencga-client/src/main/javascript/Meta.js
	opencga-client/src/main/javascript/Organization.js
	opencga-client/src/main/javascript/Project.js
	opencga-client/src/main/javascript/Sample.js
	opencga-client/src/main/javascript/Study.js
	opencga-client/src/main/javascript/User.js
	opencga-client/src/main/javascript/Variant.js
	opencga-client/src/main/javascript/VariantOperation.js
	opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/family_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/file_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/job_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/organization_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/project_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/study_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/user_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py
	opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py
    @jtarraga
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Commits on Jun 10, 2024

  1. catalog: apply data model changes, #TASK-5964

    @pfurio
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  2. app: add some migrations, #TASK-5964

    @pfurio
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Commits on Jun 11, 2024

  1. app: add new ClinicalStatus migration, #TASK-5964

    @pfurio
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  2. app: fix migration script, #TASK-5964

    @pfurio
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  3. app: improve scenario where status.id is null, #TASK-5964

    @pfurio
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  4. catalog: fix status indexes, #TASK-5964

    @pfurio
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Commits on Jun 12, 2024

  1. app: remove status name migration script, #TASK-5964

    @pfurio
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Commits on Jun 13, 2024

  1. Merge branch 'develop' into TASK-5516

    @jtarraga
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Commits on Jun 17, 2024

  1. Merge pull request #2459 from opencb/TASK-5895 

    TASK-5895 - HBaseLockManager Inconsistent lock status
    @j-coll
    j-coll authored Jun 17, 2024
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Commits on Jun 20, 2024

  1. storage: Fix compoundHet query in single-study projects. #TASK-6311

    @j-coll
    j-coll committed Jun 20, 2024
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Commits on Jun 21, 2024

  1. Merge branch 'TASK-6345' into TASK-6345-2.12.6

    @pfurio
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Commits on Jun 25, 2024

  1. Merge pull request #2471 from opencb/TASK-6311 

    TASK-6311 - Error querying by CompoundHet - Require exactly one study
    @j-coll
    j-coll authored Jun 25, 2024
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Commits on Jun 26, 2024

  1. Merge branch 'develop' into TASK-5964

    @pfurio
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  2. analysis: add config files for Exomiser versions 13.1 and 14.0 using … 

    …different default values, #TASK-6297, #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	modified:   opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/OpenCGATestExternalResource.java
	renamed:    opencga-app/app/analysis/exomiser/application.properties -> opencga-app/app/analysis/exomiser/13.1/application.properties
	renamed:    opencga-app/app/analysis/exomiser/exomiser-analysis.yml -> opencga-app/app/analysis/exomiser/13.1/exomiser-analysis.yml
	renamed:    opencga-app/app/analysis/exomiser/output.yml -> opencga-app/app/analysis/exomiser/13.1/output.yml
	new file:   opencga-app/app/analysis/exomiser/14.0/application.properties
	new file:   opencga-app/app/analysis/exomiser/14.0/exomiser-analysis.yml
	new file:   opencga-app/app/analysis/exomiser/14.0/output.yml
    @jtarraga
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  3. cicd: Modify pull request approve #TASK-6399

    @juanfeSanahuja
    juanfeSanahuja committed Jun 26, 2024
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  4. cicd: Added xetabase script #TASK-6399

    @juanfeSanahuja
    juanfeSanahuja committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. Merge branch 'TASK-6345' into TASK-6345-2.12.6

    @pfurio
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  2. Merge branch 'release-2.12.x' into TASK-6345-2.12.6

    @pfurio
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  3. catalog: check ADMIN permissions for DONE statuses, #TASK-5964

    @pfurio
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  4. app: move migration folder, #TASK-5964

    @pfurio
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Commits on Jun 28, 2024

  1. storage: Fix numTotalSamples variant result value. #TASK-6436

    @j-coll
    j-coll committed Jun 28, 2024
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  2. Merge branch 'develop' into TASK-6255 

