From f103ba5bff408b0360db8b31f677ec0e67a056f2 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 8 Mar 2024 16:24:26 +0100 Subject: [PATCH 1/9] Prepare release 3.0.0 --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 93b011f556f..86bcb471976 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -23,7 +23,7 @@ jobs: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: - cli: python3 ./build/cloud/docker/docker-build.py push --images base,init + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ needs.build.outputs.version }} secrets: inherit deploy-python: From 595b8f5612f4b03dbbc3b2ae4b61cf5bb9f58a61 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 20 May 2024 12:08:41 +0200 Subject: [PATCH 2/9] Prepare development branch 3.0.0.x #TASK-6256 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 2 +- 27 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index b207d265360..8e87f263f06 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 955c526ad6e..bfbd58793b9 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 9ec39cb0aa7..16647aebdec 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index d267e075341..832dde11be9 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index f996aa69c44..e18104a17bc 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 5b93869e400..eb2c6d0f786 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index c689e382215..7e3925bb9fe 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index dc20e3dcf3a..be27dc552d0 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6b1f0a28fb5..6eb6c110bd5 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index fb71790dc5e..80c167215df 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 3688c101f6b..2e2ee67cc27 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 44fd8cf29d7..2d5dbebf91b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 327725fd2e4..9708846e4f8 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 4f094c0a282..797c371a6a7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index be88884b590..2d1922b3655 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index d6758ba7e39..803fee44a25 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 508b1b2468b..0a7cea85134 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 177e7d79267..452570b992b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 2152ce3ec3e..7c6cbacda94 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index a0fae207eff..0cca28f1721 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index f273977d555..7e8d9e80136 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 94139ce36d5..10d9d270831 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 46501dba0bf..ac1e8071fb5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index dc9acd1a6b1..69f063a9a44 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 164e769ee99..0347eca3180 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 1076e3ad276..da8d02db513 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index ea34c50ade0..181affb30a7 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0 + 3.0.0.1.SNAPSHOT pom OpenCGA From 77876a24f4a93b4cbbde53610572f87253f59816 Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 20 May 2024 16:46:57 +0200 Subject: [PATCH 3/9] app: keep track of old migrations, #TASK-6256 - recover old v2.x migrations and marked them as deprecated - check all previous migrations were successfully run before moving to v3.0.0 - keep track of previous migrations --- .../executors/MigrationCommandExecutor.java | 2 +- .../v2/v2_0_3/catalog/java/Migration1.java | 14 ++ .../v2_0_5/catalog/java/initialiseGroups.java | 15 ++ ...removeDeletedFileReferencesFromSample.java | 16 ++ ...tationSetsInClinicalAnalysisMigration.java | 20 +++ ...pleteClinicalReportDataModelMigration.java | 19 +++ .../catalog/java/AddMissingIndexes.java | 18 +++ .../java/AddPanelsToInterpretations.java | 17 ++ .../catalog/java/CreateAuditIndexes.java | 19 +++ .../v2/v2_1_0/catalog/java/PanelLock.java | 18 +++ .../RemoveRCVersionsFromMigrationRuns.java | 18 +++ ...RenameDatastoreConfigurationToOptions.java | 18 +++ .../StudyClinicalConfigurationRelocation.java | 19 +++ .../java/VariantFileStatsRelocation.java | 18 +++ .../v2_1_0/catalog/javascript/Migration1.java | 14 ++ .../v2_1_0/catalog/javascript/Migration2.java | 14 ++ .../v2_1_0/catalog/javascript/Migration3.java | 14 ++ .../v2_1_0/catalog/javascript/Migration4.java | 14 ++ .../AddCellbaseConfigurationToProject.java | 18 +++ .../DefaultSampleIndexConfiguration.java | 18 +++ .../NewClinicalSignificanceFields.java | 18 +++ .../catalog/AddMissingClinicalAudit.java | 17 ++ .../v2_2_0/catalog/AddNameFieldInCohort.java | 16 ++ .../v2_2_0/catalog/AddNewAllowedBiotype.java | 17 ++ .../catalog/AddNewFileInternalIndex_1850.java | 17 ++ .../AddSampleInternalVariant_1851.java | 17 ++ .../catalog/ChangeInterpretationMethods.java | 16 ++ .../ClinicalVariantEvidenceMigration.java | 16 ++ .../catalog/DeleteUnusedVariableSets.java | 18 +++ .../v2_2_0/catalog/FixFamilyReferences.java | 17 ++ .../catalog/FixNonExistingMoIFromPanels.java | 18 +++ ...ImproveClinicalAnalysisQualityControl.java | 17 ++ .../catalog/ImproveFileQualityControl.java | 17 ++ .../ImproveIndividualQualityControl.java | 16 ++ ...mproveVariableSetNamesAndDescriptions.java | 16 ++ .../v2_2_0/catalog/RemoveFileDocsFromCA.java | 16 ++ .../v2_2_0/catalog/RemoveParallelIndexes.java | 16 ++ .../RenameFamilyQualityControlFields.java | 16 ++ .../RenameFileQualityControlFields.java | 16 ++ .../RenameIndividualQualityControlFields.java | 16 ++ .../RenameInterpretationFindingStats.java | 17 ++ .../RenameSampleQualityControlFields.java | 18 +++ ...allerInterpretationStudyConfiguration.java | 16 ++ .../AddInternalLastModified.java | 10 ++ ...AddModificationDateToClinicalInternal.java | 13 ++ .../AddModificationDateToCohortInternal.java | 13 ++ .../AddModificationDateToFamilyInternal.java | 13 ++ .../AddModificationDateToFileInternal.java | 13 ++ ...dModificationDateToIndividualInternal.java | 13 ++ ...ificationDateToInterpretationInternal.java | 13 ++ .../AddModificationDateToJobInternal.java | 13 ++ .../AddModificationDateToProjectInternal.java | 14 ++ .../AddModificationDateToSampleInternal.java | 13 ++ .../AddModificationDateToStudyInternal.java | 13 ++ .../catalog/addInterpretationStats.java | 17 ++ .../AddRegistrationDate.java | 10 ++ ...AddRegistrationDateToClinicalInternal.java | 13 ++ .../AddRegistrationDateToCohortInternal.java | 13 ++ .../AddRegistrationDateToFamilyInternal.java | 13 ++ .../AddRegistrationDateToFileInternal.java | 13 ++ ...dRegistrationDateToIndividualInternal.java | 13 ++ ...istrationDateToInterpretationInternal.java | 13 ++ .../AddRegistrationDateToJobInternal.java | 13 ++ .../AddRegistrationDateToProjectInternal.java | 14 ++ .../AddRegistrationDateToSampleInternal.java | 13 ++ .../AddRegistrationDateToStudyInternal.java | 13 ++ .../catalog/addRgaIndexToStudyInternal.java | 17 ++ .../issue_1795/AddFamilyIdsInIndividual.java | 15 ++ .../issue_1796/AddCohortIdsInSample.java | 15 ++ .../CompleteClinicalStatusDataModel.java | 17 ++ .../CompleteCohortStatusDataModel.java | 16 ++ .../CompleteFamilyStatusDataModel.java | 16 ++ .../CompleteFileStatusDataModel.java | 16 ++ .../CompleteIndividualStatusDataModel.java | 16 ++ ...CompleteInterpretationStatusDataModel.java | 16 ++ .../CompleteJobStatusDataModel.java | 16 ++ .../CompletePanelStatusDataModel.java | 16 ++ .../CompleteProjectStatusDataModel.java | 16 ++ .../CompleteSampleStatusDataModel.java | 16 ++ .../CompleteStudyStatusDataModel.java | 16 ++ .../CompleteUserStatusDataModel.java | 16 ++ .../IndividualOntologyTermMigration.java | 17 ++ .../NewStudyDataModelFields.java | 17 ++ .../SampleProcessingAndCollectionChanges.java | 16 ++ .../renameVariableSetFieldFromVariable.java | 18 +++ .../storage/SynchronizeCatalogStorage.java | 17 ++ .../storage/UpdateSampleIndexStatus.java | 17 ++ .../v2/v2_2_1/catalog/AddMissingBiotypes.java | 16 ++ .../v2_2_1/catalog/AddPanelGeneNameIndex.java | 17 ++ .../catalog/InitSharedProjectField.java | 16 ++ ...pleIndexConfigurationAddMissingStatus.java | 15 ++ .../catalog/AddLockedToInterpretation.java | 17 ++ .../v2_3_0/catalog/AddPanelInternalField.java | 17 ++ .../v2_3_0/catalog/AutoIncrementVersion.java | 19 +++ .../catalog/InitSampleIndexConfiguration.java | 18 +++ ...eCellbaseFromProjectInternalToProject.java | 19 +++ .../catalog/RenameDeletedCollections.java | 17 ++ .../RenameDeprecatedVariantStorageToolId.java | 18 +++ .../v2/v2_3_0/catalog/UpdateJWTSecretKey.java | 18 +++ .../storage/AddMissingColumnsToPhoenix.java | 14 ++ ...aseFromProjectInternalToProjectBugFix.java | 19 +++ .../catalog/AddClinicalStatusType_607.java | 18 +++ .../v2_4_0/catalog/AddPrivateDueDate_803.java | 18 +++ .../v2/v2_4_0/catalog/IndexPanelSource.java | 18 +++ .../AddMissingEndDateOnFinishedJobs.java | 20 +++ .../SynchronizeCatalogStorageStatuses.java | 18 +++ .../catalog/SignatureFittingsMigration.java | 18 +++ .../v2_4_2/catalog/AddClinicalDiscussion.java | 17 ++ .../catalog/RecoverProbandSamplesInCases.java | 19 +++ .../v2_4_3/catalog/MigrateToClinicalAcmg.java | 18 +++ .../catalog/ShortenIndexedFieldVariables.java | 17 ++ .../AvoidCaseStatusIdNullMigration.java | 18 +++ .../RemoveBiotypeAllowedKeysMigration.java | 17 ++ .../InvalidateVariantArchivesMigration.java | 16 ++ .../storage/AddCellbaseDataRelease.java | 20 +++ ...ncerRoleAndModeOfInheritanceMigration.java | 20 +++ .../CalculatePedigreeGraphMigration.java | 19 +++ .../MarkUnknownLargestVariantLength.java | 20 +++ .../catalog/RenameCellBaseToken2ApiKey.java | 20 +++ .../v3_0_0/OrganizationMigration.java | 152 ++++++++++++++---- .../opencga/catalog/migration/Migration.java | 5 + .../catalog/migration/MigrationManager.java | 5 + 122 files changed, 2051 insertions(+), 30 deletions(-) create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java rename opencga-app/src/main/java/org/opencb/opencga/app/migrations/{ => v3}/v3_0_0/OrganizationMigration.java (76%) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java index eb6f7ae747c..3f5f7cee80f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java @@ -6,7 +6,7 @@ import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.opencga.app.cli.admin.options.MigrationCommandOptions; import org.opencb.opencga.app.cli.main.io.Table; -import org.opencb.opencga.app.migrations.v3_0_0.OrganizationMigration; +import org.opencb.opencga.app.migrations.v3.v3_0_0.OrganizationMigration; import org.opencb.opencga.catalog.exceptions.CatalogException; import org.opencb.opencga.catalog.managers.CatalogManager; import org.opencb.opencga.catalog.migration.Migration; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java new file mode 100644 index 00000000000..ded1293c0d9 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_0_3.catalog.java; + +import org.opencb.opencga.catalog.exceptions.CatalogException; +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "recalculate_roles", description = "Recalculate roles from Family #1763", version = "2.0.3", date = 20210528, + deprecatedSince = "v3.0.0") +public class Migration1 extends MigrationTool { + + @Override + protected void run() throws CatalogException { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java new file mode 100644 index 00000000000..a5b971d44fa --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_0_5.catalog.java; + + +import org.opencb.opencga.catalog.exceptions.CatalogException; +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "initialise_groups", description = "Initialise userIds list from groups #1791", version = "2.0.5", date = 20210621, + deprecatedSince = "v3.0.0") +public class initialiseGroups extends MigrationTool { + + @Override + protected void run() throws CatalogException { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java new file mode 100644 index 00000000000..b2ffea9be48 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_0_6.catalog; + + +import org.opencb.opencga.catalog.exceptions.CatalogException; +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_file_references_from_sample", description = "Remove deleted file references from samples #1815", version = "2.0.6", + date = 20210901, deprecatedSince = "v3.0.0") +public class removeDeletedFileReferencesFromSample extends MigrationTool { + + @Override + protected void run() throws CatalogException { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java new file mode 100644 index 00000000000..79d15bbfe2d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_12_0.catalog; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_annotation_sets_to_clinical_analysis" , + description = "Add private annotation fields to ClinicalAnalysis documents #TASK-5198", + version = "2.12.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20231116, + deprecatedSince = "v3.0.0" +) +public class AddAnnotationSetsInClinicalAnalysisMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java new file mode 100644 index 00000000000..10effae5a66 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_12_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_clinical_report_data_model" , + description = "Complete Clinical Report data model #TASK-5198", + version = "2.12.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20231128, + deprecatedSince = "v3.0.0" +) +public class CompleteClinicalReportDataModelMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java new file mode 100644 index 00000000000..ecd911181d0 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_missing_indexes", + description = "Add missing indexes", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210928, + deprecatedSince = "v3.0.0") +public class AddMissingIndexes extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java new file mode 100644 index 00000000000..984e214aed5 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_panels_to_interpretations", + description = "Add panels to Interpretations #1802", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20210713, + deprecatedSince = "v3.0.0") +public class AddPanelsToInterpretations extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java new file mode 100644 index 00000000000..da1220d2595 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "create_audit_indexes", description = "Create Audit indexes", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210622, + deprecatedSince = "v3.0.0") +public class CreateAuditIndexes extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} + diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java new file mode 100644 index 00000000000..763e3568ae3 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_panel_lock", + description = "Add new panelLock to ClinicalAnalysis #1802", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210713, + deprecatedSince = "v3.0.0") +public class PanelLock extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java new file mode 100644 index 00000000000..2f6c73e610a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_rc_version_from_migration_runs", + description = "Remove RC versions from migration runs stored in catalog", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210723, + deprecatedSince = "v3.0.0") +public class RemoveRCVersionsFromMigrationRuns extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java new file mode 100644 index 00000000000..09f6facd0ae --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_datastore_configuration_to_options", description = "Rename project.internal.datastores.variant.configuration to options", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210617, + deprecatedSince = "v3.0.0") +public class RenameDatastoreConfigurationToOptions extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java new file mode 100644 index 00000000000..3a0c9fe1224 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "move_study_clinical_config_to_internal", + description = "Move Study ClinicalConfiguration to internal.configuration", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210708, + deprecatedSince = "v3.0.0") +public class StudyClinicalConfigurationRelocation extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java new file mode 100644 index 00000000000..5a61db123b9 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.java; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "move_variant_file_stats_to_qc", description = "Move opencga_file_variant_stats annotation set from variable sets to " + + "FileQualityControl", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + patch = 1, + date = 20210614, + deprecatedSince = "v3.0.0") +public class VariantFileStatsRelocation extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java new file mode 100644 index 00000000000..c531bfcbb4f --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "build_rga_indexes", description = "Create index for sample RGA status #1693", version = "2.1.0", + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") +public