From f6bba81ebd36f22c0fa82865953f35c4d54b0500 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 22 May 2023 13:51:56 +0200 Subject: [PATCH 01/23] cicd: New check-junit-test workflow #TASK-4445 --- .github/workflows/check-junit-test.yml | 41 +++++++++++++++++++ .github/workflows/scripts/get_profiles.sh | 30 ++++++++++++++ .github/workflows/test-analysis.yml | 8 +++- .github/workflows/test-long-test-analysis.yml | 14 ------- 4 files changed, 77 insertions(+), 16 deletions(-) create mode 100644 .github/workflows/check-junit-test.yml create mode 100755 .github/workflows/scripts/get_profiles.sh delete mode 100644 .github/workflows/test-long-test-analysis.yml diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml new file mode 100644 index 00000000000..183fee32ea0 --- /dev/null +++ b/.github/workflows/check-junit-test.yml @@ -0,0 +1,41 @@ +name: LONG TEST ANALYSIS + +on: + workflow_dispatch: + inputs: + short_tests: + type: boolean + required: false + default: true + medium_tests: + type: boolean + required: false + default: false + long_tests: + type: boolean + required: false + default: false + mvn_opts: + type: string + required: false + default: "" + +jobs: + test: + name: Test JUnit + runs-on: ubuntu-22.04 + steps: + - name: Building string profiles to run + id: get_profiles + run: | + if [ -f "./.github/workflows/scripts/get_profiles.sh" ]; then + chmod +x ./.github/workflows/scripts/get_profiles.sh + echo "profiles=$(./.github/workflows/scripts/get_profiles.sh ${{ inputs.short_tests }} ${{ inputs.medium_tests }} ${{ inputs.long_tests }})" >> $GITHUB_OUTPUT + fi + - name: Building string profiles to run + uses: ./.github/workflows/test-analysis.yml + secrets: inherit + with: + test_profile: ${{ steps.get_profiles.outputs.profiles }} + report_context: development + mvn_opts: ${{ inputs.mvn_opts }} diff --git a/.github/workflows/scripts/get_profiles.sh b/.github/workflows/scripts/get_profiles.sh new file mode 100755 index 00000000000..fc205968984 --- /dev/null +++ b/.github/workflows/scripts/get_profiles.sh @@ -0,0 +1,30 @@ +#!/bin/bash + +if [ $# -eq 0 ]; then + echo "The arguments must be 3" + exit 1 +fi +PROFILE="" + +if [ $1 == "true" ]; then + PROFILE="${PROFILE}runShortTests," +fi +if [ $2 == "true" ]; then + PROFILE="${PROFILE}runMediumTests," +fi +if [ $3 == "true" ]; then + PROFILE="${PROFILE}runLongTests" +fi + +if [[ "${PROFILE}" == *"," ]]; then + PROFILE="${PROFILE%?}" +fi + +if [ -z "${PROFILE}" ]; then + echo "There must be at least one active profile" + exit 1 +fi + +echo "${PROFILE}" +exit 0 + diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 8c72b649a33..37f1215a802 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -8,6 +8,10 @@ on: report_context: type: string required: true + mvn_opts: + type: string + required: false + default: "" secrets: SONAR_TOKEN: required: true @@ -61,7 +65,7 @@ jobs: mongodb-version: 6.0 mongodb-replica-set: rs-test - name: Run Junit tests - run: mvn -B verify surefire-report:report -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' + run: mvn -B verify surefire-report:report -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' ${{ inputs.mvn_opts }} - name: Upload result dir uses: actions/upload-artifact@v3 with: @@ -73,7 +77,7 @@ jobs: needs: test strategy: matrix: - module: ["opencga-app", "opencga-catalog", "opencga-client", "opencga-clinical", "opencga-core", "opencga-master", "opencga-server", "opencga-storage", "opencga-storage/opencga-storage-app", "opencga-storage/opencga-storage-benchmark", "opencga-storage/opencga-storage-core", "opencga-storage/opencga-storage-hadoop", "opencga-storage/opencga-storage-server", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps"] + module: [ "opencga-app", "opencga-catalog", "opencga-client", "opencga-clinical", "opencga-core", "opencga-master", "opencga-server", "opencga-storage", "opencga-storage/opencga-storage-app", "opencga-storage/opencga-storage-benchmark", "opencga-storage/opencga-storage-core", "opencga-storage/opencga-storage-hadoop", "opencga-storage/opencga-storage-server", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps" ] steps: - name: Download result dir uses: actions/download-artifact@v3 diff --git a/.github/workflows/test-long-test-analysis.yml b/.github/workflows/test-long-test-analysis.yml deleted file mode 100644 index fe516b75a98..00000000000 --- a/.github/workflows/test-long-test-analysis.yml +++ /dev/null @@ -1,14 +0,0 @@ -name: LONG TEST ANALYSIS - -on: - push: - branches: - - TASK-4149 - -jobs: - test: - uses: ./.github/workflows/test-analysis.yml - secrets: inherit - with: - test_profile: runLongTests,runMediumTests,runShortTests - report_context: development From bc7f00e5f0692e947f42e1f9e8f08e124e62967c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 22 May 2023 13:53:38 +0200 Subject: [PATCH 02/23] cicd: Rename check-junit-test #TASK-4445 --- .github/workflows/check-junit-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml index 183fee32ea0..58f71978a27 100644 --- a/.github/workflows/check-junit-test.yml +++ b/.github/workflows/check-junit-test.yml @@ -1,4 +1,4 @@ -name: LONG TEST ANALYSIS +name: Check junits on: workflow_dispatch: From 571f76c479ae3e3a56aa79aa6584e40cb53d0f7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 24 May 2023 16:12:01 +0100 Subject: [PATCH 03/23] storage: Fix HadoopVariantStatisticsManagerTest::testJulieTool #TASK-4445 --- .../opencga/storage/core/metadata/models/ProjectMetadata.java | 4 ---- .../storage/core/variant/annotation/DummyTestAnnotator.java | 2 +- 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/metadata/models/ProjectMetadata.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/metadata/models/ProjectMetadata.java index c27111d1c03..e64deedff64 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/metadata/models/ProjectMetadata.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/metadata/models/ProjectMetadata.java @@ -85,10 +85,6 @@ public VariantAnnotationMetadata() { sourceVersion = new ArrayList<>(); } - public VariantAnnotationMetadata(int id, String name, Date creationDate, VariantAnnotatorProgram annotator, - List sourceVersion, DataRelease dataRelease) { - - } public VariantAnnotationMetadata(int id, String name, Date creationDate, VariantAnnotatorProgram annotator, List sourceVersion, DataRelease dataRelease, List privateSources) { this.id = id; diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java index 71f5135e08c..33e2860868d 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java @@ -59,7 +59,7 @@ public List annotate(List variants) throws VariantAn public ProjectMetadata.VariantAnnotationMetadata getVariantAnnotationMetadata() throws VariantAnnotatorException { return new ProjectMetadata.VariantAnnotationMetadata(-1, null, null, new ProjectMetadata.VariantAnnotatorProgram("MyAnnotator", key, null), - Collections.singletonList(new ObjectMap("data", "genes")), null); + Collections.singletonList(new ObjectMap("data", "genes")), null, null); } } From 37ba31205a843de2f3cd5a81e6d558a751d49056 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 25 May 2023 17:13:24 +0200 Subject: [PATCH 04/23] cicd:Synch with the latest version of workflow from develop --- .github/workflows/check-junit-test.yml | 33 +++++++++++++++++++------- 1 file changed, 24 insertions(+), 9 deletions(-) diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml index 58f71978a27..f953642c9eb 100644 --- a/.github/workflows/check-junit-test.yml +++ b/.github/workflows/check-junit-test.yml @@ -21,21 +21,36 @@ on: default: "" jobs: - test: + get_profiles: name: Test JUnit runs-on: ubuntu-22.04 + outputs: + profiles: ${{ steps.getter.outputs.profiles }} steps: + - uses: actions/checkout@v3 + with: + fetch-depth: '10' - name: Building string profiles to run - id: get_profiles + id: getter run: | if [ -f "./.github/workflows/scripts/get_profiles.sh" ]; then chmod +x ./.github/workflows/scripts/get_profiles.sh echo "profiles=$(./.github/workflows/scripts/get_profiles.sh ${{ inputs.short_tests }} ${{ inputs.medium_tests }} ${{ inputs.long_tests }})" >> $GITHUB_OUTPUT fi - - name: Building string profiles to run - uses: ./.github/workflows/test-analysis.yml - secrets: inherit - with: - test_profile: ${{ steps.get_profiles.outputs.profiles }} - report_context: development - mvn_opts: ${{ inputs.mvn_opts }} + + echo_log: + needs: get_profiles + runs-on: ubuntu-22.04 + steps: + - name: Echo profiles + id: log + run: echo "Executing testing profiles -> ${{ needs.get_profiles.outputs.profiles }}" + + test: + needs: [ get_profiles, echo_log ] + uses: ./.github/workflows/test-analysis.yml + with: + test_profile: ${{ needs.get_profiles.outputs.profiles }} + report_context: development + mvn_opts: ${{ inputs.mvn_opts }} + secrets: inherit \ No newline at end of file From e68bed2ac8e7532225123a865aae1df5edc79cd2 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 8 Jun 2023 11:38:09 +0200 Subject: [PATCH 05/23] Prepare next release 2.8.3-SNAPSHOT --- .github/workflows/test-analysis.yml | 2 +- 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-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/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 | 14 +++++++------- 22 files changed, 28 insertions(+), 28 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 8c72b649a33..af9ed6209a2 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -20,7 +20,7 @@ on: SSH_TESTING_SERVER_PASSWORD: required: true env: - xb_version: "1.6.2" + xb_version: "1.6.3" jobs: analysis: name: Execute Sonar Analysis diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 8bcef458f6e..a2fed95c1b8 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 315fc675ba6..be106d38391 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index e95e81f9f7f..d43aa67b53f 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 51e8e3271b6..fc888cf42ea 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 1c3d98c36a3..7d8f216a0ea 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 5facda4944f..eb0016308f8 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 38eef6ef604..1f19d740348 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 3a1708b0d9a..c4050fb6339 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 08fd95e1d5a..3a1821c0cbd 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 - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 34771805b75..9c61a4cab94 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 - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index f89776272e5..a746892a217 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.8.2 + 2.8.3-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 3d6337f89dc..0e8e429b549 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 - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index eb2acc7aa0e..b3b9bcc68cc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index 0d533640d0e..185a923475d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 3a5fd0680de..4a1ed4cb963 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 2573492c69c..8788d1547ac 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 5287da75128..5f3b2235c63 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 9296e54be14..cf3e6549427 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 - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 9734fe45943..0f73ef09ee2 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index b13fb52d290..ab0a67d1e7e 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.8.2 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 528699344be..1dc423846c4 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2 + 2.8.3-SNAPSHOT pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.8.3 - 2.8.3 - 5.4.0 - 2.8.0 - 4.8.0 - 2.8.2 + 2.8.3_dev + 2.8.3_dev + 5.4.1-SNAPSHOT + 2.8.1-SNAPSHOT + 4.8.1-SNAPSHOT + 2.8.3-SNAPSHOT 0.2.0 2.11.4 From b80c6b115adc7a06508b3aecc4563b2fa166714c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 8 Jun 2023 12:27:18 +0200 Subject: [PATCH 06/23] pom: testing another surefire report version 3.1.0 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 1dc423846c4..182af514996 100644 --- a/pom.xml +++ b/pom.xml @@ -84,7 +84,7 @@ false false - 2.22.2 + 3.1.0 From a8c51d843df33ebebb2dc56ad3f0de0519929116 Mon Sep 17 00:00:00 2001 From: pfurio Date: Wed, 12 Jul 2023 13:54:42 +0200 Subject: [PATCH 07/23] catalog: fix include in project search method, #TASK-4712 --- .../catalog/db/mongodb/MongoDBAdaptor.java | 35 +++++++++++++++++++ .../db/mongodb/ProjectMongoDBAdaptor.java | 7 ++-- .../ProjectCatalogMongoDBIterator.java | 30 ++++++++++++++-- .../catalog/managers/ProjectManagerTest.java | 26 ++++++++++++++ 4 files changed, 94 insertions(+), 4 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MongoDBAdaptor.java index 376c835b8a8..a3b47c037dc 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MongoDBAdaptor.java @@ -376,6 +376,41 @@ protected OpenCGAResult groupBy(MongoDBCollection collection, Bson query, List(aggregate); } + public static QueryOptions addPrefixInOptions(QueryOptions options, String prefix) { + if (options == null) { + return null; + } + + QueryOptions queryOptions = new QueryOptions(options); + + if (queryOptions.containsKey(QueryOptions.INCLUDE)) { + Set includeList = new HashSet<>(queryOptions.getAsStringList(QueryOptions.INCLUDE)); + List newInclude = new ArrayList<>(includeList.size()); + for (String key : includeList) { + if (key.startsWith(prefix)) { + newInclude.add(key); + } else { + newInclude.add(prefix + key); + } + } + queryOptions.put(QueryOptions.INCLUDE, newInclude); + } + if (queryOptions.containsKey(QueryOptions.EXCLUDE)) { + Set excludeList = new HashSet<>(queryOptions.getAsStringList(QueryOptions.EXCLUDE)); + List newExclude = new ArrayList<>(excludeList.size()); + for (String key : excludeList) { + if (key.startsWith(prefix)) { + newExclude.add(key); + } else { + newExclude.add(prefix + key); + } + } + queryOptions.put(QueryOptions.EXCLUDE, newExclude); + } + + return queryOptions; + } + /** * Filter QueryOptions object to ensure the keys provided are always included. * diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java index 297ff31f27e..97de4701558 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java @@ -771,8 +771,10 @@ private MongoDBIterator getMongoCursor(ClientSession clientSession, Qu aggregates.add(Aggregates.match(bsonQuery)); // Check include - QueryOptions qOptions = options != null ? new QueryOptions(options) : new QueryOptions(); - List includeList = new ArrayList<>(); + QueryOptions qOptions = addPrefixInOptions(options, "projects."); + qOptions = filterQueryOptions(qOptions, Arrays.asList(QueryParams.UID.key(), QueryParams.FQN.key())); + + /*List includeList = new ArrayList<>(); if (options != null && options.get(QueryOptions.INCLUDE) != null) { List optionsAsStringList = options.getAsStringList(QueryOptions.INCLUDE); includeList.addAll(optionsAsStringList.stream().collect(Collectors.toList())); @@ -792,6 +794,7 @@ private MongoDBIterator getMongoCursor(ClientSession clientSession, Qu } qOptions.put(QueryOptions.INCLUDE, includeList); } + */ for (Bson aggregate : aggregates) { logger.debug("Get project: Aggregate : {}", aggregate.toBsonDocument()); diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/ProjectCatalogMongoDBIterator.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/ProjectCatalogMongoDBIterator.java index 52aa62fb1e0..f08e0cea0e6 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/ProjectCatalogMongoDBIterator.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/ProjectCatalogMongoDBIterator.java @@ -25,6 +25,7 @@ public class ProjectCatalogMongoDBIterator extends CatalogMongoDBIterator private final String user; private final QueryOptions options; + private boolean includeStudyInfo; private final StudyMongoDBAdaptor studyDBAdaptor; private QueryOptions studyQueryOptions; @@ -44,6 +45,7 @@ public ProjectCatalogMongoDBIterator(MongoDBIterator mongoCursor, Clie this.studyDBAdaptor = dbAdaptorFactory.getCatalogStudyDBAdaptor(); this.options = options != null ? new QueryOptions(options) : new QueryOptions(); + this.includeStudyInfo = includeStudyInfo(); this.studyQueryOptions = createInnerQueryOptionsForVersionedEntity(this.options, ProjectDBAdaptor.QueryParams.STUDIES.key(), false); this.studyQueryOptions = MongoDBAdaptor.filterQueryOptions(this.studyQueryOptions, Collections.singletonList(MongoDBAdaptor.PRIVATE_PROJECT)); @@ -90,8 +92,7 @@ private void fetchNextBatch() { projectListBuffer.add(projectDocument); counter++; - if (options == null || !options.containsKey(QueryOptions.EXCLUDE) - || !options.getAsStringList(QueryOptions.EXCLUDE).contains("projects.studies")) { + if (includeStudyInfo) { projectUidSet.add(projectDocument.get(UID, Long.class)); } } @@ -130,4 +131,29 @@ private void fetchNextBatch() { } } } + + private boolean includeStudyInfo() { + if (options == null) { + return true; + } + if (options.containsKey(QueryOptions.EXCLUDE)) { + List list = options.getAsStringList(QueryOptions.EXCLUDE); + for (String exclude : list) { + if (exclude.equals("studies") || exclude.equals("projects.studies")) { + return false; + } + } + return true; + } else if (options.containsKey(QueryOptions.INCLUDE)) { + List list = options.getAsStringList(QueryOptions.INCLUDE); + for (String exclude : list) { + if (exclude.equals("studies") || exclude.equals("projects.studies")) { + return true; + } + } + return false; + } else { + return true; + } + } } diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java index 2490163b781..56c29d0fbb9 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java @@ -17,6 +17,7 @@ package org.opencb.opencga.catalog.managers; import com.fasterxml.jackson.core.JsonProcessingException; +import org.apache.commons.collections4.CollectionUtils; import org.junit.Before; import org.junit.Rule; import org.junit.Test; @@ -161,6 +162,31 @@ public void searchProjects() throws CatalogException { } + @Test + public void searchProjectsUsingInclude() throws CatalogException { + OpenCGAResult projects = catalogManager.getProjectManager().search(new Query(), + new QueryOptions(QueryOptions.INCLUDE, ProjectDBAdaptor.QueryParams.ID.key()), sessionIdUser); + assertEquals(1, projects.getNumResults()); + for (Project project : projects.getResults()) { + assertNotNull(project.getId()); + assertNull(project.getDescription()); + assertNull(project.getName()); + assertNull(project.getStudies()); + assertTrue(CollectionUtils.isEmpty(project.getStudies())); + } + + projects = catalogManager.getProjectManager().search(new Query(), + new QueryOptions(QueryOptions.EXCLUDE, ProjectDBAdaptor.QueryParams.NAME.key()), sessionIdUser); + assertEquals(1, projects.getNumResults()); + for (Project project : projects.getResults()) { + assertNotNull(project.getId()); + assertNull(project.getName()); + assertNotNull(project.getDescription()); + assertNotNull(project.getStudies()); + assertFalse(CollectionUtils.isEmpty(project.getStudies())); + } + } + @Test public void getSharedProjects() throws CatalogException { try { From 88757b2ef11de00e8e1c188ba22eac9a1c9625d1 Mon Sep 17 00:00:00 2001 From: pfurio Date: Thu, 20 Jul 2023 10:23:00 +0200 Subject: [PATCH 08/23] catalog: add new test including just the studies, #TASK-4712 --- .../catalog/db/mongodb/ProjectMongoDBAdaptor.java | 4 ++-- .../opencga/catalog/managers/ProjectManagerTest.java | 11 +++++++++++ 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java index 97de4701558..1474f1ed4e1 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/ProjectMongoDBAdaptor.java @@ -771,8 +771,8 @@ private MongoDBIterator getMongoCursor(ClientSession clientSession, Qu aggregates.add(Aggregates.match(bsonQuery)); // Check include - QueryOptions qOptions = addPrefixInOptions(options, "projects."); - qOptions = filterQueryOptions(qOptions, Arrays.asList(QueryParams.UID.key(), QueryParams.FQN.key())); + QueryOptions qOptions = filterQueryOptions(options, Arrays.asList(QueryParams.UID.key(), QueryParams.FQN.key())); + qOptions = addPrefixInOptions(qOptions, "projects."); /*List includeList = new ArrayList<>(); if (options != null && options.get(QueryOptions.INCLUDE) != null) { diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java index 56c29d0fbb9..611a3a6204b 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/managers/ProjectManagerTest.java @@ -175,6 +175,17 @@ public void searchProjectsUsingInclude() throws CatalogException { assertTrue(CollectionUtils.isEmpty(project.getStudies())); } + projects = catalogManager.getProjectManager().search(new Query(), + new QueryOptions(QueryOptions.INCLUDE, ProjectDBAdaptor.QueryParams.STUDIES.key()), sessionIdUser); + assertEquals(1, projects.getNumResults()); + for (Project project : projects.getResults()) { + assertNull(project.getId()); + assertNull(project.getDescription()); + assertNull(project.getName()); + assertNotNull(project.getStudies()); + assertTrue(CollectionUtils.isNotEmpty(project.getStudies())); + } + projects = catalogManager.getProjectManager().search(new Query(), new QueryOptions(QueryOptions.EXCLUDE, ProjectDBAdaptor.QueryParams.NAME.key()), sessionIdUser); assertEquals(1, projects.getNumResults()); From 041b3bdf201060d423f5965486000c3c16c1784d Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 20 Jul 2023 11:51:56 +0200 Subject: [PATCH 09/23] Create branch Port Patch 1.6.3.1 -> 1.6.4 --- 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/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-deps/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 +- 21 files changed, 21 insertions(+), 21 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index ec07e770980..a2fed95c1b8 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 487f8a79b70..be106d38391 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index a477a10338c..d43aa67b53f 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 2253ab703c1..fc888cf42ea 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 1f4081610ce..7d8f216a0ea 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 2d20981f882..eb0016308f8 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index f1328ae8014..1f19d740348 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f31a834b58c..c4050fb6339 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index c880ba80e4d..3a1821c0cbd 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 - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 1ffa40499d6..9c61a4cab94 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 - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index e3680f726a9..a746892a217 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.8.2.1 + 2.8.3-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 4952d05abfa..0e8e429b549 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 - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index ffa0a154cd5..b3b9bcc68cc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index 1e5cc5980ab..185a923475d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 44eb9fb37a9..4a1ed4cb963 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index b3d21b69d62..8788d1547ac 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 44c89fd9b22..5f3b2235c63 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 3a7acd6082b..cf3e6549427 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 - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 21edba58336..0f73ef09ee2 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 6210dc8d2b0..ab0a67d1e7e 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.8.3-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index a71ba63f9d8..6c40385d56a 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.8.3-SNAPSHOT pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis From 1c2db28529029f8ae9e19aa51bbc5ff60a4e346d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Fri, 21 Jul 2023 11:07:29 +0100 Subject: [PATCH 10/23] storage: Add FILTER to the SampleIndexOnlyVariantQueryExecutor #TASK-4794 --- .../storage/SampleIndexConfiguration.java | 9 ++ .../SampleIndexOnlyVariantQueryExecutor.java | 102 ++++++++++++++++-- ...endelianErrorSampleIndexEntryIterator.java | 9 +- .../index/sample/SampleIndexDBLoader.java | 3 +- .../sample/SampleIndexEntryIterator.java | 11 +- .../index/sample/SampleVariantIndexEntry.java | 29 +++-- 6 files changed, 136 insertions(+), 27 deletions(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java index f2e6bf1c3f8..0dcdf5b08fc 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java @@ -386,6 +386,15 @@ public List getCustomFields() { return customFields; } + public IndexFieldConfiguration getCustomField(IndexFieldConfiguration.Source source, String key) { + for (IndexFieldConfiguration s : customFields) { + if (s.getKey().equals(key) && s.getSource() == source) { + return s; + } + } + return null; + } + public int getFilePositionBits() { return filePositionBits; } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java index 4e33e778ca4..195f35a66d2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java @@ -2,6 +2,7 @@ import com.google.common.collect.Iterators; import htsjdk.variant.vcf.VCFConstants; +import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.concurrent.BasicThreadFactory; import org.apache.commons.lang3.time.StopWatch; import org.opencb.biodata.models.variant.StudyEntry; @@ -16,7 +17,9 @@ import org.opencb.commons.run.Task; import org.opencb.opencga.core.common.BatchUtils; import org.opencb.opencga.core.common.TimeUtils; +import org.opencb.opencga.core.config.storage.IndexFieldConfiguration; import org.opencb.opencga.core.response.VariantQueryResult; +import org.opencb.opencga.storage.core.io.bit.BitBuffer; import org.opencb.opencga.storage.core.metadata.VariantStorageMetadataManager; import org.opencb.opencga.storage.core.metadata.models.SampleMetadata; import org.opencb.opencga.storage.core.metadata.models.TaskMetadata; @@ -31,10 +34,12 @@ import org.opencb.opencga.storage.core.variant.query.projection.VariantQueryProjectionParser; import org.opencb.opencga.storage.hadoop.variant.adaptors.VariantHadoopDBAdaptor; import org.opencb.opencga.storage.hadoop.variant.converters.HBaseToVariantConverter; +import org.opencb.opencga.storage.hadoop.variant.index.core.IndexField; import org.opencb.opencga.storage.hadoop.variant.index.family.GenotypeCodec; import org.opencb.opencga.storage.hadoop.variant.index.query.SampleIndexQuery; import org.opencb.opencga.storage.hadoop.variant.index.sample.SampleIndexDBAdaptor; import org.opencb.opencga.storage.hadoop.variant.index.sample.SampleIndexQueryParser; +import org.opencb.opencga.storage.hadoop.variant.index.sample.SampleIndexSchema; import org.opencb.opencga.storage.hadoop.variant.index.sample.SampleVariantIndexEntry; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -42,6 +47,7 @@ import java.io.IOException; import java.util.*; import java.util.concurrent.