      - Update JUnit tests related to Exomiser, and
  - Resolve conflicts:
	opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java
	opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java
	opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysis.java
	opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java
	opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java
	opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/VariantInternalCommandExecutor.java
	opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/VariantCommandOptions.java
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java
	opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java
	opencga-core/src/main/java/org/opencb/opencga/core/models/clinical/ExomiserWrapperParams.java
    @jtarraga
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  3. storage: Fix canUseThisExecutor on SampleIndexOnlyVariantQueryExecuto… 

    …r #TASK-6436
    @j-coll
    j-coll committed Jun 28, 2024
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Commits on Jul 1, 2024

  1. Merge pull request #2478 from opencb/TASK-6436 

    TASK-6436 - OpenCGA-Storage test failed on release-2.12.x branch
    @j-coll
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  2. Merge branch 'develop' into TASK-5964

    @pfurio
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  3. Merge branch 'develop' into TASK-5964

    @pfurio
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  4. cicd: Added xetabase script #TASK-6399

    @juanfeSanahuja
    juanfeSanahuja committed Jul 1, 2024
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Commits on Jul 3, 2024

  1. Merge branch 'release-2.12.x' into TASK-6345-2.12.6

    @pfurio
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  2. Merge branch 'develop' into TASK-5516

    @jtarraga
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  3. Merge branch 'develop' into TASK-6255

    @jtarraga
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Commits on Jul 5, 2024

  1. Prepare release 2.12.6

    @juanfeSanahuja
    juanfeSanahuja committed Jul 5, 2024
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  2. Prepare next release 2.12.7-SNAPSHOT

    @juanfeSanahuja
    juanfeSanahuja committed Jul 5, 2024
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  3. Merge branch 'develop' into TASK-5964

    @pfurio
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  4. catalog: use panelLocked constant, #TASK-5964

    @pfurio
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Commits on Jul 8, 2024

  1. Merge branch 'release-2.12.x' into TASK-6345-2.12.6

    @pfurio
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  2. pom: Added github packages to manage snapshots #TASK-6345

    @juanfeSanahuja
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  3. pom: Added sonatype also manage snapshots #TASK-6345

    @juanfeSanahuja
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  4. pom: Comment sonatype to manage snapshots #TASK-6345

    @juanfeSanahuja
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  5. pom: Comment repositories section #TASK-6345

    @juanfeSanahuja
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  6. pom: Restore repositories section #TASK-6345

    @juanfeSanahuja
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  7. Merge branch 'TASK-6345' into TASK-6345-2.12.6

    @pfurio
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  8. storage-core pom: Exclusion distlib #TASK-6345

    @juanfeSanahuja
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  9. Merge branch 'TASK-6345-2.12.6' of github.com:opencb/opencga into TAS… 

    …K-6345-2.12.6
    @juanfeSanahuja
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Commits on Jul 9, 2024

  1. Merge branch 'TASK-6345' into TASK-6345-2.12.6

    @pfurio
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Commits on Jul 10, 2024

  1. Merge branch 'TASK-6345' into TASK-6345-2.12.6

    @pfurio
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  2. Merge branch 'develop' into TASK-5448

    @j-coll
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  3. app: Fix merge issues. #TASK-5448

    @j-coll
    j-coll committed Jul 10, 2024
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  4. app: add missing migration for panelLock field, #TASK-5964

    @pfurio
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  5. storage: Allow repeat variant-setup before indexing any file. #TASK-5448

    @j-coll
    j-coll committed Jul 10, 2024
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  6. Merge branch 'develop' into TASK-6255

    @jtarraga
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  7. storage: Remove some default normalization extensions. #TASK-5448

    @j-coll
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Commits on Jul 11, 2024

  1. Merge pull request #2473 from opencb/TASK-6345-2.12.6 

    TASK-6345 - Cohort and sample double association is missing
    @pfurio
    pfurio authored Jul 11, 2024
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  2. Merge branch 'develop' into TASK-5964

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  3. Merge branch 'develop' into TASK-5964

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  4. Merge branch 'develop' into TASK-6255 

    Resolve conflicts by generating clients:
	opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
	opencga-client/src/main/R/R/Clinical-methods.R
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Commits on Jul 16, 2024