class Migration1 extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java new file mode 100644 index 00000000000..f6fff9fbd50 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "init_userId_group_arrays", description = "Initialise all userIds arrays from groups #1735", version = "2.1.0", + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") +public class Migration2 extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java new file mode 100644 index 00000000000..d449cc8fe86 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "init_ca_panel_arrays", description = "Initialise panels array in Clinical Analysis #1759", version = "2.1.0", + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") +public class Migration3 extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} \ No newline at end of file diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java new file mode 100644 index 00000000000..0093d746f08 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.catalog.javascript; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "update_qc_file_sample_fields", description = "Update QC fields from Sample and File #1730", version = "2.1.0", + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210531, patch = 4, deprecatedSince = "v3.0.0") +public class Migration4 extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java new file mode 100644 index 00000000000..a85a315e52a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.storage; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_cellbase_configuration_to_project", description = "Add cellbase configuration from storage-configuration.yml to project.internal.cellbase", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + patch = 3, + date = 20210616, + deprecatedSince = "v3.0.0") +public class AddCellbaseConfigurationToProject extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java new file mode 100644 index 00000000000..3ef78abd74f --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.storage; + + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "default_sample_index_configuration", description = "Add a default backward compatible sample index configuration", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + patch = 7, + date = 20210721, + deprecatedSince = "v3.0.0") // Needs to run after StudyClinicalConfigurationRelocation +public class DefaultSampleIndexConfiguration extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java new file mode 100644 index 00000000000..fd70c48eb00 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_1_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + + +@Migration(id = "new_clinical_significance_fields", description = "Add new clinical significance fields and combinations for variant storage and solr", version = "2.1.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + patch = 1, + date = 20210708, + deprecatedSince = "v3.0.0") +public class NewClinicalSignificanceFields extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java new file mode 100644 index 00000000000..33a03883d93 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_missing_create_interpretation_in_clinical_audit", + description = "Add missing CREATE_INTERPRETATION audits in ClinicalAnalysis", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211227, deprecatedSince = "v3.0.0") +public class AddMissingClinicalAudit extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java new file mode 100644 index 00000000000..2860f82cd1b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_name_field_in_cohort_1902", + description = "Add new name field to Cohort #1902", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220228, deprecatedSince = "v3.0.0") +public class AddNameFieldInCohort extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java new file mode 100644 index 00000000000..32324263f93 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_new_allowed_biotype", + description = "Add new allowed biotype 'guide_RNA', #1856", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20211209, deprecatedSince = "v3.0.0") +public class AddNewAllowedBiotype extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java new file mode 100644 index 00000000000..5e944869f84 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "new_file_internal_index_1850", + description = "Add new FileInternalVariant and FileInternalAlignment index #1850", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211127, deprecatedSince = "v3.0.0") +public class AddNewFileInternalIndex_1850 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java new file mode 100644 index 00000000000..0bf80272613 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_sample_internal_variant_1851", + description = "Add new SampleInternalVariant #1851", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211129, deprecatedSince = "v3.0.0") +public class AddSampleInternalVariant_1851 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java new file mode 100644 index 00000000000..f7acbb2afe1 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "change_interpretation_method", + description = "Remove list of methods from Interpretations #1841", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211112, deprecatedSince = "v3.0.0") +public class ChangeInterpretationMethods extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java new file mode 100644 index 00000000000..ac2d8053f40 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_clinical_variant_evidence_review", + description = "Add new ClinicalVariantEvidenceReview object, #1874", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220112, deprecatedSince = "v3.0.0") +public class ClinicalVariantEvidenceMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java new file mode 100644 index 00000000000..8dce7c69ff9 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "delete_unused_variablesets", + description = "Delete unused VariableSets, #1859", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20211210, deprecatedSince = "v3.0.0") +public class DeleteUnusedVariableSets extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java new file mode 100644 index 00000000000..b1884d5db2f --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "fix_family_references_in_individual", + description = "Fix Family references, #TASK-489", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220324, deprecatedSince = "v3.0.0") +public class FixFamilyReferences extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java new file mode 100644 index 00000000000..a4e46dde580 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "fix_non_existing_mois_from_panels", + description = "Remove non-existing MOIs from Panels", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20220111, deprecatedSince = "v3.0.0") +public class FixNonExistingMoIFromPanels extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java new file mode 100644 index 00000000000..29c9b704e4b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "improve_ca_quality_control", + description = "Quality control normalize comments and fields #1826", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211001, deprecatedSince = "v3.0.0") +public class ImproveClinicalAnalysisQualityControl extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java new file mode 100644 index 00000000000..e334fc6e892 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "improve_file_quality_control", + description = "Quality control normalize comments and fields #1826", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211001, deprecatedSince = "v3.0.0") +public class ImproveFileQualityControl extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java new file mode 100644 index 00000000000..aa365610323 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "improve_individual_quality_control", + description = "Quality control normalize comments and fields #1826", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211001, deprecatedSince = "v3.0.0") +public class ImproveIndividualQualityControl extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java new file mode 100644 index 00000000000..39b2df0d2a2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveVariableSetNamesAndDescriptions.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "improveVariableSetNamesAndDescriptions", + description = "Improve VariableSet names and descriptions", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211210) +public class ImproveVariableSetNamesAndDescriptions extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java new file mode 100644 index 00000000000..b39fca366f7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_file_docs_from_clinical_analyses", + description = "Store references of File in Clinical Analysis and not full File documents #1837", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211102, deprecatedSince = "v3.0.0") +public class RemoveFileDocsFromCA extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java new file mode 100644 index 00000000000..18d3359497e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_parallel_indexes", + description = "Remove parallel array indexes #CU-20jc4tx", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220310, deprecatedSince = "v3.0.0") +public class RemoveParallelIndexes extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java new file mode 100644 index 00000000000..e51a0b7a664 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_family_quality_control_fields", + description = "Rename FamilyQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211119, deprecatedSince = "v3.0.0") +public class RenameFamilyQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java new file mode 100644 index 00000000000..268d98b7ca2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_file_quality_control_fields", + description = "Rename FileQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211119, deprecatedSince = "v3.0.0") +public class RenameFileQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java new file mode 100644 index 00000000000..59d341e14fb --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_individual_quality_control_fields", + description = "Rename IndividualQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211119, deprecatedSince = "v3.0.0") +public class RenameIndividualQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java new file mode 100644 index 00000000000..c54d782361b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_interpretation_stats_field", + description = "Rename interpretation stats field #1819", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211115, deprecatedSince = "v3.0.0") +public class RenameInterpretationFindingStats extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java new file mode 100644 index 00000000000..48304e52905 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_sample_quality_control_fields", + description = "Rename SampleQualityControl fields #1844", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20211119, deprecatedSince = "v3.0.0") +public class RenameSampleQualityControlFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java new file mode 100644 index 00000000000..b461bda8aa2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_variant_caller_interpretation_configuration", + description = "Add default variant caller Interpretation Study configuration #1822", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20210916, deprecatedSince = "v3.0.0") +public class addDefaultVariantCallerInterpretationStudyConfiguration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java new file mode 100644 index 00000000000..28e32235bb0 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddInternalLastModified.java @@ -0,0 +1,10 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.MigrationTool; + +public abstract class AddInternalLastModified extends MigrationTool { + + protected void addInternalModificationDate(String collection) { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java new file mode 100644 index 00000000000..e206f4ea633 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_clinical.internal", description = "Add internal modificationDate to Clinical #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToClinicalInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java new file mode 100644 index 00000000000..051db7caee2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_cohort.internal", description = "Add internal modificationDate to Cohort #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToCohortInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java new file mode 100644 index 00000000000..dde58535dac --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_family.internal", description = "Add internal modificationDate to Family #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToFamilyInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java new file mode 100644 index 00000000000..169e97a6450 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_file.internal", description = "Add internal modificationDate to File #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToFileInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java new file mode 100644 index 00000000000..b4dac080bc4 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_individual.internal", description = "Add internal modificationDate to Individual #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToIndividualInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java new file mode 100644 index 00000000000..c86eef70177 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_interpretation.internal", description = "Add internal modificationDate to Interpretation #1810", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToInterpretationInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java new file mode 100644 index 00000000000..3afebad7f42 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_job.internal", description = "Add internal modificationDate to Job #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToJobInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java new file mode 100644 index 00000000000..06c7aa94aa4 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_modificationDate_to_project.internal", description = "Add internal modificationDate to Project #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToProjectInternal extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java new file mode 100644 index 00000000000..2d343956073 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_sample.internal", description = "Add internal modificationDate to Sample #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToSampleInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java new file mode 100644 index 00000000000..0f217355e4b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addInternalLastModified; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_modificationDate_to_study.internal", description = "Add internal modificationDate to Study #1810", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210812, deprecatedSince = "v3.0.0") +public class AddModificationDateToStudyInternal extends AddInternalLastModified { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java new file mode 100644 index 00000000000..3eee2d60222 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_interpretation_stats", + description = "Add interpretation stats #1819", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 2, + date = 20210908, deprecatedSince = "v3.0.0") +public class addInterpretationStats extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java new file mode 100644 index 00000000000..efd1107ba7b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDate.java @@ -0,0 +1,10 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.MigrationTool; + +public abstract class AddRegistrationDate extends MigrationTool { + + protected void addRegistrationDate(String collection) { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java new file mode 100644 index 00000000000..4881ae2a3f7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_clinical.internal", description = "Add registrationDate to Clinical #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToClinicalInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java new file mode 100644 index 00000000000..900d7fa7392 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_cohort.internal", description = "Add registrationDate to Cohort #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToCohortInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java new file mode 100644 index 00000000000..eca622902ff --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_family.internal", description = "Add registrationDate to Family #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToFamilyInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java new file mode 100644 index 00000000000..d8c408a9412 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_file.internal", description = "Add registrationDate to File #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToFileInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java new file mode 100644 index 00000000000..9a52e5c510f --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_individual.internal", description = "Add registrationDate to Individual #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToIndividualInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java new file mode 100644 index 00000000000..403e5ab6ca7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_interpretation.internal", description = "Add registrationDate to Interpretation #1804", + version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToInterpretationInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java new file mode 100644 index 00000000000..fffe8e9d092 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_job.internal", description = "Add registrationDate to Job #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToJobInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java new file mode 100644 index 00000000000..2648228bbdb --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_registrationDate_to_project.internal", description = "Add registrationDate to Project #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToProjectInternal extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java new file mode 100644 index 00000000000..094728d97c2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_sample.internal", description = "Add registrationDate to Sample #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToSampleInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java new file mode 100644 index 00000000000..90201d3d80d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java @@ -0,0 +1,13 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.addRegistrationDate; + +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_registrationDate_to_study.internal", description = "Add registrationDate to Study #1804", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, + date = 20210720, deprecatedSince = "v3.0.0") +public class AddRegistrationDateToStudyInternal extends AddRegistrationDate { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java new file mode 100644 index 00000000000..69939498085 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_rga_index_summary_to_study_internal", + description = "Add RGA Index information to Study Internal #", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + patch = 1, + date = 20210719, deprecatedSince = "v3.0.0") +public class addRgaIndexToStudyInternal extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java new file mode 100644 index 00000000000..343d8f4a578 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1795; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_familyIds_in_individual", description = "Add new list of familyIds in Individual #1795", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, date = 20210630, deprecatedSince = "v3.0.0") +public class AddFamilyIdsInIndividual extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} + diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java new file mode 100644 index 00000000000..60a08ba5c24 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1796; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationException; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_cohortIds_in_sample", description = "Add new list of cohortIds in Sample #1796", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, date = 20210706, deprecatedSince = "v3.0.0") +public class AddCohortIdsInSample extends MigrationTool { + + @Override + protected void run() throws MigrationException { + } +} + diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java new file mode 100644 index 00000000000..868bf9289d9 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_clinical_status_models", + description = "Complete Clinical Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, + deprecatedSince = "v3.0.0") +public class CompleteClinicalStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java new file mode 100644 index 00000000000..e5e76661b9c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_cohort_status_models", + description = "Complete Cohort Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteCohortStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java new file mode 100644 index 00000000000..7c91e83876e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_family_status_models", + description = "Complete Family Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteFamilyStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java new file mode 100644 index 00000000000..e1855bdaf34 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_file_status_models", + description = "Complete File Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteFileStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java new file mode 100644 index 00000000000..4111517a8db --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_individual_status_models", + description = "Complete Individual Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteIndividualStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java new file mode 100644 index 00000000000..4d4406e0ffe --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_interpretation_status_models", + description = "Complete Interpretation Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteInterpretationStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java new file mode 100644 index 00000000000..37ca338a57b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_job_status_models", + description = "Complete Job Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteJobStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java new file mode 100644 index 00000000000..6827d44467a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_panel_status_models", + description = "Complete Panel Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompletePanelStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java new file mode 100644 index 00000000000..a703e408fe3 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_project_status_models", + description = "Complete Project Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteProjectStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java new file mode 100644 index 00000000000..c42d6ac6a16 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_sample_status_models", + description = "Complete Sample Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteSampleStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java new file mode 100644 index 00000000000..401e823dc38 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_study_status_models", + description = "Complete Study Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteStudyStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java new file mode 100644 index 00000000000..7fd2e6bb798 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issue_1849; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "complete_user_status_models", + description = "Complete User Status data models #1849", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211126, deprecatedSince = "v3.0.0") +public class CompleteUserStatusDataModel extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java new file mode 100644 index 00000000000..14d9bf980be --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issues_1853_1855; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "individual_ontology_term_migration_#1853", + description = "Change sex and ethnicity types for OntologyTermAnnotation #1855", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211203, deprecatedSince = "v3.0.0") +public class IndividualOntologyTermMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java new file mode 100644 index 00000000000..5d8beb45356 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issues_1853_1855; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "new_study_data_model_fields_#1853", + description = "New Study 'sources', 'type' and 'additionalInfo' fields #1853", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211202, deprecatedSince = "v3.0.0") +public class NewStudyDataModelFields extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java new file mode 100644 index 00000000000..e5fdc1bd5d7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog.issues_1853_1855; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "sample_source_treatments_#1854", + description = "Sample source, treatments, processing and collection changes #1854", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20211201, patch = 2, deprecatedSince = "v3.0.0") +public class SampleProcessingAndCollectionChanges extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java new file mode 100644 index 00000000000..8a7b5d55aa2 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.catalog; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_variableset_field", + description = "Rename Variable variableSet field to variables #1823", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20210920, deprecatedSince = "v3.0.0") +public class renameVariableSetFieldFromVariable extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java new file mode 100644 index 00000000000..d7fdc3493fb --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "synchronize_catalog_storage_1850_1851", + description = "Synchronize catalog storage #1850 #1851", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220118, deprecatedSince = "v3.0.0") +public class SynchronizeCatalogStorage extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java new file mode 100644 index 00000000000..c5b1d88f3e7 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "update_sample_index_status_1901", + description = " Improve sample-index multi-schema management. #1901", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220302, deprecatedSince = "v3.0.0") +public class UpdateSampleIndexStatus extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java new file mode 100644 index 00000000000..79cda07260b --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_missing_biotypes", + description = "Add missing biotypes, #TASK-625", version = "2.2.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220412, deprecatedSince = "v3.0.0") +public class AddMissingBiotypes extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java new file mode 100644 index 00000000000..ef6f593863a --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_panel_gene_name_index", + description = "Add Panel gene.name index #TASK-602", version = "2.2.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220406, deprecatedSince = "v3.0.0") +public class AddPanelGeneNameIndex extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java new file mode 100644 index 00000000000..a87e7a0344e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "init_shared_project", + description = "Initialise sharedProjects #TASK-702", version = "2.2.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220502, deprecatedSince = "v3.0.0") +public class InitSharedProjectField extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java new file mode 100644 index 00000000000..ceb9b7ec53c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java @@ -0,0 +1,15 @@ +package org.opencb.opencga.app.migrations.v2.v2_2_1.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "sample_index_configuration_add_missing_status", + description = "Sample index configuration add missing status #TASK-512", version = "2.2.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220328, deprecatedSince = "v3.0.0") +public class SampleIndexConfigurationAddMissingStatus extends StorageMigrationTool { + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java new file mode 100644 index 00000000000..9d012bf9756 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_locked_to_interpretation_TASK-552", + description = "Add new 'locked' field to Interpretation #TASK-552", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220401, + deprecatedSince = "v3.0.0") +public class AddLockedToInterpretation extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java new file mode 100644 index 00000000000..acc9ad7f4b8 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_panel_internal_field-TASK_734", + description = "Add 'internal' to Panel data model #TASK-734", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220509, + deprecatedSince = "v3.0.0") +public class AddPanelInternalField extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java new file mode 100644 index 00000000000..1ab7ae34186 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "autoincrement_version_TASK-323", + description = "Reorganise data in new collections (autoincrement version) #TASK-323", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + offline = true, + date = 20220512, + deprecatedSince = "v3.0.0") +public class AutoIncrementVersion extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java new file mode 100644 index 00000000000..58aaee84f5c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "init_sampleIndexConfiguration-TASK550", + description = "Initialise SampleIndexConfiguration in Study internal #TASK-550", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220502, + deprecatedSince = "v3.0.0") +public class InitSampleIndexConfiguration extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java new file mode 100644 index 00000000000..17ef927ac00 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "move_cellbase_from_project_internal_to_project_TASK-354", + description = "Move cellbase from project.internal to project #TASK-354", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220422, + deprecatedSince = "v3.0.0") + +public class MoveCellbaseFromProjectInternalToProject extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java new file mode 100644 index 00000000000..907f44a7542 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_deleted_collections_TASK-359", + description = "Rename deleted collections #TASK-359", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220502, + deprecatedSince = "v3.0.0") +public class RenameDeletedCollections extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java new file mode 100644 index 00000000000..cd9daa6c5b6 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_variant_storage_tool_ids_TASK-705", + description = "Rename variant storage tool ids #TASK-705", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220506, + deprecatedSince = "v3.0.0") +public class RenameDeprecatedVariantStorageToolId extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java new file mode 100644 index 00000000000..5533165c027 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "update_jwt_secret_key_TASK-807", + description = "Update JWT secret key #TASK-807", version = "2.3.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220513, + deprecatedSince = "v3.0.0") +public class UpdateJWTSecretKey extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java new file mode 100644 index 00000000000..23b999d338d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java @@ -0,0 +1,14 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id="add_missing_columns_to_phoenix_TASK-789", description = "Add missing 1000G columns to phoenix #TASK-789", + version = "2.3.0", domain = Migration.MigrationDomain.STORAGE, date = 20220614, deprecatedSince = "v3.0.0" +) +public class AddMissingColumnsToPhoenix extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java new file mode 100644 index 00000000000..58342c39b41 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_3_1.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "bugfix_move_cellbase_from_project_internal_to_project_TASK-1100", + description = "Bugfix: Move cellbase from project.internal to project #TASK-1100", version = "2.3.1", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220620, + deprecatedSince = "v3.0.0") + +public class MoveCellbaseFromProjectInternalToProjectBugFix extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java new file mode 100644 index 00000000000..69a95f79bc6 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_clinical_status_type_TASK-607", + description = "Automatically close cases depending on the new clinical status type #TASK-607", version = "2.4.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220610, + deprecatedSince = "v3.0.0") +public class AddClinicalStatusType_607 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java new file mode 100644 index 00000000000..157ad23070d --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_private_dueDate_TASK-803", + description = "Add private _dueDate to ClinicalAnalysis #TASK-803", version = "2.4.