*; +import java.util.function.BiConsumer; import java.util.stream.Collectors; import static org.opencb.opencga.storage.core.variant.query.VariantQueryUtils.NONE; @@ -283,10 +289,12 @@ private boolean isIncludeCovered(SampleIndexQuery sampleIndexQuery, Query inputQ private static class SampleVariantIndexEntryToVariantConverter implements Converter { + + enum FamilyRole { MOTHER, FATHER, - SAMPLE + SAMPLE; } private final boolean includeStudy; @@ -296,9 +304,20 @@ enum FamilyRole { private String motherName; private String fatherName; private LinkedHashMap samplesPosition; + private final List files; + private IndexField filterField; + private IndexField qualField; + private final SampleIndexSchema schema; + SampleVariantIndexEntryToVariantConverter(ParsedVariantQuery parseQuery, SampleIndexQuery sampleIndexQuery, VariantStorageMetadataManager metadataManager) { + schema = sampleIndexQuery.getSchema(); + filterField = schema.getFileIndex() + .getCustomField(IndexFieldConfiguration.Source.FILE, StudyEntry.FILTER); + qualField = schema.getFileIndex() + .getCustomField(IndexFieldConfiguration.Source.FILE, StudyEntry.QUAL); + VariantQueryProjection projection = parseQuery.getProjection(); includeStudy = !projection.getStudyIds().isEmpty(); if (includeStudy) { @@ -348,6 +367,13 @@ enum FamilyRole { this.fatherName = null; } + List fileIds = metadataManager.getFileIdsFromSampleId(studyId, sampleId, true); + files = new ArrayList<>(fileIds.size()); + for (Integer fileId : fileIds) { + files.add(metadataManager.getFileName(studyId, fileId)); + } + } else { + files = null; } } @@ -378,6 +404,22 @@ public Variant convert(SampleVariantIndexEntry entry) { throw new IllegalStateException("Unexpected value: " + role); } } + HashMap fileAttributes = new HashMap<>(); + // TODO: What if multi-files? + BitBuffer fileIndexBitBuffer = entry.getFileIndex(); + String filter = filterField.readAndDecode(fileIndexBitBuffer); + if (filter == null) { + filter = "NA"; + } + fileAttributes.put(StudyEntry.FILTER, filter); +// String qual = qualField.readAndDecode(fileIndexBitBuffer); +// if (qual == null) { +// qual = "NA"; +// } +// fileAttributes.put(StudyEntry.QUAL, qual); + String fileName = files.get(0); + studyEntry.setFiles(new ArrayList<>()); + studyEntry.getFiles().add(new FileEntry(fileName, null, fileAttributes)); studyEntry.setSortedSamplesPosition(samplesPosition); v.setStudies(Collections.singletonList(studyEntry)); } @@ -391,6 +433,7 @@ private class AddMissingDataTask implements Task { private final List samples; private final List files; private final List allFiles; + private final int gtIdx; AddMissingDataTask(ParsedVariantQuery parsedQuery, SampleIndexQuery sampleIndexQuery, VariantStorageMetadataManager metadataManager) { @@ -423,6 +466,8 @@ private class AddMissingDataTask implements Task { for (Integer fileId : fileIds) { files.add(metadataManager.getFileName(studyId, fileId)); } + List includeSampleData = VariantQueryUtils.getIncludeSampleData(parsedQuery.getInputQuery()); + gtIdx = includeSampleData.indexOf("GT"); } @Override @@ -478,6 +523,10 @@ public List apply(List variants) { return variants; } + /** + * Fetch the Secondary alternates, sample GTs and original call of these variants. + * @param toReadFull variants to complete + */ private void addSecondaryAlternates(List toReadFull) { // StopWatch stopWatch = StopWatch.createStarted(); Set includeFields = new HashSet<>(VariantField.getIncludeFields(parsedQuery.getInputOptions())); @@ -491,27 +540,41 @@ private void addSecondaryAlternates(List toReadFull) { options.put(VariantHadoopDBAdaptor.QUIET, true); options.put(VariantHadoopDBAdaptor.NATIVE, true); - Map fullVariants = dbAdaptor.get(new VariantQuery() + Map variantsExtra = dbAdaptor.get(new VariantQuery() .id(toReadFull) .study(studyName) .includeSample(samples) - .includeSampleData(VariantQueryUtils.getIncludeSampleData(parsedQuery.getInputQuery())) + .includeSampleData("GT") // read only GT .includeFile(allFiles), options) .getResults().stream().collect(Collectors.toMap(Variant::toString, v -> v)); for (Variant variant : toReadFull) { - Variant fullVariant = fullVariants.get(variant.toString()); - if (fullVariant == null) { + Variant variantExtra = variantsExtra.get(variant.toString()); + if (variantExtra == null) { // TODO: Should we fail here? // throw new VariantQueryException("Variant " + variant + " not found!"); logger.warn("Variant " + variant + " not found!"); continue; } - StudyEntry fullStudy = fullVariant.getStudies().get(0); - fullStudy.getFiles().forEach(f -> f.setData(Collections.emptyMap())); - fullStudy.setStats(Collections.emptyList()); - variant.setStudies(Collections.singletonList(fullStudy)); + StudyEntry studyExtra = variantExtra.getStudies().get(0); + StudyEntry study = variant.getStudies().get(0); + + mergeFileEntries(study, studyExtra.getFiles(), (fe, newFe) -> { + fe.setCall(newFe.getCall()); + }); + // merge sampleEntries + for (SampleEntry sampleExtra : studyExtra.getSamples()) { + SampleEntry sample = study.getSample(sampleExtra.getSampleId()); + sample.getData().set(gtIdx, sampleExtra.getData().get(0)); +// if (sampleExtra.getFileIndex() != null) { +// String fileIdFromFull = fullStudy.getFiles().get(sampleExtra.getFileIndex()).getFileId(); +// if (sample.getFileIndex() == null) { +// actualStudy.getFiles(). +// String fileIdFrmoFull = fullStudy.getFiles().get(sampleExtra.getFileIndex()).getFileId(); +// } +// } + } } // logger.info(" # Fetch {} SEC_ALTS in {}", toReadFull.size(), TimeUtils.durationToString(stopWatch)); } @@ -544,11 +607,30 @@ private void addOriginalCall(List variants, String study) { logger.warn("Variant " + variant + " not found!"); continue; } - variant.getStudies().get(0).setFiles(fileEntries); + StudyEntry studyEntry = variant.getStudies().get(0); + mergeFileEntries(studyEntry, fileEntries, (fe, newFe)->{ + fe.setCall(newFe.getCall()); + }); } // logger.info(" # Fetch {} INDEL original call in {}", filesMap.size(), TimeUtils.durationToString(stopWatch)); } + private void mergeFileEntries(StudyEntry studyEntry, List newFileEntries, + BiConsumer merge) { + if (CollectionUtils.isEmpty(studyEntry.getFiles())) { + studyEntry.setFiles(newFileEntries); + } else { + for (FileEntry newFileEntry : newFileEntries) { + FileEntry fileEntry = studyEntry.getFile(newFileEntry.getFileId()); + if (fileEntry == null) { + studyEntry.getFiles().add(newFileEntry); + } else { + merge.accept(fileEntry, newFileEntry); + } + } + } + } + } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/family/MendelianErrorSampleIndexEntryIterator.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/family/MendelianErrorSampleIndexEntryIterator.java index 233129ef337..f089c82f20e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/family/MendelianErrorSampleIndexEntryIterator.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/family/MendelianErrorSampleIndexEntryIterator.java @@ -125,9 +125,12 @@ public Variant next() { @Override public SampleVariantIndexEntry nextSampleVariantIndexEntry() { AnnotationIndexEntry annotationIndexEntry = nextAnnotationIndexEntry(); - BitBuffer fileIndex = null; + List filesIndex = new ArrayList<>(); if (hasFileIndex()) { - fileIndex = nextFileIndexEntry(); + filesIndex.add(nextFileIndexEntry()); + while (isMultiFileIndex()) { + filesIndex.add(nextMultiFileIndexEntry()); + } } String genotype = nextGenotype(); int meCode = nextMendelianErrorCode(); @@ -136,7 +139,7 @@ public SampleVariantIndexEntry nextSampleVariantIndexEntry() { parentsCode = nextParentsIndexEntry(); } Variant variant = next(); - return new SampleVariantIndexEntry(variant, fileIndex, genotype, annotationIndexEntry, parentsCode, meCode); + return new SampleVariantIndexEntry(variant, filesIndex, genotype, annotationIndexEntry, parentsCode, meCode); } @Override diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexDBLoader.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexDBLoader.java index 428e835025c..f2700831e94 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexDBLoader.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexDBLoader.java @@ -143,7 +143,8 @@ public void addVariant(int sampleIdx, String gt, SampleVariantIndexEntry variant throw new IllegalArgumentException("Already loaded variant " + variantIndexEntry.getVariant()); } } - if (schema.getFileIndex().isMultiFile(variantIndexEntry.getFileIndex())) { + if (variantIndexEntry.getFilesIndex().size() > 1 + || schema.getFileIndex().isMultiFile(variantIndexEntry.getFilesIndex().get(0))) { throw new IllegalArgumentException("Unexpected multi-file at variant " + variantIndexEntry.getVariant()); } sampleEntry.add(gt, variantIndexEntry); diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexEntryIterator.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexEntryIterator.java index 61627ddfd7b..da9c4a3a517 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexEntryIterator.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexEntryIterator.java @@ -4,7 +4,9 @@ import org.opencb.opencga.storage.core.io.bit.BitBuffer; import org.opencb.opencga.storage.hadoop.variant.index.annotation.AnnotationIndexEntry; +import java.util.ArrayList; import java.util.Iterator; +import java.util.List; /** * Iterate through the variants of a SampleIndexEntry. @@ -36,9 +38,12 @@ default SampleVariantIndexEntry nextSampleVariantIndexEntry() { // This object could be reused annotationIndexEntry = new AnnotationIndexEntry(annotationIndexEntry); } - BitBuffer fileIndex = null; + List filesIndex = new ArrayList<>(); if (hasFileIndex()) { - fileIndex = nextFileIndexEntry(); + filesIndex.add(nextFileIndexEntry()); + while (isMultiFileIndex()) { + filesIndex.add(nextMultiFileIndexEntry()); + } } Byte parentsCode = null; if (hasParentsIndex()) { @@ -46,7 +51,7 @@ default SampleVariantIndexEntry nextSampleVariantIndexEntry() { } String genotype = nextGenotype(); Variant variant = next(); - return new SampleVariantIndexEntry(variant, fileIndex, genotype, annotationIndexEntry, parentsCode); + return new SampleVariantIndexEntry(variant, filesIndex, genotype, annotationIndexEntry, parentsCode, null); } /** diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleVariantIndexEntry.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleVariantIndexEntry.java index 359591ed3d1..3d919ce846f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleVariantIndexEntry.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleVariantIndexEntry.java @@ -6,7 +6,9 @@ import org.opencb.opencga.storage.core.io.bit.BitBuffer; import org.opencb.opencga.storage.hadoop.variant.index.annotation.AnnotationIndexEntry; +import java.util.Collections; import java.util.Comparator; +import java.util.List; import java.util.Objects; import static org.opencb.opencga.storage.hadoop.variant.index.sample.SampleIndexSchema.INTRA_CHROMOSOME_VARIANT_COMPARATOR; @@ -15,21 +17,18 @@ public class SampleVariantIndexEntry { private final Variant variant; private final String genotype; + @Deprecated private final BitBuffer fileIndex; + private final List filesIndex; private final AnnotationIndexEntry annotationIndexEntry; private final Integer meCode; private final Byte parentsCode; public SampleVariantIndexEntry(Variant variant, BitBuffer fileIndex) { - this(variant, fileIndex, null, null, null); + this(variant, Collections.singletonList(fileIndex), null, null, null, null); } - public SampleVariantIndexEntry(Variant variant, BitBuffer fileIndex, String genotype, AnnotationIndexEntry annotationIndexEntry, - Byte parentsCode) { - this(variant, fileIndex, genotype, annotationIndexEntry, parentsCode, null); - } - - public SampleVariantIndexEntry(Variant variant, BitBuffer fileIndex, String genotype, AnnotationIndexEntry annotationIndexEntry, + public SampleVariantIndexEntry(Variant variant, List filesIndex, String genotype, AnnotationIndexEntry annotationIndexEntry, Byte parentsCode, Integer meCode) { if (CollectionUtils.isEmpty(variant.getImpl().getStudies())) { this.variant = variant; @@ -48,7 +47,12 @@ public SampleVariantIndexEntry(Variant variant, BitBuffer fileIndex, String geno variant.getType(), null, null)); } - this.fileIndex = fileIndex; + this.filesIndex = filesIndex; + if (filesIndex == null) { + this.fileIndex = null; + } else { + this.fileIndex = filesIndex.get(0); + } this.genotype = genotype; this.annotationIndexEntry = annotationIndexEntry; this.meCode = meCode; @@ -59,10 +63,15 @@ public Variant getVariant() { return variant; } + @Deprecated public BitBuffer getFileIndex() { return fileIndex; } + public List getFilesIndex() { + return filesIndex; + } + public String getGenotype() { return genotype; } @@ -88,7 +97,7 @@ public boolean equals(Object o) { return false; } SampleVariantIndexEntry that = (SampleVariantIndexEntry) o; - return fileIndex.equals(that.fileIndex) && Objects.equals(variant, that.variant); + return filesIndex.equals(that.filesIndex) && Objects.equals(variant, that.variant); } @Override @@ -106,7 +115,7 @@ public String toString(SampleIndexSchema schema, String separator) { sb.append(separator).append("gt: ") .append(this.getGenotype()); sb.append(separator).append("file: ") - .append(this.getFileIndex()); + .append(this.getFilesIndex()); if (annotationIndexEntry != null) { annotationIndexEntry.toString(schema, separator, sb); } From c21e416ebb1c66f4b4ab3bd43eb65039292311be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Fri, 21 Jul 2023 12:55:35 +0100 Subject: [PATCH 11/23] storage: Fix multi-allelic fetch. Add QUAL. #TASK-4794 --- .../SampleIndexOnlyVariantQueryExecutor.java | 27 ++++++++++--------- .../variant/index/core/RangeIndexField.java | 2 +- 2 files changed, 16 insertions(+), 13 deletions(-) diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java index 195f35a66d2..6c0668aa1e2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java @@ -390,15 +390,15 @@ public Variant convert(SampleVariantIndexEntry entry) { switch (role) { case MOTHER: studyEntry.getSamples().add(new SampleEntry(motherName, null, - Collections.singletonList(GenotypeCodec.decodeMother(entry.getParentsCode())))); + Arrays.asList(GenotypeCodec.decodeMother(entry.getParentsCode())))); break; case FATHER: studyEntry.getSamples().add(new SampleEntry(fatherName, null, - Collections.singletonList(GenotypeCodec.decodeFather(entry.getParentsCode())))); + Arrays.asList(GenotypeCodec.decodeFather(entry.getParentsCode())))); break; case SAMPLE: studyEntry.getSamples().add(new SampleEntry(sampleName, null, - Collections.singletonList(entry.getGenotype()))); + Arrays.asList(entry.getGenotype()))); break; default: throw new IllegalStateException("Unexpected value: " + role); @@ -412,11 +412,11 @@ public Variant convert(SampleVariantIndexEntry entry) { filter = "NA"; } fileAttributes.put(StudyEntry.FILTER, filter); -// String qual = qualField.readAndDecode(fileIndexBitBuffer); -// if (qual == null) { -// qual = "NA"; -// } -// fileAttributes.put(StudyEntry.QUAL, qual); + String qual = qualField.readAndDecode(fileIndexBitBuffer); + if (qual == null) { + qual = "NA"; + } + fileAttributes.put(StudyEntry.QUAL, qual); String fileName = files.get(0); studyEntry.setFiles(new ArrayList<>()); studyEntry.getFiles().add(new FileEntry(fileName, null, fileAttributes)); @@ -513,7 +513,7 @@ public List apply(List variants) { // Should end in few seconds future.get(90, TimeUnit.SECONDS); } catch (InterruptedException | ExecutionException | TimeoutException e) { - throw new VariantQueryException("Error fetching original call for INDELs"); + throw new VariantQueryException("Error fetching extra data", e); } } logger.info("Fetch {} partial variants in {} in {} threads", @@ -564,8 +564,11 @@ private void addSecondaryAlternates(List toReadFull) { fe.setCall(newFe.getCall()); }); // merge sampleEntries - for (SampleEntry sampleExtra : studyExtra.getSamples()) { - SampleEntry sample = study.getSample(sampleExtra.getSampleId()); + for (int i = 0; i < samples.size(); i++) { +// String sampleName = samples.get(i); + SampleEntry sample = study.getSample(i); + SampleEntry sampleExtra = studyExtra.getSample(i); + sample.getData().set(gtIdx, sampleExtra.getData().get(0)); // if (sampleExtra.getFileIndex() != null) { // String fileIdFromFull = fullStudy.getFiles().get(sampleExtra.getFileIndex()).getFileId(); @@ -608,7 +611,7 @@ private void addOriginalCall(List variants, String study) { continue; } StudyEntry studyEntry = variant.getStudies().get(0); - mergeFileEntries(studyEntry, fileEntries, (fe, newFe)->{ + mergeFileEntries(studyEntry, fileEntries, (fe, newFe) -> { fe.setCall(newFe.getCall()); }); } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/RangeIndexField.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/RangeIndexField.java index 5cf4d9e75c0..8f5d6a8f4f8 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/RangeIndexField.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/RangeIndexField.java @@ -120,7 +120,7 @@ public int encode(Double value) { @Override public Double decode(int code) { - return code == thresholds.length ? max : code < 0 ? min : thresholds[code]; + return code <= 0 ? min : thresholds[code - 1]; } @Override From 4de465a5a1dedbd5c5e1d2dff2ffabfebed3e81d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Tue, 25 Jul 2023 16:20:56 +0100 Subject: [PATCH 12/23] storage: Do not return extra files information. #TASK-4794 --- .../ExomiserWrapperAnalysisExecutor.java | 8 +- .../storage/SampleIndexConfiguration.java | 2 +- .../test/resources/variant-multiallelic.vcf | 20 +++ .../SampleIndexOnlyVariantQueryExecutor.java | 141 ++++++++++-------- .../variant/index/sample/FileIndexSchema.java | 27 +++- .../index/core/CategoricalIndexFieldTest.java | 50 ++++++- .../variant/index/sample/SampleIndexTest.java | 61 +++++++- 7 files changed, 233 insertions(+), 76 deletions(-) create mode 100644 opencga-storage/opencga-storage-core/src/test/resources/variant-multiallelic.vcf diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java index 1b19e410b5b..099d3c6c7db 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/exomiser/ExomiserWrapperAnalysisExecutor.java @@ -7,7 +7,6 @@ import org.opencb.biodata.models.clinical.Phenotype; import org.opencb.biodata.models.clinical.pedigree.Member; import org.opencb.biodata.models.clinical.pedigree.Pedigree; -import org.opencb.biodata.models.core.SexOntologyTermAnnotation; import org.opencb.biodata.models.pedigree.IndividualProperty; import org.opencb.commons.datastore.core.QueryOptions; import org.opencb.commons.exec.Command; @@ -21,12 +20,9 @@ import org.opencb.opencga.core.exceptions.ToolExecutorException; import org.opencb.opencga.core.models.family.Family; import org.opencb.opencga.core.models.individual.Individual; -import org.opencb.opencga.core.models.sample.Sample; import org.opencb.opencga.core.tools.annotations.ToolExecutor; import org.opencb.opencga.storage.core.exceptions.StorageEngineException; -import org.opencb.opencga.storage.core.variant.adaptors.VariantField; import org.opencb.opencga.storage.core.variant.adaptors.VariantQuery; -import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam; import org.opencb.opencga.storage.core.variant.io.VariantWriterFactory; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -36,7 +32,6 @@ import java.nio.file.Path; import java.nio.file.Paths; import java.util.*; -import java.util.stream.Collectors; @ToolExecutor(id = ExomiserWrapperAnalysisExecutor.ID, tool = ExomiserWrapperAnalysis.ID, @@ -133,7 +128,8 @@ public void run() throws ToolException { .sample(sampleId) .includeSample(samples) .includeSampleData("GT") - .unknownGenotype("./."); + .unknownGenotype("./.") + .append("includeAllFromSampleIndex", true); QueryOptions queryOptions = new QueryOptions(QueryOptions.INCLUDE, "id,studies.samples"); diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java index 0dcdf5b08fc..31b1bd45a45 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java @@ -169,7 +169,7 @@ public static SampleIndexConfiguration defaultConfiguration(boolean cellbaseV4) .addFileIndexField(new IndexFieldConfiguration( IndexFieldConfiguration.Source.FILE, StudyEntry.FILTER, - IndexFieldConfiguration.Type.CATEGORICAL, + IndexFieldConfiguration.Type.CATEGORICAL_MULTI_VALUE, VCFConstants.PASSES_FILTERS_v4)) .addFileIndexField(new IndexFieldConfiguration( IndexFieldConfiguration.Source.FILE, StudyEntry.QUAL, QUAL_THRESHOLDS).setNullable(false)) diff --git a/opencga-storage/opencga-storage-core/src/test/resources/variant-multiallelic.vcf b/opencga-storage/opencga-storage-core/src/test/resources/variant-multiallelic.vcf new file mode 100644 index 00000000000..dc1cfc5d784 --- /dev/null +++ b/opencga-storage/opencga-storage-core/src/test/resources/variant-multiallelic.vcf @@ -0,0 +1,20 @@ +##fileformat=VCFv4.1 +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##command=seq 1000000 500 3000000 | while read i ; do echo -e "chr1\t$i\t.\tA\tC\t$RANDOM\tPASS\t.\tGT\t0/1\t1/1\t1|0\t0|1" ; done +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA19600 NA19660 NA19661 NA19685 +chr1 1000000 . A C,T 5 noPass,noPass2 . GT 1/2 1/1 0|0 0|1 +chr1 1000010 . A AC,CA 20 PASS . GT 1/2 1/1 0|0 0|1 +chr1 1000020 . AT T,A 60 . . GT 1/2 1/1 0|0 0|1 +chr1 1000030 . C G 60 . PASS GT 1/0 1/1 0|0 0|1 +chr1 1000040 . C G 60 . PASS GT 1/0 1/1 0|0 0|1 +chr1 1000050 . C G 60 . PASS GT 1/0 1/1 0|0 0|1 +chr1 1000060 . C G 60 . PASS GT 1/0 1/1 0|0 0|1 +chr1 1000070 . C G 60 . PASS GT 1/0 1/1 0|0 0|1 +chr1 1000080 . C G 60 . PASS GT 1/0 1/1 0|0 0|1 +chr1 1000090 . C G 60 . PASS GT 1/0 1/1 0|0 0|1 \ No newline at end of file diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java index 6c0668aa1e2..8b4f5d1c347 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java @@ -2,7 +2,6 @@ import com.google.common.collect.Iterators; import htsjdk.variant.vcf.VCFConstants; -import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.concurrent.BasicThreadFactory; import org.apache.commons.lang3.time.StopWatch; import org.opencb.biodata.models.variant.StudyEntry; @@ -177,8 +176,9 @@ private VariantDBIterator getVariantDBIterator(SampleIndexQuery sampleIndexQuery } catch (IOException e) { throw VariantQueryException.internalException(e).setQuery(inputQuery); } - SampleVariantIndexEntryToVariantConverter converter = - new SampleVariantIndexEntryToVariantConverter(parsedQuery, sampleIndexQuery, dbAdaptor.getMetadataManager()); + boolean includeAll = inputQuery.getBoolean("includeAllFromSampleIndex", false); + SampleVariantIndexEntryToVariantConverter converter = new SampleVariantIndexEntryToVariantConverter( + parsedQuery, sampleIndexQuery, dbAdaptor.getMetadataManager(), includeAll); variantIterator = VariantDBIterator.wrapper(Iterators.transform(rawIterator, converter::convert)); AddMissingDataTask task = new AddMissingDataTask( parsedQuery, sampleIndexQuery, dbAdaptor.getMetadataManager()); @@ -289,8 +289,6 @@ private boolean isIncludeCovered(SampleIndexQuery sampleIndexQuery, Query inputQ private static class SampleVariantIndexEntryToVariantConverter implements Converter { - - enum FamilyRole { MOTHER, FATHER, @@ -304,19 +302,17 @@ enum FamilyRole { private String motherName; private String fatherName; private LinkedHashMap samplesPosition; - private final List files; + private List sampleFiles; private IndexField filterField; private IndexField qualField; private final SampleIndexSchema schema; + private final boolean includeAll; SampleVariantIndexEntryToVariantConverter(ParsedVariantQuery parseQuery, SampleIndexQuery sampleIndexQuery, - VariantStorageMetadataManager metadataManager) { + VariantStorageMetadataManager metadataManager, boolean includeAll) { schema = sampleIndexQuery.getSchema(); - filterField = schema.getFileIndex() - .getCustomField(IndexFieldConfiguration.Source.FILE, StudyEntry.FILTER); - qualField = schema.getFileIndex() - .getCustomField(IndexFieldConfiguration.Source.FILE, StudyEntry.QUAL); + this.includeAll = includeAll; VariantQueryProjection projection = parseQuery.getProjection(); includeStudy = !projection.getStudyIds().isEmpty(); @@ -367,13 +363,22 @@ enum FamilyRole { this.fatherName = null; } - List fileIds = metadataManager.getFileIdsFromSampleId(studyId, sampleId, true); - files = new ArrayList<>(fileIds.size()); - for (Integer fileId : fileIds) { - files.add(metadataManager.getFileName(studyId, fileId)); + if (includeAll) { + if (sampleMetadata == null) { + sampleMetadata = metadataManager.getSampleMetadata(studyId, sampleId); + } + if (sampleMetadata.isMultiFileSample()) { + List sampleFileIds = sampleMetadata.getFiles(); + sampleFiles = new ArrayList<>(sampleFileIds.size()); + for (Integer fileId : sampleFileIds) { + sampleFiles.add(metadataManager.getFileName(studyId, fileId)); + } + } + filterField = schema.getFileIndex() + .getCustomField(IndexFieldConfiguration.Source.FILE, StudyEntry.FILTER); + qualField = schema.getFileIndex() + .getCustomField(IndexFieldConfiguration.Source.FILE, StudyEntry.QUAL); } - } else { - files = null; } } @@ -386,6 +391,7 @@ public Variant convert(SampleVariantIndexEntry entry) { studyEntry.setStudyId(studyName); studyEntry.setSampleDataKeys(Collections.singletonList("GT")); studyEntry.setSamples(new ArrayList<>(familyRoleOrder.size())); + SampleEntry sampleEntry = null; for (FamilyRole role : familyRoleOrder) { switch (role) { case MOTHER: @@ -397,29 +403,37 @@ public Variant convert(SampleVariantIndexEntry entry) { Arrays.asList(GenotypeCodec.decodeFather(entry.getParentsCode())))); break; case SAMPLE: - studyEntry.getSamples().add(new SampleEntry(sampleName, null, - Arrays.asList(entry.getGenotype()))); + sampleEntry = new SampleEntry(sampleName, null, + Arrays.asList(entry.getGenotype())); + studyEntry.getSamples().add(sampleEntry); break; default: throw new IllegalStateException("Unexpected value: " + role); } } - HashMap fileAttributes = new HashMap<>(); - // TODO: What if multi-files? - BitBuffer fileIndexBitBuffer = entry.getFileIndex(); - String filter = filterField.readAndDecode(fileIndexBitBuffer); - if (filter == null) { - filter = "NA"; - } - fileAttributes.put(StudyEntry.FILTER, filter); - String qual = qualField.readAndDecode(fileIndexBitBuffer); - if (qual == null) { - qual = "NA"; + if (includeAll) { + HashMap fileAttributes = new HashMap<>(); + for (BitBuffer fileIndexBitBuffer : entry.getFilesIndex()) { + String filter = filterField.readAndDecode(fileIndexBitBuffer); + if (filter == null) { + filter = "NA"; + } + fileAttributes.put(StudyEntry.FILTER, filter); + String qual = qualField.readAndDecode(fileIndexBitBuffer); + if (qual == null) { + qual = "NA"; + } + fileAttributes.put(StudyEntry.QUAL, qual); + + Integer idx = schema.getFileIndex().getFilePositionIndex().readAndDecode(fileIndexBitBuffer); + String fileName = sampleFiles.get(idx); + studyEntry.setFiles(new ArrayList<>()); + studyEntry.getFiles().add(new FileEntry(fileName, null, fileAttributes)); + if (sampleEntry != null) { + sampleEntry.setFileIndex(0); + } + } } - fileAttributes.put(StudyEntry.QUAL, qual); - String fileName = files.get(0); - studyEntry.setFiles(new ArrayList<>()); - studyEntry.getFiles().add(new FileEntry(fileName, null, fileAttributes)); studyEntry.setSortedSamplesPosition(samplesPosition); v.setStudies(Collections.singletonList(studyEntry)); } @@ -430,9 +444,10 @@ public Variant convert(SampleVariantIndexEntry entry) { private class AddMissingDataTask implements Task { private final ParsedVariantQuery parsedQuery; private final String studyName; - private final List samples; - private final List files; - private final List allFiles; + private final String sampleName; + private final List filesFromSample; + private final List includeSamples; + private final List allFiles; // from all includedSamples private final int gtIdx; AddMissingDataTask(ParsedVariantQuery parsedQuery, SampleIndexQuery sampleIndexQuery, @@ -449,9 +464,9 @@ private class AddMissingDataTask implements Task { throw new IllegalStateException("Unexpected number of samples. Expected one, found " + sampleIndexQuery.getSamplesMap().keySet()); } - samples = new ArrayList<>(projectionStudy.getSamples().size()); + includeSamples = new ArrayList<>(projectionStudy.getSamples().size()); for (Integer sample : projectionStudy.getSamples()) { - samples.add(metadataManager.getSampleName(studyId, sample)); + includeSamples.add(metadataManager.getSampleName(studyId, sample)); } Set allFileIds = metadataManager.getFileIdsFromSampleIds(studyId, projectionStudy.getSamples(), true); allFiles = new ArrayList<>(allFileIds.size()); @@ -459,12 +474,12 @@ private class AddMissingDataTask implements Task { allFiles.add(metadataManager.getFileName(studyId, fileId)); } - String sampleName = sampleIndexQuery.getSamplesMap().keySet().iterator().next(); + sampleName = sampleIndexQuery.getSamplesMap().keySet().iterator().next(); Integer sampleId = metadataManager.getSampleId(studyId, sampleName); List fileIds = metadataManager.getFileIdsFromSampleId(studyId, sampleId, true); - files = new ArrayList<>(fileIds.size()); + filesFromSample = new ArrayList<>(fileIds.size()); for (Integer fileId : fileIds) { - files.add(metadataManager.getFileName(studyId, fileId)); + filesFromSample.add(metadataManager.getFileName(studyId, fileId)); } List includeSampleData = VariantQueryUtils.getIncludeSampleData(parsedQuery.getInputQuery()); gtIdx = includeSampleData.indexOf("GT"); @@ -543,7 +558,7 @@ private void addSecondaryAlternates(List toReadFull) { Map variantsExtra = dbAdaptor.get(new VariantQuery() .id(toReadFull) .study(studyName) - .includeSample(samples) + .includeSample(includeSamples) .includeSampleData("GT") // read only GT .includeFile(allFiles), options) @@ -560,23 +575,17 @@ private void addSecondaryAlternates(List toReadFull) { StudyEntry studyExtra = variantExtra.getStudies().get(0); StudyEntry study = variant.getStudies().get(0); + study.setSecondaryAlternates(studyExtra.getSecondaryAlternates()); + mergeFileEntries(study, studyExtra.getFiles(), (fe, newFe) -> { fe.setCall(newFe.getCall()); }); // merge sampleEntries - for (int i = 0; i < samples.size(); i++) { -// String sampleName = samples.get(i); + for (int i = 0; i < includeSamples.size(); i++) { SampleEntry sample = study.getSample(i); SampleEntry sampleExtra = studyExtra.getSample(i); sample.getData().set(gtIdx, sampleExtra.getData().get(0)); -// if (sampleExtra.getFileIndex() != null) { -// String fileIdFromFull = fullStudy.getFiles().get(sampleExtra.getFileIndex()).getFileId(); -// if (sample.getFileIndex() == null) { -// actualStudy.getFiles(). -// String fileIdFrmoFull = fullStudy.getFiles().get(sampleExtra.getFileIndex()).getFileId(); -// } -// } } } // logger.info(" # Fetch {} SEC_ALTS in {}", toReadFull.size(), TimeUtils.durationToString(stopWatch)); @@ -588,7 +597,7 @@ private void addOriginalCall(List variants, String study) { for (Variant variant : dbAdaptor.iterable( new Query() .append(VariantQueryParam.ID.key(), variants) - .append(VariantQueryParam.INCLUDE_FILE.key(), files) + .append(VariantQueryParam.INCLUDE_FILE.key(), filesFromSample) .append(VariantQueryParam.INCLUDE_SAMPLE.key(), NONE) .append(VariantQueryParam.INCLUDE_STUDY.key(), study), new QueryOptions() @@ -620,21 +629,23 @@ private void addOriginalCall(List variants, String study) { private void mergeFileEntries(StudyEntry studyEntry, List newFileEntries, BiConsumer merge) { - if (CollectionUtils.isEmpty(studyEntry.getFiles())) { - studyEntry.setFiles(newFileEntries); - } else { - for (FileEntry newFileEntry : newFileEntries) { - FileEntry fileEntry = studyEntry.getFile(newFileEntry.getFileId()); - if (fileEntry == null) { - studyEntry.getFiles().add(newFileEntry); - } else { - merge.accept(fileEntry, newFileEntry); + if (studyEntry.getFiles() == null) { + studyEntry.setFiles(new ArrayList<>(newFileEntries.size())); + } + for (FileEntry newFileEntry : newFileEntries) { + FileEntry fileEntry = studyEntry.getFile(newFileEntry.getFileId()); + if (fileEntry == null) { + fileEntry = new FileEntry(newFileEntry.getFileId(), null, new HashMap<>()); + studyEntry.getFiles().add(fileEntry); + if (filesFromSample.contains(fileEntry.getFileId())) { + SampleEntry sampleEntry = studyEntry.getSample(sampleName); + if (sampleEntry.getFileIndex() == null) { + sampleEntry.setFileIndex(studyEntry.getFiles().size() - 1); + } } } + merge.accept(fileEntry, newFileEntry); } } - - } - } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/FileIndexSchema.