  1. storage: Do not use CIEND on INSERTIONS to build HBase RowKey. #TASK-… 

    …6558
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  1. Merge branch 'release-3.2.x'

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  2. Prepare new development branch release-3.2.x

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  3. storage: Remove uneeded assumptions in tests. #TASK-6558

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  1. server: add new tagsAction query parameter, #TASK-6568

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  2. server: add tagsAction to study notes update, #TASK-6568

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  3. catalog: ensure password change and reset use same policy, #TASK-6494

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  4. client: regenerate clients, #TASK-6568

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  1. Merge branch 'release-3.2.x' into TASK-5964

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  2. Merge remote-tracking branch 'origin/release-3.2.x' into TASK-5448

    @j-coll
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  3. analysis: Fix compilation issues. #TASK-5448

    @j-coll
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  4. app: improve migration, #TASK-5964

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  1. Merge branch 'release-3.2.x' into TASK-6255

    @jtarraga
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  2. Merge branch 'release-3.2.x' into TASK-5516

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  1. catalog: archive old password, #TASK-6494

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  1. core: rename lastChangeDate for lastModified, #TASK-6494

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  2. server: change executor cli generator to consider maps, #TASK-6626

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  3. app: regenerate cli executors, #TASK-6626

    @pfurio
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  4. Prepare next release 2.12.6.1-SNAPSHOT

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  5. storage: Hash large vairants into solr collections. Add unhashed attr… 

    …_id #TASK-6596
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  6. storage: Fix some tests. #TASK-6596

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  7. storage: Fix NPE at some tests. #TASK-6596

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Commits on Jul 25, 2024

  1. storage: Fix VariantDBAdaptorTest. #TASK-6596

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  2. Merge pull request #2490 from opencb/TASK-6596 

    TASK-6596 - Error loading long variants: DocValuesField "variantId" is too large, must be <=32766
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  1. Prepare release 2.12.6.1

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Commits on Jul 29, 2024

  1. storage-core: call the function parseConsequenceTypes from VariantQue… 

    …ryUtils to replace the aliases "loss_of_function" and "protein_altering" with their corresponding list of values, #TASK-6492
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  2. Merge branch 'release-3.2.x' into TASK-6399

    @juanfeSanahuja
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  1. Prepare Port Patch 1.10.6.1 -> 2.2.1 #TASK-6515

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  2. Merge branch 'release-3.2.x' into TASK-6515

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Commits on Jul 31, 2024

  1. Merge pull request #2465 from opencb/TASK-5516 

    TASK-5516 Speed-up CVDB queries
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  1. Merge branch 'release-3.2.x' into TASK-6492

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  1. catalog: query case by version, #TASK-5964

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  2. Merge branch 'release-3.2.x' into TASK-5964

    @pfurio
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  3. Merge branch 'release-3.2.x' into TASK-6568

    @pfurio
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  4. Merge pull request #2485 from opencb/TASK-6568 

    TASK-6568 - missing tagsAction in notes/update
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  5. Merge branch 'release-3.2.x' into TASK-6492

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  6. Merge pull request #2492 from opencb/TASK-6492 

    TASK-6492 Clinical Case query failed with cvCt value loss_of_function
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Commits on Aug 6, 2024

  1. Merge pull request #2484 from opencb/TASK-6558 

    TASK-6558 - Issue indexing variants with length 0 (i.e. start > end) and CIEND
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  2. Merge branch 'release-3.2.x' into TASK-6494

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  3. core: update configuration.yml, #TASK-6494

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  4. Merge branch 'release-3.2.x' into TASK-5964

    @pfurio
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Commits on Aug 7, 2024

  1. Merge branch 'release-3.2.x' into TASK-6626

    @pfurio
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  2. analysis: Fix ClinicalInterpretationAnalysisTest tests. #TASK-6703 

    Cherry-pick from 8495dd2
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  3. storage: Fix VariantLocalConflictResolverTest tests. #TASK-6703

    @j-coll
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  4. analysis: Fix test VariantOperationsTest#testCellbaseConfigure #TASK-… 

    …6703

Cherry-pick fdd88bc
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  5. storage: Fix tests VariantQueryExecutorTest. #TASK-6703