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220530, + deprecatedSince = "v3.0.0") +public class AddPrivateDueDate_803 extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java new file mode 100644 index 00000000000..4b4839eba62 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "index_panel_source_TASK-473", + description = "Index panel source #TASK-473", version = "2.4.0", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220530, + deprecatedSince = "v3.0.0") +public class IndexPanelSource extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java new file mode 100644 index 00000000000..55b102ce06e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_10.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_missing_endDate_on_finished_jobs" , + description = "Add missing end date on finished jobs", + version = "2.4.10", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20221026, + deprecatedSince = "v3.0.0" +) +public class AddMissingEndDateOnFinishedJobs extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java new file mode 100644 index 00000000000..c4428b3204c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_11; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "synchronize_catalog_storage_statuses", + description = "Synchronize catalog internal statuses from storage, #TASK-1304", version = "2.4.11", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20221117, + deprecatedSince = "v3.0.0") +public class SynchronizeCatalogStorageStatuses extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java new file mode 100644 index 00000000000..0300dd60eae --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_11.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "signature_fittings" , + description = "Replace fitting for fittings in Signature", + version = "2.4.11", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20221109, + deprecatedSince = "v3.0.0" +) +public class SignatureFittingsMigration extends MigrationTool { + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java new file mode 100644 index 00000000000..a20caa8ac9c --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_2.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "add_clinical_discussion_TASK-1472", + description = "Add ClinicalDiscussion #TASK-1472", version = "2.4.2", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220727, + deprecatedSince = "v3.0.0") +public class AddClinicalDiscussion extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java new file mode 100644 index 00000000000..5fb3e88f9d5 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_2.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "recover_proband_samples_in_cases_TASK-1470", + description = "Recover lost samples in clinical collection #TASK-1470", version = "2.4.2", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220725, + patch = 2, + deprecatedSince = "v3.0.0") +public class RecoverProbandSamplesInCases extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java new file mode 100644 index 00000000000..c92a6789215 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_3.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "migrate_to_clinical_acmg_TASK-1194", + description = "Migrate to ClinicalAcmg #TASK-1194", version = "2.4.3", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220809, + deprecatedSince = "v3.0.0") +public class MigrateToClinicalAcmg extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java new file mode 100644 index 00000000000..2dde0ff7165 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_3.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "shorten_indexed_field_variables-1386", + description = "Shorten indexed field variables #TASK-1386", version = "2.4.3", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220809, + deprecatedSince = "v3.0.0") +public class ShortenIndexedFieldVariables extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java new file mode 100644 index 00000000000..bd1f1a496e0 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java @@ -0,0 +1,18 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_4.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "avoidCaseStatusIdNull-1938", + description = "Avoid nullable status id in Clinical Analysis #TASK-1938", version = "2.4.4", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220914, + deprecatedSince = "v3.0.0") +public class AvoidCaseStatusIdNullMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java new file mode 100644 index 00000000000..05d6967de74 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java @@ -0,0 +1,17 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_4.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "remove_biotype_allowed_keys_TASK-1849", + description = "Remove biotype and consequence type allowed keys from variable sets #TASK-1849", version = "2.4.4", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.CATALOG, + date = 20220905, + deprecatedSince = "v3.0.0") +public class RemoveBiotypeAllowedKeysMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java new file mode 100644 index 00000000000..4283c433ede --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java @@ -0,0 +1,16 @@ +package org.opencb.opencga.app.migrations.v2.v2_4_4.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "invalidate_variant_archives_migration-633", + description = "Invalidate variant archives from variant storage hadoop #TASK-633", version = "2.4.4", + language = Migration.MigrationLanguage.JAVA, + domain = Migration.MigrationDomain.STORAGE, + date = 20220825, + deprecatedSince = "v3.0.0") +public class InvalidateVariantArchivesMigration extends StorageMigrationTool { + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java new file mode 100644 index 00000000000..4dc66aabcea --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_6_0.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "add_cellbase_data_release" , + description = "Add default cellbase data release if missing", + version = "2.6.0", + domain = Migration.MigrationDomain.STORAGE, + language = Migration.MigrationLanguage.JAVA, + patch = 2, + date = 20230104, + deprecatedSince = "v3.0.0" +) +public class AddCellbaseDataRelease extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java new file mode 100644 index 00000000000..f7fcaa12a55 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_7_0.catalog; + + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "panel_roles_and_modesOfInheritance" , + description = "Change panel cancer.role and modeOfInheritance for cancer.roles[] and modesOfInheritance[]", + version = "2.7.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20230117, + deprecatedSince = "v3.0.0" +) +public class CancerRoleAndModeOfInheritanceMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java new file mode 100644 index 00000000000..d3f44141067 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java @@ -0,0 +1,19 @@ +package org.opencb.opencga.app.migrations.v2.v2_8_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "calculate_pedigree_graph" , + description = "Calculate Pedigree Graph for all the families", + version = "2.8.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20230313, + deprecatedSince = "v3.0.0" +) +public class CalculatePedigreeGraphMigration extends MigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java new file mode 100644 index 00000000000..fdb1a44da12 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_8_6.storage; + +import org.opencb.opencga.app.migrations.StorageMigrationTool; +import org.opencb.opencga.catalog.migration.Migration; + +@Migration(id = "mark_unknown_largest_variant_length" , + description = "Mark as unknown largest variant length", + version = "2.8.6", + domain = Migration.MigrationDomain.STORAGE, + language = Migration.MigrationLanguage.JAVA, + patch = 1, + date = 20230927, + deprecatedSince = "v3.0.0" +) +public class MarkUnknownLargestVariantLength extends StorageMigrationTool { + + @Override + protected void run() throws Exception { + } +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java new file mode 100644 index 00000000000..79dd1aab762 --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java @@ -0,0 +1,20 @@ +package org.opencb.opencga.app.migrations.v2.v2_9_0.catalog; + +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +@Migration(id = "rename_cellbase_token_2_api_key" , + description = "Rename CellBase Token to ApiKey", + version = "2.9.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20230829, + deprecatedSince = "v3.0.0" +) +public class RenameCellBaseToken2ApiKey extends MigrationTool { + + @Override + protected void run() throws Exception { + } + +} diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java similarity index 76% rename from opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java rename to opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java index 04c976812c4..d1f749bafe0 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3_0_0/OrganizationMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v3/v3_0_0/OrganizationMigration.java @@ -1,4 +1,4 @@ -package org.opencb.opencga.app.migrations.v3_0_0; +package org.opencb.opencga.app.migrations.v3.v3_0_0; import com.mongodb.client.*; import com.mongodb.client.model.Filters; @@ -28,7 +28,14 @@ import org.opencb.opencga.core.config.Configuration; import org.opencb.opencga.core.models.migration.MigrationRun; import org.opencb.opencga.core.models.organizations.OrganizationCreateParams; - +import org.reflections.Reflections; +import org.reflections.scanners.SubTypesScanner; +import org.reflections.scanners.TypeAnnotationsScanner; +import org.reflections.util.ClasspathHelper; +import org.reflections.util.ConfigurationBuilder; + +import java.lang.reflect.Modifier; +import java.net.URL; import java.nio.file.Files; import java.nio.file.Paths; import java.security.NoSuchAlgorithmException; @@ -102,13 +109,52 @@ private MigrationStatus checkAndInit() throws CatalogException { throw new CatalogException("Please grant write access to path '" + configuration.getWorkspace() + "'"); } - // TODO: Check last migration is 2.2.?? + Set> availableMigrations = getAvailableMigrations(); + + // Check all previous v2.x migrations have been run successfully MongoCollection migrationCol = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.MIGRATION_COLLECTION); - long count = migrationCol.countDocuments(Filters.in("status", MigrationRun.MigrationStatus.PENDING, + long count = migrationCol.countDocuments(); + // We take out 1 to the availableMigrations.size() because it will consider the present migration, which is not part of the check + logger.debug("Found '{}' Java migrations", availableMigrations.size() - 1); + logger.debug("Found '{}' migrations registered in the database", count); + if (count < availableMigrations.size() - 1) { + Set migrations = new HashSet<>(); + for (Class availableMigration : availableMigrations) { + Migration annotation = availableMigration.getAnnotation(Migration.class); + // Only consider previous migrations, not the present one + if (!annotation.version().equals("3.0.0")) { + migrations.add(annotation.id() + ":v" + annotation.version()); + } + } + + Set processedMigrations = new HashSet<>(); + Set onlyInJava = new HashSet<>(); + Set onlyInDB = new HashSet<>(); + migrationCol.find().forEach((document) -> { + String migrationId = document.getString("id") + ":v" + document.getString("version"); + processedMigrations.add(migrationId); + if (!migrations.contains(migrationId)) { + onlyInDB.add(migrationId); + } + }); + for (String migration : migrations) { + if (!processedMigrations.contains(migration)) { + onlyInJava.add(migration); + } + } + logger.debug("Migrations not registered in the database: {}", String.join(", ", onlyInJava)); + logger.debug("Migrations only found in the DB: {}", String.join(", ", onlyInDB)); + + throw new CatalogException("Please check past migrations before moving to v3.0.0. Found " + + (availableMigrations.size() -1 - count) + " missing migrations available."); + } + + count = migrationCol.countDocuments(Filters.in("status", MigrationRun.MigrationStatus.PENDING, MigrationRun.MigrationStatus.ON_HOLD, MigrationRun.MigrationStatus.ERROR)); if (count > 0) { - throw new CatalogException("Please check past migrations. Found migrations with status '" + MigrationRun.MigrationStatus.PENDING - + "', '" + MigrationRun.MigrationStatus.ON_HOLD + "', or '" + MigrationRun.MigrationStatus.ERROR + "'."); + throw new CatalogException("Please check past migrations. Found " + count + " migrations with status '" + + MigrationRun.MigrationStatus.PENDING + "', '" + MigrationRun.MigrationStatus.ON_HOLD + "', or '" + + MigrationRun.MigrationStatus.ERROR + "'."); } // Retrieve all users with data @@ -226,25 +272,23 @@ protected void run() throws Exception { queryMongo(oldUserCollection, Filters.eq("id", ParamConstants.OPENCGA_USER_ID), Projections.exclude("_id"), document -> { String organizationId = ParamConstants.ADMIN_ORGANIZATION; try { - MongoCollection userCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION); - MongoCollection projectCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.PROJECT_COLLECTION); - MongoCollection studyCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION); - MongoCollection fileCollection = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb() - .getCollection(OrganizationMongoDBAdaptorFactory.FILE_COLLECTION); + MongoDatabase orgDatabase = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb(); + + MongoCollection userCollection = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.USER_COLLECTION); + MongoCollection projectCollection = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.PROJECT_COLLECTION); + MongoCollection studyCollection = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.STUDY_COLLECTION); + MongoCollection fileCollection = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.FILE_COLLECTION); + MongoCollection migrationCollection = orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.MIGRATION_COLLECTION); // Empty data from collections with default data userCollection.deleteMany(new Document()); projectCollection.deleteMany(new Document()); studyCollection.deleteMany(new Document()); fileCollection.deleteMany(new Document()); + migrationCollection.deleteMany(new Document()); // Replace user in organization userCollection.insertOne(document); - MongoDatabase orgDatabase = mongoDBAdaptorFactory.getMongoDataStore(organizationId).getDb(); - // Extract projects List projects = document.getList("projects", Document.class); for (Document project : projects) { @@ -280,12 +324,16 @@ protected void run() throws Exception { replicateData(studyUid, oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.INTERPRETATION_COLLECTION), orgDatabase.getCollection(OrganizationMongoDBAdaptorFactory.INTERPRETATION_COLLECTION)); - oldStudyCol.deleteOne(Filters.eq("uid", studyUid)); }); - } + // Copy migration history + MongoCollection oldMigrationCollection = oldDatastore.getDb().getCollection(OrganizationMongoDBAdaptorFactory.MIGRATION_COLLECTION); + logger.info("Copying Migration data from {} to {}", oldMigrationCollection.getNamespace(), migrationCollection.getNamespace()); + migrateCollection(oldMigrationCollection, migrationCollection, new Document(), Projections.exclude("_id"), + (tmpDocument, bulk) -> bulk.add(new InsertOneModel<>(tmpDocument))); + // Remove user from the source database oldUserCollection.deleteOne(Filters.eq("id", ParamConstants.OPENCGA_USER_ID)); } catch (CatalogException e) { @@ -302,17 +350,12 @@ protected void run() throws Exception { // Rename database to main organization database MongoDataStore adminDatastore = mongoDBAdaptorFactory.getMongoManager().get("admin", mongoDBAdaptorFactory.getMongoDbConfiguration()); for (String collectionName : oldDatastore.getCollectionNames()) { - if (!OrganizationMongoDBAdaptorFactory.MIGRATION_COLLECTION.equals(collectionName)) { - logger.info("Renaming collection {} to {}", oldDatabase + "." + collectionName, newDatabase + "." + collectionName); - adminDatastore.getDb().runCommand(new Document() - .append("renameCollection", oldDatabase + "." + collectionName) - .append("to", newDatabase + "." + collectionName) - .append("dropTarget", true) - ); - } else { - // Remove collections - oldDatastore.getDb().getCollection(collectionName).drop(); - } + logger.info("Renaming collection {} to {}", oldDatabase + "." + collectionName, newDatabase + "." + collectionName); + adminDatastore.getDb().runCommand(new Document() + .append("renameCollection", oldDatabase + "." + collectionName) + .append("to", newDatabase + "." + collectionName) + .append("dropTarget", true) + ); } CatalogIOManager