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/FileIndexSchema.java index 4ea023e75e5..a383109139d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/FileIndexSchema.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/FileIndexSchema.java @@ -213,7 +213,32 @@ private static IndexField buildCustomIndexField(IndexFieldConfiguration } else { return Arrays.asList(s.split(VCFConstants.FILTER_CODE_SEPARATOR)); } - }, v -> v == null ? null : String.join(VCFConstants.FILTER_CODE_SEPARATOR, v)); + }, values -> { + if (values == null || values.isEmpty()) { + return null; + } + if (values.size() == 1) { + String value = values.get(0); + if (value == null) { + return null; + } else { + return value; + } + } else { + StringBuilder sb = new StringBuilder(); + for (String v : values) { + if (sb.length() != 0) { + sb.append(VCFConstants.FILTER_CODE_SEPARATOR); + } + if (v == null) { + sb.append("NA"); + } else { + sb.append(v); + } + } + return sb.toString(); + } + }); } else { return new CategoricalMultiValuedIndexField<>(conf, bitOffset, conf.getValues()) .from(s -> { diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexFieldTest.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexFieldTest.java index a062617da1f..0abaa66893a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexFieldTest.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexFieldTest.java @@ -1,7 +1,9 @@ package org.opencb.opencga.storage.hadoop.variant.index.core; +import org.apache.commons.lang3.tuple.Pair; import org.junit.Test; import org.junit.experimental.categories.Category; +import org.opencb.biodata.models.variant.StudyEntry; import org.opencb.opencga.core.config.storage.IndexFieldConfiguration; import org.opencb.opencga.core.config.storage.SampleIndexConfiguration; import org.opencb.opencga.core.testclassification.duration.ShortTests; @@ -15,6 +17,7 @@ import java.util.Set; import static org.junit.Assert.assertEquals; +import static org.opencb.opencga.core.config.storage.IndexFieldConfiguration.Source.FILE; import static org.opencb.opencga.core.config.storage.IndexFieldConfiguration.Source.SAMPLE; @Category(ShortTests.class) @@ -39,10 +42,55 @@ public void testLength() { assertEquals(3, CategoricalIndexField.create(new IndexFieldConfiguration(SAMPLE, "K", IndexFieldConfiguration.Type.CATEGORICAL, "1", "2", "3", "4", "5", "6").setNullable(nullable), 0).getBitLength()); } + @Test + public void testEncodeDecodeQual() { + SampleIndexSchema indexSchema = SampleIndexSchema.defaultSampleIndexSchema(); + IndexField qualfield = indexSchema.getFileIndex().getCustomField(FILE, StudyEntry.QUAL); + + List> pairs = Arrays.asList( + Pair.of("45", "30.0"), + Pair.of("25", "20.0"), + Pair.of("30", "30.0"), + Pair.of("10", "10.0"), + Pair.of("0", Double.toString(Double.MIN_VALUE)) + ); + for (Pair pair : pairs) { + String qual = pair.getKey(); + String expectedQual = pair.getValue(); + int encode = qualfield.encode(qual); + String actualQual = qualfield.decode(encode); + assertEquals(expectedQual, actualQual); + } + } + + @Test + public void testEncodeDecodeFilter() { + SampleIndexConfiguration indexConfiguration = SampleIndexConfiguration.defaultConfiguration(); + indexConfiguration.getFileIndexConfiguration().getCustomField(FILE, StudyEntry.FILTER).setValues("PASS", "noPass"); + SampleIndexSchema indexSchema = new SampleIndexSchema(indexConfiguration, 0); + IndexField field = indexSchema.getFileIndex().getCustomField(FILE, StudyEntry.FILTER); + + List> pairs = Arrays.asList( + Pair.of("PASS", "PASS"), + Pair.of("asdfasdf", null), + Pair.of("noPass", "noPass"), + Pair.of("PASS;noPass", "PASS;noPass"), + Pair.of("PASS;noPass;other;another", "PASS;noPass;NA"), + Pair.of(".", null) + ); + for (Pair pair : pairs) { + String filter = pair.getKey(); + String expectedFilter = pair.getValue(); + int encode = field.encode(filter); + String actualFilter = field.decode(encode); + assertEquals(expectedFilter, actualFilter); + } + } + @Test public void testEncodeDecode() { SampleIndexSchema indexSchema = SampleIndexSchema.defaultSampleIndexSchema(); - CategoricalMultiValuedIndexField field = (CategoricalMultiValuedIndexField) indexSchema.getCtIndex().getField(); + CategoricalMultiValuedIndexField field = indexSchema.getCtIndex().getField(); List expected = Arrays.asList("synonymous_variant", "missense_variant"); int encode = field.encode(expected); diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexTest.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexTest.java index 7693fc1a53e..3cea4d62452 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexTest.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexTest.java @@ -14,8 +14,10 @@ import org.junit.experimental.categories.Category; import org.junit.rules.ExternalResource; import org.opencb.biodata.models.core.Region; +import org.opencb.biodata.models.variant.StudyEntry; import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.models.variant.avro.ConsequenceType; +import org.opencb.biodata.models.variant.avro.FileEntry; import org.opencb.biodata.models.variant.avro.VariantType; import org.opencb.biodata.models.variant.metadata.SampleVariantStats; import org.opencb.commons.datastore.core.*; @@ -59,6 +61,7 @@ import java.util.*; import java.util.concurrent.TimeUnit; import java.util.concurrent.atomic.AtomicInteger; +import java.util.function.Function; import java.util.stream.Collectors; import static java.util.stream.Collectors.*; @@ -84,8 +87,15 @@ public class SampleIndexTest extends VariantStorageBaseTest implements HadoopVar private static boolean loaded = false; public static final String STUDY_NAME_3 = "study_3"; public static final String STUDY_NAME_4 = "study_4"; - public static final String STUDY_NAME_5 = "study_5"; - private static final List studies = Arrays.asList(STUDY_NAME, STUDY_NAME_2, STUDY_NAME_3, STUDY_NAME_4, STUDY_NAME_5); + public static final String STUDY_NAME_5 = "study_5"; // large SV + public static final String STUDY_NAME_6 = "study_6"; // multiallelic + private static final List studies = Arrays.asList( + STUDY_NAME, + STUDY_NAME_2, + STUDY_NAME_3, + STUDY_NAME_4, + STUDY_NAME_5, + STUDY_NAME_6); private static final Map> sampleNames = new HashMap>() {{ put(STUDY_NAME, Arrays.asList("NA19600", "NA19660", "NA19661", "NA19685")); put(STUDY_NAME_2, Arrays.asList("NA19600", "NA19660", "NA19661", "NA19685")); @@ -192,6 +202,20 @@ public void load() throws Exception { runETL(engine, getResourceUri("variant-large-sv.vcf"), outputUri, params, true, true, true); engine.familyIndex(STUDY_NAME_5, trios, new ObjectMap()); + // Study 6, multiallelic + SampleIndexConfiguration sampleIndexConfiguration = SampleIndexConfiguration.defaultConfiguration(); + System.out.println("sampleIndexConfiguration.getFileIndexConfiguration() = " + sampleIndexConfiguration.getFileIndexConfiguration()); + sampleIndexConfiguration.getFileIndexConfiguration().getCustomField(IndexFieldConfiguration.Source.FILE, "FILTER") + .setValues("PASS", "noPass", "noPass2"); + engine.getMetadataManager().addSampleIndexConfiguration(STUDY_NAME_6, sampleIndexConfiguration, true); + + params = new ObjectMap() + .append(VariantStorageOptions.STUDY.key(), STUDY_NAME_6) + .append(VariantStorageOptions.ANNOTATE.key(), false) + .append(VariantStorageOptions.STATS_CALCULATE.key(), false); + runETL(engine, getResourceUri("variant-multiallelic.vcf"), outputUri, params, true, true, true); + engine.familyIndex(STUDY_NAME_6, trios, new ObjectMap()); + // ---------------- Annotate // variantStorageEngine.getConfiguration().getCellbase().setUrl(ParamConstants.CELLBASE_URL); @@ -1122,9 +1146,41 @@ public void testSampleIndexOnlyVariantQueryExecutor() { new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(VariantField.ID, VariantField.STUDIES_SAMPLES)), SampleIndexOnlyVariantQueryExecutor.class); + testSampleIndexOnlyVariantQueryExecutor( + new VariantQuery() + .study(STUDY_NAME_6) + .sample("NA19600") + .includeGenotype(true), + new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(VariantField.ID, VariantField.STUDIES_SAMPLES)), + SampleIndexOnlyVariantQueryExecutor.class); + + testSampleIndexOnlyVariantQueryExecutor( + new VariantQuery() + .study(STUDY_NAME_6) + .sample("NA19600") + .includeGenotype(true) + .append("includeAllFromSampleIndex", true), + new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(VariantField.ID, VariantField.STUDIES_SAMPLES)), + SampleIndexOnlyVariantQueryExecutor.class, + v -> { + for (FileEntry fe : v.getStudies().get(0).getFiles()) { + assertNotNull(fe.getData().get(StudyEntry.FILTER)); + fe.setData(Collections.emptyMap()); + } + v.getStudies().get(0).getFiles().removeIf(fe -> fe.getCall() == null); + if (v.getStudies().get(0).getFiles().isEmpty()) { + v.getStudies().get(0).getSamples().forEach(s -> s.setFileIndex(null)); + } + return v; + }); } private void testSampleIndexOnlyVariantQueryExecutor(VariantQuery query, QueryOptions options, Class expected) { + testSampleIndexOnlyVariantQueryExecutor(query, options, expected, v -> v); + } + + private void testSampleIndexOnlyVariantQueryExecutor(VariantQuery query, QueryOptions options, Class expected, + Function mapper) { VariantQueryExecutor variantQueryExecutor = variantStorageEngine.getVariantQueryExecutor( query, options); @@ -1158,6 +1214,7 @@ private void testSampleIndexOnlyVariantQueryExecutor(VariantQuery query, QueryOp for (int i = 0; i < actualVariants.size(); i++) { Variant av = actualVariants.get(i); Variant ev = expectedVariants.get(i); + mapper.apply(av); if (!ev.getStudies().isEmpty()) { if (av.getLengthAlternate() == 0 || av.getLengthReference() == 0) { // System.out.println("-------" + av + "----------"); From 2943017fa577df1eadf160ecb99987492fd7dd4a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 26 Jul 2023 10:59:38 +0100 Subject: [PATCH 13/23] storage: Fix NPE at SampleIndexOnlyVariantQueryExecutor for non multi-file samples #TASK-4794 --- .../index/SampleIndexOnlyVariantQueryExecutor.java | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java index 8b4f5d1c347..5829a9580a8 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/SampleIndexOnlyVariantQueryExecutor.java @@ -66,7 +66,7 @@ public class SampleIndexOnlyVariantQueryExecutor extends VariantQueryExecutor { private final VariantHadoopDBAdaptor dbAdaptor; private final VariantQueryParser variantQueryParser; private final VariantQueryProjectionParser variantQueryProjectionParser; - private Logger logger = LoggerFactory.getLogger(SampleIndexOnlyVariantQueryExecutor.class); + private static Logger logger = LoggerFactory.getLogger(SampleIndexOnlyVariantQueryExecutor.class); private static final ExecutorService THREAD_POOL = Executors.newCachedThreadPool(new BasicThreadFactory.Builder() .namingPattern("sample-index-async-count-%s") @@ -373,6 +373,15 @@ enum FamilyRole { for (Integer fileId : sampleFileIds) { sampleFiles.add(metadataManager.getFileName(studyId, fileId)); } + } else { + List fileIds = metadataManager.getFileIdsFromSampleId(studyId, sampleId, true); + if (fileIds.isEmpty()) { + logger.warn("Sample without indexed files!"); + sampleFiles = Collections.singletonList("sample_without_indexed_files.vcf"); + } else { + String fileName = metadataManager.getFileName(studyId, fileIds.get(0)); + sampleFiles = Collections.singletonList(fileName); + } } filterField = schema.getFileIndex() .getCustomField(IndexFieldConfiguration.Source.FILE, StudyEntry.FILTER); From b2f354aca1d5f30c2d251363fc1ff465e38fb784 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 26 Jul 2023 11:00:03 +0100 Subject: [PATCH 14/23] storage: Revert default SampleIndexConfiguration changes. #TASK-4794 --- .../storage/SampleIndexConfiguration.java | 11 ++++- .../index/core/CategoricalIndexField.java | 47 +++++++++++++++---- .../CategoricalMultiValuedIndexField.java | 28 +++++++++-- .../index/core/FixedSizeIndexSchema.java | 8 ++++ .../hadoop/variant/index/core/IndexField.java | 8 ++++ .../variant/index/core/RangeIndexField.java | 36 ++++++++++++-- .../index/core/SingleFieldIndexSchema.java | 8 ++++ .../AbstractSampleIndexEntryFilter.java | 7 ++- .../index/sample/SampleIndexSchema.java | 16 +++++++ .../sample/SampleIndexVariantBiConverter.java | 4 ++ .../index/sample/VariantTypeIndexCodec.java | 7 +++ 11 files changed, 164 insertions(+), 16 deletions(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java index 31b1bd45a45..21178f7fdf4 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/SampleIndexConfiguration.java @@ -169,7 +169,7 @@ public static SampleIndexConfiguration defaultConfiguration(boolean cellbaseV4) .addFileIndexField(new IndexFieldConfiguration( IndexFieldConfiguration.Source.FILE, StudyEntry.FILTER, - IndexFieldConfiguration.Type.CATEGORICAL_MULTI_VALUE, + IndexFieldConfiguration.Type.CATEGORICAL, VCFConstants.PASSES_FILTERS_v4)) .addFileIndexField(new IndexFieldConfiguration( IndexFieldConfiguration.Source.FILE, StudyEntry.QUAL, QUAL_THRESHOLDS).setNullable(false)) @@ -714,4 +714,13 @@ public boolean equals(Object o) { public int hashCode() { return Objects.hash(fileIndexConfiguration, annotationIndexConfiguration); } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("SampleIndexConfiguration{"); + sb.append("fileIndexConfiguration=").append(fileIndexConfiguration); + sb.append(", annotationIndexConfiguration=").append(annotationIndexConfiguration); + sb.append('}'); + return sb.toString(); + } } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexField.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexField.java index 1ebc25bbe97..59e373257d7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexField.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexField.java @@ -8,10 +8,7 @@ import org.opencb.opencga.storage.hadoop.variant.index.core.filters.MultiValueIndexFieldFilter; import org.opencb.opencga.storage.hadoop.variant.index.core.filters.SingleValueIndexFieldFilter; -import java.util.Collections; -import java.util.HashMap; -import java.util.List; -import java.util.Map; +import java.util.*; import java.util.stream.Collectors; /** @@ -22,7 +19,7 @@ * Value "0" represents NA. */ public class CategoricalIndexField extends IndexField implements IndexCodec { - private final int numBits; + private final int bitLength; private final IndexCodec codec; public static CategoricalIndexField create(IndexFieldConfiguration configuration, int bitOffset) { @@ -43,18 +40,18 @@ public CategoricalIndexField(IndexFieldConfiguration configuration, int bitOffse numValues = values.length; codec = new BasicCodec<>(values, valuesMapping); } - this.numBits = Math.max(1, IndexUtils.log2(numValues - 1) + 1); + this.bitLength = Math.max(1, IndexUtils.log2(numValues - 1) + 1); } public CategoricalIndexField(IndexFieldConfiguration configuration, int bitOffset, int numValues, IndexCodec codec) { super(configuration, bitOffset); - this.numBits = IndexUtils.log2(numValues - 1) + 1; + this.bitLength = IndexUtils.log2(numValues - 1) + 1; this.codec = codec; } @Override public int getBitLength() { - return numBits; + return bitLength; } @Override @@ -124,6 +121,16 @@ public T decode(int code) { public boolean ambiguous(int code) { return ambiguousValues[code]; } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("BasicCodec{"); + sb.append("values=").append(Arrays.toString(values)); + sb.append(", valuesMappingRev=").append(valuesMappingRev); + sb.append(", ambiguousValues=").append(Arrays.toString(ambiguousValues)); + sb.append('}'); + return sb.toString(); + } } private static class BasicCodecWithNa implements IndexCodec { @@ -178,6 +185,20 @@ public T decode(int code) { public boolean ambiguous(int code) { return ambiguousValues[code]; } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("BasicCodecWithNa{"); + sb.append("values=").append(Arrays.toString(values)); + sb.append(", valuesMappingRev=").append(valuesMappingRev); + sb.append(", ambiguousValues=").append(Arrays.toString(ambiguousValues)); + sb.append('}'); + return sb.toString(); + } + } + + protected IndexCodec getCodec() { + return codec; } @Override @@ -195,4 +216,14 @@ public boolean ambiguous(int code) { return codec.ambiguous(code); } + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("CategoricalIndexField{"); + sb.append("configuration=").append(getConfiguration()); + sb.append(", bitOffset=").append(getBitOffset()); + sb.append(", bitLength=").append(bitLength); + sb.append(", codec=").append(codec); + sb.append('}'); + return sb.toString(); + } } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalMultiValuedIndexField.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalMultiValuedIndexField.java index 3f172f9db72..e7bafeb4b11 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalMultiValuedIndexField.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalMultiValuedIndexField.java @@ -20,7 +20,7 @@ */ public class CategoricalMultiValuedIndexField extends CategoricalIndexField> { - private final int numBits; + private final int bitLength; public static CategoricalMultiValuedIndexField createMultiValued(IndexFieldConfiguration configuration, int bitOffset) { return new CategoricalMultiValuedIndexField<>( @@ -41,7 +41,7 @@ public CategoricalMultiValuedIndexField(IndexFieldConfiguration configuration, i private CategoricalMultiValuedIndexField(IndexFieldConfiguration configuration, int bitOffset, T[] values, MaskValueCodec codec) { super(configuration, bitOffset, values.length, codec); - numBits = codec.numBits; + bitLength = codec.numBits; } @Override @@ -59,7 +59,7 @@ protected IndexFieldFilter getSingleValueIndexFilter(OpValue> opValue) { @Override public int getBitLength() { - return numBits; + return bitLength; } /** @@ -145,6 +145,28 @@ public List decode(int code) { public boolean ambiguous(int code) { return code == NA || (code & ambiguousValues) != 0; } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("MaskValueCodec{"); + sb.append("values=").append(Arrays.toString(values)); + sb.append(", otherValuePosition=").append(otherValuePosition); + sb.append(", valuesPosition=").append(valuesPosition); + sb.append(", numBits=").append(numBits); + sb.append(", ambiguousValues=").append(ambiguousValues); + sb.append('}'); + return sb.toString(); + } } + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("CategoricalMultiValuedIndexField{"); + sb.append("configuration=").append(getConfiguration()); + sb.append(", codec=").append(getCodec()); + sb.append(", bitOffset=").append(getBitOffset()); + sb.append(", bitLength=").append(bitLength); + sb.append('}'); + return sb.toString(); + } } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/FixedSizeIndexSchema.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/FixedSizeIndexSchema.java index 727d21c6ae6..1b2592caec9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/FixedSizeIndexSchema.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/FixedSizeIndexSchema.java @@ -38,4 +38,12 @@ public BitBuffer read(BitBuffer buffer, int i) { return buffer.getBitBuffer(i * indexSizeBits, indexSizeBits); } + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("FixedSizeIndexSchema{"); + sb.append("indexSizeBits=").append(indexSizeBits); + sb.append(", fields=").append(fields); + sb.append('}'); + return sb.toString(); + } } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/IndexField.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/IndexField.java index aa12c98653f..ae0715ff52e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/IndexField.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/IndexField.java @@ -170,4 +170,12 @@ public R decode(int code) { }; } + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("IndexField{"); + sb.append("configuration=").append(configuration); + sb.append(", bitOffset=").append(bitOffset); + sb.append('}'); + return sb.toString(); + } } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/RangeIndexField.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/RangeIndexField.java index 8f5d6a8f4f8..5e37863cee7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/RangeIndexField.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/RangeIndexField.java @@ -7,6 +7,7 @@ import org.opencb.opencga.storage.hadoop.variant.index.core.filters.IndexFieldFilter; import org.opencb.opencga.storage.hadoop.variant.index.core.filters.RangeIndexFieldFilter; +import java.util.Arrays; import java.util.List; /** @@ -18,7 +19,7 @@ public class RangeIndexField extends IndexField { private final double[] thresholds; private final double min; private final double max; - private final int numBits; + private final int bitLength; private final IndexCodec codec; private int numRanges; @@ -40,7 +41,7 @@ public RangeIndexField(IndexFieldConfiguration configuration, int bitOffset, dou } else { codec = new NonNullableRangeCodec(); } - numBits = Math.max(1, IndexUtils.log2(numRanges - 1) + 1); + bitLength = Math.max(1, IndexUtils.log2(numRanges - 1) + 1); if (configuration.getType().equals(IndexFieldConfiguration.Type.RANGE_GT)) { // Add one DELTA to each value to invert ranges from [s, e) to (s, e], therefore the operation ">" is exact for (int i = 0; i < thresholds.length; i++) { @@ -77,7 +78,7 @@ public double getMax() { @Override public int getBitLength() { - return numBits; + return bitLength; } @Override @@ -127,6 +128,13 @@ public Double decode(int code) { public boolean ambiguous(int code) { return true; } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("NonNullableRangeCodec{"); + sb.append('}'); + return sb.toString(); + } } public class NullableRangeCodec extends NonNullableRangeCodec { @@ -142,6 +150,13 @@ public int encode(Double value) { public Double decode(int code) { return code == NA ? null : super.decode(code - 1); } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("NullableRangeCodec{"); + sb.append('}'); + return sb.toString(); + } } /** @@ -174,4 +189,19 @@ public static boolean lessThan(double a, double b) { public static boolean equalsTo(double a, double b) { return Math.abs(a - b) < (DELTA / 10); } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("RangeIndexField{"); + sb.append("configuration=").append(getConfiguration()); + sb.append(", bitOffset=").append(getBitOffset()); + sb.append(", bitLength=").append(bitLength); + sb.append(", thresholds=").append(Arrays.toString(thresholds)); + sb.append(", min=").append(min); + sb.append(", max=").append(max); + sb.append(", codec=").append(codec); + sb.append(", numRanges=").append(numRanges); + sb.append('}'); + return sb.toString(); + } } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/SingleFieldIndexSchema.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/SingleFieldIndexSchema.java index 58da9585b8f..2f2cf67409a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/SingleFieldIndexSchema.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/core/SingleFieldIndexSchema.java @@ -21,4 +21,12 @@ public int readFieldValue(BitBuffer buffer, int i) { // return getField().read(read(buffer, i)); return buffer.getIntPartial(i * getBitsLength(), getBitsLength()); } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("SingleFieldIndexSchema{"); + sb.append("field=").append(field); + sb.append('}'); + return sb.toString(); + } } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/AbstractSampleIndexEntryFilter.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/AbstractSampleIndexEntryFilter.java index 7cb87773f0c..1a0fd0935d9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/AbstractSampleIndexEntryFilter.