    @j-coll
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Commits on Aug 8, 2024

  1. Merge pull request #2489 from opencb/TASK-6626 

    TASK-6626 - CLI file update sets empty attributes object
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  2. Merge branch 'release-3.2.x' into TASK-6494

    @pfurio
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  3. Merge pull request #2493 from opencb/TASK-6703 

    TASK-6703 - Fix junit tests
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  4. Merge branch 'release-3.2.x' into TASK-5964

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Commits on Aug 9, 2024

  1. catalog: add salt to passwords, #TASK-6494

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  2. Fix Kill job method #TASK-6636

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  3. catalog: backwards compatibility, #TASK-6494

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  4. catalog: increase random salt length to 32, #TASK-6494

    @pfurio
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  5. core: add constant variable for the salt lenght, #TASK-6494

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  6. Merge branch 'release-3.2.x' into TASK-6515

    @juanfeSanahuja
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  7. Fix compile error CELLBASE_DATA_RELEASE_GRCH38 #TASK-6515

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  8. catalog: add salt to encryptPassword method, #TASK-6494

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Commits on Aug 13, 2024

  1. Merge pull request #2494 from opencb/TASK-6636 

    TASK-6636 - Job Kill method in JavaScript client of OpenCGA sends the params as POST body data
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  2. storage: Fix merge issue with ASSEMBLY. #TASK-6515

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  3. Merge branch 'release-3.2.x' into TASK-6255 

    Resolve conflicts:
    @jtarraga
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  4. storage: Embedded solr should be optional in tests. #TASK-6515

    @j-coll
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Commits on Aug 14, 2024

  1. Merge branch 'release-3.2.x' into TASK-6399

    @juanfeSanahuja
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  2. Merge pull request #2477 from opencb/TASK-6399 

    TASK-6399 - CI/CD: Include save reports option for tasks workflows
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Commits on Aug 19, 2024

  1. catalog: simplify code, #TASK-6494

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  2. Merge branch 'release-3.2.x' into TASK-6494

    @pfurio
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  3. Merge branch 'release-3.2.x' into TASK-5964

    @pfurio
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  4. Merge branch 'release-3.2.x' into TASK-6515

    @pfurio
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  5. catalog: add missing snapshot to parse query method, #TASK-5964

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Commits on Aug 20, 2024

  1. Merge pull request #2491 from opencb/TASK-6515 

    TASK-6515 - Port Patch 1.10.6.1 -> 2.2.1
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  2. Merge branch 'release-3.2.x' into TASK-6255

    @pfurio
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  3. Merge pull request #2462 from opencb/TASK-6255 

    Task 6255 Update Exomiser Docker image to v14.0.0
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  4. catalog: allow users with ADMIN to update Interpretations, #TASK-5964

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Commits on Aug 21, 2024

  1. catalog: check Interpretations can't be touched when CLOSED, #TASK-5964

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Commits on Aug 22, 2024

  1. storage: Define start-stop row scan for deleting files from archive t… 

    …able. #TASK-6756
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  2. storage: Fix param --force for vairant-file-delete #TASK-6737

    @j-coll
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  3. storage: Add tests for variant-file-delete --force. #TASK-6737

    @j-coll
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  4. catalog: allow updating status from type CLOSED, #TASK-5964

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  5. Merge branch 'release-3.2.x' into TASK-6494

    @pfurio
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  6. Merge pull request #2488 from opencb/TASK-6494 

    TASK-6494 - Improve our current Password Policy for built-in authentication in OpenCGA
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  7. Merge branch 'release-3.2.x' into TASK-5964

    @pfurio
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Commits on Aug 28, 2024

  1. Merge pull request #2474 from opencb/TASK-5964 

    TASK-5964 - Clinical Improvements
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Commits on Aug 29, 2024

  1. Merge branch 'release-3.2.x' into TASK-5448

    @j-coll
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Commits on Aug 30, 2024

  1. storage: Ensure SearchIndexVariantQueryExecutor is used with skip>500… 

    …. #TASK-6789
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  2. Merge pull request #2498 from opencb/TASK-6789 