ioManager = new CatalogIOManager(configuration); @@ -395,6 +438,57 @@ protected void run() throws Exception { Updates.set("configuration.authenticationOrigins", authOrigins) )); } + + // Skip current migration for both organizations + catalogManager.getMigrationManager().skipPendingMigrations(ParamConstants.ADMIN_ORGANIZATION, opencgaToken); + catalogManager.getMigrationManager().skipPendingMigrations(organizationId, opencgaToken); + } + + Set> getAvailableMigrations() { + Reflections reflections = new Reflections(new ConfigurationBuilder() + .setScanners( + new SubTypesScanner(), + new TypeAnnotationsScanner().filterResultsBy(s -> StringUtils.equals(s, Migration.class.getName())) + ) + .addUrls(getUrls()) + .filterInputsBy(input -> input != null && input.endsWith(".class")) + ); + + Set> migrations = reflections.getSubTypesOf(MigrationTool.class); + migrations.removeIf(c -> Modifier.isAbstract(c.getModifiers())); + + // Validate unique ids and rank + Map> versionIdMap = new HashMap<>(); + + for (Class migration : migrations) { + Migration annotation = migration.getAnnotation(Migration.class); + + if (!versionIdMap.containsKey(annotation.version())) { + versionIdMap.put(annotation.version(), new HashSet<>()); + } + if (versionIdMap.get(annotation.version()).contains(annotation.id())) { + throw new IllegalStateException("Found duplicated migration id '" + annotation.id() + "' in version " + + annotation.version()); + } + if (String.valueOf(annotation.date()).length() != 8) { + throw new IllegalStateException("Found unexpected date '" + annotation.date() + "' in migration '" + annotation.id() + + "' from version " + annotation.version() + ". Date format is YYYYMMDD."); + } + versionIdMap.get(annotation.version()).add(annotation.id()); + } + + return migrations; + } + + private Collection getUrls() { + Collection urls = new LinkedList<>(); + for (URL url : ClasspathHelper.forPackage("org.opencb.opencga")) { + String name = url.getPath().substring(url.getPath().lastIndexOf('/') + 1); + if (name.isEmpty() || (name.contains("opencga") && !name.contains("opencga-hadoop-shaded"))) { + urls.add(url); + } + } + return urls; } private void replicateData(long studyUid, MongoCollection sourceCol, MongoCollection targetCol) { diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java index 7fb3b1dabf8..3c5ddea26d3 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/Migration.java @@ -54,6 +54,11 @@ */ boolean manual() default false; + /** + * @return the version when the migration was deprecated. + */ + String deprecatedSince() default ""; + enum MigrationDomain { CATALOG, STORAGE diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java index 7809f4fb0f7..543e378cba3 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java @@ -622,6 +622,11 @@ private MigrationRun run(String organizationId, Class r String token) throws MigrationException { Migration annotation = getMigrationAnnotation(runnableMigration); + if (StringUtils.isNotEmpty(annotation.deprecatedSince())) { + throw new MigrationException("Migration '" + annotation.id() + "' can't be run since version '" + annotation.deprecatedSince() + + "'. Please, run this migration from a previous OpenCGA version."); + } + MigrationTool migrationTool; try { migrationTool = runnableMigration.newInstance(); From ec4691c21839f30b13dc97d9d639e7a88f16eaf3 Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 20 May 2024 16:57:48 +0200 Subject: [PATCH 4/9] app: remove v from deprecatedSince version field, #TASK-6256 --- .../app/migrations/v2/v2_0_3/catalog/java/Migration1.java | 2 +- .../app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java | 2 +- .../v2_0_6/catalog/removeDeletedFileReferencesFromSample.java | 2 +- .../catalog/AddAnnotationSetsInClinicalAnalysisMigration.java | 2 +- .../catalog/CompleteClinicalReportDataModelMigration.java | 2 +- .../migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java | 2 +- .../v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java | 2 +- .../migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java | 2 +- .../app/migrations/v2/v2_1_0/catalog/java/PanelLock.java | 2 +- .../v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java | 2 +- .../catalog/java/RenameDatastoreConfigurationToOptions.java | 2 +- .../catalog/java/StudyClinicalConfigurationRelocation.java | 2 +- .../v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java | 2 +- .../app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java | 2 +- .../app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java | 2 +- .../app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java | 2 +- .../app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java | 2 +- .../v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java | 2 +- .../v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java | 2 +- .../v2/v2_1_0/storage/NewClinicalSignificanceFields.java | 2 +- .../migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java | 2 +- .../app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java | 2 +- .../app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java | 2 +- .../v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java | 2 +- .../v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java | 2 +- .../v2/v2_2_0/catalog/ChangeInterpretationMethods.java | 2 +- .../v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java | 2 +- .../migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java | 2 +- .../app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java | 2 +- .../v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java | 2 +- .../v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java | 2 +- .../migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java | 2 +- .../v2/v2_2_0/catalog/ImproveIndividualQualityControl.java | 2 +- .../app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java | 2 +- .../app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java | 2 +- .../v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java | 2 +- .../v2/v2_2_0/catalog/RenameFileQualityControlFields.java | 2 +- .../v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java | 2 +- .../v2/v2_2_0/catalog/RenameInterpretationFindingStats.java | 2 +- .../v2/v2_2_0/catalog/RenameSampleQualityControlFields.java | 2 +- ...addDefaultVariantCallerInterpretationStudyConfiguration.java | 2 +- .../AddModificationDateToClinicalInternal.java | 2 +- .../AddModificationDateToCohortInternal.java | 2 +- .../AddModificationDateToFamilyInternal.java | 2 +- .../AddModificationDateToFileInternal.java | 2 +- .../AddModificationDateToIndividualInternal.java | 2 +- .../AddModificationDateToInterpretationInternal.java | 2 +- .../AddModificationDateToJobInternal.java | 2 +- .../AddModificationDateToProjectInternal.java | 2 +- .../AddModificationDateToSampleInternal.java | 2 +- .../AddModificationDateToStudyInternal.java | 2 +- .../migrations/v2/v2_2_0/catalog/addInterpretationStats.java | 2 +- .../AddRegistrationDateToClinicalInternal.java | 2 +- .../AddRegistrationDateToCohortInternal.java | 2 +- .../AddRegistrationDateToFamilyInternal.java | 2 +- .../addRegistrationDate/AddRegistrationDateToFileInternal.java | 2 +- .../AddRegistrationDateToIndividualInternal.java | 2 +- .../AddRegistrationDateToInterpretationInternal.java | 2 +- .../addRegistrationDate/AddRegistrationDateToJobInternal.java | 2 +- .../AddRegistrationDateToProjectInternal.java | 2 +- .../AddRegistrationDateToSampleInternal.java | 2 +- .../addRegistrationDate/AddRegistrationDateToStudyInternal.java | 2 +- .../v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java | 2 +- .../v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java | 2 +- .../v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java | 2 +- .../catalog/issue_1849/CompleteClinicalStatusDataModel.java | 2 +- .../catalog/issue_1849/CompleteCohortStatusDataModel.java | 2 +- .../catalog/issue_1849/CompleteFamilyStatusDataModel.java | 2 +- .../v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java | 2 +- .../catalog/issue_1849/CompleteIndividualStatusDataModel.java | 2 +- .../issue_1849/CompleteInterpretationStatusDataModel.java | 2 +- .../v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java | 2 +- .../v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java | 2 +- .../catalog/issue_1849/CompleteProjectStatusDataModel.java | 2 +- .../catalog/issue_1849/CompleteSampleStatusDataModel.java | 2 +- .../v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java | 2 +- .../v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java | 2 +- .../issues_1853_1855/IndividualOntologyTermMigration.java | 2 +- .../catalog/issues_1853_1855/NewStudyDataModelFields.java | 2 +- .../issues_1853_1855/SampleProcessingAndCollectionChanges.java | 2 +- .../v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java | 2 +- .../migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java | 2 +- .../migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java | 2 +- .../app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java | 2 +- .../app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java | 2 +- .../migrations/v2/v2_2_1/catalog/InitSharedProjectField.java | 2 +- .../storage/SampleIndexConfigurationAddMissingStatus.java | 2 +- .../migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java | 2 +- .../app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java | 2 +- .../app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java | 2 +- .../v2/v2_3_0/catalog/InitSampleIndexConfiguration.java | 2 +- .../catalog/MoveCellbaseFromProjectInternalToProject.java | 2 +- .../migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java | 2 +- .../v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java | 2 +- .../app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java | 2 +- .../v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java | 2 +- .../catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java | 2 +- .../migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java | 2 +- .../app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java | 2 +- .../app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java | 2 +- .../v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java | 2 +- .../v2/v2_4_11/SynchronizeCatalogStorageStatuses.java | 2 +- .../v2/v2_4_11/catalog/SignatureFittingsMigration.java | 2 +- .../app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java | 2 +- .../v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java | 2 +- .../app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java | 2 +- .../v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java | 2 +- .../v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java | 2 +- .../v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java | 2 +- .../v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java | 2 +- .../migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java | 2 +- .../v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java | 2 +- .../v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java | 2 +- .../v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java | 2 +- .../v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java | 2 +- 115 files changed, 115 insertions(+), 115 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java index ded1293c0d9..425fd72353f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_3/catalog/java/Migration1.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "recalculate_roles", description = "Recalculate roles from Family #1763", version = "2.0.3", date = 20210528, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class Migration1 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java index a5b971d44fa..0c0273e7820 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_5/catalog/java/initialiseGroups.java @@ -6,7 +6,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "initialise_groups", description = "Initialise userIds list from groups #1791", version = "2.0.5", date = 20210621, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class initialiseGroups extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java index b2ffea9be48..b99e0a9f1d5 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_0_6/catalog/removeDeletedFileReferencesFromSample.java @@ -6,7 +6,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "remove_file_references_from_sample", description = "Remove deleted file references from samples #1815", version = "2.0.6", - date = 20210901, deprecatedSince = "v3.0.0") + date = 20210901, deprecatedSince = "3.0.0") public class removeDeletedFileReferencesFromSample extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java index 79d15bbfe2d..06a78900ab0 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/AddAnnotationSetsInClinicalAnalysisMigration.java @@ -10,7 +10,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20231116, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class AddAnnotationSetsInClinicalAnalysisMigration extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java index 10effae5a66..96f702d96f4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_12_0/catalog/CompleteClinicalReportDataModelMigration.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20231128, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class CompleteClinicalReportDataModelMigration extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java index ecd911181d0..7efdea6a56a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddMissingIndexes.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210928, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddMissingIndexes extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java index 984e214aed5..a35f794d130 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/AddPanelsToInterpretations.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20210713, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddPanelsToInterpretations extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java index da1220d2595..48cd8ce2f3b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/CreateAuditIndexes.java @@ -8,7 +8,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210622, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class CreateAuditIndexes extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java index 763e3568ae3..747feb3bbcb 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/PanelLock.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210713, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class PanelLock extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java index 2f6c73e610a..58625266d9b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RemoveRCVersionsFromMigrationRuns.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210723, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RemoveRCVersionsFromMigrationRuns extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java index 09f6facd0ae..452e99d627f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/RenameDatastoreConfigurationToOptions.java @@ -8,7 +8,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210617, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RenameDatastoreConfigurationToOptions extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java index 3a0c9fe1224..18e6272d7a6 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/StudyClinicalConfigurationRelocation.java @@ -10,7 +10,7 @@ domain = Migration.MigrationDomain.CATALOG, patch = 1, date = 20210708, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class StudyClinicalConfigurationRelocation extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java index 5a61db123b9..f37d46cb9f2 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/java/VariantFileStatsRelocation.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.STORAGE, patch = 1, date = 20210614, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class VariantFileStatsRelocation extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java index c531bfcbb4f..0530e369b04 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration1.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "build_rga_indexes", description = "Create index for sample RGA status #1693", version = "2.1.0", - language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "3.0.0") public class Migration1 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java index f6fff9fbd50..a0c0938de73 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration2.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "init_userId_group_arrays", description = "Initialise all userIds arrays from groups #1735", version = "2.1.0", - language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "3.0.0") public class Migration2 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java index d449cc8fe86..9b21dcdbc9c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration3.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "init_ca_panel_arrays", description = "Initialise panels array in Clinical Analysis #1759", version = "2.1.0", - language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210528, deprecatedSince = "3.0.0") public class Migration3 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java index 0093d746f08..ef72a501f44 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/catalog/javascript/Migration4.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "update_qc_file_sample_fields", description = "Update QC fields from Sample and File #1730", version = "2.1.0", - language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210531, patch = 4, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVASCRIPT, date = 20210531, patch = 4, deprecatedSince = "3.0.0") public class Migration4 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java index a85a315e52a..5dac53d4688 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/AddCellbaseConfigurationToProject.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.STORAGE, patch = 3, date = 20210616, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddCellbaseConfigurationToProject extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java index 3ef78abd74f..7b33bd7d709 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/DefaultSampleIndexConfiguration.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.STORAGE, patch = 7, date = 20210721, - deprecatedSince = "v3.0.0") // Needs to run after StudyClinicalConfigurationRelocation + deprecatedSince = "3.0.0") // Needs to run after StudyClinicalConfigurationRelocation public class DefaultSampleIndexConfiguration extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java index fd70c48eb00..b4d243ee279 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_1_0/storage/NewClinicalSignificanceFields.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.STORAGE, patch = 1, date = 20210708, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class NewClinicalSignificanceFields extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java index 33a03883d93..7008388f42e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddMissingClinicalAudit.java @@ -7,7 +7,7 @@ description = "Add missing CREATE_INTERPRETATION audits in ClinicalAnalysis", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211227, deprecatedSince = "v3.0.0") + date = 20211227, deprecatedSince = "3.0.0") public class AddMissingClinicalAudit extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java index 2860f82cd1b..1f23c1b331c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNameFieldInCohort.java @@ -7,7 +7,7 @@ description = "Add new name field to Cohort #1902", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220228, deprecatedSince = "v3.0.0") + date = 20220228, deprecatedSince = "3.0.0") public class AddNameFieldInCohort extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java index 32324263f93..1aa51b53014 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewAllowedBiotype.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 2, - date = 20211209, deprecatedSince = "v3.0.0") + date = 20211209, deprecatedSince = "3.0.0") public class AddNewAllowedBiotype extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java index 5e944869f84..099dd960790 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddNewFileInternalIndex_1850.java @@ -7,7 +7,7 @@ description = "Add new FileInternalVariant and FileInternalAlignment index #1850", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211127, deprecatedSince = "v3.0.0") + date = 20211127, deprecatedSince = "3.0.0") public class AddNewFileInternalIndex_1850 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java index 0bf80272613..21218e3222d 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/AddSampleInternalVariant_1851.java @@ -7,7 +7,7 @@ description = "Add new SampleInternalVariant #1851", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211129, deprecatedSince = "v3.0.0") + date = 20211129, deprecatedSince = "3.0.0") public class AddSampleInternalVariant_1851 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java index f7acbb2afe1..7731a4510fe 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ChangeInterpretationMethods.java @@ -7,7 +7,7 @@ description = "Remove list of methods from Interpretations #1841", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211112, deprecatedSince = "v3.0.0") + date = 20211112, deprecatedSince = "3.0.0") public class ChangeInterpretationMethods extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java index ac2d8053f40..6de2592fbaa 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ClinicalVariantEvidenceMigration.java @@ -7,7 +7,7 @@ description = "Add new ClinicalVariantEvidenceReview object, #1874", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220112, deprecatedSince = "v3.0.0") + date = 20220112, deprecatedSince = "3.0.0") public class ClinicalVariantEvidenceMigration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java index 8dce7c69ff9..7ddea73508c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/DeleteUnusedVariableSets.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 2, - date = 20211210, deprecatedSince = "v3.0.0") + date = 20211210, deprecatedSince = "3.0.0") public class DeleteUnusedVariableSets extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java index b1884d5db2f..fd160750475 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixFamilyReferences.java @@ -7,7 +7,7 @@ description = "Fix Family references, #TASK-489", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220324, deprecatedSince = "v3.0.0") + date = 20220324, deprecatedSince = "3.0.0") public class FixFamilyReferences extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java index a4e46dde580..d642d8499af 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/FixNonExistingMoIFromPanels.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 2, - date = 20220111, deprecatedSince = "v3.0.0") + date = 20220111, deprecatedSince = "3.0.0") public class FixNonExistingMoIFromPanels extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java index 29c9b704e4b..b7ff196615b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveClinicalAnalysisQualityControl.java @@ -7,7 +7,7 @@ description = "Quality control normalize comments and fields #1826", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211001, deprecatedSince = "v3.0.0") + date = 20211001, deprecatedSince = "3.0.0") public class ImproveClinicalAnalysisQualityControl extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java index e334fc6e892..16043d38b26 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveFileQualityControl.java @@ -7,7 +7,7 @@ description = "Quality control normalize comments and fields #1826", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211001, deprecatedSince = "v3.0.0") + date = 20211001, deprecatedSince = "3.0.0") public class ImproveFileQualityControl extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java index aa365610323..b3350e099f3 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/ImproveIndividualQualityControl.java @@ -7,7 +7,7 @@ description = "Quality control normalize comments and fields #1826", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211001, deprecatedSince = "v3.0.0") + date = 20211001, deprecatedSince = "3.0.0") public class ImproveIndividualQualityControl extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java index b39fca366f7..af85465d69e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveFileDocsFromCA.java @@ -7,7 +7,7 @@ description = "Store references of File in Clinical Analysis and not full File documents #1837", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211102, deprecatedSince = "v3.0.0") + date = 20211102, deprecatedSince = "3.0.0") public class RemoveFileDocsFromCA extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java index 18d3359497e..7b00543f9a5 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RemoveParallelIndexes.java @@ -7,7 +7,7 @@ description = "Remove parallel array indexes #CU-20jc4tx", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220310, deprecatedSince = "v3.0.0") + date = 20220310, deprecatedSince = "3.0.0") public class RemoveParallelIndexes extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java index e51a0b7a664..821fb020a28 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFamilyQualityControlFields.java @@ -7,7 +7,7 @@ description = "Rename FamilyQualityControl fields #1844", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211119, deprecatedSince = "v3.0.0") + date = 20211119, deprecatedSince = "3.0.0") public class RenameFamilyQualityControlFields extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java index 268d98b7ca2..c3c5d4ff7f8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameFileQualityControlFields.java @@ -7,7 +7,7 @@ description = "Rename FileQualityControl fields #1844", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211119, deprecatedSince = "v3.0.0") + date = 20211119, deprecatedSince = "3.0.0") public class RenameFileQualityControlFields extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java index 59d341e14fb..6df5fc82131 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameIndividualQualityControlFields.java @@ -7,7 +7,7 @@ description = "Rename IndividualQualityControl fields #1844", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211119, deprecatedSince = "v3.0.0") + date = 20211119, deprecatedSince = "3.0.0") public class RenameIndividualQualityControlFields extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java index c54d782361b..bd4ad966774 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameInterpretationFindingStats.java @@ -7,7 +7,7 @@ description = "Rename interpretation stats field #1819", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211115, deprecatedSince = "v3.0.0") + date = 20211115, deprecatedSince = "3.0.0") public class RenameInterpretationFindingStats extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java index 48304e52905..0c5b36cdf93 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/RenameSampleQualityControlFields.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 2, - date = 20211119, deprecatedSince = "v3.0.0") + date = 20211119, deprecatedSince = "3.0.0") public class RenameSampleQualityControlFields extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java index b461bda8aa2..9a43d99ac53 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addDefaultVariantCallerInterpretationStudyConfiguration.java @@ -7,7 +7,7 @@ description = "Add default variant caller Interpretation Study configuration #1822", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210916, deprecatedSince = "v3.0.0") + date = 20210916, deprecatedSince = "3.0.0") public class addDefaultVariantCallerInterpretationStudyConfiguration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java index e206f4ea633..c127e7b2695 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToClinicalInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_clinical.internal", description = "Add internal modificationDate to Clinical #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToClinicalInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java index 051db7caee2..0aaccf98b74 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToCohortInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_cohort.internal", description = "Add internal modificationDate to Cohort #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToCohortInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java index dde58535dac..914b6351a0c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFamilyInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_family.internal", description = "Add internal modificationDate to Family #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToFamilyInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java index 169e97a6450..7ffc3cf7f37 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToFileInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_file.internal", description = "Add internal modificationDate to File #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToFileInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java index b4dac080bc4..05ca7bc522d 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToIndividualInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_individual.internal", description = "Add internal modificationDate to Individual #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToIndividualInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java index c86eef70177..9340231dfde 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToInterpretationInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_interpretation.internal", description = "Add internal modificationDate to Interpretation #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToInterpretationInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java index 3afebad7f42..543e02f328e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToJobInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_job.internal", description = "Add internal modificationDate to Job #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToJobInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java index 06c7aa94aa4..82a3142a222 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToProjectInternal.java @@ -5,7 +5,7 @@ @Migration(id = "add_modificationDate_to_project.internal", description = "Add internal modificationDate to Project #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToProjectInternal extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java index 2d343956073..875bbaa26a7 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToSampleInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_sample.internal", description = "Add internal modificationDate to Sample #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToSampleInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java index 0f217355e4b..987a742cb5d 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInternalLastModified/AddModificationDateToStudyInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_modificationDate_to_study.internal", description = "Add internal modificationDate to Study #1810", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210812, deprecatedSince = "v3.0.0") + date = 20210812, deprecatedSince = "3.0.0") public class AddModificationDateToStudyInternal extends AddInternalLastModified { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java index 3eee2d60222..ac1c112d0a1 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addInterpretationStats.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 2, - date = 20210908, deprecatedSince = "v3.0.0") + date = 20210908, deprecatedSince = "3.0.0") public class addInterpretationStats extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java index 4881ae2a3f7..14a48ed90be 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToClinicalInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_clinical.internal", description = "Add registrationDate to Clinical #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToClinicalInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java index 900d7fa7392..a7dcf145b33 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToCohortInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_cohort.internal", description = "Add registrationDate to Cohort #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToCohortInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java index eca622902ff..66f375ce955 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFamilyInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_family.internal", description = "Add registrationDate to Family #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToFamilyInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java index d8c408a9412..cfa29de842a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToFileInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_file.internal", description = "Add registrationDate to File #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToFileInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java index 9a52e5c510f..58d233f6d7f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToIndividualInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_individual.internal", description = "Add registrationDate to Individual #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToIndividualInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java index 403e5ab6ca7..115b4e4fc6c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToInterpretationInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_interpretation.internal", description = "Add registrationDate to Interpretation #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToInterpretationInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java index fffe8e9d092..c56124cdda6 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToJobInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_job.internal", description = "Add registrationDate to Job #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToJobInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java index 2648228bbdb..ae3f65b70d9 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToProjectInternal.java @@ -5,7 +5,7 @@ @Migration(id = "add_registrationDate_to_project.internal", description = "Add registrationDate to Project #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToProjectInternal extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java index 094728d97c2..e317c667a98 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToSampleInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_sample.internal", description = "Add registrationDate to Sample #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToSampleInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java index 90201d3d80d..7d036f65bc4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRegistrationDate/AddRegistrationDateToStudyInternal.java @@ -4,7 +4,7 @@ @Migration(id = "add_registrationDate_to_study.internal", description = "Add registrationDate to Study #1804", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210720, deprecatedSince = "v3.0.0") + date = 20210720, deprecatedSince = "3.0.0") public class AddRegistrationDateToStudyInternal extends AddRegistrationDate { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java index 69939498085..d995f4ba97f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/addRgaIndexToStudyInternal.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, patch = 1, - date = 20210719, deprecatedSince = "v3.0.0") + date = 20210719, deprecatedSince = "3.0.0") public class addRgaIndexToStudyInternal extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java index 343d8f4a578..25e93347812 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1795/AddFamilyIdsInIndividual.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "add_familyIds_in_individual", description = "Add new list of familyIds in Individual #1795", version = "2.2.0", - language = Migration.MigrationLanguage.JAVA, date = 20210630, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVA, date = 20210630, deprecatedSince = "3.0.0") public class AddFamilyIdsInIndividual extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java index 60a08ba5c24..b6d1d3ff298 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1796/AddCohortIdsInSample.java @@ -5,7 +5,7 @@ import org.opencb.opencga.catalog.migration.MigrationTool; @Migration(id = "add_cohortIds_in_sample", description = "Add new list of cohortIds in Sample #1796", version = "2.2.0", - language = Migration.MigrationLanguage.JAVA, date = 20210706, deprecatedSince = "v3.0.0") + language = Migration.MigrationLanguage.JAVA, date = 20210706, deprecatedSince = "3.0.0") public class AddCohortIdsInSample extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java index 868bf9289d9..fcb2313cb39 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteClinicalStatusDataModel.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20211126, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class CompleteClinicalStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java index e5e76661b9c..692e58cc397 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteCohortStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Cohort Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteCohortStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java index 7c91e83876e..5c1bfbfc2aa 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFamilyStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Family Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteFamilyStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java index e1855bdaf34..c1c84058b5c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteFileStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete File Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteFileStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java index 4111517a8db..cb7fda578ca 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteIndividualStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Individual Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteIndividualStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java index 4d4406e0ffe..dad8a984810 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteInterpretationStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Interpretation Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteInterpretationStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java index 37ca338a57b..4a08d4695e7 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteJobStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Job Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteJobStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java index 6827d44467a..8311dcc2153 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompletePanelStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Panel Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompletePanelStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java index a703e408fe3..09ce8a4fc88 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteProjectStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Project Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteProjectStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java index c42d6ac6a16..bb9b3e54086 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteSampleStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Sample Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteSampleStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java index 401e823dc38..8b119d92cc4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteStudyStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete Study Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteStudyStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java index 7fd2e6bb798..937e6d3f9fb 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issue_1849/CompleteUserStatusDataModel.java @@ -7,7 +7,7 @@ description = "Complete User Status data models #1849", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211126, deprecatedSince = "v3.0.0") + date = 20211126, deprecatedSince = "3.0.0") public class CompleteUserStatusDataModel extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java index 14d9bf980be..9a5eb6cec84 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/IndividualOntologyTermMigration.java @@ -7,7 +7,7 @@ description = "Change sex and ethnicity types for OntologyTermAnnotation #1855", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211203, deprecatedSince = "v3.0.0") + date = 20211203, deprecatedSince = "3.0.0") public class IndividualOntologyTermMigration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java index 5d8beb45356..e6659fb4ad7 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/NewStudyDataModelFields.java @@ -7,7 +7,7 @@ description = "New Study 'sources', 'type' and 'additionalInfo' fields #1853", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211202, deprecatedSince = "v3.0.0") + date = 20211202, deprecatedSince = "3.0.0") public class NewStudyDataModelFields extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java index e5fdc1bd5d7..a054a6a0566 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/issues_1853_1855/SampleProcessingAndCollectionChanges.java @@ -7,7 +7,7 @@ description = "Sample source, treatments, processing and collection changes #1854", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20211201, patch = 2, deprecatedSince = "v3.0.0") + date = 20211201, patch = 2, deprecatedSince = "3.0.0") public class SampleProcessingAndCollectionChanges extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java index 8a7b5d55aa2..bd3f00937e9 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/catalog/renameVariableSetFieldFromVariable.java @@ -8,7 +8,7 @@ description = "Rename Variable variableSet field to variables #1823", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20210920, deprecatedSince = "v3.0.0") + date = 20210920, deprecatedSince = "3.0.0") public class renameVariableSetFieldFromVariable extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java index d7fdc3493fb..609d50c915a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/SynchronizeCatalogStorage.java @@ -7,7 +7,7 @@ description = "Synchronize catalog storage #1850 #1851", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.STORAGE, - date = 20220118, deprecatedSince = "v3.0.0") + date = 20220118, deprecatedSince = "3.0.0") public class SynchronizeCatalogStorage extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java index c5b1d88f3e7..2965c326760 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_0/storage/UpdateSampleIndexStatus.java @@ -7,7 +7,7 @@ description = " Improve sample-index multi-schema management. #1901", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.STORAGE, - date = 20220302, deprecatedSince = "v3.0.0") + date = 20220302, deprecatedSince = "3.0.0") public class UpdateSampleIndexStatus extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java index 79cda07260b..7173a402e96 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddMissingBiotypes.java @@ -7,7 +7,7 @@ description = "Add missing biotypes, #TASK-625", version = "2.2.1", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220412, deprecatedSince = "v3.0.0") + date = 20220412, deprecatedSince = "3.0.0") public class AddMissingBiotypes extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java index ef6f593863a..0cd9ba5ff1b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/AddPanelGeneNameIndex.java @@ -7,7 +7,7 @@ description = "Add Panel gene.name index #TASK-602", version = "2.2.1", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220406, deprecatedSince = "v3.0.0") + date = 20220406, deprecatedSince = "3.0.0") public class AddPanelGeneNameIndex extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java index a87e7a0344e..49b4b252f60 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/catalog/InitSharedProjectField.java @@ -7,7 +7,7 @@ description = "Initialise sharedProjects #TASK-702", version = "2.2.1", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, - date = 20220502, deprecatedSince = "v3.0.0") + date = 20220502, deprecatedSince = "3.0.0") public class InitSharedProjectField extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java index ceb9b7ec53c..cd11e50f8aa 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_2_1/storage/SampleIndexConfigurationAddMissingStatus.java @@ -7,7 +7,7 @@ description = "Sample index configuration add missing status #TASK-512", version = "2.2.0", language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.STORAGE, - date = 20220328, deprecatedSince = "v3.0.0") + date = 20220328, deprecatedSince = "3.0.0") public class SampleIndexConfigurationAddMissingStatus extends StorageMigrationTool { @Override protected void run() throws Exception { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java index 9d012bf9756..52a95ccf66e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddLockedToInterpretation.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220401, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddLockedToInterpretation extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java index acc9ad7f4b8..e2edbf68060 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AddPanelInternalField.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220509, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddPanelInternalField extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java index 1ab7ae34186..8cbd5a59eef 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/AutoIncrementVersion.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, offline = true, date = 20220512, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AutoIncrementVersion extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java index 58aaee84f5c..81d3f1e8628 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/InitSampleIndexConfiguration.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220502, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class InitSampleIndexConfiguration extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java index 17ef927ac00..9f4f30213fb 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/MoveCellbaseFromProjectInternalToProject.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220422, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class MoveCellbaseFromProjectInternalToProject extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java index 907f44a7542..2a1532c6da4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeletedCollections.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220502, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RenameDeletedCollections extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java index cd9daa6c5b6..b39a56cdbec 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/RenameDeprecatedVariantStorageToolId.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220506, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RenameDeprecatedVariantStorageToolId extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java index 5533165c027..be328bbeb6a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/catalog/UpdateJWTSecretKey.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220513, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class UpdateJWTSecretKey extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java index 23b999d338d..df2e308a727 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_0/storage/AddMissingColumnsToPhoenix.java @@ -4,7 +4,7 @@ import org.opencb.opencga.catalog.migration.Migration; @Migration(id="add_missing_columns_to_phoenix_TASK-789", description = "Add missing 1000G columns to phoenix #TASK-789", - version = "2.3.0", domain = Migration.MigrationDomain.STORAGE, date = 20220614, deprecatedSince = "v3.0.0" + version = "2.3.0", domain = Migration.MigrationDomain.STORAGE, date = 20220614, deprecatedSince = "3.0.0" ) public class AddMissingColumnsToPhoenix extends StorageMigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java index 58342c39b41..2c645980391 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_3_1/catalog/MoveCellbaseFromProjectInternalToProjectBugFix.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220620, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class MoveCellbaseFromProjectInternalToProjectBugFix extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java index 69a95f79bc6..8f3886c50e8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddClinicalStatusType_607.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220610, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddClinicalStatusType_607 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java index 157ad23070d..6dcab05694a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/AddPrivateDueDate_803.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220530, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddPrivateDueDate_803 extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java index 4b4839eba62..af93d04de7d 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_0/catalog/IndexPanelSource.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220530, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class IndexPanelSource extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java index 55b102ce06e..0759d4c7bf1 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_10/catalog/AddMissingEndDateOnFinishedJobs.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20221026, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class AddMissingEndDateOnFinishedJobs extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java index c4428b3204c..e2fb99933cf 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/SynchronizeCatalogStorageStatuses.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.STORAGE, date = 20221117, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class SynchronizeCatalogStorageStatuses extends StorageMigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java index 0300dd60eae..ec0b49baae3 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_11/catalog/SignatureFittingsMigration.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20221109, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class SignatureFittingsMigration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java index a20caa8ac9c..8e5825e3de7 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/AddClinicalDiscussion.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220727, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AddClinicalDiscussion extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java index 5fb3e88f9d5..aba0267d65b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_2/catalog/RecoverProbandSamplesInCases.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, date = 20220725, patch = 2, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RecoverProbandSamplesInCases extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java index c92a6789215..7951810b105 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/MigrateToClinicalAcmg.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220809, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class MigrateToClinicalAcmg extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java index 2dde0ff7165..2d4e2cb14a8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_3/catalog/ShortenIndexedFieldVariables.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220809, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class ShortenIndexedFieldVariables extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java index bd1f1a496e0..e26df11c03c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/AvoidCaseStatusIdNullMigration.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220914, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class AvoidCaseStatusIdNullMigration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java index 05d6967de74..07a19a12fdb 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/catalog/RemoveBiotypeAllowedKeysMigration.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.CATALOG, date = 20220905, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class RemoveBiotypeAllowedKeysMigration extends MigrationTool { @Override diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java index 4283c433ede..069e1a86e6e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_4_4/storage/InvalidateVariantArchivesMigration.java @@ -8,7 +8,7 @@ language = Migration.MigrationLanguage.JAVA, domain = Migration.MigrationDomain.STORAGE, date = 20220825, - deprecatedSince = "v3.0.0") + deprecatedSince = "3.0.0") public class InvalidateVariantArchivesMigration extends StorageMigrationTool { @Override protected void run() throws Exception { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java index 4dc66aabcea..06f1d871a80 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_6_0/storage/AddCellbaseDataRelease.java @@ -10,7 +10,7 @@ language = Migration.MigrationLanguage.JAVA, patch = 2, date = 20230104, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class AddCellbaseDataRelease extends StorageMigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java index f7fcaa12a55..ce425e3434b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_7_0/catalog/CancerRoleAndModeOfInheritanceMigration.java @@ -10,7 +10,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20230117, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class CancerRoleAndModeOfInheritanceMigration extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java index d3f44141067..0be802202c4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_0/catalog/CalculatePedigreeGraphMigration.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20230313, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class CalculatePedigreeGraphMigration extends MigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java index fdb1a44da12..e3b093906c4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_8_6/storage/MarkUnknownLargestVariantLength.java @@ -10,7 +10,7 @@ language = Migration.MigrationLanguage.JAVA, patch = 1, date = 20230927, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class MarkUnknownLargestVariantLength extends StorageMigrationTool { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java index 79dd1aab762..7dbd590c27e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java @@ -9,7 +9,7 @@ domain = Migration.MigrationDomain.CATALOG, language = Migration.MigrationLanguage.JAVA, date = 20230829, - deprecatedSince = "v3.0.0" + deprecatedSince = "3.0.0" ) public class RenameCellBaseToken2ApiKey extends MigrationTool { From 65015f3a5d69e62b4ec432e255c168420aaa16af Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 20 May 2024 17:07:41 +0200 Subject: [PATCH 5/9] catalog: add deprecatedSince migration check in MigrationTool,#TASK-6256 --- .../org/opencb/opencga/catalog/migration/MigrationTool.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java index 6d2a7215035..805f43eb41d 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java @@ -4,6 +4,7 @@ import com.mongodb.client.MongoCursor; import com.mongodb.client.model.IndexOptions; import com.mongodb.client.model.WriteModel; +import org.apache.commons.lang3.StringUtils; import org.bson.Document; import org.bson.conversions.Bson; import org.opencb.commons.ProgressLogger; @@ -78,6 +79,11 @@ public final void setup(Configuration configuration, CatalogManager catalogManag public final void execute() throws MigrationException { try { + Migration annotation = getAnnotation(); + if (StringUtils.isNotEmpty(annotation.deprecatedSince())) { + throw new MigrationException("Migration '" + annotation.id() + "' can't be run since version '" + + annotation.deprecatedSince() + "'. Please, run this migration from a previous OpenCGA version."); + } run(); } catch (MigrationException e) { throw e; From 37f023585a1c66c4b37fe70433d953a14cf8ac31 Mon Sep 17 00:00:00 2001 From: pfurio Date: Tue, 21 May 2024 12:42:29 +0200 Subject: [PATCH 6/9] catalog: add new static MigrationException message, #TASK-6256 --- .../opencga/catalog/migration/MigrationException.java | 6 ++++++ .../opencb/opencga/catalog/migration/MigrationManager.java | 3 +-- .../org/opencb/opencga/catalog/migration/MigrationTool.java | 3 +-- 3 files changed, 8 insertions(+), 4 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java index 63f666eac14..000c46d57dc 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationException.java @@ -20,4 +20,10 @@ public static MigrationException offlineMigrationException(Migration migration) return new MigrationException("Migration '" + migration.id() + "' requires database to be offline. Please, ensure the database " + "cannot be accessed and run try again with '--offline' flag."); } + + public static MigrationException deprecatedMigration(Migration migration) { + return new MigrationException("Migration '" + migration.id() + "' can't be run since version '" + + migration.deprecatedSince() + "'. Please, run this migration from a previous OpenCGA version."); + } + } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java index 543e378cba3..10b247a6d0d 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationManager.java @@ -623,8 +623,7 @@ private MigrationRun run(String organizationId, Class r Migration annotation = getMigrationAnnotation(runnableMigration); if (StringUtils.isNotEmpty(annotation.deprecatedSince())) { - throw new MigrationException("Migration '" + annotation.id() + "' can't be run since version '" + annotation.deprecatedSince() - + "'. Please, run this migration from a previous OpenCGA version."); + throw MigrationException.deprecatedMigration(annotation); } MigrationTool migrationTool; diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java index 805f43eb41d..f46e54277d2 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/migration/MigrationTool.java @@ -81,8 +81,7 @@ public final void execute() throws MigrationException { try { Migration annotation = getAnnotation(); if (StringUtils.isNotEmpty(annotation.deprecatedSince())) { - throw new MigrationException("Migration '" + annotation.id() + "' can't be run since version '" - + annotation.deprecatedSince() + "'. Please, run this migration from a previous OpenCGA version."); + throw MigrationException.deprecatedMigration(annotation); } run(); } catch (MigrationException e) { From f9291aef0b4d7607d8ba2cf09a4bc1237152535b Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 24 May 2024 13:09:33 +0200 Subject: [PATCH 7/9] pom:Fix number version #TASK-6256 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 2 +- 27 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 8e87f263f06..e0b30a8882d 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index bfbd58793b9..69ea6975e71 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 16647aebdec..b078878178e 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 832dde11be9..183d0de46d6 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index e18104a17bc..d309c1542dd 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index eb2c6d0f786..05ca25079e5 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 7e3925bb9fe..87f8dd26c76 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index be27dc552d0..3a54e9267c6 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 6eb6c110bd5..b920b27a6bf 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 80c167215df..4ffcee0a682 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 2e2ee67cc27..14d41561c1f 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 2d5dbebf91b..2723f7bdd83 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 9708846e4f8..557b499da4a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 797c371a6a7..943104d930b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index 2d1922b3655..bc7929a5e5b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 803fee44a25..3ead859cde8 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 0a7cea85134..3aa6c664266 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 452570b992b..0afb37a331e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 7c6cbacda94..29d98c3fb1e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 0cca28f1721..35bfaf2b683 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 7e8d9e80136..b39ecfa1c28 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 10d9d270831..c799f4e1278 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index ac1e8071fb5..b9dc4e7afe0 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 69f063a9a44..e6f50d31070 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 0347eca3180..45b0e418665 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index da8d02db513..c8a06679244 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 181affb30a7..0d8e82fe5e3 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1.SNAPSHOT + 3.0.0.1-SNAPSHOT pom OpenCGA From 39fed2253b2af85dae6cf961208b748244b9a231 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 29 May 2024 16:33:26 +0200 Subject: [PATCH 8/9] Prepare release 3.0.0.1 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 6 +++--- 27 files changed, 29 insertions(+), 29 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index e0b30a8882d..f360b51b820 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 69ea6975e71..a211147e294 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index b078878178e..4b0827a1058 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 183d0de46d6..b86efb944d4 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index d309c1542dd..ef56059fcb1 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 05ca25079e5..8942fdd2d11 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 87f8dd26c76..fb06b5d2b98 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 3a54e9267c6..846323d417d 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index b920b27a6bf..2715a9b06ac 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 4ffcee0a682..896868defdb 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 14d41561c1f..b62ec3d581f 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 2723f7bdd83..35d022c328d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 557b499da4a..48b48e0a406 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index 943104d930b..b2ad7976f66 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index bc7929a5e5b..e10b7910ee9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 3ead859cde8..87a073c4d53 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 3aa6c664266..8da62fe6c4d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 0afb37a331e..298103a6ce9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 29d98c3fb1e..1062a0712d9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 35bfaf2b683..392730030fa 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index b39ecfa1c28..608cab88861 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index c799f4e1278..1b0e3907b90 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index b9dc4e7afe0..440a1fec50a 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index e6f50d31070..98bfb2231ee 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 45b0e418665..0615d0daa9b 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index c8a06679244..d43e29d0f30 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 ../pom.xml diff --git a/pom.xml b/pom.xml index 0d8e82fe5e3..efdab0d6520 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1-SNAPSHOT + 3.0.0.1 pom OpenCGA @@ -43,8 +43,8 @@ - 3.0.0 - 3.0.0 + + 3.0.0.1 6.0.0 3.0.0 5.0.0 From 79eafc9be1feae4ed488092c3e864aeaae71c57a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 10 Jun 2024 12:08:54 +0200 Subject: [PATCH 9/9] Prepare port patch #TASK-6281 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-compat-api/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.0/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.2/pom.xml | 2 +- .../opencga-storage-hadoop-compat-hbase2.4/pom.xml | 2 +- .../opencga-storage-hadoop-compat/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-emr6.13/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdi5.1/pom.xml | 2 +- .../opencga-storage-hadoop-lib-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 2 +- 27 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index f360b51b820..185192a6227 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index a211147e294..1c77750c7f7 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 4b0827a1058..096c7abfae1 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index b86efb944d4..2582a5f2003 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index ef56059fcb1..16aff526b3e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 8942fdd2d11..73047a516e9 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index fb06b5d2b98..2348ef6f6f7 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 846323d417d..294acb88305 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 2715a9b06ac..1834d5c7e64 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 896868defdb..02953389c2d 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index b62ec3d581f..a7a2c8adbbb 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml index 35d022c328d..ea3dbc32689 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-api/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml index 48b48e0a406..927d616c88c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.0/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml index b2ad7976f66..a84279ad4de 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.2/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml index e10b7910ee9..ea5b63a7b6f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/opencga-storage-hadoop-compat-hbase2.4/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-compat - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml index 87a073c4d53..705f7b4104c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-compat/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8da62fe6c4d..19c1294d041 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml index 298103a6ce9..3675d760a35 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml index 1062a0712d9..ee08e659ae7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-emr6.13/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml index 392730030fa..ffd41bdf7ca 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdi5.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml index 608cab88861..435818c24cf 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/opencga-storage-hadoop-lib-hdp3.1/pom.xml @@ -7,7 +7,7 @@ org.opencb.opencga opencga-storage-hadoop-lib - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml index 1b0e3907b90..495de2ebf89 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-lib/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 440a1fec50a..7de2add12c5 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 98bfb2231ee..d6d92f43dda 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 0615d0daa9b..2cbf9a9aa24 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index d43e29d0f30..76a6360d5e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index efdab0d6520..a15be286fbd 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 3.0.0.1 + 3.2.0-SNAPSHOT pom OpenCGA