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/AbstractSampleIndexEntryFilter.java @@ -206,7 +206,12 @@ private Collection filter(SampleIndexEntry entry, boolean count) { entry.getSampleId(), entry.getChromosome(), entry.getBatchStart(), gtEntry.getGt()); - logger.warn(gtEntry.toStringSummary()); + try { + logger.warn(gtEntry.toStringSummary()); + logger.warn(converter.getSchema().toString()); + } catch (Exception exception) { + e.addSuppressed(exception); + } throw e; } if (!variants.isEmpty()) { diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexSchema.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexSchema.java index 2a82e5d1750..d050421a160 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexSchema.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexSchema.java @@ -198,6 +198,22 @@ public FileIndexSchema getFileIndex() { return fileIndex; } + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("SampleIndexSchema{"); + sb.append("version=").append(version); + sb.append(", configuration=").append(configuration); + sb.append(", fileIndex=").append(fileIndex); + sb.append(", popFreqIndex=").append(popFreqIndex); + sb.append(", ctIndex=").append(ctIndex); + sb.append(", biotypeIndex=").append(biotypeIndex); + sb.append(", transcriptFlagIndexSchema=").append(transcriptFlagIndexSchema); + sb.append(", ctBtTfIndex=").append(ctBtTfIndex); + sb.append(", clinicalIndexSchema=").append(clinicalIndexSchema); + sb.append('}'); + return sb.toString(); + } + public static int getChunkStart(Integer start) { return (start / BATCH_SIZE) * BATCH_SIZE; } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexVariantBiConverter.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexVariantBiConverter.java index 4c0fb21701f..d8961251205 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexVariantBiConverter.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexVariantBiConverter.java @@ -196,6 +196,10 @@ public MendelianErrorSampleIndexEntryIterator toMendelianIterator(SampleIndexEnt return new MendelianErrorSampleIndexEntryIterator(sampleIndexEntry, schema); } + public SampleIndexSchema getSchema() { + return schema; + } + private abstract static class SampleIndexGtEntryIterator implements SampleIndexEntryIterator { protected SampleIndexEntry.SampleIndexGtEntry gtEntry; private final SampleIndexSchema schema; diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/VariantTypeIndexCodec.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/VariantTypeIndexCodec.java index dd4acb565b2..a385183398f 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/VariantTypeIndexCodec.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/index/sample/VariantTypeIndexCodec.java @@ -74,4 +74,11 @@ public VariantType decode(int code) { public boolean ambiguous(int code) { return code == TYPE_OTHER_CODE || code == TYPE_CNV_CODE; } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("VariantTypeIndexCodec{"); + sb.append('}'); + return sb.toString(); + } } From 53c5ef3ee03427be5621807cc09eb2ff39cb7ef5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 26 Jul 2023 11:14:02 +0100 Subject: [PATCH 15/23] storage: Fix variant parse for unusual contigs. #TASK-4816 --- .../core/variant/query/VariantQueryUtils.java | 16 +++++++++++++--- .../variant/adaptors/VariantQueryUtilsTest.java | 9 +++++++-- 2 files changed, 20 insertions(+), 5 deletions(-) diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryUtils.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryUtils.java index 6e7831c69ed..114379c77a9 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryUtils.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryUtils.java @@ -25,6 +25,7 @@ import org.opencb.biodata.models.core.Region; import org.opencb.biodata.models.variant.StudyEntry; import org.opencb.biodata.models.variant.Variant; +import org.opencb.biodata.models.variant.VariantBuilder; import org.opencb.biodata.models.variant.annotation.ConsequenceTypeMappings; import org.opencb.biodata.models.variant.avro.*; import org.opencb.commons.datastore.core.*; @@ -515,9 +516,18 @@ public static boolean isHpo(String value) { */ public static boolean isVariantId(String value) { int count = StringUtils.countMatches(value, ':'); - return count == 3 - // It may have more colons if is a symbolic alternate like , or a breakend 4:100:C:]15:300]A - || count > 3 && StringUtils.containsAny(value, '<', '[', ']'); + if (count == 3) { + return true; + } + if (count > 3) { + try { + new VariantBuilder(value); + } catch (RuntimeException e) { + return false; + } + return true; + } + return false; } /** diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQueryUtilsTest.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQueryUtilsTest.java index 8f14f1a202b..c939064307e 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQueryUtilsTest.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQueryUtilsTest.java @@ -435,6 +435,8 @@ public void isVariantId() { checkIsVariantId("1:1000:A:T"); checkIsVariantId("1:1000-2000:A:T"); checkIsVariantId("1:1000-2000:A:"); + checkIsVariantId("HLA-DRB1*04:03:01:3349:GAGACAGAG:-", true); + checkIsVariantId("HLA-DRB1*04:03:01:3349:GAGACAGAG:-:2", false); checkIsVariantId("11:14525312:-:]11:14521700]."); checkIsVariantId("4:100:C:[15:300[A"); checkIsVariantId("4:100:C:]15:300]A"); @@ -442,8 +444,6 @@ public void isVariantId() { } public void checkIsVariantId(String v) { - - boolean actual = VariantQueryUtils.isVariantId(v); boolean expected; try { new Variant(v); @@ -451,6 +451,11 @@ public void checkIsVariantId(String v) { } catch (Exception e) { expected = false; } + checkIsVariantId(v, expected); + } + + public void checkIsVariantId(String v, boolean expected) { + boolean actual = VariantQueryUtils.isVariantId(v); assertEquals(v, expected, actual); } From d37174e6caa5c85cfe114f87bdde86df2a8618ec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 26 Jul 2023 11:38:37 +0100 Subject: [PATCH 16/23] storage: Fix test CategoricalIndexFieldTest#testEncodeDecodeFilter #TASK-4794 --- .../hadoop/variant/index/core/CategoricalIndexFieldTest.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexFieldTest.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexFieldTest.java index 0abaa66893a..feae2ca31e6 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexFieldTest.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/core/CategoricalIndexFieldTest.java @@ -66,7 +66,9 @@ public void testEncodeDecodeQual() { @Test public void testEncodeDecodeFilter() { SampleIndexConfiguration indexConfiguration = SampleIndexConfiguration.defaultConfiguration(); - indexConfiguration.getFileIndexConfiguration().getCustomField(FILE, StudyEntry.FILTER).setValues("PASS", "noPass"); + indexConfiguration.getFileIndexConfiguration().getCustomField(FILE, StudyEntry.FILTER) + .setType(IndexFieldConfiguration.Type.CATEGORICAL_MULTI_VALUE) + .setValues("PASS", "noPass"); SampleIndexSchema indexSchema = new SampleIndexSchema(indexConfiguration, 0); IndexField field = indexSchema.getFileIndex().getCustomField(FILE, StudyEntry.FILTER); From 83dfca3df976946fba2d46e232dab8f68cc3632f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 26 Jul 2023 16:25:14 +0100 Subject: [PATCH 17/23] storage: Fix tests from SampleIndexTest #TASK-4794 --- .../hadoop/variant/index/sample/SampleIndexTest.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexTest.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexTest.java index 3cea4d62452..0319c2bc43b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexTest.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/test/java/org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexTest.java @@ -95,12 +95,15 @@ public class SampleIndexTest extends VariantStorageBaseTest implements HadoopVar STUDY_NAME_3, STUDY_NAME_4, STUDY_NAME_5, - STUDY_NAME_6); + STUDY_NAME_6 + ); private static final Map> sampleNames = new HashMap>() {{ put(STUDY_NAME, Arrays.asList("NA19600", "NA19660", "NA19661", "NA19685")); put(STUDY_NAME_2, Arrays.asList("NA19600", "NA19660", "NA19661", "NA19685")); put(STUDY_NAME_3, Arrays.asList("NA12877", "NA12878")); put(STUDY_NAME_4, Arrays.asList("NA19600", "NA19660", "NA19661", "NA19685")); + put(STUDY_NAME_5, Arrays.asList("NA19600", "NA19660", "NA19661", "NA19685")); + put(STUDY_NAME_6, Arrays.asList("NA19600", "NA19660", "NA19661", "NA19685")); }}; // private static List> trios = Arrays.asList( // Arrays.asList("NA19600", "NA19660", "NA19661"), @@ -204,7 +207,6 @@ public void load() throws Exception { // Study 6, multiallelic SampleIndexConfiguration sampleIndexConfiguration = SampleIndexConfiguration.defaultConfiguration(); - System.out.println("sampleIndexConfiguration.getFileIndexConfiguration() = " + sampleIndexConfiguration.getFileIndexConfiguration()); sampleIndexConfiguration.getFileIndexConfiguration().getCustomField(IndexFieldConfiguration.Source.FILE, "FILTER") .setValues("PASS", "noPass", "noPass2"); engine.getMetadataManager().addSampleIndexConfiguration(STUDY_NAME_6, sampleIndexConfiguration, true); @@ -1163,6 +1165,7 @@ public void testSampleIndexOnlyVariantQueryExecutor() { new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(VariantField.ID, VariantField.STUDIES_SAMPLES)), SampleIndexOnlyVariantQueryExecutor.class, v -> { + assertEquals(v.toString(), 1, v.getStudies().get(0).getFiles().size()); for (FileEntry fe : v.getStudies().get(0).getFiles()) { assertNotNull(fe.getData().get(StudyEntry.FILTER)); fe.setData(Collections.emptyMap()); From b176eb7b2ae7b132c5f6a570016eb17654f02be6 Mon Sep 17 00:00:00 2001 From: pfurio Date: Wed, 9 Aug 2023 13:20:03 +0200 Subject: [PATCH 18/23] catalog: fix project include issues, #TASK-4851 --- .../opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java | 6 +++--- .../db/mongodb/iterators/ProjectCatalogMongoDBIterator.java | 4 ++-- .../org/opencb/opencga/catalog/managers/ProjectManager.java | 4 +++- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java index 0a3539870bb..7b88fb6ce1f 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java @@ -318,10 +318,10 @@ Study insert(ClientSession clientSession, Project project, Study study) } @Override - public OpenCGAResult getAllStudiesInProject(long projectId, QueryOptions options) throws CatalogDBException { + public OpenCGAResult getAllStudiesInProject(long projectUid, QueryOptions options) throws CatalogDBException { long startTime = startQuery(); - dbAdaptorFactory.getCatalogProjectDbAdaptor().checkId(projectId); - Query query = new Query(QueryParams.PROJECT_ID.key(), projectId); + dbAdaptorFactory.getCatalogProjectDbAdaptor().checkId(projectUid); + Query query = new Query(QueryParams.PROJECT_UID.key(), projectUid); return endQuery(startTime, get(query, options)); } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/ProjectCatalogMongoDBIterator.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/ProjectCatalogMongoDBIterator.java index f08e0cea0e6..0cc8fc56180 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/ProjectCatalogMongoDBIterator.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/iterators/ProjectCatalogMongoDBIterator.java @@ -146,8 +146,8 @@ private boolean includeStudyInfo() { return true; } else if (options.containsKey(QueryOptions.INCLUDE)) { List list = options.getAsStringList(QueryOptions.INCLUDE); - for (String exclude : list) { - if (exclude.equals("studies") || exclude.equals("projects.studies")) { + for (String include : list) { + if (include.startsWith("studies") || include.startsWith("projects.studies")) { return true; } } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ProjectManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ProjectManager.java index 249d14ab057..7900d958a42 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ProjectManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/ProjectManager.java @@ -610,7 +610,9 @@ public OpenCGAResult incrementRelease(String projectStr, String session int currentRelease = project.getCurrentRelease(); // Check current release has been used at least in one study or file or cohort or individual... - List allStudiesInProject = project.getStudies(); + QueryOptions studyOptions = keepFieldInQueryOptions(StudyManager.INCLUDE_STUDY_IDS, StudyDBAdaptor.QueryParams.RELEASE.key()); + OpenCGAResult studyResult = studyDBAdaptor.getAllStudiesInProject(projectUid, studyOptions); + List allStudiesInProject = studyResult.getResults(); if (allStudiesInProject.isEmpty()) { throw new CatalogException("Cannot increment current release number. No studies found for release " + currentRelease); } From 6137680dd01c58e201059cfd9e8b430088e1da3a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 11 Aug 2023 15:27:30 +0200 Subject: [PATCH 19/23] Prepare release 2.8.3 --- 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-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/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 | 14 +++++++------- 21 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index a2fed95c1b8..260955d38c6 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index be106d38391..4d18a6476ca 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index d43aa67b53f..a0ea06ca14c 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index fc888cf42ea..191a5319867 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 7d8f216a0ea..a9630add90e 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index eb0016308f8..508d50cede8 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 1f19d740348..d45f901844c 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index c4050fb6339..0d66c9f3a74 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 3a1821c0cbd..9d41b4d028d 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 - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 9c61a4cab94..89d8c6c9d7e 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 - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index a746892a217..3b2f329ccb0 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.8.3-SNAPSHOT + 2.8.3 ../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 0e8e429b549..bd7a7c7baa4 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 - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index b3b9bcc68cc..f64c1bc25ba 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index 185a923475d..a5852716f29 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 4a1ed4cb963..cbbfa9c0e83 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 8788d1547ac..3dc7eedf5dc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 5f3b2235c63..202510b2e48 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index cf3e6549427..bbe30f1aa3b 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 - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 0f73ef09ee2..ab93e1a8071 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index ab0a67d1e7e..8f13ebd49ab 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.8.3-SNAPSHOT + 2.8.3 ../pom.xml diff --git a/pom.xml b/pom.xml index c9d53b1bfb7..a91ad02aa54 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3-SNAPSHOT + 2.8.3 pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.8.3_dev - 2.8.3_dev - 5.4.1-SNAPSHOT - 2.8.1-SNAPSHOT - 4.8.1-SNAPSHOT - 2.8.3-SNAPSHOT + 2.8.3 + 2.8.3 + 5.4.0 + 2.8.0 + 4.8.0 + 2.8.3 0.2.0 From aed710fdd2ab13f3bd4d81754717133689a547bb Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 28 Aug 2023 10:52:08 +0200 Subject: [PATCH 20/23] core: add REGEX comment to /search and /distinct, #TASK-4248 --- .../opencga/core/api/ParamConstants.java | 65 ++++++++++--------- 1 file changed, 33 insertions(+), 32 deletions(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java index b65214a9ba4..6a42182cf34 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java @@ -38,6 +38,7 @@ public class ParamConstants { public static final String RELEASE_DESCRIPTION = "Release when it was created"; public static final String INTERNAL_STATUS_PARAM = "internalStatus"; public static final String INTERNAL_STATUS_DESCRIPTION = "Filter by internal status"; + private static final String REGEX_SUPPORT = ". Also admits basic regular expressions like '~/^value/i'"; @Deprecated // Use INTERNAL_VARIANT_INDEX_STATUS_PARAM public static final String INTERNAL_INDEX_STATUS_PARAM = "internalIndexStatus"; public static final String INTERNAL_VARIANT_INDEX_STATUS_PARAM = "internalVariantIndexStatus"; @@ -169,12 +170,12 @@ public class ParamConstants { + "exception whenever one of the entries looked for cannot be shown for whichever reason"; public static final String FILE_ID_DESCRIPTION = "File ID"; public static final String FILE_NAME_DESCRIPTION = "File name"; - public static final String FILE_NAMES_DESCRIPTION = "Comma separated list of file names"; + public static final String FILE_NAMES_DESCRIPTION = "Comma separated list of file names" + REGEX_SUPPORT; // --------------------------------------------- public static final String FILE_PATH_PARAM = "path"; public static final String FILE_PATH_DESCRIPTION = "File path"; - public static final String FILE_PATHS_DESCRIPTION = "Comma separated list of paths"; - public static final String FILE_URIS_DESCRIPTION = "Comma separated list of uris"; + public static final String FILE_PATHS_DESCRIPTION = "Comma separated list of paths" + REGEX_SUPPORT; + public static final String FILE_URIS_DESCRIPTION = "Comma separated list of uris" + REGEX_SUPPORT; public static final String FILE_TYPE_DESCRIPTION = "File type, either FILE or DIRECTORY"; public static final String FILE_FORMAT_DESCRIPTION = "Comma separated Format values. For existing Formats see files/formats"; public static final String FILE_EXTERNAL_DESCRIPTION = "Boolean field indicating whether to filter by external or non external files"; @@ -182,7 +183,7 @@ public class ParamConstants { "files/bioformats"; public static final String FILE_STATUS_DESCRIPTION = "File status"; public static final String FILE_DESCRIPTION_DESCRIPTION = "Description"; - public static final String FILE_TAGS_DESCRIPTION = "Tags"; + public static final String FILE_TAGS_DESCRIPTION = "Tags" + REGEX_SUPPORT; public static final String FILE_SOFTWARE_NAME_PARAM = "softwareName"; public static final String FILE_SOFTWARE_NAME_DESCRIPTION = "Software name"; public static final String FILE_JOB_ID_DESCRIPTION = "Job ID that created the file(s) or folder(s)"; @@ -316,12 +317,12 @@ public class ParamConstants { public static final String INDIVIDUAL_MOTHER_DESCRIPTION = "Mother ID, name or UUID"; public static final String INDIVIDUAL_SAMPLES_DESCRIPTION = "Sample ID, name or UUID"; public static final String INDIVIDUAL_SEX_DESCRIPTION = "Individual sex"; - public static final String INDIVIDUAL_ETHNICITY_DESCRIPTION = "Individual ethnicity"; + public static final String INDIVIDUAL_ETHNICITY_DESCRIPTION = "Individual ethnicity" + REGEX_SUPPORT; public static final String INDIVIDUAL_DATE_OF_BIRTH_DESCRIPTION = "Individual date of birth"; - public static final String INDIVIDUAL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION; - public static final String INDIVIDUAL_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION; - public static final String INDIVIDUAL_POPULATION_NAME_DESCRIPTION = "Population name"; - public static final String INDIVIDUAL_POPULATION_SUBPOPULATION_DESCRIPTION = "Subpopulation name"; + public static final String INDIVIDUAL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT; + public static final String INDIVIDUAL_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION + REGEX_SUPPORT; + public static final String INDIVIDUAL_POPULATION_NAME_DESCRIPTION = "Population name" + REGEX_SUPPORT; + public static final String INDIVIDUAL_POPULATION_SUBPOPULATION_DESCRIPTION = "Subpopulation name" + REGEX_SUPPORT; public static final String INDIVIDUAL_KARYOTYPIC_SEX_DESCRIPTION = "Individual karyotypic sex"; public static final String INDIVIDUAL_LIFE_STATUS_DESCRIPTION = "Individual life status"; public static final String INDIVIDUAL_DELETED_DESCRIPTION = DELETED_DESCRIPTION; @@ -358,8 +359,8 @@ public class ParamConstants { public static final String FAMILY_MEMBERS_DESCRIPTION = "Comma separated list of family members"; public static final String FAMILY_SAMPLES_DESCRIPTION = "Comma separated list of member's samples"; public static final String FAMILY_EXPECTED_SIZE_DESCRIPTION = "Expected size of the family (number of members)"; - public static final String FAMILY_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION; - public static final String FAMILY_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION; + public static final String FAMILY_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION + REGEX_SUPPORT; + public static final String FAMILY_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT; public static final String FAMILY_CREATION_DATE_DESCRIPTION = CREATION_DATE_DESCRIPTION; public static final String FAMILY_MODIFICATION_DATE_DESCRIPTION = MODIFICATION_DATE_DESCRIPTION; public static final String FAMILY_DELETED_DESCRIPTION = DELETED_DESCRIPTION; @@ -422,7 +423,7 @@ public class ParamConstants { public static final String CLINICAL_STATUS_PARAM = STATUS_PARAM; public static final String CLINICAL_INTERNAL_STATUS_PARAM = INTERNAL_STATUS_PARAM; public static final String CLINICAL_TYPE_DESCRIPTION = "Clinical Analysis type"; - public static final String CLINICAL_DISORDER_DESCRIPTION = "Clinical Analysis disorder"; + public static final String CLINICAL_DISORDER_DESCRIPTION = "Clinical Analysis disorder" + REGEX_SUPPORT; public static final String CLINICAL_FILES_DESCRIPTION = "Clinical Analysis files"; public static final String CLINICAL_SAMPLE_DESCRIPTION = "Sample associated to the proband or any member of a family"; public static final String CLINICAL_INDIVIDUAL_DESCRIPTION = "Proband or any member of a family"; @@ -466,7 +467,7 @@ public class ParamConstants { public static final String INTERPRETATION_LOCKED_PARAM = "locked"; public static final String INTERPRETATION_CLINICAL_ANALYSIS_ID_DESCRIPTION = "Clinical Analysis id"; public static final String INTERPRETATION_ANALYST_ID_DESCRIPTION = "Analyst ID"; - public static final String INTERPRETATION_METHOD_NAME_DESCRIPTION = "Interpretation method name"; + public static final String INTERPRETATION_METHOD_NAME_DESCRIPTION = "Interpretation method name" + REGEX_SUPPORT; public static final String INTERPRETATION_PANELS_DESCRIPTION = "Interpretation panels"; public static final String INTERPRETATION_PRIMARY_FINDINGS_IDS_DESCRIPTION = "Interpretation primary findings"; public static final String INTERPRETATION_SECONDARY_FINDINGS_IDS_DESCRIPTION = "Interpretation secondary findings"; @@ -498,12 +499,12 @@ public class ParamConstants { public static final String PANEL_ACL_PARAM = ACL_PARAM; public static final String PANEL_RELEASE_PARAM = RELEASE_PARAM; public static final String PANEL_SNAPSHOT_PARAM = SNAPSHOT_PARAM; - public static final String PANEL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION; - public static final String PANEL_VARIANTS_DESCRIPTION = "Comma separated list of variant ids"; - public static final String PANEL_GENES_DESCRIPTION = "Comma separated list of gene ids"; - public static final String PANEL_REGIONS_DESCRIPTION = "Comma separated list of regions"; - public static final String PANEL_CATEGORIES_DESCRIPTION = "Comma separated list of category names"; - public static final String PANEL_TAGS_DESCRIPTION = "Panel tags"; + public static final String PANEL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT; + public static final String PANEL_VARIANTS_DESCRIPTION = "Comma separated list of variant ids" + REGEX_SUPPORT; + public static final String PANEL_GENES_DESCRIPTION = "Comma separated list of gene ids" + REGEX_SUPPORT; + public static final String PANEL_REGIONS_DESCRIPTION = "Comma separated list of regions" + REGEX_SUPPORT; + public static final String PANEL_CATEGORIES_DESCRIPTION = "Comma separated list of category names" + REGEX_SUPPORT; + public static final String PANEL_TAGS_DESCRIPTION = "Panel tags" + REGEX_SUPPORT; public static final String PANEL_DELETED_DESCRIPTION = DELETED_DESCRIPTION; public static final String PANEL_STATUS_DESCRIPTION = STATUS_DESCRIPTION; @@ -539,7 +540,7 @@ public class ParamConstants { public static final String JOB_DEPENDS_ON_DESCRIPTION = "Comma separated list of existing job IDs the job will depend on."; public static final String JOB_TOOL_ID_PARAM = "toolId"; public static final String JOB_TOOL_TYPE_PARAM = "toolType"; - public static final String JOB_TOOL_ID_DESCRIPTION = "Tool ID executed by the job"; + public static final String JOB_TOOL_ID_DESCRIPTION = "Tool ID executed by the job" + REGEX_SUPPORT; public static final String JOB_TOOL_TYPE_DESCRIPTION = "Tool type executed by the job [OPERATION, ANALYSIS]"; public static final String JOB_USER_PARAM = "userId"; public static final String JOB_USER_DESCRIPTION = "User that created the job"; @@ -1475,34 +1476,34 @@ public class ParamConstants { public static final String ADMIN_CATALOG_JWT_SECRETKEY = "The body web service secretKey parameter"; private static final String UP_TO_100 = " up to a maximum of 100"; public static final String FILES_DESCRIPTION = "Comma separated list of file IDs or names" + UP_TO_100; - public static final String FILES_ID_DESCRIPTION = "Comma separated list of file IDs" + UP_TO_100; + public static final String FILES_ID_DESCRIPTION = "Comma separated list of file IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String FILES_UUID_DESCRIPTION = "Comma separated list file UUIDs" + UP_TO_100; public static final String SAMPLES_DESCRIPTION = "Comma separated list sample IDs or UUIDs" + UP_TO_100; public static final String SAMPLES_ID_DESCRIPTION = "Comma separated list sample IDs" + UP_TO_100; public static final String SAMPLES_UUID_DESCRIPTION = "Comma separated list sample UUIDs" + UP_TO_100; public static final String INDIVIDUALS_DESCRIPTION = "Comma separated list of individual IDs, names or UUIDs" + UP_TO_100; - public static final String INDIVIDUALS_ID_DESCRIPTION = "Comma separated list individual IDs" + UP_TO_100; - public static final String INDIVIDUAL_NAME_DESCRIPTION = "Comma separated list individual names" + UP_TO_100; + public static final String INDIVIDUALS_ID_DESCRIPTION = "Comma separated list individual IDs" + UP_TO_100 + REGEX_SUPPORT; + public static final String INDIVIDUAL_NAME_DESCRIPTION = "Comma separated list individual names" + UP_TO_100 + REGEX_SUPPORT; public static final String INDIVIDUAL_UUID_DESCRIPTION = "Comma separated list individual UUIDs" + UP_TO_100; public static final String FAMILIES_DESCRIPTION = "Comma separated list of family IDs or names" + UP_TO_100; - public static final String FAMILY_ID_DESCRIPTION = "Comma separated list family IDs" + UP_TO_100; - public static final String FAMILY_NAME_DESCRIPTION = "Comma separated list family names" + UP_TO_100; + public static final String FAMILY_ID_DESCRIPTION = "Comma separated list family IDs" + UP_TO_100 + REGEX_SUPPORT; + public static final String FAMILY_NAME_DESCRIPTION = "Comma separated list family names" + UP_TO_100 + REGEX_SUPPORT; public static final String FAMILY_UUID_DESCRIPTION = "Comma separated list family UUIDs" + UP_TO_100; public static final String COHORTS_DESCRIPTION = "Comma separated list of cohort IDs or UUIDs" + UP_TO_100; - public static final String COHORT_IDS_DESCRIPTION = "Comma separated list of cohort IDs" + UP_TO_100; - public static final String COHORT_NAMES_DESCRIPTION = "Comma separated list of cohort names" + UP_TO_100; + public static final String COHORT_IDS_DESCRIPTION = "Comma separated list of cohort IDs" + UP_TO_100 + REGEX_SUPPORT; + public static final String COHORT_NAMES_DESCRIPTION = "Comma separated list of cohort names" + UP_TO_100 + REGEX_SUPPORT; public static final String COHORT_UUIDS_DESCRIPTION = "Comma separated list of cohort IDs" + UP_TO_100; - public static final String CLINICAL_ID_DESCRIPTION = "Comma separated list of Clinical Analysis IDs" + UP_TO_100; + public static final String CLINICAL_ID_DESCRIPTION = "Comma separated list of Clinical Analysis IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String CLINICAL_UUID_DESCRIPTION = "Comma separated list of Clinical Analysis UUIDs" + UP_TO_100; public static final String CLINICAL_ANALYSES_DESCRIPTION = "Comma separated list of clinical analysis IDs or names" + UP_TO_100; - public static final String INTERPRETATION_ID_DESCRIPTION = "Comma separated list of Interpretation IDs" + UP_TO_100; + public static final String INTERPRETATION_ID_DESCRIPTION = "Comma separated list of Interpretation IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String INTERPRETATION_UUID_DESCRIPTION = "Comma separated list of Interpretation UUIDs" + UP_TO_100; public static final String INTERPRETATION_DESCRIPTION = "Comma separated list of clinical interpretation IDs " + UP_TO_100; - public static final String PANEL_ID_DESCRIPTION = "Comma separated list of panel IDs " + UP_TO_100; + public static final String PANEL_ID_DESCRIPTION = "Comma separated list of panel IDs " + UP_TO_100 + REGEX_SUPPORT; public static final String PANEL_UUID_DESCRIPTION = "Comma separated list of panel UUIDs " + UP_TO_100; - public static final String PANEL_NAME_DESCRIPTION = "Comma separated list of panel names " + UP_TO_100; + public static final String PANEL_NAME_DESCRIPTION = "Comma separated list of panel names " + UP_TO_100 + REGEX_SUPPORT; public static final String JOBS_DESCRIPTION = "Comma separated list of job IDs or UUIDs" + UP_TO_100; - public static final String JOB_IDS_DESCRIPTION = "Comma separated list of job IDs" + UP_TO_100; + public static final String JOB_IDS_DESCRIPTION = "Comma separated list of job IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String JOB_UUIDS_DESCRIPTION = "Comma separated list of job UUIDs" + UP_TO_100; // --------------------------------------------- public static final String PROJECTS_DESCRIPTION = "Comma separated list of projects [user@]project" + UP_TO_100; From 88ed0ea4ef071c2257b2fa5e6c3e1422f48cdb49 Mon Sep 17 00:00:00 2001 From: pfurio Date: Wed, 30 Aug 2023 09:40:17 +0200 Subject: [PATCH 21/23] core: improve regex description, #TASK-4906 --- .../main/java/org/opencb/opencga/core/api/ParamConstants.