    TASK-6789 - Variant query fails with large skip values
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  3. Merge pull request #2497 from opencb/TASK-6737 

    TASK-6737 - Force parameter is not recognised in the variant delete operation
    @j-coll
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  4. Merge pull request #2496 from opencb/TASK-6756 

    TAKS-6756 - Error deleting files from archive table
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Commits on Sep 2, 2024

  1. Prepare release 2.12.7

    @juanfeSanahuja
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  2. storage: Remove verbose logging. #TASK-5448

    @j-coll
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  3. Merge branch 'release-3.2.x' into TASK-5448

    @j-coll
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  4. storage: Fix compilation issue. #TASK-5448

    @j-coll
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Commits on Sep 3, 2024

  1. Merge pull request #2454 from opencb/TASK-5448 

    TASK-5448 - Add mandatory variant setup step
    @j-coll
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  2. preparing Port Patch 1.10.7 -> 2.2.1

    @juanfeSanahuja
    juanfeSanahuja committed Sep 3, 2024
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  3. Merge branch 'release-3.2.x' into TASK-6708

    @juanfeSanahuja
    juanfeSanahuja committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. cicd: Upload reference to develop branch in pull-request-approve to t… 

    …est-xetabase-workflow #TASK-6807
    @juanfeSanahuja
    juanfeSanahuja committed Sep 4, 2024
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Commits on Sep 6, 2024

  1. storage: Fix junit tests. #TASK-6708

    @j-coll
    j-coll committed Sep 6, 2024
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  2. app: Fix migration test. Missing projectMetadata #TASK-6708

    @j-coll
    j-coll committed Sep 6, 2024
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  3. anaysis: Fix OpenCGATestExternalResource creating analysis/exomiser. … 

    …#TASK-6708
    @j-coll
    j-coll committed Sep 6, 2024
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  4. Merge pull request #2499 from opencb/TASK-6708 

    TASK-6708 - Port Patch 2.12.7 -> 3.2.1 (Xetabase 1.10.7 -> 2.2.1)
    @juanfeSanahuja
    juanfeSanahuja authored Sep 6, 2024
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  5. Merge branch 'release-3.2.x' into TASK-6807

    @juanfeSanahuja
    juanfeSanahuja committed Sep 6, 2024
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Commits on Sep 9, 2024

  1. cicd: Fix xetabase branch calculation #TASK-6807

    @juanfeSanahuja
    juanfeSanahuja committed Sep 9, 2024
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Commits on Sep 10, 2024

  1. cicd: Fix xetabase branch calculation #TASK-6807

    @juanfeSanahuja
    juanfeSanahuja committed Sep 10, 2024
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  2. cicd: Fix xetabase branch calculation #TASK-6807

    @juanfeSanahuja
    juanfeSanahuja committed Sep 10, 2024
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Commits on Sep 12, 2024

  1. Merge pull request #2500 from opencb/TASK-6807 

    TASK-6807 - Pull request approve workflow Fail
    @juanfeSanahuja
    juanfeSanahuja authored Sep 12, 2024
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Commits on Sep 13, 2024

  1. Prepare release 3.2.1

    @juanfeSanahuja
    juanfeSanahuja committed Sep 13, 2024
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  2. Merge branch 'release-3.2.x'

    @juanfeSanahuja
    juanfeSanahuja committed Sep 13, 2024
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Commits on Oct 3, 2024

  1. Port Patch 3.2.1 -> 4.0.0 XB 2.2.1 -> 3.0.0 #TASK-6780

    @juanfeSanahuja
    juanfeSanahuja committed Oct 3, 2024
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  2. Merge branch 'develop' into TASK-6780

    @juanfeSanahuja
    juanfeSanahuja committed Oct 3, 2024
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Commits on Oct 8, 2024

  1. test: fix FamilyAnalysisTest JUnit tests, #TASK-6780

    @jtarraga
    jtarraga committed Oct 8, 2024
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  2. Merge branch 'TASK-6780' of https://github.com/opencb/opencga into TA… 

    …SK-6780
    @jtarraga
    jtarraga committed Oct 8, 2024
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