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java index 6a42182cf34..a34b818924a 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java @@ -38,7 +38,8 @@ public class ParamConstants { public static final String RELEASE_DESCRIPTION = "Release when it was created"; public static final String INTERNAL_STATUS_PARAM = "internalStatus"; public static final String INTERNAL_STATUS_DESCRIPTION = "Filter by internal status"; - private static final String REGEX_SUPPORT = ". Also admits basic regular expressions like '~/^value/i'"; + private static final String REGEX_SUPPORT = ". Also admits basic regular expressions using the operator '~', " + + "i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search."; @Deprecated // Use INTERNAL_VARIANT_INDEX_STATUS_PARAM public static final String INTERNAL_INDEX_STATUS_PARAM = "internalIndexStatus"; public static final String INTERNAL_VARIANT_INDEX_STATUS_PARAM = "internalVariantIndexStatus"; From 48889d0218db3d0c3779fa15ee956e4d72d2e350 Mon Sep 17 00:00:00 2001 From: pfurio Date: Fri, 1 Sep 2023 10:43:15 +0200 Subject: [PATCH 22/23] app: generate cli automatically, #TASK-4248 --- .../app/cli/main/OpenCgaCompleter.java | 2 +- .../app/cli/main/OpencgaCliOptionsParser.java | 2 +- .../AnalysisClinicalCommandOptions.java | 16 ++-- .../main/options/CohortsCommandOptions.java | 10 +-- .../options/DiseasePanelsCommandOptions.java | 32 ++++---- .../main/options/FamiliesCommandOptions.java | 16 ++-- .../cli/main/options/FilesCommandOptions.java | 20 ++--- .../options/IndividualsCommandOptions.java | 28 +++---- .../cli/main/options/JobsCommandOptions.java | 8 +- .../main/options/SamplesCommandOptions.java | 8 +- opencga-client/src/main/R/R/Admin-methods.R | 2 +- .../src/main/R/R/Alignment-methods.R | 2 +- opencga-client/src/main/R/R/AllGenerics.R | 20 ++--- .../src/main/R/R/Clinical-methods.R | 20 ++--- opencga-client/src/main/R/R/Cohort-methods.R | 14 ++-- opencga-client/src/main/R/R/Family-methods.R | 20 ++--- opencga-client/src/main/R/R/File-methods.R | 24 +++--- opencga-client/src/main/R/R/GA4GH-methods.R | 4 +- .../src/main/R/R/Individual-methods.R | 32 ++++---- opencga-client/src/main/R/R/Job-methods.R | 14 ++-- opencga-client/src/main/R/R/Meta-methods.R | 2 +- .../src/main/R/R/Operation-methods.R | 2 +- opencga-client/src/main/R/R/Panel-methods.R | 34 ++++----- opencga-client/src/main/R/R/Project-methods.R | 2 +- opencga-client/src/main/R/R/Sample-methods.R | 12 +-- opencga-client/src/main/R/R/Study-methods.R | 4 +- opencga-client/src/main/R/R/User-methods.R | 4 +- opencga-client/src/main/R/R/Variant-methods.R | 2 +- .../client/rest/clients/AdminClient.java | 2 +- .../client/rest/clients/AlignmentClient.java | 2 +- .../rest/clients/ClinicalAnalysisClient.java | 26 ++++--- .../client/rest/clients/CohortClient.java | 17 +++-- .../rest/clients/DiseasePanelClient.java | 54 ++++++++----- .../client/rest/clients/FamilyClient.java | 26 ++++--- .../client/rest/clients/FileClient.java | 32 +++++--- .../client/rest/clients/GA4GHClient.java | 2 +- .../client/rest/clients/IndividualClient.java | 44 +++++++---- .../client/rest/clients/JobClient.java | 17 +++-- .../client/rest/clients/MetaClient.java | 2 +- .../client/rest/clients/ProjectClient.java | 2 +- .../client/rest/clients/SampleClient.java | 14 ++-- .../client/rest/clients/StudyClient.java | 2 +- .../client/rest/clients/UserClient.java | 2 +- .../client/rest/clients/VariantClient.java | 2 +- .../rest/clients/VariantOperationClient.java | 2 +- opencga-client/src/main/javascript/Admin.js | 2 +- .../src/main/javascript/Alignment.js | 2 +- .../src/main/javascript/ClinicalAnalysis.js | 26 ++++--- opencga-client/src/main/javascript/Cohort.js | 17 +++-- .../src/main/javascript/DiseasePanel.js | 54 ++++++++----- opencga-client/src/main/javascript/Family.js | 26 ++++--- opencga-client/src/main/javascript/File.js | 32 +++++--- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 44 +++++++---- opencga-client/src/main/javascript/Job.js | 17 +++-- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 14 ++-- opencga-client/src/main/javascript/Study.js | 2 +- opencga-client/src/main/javascript/User.js | 2 +- opencga-client/src/main/javascript/Variant.js | 2 +- .../src/main/javascript/VariantOperation.js | 2 +- .../pyopencga/rest_clients/admin_client.py | 2 +- .../rest_clients/alignment_client.py | 2 +- .../rest_clients/clinical_analysis_client.py | 38 +++++++--- .../pyopencga/rest_clients/cohort_client.py | 21 +++-- .../rest_clients/disease_panel_client.py | 76 +++++++++++++++---- .../pyopencga/rest_clients/family_client.py | 28 ++++++- .../pyopencga/rest_clients/file_client.py | 48 +++++++++--- .../pyopencga/rest_clients/ga4gh_client.py | 2 +- .../rest_clients/individual_client.py | 60 ++++++++++++--- .../pyopencga/rest_clients/job_client.py | 23 +++++- .../pyopencga/rest_clients/meta_client.py | 2 +- .../pyopencga/rest_clients/project_client.py | 2 +- .../pyopencga/rest_clients/sample_client.py | 14 +++- .../pyopencga/rest_clients/study_client.py | 2 +- .../pyopencga/rest_clients/user_client.py | 2 +- .../pyopencga/rest_clients/variant_client.py | 2 +- .../rest_clients/variant_operation_client.py | 2 +- .../opencga/core/api/ParamConstants.java | 14 ++-- 80 files changed, 765 insertions(+), 427 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index 6627d4d82f1..07cb922d522 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-08-30 OpenCB +* Copyright 2015-2023-09-01 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index b619c612c32..4e3e7ed1c1f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-08-30 OpenCB +* Copyright 2015-2023-09-01 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java index 48261ca8a3c..95636ad4c3f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java @@ -275,7 +275,7 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of Clinical Analysis UUIDs up to a maximum of 100", required = false, arity = 1) @@ -284,7 +284,7 @@ public class DistinctCommandOptions { @Parameter(names = {"--type"}, description = "Clinical Analysis type", required = false, arity = 1) public String type; - @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder", required = false, arity = 1) + @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorder; @Parameter(names = {"--files"}, description = "Clinical Analysis files", required = false, arity = 1) @@ -364,7 +364,7 @@ public class DistinctInterpretationCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1) @@ -376,7 +376,7 @@ public class DistinctInterpretationCommandOptions { @Parameter(names = {"--analyst-id"}, description = "Analyst ID", required = false, arity = 1) public String analystId; - @Parameter(names = {"--method-name"}, description = "Interpretation method name", required = false, arity = 1) + @Parameter(names = {"--method-name"}, description = "Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String methodName; @Parameter(names = {"--panels"}, description = "Interpretation panels", required = false, arity = 1) @@ -432,7 +432,7 @@ public class SearchInterpretationCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1) @@ -444,7 +444,7 @@ public class SearchInterpretationCommandOptions { @Parameter(names = {"--analyst-id"}, description = "Analyst ID", required = false, arity = 1) public String analystId; - @Parameter(names = {"--method-name"}, description = "Interpretation method name", required = false, arity = 1) + @Parameter(names = {"--method-name"}, description = "Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String methodName; @Parameter(names = {"--panels"}, description = "Interpretation panels", required = false, arity = 1) @@ -1488,7 +1488,7 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of Clinical Analysis UUIDs up to a maximum of 100", required = false, arity = 1) @@ -1497,7 +1497,7 @@ public class SearchCommandOptions { @Parameter(names = {"--type"}, description = "Clinical Analysis type", required = false, arity = 1) public String type; - @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder", required = false, arity = 1) + @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorder; @Parameter(names = {"--files"}, description = "Clinical Analysis files", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java index 13373914df4..03f08e58c9e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java @@ -242,10 +242,10 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--uuid"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1) @@ -334,7 +334,7 @@ public class GenerateCommandOptions { @Parameter(names = {"--status"}, description = "Filter by status", required = false, arity = 1) public String status; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; @Parameter(names = {"--annotation"}, description = "Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0", required = false, arity = 1) @@ -411,10 +411,10 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--uuid"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java index c6e353a7dca..1f0f1cbb9bc 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java @@ -157,37 +157,37 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of panel UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--internal-status"}, description = "Filter by internal status", required = false, arity = 1) public String internalStatus; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; - @Parameter(names = {"--variants"}, description = "Comma separated list of variant ids", required = false, arity = 1) + @Parameter(names = {"--variants"}, description = "Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String variants; - @Parameter(names = {"--genes"}, description = "Comma separated list of gene ids", required = false, arity = 1) + @Parameter(names = {"--genes"}, description = "Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String genes; @Parameter(names = {"--source"}, description = "Comma separated list of source ids or names.", required = false, arity = 1) public String source; - @Parameter(names = {"--regions"}, description = "Comma separated list of regions", required = false, arity = 1) + @Parameter(names = {"--regions"}, description = "Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String regions; - @Parameter(names = {"--categories"}, description = "Comma separated list of category names", required = false, arity = 1) + @Parameter(names = {"--categories"}, description = "Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String categories; - @Parameter(names = {"--tags"}, description = "Panel tags", required = false, arity = 1) + @Parameter(names = {"--tags"}, description = "Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String tags; @Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0) @@ -275,37 +275,37 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of panel UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--internal-status"}, description = "Filter by internal status", required = false, arity = 1) public String internalStatus; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; - @Parameter(names = {"--variants"}, description = "Comma separated list of variant ids", required = false, arity = 1) + @Parameter(names = {"--variants"}, description = "Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String variants; - @Parameter(names = {"--genes"}, description = "Comma separated list of gene ids", required = false, arity = 1) + @Parameter(names = {"--genes"}, description = "Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String genes; @Parameter(names = {"--source"}, description = "Comma separated list of source ids or names.", required = false, arity = 1) public String source; - @Parameter(names = {"--regions"}, description = "Comma separated list of regions", required = false, arity = 1) + @Parameter(names = {"--regions"}, description = "Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String regions; - @Parameter(names = {"--categories"}, description = "Comma separated list of category names", required = false, arity = 1) + @Parameter(names = {"--categories"}, description = "Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String categories; - @Parameter(names = {"--tags"}, description = "Panel tags", required = false, arity = 1) + @Parameter(names = {"--tags"}, description = "Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String tags; @Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java index 9530f60074d..3c57ef335ba 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java @@ -252,10 +252,10 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list family IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list family names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--uuid"}, description = "Comma separated list family UUIDs up to a maximum of 100", required = false, arity = 1) @@ -270,10 +270,10 @@ public class DistinctCommandOptions { @Parameter(names = {"--samples"}, description = "Comma separated list of member's samples", required = false, arity = 1) public String samples; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; @Parameter(names = {"--creation-date", "--cd"}, description = "Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805", required = false, arity = 1) @@ -335,10 +335,10 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list family IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list family names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--uuid"}, description = "Comma separated list family UUIDs up to a maximum of 100", required = false, arity = 1) @@ -353,10 +353,10 @@ public class SearchCommandOptions { @Parameter(names = {"--samples"}, description = "Comma separated list of member's samples", required = false, arity = 1) public String samples; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; @Parameter(names = {"--creation-date", "--cd"}, description = "Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java index d1d4e0bf0a8..5ea18955f58 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java @@ -327,19 +327,19 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of file IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list file UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of file names", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; - @Parameter(names = {"--path"}, description = "Comma separated list of paths", required = false, arity = 1) + @Parameter(names = {"--path"}, description = "Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String path; - @Parameter(names = {"--uri", "--input", "-i"}, description = "Comma separated list of uris", required = false, arity = 1) + @Parameter(names = {"--uri", "--input", "-i"}, description = "Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String uri; @Parameter(names = {"--type"}, description = "File type, either FILE or DIRECTORY", required = false, arity = 1) @@ -378,7 +378,7 @@ public class DistinctCommandOptions { @Parameter(names = {"--description"}, description = "Description", required = false, arity = 1) public String description; - @Parameter(names = {"--tags"}, description = "Tags", required = false, arity = 1) + @Parameter(names = {"--tags"}, description = "Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String tags; @Parameter(names = {"--size"}, description = "File size", required = false, arity = 1) @@ -609,19 +609,19 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of file IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list file UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of file names", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; - @Parameter(names = {"--path"}, description = "Comma separated list of paths", required = false, arity = 1) + @Parameter(names = {"--path"}, description = "Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String path; - @Parameter(names = {"--uri", "--input", "-i"}, description = "Comma separated list of uris", required = false, arity = 1) + @Parameter(names = {"--uri", "--input", "-i"}, description = "Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String uri; @Parameter(names = {"--type"}, description = "File type, either FILE or DIRECTORY", required = false, arity = 1) @@ -660,7 +660,7 @@ public class SearchCommandOptions { @Parameter(names = {"--description"}, description = "Description", required = false, arity = 1) public String description; - @Parameter(names = {"--tags"}, description = "Tags", required = false, arity = 1) + @Parameter(names = {"--tags"}, description = "Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String tags; @Parameter(names = {"--size"}, description = "File size", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java index a9e20c70232..d0238597f52 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java @@ -350,13 +350,13 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list individual IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list individual UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list individual names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--family-ids"}, description = "Comma separated list of family ids the individuals may belong to.", required = false, arity = 1) @@ -374,22 +374,22 @@ public class DistinctCommandOptions { @Parameter(names = {"--sex"}, description = "Individual sex", required = false, arity = 1) public String sex; - @Parameter(names = {"--ethnicity"}, description = "Individual ethnicity", required = false, arity = 1) + @Parameter(names = {"--ethnicity"}, description = "Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String ethnicity; @Parameter(names = {"--date-of-birth"}, description = "Individual date of birth", required = false, arity = 1) public String dateOfBirth; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; - @Parameter(names = {"--population-name"}, description = "Population name", required = false, arity = 1) + @Parameter(names = {"--population-name"}, description = "Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String populationName; - @Parameter(names = {"--population-subpopulation"}, description = "Subpopulation name", required = false, arity = 1) + @Parameter(names = {"--population-subpopulation"}, description = "Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String populationSubpopulation; @Parameter(names = {"--karyotypic-sex"}, description = "Individual karyotypic sex", required = false, arity = 1) @@ -457,13 +457,13 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list individual IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list individual UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list individual names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--father"}, description = "Father ID, name or UUID", required = false, arity = 1) @@ -484,19 +484,19 @@ public class SearchCommandOptions { @Parameter(names = {"--date-of-birth"}, description = "Individual date of birth", required = false, arity = 1) public String dateOfBirth; - @Parameter(names = {"--ethnicity"}, description = "Individual ethnicity", required = false, arity = 1) + @Parameter(names = {"--ethnicity"}, description = "Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String ethnicity; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; - @Parameter(names = {"--population-name"}, description = "Population name", required = false, arity = 1) + @Parameter(names = {"--population-name"}, description = "Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String populationName; - @Parameter(names = {"--population-subpopulation"}, description = "Subpopulation name", required = false, arity = 1) + @Parameter(names = {"--population-subpopulation"}, description = "Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String populationSubpopulation; @Parameter(names = {"--karyotypic-sex"}, description = "Individual karyotypic sex", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java index 44eac65bf28..04b6caae03c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java @@ -241,13 +241,13 @@ public class DistinctCommandOptions { @Parameter(names = {"--other-studies"}, description = "Flag indicating the entries being queried can belong to any related study, not just the primary one.", required = false, help = true, arity = 0) public boolean otherStudies = false; - @Parameter(names = {"--id"}, description = "Comma separated list of job IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of job UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--tool-id"}, description = "Tool ID executed by the job", required = false, arity = 1) + @Parameter(names = {"--tool-id"}, description = "Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String toolId; @Parameter(names = {"--tool-type"}, description = "Tool type executed by the job [OPERATION, ANALYSIS]", required = false, arity = 1) @@ -362,13 +362,13 @@ public class SearchCommandOptions { @Parameter(names = {"--other-studies"}, description = "Flag indicating the entries being queried can belong to any related study, not just the primary one.", required = false, help = true, arity = 0) public boolean otherStudies = false; - @Parameter(names = {"--id"}, description = "Comma separated list of job IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of job UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--tool-id"}, description = "Tool ID executed by the job", required = false, arity = 1) + @Parameter(names = {"--tool-id"}, description = "Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String toolId; @Parameter(names = {"--tool-type"}, description = "Tool type executed by the job [OPERATION, ANALYSIS]", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java index 0099fbf2a90..8cfc8fed346 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java @@ -305,7 +305,7 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list sample IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list sample UUIDs up to a maximum of 100", required = false, arity = 1) @@ -356,7 +356,7 @@ public class DistinctCommandOptions { @Parameter(names = {"--collection-method"}, description = "Collection method", required = false, arity = 1) public String collectionMethod; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; @Parameter(names = {"--annotation"}, description = "Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0", required = false, arity = 1) @@ -468,7 +468,7 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list sample IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list sample UUIDs up to a maximum of 100", required = false, arity = 1) @@ -519,7 +519,7 @@ public class SearchCommandOptions { @Parameter(names = {"--collection-method"}, description = "Collection method", required = false, arity = 1) public String collectionMethod; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; @Parameter(names = {"--annotation"}, description = "Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0", required = false, arity = 1) diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 5d46536451d..da576e61ed5 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index 206b0aa2646..e8d0ded651f 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index 8e9baedd284..64aa34c799c 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,6 +1,6 @@ # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -10,37 +10,37 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, members, variableSet, studies, group, study, templateId, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, variableSet, studies, members, group, study, templateId, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, files, members, file, annotationSet, folder, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, members, folder, annotationSet, files, file, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, members, sample, samples, annotationSet, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, annotationSet, sample, samples, members, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, members, individuals, annotationSet, individual, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, individual, individuals, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, members, family, annotationSet, families, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, families, family, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, annotationSet, cohorts, members, cohort, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, interpretation, members, interpretations, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## @@ -75,7 +75,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## GA4GHClient -setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=NULL, ...) +setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...) standardGeneric("ga4ghClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index f0652ba64dd..ae64c192aeb 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -58,7 +58,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretation, members, interpretations, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: @@ -94,10 +94,10 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, memb #' @section Endpoint /{apiVersion}/analysis/clinical/distinct: #' Clinical Analysis distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of Clinical Analysis IDs up to a maximum of 100. + #' @param id Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. #' @param type Clinical Analysis type. - #' @param disorder Clinical Analysis disorder. + #' @param disorder Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param files Clinical Analysis files. #' @param sample Sample associated to the proband or any member of a family. #' @param individual Proband or any member of a family. @@ -126,11 +126,11 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, memb #' @section Endpoint /{apiVersion}/analysis/clinical/interpretation/distinct: #' Interpretation distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of Interpretation IDs up to a maximum of 100. + #' @param id Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of Interpretation UUIDs up to a maximum of 100. #' @param clinicalAnalysisId Clinical Analysis id. #' @param analystId Analyst ID. - #' @param methodName Interpretation method name. + #' @param methodName Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param panels Interpretation panels. #' @param primaryFindings Interpretation primary findings. #' @param secondaryFindings Interpretation secondary findings. @@ -152,11 +152,11 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, memb #' @param skip Number of results to skip. #' @param sort Sort the results. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of Interpretation IDs up to a maximum of 100. + #' @param id Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of Interpretation UUIDs up to a maximum of 100. #' @param clinicalAnalysisId Clinical Analysis id. #' @param analystId Analyst ID. - #' @param methodName Interpretation method name. + #' @param methodName Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param panels Interpretation panels. #' @param primaryFindings Interpretation primary findings. #' @param secondaryFindings Interpretation secondary findings. @@ -484,10 +484,10 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, memb #' @param skip Number of results to skip. #' @param count Get the total number of results matching the query. Deactivated by default. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of Clinical Analysis IDs up to a maximum of 100. + #' @param id Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. #' @param type Clinical Analysis type. - #' @param disorder Clinical Analysis disorder. + #' @param disorder Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param files Clinical Analysis files. #' @param sample Sample associated to the proband or any member of a family. #' @param individual Proband or any member of a family. diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 2bcb87bbbbc..3dbf84870e5 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohorts, members, cohort, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: @@ -97,8 +97,8 @@ setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, #' @section Endpoint /{apiVersion}/cohorts/distinct: #' Cohort distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of cohort IDs up to a maximum of 100. - #' @param name Comma separated list of cohort names up to a maximum of 100. + #' @param id Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param name Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of cohort IDs up to a maximum of 100. #' @param type Cohort type. #' @param creationDate creationDate. @@ -128,7 +128,7 @@ setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param internalStatus Filter by internal status. #' @param status Filter by status. - #' @param phenotypes Comma separated list of phenotype ids or names. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. . #' @param release Release when it was created. @@ -147,8 +147,8 @@ setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, #' @param count Get the total number of results matching the query. Deactivated by default. #' @param flattenAnnotations Flatten the annotations?. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of cohort IDs up to a maximum of 100. - #' @param name Comma separated list of cohort names up to a maximum of 100. + #' @param id Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param name Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of cohort IDs up to a maximum of 100. #' @param type Cohort type. #' @param creationDate creationDate. diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index 5993bbe8de9..c5d4cbc0485 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, annotationSet, families, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, families, family, annotationSet, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: @@ -98,14 +98,14 @@ setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, annota #' @section Endpoint /{apiVersion}/families/distinct: #' Family distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list family IDs up to a maximum of 100. - #' @param name Comma separated list family names up to a maximum of 100. + #' @param id Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param name Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list family UUIDs up to a maximum of 100. #' @param members Comma separated list of family members. #' @param expectedSize Expected size of the family (number of members). #' @param samples Comma separated list of member's samples. - #' @param phenotypes Comma separated list of phenotype ids or names. - #' @param disorders Comma separated list of disorder ids or names. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param deleted Boolean to retrieve deleted entries. @@ -128,14 +128,14 @@ setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, annota #' @param count Get the total number of results matching the query. Deactivated by default. #' @param flattenAnnotations Flatten the annotations?. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list family IDs up to a maximum of 100. - #' @param name Comma separated list family names up to a maximum of 100. + #' @param id Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param name Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list family UUIDs up to a maximum of 100. #' @param members Comma separated list of family members. #' @param expectedSize Expected size of the family (number of members). #' @param samples Comma separated list of member's samples. - #' @param phenotypes Comma separated list of phenotype ids or names. - #' @param disorders Comma separated list of disorder ids or names. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param deleted Boolean to retrieve deleted entries. diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 0ef0d2c83d8..3145654d92d 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +54,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, annotationSet, folder, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, annotationSet, files, file, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: @@ -122,11 +122,11 @@ setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, ann #' @section Endpoint /{apiVersion}/files/distinct: #' File distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of file IDs up to a maximum of 100. + #' @param id Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list file UUIDs up to a maximum of 100. - #' @param name Comma separated list of file names. - #' @param path Comma separated list of paths. - #' @param uri Comma separated list of uris. + #' @param name Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param path Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param uri Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param type File type, either FILE or DIRECTORY. #' @param bioformat Comma separated Bioformat values. For existing Bioformats see files/bioformats. #' @param format Comma separated Format values. For existing Formats see files/formats. @@ -139,7 +139,7 @@ setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, ann #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param description Description. - #' @param tags Tags. + #' @param tags Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param size File size. #' @param sampleIds Comma separated list sample IDs or UUIDs up to a maximum of 100. #' @param jobId Job ID that created the file(s) or folder(s). @@ -207,11 +207,11 @@ setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, ann #' @param count Get the total number of results matching the query. Deactivated by default. #' @param flattenAnnotations Boolean indicating to flatten the annotations. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of file IDs up to a maximum of 100. + #' @param id Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list file UUIDs up to a maximum of 100. - #' @param name Comma separated list of file names. - #' @param path Comma separated list of paths. - #' @param uri Comma separated list of uris. + #' @param name Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param path Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param uri Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param type File type, either FILE or DIRECTORY. #' @param bioformat Comma separated Bioformat values. For existing Bioformats see files/bioformats. #' @param format Comma separated Format values. For existing Formats see files/formats. @@ -224,7 +224,7 @@ setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, ann #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param description Description. - #' @param tags Tags. + #' @param tags Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param size File size. #' @param sampleIds Comma separated list sample IDs or UUIDs up to a maximum of 100. #' @param jobId Job ID that created the file(s) or folder(s). diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index 534e75260ad..7ec25d1cb31 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -31,7 +31,7 @@ #' [*]: Required parameter #' @export -setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, endpointName, params=NULL, ...) { +setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, study, file, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/ga4gh/reads/search: diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 019acd410c2..fa208ff5bf2 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individuals, annotationSet, individual, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, individuals, annotationSet, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: @@ -106,20 +106,20 @@ setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individual #' @section Endpoint /{apiVersion}/individuals/distinct: #' Individual distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list individual IDs up to a maximum of 100. + #' @param id Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list individual UUIDs up to a maximum of 100. - #' @param name Comma separated list individual names up to a maximum of 100. + #' @param name Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param familyIds Comma separated list of family ids the individuals may belong to. #' @param father Father ID, name or UUID. #' @param mother Mother ID, name or UUID. #' @param samples Sample ID, name or UUID. #' @param sex Individual sex. - #' @param ethnicity Individual ethnicity. + #' @param ethnicity Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param dateOfBirth Individual date of birth. - #' @param disorders Comma separated list of disorder ids or names. - #' @param phenotypes Comma separated list of phenotype ids or names. - #' @param populationName Population name. - #' @param populationSubpopulation Subpopulation name. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param populationName Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param populationSubpopulation Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param karyotypicSex Individual karyotypic sex. #' @param lifeStatus Individual life status. #' @param internalStatus Filter by internal status. @@ -144,20 +144,20 @@ setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individual #' @param count Get the total number of results matching the query. Deactivated by default. #' @param flattenAnnotations Flatten the annotations?. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list individual IDs up to a maximum of 100. + #' @param id Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list individual UUIDs up to a maximum of 100. - #' @param name Comma separated list individual names up to a maximum of 100. + #' @param name Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param father Father ID, name or UUID. #' @param mother Mother ID, name or UUID. #' @param samples Sample ID, name or UUID. #' @param familyIds Comma separated list of family ids the individuals may belong to. #' @param sex Individual sex. #' @param dateOfBirth Individual date of birth. - #' @param ethnicity Individual ethnicity. - #' @param disorders Comma separated list of disorder ids or names. - #' @param phenotypes Comma separated list of phenotype ids or names. - #' @param populationName Population name. - #' @param populationSubpopulation Subpopulation name. + #' @param ethnicity Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param populationName Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param populationSubpopulation Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param karyotypicSex Individual karyotypic sex. #' @param lifeStatus Individual life status. #' @param internalStatus Filter by internal status. diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index f85fe4840f7..00c06ed1483 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -40,7 +40,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: @@ -87,9 +87,9 @@ setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpoi #' Job distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. #' @param otherStudies Flag indicating the entries being queried can belong to any related study, not just the primary one. - #' @param id Comma separated list of job IDs up to a maximum of 100. + #' @param id Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of job UUIDs up to a maximum of 100. - #' @param toolId Tool ID executed by the job. + #' @param toolId Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param toolType Tool type executed by the job [OPERATION, ANALYSIS]. #' @param userId User that created the job. #' @param priority Priority of the job. @@ -128,9 +128,9 @@ setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpoi #' @param count Get the total number of results matching the query. Deactivated by default. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. #' @param otherStudies Flag indicating the entries being queried can belong to any related study, not just the primary one. - #' @param id Comma separated list of job IDs up to a maximum of 100. + #' @param id Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of job UUIDs up to a maximum of 100. - #' @param toolId Tool ID executed by the job. + #' @param toolId Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param toolType Tool type executed by the job [OPERATION, ANALYSIS]. #' @param userId User that created the job. #' @param priority Priority of the job. @@ -155,7 +155,7 @@ setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpoi #' @param internalStatus Filter by internal status. #' @param priority Priority of the job. #' @param userId User that created the job. - #' @param toolId Tool ID executed by the job. + #' @param toolId Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. top=fetchOpenCGA(object=OpencgaR, category="jobs", categoryId=NULL, subcategory=NULL, subcategoryId=NULL, action="top", params=params, httpMethod="GET", as.queryParam=NULL, ...), diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index d4de1c866b8..360a9dacb50 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 902a0403f47..f95d93bc801 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index e7d661d3a2c..fe01d294f0b 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -62,17 +62,17 @@ setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpoin #' @section Endpoint /{apiVersion}/panels/distinct: #' Panel distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of panel IDs up to a maximum of 100. + #' @param id Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of panel UUIDs up to a maximum of 100. - #' @param name Comma separated list of panel names up to a maximum of 100. + #' @param name Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param internalStatus Filter by internal status. - #' @param disorders Comma separated list of disorder ids or names. - #' @param variants Comma separated list of variant ids. - #' @param genes Comma separated list of gene ids. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param variants Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param genes Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param source Comma separated list of source ids or names. - #' @param regions Comma separated list of regions. - #' @param categories Comma separated list of category names. - #' @param tags Panel tags. + #' @param regions Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param categories Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param tags Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param deleted Boolean to retrieve deleted entries. #' @param status Filter by status. #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. @@ -103,17 +103,17 @@ setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpoin #' @param skip Number of results to skip. #' @param count Get the total number of results matching the query. Deactivated by default. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of panel IDs up to a maximum of 100. + #' @param id Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of panel UUIDs up to a maximum of 100. - #' @param name Comma separated list of panel names up to a maximum of 100. + #' @param name Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param internalStatus Filter by internal status. - #' @param disorders Comma separated list of disorder ids or names. - #' @param variants Comma separated list of variant ids. - #' @param genes Comma separated list of gene ids. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param variants Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param genes Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param source Comma separated list of source ids or names. - #' @param regions Comma separated list of regions. - #' @param categories Comma separated list of category names. - #' @param tags Panel tags. + #' @param regions Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param categories Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param tags Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param deleted Boolean to retrieve deleted entries. #' @param status Filter by status. #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index b4ab8a5b98e..d9cb522a4e2 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index 89b2d7b5876..8a8d00d9796 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, samples, annotationSet, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, sample, samples, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: @@ -98,7 +98,7 @@ setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, sample #' @section Endpoint /{apiVersion}/samples/distinct: #' Sample distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list sample IDs up to a maximum of 100. + #' @param id Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list sample UUIDs up to a maximum of 100. #' @param somatic Somatic sample. #' @param individualId Individual ID or UUID. @@ -115,7 +115,7 @@ setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, sample #' @param collectionFrom Collection from. #' @param collectionType Collection type. #' @param collectionMethod Collection method. - #' @param phenotypes Comma separated list of phenotype ids or names. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. . #' @param internalRgaStatus Index status of the sample for the Recessive Gene Analysis. Allowed values: ['NOT_INDEXED INDEXED INVALID_PERMISSIONS INVALID_METADATA INVALID'] @@ -157,7 +157,7 @@ setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, sample #' @param includeIndividual Include Individual object as an attribute. #' @param flattenAnnotations Flatten the annotations?. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list sample IDs up to a maximum of 100. + #' @param id Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list sample UUIDs up to a maximum of 100. #' @param somatic Somatic sample. #' @param individualId Individual ID or UUID. @@ -174,7 +174,7 @@ setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, sample #' @param collectionFrom Collection from. #' @param collectionType Collection type. #' @param collectionMethod Collection method. - #' @param phenotypes Comma separated list of phenotype ids or names. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. . #' @param internalRgaStatus Index status of the sample for the Recessive Gene Analysis. Allowed values: ['NOT_INDEXED INDEXED INVALID_PERMISSIONS INVALID_METADATA INVALID'] diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 754fa677dea..84227b71b68 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +46,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, members, variableSet, studies, group, study, templateId, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, variableSet, studies, members, group, study, templateId, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index 7fb54a32ff1..51b6157fe7a 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/login: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 0b7a706cb8f..6d17848726b 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index 2a375bb7b83..df137812b2f 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index 08257cc1a1a..759e68f1b90 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index 32ab712003e..22eeeca0ccd 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -51,7 +51,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -127,10 +127,12 @@ public RestResponse create(ClinicalAnalysisCreateParams data, * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. + * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. * type: Clinical Analysis type. - * disorder: Clinical Analysis disorder. + * disorder: Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * files: Clinical Analysis files. * sample: Sample associated to the proband or any member of a family. * individual: Proband or any member of a family. @@ -166,11 +168,13 @@ public RestResponse distinct(String field, ObjectMap params) throws C * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Interpretation IDs up to a maximum of 100. + * id: Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. * clinicalAnalysisId: Clinical Analysis id. * analystId: Analyst ID. - * methodName: Interpretation method name. + * methodName: Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * panels: Interpretation panels. * primaryFindings: Interpretation primary findings. * secondaryFindings: Interpretation secondary findings. @@ -197,11 +201,13 @@ public RestResponse distinctInterpretation(String field, ObjectMap pa * skip: Number of results to skip. * sort: Sort the results. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Interpretation IDs up to a maximum of 100. + * id: Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. * clinicalAnalysisId: Clinical Analysis id. * analystId: Analyst ID. - * methodName: Interpretation method name. + * methodName: Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * panels: Interpretation panels. * primaryFindings: Interpretation primary findings. * secondaryFindings: Interpretation secondary findings. @@ -614,10 +620,12 @@ public RestResponse summaryRgaVariant(ObjectMap params * skip: Number of results to skip. * count: Get the total number of results matching the query. Deactivated by default. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. + * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. * type: Clinical Analysis type. - * disorder: Clinical Analysis disorder. + * disorder: Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * files: Clinical Analysis files. * sample: Sample associated to the proband or any member of a family. * individual: Proband or any member of a family. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 547601b9329..4afa30f7993 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -144,8 +144,10 @@ public RestResponse create(CohortCreateParams data, ObjectMap params) th * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of cohort IDs up to a maximum of 100. - * name: Comma separated list of cohort names up to a maximum of 100. + * id: Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * name: Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of cohort IDs up to a maximum of 100. * type: Cohort type. * creationDate: creationDate. @@ -182,7 +184,8 @@ public RestResponse distinct(String field, ObjectMap params) throws Clie * modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * internalStatus: Filter by internal status. * status: Filter by status. - * phenotypes: Comma separated list of phenotype ids or names. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * acl: Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: @@ -210,8 +213,10 @@ public RestResponse generate(CohortGenerateParams data, ObjectMap params * count: Get the total number of results matching the query. Deactivated by default. * flattenAnnotations: Flatten the annotations?. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of cohort IDs up to a maximum of 100. - * name: Comma separated list of cohort names up to a maximum of 100. + * id: Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * name: Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of cohort IDs up to a maximum of 100. * type: Cohort type. * creationDate: creationDate. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index ad5ea1a7047..ec146dbae49 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -93,17 +93,27 @@ public RestResponse create(PanelCreateParams data, ObjectMap params) thro * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of panel IDs up to a maximum of 100. + * id: Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of panel UUIDs up to a maximum of 100. - * name: Comma separated list of panel names up to a maximum of 100. + * name: Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * internalStatus: Filter by internal status. - * disorders: Comma separated list of disorder ids or names. - * variants: Comma separated list of variant ids. - * genes: Comma separated list of gene ids. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular + * expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case + * insensitive search. + * variants: Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * genes: Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * source: Comma separated list of source ids or names. - * regions: Comma separated list of regions. - * categories: Comma separated list of category names. - * tags: Panel tags. + * regions: Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * categories: Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * tags: Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + * sensitive, '~/value/i' for case insensitive search. * deleted: Boolean to retrieve deleted entries. * status: Filter by status. * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. @@ -149,17 +159,27 @@ public RestResponse importPanels(PanelImportParams data, ObjectMap params) * skip: Number of results to skip. * count: Get the total number of results matching the query. Deactivated by default. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of panel IDs up to a maximum of 100. + * id: Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of panel UUIDs up to a maximum of 100. - * name: Comma separated list of panel names up to a maximum of 100. + * name: Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * internalStatus: Filter by internal status. - * disorders: Comma separated list of disorder ids or names. - * variants: Comma separated list of variant ids. - * genes: Comma separated list of gene ids. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular + * expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case + * insensitive search. + * variants: Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * genes: Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * source: Comma separated list of source ids or names. - * regions: Comma separated list of regions. - * categories: Comma separated list of category names. - * tags: Panel tags. + * regions: Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * categories: Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * tags: Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + * sensitive, '~/value/i' for case insensitive search. * deleted: Boolean to retrieve deleted entries. * status: Filter by status. * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index d113cbdaf09..cbd554fe8d4 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -145,14 +145,18 @@ public RestResponse create(FamilyCreateParams data, ObjectMap params) th * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list family IDs up to a maximum of 100. - * name: Comma separated list family names up to a maximum of 100. + * id: Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * name: Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list family UUIDs up to a maximum of 100. * members: Comma separated list of family members. * expectedSize: Expected size of the family (number of members). * samples: Comma separated list of member's samples. - * phenotypes: Comma separated list of phenotype ids or names. - * disorders: Comma separated list of disorder ids or names. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * deleted: Boolean to retrieve deleted entries. @@ -184,14 +188,18 @@ public RestResponse distinct(String field, ObjectMap params) throws Clie * count: Get the total number of results matching the query. Deactivated by default. * flattenAnnotations: Flatten the annotations?. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list family IDs up to a maximum of 100. - * name: Comma separated list family names up to a maximum of 100. + * id: Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * name: Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list family UUIDs up to a maximum of 100. * members: Comma separated list of family members. * expectedSize: Expected size of the family (number of members). * samples: Comma separated list of member's samples. - * phenotypes: Comma separated list of phenotype ids or names. - * disorders: Comma separated list of disorder ids or names. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * deleted: Boolean to retrieve deleted entries. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 72be6ed305b..fc31ad2bec2 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -43,7 +43,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -164,11 +164,15 @@ public RestResponse create(FileCreateParams data, ObjectMap params) throws * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of file IDs up to a maximum of 100. + * id: Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list file UUIDs up to a maximum of 100. - * name: Comma separated list of file names. - * path: Comma separated list of paths. - * uri: Comma separated list of uris. + * name: Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * path: Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. + * uri: Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * type: File type, either FILE or DIRECTORY. * bioformat: Comma separated Bioformat values. For existing Bioformats see files/bioformats. * format: Comma separated Format values. For existing Formats see files/formats. @@ -181,7 +185,8 @@ public RestResponse create(FileCreateParams data, ObjectMap params) throws * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * description: Description. - * tags: Tags. + * tags: Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + * sensitive, '~/value/i' for case insensitive search. * size: File size. * sampleIds: Comma separated list sample IDs or UUIDs up to a maximum of 100. * jobId: Job ID that created the file(s) or folder(s). @@ -290,11 +295,15 @@ public RestResponse runPostlink(PostLinkToolParams data, ObjectMap params) * count: Get the total number of results matching the query. Deactivated by default. * flattenAnnotations: Boolean indicating to flatten the annotations. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of file IDs up to a maximum of 100. + * id: Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list file UUIDs up to a maximum of 100. - * name: Comma separated list of file names. - * path: Comma separated list of paths. - * uri: Comma separated list of uris. + * name: Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * path: Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. + * uri: Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * type: File type, either FILE or DIRECTORY. * bioformat: Comma separated Bioformat values. For existing Bioformats see files/bioformats. * format: Comma separated Format values. For existing Formats see files/formats. @@ -307,7 +316,8 @@ public RestResponse runPostlink(PostLinkToolParams data, ObjectMap params) * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * description: Description. - * tags: Tags. + * tags: Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + * sensitive, '~/value/i' for case insensitive search. * size: File size. * sampleIds: Comma separated list sample IDs or UUIDs up to a maximum of 100. * jobId: Job ID that created the file(s) or folder(s). diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index fbb84f972a4..b0afdac763a 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index 5803d125e54..27a9af45ed5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -153,20 +153,27 @@ public RestResponse create(IndividualCreateParams data, ObjectMap pa * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list individual IDs up to a maximum of 100. + * id: Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list individual UUIDs up to a maximum of 100. - * name: Comma separated list individual names up to a maximum of 100. + * name: Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * familyIds: Comma separated list of family ids the individuals may belong to. * father: Father ID, name or UUID. * mother: Mother ID, name or UUID. * samples: Sample ID, name or UUID. * sex: Individual sex. - * ethnicity: Individual ethnicity. + * ethnicity: Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * dateOfBirth: Individual date of birth. - * disorders: Comma separated list of disorder ids or names. - * phenotypes: Comma separated list of phenotype ids or names. - * populationName: Population name. - * populationSubpopulation: Subpopulation name. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * populationName: Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. + * populationSubpopulation: Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * karyotypicSex: Individual karyotypic sex. * lifeStatus: Individual life status. * internalStatus: Filter by internal status. @@ -200,20 +207,27 @@ public RestResponse distinct(String field, ObjectMap params) throws Clie * count: Get the total number of results matching the query. Deactivated by default. * flattenAnnotations: Flatten the annotations?. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list individual IDs up to a maximum of 100. + * id: Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list individual UUIDs up to a maximum of 100. - * name: Comma separated list individual names up to a maximum of 100. + * name: Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * father: Father ID, name or UUID. * mother: Mother ID, name or UUID. * samples: Sample ID, name or UUID. * familyIds: Comma separated list of family ids the individuals may belong to. * sex: Individual sex. * dateOfBirth: Individual date of birth. - * ethnicity: Individual ethnicity. - * disorders: Comma separated list of disorder ids or names. - * phenotypes: Comma separated list of phenotype ids or names. - * populationName: Population name. - * populationSubpopulation: Subpopulation name. + * ethnicity: Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * populationName: Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. + * populationSubpopulation: Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * karyotypicSex: Individual karyotypic sex. * lifeStatus: Individual life status. * internalStatus: Filter by internal status. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index 27245d4011c..f880ed1d600 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -120,9 +120,11 @@ public RestResponse create(JobCreateParams data, ObjectMap params) throws C * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. * otherStudies: Flag indicating the entries being queried can belong to any related study, not just the primary one. - * id: Comma separated list of job IDs up to a maximum of 100. + * id: Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of job UUIDs up to a maximum of 100. - * toolId: Tool ID executed by the job. + * toolId: Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * toolType: Tool type executed by the job [OPERATION, ANALYSIS]. * userId: User that created the job. * priority: Priority of the job. @@ -176,9 +178,11 @@ public RestResponse retry(JobRetryParams data, ObjectMap params) throws Cli * count: Get the total number of results matching the query. Deactivated by default. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. * otherStudies: Flag indicating the entries being queried can belong to any related study, not just the primary one. - * id: Comma separated list of job IDs up to a maximum of 100. + * id: Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of job UUIDs up to a maximum of 100. - * toolId: Tool ID executed by the job. + * toolId: Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * toolType: Tool type executed by the job [OPERATION, ANALYSIS]. * userId: User that created the job. * priority: Priority of the job. @@ -211,7 +215,8 @@ public RestResponse search(ObjectMap params) throws ClientException { * internalStatus: Filter by internal status. * priority: Priority of the job. * userId: User that created the job. - * toolId: Tool ID executed by the job. + * toolId: Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * @return a RestResponse object. * @throws ClientException ClientException if there is any server error. */ diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index c2c015b670d..15ca508dc41 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 47aeec33622..fb3f13b0077 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -32,7 +32,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index d2dd71bc2f3..5399ebea102 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -145,7 +145,8 @@ public RestResponse create(SampleCreateParams data, ObjectMap params) th * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list sample IDs up to a maximum of 100. + * id: Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list sample UUIDs up to a maximum of 100. * somatic: Somatic sample. * individualId: Individual ID or UUID. @@ -162,7 +163,8 @@ public RestResponse create(SampleCreateParams data, ObjectMap params) th * collectionFrom: Collection from. * collectionType: Collection type. * collectionMethod: Collection method. - * phenotypes: Comma separated list of phenotype ids or names. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * acl: Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: @@ -221,7 +223,8 @@ public RestResponse load(String file, ObjectMap params) throws ClientExc * includeIndividual: Include Individual object as an attribute. * flattenAnnotations: Flatten the annotations?. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list sample IDs up to a maximum of 100. + * id: Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list sample UUIDs up to a maximum of 100. * somatic: Somatic sample. * individualId: Individual ID or UUID. @@ -238,7 +241,8 @@ public RestResponse load(String file, ObjectMap params) throws ClientExc * collectionFrom: Collection from. * collectionType: Collection type. * collectionMethod: Collection method. - * phenotypes: Comma separated list of phenotype ids or names. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * acl: Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 53502e91c7e..f5cc56d0d9c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -45,7 +45,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index eda89cb9228..e6c291036f5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index 0d25391978a..0e88f0a112c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index ae6bef9d18d..e0e2f076484 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 26d6d454012..d372e15a01c 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index 33aa92db017..7a1e4809128 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 4434d811346..1054e70f292 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -76,10 +76,12 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular + * expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. * @param {String} [params.type] - Clinical Analysis type. - * @param {String} [params.disorder] - Clinical Analysis disorder. + * @param {String} [params.disorder] - Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.files] - Clinical Analysis files. * @param {String} [params.sample] - Sample associated to the proband or any member of a family. * @param {String} [params.individual] - Proband or any member of a family. @@ -112,11 +114,13 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. * @param {String} [params.analystId] - Analyst ID. - * @param {String} [params.methodName] - Interpretation method name. + * @param {String} [params.methodName] - Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.panels] - Interpretation panels. * @param {String} [params.primaryFindings] - Interpretation primary findings. * @param {String} [params.secondaryFindings] - Interpretation secondary findings. @@ -140,11 +144,13 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {Number} [params.skip] - Number of results to skip. * @param {Boolean} [params.sort] - Sort the results. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. * @param {String} [params.analystId] - Analyst ID. - * @param {String} [params.methodName] - Interpretation method name. + * @param {String} [params.methodName] - Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.panels] - Interpretation panels. * @param {String} [params.primaryFindings] - Interpretation primary findings. * @param {String} [params.secondaryFindings] - Interpretation secondary findings. @@ -513,10 +519,12 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {Boolean} [params.count = "false"] - Get the total number of results matching the query. Deactivated by default. The default * value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular + * expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. * @param {String} [params.type] - Clinical Analysis type. - * @param {String} [params.disorder] - Clinical Analysis disorder. + * @param {String} [params.disorder] - Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.files] - Clinical Analysis files. * @param {String} [params.sample] - Sample associated to the proband or any member of a family. * @param {String} [params.individual] - Proband or any member of a family. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index cb53c5278a3..11d9d5906f6 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -101,8 +101,10 @@ export default class Cohort extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of cohort IDs up to a maximum of 100. * @param {String} [params.type] - Cohort type. * @param {String} [params.creationDate] - creationDate. @@ -135,7 +137,8 @@ export default class Cohort extends OpenCGAParentClass { * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.internalStatus] - Filter by internal status. * @param {String} [params.status] - Filter by status. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {String} [params.acl] - Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. @@ -161,8 +164,10 @@ export default class Cohort extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of cohort IDs up to a maximum of 100. * @param {String} [params.type] - Cohort type. * @param {String} [params.creationDate] - creationDate. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index a4bc253c0bd..1c427e0629f 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -62,17 +62,27 @@ export default class DiseasePanel extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of panel UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.internalStatus] - Filter by internal status. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.variants] - Comma separated list of variant ids. - * @param {String} [params.genes] - Comma separated list of gene ids. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic + * regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive + * search. + * @param {String} [params.variants] - Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.genes] - Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.source] - Comma separated list of source ids or names. - * @param {String} [params.regions] - Comma separated list of regions. - * @param {String} [params.categories] - Comma separated list of category names. - * @param {String} [params.tags] - Panel tags. + * @param {String} [params.regions] - Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.categories] - Comma separated list of category names. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.tags] - Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. * @param {String} [params.status] - Filter by status. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. @@ -112,17 +122,27 @@ export default class DiseasePanel extends OpenCGAParentClass { * @param {Boolean} [params.count = "false"] - Get the total number of results matching the query. Deactivated by default. The default * value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of panel UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.internalStatus] - Filter by internal status. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.variants] - Comma separated list of variant ids. - * @param {String} [params.genes] - Comma separated list of gene ids. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic + * regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive + * search. + * @param {String} [params.variants] - Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.genes] - Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.source] - Comma separated list of source ids or names. - * @param {String} [params.regions] - Comma separated list of regions. - * @param {String} [params.categories] - Comma separated list of category names. - * @param {String} [params.tags] - Panel tags. + * @param {String} [params.regions] - Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.categories] - Comma separated list of category names. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.tags] - Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. * @param {String} [params.status] - Filter by status. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index e971b3b2e81..90d31e15443 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -104,14 +104,18 @@ export default class Family extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list family UUIDs up to a maximum of 100. * @param {String} [params.members] - Comma separated list of family members. * @param {Number} [params.expectedSize] - Expected size of the family (number of members). * @param {String} [params.samples] - Comma separated list of member's samples. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. @@ -140,14 +144,18 @@ export default class Family extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list family UUIDs up to a maximum of 100. * @param {String} [params.members] - Comma separated list of family members. * @param {Number} [params.expectedSize] - Expected size of the family (number of members). * @param {String} [params.samples] - Comma separated list of member's samples. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index b3219c4f08a..d5678f46153 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -112,11 +112,15 @@ export default class File extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list file UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of file names. - * @param {String} [params.path] - Comma separated list of paths. - * @param {String} [params.uri] - Comma separated list of uris. + * @param {String} [params.name] - Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.path] - Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.uri] - Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.type] - File type, either FILE or DIRECTORY. * @param {String} [params.bioformat] - Comma separated Bioformat values. For existing Bioformats see files/bioformats. * @param {String} [params.format] - Comma separated Format values. For existing Formats see files/formats. @@ -129,7 +133,8 @@ export default class File extends OpenCGAParentClass { * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.description] - Description. - * @param {String} [params.tags] - Tags. + * @param {String} [params.tags] - Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' + * for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.size] - File size. * @param {String} [params.sampleIds] - Comma separated list sample IDs or UUIDs up to a maximum of 100. * @param {String} [params.jobId] - Job ID that created the file(s) or folder(s). @@ -220,11 +225,15 @@ export default class File extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Boolean indicating to flatten the annotations. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list file UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of file names. - * @param {String} [params.path] - Comma separated list of paths. - * @param {String} [params.uri] - Comma separated list of uris. + * @param {String} [params.name] - Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.path] - Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.uri] - Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.type] - File type, either FILE or DIRECTORY. * @param {String} [params.bioformat] - Comma separated Bioformat values. For existing Bioformats see files/bioformats. * @param {String} [params.format] - Comma separated Format values. For existing Formats see files/formats. @@ -237,7 +246,8 @@ export default class File extends OpenCGAParentClass { * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.description] - Description. - * @param {String} [params.tags] - Tags. + * @param {String} [params.tags] - Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' + * for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.size] - File size. * @param {String} [params.sampleIds] - Comma separated list sample IDs or UUIDs up to a maximum of 100. * @param {String} [params.jobId] - Job ID that created the file(s) or folder(s). diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index ec01beb21de..52d93be35f7 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index 71eb45dbafd..b66f0fc8aee 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -111,20 +111,27 @@ export default class Individual extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list individual UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.familyIds] - Comma separated list of family ids the individuals may belong to. * @param {String} [params.father] - Father ID, name or UUID. * @param {String} [params.mother] - Mother ID, name or UUID. * @param {String} [params.samples] - Sample ID, name or UUID. * @param {String} [params.sex] - Individual sex. - * @param {String} [params.ethnicity] - Individual ethnicity. + * @param {String} [params.ethnicity] - Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.dateOfBirth] - Individual date of birth. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.populationName] - Population name. - * @param {String} [params.populationSubpopulation] - Subpopulation name. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationName] - Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationSubpopulation] - Subpopulation name. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.karyotypicSex] - Individual karyotypic sex. * @param {String} [params.lifeStatus] - Individual life status. * @param {String} [params.internalStatus] - Filter by internal status. @@ -155,20 +162,27 @@ export default class Individual extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list individual UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.father] - Father ID, name or UUID. * @param {String} [params.mother] - Mother ID, name or UUID. * @param {String} [params.samples] - Sample ID, name or UUID. * @param {String} [params.familyIds] - Comma separated list of family ids the individuals may belong to. * @param {String} [params.sex] - Individual sex. * @param {String} [params.dateOfBirth] - Individual date of birth. - * @param {String} [params.ethnicity] - Individual ethnicity. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.populationName] - Population name. - * @param {String} [params.populationSubpopulation] - Subpopulation name. + * @param {String} [params.ethnicity] - Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationName] - Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationSubpopulation] - Subpopulation name. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.karyotypicSex] - Individual karyotypic sex. * @param {String} [params.lifeStatus] - Individual life status. * @param {String} [params.internalStatus] - Filter by internal status. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index 1e1cc91bc52..8128ce9db7d 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -85,9 +85,11 @@ export default class Job extends OpenCGAParentClass { * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. * @param {Boolean} [params.otherStudies = "false"] - Flag indicating the entries being queried can belong to any related study, not just * the primary one. The default value is false. - * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of job UUIDs up to a maximum of 100. - * @param {String} [params.toolId] - Tool ID executed by the job. + * @param {String} [params.toolId] - Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.toolType] - Tool type executed by the job [OPERATION, ANALYSIS]. * @param {String} [params.userId] - User that created the job. * @param {String} [params.priority] - Priority of the job. @@ -136,9 +138,11 @@ export default class Job extends OpenCGAParentClass { * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. * @param {Boolean} [params.otherStudies = "false"] - Flag indicating the entries being queried can belong to any related study, not just * the primary one. The default value is false. - * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of job UUIDs up to a maximum of 100. - * @param {String} [params.toolId] - Tool ID executed by the job. + * @param {String} [params.toolId] - Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.toolType] - Tool type executed by the job [OPERATION, ANALYSIS]. * @param {String} [params.userId] - User that created the job. * @param {String} [params.priority] - Priority of the job. @@ -168,7 +172,8 @@ export default class Job extends OpenCGAParentClass { * @param {String} [params.internalStatus] - Filter by internal status. * @param {String} [params.priority] - Priority of the job. * @param {String} [params.userId] - User that created the job. - * @param {String} [params.toolId] - Tool ID executed by the job. + * @param {String} [params.toolId] - Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @returns {Promise} Promise object in the form of RestResponse instance. */ top(params) { diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index 24dfe87c63d..96fcc5b6d68 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index e240c25cb46..8c4e02f956e 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index 03c6a5b8d8f..74c71a5206f 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -103,7 +103,8 @@ export default class Sample extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list sample UUIDs up to a maximum of 100. * @param {Boolean} [params.somatic] - Somatic sample. * @param {String} [params.individualId] - Individual ID or UUID. @@ -120,7 +121,8 @@ export default class Sample extends OpenCGAParentClass { * @param {String} [params.collectionFrom] - Collection from. * @param {String} [params.collectionType] - Collection type. * @param {String} [params.collectionMethod] - Collection method. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {String} [params.acl] - Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. @@ -173,7 +175,8 @@ export default class Sample extends OpenCGAParentClass { * @param {Boolean} [params.includeIndividual = "false"] - Include Individual object as an attribute. The default value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list sample UUIDs up to a maximum of 100. * @param {Boolean} [params.somatic] - Somatic sample. * @param {String} [params.individualId] - Individual ID or UUID. @@ -190,7 +193,8 @@ export default class Sample extends OpenCGAParentClass { * @param {String} [params.collectionFrom] - Collection from. * @param {String} [params.collectionType] - Collection type. * @param {String} [params.collectionMethod] - Collection method. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {String} [params.acl] - Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index e99e8c7606b..54186dac4ec 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index bfed2a7bfec..ac91b91b891 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index ae9365d5448..27eb9763570 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index f9837f69e25..192a736a775 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index e982694d126..2a5439b0d00 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index b94f350449a..012e5296968 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index ca4e1438978..6bd79233875 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -86,11 +86,16 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of Clinical Analysis IDs up to a - maximum of 100. + maximum of 100. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. :param str type: Clinical Analysis type. - :param str disorder: Clinical Analysis disorder. + :param str disorder: Clinical Analysis disorder. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str files: Clinical Analysis files. :param str sample: Sample associated to the proband or any member of a family. @@ -133,12 +138,17 @@ def distinct_interpretation(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of Interpretation IDs up to a - maximum of 100. + maximum of 100. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. :param str clinical_analysis_id: Clinical Analysis id. :param str analyst_id: Analyst ID. - :param str method_name: Interpretation method name. + :param str method_name: Interpretation method name. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str panels: Interpretation panels. :param str primary_findings: Interpretation primary findings. :param str secondary_findings: Interpretation secondary findings. @@ -169,12 +179,17 @@ def search_interpretation(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of Interpretation IDs up to a - maximum of 100. + maximum of 100. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. :param str clinical_analysis_id: Clinical Analysis id. :param str analyst_id: Analyst ID. - :param str method_name: Interpretation method name. + :param str method_name: Interpretation method name. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str panels: Interpretation panels. :param str primary_findings: Interpretation primary findings. :param str secondary_findings: Interpretation secondary findings. @@ -606,11 +621,16 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of Clinical Analysis IDs up to a - maximum of 100. + maximum of 100. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. :param str type: Clinical Analysis type. - :param str disorder: Clinical Analysis disorder. + :param str disorder: Clinical Analysis disorder. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str files: Clinical Analysis files. :param str sample: Sample associated to the proband or any member of a family. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index fef4cafa48d..4b1be07e92a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -121,9 +121,13 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of cohort IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str name: Comma separated list of cohort names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str uuid: Comma separated list of cohort IDs up to a maximum of 100. :param str type: Cohort type. @@ -166,6 +170,9 @@ def generate(self, data=None, **options): :param str internal_status: Filter by internal status. :param str status: Filter by status. :param str phenotypes: Comma separated list of phenotype ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. @@ -200,9 +207,13 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of cohort IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str name: Comma separated list of cohort names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str uuid: Comma separated list of cohort IDs up to a maximum of 100. :param str type: Cohort type. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index 8382900c307..a6fe0e432a5 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -67,19 +67,42 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of panel IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list of panel UUIDs up to a maximum of 100. :param str name: Comma separated list of panel names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str internal_status: Filter by internal status. :param str disorders: Comma separated list of disorder ids or names. - :param str variants: Comma separated list of variant ids. - :param str genes: Comma separated list of gene ids. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search.. Also admits basic regular expressions + using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. + :param str variants: Comma separated list of variant ids. Also admits + basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str genes: Comma separated list of gene ids. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str source: Comma separated list of source ids or names. - :param str regions: Comma separated list of regions. - :param str categories: Comma separated list of category names. - :param str tags: Panel tags. + :param str regions: Comma separated list of regions. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str categories: Comma separated list of category names. Also + admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str tags: Panel tags. Also admits basic regular expressions + using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param bool deleted: Boolean to retrieve deleted entries. :param str status: Filter by status. :param str creation_date: Creation date. Format: yyyyMMddHHmmss. @@ -133,19 +156,42 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of panel IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list of panel UUIDs up to a maximum of 100. :param str name: Comma separated list of panel names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str internal_status: Filter by internal status. :param str disorders: Comma separated list of disorder ids or names. - :param str variants: Comma separated list of variant ids. - :param str genes: Comma separated list of gene ids. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search.. Also admits basic regular expressions + using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. + :param str variants: Comma separated list of variant ids. Also admits + basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str genes: Comma separated list of gene ids. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str source: Comma separated list of source ids or names. - :param str regions: Comma separated list of regions. - :param str categories: Comma separated list of category names. - :param str tags: Panel tags. + :param str regions: Comma separated list of regions. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str categories: Comma separated list of category names. Also + admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str tags: Panel tags. Also admits basic regular expressions + using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param bool deleted: Boolean to retrieve deleted entries. :param str status: Filter by status. :param str creation_date: Creation date. Format: yyyyMMddHHmmss. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index 0637f728a08..1d41d4a8488 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -124,8 +124,13 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list family IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str name: Comma separated list family names up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list family UUIDs up to a maximum of 100. :param str members: Comma separated list of family members. @@ -133,7 +138,13 @@ def distinct(self, field, **options): members). :param str samples: Comma separated list of member's samples. :param str phenotypes: Comma separated list of phenotype ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str disorders: Comma separated list of disorder ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str creation_date: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. :param str modification_date: Modification date. Format: @@ -174,8 +185,13 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list family IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str name: Comma separated list family names up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list family UUIDs up to a maximum of 100. :param str members: Comma separated list of family members. @@ -183,7 +199,13 @@ def search(self, **options): members). :param str samples: Comma separated list of member's samples. :param str phenotypes: Comma separated list of phenotype ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str disorders: Comma separated list of disorder ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str creation_date: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. :param str modification_date: Modification date. Format: diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 816cdf83c0b..e3a5a9b8988 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -129,12 +129,23 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of file IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list file UUIDs up to a maximum of 100. - :param str name: Comma separated list of file names. - :param str path: Comma separated list of paths. - :param str uri: Comma separated list of uris. + :param str name: Comma separated list of file names. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str path: Comma separated list of paths. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str uri: Comma separated list of uris. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str type: File type, either FILE or DIRECTORY. :param str bioformat: Comma separated Bioformat values. For existing Bioformats see files/bioformats. @@ -154,7 +165,9 @@ def distinct(self, field, **options): :param str modification_date: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. :param str description: Description. - :param str tags: Tags. + :param str tags: Tags. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str size: File size. :param str sample_ids: Comma separated list sample IDs or UUIDs up to a maximum of 100. @@ -269,12 +282,23 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of file IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list file UUIDs up to a maximum of 100. - :param str name: Comma separated list of file names. - :param str path: Comma separated list of paths. - :param str uri: Comma separated list of uris. + :param str name: Comma separated list of file names. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str path: Comma separated list of paths. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str uri: Comma separated list of uris. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str type: File type, either FILE or DIRECTORY. :param str bioformat: Comma separated Bioformat values. For existing Bioformats see files/bioformats. @@ -294,7 +318,9 @@ def search(self, **options): :param str modification_date: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. :param str description: Description. - :param str tags: Tags. + :param str tags: Tags. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str size: File size. :param str sample_ids: Comma separated list sample IDs or UUIDs up to a maximum of 100. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index 6f62ec62786..0b077f4a7c6 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index 3982f010208..e8213458d7b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -132,23 +132,42 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list individual IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list individual UUIDs up to a maximum of 100. :param str name: Comma separated list individual names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str family_ids: Comma separated list of family ids the individuals may belong to. :param str father: Father ID, name or UUID. :param str mother: Mother ID, name or UUID. :param str samples: Sample ID, name or UUID. :param str sex: Individual sex. - :param str ethnicity: Individual ethnicity. + :param str ethnicity: Individual ethnicity. Also admits basic regular + expressions using the operator '~', i.e. '~{perl-regex}' e.g. + '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str date_of_birth: Individual date of birth. :param str disorders: Comma separated list of disorder ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str phenotypes: Comma separated list of phenotype ids or names. - :param str population_name: Population name. - :param str population_subpopulation: Subpopulation name. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str population_name: Population name. Also admits basic regular + expressions using the operator '~', i.e. '~{perl-regex}' e.g. + '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str population_subpopulation: Subpopulation name. Also admits + basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str karyotypic_sex: Individual karyotypic sex. :param str life_status: Individual life status. :param str internal_status: Filter by internal status. @@ -191,11 +210,15 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list individual IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list individual UUIDs up to a maximum of 100. :param str name: Comma separated list individual names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str father: Father ID, name or UUID. :param str mother: Mother ID, name or UUID. :param str samples: Sample ID, name or UUID. @@ -203,11 +226,26 @@ def search(self, **options): individuals may belong to. :param str sex: Individual sex. :param str date_of_birth: Individual date of birth. - :param str ethnicity: Individual ethnicity. + :param str ethnicity: Individual ethnicity. Also admits basic regular + expressions using the operator '~', i.e. '~{perl-regex}' e.g. + '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str disorders: Comma separated list of disorder ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str phenotypes: Comma separated list of phenotype ids or names. - :param str population_name: Population name. - :param str population_subpopulation: Subpopulation name. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str population_name: Population name. Also admits basic regular + expressions using the operator '~', i.e. '~{perl-regex}' e.g. + '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str population_subpopulation: Subpopulation name. Also admits + basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str karyotypic_sex: Individual karyotypic sex. :param str life_status: Individual life status. :param str internal_status: Filter by internal status. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index 313cf0df796..fd4ac0a9386 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -92,9 +92,15 @@ def distinct(self, field, **options): :param bool other_studies: Flag indicating the entries being queried can belong to any related study, not just the primary one. :param str id: Comma separated list of job IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str uuid: Comma separated list of job UUIDs up to a maximum of 100. - :param str tool_id: Tool ID executed by the job. + :param str tool_id: Tool ID executed by the job. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str tool_type: Tool type executed by the job [OPERATION, ANALYSIS]. :param str user_id: User that created the job. @@ -157,9 +163,15 @@ def search(self, **options): :param bool other_studies: Flag indicating the entries being queried can belong to any related study, not just the primary one. :param str id: Comma separated list of job IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str uuid: Comma separated list of job UUIDs up to a maximum of 100. - :param str tool_id: Tool ID executed by the job. + :param str tool_id: Tool ID executed by the job. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str tool_type: Tool type executed by the job [OPERATION, ANALYSIS]. :param str user_id: User that created the job. @@ -196,7 +208,10 @@ def top(self, **options): :param str internal_status: Filter by internal status. :param str priority: Priority of the job. :param str user_id: User that created the job. - :param str tool_id: Tool ID executed by the job. + :param str tool_id: Tool ID executed by the job. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. """ return self._get(category='jobs', resource='top', **options) diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index 189a5ab62ea..d9f841bb69d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index 0784b20594c..b5eac020645 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index 258189685ef..dbd8d313d8a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -122,6 +122,9 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list sample IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str uuid: Comma separated list sample UUIDs up to a maximum of 100. :param bool somatic: Somatic sample. @@ -143,6 +146,9 @@ def distinct(self, field, **options): :param str collection_type: Collection type. :param str collection_method: Collection method. :param str phenotypes: Comma separated list of phenotype ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. @@ -215,6 +221,9 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list sample IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str uuid: Comma separated list sample UUIDs up to a maximum of 100. :param bool somatic: Somatic sample. @@ -236,6 +245,9 @@ def search(self, **options): :param str collection_type: Collection type. :param str collection_method: Collection method. :param str phenotypes: Comma separated list of phenotype ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 3726c1e0a3a..82c241c0eb2 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index 80ac433566b..e7de326420c 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index 32dfa804648..9e447940a11 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index 4070484d219..87b0d72a7d2 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java index a34b818924a..10cd2f3cdf2 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java @@ -68,9 +68,9 @@ public class ParamConstants { public static final String DISTINCT_FIELD_PARAM = "field"; public static final String DISTINCT_FIELD_DESCRIPTION = "Comma separated list of fields for which to obtain the distinct values"; public static final String PHENOTYPES_PARAM = "phenotypes"; - public static final String PHENOTYPES_DESCRIPTION = "Comma separated list of phenotype ids or names"; + public static final String PHENOTYPES_DESCRIPTION = "Comma separated list of phenotype ids or names" + REGEX_SUPPORT; public static final String DISORDERS_PARAM = "disorders"; - public static final String DISORDERS_DESCRIPTION = "Comma separated list of disorder ids or names"; + public static final String DISORDERS_DESCRIPTION = "Comma separated list of disorder ids or names" + REGEX_SUPPORT; public static final String BODY_PARAM = "body"; public static final String OVERWRITE = "overwrite"; @@ -320,8 +320,8 @@ public class ParamConstants { public static final String INDIVIDUAL_SEX_DESCRIPTION = "Individual sex"; public static final String INDIVIDUAL_ETHNICITY_DESCRIPTION = "Individual ethnicity" + REGEX_SUPPORT; public static final String INDIVIDUAL_DATE_OF_BIRTH_DESCRIPTION = "Individual date of birth"; - public static final String INDIVIDUAL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT; - public static final String INDIVIDUAL_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION + REGEX_SUPPORT; + public static final String INDIVIDUAL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION; + public static final String INDIVIDUAL_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION; public static final String INDIVIDUAL_POPULATION_NAME_DESCRIPTION = "Population name" + REGEX_SUPPORT; public static final String INDIVIDUAL_POPULATION_SUBPOPULATION_DESCRIPTION = "Subpopulation name" + REGEX_SUPPORT; public static final String INDIVIDUAL_KARYOTYPIC_SEX_DESCRIPTION = "Individual karyotypic sex"; @@ -360,8 +360,8 @@ public class ParamConstants { public static final String FAMILY_MEMBERS_DESCRIPTION = "Comma separated list of family members"; public static final String FAMILY_SAMPLES_DESCRIPTION = "Comma separated list of member's samples"; public static final String FAMILY_EXPECTED_SIZE_DESCRIPTION = "Expected size of the family (number of members)"; - public static final String FAMILY_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION + REGEX_SUPPORT; - public static final String FAMILY_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT; + public static final String FAMILY_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION; + public static final String FAMILY_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION; public static final String FAMILY_CREATION_DATE_DESCRIPTION = CREATION_DATE_DESCRIPTION; public static final String FAMILY_MODIFICATION_DATE_DESCRIPTION = MODIFICATION_DATE_DESCRIPTION; public static final String FAMILY_DELETED_DESCRIPTION = DELETED_DESCRIPTION; @@ -1480,7 +1480,7 @@ public class ParamConstants { public static final String FILES_ID_DESCRIPTION = "Comma separated list of file IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String FILES_UUID_DESCRIPTION = "Comma separated list file UUIDs" + UP_TO_100; public static final String SAMPLES_DESCRIPTION = "Comma separated list sample IDs or UUIDs" + UP_TO_100; - public static final String SAMPLES_ID_DESCRIPTION = "Comma separated list sample IDs" + UP_TO_100; + public static final String SAMPLES_ID_DESCRIPTION = "Comma separated list sample IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String SAMPLES_UUID_DESCRIPTION = "Comma separated list sample UUIDs" + UP_TO_100; public static final String INDIVIDUALS_DESCRIPTION = "Comma separated list of individual IDs, names or UUIDs" + UP_TO_100; public static final String INDIVIDUALS_ID_DESCRIPTION = "Comma separated list individual IDs" + UP_TO_100 + REGEX_SUPPORT; From 7e29141346bf4153eff9d13c8f4dbe8de947f237 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 4 Sep 2023 12:31:29 +0200 Subject: [PATCH 23/23] Prepare merge --- 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/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-deps/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 +- 21 files changed, 21 insertions(+), 21 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 260955d38c6..adcb53e2d0e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 4d18a6476ca..b787e5d11d2 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index a0ea06ca14c..fac7d8e548a 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 191a5319867..22a563296b0 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index a9630add90e..de52a8ef4e1 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 508d50cede8..e2d8fc127e4 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index d45f901844c..2d6fd5a8da6 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 0d66c9f3a74..65cebaebdda 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 9d41b4d028d..cafb6d1c2ac 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 - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 89d8c6c9d7e..aa79ec720fd 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 - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 3b2f329ccb0..b97d0472984 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.8.3 + 2.11.0-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 bd7a7c7baa4..97db69b63b9 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 - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index f64c1bc25ba..1c27bd10350 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index a5852716f29..f1f99b70468 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index cbbfa9c0e83..03561e6c93d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 3dc7eedf5dc..c0e60a63db5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 202510b2e48..1ea5e5a91d1 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index bbe30f1aa3b..c9a6b5604a3 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 - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index ab93e1a8071..49b680170d0 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 8f13ebd49ab..caa613c03e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index a91ad02aa54..6cdcc114b77 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis