From e4962c8a9967b6198c81bb8bc3e5541e811ab95c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 27 Oct 2023 15:39:23 +0200 Subject: [PATCH 1/5] CLI: getObjetcJson method params are now category and path --- .../app/cli/main/OpenCgaCompleter.java | 2 +- .../app/cli/main/OpencgaCliOptionsParser.java | 2 +- .../main/executors/AdminCommandExecutor.java | 13 ++--- .../AnalysisAlignmentCommandExecutor.java | 19 +++---- .../AnalysisClinicalCommandExecutor.java | 25 ++++----- .../AnalysisVariantCommandExecutor.java | 49 +++++++++--------- .../executors/CohortsCommandExecutor.java | 13 ++--- .../DiseasePanelsCommandExecutor.java | 9 ++-- .../executors/FamiliesCommandExecutor.java | 11 ++-- .../main/executors/FilesCommandExecutor.java | 19 +++---- .../executors/IndividualsCommandExecutor.java | 11 ++-- .../main/executors/JobsCommandExecutor.java | 9 ++-- .../main/executors/MetaCommandExecutor.java | 1 + .../executors/OpencgaCommandExecutor.java | 30 +++++++++-- ...erationsVariantStorageCommandExecutor.java | 51 ++++++++++--------- .../executors/ProjectsCommandExecutor.java | 5 +- .../executors/SamplesCommandExecutor.java | 11 ++-- .../executors/StudiesCommandExecutor.java | 17 ++++--- .../main/executors/UsersCommandExecutor.java | 7 +-- 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 | 18 +++---- .../src/main/R/R/Clinical-methods.R | 4 +- opencga-client/src/main/R/R/Cohort-methods.R | 4 +- opencga-client/src/main/R/R/Family-methods.R | 4 +- opencga-client/src/main/R/R/File-methods.R | 4 +- opencga-client/src/main/R/R/GA4GH-methods.R | 2 +- .../src/main/R/R/Individual-methods.R | 4 +- opencga-client/src/main/R/R/Job-methods.R | 4 +- 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 | 2 +- opencga-client/src/main/R/R/Project-methods.R | 2 +- opencga-client/src/main/R/R/Sample-methods.R | 4 +- 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 | 4 +- .../client/rest/clients/AlignmentClient.java | 4 +- .../rest/clients/ClinicalAnalysisClient.java | 4 +- .../client/rest/clients/CohortClient.java | 4 +- .../rest/clients/DiseasePanelClient.java | 4 +- .../client/rest/clients/FamilyClient.java | 4 +- .../client/rest/clients/FileClient.java | 4 +- .../client/rest/clients/GA4GHClient.java | 4 +- .../client/rest/clients/IndividualClient.java | 4 +- .../client/rest/clients/JobClient.java | 4 +- .../client/rest/clients/MetaClient.java | 4 +- .../client/rest/clients/ProjectClient.java | 4 +- .../client/rest/clients/SampleClient.java | 4 +- .../client/rest/clients/StudyClient.java | 4 +- .../client/rest/clients/UserClient.java | 4 +- .../client/rest/clients/VariantClient.java | 4 +- .../rest/clients/VariantOperationClient.java | 4 +- opencga-client/src/main/javascript/Admin.js | 2 +- .../src/main/javascript/Alignment.js | 2 +- .../src/main/javascript/ClinicalAnalysis.js | 2 +- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- 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 | 4 +- .../rest_clients/alignment_client.py | 4 +- .../rest_clients/clinical_analysis_client.py | 4 +- .../pyopencga/rest_clients/cohort_client.py | 4 +- .../rest_clients/disease_panel_client.py | 4 +- .../pyopencga/rest_clients/family_client.py | 4 +- .../pyopencga/rest_clients/file_client.py | 4 +- .../pyopencga/rest_clients/ga4gh_client.py | 4 +- .../rest_clients/individual_client.py | 4 +- .../pyopencga/rest_clients/job_client.py | 4 +- .../pyopencga/rest_clients/meta_client.py | 4 +- .../pyopencga/rest_clients/project_client.py | 4 +- .../pyopencga/rest_clients/sample_client.py | 4 +- .../pyopencga/rest_clients/study_client.py | 4 +- .../pyopencga/rest_clients/user_client.py | 4 +- .../pyopencga/rest_clients/variant_client.py | 4 +- .../rest_clients/variant_operation_client.py | 4 +- .../cli/ExecutorsCliRestApiWriter.java | 3 +- 89 files changed, 293 insertions(+), 254 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 ee9f603f739..7d088edef53 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 2015-2023-09-12 OpenCB +* Copyright 2015-2023-10-27 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 832d5638d49..279ccd36197 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 2015-2023-09-12 OpenCB +* Copyright 2015-2023-10-27 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/executors/AdminCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java index a16efb4df47..0ab7c6405dc 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java @@ -48,6 +48,7 @@ */ public class AdminCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "admin"; public AdminCommandOptions adminCommandOptions; public AdminCommandExecutor(AdminCommandOptions adminCommandOptions) throws CatalogAuthenticationException { @@ -138,7 +139,7 @@ private RestResponse installCatalog() throws Exception { installationParams = new InstallationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(installationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/install")); return res; } else if (commandOptions.jsonFile != null) { installationParams = JacksonUtils.getDefaultObjectMapper() @@ -167,7 +168,7 @@ private RestResponse jwtCatalog() throws Exception { jWTParams = new JWTParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(jWTParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/jwt")); return res; } else if (commandOptions.jsonFile != null) { jWTParams = JacksonUtils.getDefaultObjectMapper() @@ -193,7 +194,7 @@ private RestResponse createUsers() throws Exception { userCreateParams = new UserCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(userCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/create")); return res; } else if (commandOptions.jsonFile != null) { userCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -224,7 +225,7 @@ private RestResponse importUsers() throws Exception { userImportParams = new UserImportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(userImportParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/import")); return res; } else if (commandOptions.jsonFile != null) { userImportParams = JacksonUtils.getDefaultObjectMapper() @@ -272,7 +273,7 @@ private RestResponse syncUsers() throws Exception { groupSyncParams = new GroupSyncParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(groupSyncParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/sync")); return res; } else if (commandOptions.jsonFile != null) { groupSyncParams = JacksonUtils.getDefaultObjectMapper() @@ -308,7 +309,7 @@ private RestResponse usersUpdateGroups() throws Exception { userUpdateGroup = new UserUpdateGroup(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(userUpdateGroup)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/{user}/groups/update")); return res; } else if (commandOptions.jsonFile != null) { userUpdateGroup = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java index 328a83daeb4..60c7752ddbe 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java @@ -48,6 +48,7 @@ */ public class AnalysisAlignmentCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "analysisAlignment"; public AnalysisAlignmentCommandOptions analysisAlignmentCommandOptions; public AnalysisAlignmentCommandExecutor(AnalysisAlignmentCommandOptions analysisAlignmentCommandOptions) throws CatalogAuthenticationException { @@ -134,7 +135,7 @@ private RestResponse runBwa() throws Exception { bwaWrapperParams = new BwaWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(bwaWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/bwa/run")); return res; } else if (commandOptions.jsonFile != null) { bwaWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -176,7 +177,7 @@ private RestResponse runCoverageIndex() throws Exception { coverageIndexParams = new CoverageIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(coverageIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/coverage/index/run")); return res; } else if (commandOptions.jsonFile != null) { coverageIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -215,7 +216,7 @@ private RestResponse coverageQcGeneCoverageStatsRun() throws Exception { alignmentGeneCoverageStatsParams = new AlignmentGeneCoverageStatsParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(alignmentGeneCoverageStatsParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/coverage/qc/geneCoverageStats/run")); return res; } else if (commandOptions.jsonFile != null) { alignmentGeneCoverageStatsParams = JacksonUtils.getDefaultObjectMapper() @@ -311,7 +312,7 @@ private RestResponse runDeeptools() throws Exception { deeptoolsWrapperParams = new DeeptoolsWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(deeptoolsWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/deeptools/run")); return res; } else if (commandOptions.jsonFile != null) { deeptoolsWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -350,7 +351,7 @@ private RestResponse runFastqc() throws Exception { fastqcWrapperParams = new FastqcWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fastqcWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/fastqc/run")); return res; } else if (commandOptions.jsonFile != null) { fastqcWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -389,7 +390,7 @@ private RestResponse runIndex() throws Exception { alignmentIndexParams = new AlignmentIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(alignmentIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/index/run")); return res; } else if (commandOptions.jsonFile != null) { alignmentIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -427,7 +428,7 @@ private RestResponse runPicard() throws Exception { picardWrapperParams = new PicardWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(picardWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/picard/run")); return res; } else if (commandOptions.jsonFile != null) { picardWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -466,7 +467,7 @@ private RestResponse runQc() throws Exception { alignmentQcParams = new AlignmentQcParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(alignmentQcParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/qc/run")); return res; } else if (commandOptions.jsonFile != null) { alignmentQcParams = JacksonUtils.getDefaultObjectMapper() @@ -538,7 +539,7 @@ private RestResponse runSamtools() throws Exception { samtoolsWrapperParams = new SamtoolsWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(samtoolsWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/samtools/run")); return res; } else if (commandOptions.jsonFile != null) { samtoolsWrapperParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java index 3039ab1cc68..0bd8b87285e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java @@ -80,6 +80,7 @@ */ public class AnalysisClinicalCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "analysisClinical"; public AnalysisClinicalCommandOptions analysisClinicalCommandOptions; public AnalysisClinicalCommandExecutor(AnalysisClinicalCommandOptions analysisClinicalCommandOptions) throws CatalogAuthenticationException { @@ -217,7 +218,7 @@ private RestResponse updateAcl() throws Exception clinicalAnalysisAclUpdateParams = new ClinicalAnalysisAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(clinicalAnalysisAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { clinicalAnalysisAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -251,7 +252,7 @@ private RestResponse updateClinicalConfiguration() throws Exception { clinicalAnalysisStudyConfiguration = new ClinicalAnalysisStudyConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(clinicalAnalysisStudyConfiguration)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/clinical/configuration/update")); return res; } else if (commandOptions.jsonFile != null) { clinicalAnalysisStudyConfiguration = JacksonUtils.getDefaultObjectMapper() @@ -288,7 +289,7 @@ private RestResponse create() throws Exception { clinicalAnalysisCreateParams = new ClinicalAnalysisCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(clinicalAnalysisCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/create")); return res; } else if (commandOptions.jsonFile != null) { clinicalAnalysisCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -467,7 +468,7 @@ private RestResponse runInterpreterCancerTiering() throws Exception { cancerTieringInterpretationAnalysisParams = new CancerTieringInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cancerTieringInterpretationAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/cancerTiering/run")); return res; } else if (commandOptions.jsonFile != null) { cancerTieringInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -506,7 +507,7 @@ private RestResponse runInterpreterExomiser() throws Exception { exomiserInterpretationAnalysisParams = new ExomiserInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(exomiserInterpretationAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/exomiser/run")); return res; } else if (commandOptions.jsonFile != null) { exomiserInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -543,7 +544,7 @@ private RestResponse runInterpreterTeam() throws Exception { teamInterpretationAnalysisParams = new TeamInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(teamInterpretationAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/team/run")); return res; } else if (commandOptions.jsonFile != null) { teamInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -583,7 +584,7 @@ private RestResponse runInterpreterTiering() throws Exception { tieringInterpretationAnalysisParams = new TieringInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tieringInterpretationAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/tiering/run")); return res; } else if (commandOptions.jsonFile != null) { tieringInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -623,7 +624,7 @@ private RestResponse runInterpreterZetta() throws Exception { zettaInterpretationAnalysisParams = new ZettaInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(zettaInterpretationAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/zetta/run")); return res; } else if (commandOptions.jsonFile != null) { zettaInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -826,7 +827,7 @@ private RestResponse runRgaIndex() throws Exception { rgaAnalysisParams = new RgaAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(rgaAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/rga/index/run")); return res; } else if (commandOptions.jsonFile != null) { rgaAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1166,7 +1167,7 @@ private RestResponse update() throws Exception { clinicalAnalysisUpdateParams = new ClinicalAnalysisUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(clinicalAnalysisUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalyses}/update")); return res; } else if (commandOptions.jsonFile != null) { clinicalAnalysisUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -1241,7 +1242,7 @@ private RestResponse createInterpretation() throws Exception { interpretationCreateParams = new InterpretationCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(interpretationCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create")); return res; } else if (commandOptions.jsonFile != null) { interpretationCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -1331,7 +1332,7 @@ private RestResponse updateInterpretation() throws Exception { interpretationUpdateParams = new InterpretationUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(interpretationUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update")); return res; } else if (commandOptions.jsonFile != null) { interpretationUpdateParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java index 601ea3739bf..418b0c3ac40 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java @@ -76,6 +76,7 @@ */ public class AnalysisVariantCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "analysisVariant"; public AnalysisVariantCommandOptions analysisVariantCommandOptions; public AnalysisVariantCommandExecutor(AnalysisVariantCommandOptions analysisVariantCommandOptions) throws CatalogAuthenticationException { @@ -315,7 +316,7 @@ private RestResponse runCircos() throws Exception { circosAnalysisParams = new CircosAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(circosAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/circos/run")); return res; } else if (commandOptions.jsonFile != null) { circosAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -384,7 +385,7 @@ private RestResponse runCohortStats() throws Exception { cohortVariantStatsAnalysisParams = new CohortVariantStatsAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cohortVariantStatsAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/cohort/stats/run")); return res; } else if (commandOptions.jsonFile != null) { cohortVariantStatsAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -425,7 +426,7 @@ private RestResponse runExomiser() throws Exception { exomiserWrapperParams = new ExomiserWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(exomiserWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/exomiser/run")); return res; } else if (commandOptions.jsonFile != null) { exomiserWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -466,7 +467,7 @@ private RestResponse runExport() throws Exception { variantExportParams = new VariantExportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantExportParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/export/run")); return res; } else if (commandOptions.jsonFile != null) { variantExportParams = JacksonUtils.getDefaultObjectMapper() @@ -607,7 +608,7 @@ private RestResponse runFamilyQc() throws Exception { familyQcAnalysisParams = new FamilyQcAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(familyQcAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/family/qc/run")); return res; } else if (commandOptions.jsonFile != null) { familyQcAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -667,7 +668,7 @@ private RestResponse runGatk() throws Exception { gatkWrapperParams = new GatkWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(gatkWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/gatk/run")); return res; } else if (commandOptions.jsonFile != null) { gatkWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -706,7 +707,7 @@ private RestResponse runGenomePlot() throws Exception { genomePlotAnalysisParams = new GenomePlotAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(genomePlotAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/genomePlot/run")); return res; } else if (commandOptions.jsonFile != null) { genomePlotAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -747,7 +748,7 @@ private RestResponse runGwas() throws Exception { gwasAnalysisParams = new GwasAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(gwasAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/gwas/run")); return res; } else if (commandOptions.jsonFile != null) { gwasAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -795,7 +796,7 @@ private RestResponse runHrDetect() throws Exception { hRDetectAnalysisParams = new HRDetectAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(hRDetectAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/hrDetect/run")); return res; } else if (commandOptions.jsonFile != null) { hRDetectAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -844,7 +845,7 @@ private RestResponse runIndex() throws Exception { variantIndexParams = new VariantIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/index/run")); return res; } else if (commandOptions.jsonFile != null) { variantIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -909,7 +910,7 @@ private RestResponse runIndividualQc() throws Exception { individualQcAnalysisParams = new IndividualQcAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(individualQcAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/individual/qc/run")); return res; } else if (commandOptions.jsonFile != null) { individualQcAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -949,7 +950,7 @@ private RestResponse runInferredSex() throws Exception { inferredSexAnalysisParams = new InferredSexAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(inferredSexAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/inferredSex/run")); return res; } else if (commandOptions.jsonFile != null) { inferredSexAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1022,7 +1023,7 @@ private RestResponse runKnockout() throws Exception { knockoutAnalysisParams = new KnockoutAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(knockoutAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/knockout/run")); return res; } else if (commandOptions.jsonFile != null) { knockoutAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1068,7 +1069,7 @@ private RestResponse runMendelianError() throws Exception { mendelianErrorAnalysisParams = new MendelianErrorAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(mendelianErrorAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/mendelianError/run")); return res; } else if (commandOptions.jsonFile != null) { mendelianErrorAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1161,7 +1162,7 @@ private RestResponse runMutationalSignature() throws Exception { mutationalSignatureAnalysisParams = new MutationalSignatureAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(mutationalSignatureAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/mutationalSignature/run")); return res; } else if (commandOptions.jsonFile != null) { mutationalSignatureAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1213,7 +1214,7 @@ private RestResponse runPlink() throws Exception { plinkWrapperParams = new PlinkWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(plinkWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/plink/run")); return res; } else if (commandOptions.jsonFile != null) { plinkWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -1341,7 +1342,7 @@ private RestResponse runRelatedness() throws Exception { relatednessAnalysisParams = new RelatednessAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(relatednessAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/relatedness/run")); return res; } else if (commandOptions.jsonFile != null) { relatednessAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1382,7 +1383,7 @@ private RestResponse runRvtests() throws Exception { rvtestsWrapperParams = new RvtestsWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(rvtestsWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/rvtests/run")); return res; } else if (commandOptions.jsonFile != null) { rvtestsWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -1456,7 +1457,7 @@ private RestResponse runSampleEligibility() throws Exception { sampleEligibilityAnalysisParams = new SampleEligibilityAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleEligibilityAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/eligibility/run")); return res; } else if (commandOptions.jsonFile != null) { sampleEligibilityAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1495,7 +1496,7 @@ private RestResponse runSampleQc() throws Exception { sampleQcAnalysisParams = new SampleQcAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleQcAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/qc/run")); return res; } else if (commandOptions.jsonFile != null) { sampleQcAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1596,7 +1597,7 @@ private RestResponse runSample() throws Exception { sampleVariantFilterParams = new SampleVariantFilterParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleVariantFilterParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/run")); return res; } else if (commandOptions.jsonFile != null) { sampleVariantFilterParams = JacksonUtils.getDefaultObjectMapper() @@ -1690,7 +1691,7 @@ private RestResponse runSampleStats() throws Exception { sampleVariantStatsAnalysisParams = new SampleVariantStatsAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleVariantStatsAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/stats/run")); return res; } else if (commandOptions.jsonFile != null) { sampleVariantStatsAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1763,7 +1764,7 @@ private RestResponse runStatsExport() throws Exception { variantStatsExportParams = new VariantStatsExportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStatsExportParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/stats/export/run")); return res; } else if (commandOptions.jsonFile != null) { variantStatsExportParams = JacksonUtils.getDefaultObjectMapper() @@ -1804,7 +1805,7 @@ private RestResponse runStats() throws Exception { variantStatsAnalysisParams = new VariantStatsAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStatsAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/stats/run")); return res; } else if (commandOptions.jsonFile != null) { variantStatsAnalysisParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java index 92677f27fa4..4767a83173c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java @@ -50,6 +50,7 @@ */ public class CohortsCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "cohorts"; public CohortsCommandOptions cohortsCommandOptions; public CohortsCommandExecutor(CohortsCommandOptions cohortsCommandOptions) throws CatalogAuthenticationException { @@ -129,7 +130,7 @@ private RestResponse updateAcl() throws Exception { cohortAclUpdateParams = new CohortAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cohortAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { cohortAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -190,7 +191,7 @@ private RestResponse loadAnnotationSets() throws Exception { tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tsvAnnotationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/annotationSets/load")); return res; } else if (commandOptions.jsonFile != null) { tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper() @@ -228,7 +229,7 @@ private RestResponse create() throws Exception { cohortCreateParams = new CohortCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cohortCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/create")); return res; } else if (commandOptions.jsonFile != null) { cohortCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -314,7 +315,7 @@ private RestResponse generate() throws Exception { cohortGenerateParams = new CohortGenerateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cohortGenerateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/generate")); return res; } else if (commandOptions.jsonFile != null) { cohortGenerateParams = JacksonUtils.getDefaultObjectMapper() @@ -441,7 +442,7 @@ private RestResponse update() throws Exception { cohortUpdateParams = new CohortUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cohortUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/{cohorts}/update")); return res; } else if (commandOptions.jsonFile != null) { cohortUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -484,7 +485,7 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(objectMap)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/{cohort}/annotationSets/{annotationSet}/annotations/update")); return res; } else if (commandOptions.jsonFile != null) { objectMap = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java index 3e05c22aa5f..5c6446b45e4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java @@ -44,6 +44,7 @@ */ public class DiseasePanelsCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "diseasePanels"; public DiseasePanelsCommandOptions diseasePanelsCommandOptions; public DiseasePanelsCommandExecutor(DiseasePanelsCommandOptions diseasePanelsCommandOptions) throws CatalogAuthenticationException { @@ -114,7 +115,7 @@ private RestResponse updateAcl() throws Exception { panelAclUpdateParams = new PanelAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(panelAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { panelAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -151,7 +152,7 @@ private RestResponse create() throws Exception { panelCreateParams = new PanelCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(panelCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/create")); return res; } else if (commandOptions.jsonFile != null) { panelCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -230,7 +231,7 @@ private RestResponse importPanels() throws Exception { panelImportParams = new PanelImportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(panelImportParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/import")); return res; } else if (commandOptions.jsonFile != null) { panelImportParams = JacksonUtils.getDefaultObjectMapper() @@ -352,7 +353,7 @@ private RestResponse update() throws Exception { panelUpdateParams = new PanelUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(panelUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/{panels}/update")); return res; } else if (commandOptions.jsonFile != null) { panelUpdateParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java index 35e1596aba4..60a56535f4a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java @@ -50,6 +50,7 @@ */ public class FamiliesCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "families"; public FamiliesCommandOptions familiesCommandOptions; public FamiliesCommandExecutor(FamiliesCommandOptions familiesCommandOptions) throws CatalogAuthenticationException { @@ -127,7 +128,7 @@ private RestResponse updateAcl() throws Exception { familyAclUpdateParams = new FamilyAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(familyAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { familyAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -192,7 +193,7 @@ private RestResponse loadAnnotationSets() throws Exception { tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tsvAnnotationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/annotationSets/load")); return res; } else if (commandOptions.jsonFile != null) { tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper() @@ -229,7 +230,7 @@ private RestResponse create() throws Exception { familyCreateParams = new FamilyCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(familyCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/create")); return res; } else if (commandOptions.jsonFile != null) { familyCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -393,7 +394,7 @@ private RestResponse update() throws Exception { familyUpdateParams = new FamilyUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(familyUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/{families}/update")); return res; } else if (commandOptions.jsonFile != null) { familyUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -437,7 +438,7 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(objectMap)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/{family}/annotationSets/{annotationSet}/annotations/update")); return res; } else if (commandOptions.jsonFile != null) { objectMap = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java index 039e0d536e3..b4cfc6fdb9f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java @@ -96,6 +96,7 @@ */ public class FilesCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "files"; public FilesCommandOptions filesCommandOptions; public FilesCommandExecutor(FilesCommandOptions filesCommandOptions) throws CatalogAuthenticationException { @@ -220,7 +221,7 @@ private RestResponse updateAcl() throws Exception { fileAclUpdateParams = new FileAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { fileAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -290,7 +291,7 @@ private RestResponse loadAnnotationSets() throws Exception { tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tsvAnnotationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/annotationSets/load")); return res; } else if (commandOptions.jsonFile != null) { tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper() @@ -331,7 +332,7 @@ private RestResponse create() throws Exception { fileCreateParams = new FileCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/create")); return res; } else if (commandOptions.jsonFile != null) { fileCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -427,7 +428,7 @@ private RestResponse fetch() throws Exception { fileFetch = new FileFetch(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileFetch)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/fetch")); return res; } else if (commandOptions.jsonFile != null) { fileFetch = JacksonUtils.getDefaultObjectMapper() @@ -469,7 +470,7 @@ private RestResponse link() throws Exception { fileLinkParams = new FileLinkParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileLinkParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/link")); return res; } else if (commandOptions.jsonFile != null) { fileLinkParams = JacksonUtils.getDefaultObjectMapper() @@ -515,7 +516,7 @@ private RestResponse runLink() throws Exception { fileLinkToolParams = new FileLinkToolParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileLinkToolParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/link/run")); return res; } else if (commandOptions.jsonFile != null) { fileLinkToolParams = JacksonUtils.getDefaultObjectMapper() @@ -557,7 +558,7 @@ private RestResponse runPostlink() throws Exception { postLinkToolParams = new PostLinkToolParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(postLinkToolParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/postlink/run")); return res; } else if (commandOptions.jsonFile != null) { postLinkToolParams = JacksonUtils.getDefaultObjectMapper() @@ -723,7 +724,7 @@ private RestResponse update() throws Exception { fileUpdateParams = new FileUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/{files}/update")); return res; } else if (commandOptions.jsonFile != null) { fileUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -790,7 +791,7 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception { objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(objectMap)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/{file}/annotationSets/{annotationSet}/annotations/update")); return res; } else if (commandOptions.jsonFile != null) { objectMap = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java index 86fcc2f8d58..0675de1255f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java @@ -56,6 +56,7 @@ */ public class IndividualsCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "individuals"; public IndividualsCommandOptions individualsCommandOptions; public IndividualsCommandExecutor(IndividualsCommandOptions individualsCommandOptions) throws CatalogAuthenticationException { @@ -136,7 +137,7 @@ private RestResponse updateAcl() throws Exception { individualAclUpdateParams = new IndividualAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(individualAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { individualAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -207,7 +208,7 @@ private RestResponse loadAnnotationSets() throws Exception { tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tsvAnnotationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/annotationSets/load")); return res; } else if (commandOptions.jsonFile != null) { tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper() @@ -244,7 +245,7 @@ private RestResponse create() throws Exception { individualCreateParams = new IndividualCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(individualCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/create")); return res; } else if (commandOptions.jsonFile != null) { individualCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -449,7 +450,7 @@ private RestResponse update() throws Exception { individualUpdateParams = new IndividualUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(individualUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/{individuals}/update")); return res; } else if (commandOptions.jsonFile != null) { individualUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -519,7 +520,7 @@ private RestResponse updateAnnotationSetsAnnotations() throws Except objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(objectMap)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/{individual}/annotationSets/{annotationSet}/annotations/update")); return res; } else if (commandOptions.jsonFile != null) { objectMap = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java index 93723bdc05e..846c568724e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java @@ -67,6 +67,7 @@ */ public class JobsCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "jobs"; public JobsCommandOptions jobsCommandOptions; public JobsCommandExecutor(JobsCommandOptions jobsCommandOptions) throws CatalogAuthenticationException { @@ -142,7 +143,7 @@ private RestResponse updateAcl() throws Exception { jobAclUpdateParams = new JobAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(jobAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { jobAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -207,7 +208,7 @@ private RestResponse create() throws Exception { jobCreateParams = new JobCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(jobCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/create")); return res; } else if (commandOptions.jsonFile != null) { jobCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -294,7 +295,7 @@ private RestResponse retry() throws Exception { jobRetryParams = new JobRetryParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(jobRetryParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/retry")); return res; } else if (commandOptions.jsonFile != null) { jobRetryParams = JacksonUtils.getDefaultObjectMapper() @@ -430,7 +431,7 @@ private RestResponse update() throws Exception { jobUpdateParams = new JobUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(jobUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/{jobs}/update")); return res; } else if (commandOptions.jsonFile != null) { jobUpdateParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java index 3f8448898be..0cc03b91ef7 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java @@ -37,6 +37,7 @@ */ public class MetaCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "meta"; public MetaCommandOptions metaCommandOptions; public MetaCommandExecutor(MetaCommandOptions metaCommandOptions) throws CatalogAuthenticationException { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java index 8360af46f00..fc2357c14ad 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java @@ -17,11 +17,11 @@ package org.opencb.opencga.app.cli.main.executors; import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.lang3.StringUtils; import org.opencb.commons.datastore.core.ObjectMap; -import org.opencb.commons.utils.DataModelsUtils; import org.opencb.opencga.app.cli.CommandExecutor; import org.opencb.opencga.app.cli.GeneralCliOptions; import org.opencb.opencga.app.cli.main.io.*; @@ -36,6 +36,9 @@ import org.opencb.opencga.core.models.user.AuthenticationResponse; import org.opencb.opencga.core.response.QueryType; import org.opencb.opencga.core.response.RestResponse; +import org.opencb.opencga.server.generator.models.RestCategory; +import org.opencb.opencga.server.generator.models.RestEndpoint; +import org.opencb.opencga.server.generator.models.RestParameter; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -221,11 +224,30 @@ public OpencgaCommandExecutor setOpenCGAClient(OpenCGAClient openCGAClient) { return this; } - public String getObjectAsJSON(Object o) throws Exception { - String jsonInString = "Data model not found."; + public String getObjectAsJSON(String objectCategory, String objectPath) throws Exception { + String jsonInString = ""; try { - jsonInString = DataModelsUtils.dataModelToJsonString(o.getClass()); + ObjectMap queryParams = new ObjectMap(); + queryParams.putIfNotEmpty("category", String.valueOf(objectCategory)); + RestResponse response = openCGAClient.getMetaClient().api(queryParams); + ObjectMapper jsonObjectMapper = new ObjectMapper(); + for (List list : response.getResponses().get(0).getResults()) { + List categories = jsonObjectMapper.convertValue(list, new TypeReference>() {}); + for (RestCategory category : categories) { + for (RestEndpoint endpoint: category.getEndpoints()){ + if(objectPath.equals(endpoint.getPath())){ + for (RestParameter parameter:endpoint.getParameters()){ + //jsonInString += parameter.getName()+":"+parameter.getAllowedValues()+"\n"; + jsonInString += parameter.toString()+"\n"; + } + // + } + } + } + } + // jsonInString = DataModelsUtils.dataModelToJsonString(o.getClass()); } catch (Exception e) { + jsonInString = "Data model not found."; CommandLineUtils.error(e); } return jsonInString; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java index 78ed32b92dc..7e1faf04dfd 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java @@ -61,6 +61,7 @@ */ public class OperationsVariantStorageCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "operationsVariantStorage"; public OperationsVariantStorageCommandOptions operationsVariantStorageCommandOptions; public OperationsVariantStorageCommandExecutor(OperationsVariantStorageCommandOptions operationsVariantStorageCommandOptions) throws CatalogAuthenticationException { @@ -187,7 +188,7 @@ private RestResponse configureCellbase() throws Exception { cellBaseConfiguration = new CellBaseConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cellBaseConfiguration)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/cellbase/configure")); return res; } else if (commandOptions.jsonFile != null) { cellBaseConfiguration = JacksonUtils.getDefaultObjectMapper() @@ -227,7 +228,7 @@ private RestResponse aggregateVariant() throws Exception { variantAggregateParams = new VariantAggregateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantAggregateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/aggregate")); return res; } else if (commandOptions.jsonFile != null) { variantAggregateParams = JacksonUtils.getDefaultObjectMapper() @@ -282,7 +283,7 @@ private RestResponse indexVariantAnnotation() throws Exception { variantAnnotationIndexParams = new VariantAnnotationIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantAnnotationIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/annotation/index")); return res; } else if (commandOptions.jsonFile != null) { variantAnnotationIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -324,7 +325,7 @@ private RestResponse saveVariantAnnotation() throws Exception { variantAnnotationSaveParams = new VariantAnnotationSaveParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantAnnotationSaveParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/annotation/save")); return res; } else if (commandOptions.jsonFile != null) { variantAnnotationSaveParams = JacksonUtils.getDefaultObjectMapper() @@ -358,7 +359,7 @@ private RestResponse configureVariant() throws Exception { variantConfigureParams = new VariantConfigureParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantConfigureParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/configure")); return res; } else if (commandOptions.jsonFile != null) { variantConfigureParams = JacksonUtils.getDefaultObjectMapper() @@ -395,7 +396,7 @@ private RestResponse deleteVariant() throws Exception { variantFileDeleteParams = new VariantFileDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantFileDeleteParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/delete")); return res; } else if (commandOptions.jsonFile != null) { variantFileDeleteParams = JacksonUtils.getDefaultObjectMapper() @@ -433,7 +434,7 @@ private RestResponse aggregateVariantFamily() throws Exception { variantAggregateFamilyParams = new VariantAggregateFamilyParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantAggregateFamilyParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/family/aggregate")); return res; } else if (commandOptions.jsonFile != null) { variantAggregateFamilyParams = JacksonUtils.getDefaultObjectMapper() @@ -472,7 +473,7 @@ private RestResponse indexVariantFamily() throws Exception { variantFamilyIndexParams = new VariantFamilyIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantFamilyIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/family/index")); return res; } else if (commandOptions.jsonFile != null) { variantFamilyIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -512,7 +513,7 @@ private RestResponse indexVariant() throws Exception { variantIndexParams = new VariantIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/index")); return res; } else if (commandOptions.jsonFile != null) { variantIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -577,7 +578,7 @@ private RestResponse launcherVariantIndex() throws Exception { variantFileIndexJobLauncherParams = new VariantFileIndexJobLauncherParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantFileIndexJobLauncherParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/index/launcher")); return res; } else if (commandOptions.jsonFile != null) { variantFileIndexJobLauncherParams = JacksonUtils.getDefaultObjectMapper() @@ -644,7 +645,7 @@ private RestResponse runVariantJulie() throws Exception { julieParams = new JulieParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(julieParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/julie/run")); return res; } else if (commandOptions.jsonFile != null) { julieParams = JacksonUtils.getDefaultObjectMapper() @@ -679,7 +680,7 @@ private RestResponse repairVariantMetadata() throws Exception { variantStorageMetadataRepairToolParams = new VariantStorageMetadataRepairToolParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStorageMetadataRepairToolParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/metadata/repair")); return res; } else if (commandOptions.jsonFile != null) { variantStorageMetadataRepairToolParams = JacksonUtils.getDefaultObjectMapper() @@ -717,7 +718,7 @@ private RestResponse synchronizeVariantMetadata() throws Exception { variantStorageMetadataSynchronizeParams = new VariantStorageMetadataSynchronizeParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStorageMetadataSynchronizeParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/metadata/synchronize")); return res; } else if (commandOptions.jsonFile != null) { variantStorageMetadataSynchronizeParams = JacksonUtils.getDefaultObjectMapper() @@ -751,7 +752,7 @@ private RestResponse pruneVariant() throws Exception { variantPruneParams = new VariantPruneParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantPruneParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/prune")); return res; } else if (commandOptions.jsonFile != null) { variantPruneParams = JacksonUtils.getDefaultObjectMapper() @@ -790,7 +791,7 @@ private RestResponse deleteVariantSample() throws Exception { variantSampleDeleteParams = new VariantSampleDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantSampleDeleteParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/sample/delete")); return res; } else if (commandOptions.jsonFile != null) { variantSampleDeleteParams = JacksonUtils.getDefaultObjectMapper() @@ -829,7 +830,7 @@ private RestResponse indexVariantSample() throws Exception { variantSecondarySampleIndexParams = new VariantSecondarySampleIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantSecondarySampleIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/sample/index")); return res; } else if (commandOptions.jsonFile != null) { variantSecondarySampleIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -867,7 +868,7 @@ private RestResponse variantSampleIndexConfigure() throws Exception { sampleIndexConfiguration = new SampleIndexConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleIndexConfiguration)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/sample/index/configure")); return res; } else if (commandOptions.jsonFile != null) { sampleIndexConfiguration = JacksonUtils.getDefaultObjectMapper() @@ -918,7 +919,7 @@ private RestResponse indexVariantScore() throws Exception { variantScoreIndexParams = new VariantScoreIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantScoreIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/score/index")); return res; } else if (commandOptions.jsonFile != null) { variantScoreIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -961,7 +962,7 @@ private RestResponse variantSecondaryAnnotationIndex() throws Exception { variantSecondaryAnnotationIndexParams = new VariantSecondaryAnnotationIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantSecondaryAnnotationIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondary/annotation/index")); return res; } else if (commandOptions.jsonFile != null) { variantSecondaryAnnotationIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -1000,7 +1001,7 @@ private RestResponse variantSecondarySampleIndex() throws Exception { variantSecondarySampleIndexParams = new VariantSecondarySampleIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantSecondarySampleIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondary/sample/index")); return res; } else if (commandOptions.jsonFile != null) { variantSecondarySampleIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -1038,7 +1039,7 @@ private RestResponse configureVariantSecondarySampleIndex() throws Exceptio sampleIndexConfiguration = new SampleIndexConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleIndexConfiguration)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondary/sample/index/configure")); return res; } else if (commandOptions.jsonFile != null) { sampleIndexConfiguration = JacksonUtils.getDefaultObjectMapper() @@ -1069,7 +1070,7 @@ private RestResponse secondaryIndexVariant() throws Exception { variantSecondaryAnnotationIndexParams = new VariantSecondaryAnnotationIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantSecondaryAnnotationIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondaryIndex")); return res; } else if (commandOptions.jsonFile != null) { variantSecondaryAnnotationIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -1127,7 +1128,7 @@ private RestResponse deleteVariantStats() throws Exception { variantStatsDeleteParams = new VariantStatsDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStatsDeleteParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/stats/delete")); return res; } else if (commandOptions.jsonFile != null) { variantStatsDeleteParams = JacksonUtils.getDefaultObjectMapper() @@ -1165,7 +1166,7 @@ private RestResponse indexVariantStats() throws Exception { variantStatsIndexParams = new VariantStatsIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStatsIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/stats/index")); return res; } else if (commandOptions.jsonFile != null) { variantStatsIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -1207,7 +1208,7 @@ private RestResponse deleteVariantStudy() throws Exception { variantStudyDeleteParams = new VariantStudyDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStudyDeleteParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/study/delete")); return res; } else if (commandOptions.jsonFile != null) { variantStudyDeleteParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java index 2ed3593e612..98bb7eb2814 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java @@ -42,6 +42,7 @@ */ public class ProjectsCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "projects"; public ProjectsCommandOptions projectsCommandOptions; public ProjectsCommandExecutor(ProjectsCommandOptions projectsCommandOptions) throws CatalogAuthenticationException { @@ -105,7 +106,7 @@ private RestResponse create() throws Exception { projectCreateParams = new ProjectCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(projectCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/projects/create")); return res; } else if (commandOptions.jsonFile != null) { projectCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -227,7 +228,7 @@ private RestResponse update() throws Exception { projectUpdateParams = new ProjectUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(projectUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/projects/{project}/update")); return res; } else if (commandOptions.jsonFile != null) { projectUpdateParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java index a88c8330a26..7d0ebf47cc8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java @@ -55,6 +55,7 @@ */ public class SamplesCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "samples"; public SamplesCommandOptions samplesCommandOptions; public SamplesCommandExecutor(SamplesCommandOptions samplesCommandOptions) throws CatalogAuthenticationException { @@ -134,7 +135,7 @@ private RestResponse updateAcl() throws Exception { sampleAclUpdateParams = new SampleAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { sampleAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -202,7 +203,7 @@ private RestResponse loadAnnotationSets() throws Exception { tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tsvAnnotationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/annotationSets/load")); return res; } else if (commandOptions.jsonFile != null) { tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper() @@ -238,7 +239,7 @@ private RestResponse create() throws Exception { sampleCreateParams = new SampleCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/create")); return res; } else if (commandOptions.jsonFile != null) { sampleCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -476,7 +477,7 @@ private RestResponse update() throws Exception { sampleUpdateParams = new SampleUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/{samples}/update")); return res; } else if (commandOptions.jsonFile != null) { sampleUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -536,7 +537,7 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(objectMap)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/{sample}/annotationSets/{annotationSet}/annotations/update")); return res; } else if (commandOptions.jsonFile != null) { objectMap = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java index 944262e77f1..fef8f85a042 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java @@ -90,6 +90,7 @@ */ public class StudiesCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "studies"; public StudiesCommandOptions studiesCommandOptions; public StudiesCommandExecutor(StudiesCommandOptions studiesCommandOptions) throws CatalogAuthenticationException { @@ -183,7 +184,7 @@ private RestResponse updateAcl() throws Exception { studyAclUpdateParams = new StudyAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(studyAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { studyAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -218,7 +219,7 @@ private RestResponse create() throws Exception { studyCreateParams = new StudyCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(studyCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/create")); return res; } else if (commandOptions.jsonFile != null) { studyCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -360,7 +361,7 @@ private RestResponse updateGroups() throws Exception { groupCreateParams = new GroupCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(groupCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/groups/update")); return res; } else if (commandOptions.jsonFile != null) { groupCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -391,7 +392,7 @@ private RestResponse updateGroupsUsers() throws Exception { groupUpdateParams = new GroupUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(groupUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/groups/{group}/users/update")); return res; } else if (commandOptions.jsonFile != null) { groupUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -428,7 +429,7 @@ private RestResponse updatePermissionRules() throws Exception { permissionRule = new PermissionRule(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(permissionRule)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/permissionRules/update")); return res; } else if (commandOptions.jsonFile != null) { permissionRule = JacksonUtils.getDefaultObjectMapper() @@ -511,7 +512,7 @@ private RestResponse update() throws Exception { studyUpdateParams = new StudyUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(studyUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/update")); return res; } else if (commandOptions.jsonFile != null) { studyUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -562,7 +563,7 @@ private RestResponse updateVariableSets() throws Exception { variableSetCreateParams = new VariableSetCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variableSetCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/variableSets/update")); return res; } else if (commandOptions.jsonFile != null) { variableSetCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -596,7 +597,7 @@ private RestResponse updateVariableSetsVariables() throws Exception variable = new Variable(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variable)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/variableSets/{variableSet}/variables/update")); return res; } else if (commandOptions.jsonFile != null) { variable = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java index b2cca1037ba..f44e3449cc5 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java @@ -61,6 +61,7 @@ */ public class UsersCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "users"; public UsersCommandOptions usersCommandOptions; public UsersCommandExecutor(UsersCommandOptions usersCommandOptions) throws CatalogAuthenticationException { @@ -136,7 +137,7 @@ private RestResponse password() throws Exception { passwordChangeParams = new PasswordChangeParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(passwordChangeParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/users/password")); return res; } else if (commandOptions.jsonFile != null) { passwordChangeParams = JacksonUtils.getDefaultObjectMapper() @@ -192,7 +193,7 @@ private RestResponse updateConfigs() throws Exception { configUpdateParams = new ConfigUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(configUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/users/{user}/configs/update")); return res; } else if (commandOptions.jsonFile != null) { configUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -257,7 +258,7 @@ private RestResponse update() throws Exception { userUpdateParams = new UserUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(userUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/users/{user}/update")); return res; } else if (commandOptions.jsonFile != null) { userUpdateParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index f36ae979df6..ca588e36aec 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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 7f1a6a2d745..42453c4b949 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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 5756f579584..1094354e3de 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, filterId, user, users, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -10,37 +10,37 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, study, group, variableSet, studies, members, templateId, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, templateId, variableSet, study, group, studies, members, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, file, files, folder, members, annotationSet, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, files, file, folder, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, sample, members, annotationSet, samples, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, sample, samples, members, annotationSet, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, families, members, annotationSet, family, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, annotationSet, members, family, families, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, cohort, members, cohorts, annotationSet, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, interpretation, interpretations, clinicalAnalysis, clinicalAnalyses, members, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretations, members, interpretation, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index 5d84fa14614..063b5ca56bf 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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, interpretation, interpretations, clinicalAnalysis, clinicalAnalyses, members, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretations, members, interpretation, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index d192d6feec1..86c256ad13c 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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, cohort, members, cohorts, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index c582b23a93a..f61994486fa 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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, families, members, annotationSet, family, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, members, family, families, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index f3eeac80df2..12a692cba71 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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, file, files, folder, members, annotationSet, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, files, file, folder, annotationSet, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index 639683e171c..d03fe839d00 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 1839f2cb8c9..6c6db781f0f 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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, annotationSet, individuals, individual, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index ed70e8df6cf..2336177e4e3 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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, jobs, members, job, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index c278a0c47e4..10888d84a65 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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 11621e2cf87..492c6a7c654 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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 20fb425cc31..9ff4ec9416b 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 80d88c4cc79..a0cdf42263b 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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 32e64a3ecc9..e154dbdea1d 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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, sample, members, annotationSet, samples, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, sample, samples, members, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index a9c9a3c90f8..ec660266b5a 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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, study, group, variableSet, studies, members, templateId, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, templateId, variableSet, study, group, studies, members, 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 2a1d1bc3e82..65db531b18c 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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, filterId, user, users, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, user, filterId, users, 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 ad760abcd16..70d0f7406a2 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: 2023-09-12 +# Autogenerated on: 2023-10-27 # # 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 6aad0bc7842..b8650868796 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -45,7 +45,7 @@ /** * This class contains methods for the Admin webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: admin */ public class AdminClient extends AbstractParentClient { 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 16c679f642f..e979ae69978 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -49,7 +49,7 @@ /** * This class contains methods for the Alignment webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: analysis/alignment */ public class AlignmentClient extends AbstractParentClient { 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 94ab79f677d..8e45768167c 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -60,7 +60,7 @@ /** * This class contains methods for the ClinicalAnalysis webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: analysis/clinical */ public class ClinicalAnalysisClient extends AbstractParentClient { 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 2320ca7bbcd..a6c7798a94b 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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 @@ /** * This class contains methods for the Cohort webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: cohorts */ public class CohortClient extends AbstractParentClient { 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 ad9ef470eaa..979f96e572e 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -44,7 +44,7 @@ /** * This class contains methods for the DiseasePanel webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: panels */ public class DiseasePanelClient extends AbstractParentClient { 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 94b0e7cf66d..60b4ca25d77 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -45,7 +45,7 @@ /** * This class contains methods for the Family webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: families */ public class FamilyClient extends AbstractParentClient { 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 94eeead7197..795aeff6846 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -52,7 +52,7 @@ /** * This class contains methods for the File webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: files */ public class FileClient extends AbstractParentClient { 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 48b4524ea7f..b843ea82794 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -36,7 +36,7 @@ /** * This class contains methods for the GA4GH webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: ga4gh */ public class GA4GHClient extends AbstractParentClient { 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 b89c47024df..71a2b12acb5 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -45,7 +45,7 @@ /** * This class contains methods for the Individual webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: individuals */ public class IndividualClient extends AbstractParentClient { 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 7945a8d65cc..a3ba8a9fcd1 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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 @@ /** * This class contains methods for the Job webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: jobs */ public class JobClient extends AbstractParentClient { 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 794c6ad3394..49ec8ae0eed 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -37,7 +37,7 @@ /** * This class contains methods for the Meta webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: meta */ public class MetaClient extends AbstractParentClient { 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 317a4af226c..0b92cedd97b 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -41,7 +41,7 @@ /** * This class contains methods for the Project webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: projects */ public class ProjectClient extends AbstractParentClient { 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 5cbb8f10fd4..4dfeecc596d 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -45,7 +45,7 @@ /** * This class contains methods for the Sample webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: samples */ public class SampleClient extends AbstractParentClient { 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 8f018861260..e86ac389d40 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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 @@ /** * This class contains methods for the Study webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: studies */ public class StudyClient extends AbstractParentClient { 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 adb4ce85938..e5984ffeff2 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -45,7 +45,7 @@ /** * This class contains methods for the User webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: users */ public class UserClient extends AbstractParentClient { 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 4801650a0f9..07360eddb66 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -71,7 +71,7 @@ /** * This class contains methods for the Variant webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: analysis/variant */ public class VariantClient extends AbstractParentClient { 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 c1ffc952c9d..27222047a76 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: 2023-09-12 +* Autogenerated on: 2023-10-27 * * 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. @@ -59,7 +59,7 @@ /** * This class contains methods for the VariantOperation webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: operation */ public class VariantOperationClient extends AbstractParentClient { diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 2466edfccfd..fdfb9de6aa6 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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 446219c5a59..8c967d31de0 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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 221fa4a68da..b814ab17d37 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 9d070dc8ec8..8a3379c7348 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index 1d97f0d3b6f..a0967fc19f7 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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/Family.js b/opencga-client/src/main/javascript/Family.js index 5b11ceacd3a..a1183ca4f60 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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/File.js b/opencga-client/src/main/javascript/File.js index 27d76b733e7..58e1343ad16 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index 2e3f968ab05..e61030ad0e3 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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 160bb589c50..8e5089be7fd 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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/Job.js b/opencga-client/src/main/javascript/Job.js index 52f5cdde599..21d175e0ca3 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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/Meta.js b/opencga-client/src/main/javascript/Meta.js index 0207e95847a..02c96c1dade 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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 f43c7394d71..e38753e0c87 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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 edefccf3e5a..abbe89cf5ac 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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/Study.js b/opencga-client/src/main/javascript/Study.js index d153ba9d316..d0eb2bb02fe 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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 d8c60b8d409..b65022b6a8b 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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 35617fde07f..d3ced6ac6ad 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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 daa6917728a..7044b256894 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: 2023-09-12 + * Autogenerated on: 2023-10-27 * * 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 28598b602eb..90d868b6533 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Admin(_ParentRestClient): """ This class contains methods for the 'Admin' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/admin """ 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 d19895d21ba..b3fd66f2f86 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Alignment(_ParentRestClient): """ This class contains methods for the 'Analysis - Alignment' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/analysis/alignment """ 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 cf8de0798c5..359a1bdcb5b 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class ClinicalAnalysis(_ParentRestClient): """ This class contains methods for the 'Analysis - Clinical' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/analysis/clinical """ 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 f7d6ad80542..021ca07f480 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Cohort(_ParentRestClient): """ This class contains methods for the 'Cohorts' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/cohorts """ 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 6d47ea09d3c..e02a70f6560 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class DiseasePanel(_ParentRestClient): """ This class contains methods for the 'Disease Panels' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/panels """ 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 65e3a070dce..a321fc45b54 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Family(_ParentRestClient): """ This class contains methods for the 'Families' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/families """ 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 c6c028d3b3a..7a0f41fcb5a 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class File(_ParentRestClient): """ This class contains methods for the 'Files' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/files """ 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 48e5b17de75..c9966af7a5e 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class GA4GH(_ParentRestClient): """ This class contains methods for the 'GA4GH' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/ga4gh """ 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 07dd3d04b0d..2c811e6c501 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Individual(_ParentRestClient): """ This class contains methods for the 'Individuals' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/individuals """ 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 d692f8e099c..80078af84e6 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Job(_ParentRestClient): """ This class contains methods for the 'Jobs' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/jobs """ 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 d43227b33f8..6e7cc082b1f 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Meta(_ParentRestClient): """ This class contains methods for the 'Meta' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/meta """ 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 bd29b4b1013..1b063026bd1 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Project(_ParentRestClient): """ This class contains methods for the 'Projects' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/projects """ 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 fcb5c944884..9d4c3d3b56a 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Sample(_ParentRestClient): """ This class contains methods for the 'Samples' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/samples """ 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 40cc9a63c08..0c67bc31819 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Study(_ParentRestClient): """ This class contains methods for the 'Studies' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/studies """ 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 3f2ed4eae3e..bfc4b7d4d9a 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class User(_ParentRestClient): """ This class contains methods for the 'Users' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/users """ 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 80e1746470a..b7e2829b208 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class Variant(_ParentRestClient): """ This class contains methods for the 'Analysis - Variant' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/analysis/variant """ 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 4297fbf08ae..6736e33528e 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: 2023-09-12 + Autogenerated on: 2023-10-27 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. @@ -14,7 +14,7 @@ class VariantOperation(_ParentRestClient): """ This class contains methods for the 'Operations - Variant Storage' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/operation """ diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java index f75776a7dfa..9a7c35caa86 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java @@ -170,6 +170,7 @@ protected String getClassHeader(String key) { CategoryConfig config = availableCategoryConfigs.get(key); sb.append("public class " + getAsClassName(restCategory.getName()) + "CommandExecutor extends " + getExtendedClass() + " {\n\n"); + sb.append(" public String categoryName = \"" + getAsVariableName(getAsCamelCase(restCategory.getName())) + "\";\n"); sb.append(" public " + getAsClassName(restCategory.getName()) + "CommandOptions " + getAsVariableName(getAsCamelCase(restCategory.getName())) + "CommandOptions;\n\n"); sb.append(" public " + getAsClassName(restCategory.getName()) + "CommandExecutor(" + getAsClassName(restCategory.getName()) @@ -373,7 +374,7 @@ private String getBodyParams(RestCategory restCategory, RestEndpoint restEndpoin sb.append("\n " + variableName + " = new " + bodyClassName + "();"); sb.append("\n RestResponse<" + getValidResponseNames(restEndpoint.getResponse()) + "> res = new RestResponse<>();"); sb.append("\n res.setType(QueryType.VOID);"); - sb.append("\n PrintUtils.println(getObjectAsJSON(" + variableName + "));"); + sb.append("\n PrintUtils.println(getObjectAsJSON(categoryName,\""+restEndpoint.getPath()+"\"));"); sb.append("\n return res;"); sb.append("\n } else if (commandOptions.jsonFile != null) {"); sb.append("\n " + getAsVariableName(bodyClassName) + " = JacksonUtils.getDefaultObjectMapper()"); From 5226ae7d3ec3116d920da601f3a2e0ee9f67cb32 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 2 Nov 2023 17:32:16 +0100 Subject: [PATCH 2/5] cli:getObjectAsJSON completo #TASK-5160 --- .../app/cli/main/OpenCgaCompleter.java | 2 +- .../app/cli/main/OpencgaCliOptionsParser.java | 2 +- .../AnalysisAlignmentCommandExecutor.java | 2 +- .../AnalysisClinicalCommandExecutor.java | 2 +- .../AnalysisVariantCommandExecutor.java | 2 +- .../DiseasePanelsCommandExecutor.java | 2 +- .../executors/OpencgaCommandExecutor.java | 79 +++++++++++++++++-- ...erationsVariantStorageCommandExecutor.java | 2 +- 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 | 14 ++-- .../src/main/R/R/Clinical-methods.R | 4 +- opencga-client/src/main/R/R/Cohort-methods.R | 2 +- opencga-client/src/main/R/R/Family-methods.R | 4 +- opencga-client/src/main/R/R/File-methods.R | 4 +- opencga-client/src/main/R/R/GA4GH-methods.R | 2 +- .../src/main/R/R/Individual-methods.R | 2 +- opencga-client/src/main/R/R/Job-methods.R | 2 +- 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 | 2 +- opencga-client/src/main/R/R/Project-methods.R | 4 +- opencga-client/src/main/R/R/Sample-methods.R | 4 +- 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 | 2 +- .../client/rest/clients/CohortClient.java | 2 +- .../rest/clients/DiseasePanelClient.java | 2 +- .../client/rest/clients/FamilyClient.java | 2 +- .../client/rest/clients/FileClient.java | 2 +- .../client/rest/clients/GA4GHClient.java | 2 +- .../client/rest/clients/IndividualClient.java | 2 +- .../client/rest/clients/JobClient.java | 2 +- .../client/rest/clients/MetaClient.java | 2 +- .../client/rest/clients/ProjectClient.java | 2 +- .../client/rest/clients/SampleClient.java | 2 +- .../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 | 2 +- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- 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 | 2 +- .../pyopencga/rest_clients/cohort_client.py | 2 +- .../rest_clients/disease_panel_client.py | 2 +- .../pyopencga/rest_clients/family_client.py | 2 +- .../pyopencga/rest_clients/file_client.py | 2 +- .../pyopencga/rest_clients/ga4gh_client.py | 2 +- .../rest_clients/individual_client.py | 2 +- .../pyopencga/rest_clients/job_client.py | 2 +- .../pyopencga/rest_clients/meta_client.py | 2 +- .../pyopencga/rest_clients/project_client.py | 2 +- .../pyopencga/rest_clients/sample_client.py | 2 +- .../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 +- .../writers/ParentClientRestApiWriter.java | 6 +- .../cli/ExecutorsCliRestApiWriter.java | 2 +- 79 files changed, 166 insertions(+), 99 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 7d088edef53..db447fe40b6 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 2015-2023-10-27 OpenCB +* Copyright 2015-2023-11-02 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 279ccd36197..1dfe8779b88 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 2015-2023-10-27 OpenCB +* Copyright 2015-2023-11-02 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/executors/AnalysisAlignmentCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java index 60c7752ddbe..28e02d2ad67 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java @@ -48,7 +48,7 @@ */ public class AnalysisAlignmentCommandExecutor extends OpencgaCommandExecutor { - public String categoryName = "analysisAlignment"; + public String categoryName = "alignment"; public AnalysisAlignmentCommandOptions analysisAlignmentCommandOptions; public AnalysisAlignmentCommandExecutor(AnalysisAlignmentCommandOptions analysisAlignmentCommandOptions) throws CatalogAuthenticationException { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java index 0bd8b87285e..284aff68cc4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java @@ -80,7 +80,7 @@ */ public class AnalysisClinicalCommandExecutor extends OpencgaCommandExecutor { - public String categoryName = "analysisClinical"; + public String categoryName = "clinical"; public AnalysisClinicalCommandOptions analysisClinicalCommandOptions; public AnalysisClinicalCommandExecutor(AnalysisClinicalCommandOptions analysisClinicalCommandOptions) throws CatalogAuthenticationException { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java index 418b0c3ac40..5ae64623bb5 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java @@ -76,7 +76,7 @@ */ public class AnalysisVariantCommandExecutor extends OpencgaCommandExecutor { - public String categoryName = "analysisVariant"; + public String categoryName = "variant"; public AnalysisVariantCommandOptions analysisVariantCommandOptions; public AnalysisVariantCommandExecutor(AnalysisVariantCommandOptions analysisVariantCommandOptions) throws CatalogAuthenticationException { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java index 5c6446b45e4..29e5e25e4b9 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java @@ -44,7 +44,7 @@ */ public class DiseasePanelsCommandExecutor extends OpencgaCommandExecutor { - public String categoryName = "diseasePanels"; + public String categoryName = "panels"; public DiseasePanelsCommandOptions diseasePanelsCommandOptions; public DiseasePanelsCommandExecutor(DiseasePanelsCommandOptions diseasePanelsCommandOptions) throws CatalogAuthenticationException { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java index fc2357c14ad..b46e5f387ab 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java @@ -225,27 +225,33 @@ public OpencgaCommandExecutor setOpenCGAClient(OpenCGAClient openCGAClient) { } public String getObjectAsJSON(String objectCategory, String objectPath) throws Exception { - String jsonInString = ""; + String jsonInString = "\n"; try { ObjectMap queryParams = new ObjectMap(); - queryParams.putIfNotEmpty("category", String.valueOf(objectCategory)); + queryParams.putIfNotEmpty("category", objectCategory); RestResponse response = openCGAClient.getMetaClient().api(queryParams); ObjectMapper jsonObjectMapper = new ObjectMapper(); for (List list : response.getResponses().get(0).getResults()) { List categories = jsonObjectMapper.convertValue(list, new TypeReference>() {}); for (RestCategory category : categories) { - for (RestEndpoint endpoint: category.getEndpoints()){ - if(objectPath.equals(endpoint.getPath())){ - for (RestParameter parameter:endpoint.getParameters()){ + for (RestEndpoint endpoint : category.getEndpoints()) { + if (objectPath.equals(endpoint.getPath())) { + boolean enc = false; + for (RestParameter parameter : endpoint.getParameters()) { //jsonInString += parameter.getName()+":"+parameter.getAllowedValues()+"\n"; - jsonInString += parameter.toString()+"\n"; + if (parameter.getData() != null) { + enc = true; + jsonInString += printBody(parameter.getData(), ""); + } + } + if (!enc) { + jsonInString += "No model available"; } // } } } - } - // jsonInString = DataModelsUtils.dataModelToJsonString(o.getClass()); + } } catch (Exception e) { jsonInString = "Data model not found."; CommandLineUtils.error(e); @@ -253,6 +259,63 @@ public String getObjectAsJSON(String objectCategory, String objectPath) throws E return jsonInString; } + private String printBody(List data, String tabs) { + String res = ""; + res += "{\n"; + String tab = " " + tabs; + for (RestParameter parameter : data) { + if (parameter.getData() == null) { + res += printParameter(parameter, tab); + } else { + res += tab + parameter.getName() + "\"" + ": [" + printBody(parameter.getData(), tab) + "],\n"; + } + } + res += tabs + "}"; + return res; + + } + + private String printParameter(RestParameter parameter, String tab) { + + return tab + "\"" + parameter.getName() + "\"" + ":" + printParameterValue(parameter) + ",\n"; + } + + private String printParameterValue(RestParameter parameter) { + + if(!StringUtils.isEmpty(parameter.getAllowedValues())){ + return parameter.getAllowedValues().replace(" ", "|"); + } + switch (parameter.getType()) { + case "Boolean": + case "java.lang.Boolean": + return "false"; + case "Long": + case "Float": + case "Double": + case "Integer": + case "int": + case "double": + case "float": + case "long": + return "0"; + case "List": + return "[\"\"]"; + case "Date": + return "\"dd/mm/yyyy\""; + case "Map": + return "{\"key\": \"value\"}"; + case "String": + return "\"\""; + default: + return "\"-\""; + } + } + + private boolean isNumeric(String type) { + + return "int".equals(type) || "Long".equals(type) || "Float".equals(type) || "double".equals(type); + } + public RestResponse saveSession(String user, AuthenticationResponse response) throws ClientException, IOException { RestResponse res = new RestResponse<>(); if (response != null) { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java index 7e1faf04dfd..6197d5eb410 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java @@ -61,7 +61,7 @@ */ public class OperationsVariantStorageCommandExecutor extends OpencgaCommandExecutor { - public String categoryName = "operationsVariantStorage"; + public String categoryName = "operation"; public OperationsVariantStorageCommandOptions operationsVariantStorageCommandOptions; public OperationsVariantStorageCommandExecutor(OperationsVariantStorageCommandOptions operationsVariantStorageCommandOptions) throws CatalogAuthenticationException { diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index ca588e36aec..1c4a4479bb0 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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 42453c4b949..5c97d7f69d1 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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 1094354e3de..85629266564 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,21 +1,21 @@ # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## ## ProjectClient -setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...) +setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...) standardGeneric("projectClient")) # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, templateId, variableSet, study, group, studies, members, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, group, members, studies, study, templateId, variableSet, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, files, file, folder, annotationSet, members, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, files, file, members, annotationSet, folder, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## @@ -25,7 +25,7 @@ setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, par # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, sample, samples, members, annotationSet, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## @@ -35,7 +35,7 @@ setGeneric("individualClient", function(OpencgaR, individual, members, individua # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, annotationSet, members, family, families, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, members, family, families, annotationSet, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretations, members, interpretation, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, members, interpretation, interpretations, clinicalAnalyses, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index 063b5ca56bf..58c38ecb630 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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, clinicalAnalysis, clinicalAnalyses, interpretations, members, interpretation, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, members, interpretation, interpretations, clinicalAnalyses, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 86c256ad13c..aeca965c7b2 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index f61994486fa..747382a2b15 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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, annotationSet, members, family, families, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, families, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 12a692cba71..89b8034de42 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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, file, folder, annotationSet, members, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, files, file, members, annotationSet, folder, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index d03fe839d00..98aaad0e987 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 6c6db781f0f..bf6750fc941 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index 2336177e4e3..37e3a2c9548 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index 10888d84a65..481bae671e6 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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 492c6a7c654..93934f11fef 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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 9ff4ec9416b..4d45393c182 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index a0cdf42263b..570ebfc9cf7 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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. @@ -34,7 +34,7 @@ #' [*]: Required parameter #' @export -setMethod("projectClient", "OpencgaR", function(OpencgaR, projects, project, endpointName, params=NULL, ...) { +setMethod("projectClient", "OpencgaR", function(OpencgaR, project, projects, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/projects/create: diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index e154dbdea1d..319ded3abbb 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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, sample, samples, members, annotationSet, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index ec660266b5a..9873110e560 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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, templateId, variableSet, study, group, studies, members, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, group, members, studies, study, templateId, variableSet, 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 65db531b18c..458947e9b4e 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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, user, users, 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 70d0f7406a2..1957998638d 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: 2023-10-27 +# Autogenerated on: 2023-11-02 # # 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 b8650868796..5460d28052e 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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 e979ae69978..33a9c268320 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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 8e45768167c..a322c2c9e3b 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index a6c7798a94b..9631f0aacb0 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index 979f96e572e..7e60a93d950 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index 60b4ca25d77..25e941e8b0b 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 795aeff6846..7abe70688b7 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index b843ea82794..45eea839db8 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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 71a2b12acb5..478a20a285a 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index a3ba8a9fcd1..cf96ffaaf61 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index 49ec8ae0eed..6dd12a34e12 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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 0b92cedd97b..3db333e8d16 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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 4dfeecc596d..e80e58efb11 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index e86ac389d40..df90b1e2153 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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 e5984ffeff2..736744268b5 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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 07360eddb66..d85feb6f179 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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 27222047a76..2e20373c6d7 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: 2023-10-27 +* Autogenerated on: 2023-11-02 * * 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 fdfb9de6aa6..0522ec1c5a9 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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 8c967d31de0..6f3df1f5998 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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 b814ab17d37..6431faa5cf3 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 8a3379c7348..6a234b6554e 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index a0967fc19f7..21eb1f0422e 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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/Family.js b/opencga-client/src/main/javascript/Family.js index a1183ca4f60..cae578e4413 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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/File.js b/opencga-client/src/main/javascript/File.js index 58e1343ad16..63ce3b943da 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index e61030ad0e3..611b81c5727 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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 8e5089be7fd..534e2d3c7ed 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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/Job.js b/opencga-client/src/main/javascript/Job.js index 21d175e0ca3..be7c71c00e7 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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/Meta.js b/opencga-client/src/main/javascript/Meta.js index 02c96c1dade..07bd4c5b07c 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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 e38753e0c87..54dd86064a5 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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 abbe89cf5ac..42cd10689ae 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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/Study.js b/opencga-client/src/main/javascript/Study.js index d0eb2bb02fe..4c6931b0c89 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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 b65022b6a8b..2db00a202b2 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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 d3ced6ac6ad..5edd6753b11 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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 7044b256894..b9f8f029258 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: 2023-10-27 + * Autogenerated on: 2023-11-02 * * 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 90d868b6533..972e456556c 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: 2023-10-27 + Autogenerated on: 2023-11-02 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 b3fd66f2f86..1b598296913 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: 2023-10-27 + Autogenerated on: 2023-11-02 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 359a1bdcb5b..3bd95f48564 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: 2023-10-27 + Autogenerated on: 2023-11-02 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/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index 021ca07f480..1eea42c98a3 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: 2023-10-27 + Autogenerated on: 2023-11-02 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/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index e02a70f6560..eb9aea88c65 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: 2023-10-27 + Autogenerated on: 2023-11-02 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/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index a321fc45b54..f78c61e2a5a 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: 2023-10-27 + Autogenerated on: 2023-11-02 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/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 7a0f41fcb5a..a65add7cf7e 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: 2023-10-27 + Autogenerated on: 2023-11-02 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/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index c9966af7a5e..f4e96d25df2 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: 2023-10-27 + Autogenerated on: 2023-11-02 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 2c811e6c501..fadca48f497 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: 2023-10-27 + Autogenerated on: 2023-11-02 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/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index 80078af84e6..e8f18894ef9 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: 2023-10-27 + Autogenerated on: 2023-11-02 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/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index 6e7cc082b1f..dd437e17394 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: 2023-10-27 + Autogenerated on: 2023-11-02 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 1b063026bd1..dac784edf9a 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: 2023-10-27 + Autogenerated on: 2023-11-02 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 9d4c3d3b56a..b13fec2f082 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: 2023-10-27 + Autogenerated on: 2023-11-02 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/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 0c67bc31819..d4312e58800 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: 2023-10-27 + Autogenerated on: 2023-11-02 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 bfc4b7d4d9a..2d6a136c750 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: 2023-10-27 + Autogenerated on: 2023-11-02 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 b7e2829b208..c3c298dbbc6 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: 2023-10-27 + Autogenerated on: 2023-11-02 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 6736e33528e..f0357486079 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: 2023-10-27 + Autogenerated on: 2023-11-02 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-server/src/main/java/org/opencb/opencga/server/generator/writers/ParentClientRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/ParentClientRestApiWriter.java index 72857bc2aec..940c6e56427 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/ParentClientRestApiWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/ParentClientRestApiWriter.java @@ -83,11 +83,15 @@ protected static String reverseCommandName(String commandName) { return commandName.toLowerCase(); } + public String getCategoryRestName(RestCategory restCategory, CategoryConfig categoryConfig) { + return restCategory.getPath().substring(restCategory.getPath().lastIndexOf("/") + 1); + } + public String getCategoryCommandName(RestCategory restCategory, CategoryConfig categoryConfig) { if (!StringUtils.isEmpty(categoryConfig.getCommandName())) { return categoryConfig.getCommandName(); } - return restCategory.getPath().substring(restCategory.getPath().lastIndexOf("/") + 1); + return getCategoryRestName(restCategory, categoryConfig); } protected void writeToFile(File file, StringBuffer sb) throws IOException { diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java index 9a7c35caa86..f9c5c7d0f18 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java @@ -170,7 +170,7 @@ protected String getClassHeader(String key) { CategoryConfig config = availableCategoryConfigs.get(key); sb.append("public class " + getAsClassName(restCategory.getName()) + "CommandExecutor extends " + getExtendedClass() + " {\n\n"); - sb.append(" public String categoryName = \"" + getAsVariableName(getAsCamelCase(restCategory.getName())) + "\";\n"); + sb.append(" public String categoryName = \"" + getCategoryRestName(restCategory, config) + "\";\n"); sb.append(" public " + getAsClassName(restCategory.getName()) + "CommandOptions " + getAsVariableName(getAsCamelCase(restCategory.getName())) + "CommandOptions;\n\n"); sb.append(" public " + getAsClassName(restCategory.getName()) + "CommandExecutor(" + getAsClassName(restCategory.getName()) From 98d42e3bb2ea5a30eb897fb43714586fee134915 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 3 Nov 2023 11:27:42 +0100 Subject: [PATCH 3/5] cli:Deleted unused object in executors #TASK-5160 --- .../app/cli/main/OpenCgaCompleter.java | 2 +- .../app/cli/main/OpencgaCliOptionsParser.java | 2 +- .../main/executors/AdminCommandExecutor.java | 6 ----- .../AnalysisAlignmentCommandExecutor.java | 9 ------- .../AnalysisClinicalCommandExecutor.java | 12 --------- .../AnalysisVariantCommandExecutor.java | 24 ------------------ .../executors/CohortsCommandExecutor.java | 6 ----- .../DiseasePanelsCommandExecutor.java | 4 --- .../executors/FamiliesCommandExecutor.java | 5 ---- .../main/executors/FilesCommandExecutor.java | 9 ------- .../executors/IndividualsCommandExecutor.java | 5 ---- .../main/executors/JobsCommandExecutor.java | 4 --- ...erationsVariantStorageCommandExecutor.java | 25 ------------------- .../executors/ProjectsCommandExecutor.java | 2 -- .../executors/SamplesCommandExecutor.java | 5 ---- .../executors/StudiesCommandExecutor.java | 8 ------ .../main/executors/UsersCommandExecutor.java | 3 --- 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 | 18 ++++++------- .../src/main/R/R/Clinical-methods.R | 4 +-- opencga-client/src/main/R/R/Cohort-methods.R | 4 +-- opencga-client/src/main/R/R/Family-methods.R | 4 +-- opencga-client/src/main/R/R/File-methods.R | 4 +-- opencga-client/src/main/R/R/GA4GH-methods.R | 2 +- .../src/main/R/R/Individual-methods.R | 4 +-- opencga-client/src/main/R/R/Job-methods.R | 4 +-- 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 | 2 +- opencga-client/src/main/R/R/Project-methods.R | 2 +- opencga-client/src/main/R/R/Sample-methods.R | 4 +-- 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 | 2 +- .../client/rest/clients/CohortClient.java | 2 +- .../rest/clients/DiseasePanelClient.java | 2 +- .../client/rest/clients/FamilyClient.java | 2 +- .../client/rest/clients/FileClient.java | 2 +- .../client/rest/clients/GA4GHClient.java | 2 +- .../client/rest/clients/IndividualClient.java | 2 +- .../client/rest/clients/JobClient.java | 2 +- .../client/rest/clients/MetaClient.java | 2 +- .../client/rest/clients/ProjectClient.java | 2 +- .../client/rest/clients/SampleClient.java | 2 +- .../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 | 2 +- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- 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 | 2 +- .../pyopencga/rest_clients/cohort_client.py | 2 +- .../rest_clients/disease_panel_client.py | 2 +- .../pyopencga/rest_clients/family_client.py | 2 +- .../pyopencga/rest_clients/file_client.py | 2 +- .../pyopencga/rest_clients/ga4gh_client.py | 2 +- .../rest_clients/individual_client.py | 2 +- .../pyopencga/rest_clients/job_client.py | 2 +- .../pyopencga/rest_clients/meta_client.py | 2 +- .../pyopencga/rest_clients/project_client.py | 2 +- .../pyopencga/rest_clients/sample_client.py | 2 +- .../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 +- .../cli/ExecutorsCliRestApiWriter.java | 1 - 87 files changed, 88 insertions(+), 216 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 db447fe40b6..3c30b6d022e 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 2015-2023-11-02 OpenCB +* Copyright 2015-2023-11-03 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 1dfe8779b88..19ca44161d1 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 2015-2023-11-02 OpenCB +* Copyright 2015-2023-11-03 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/executors/AdminCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java index 0ab7c6405dc..554a475732c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java @@ -136,7 +136,6 @@ private RestResponse installCatalog() throws Exception { InstallationParams installationParams = null; if (commandOptions.jsonDataModel) { - installationParams = new InstallationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/install")); @@ -165,7 +164,6 @@ private RestResponse jwtCatalog() throws Exception { JWTParams jWTParams = null; if (commandOptions.jsonDataModel) { - jWTParams = new JWTParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/jwt")); @@ -191,7 +189,6 @@ private RestResponse createUsers() throws Exception { UserCreateParams userCreateParams = null; if (commandOptions.jsonDataModel) { - userCreateParams = new UserCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/create")); @@ -222,7 +219,6 @@ private RestResponse importUsers() throws Exception { UserImportParams userImportParams = null; if (commandOptions.jsonDataModel) { - userImportParams = new UserImportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/import")); @@ -270,7 +266,6 @@ private RestResponse syncUsers() throws Exception { GroupSyncParams groupSyncParams = null; if (commandOptions.jsonDataModel) { - groupSyncParams = new GroupSyncParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/sync")); @@ -306,7 +301,6 @@ private RestResponse usersUpdateGroups() throws Exception { UserUpdateGroup userUpdateGroup = null; if (commandOptions.jsonDataModel) { - userUpdateGroup = new UserUpdateGroup(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/{user}/groups/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java index 28e02d2ad67..5e9f53fb2cf 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java @@ -132,7 +132,6 @@ private RestResponse runBwa() throws Exception { BwaWrapperParams bwaWrapperParams = null; if (commandOptions.jsonDataModel) { - bwaWrapperParams = new BwaWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/bwa/run")); @@ -174,7 +173,6 @@ private RestResponse runCoverageIndex() throws Exception { CoverageIndexParams coverageIndexParams = null; if (commandOptions.jsonDataModel) { - coverageIndexParams = new CoverageIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/coverage/index/run")); @@ -213,7 +211,6 @@ private RestResponse coverageQcGeneCoverageStatsRun() throws Exception { AlignmentGeneCoverageStatsParams alignmentGeneCoverageStatsParams = null; if (commandOptions.jsonDataModel) { - alignmentGeneCoverageStatsParams = new AlignmentGeneCoverageStatsParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/coverage/qc/geneCoverageStats/run")); @@ -309,7 +306,6 @@ private RestResponse runDeeptools() throws Exception { DeeptoolsWrapperParams deeptoolsWrapperParams = null; if (commandOptions.jsonDataModel) { - deeptoolsWrapperParams = new DeeptoolsWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/deeptools/run")); @@ -348,7 +344,6 @@ private RestResponse runFastqc() throws Exception { FastqcWrapperParams fastqcWrapperParams = null; if (commandOptions.jsonDataModel) { - fastqcWrapperParams = new FastqcWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/fastqc/run")); @@ -387,7 +382,6 @@ private RestResponse runIndex() throws Exception { AlignmentIndexParams alignmentIndexParams = null; if (commandOptions.jsonDataModel) { - alignmentIndexParams = new AlignmentIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/index/run")); @@ -425,7 +419,6 @@ private RestResponse runPicard() throws Exception { PicardWrapperParams picardWrapperParams = null; if (commandOptions.jsonDataModel) { - picardWrapperParams = new PicardWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/picard/run")); @@ -464,7 +457,6 @@ private RestResponse runQc() throws Exception { AlignmentQcParams alignmentQcParams = null; if (commandOptions.jsonDataModel) { - alignmentQcParams = new AlignmentQcParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/qc/run")); @@ -536,7 +528,6 @@ private RestResponse runSamtools() throws Exception { SamtoolsWrapperParams samtoolsWrapperParams = null; if (commandOptions.jsonDataModel) { - samtoolsWrapperParams = new SamtoolsWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/samtools/run")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java index 284aff68cc4..2cf48aa5a8c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java @@ -215,7 +215,6 @@ private RestResponse updateAcl() throws Exception ClinicalAnalysisAclUpdateParams clinicalAnalysisAclUpdateParams = null; if (commandOptions.jsonDataModel) { - clinicalAnalysisAclUpdateParams = new ClinicalAnalysisAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/acl/{members}/update")); @@ -249,7 +248,6 @@ private RestResponse updateClinicalConfiguration() throws Exception { ClinicalAnalysisStudyConfiguration clinicalAnalysisStudyConfiguration = null; if (commandOptions.jsonDataModel) { - clinicalAnalysisStudyConfiguration = new ClinicalAnalysisStudyConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/clinical/configuration/update")); @@ -286,7 +284,6 @@ private RestResponse create() throws Exception { ClinicalAnalysisCreateParams clinicalAnalysisCreateParams = null; if (commandOptions.jsonDataModel) { - clinicalAnalysisCreateParams = new ClinicalAnalysisCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/create")); @@ -465,7 +462,6 @@ private RestResponse runInterpreterCancerTiering() throws Exception { CancerTieringInterpretationAnalysisParams cancerTieringInterpretationAnalysisParams = null; if (commandOptions.jsonDataModel) { - cancerTieringInterpretationAnalysisParams = new CancerTieringInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/cancerTiering/run")); @@ -504,7 +500,6 @@ private RestResponse runInterpreterExomiser() throws Exception { ExomiserInterpretationAnalysisParams exomiserInterpretationAnalysisParams = null; if (commandOptions.jsonDataModel) { - exomiserInterpretationAnalysisParams = new ExomiserInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/exomiser/run")); @@ -541,7 +536,6 @@ private RestResponse runInterpreterTeam() throws Exception { TeamInterpretationAnalysisParams teamInterpretationAnalysisParams = null; if (commandOptions.jsonDataModel) { - teamInterpretationAnalysisParams = new TeamInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/team/run")); @@ -581,7 +575,6 @@ private RestResponse runInterpreterTiering() throws Exception { TieringInterpretationAnalysisParams tieringInterpretationAnalysisParams = null; if (commandOptions.jsonDataModel) { - tieringInterpretationAnalysisParams = new TieringInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/tiering/run")); @@ -621,7 +614,6 @@ private RestResponse runInterpreterZetta() throws Exception { ZettaInterpretationAnalysisParams zettaInterpretationAnalysisParams = null; if (commandOptions.jsonDataModel) { - zettaInterpretationAnalysisParams = new ZettaInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/zetta/run")); @@ -824,7 +816,6 @@ private RestResponse runRgaIndex() throws Exception { RgaAnalysisParams rgaAnalysisParams = null; if (commandOptions.jsonDataModel) { - rgaAnalysisParams = new RgaAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/rga/index/run")); @@ -1164,7 +1155,6 @@ private RestResponse update() throws Exception { ClinicalAnalysisUpdateParams clinicalAnalysisUpdateParams = null; if (commandOptions.jsonDataModel) { - clinicalAnalysisUpdateParams = new ClinicalAnalysisUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalyses}/update")); @@ -1239,7 +1229,6 @@ private RestResponse createInterpretation() throws Exception { InterpretationCreateParams interpretationCreateParams = null; if (commandOptions.jsonDataModel) { - interpretationCreateParams = new InterpretationCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create")); @@ -1329,7 +1318,6 @@ private RestResponse updateInterpretation() throws Exception { InterpretationUpdateParams interpretationUpdateParams = null; if (commandOptions.jsonDataModel) { - interpretationUpdateParams = new InterpretationUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java index 5ae64623bb5..45346945d18 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java @@ -313,7 +313,6 @@ private RestResponse runCircos() throws Exception { CircosAnalysisParams circosAnalysisParams = null; if (commandOptions.jsonDataModel) { - circosAnalysisParams = new CircosAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/circos/run")); @@ -382,7 +381,6 @@ private RestResponse runCohortStats() throws Exception { CohortVariantStatsAnalysisParams cohortVariantStatsAnalysisParams = null; if (commandOptions.jsonDataModel) { - cohortVariantStatsAnalysisParams = new CohortVariantStatsAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/cohort/stats/run")); @@ -423,7 +421,6 @@ private RestResponse runExomiser() throws Exception { ExomiserWrapperParams exomiserWrapperParams = null; if (commandOptions.jsonDataModel) { - exomiserWrapperParams = new ExomiserWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/exomiser/run")); @@ -464,7 +461,6 @@ private RestResponse runExport() throws Exception { VariantExportParams variantExportParams = null; if (commandOptions.jsonDataModel) { - variantExportParams = new VariantExportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/export/run")); @@ -605,7 +601,6 @@ private RestResponse runFamilyQc() throws Exception { FamilyQcAnalysisParams familyQcAnalysisParams = null; if (commandOptions.jsonDataModel) { - familyQcAnalysisParams = new FamilyQcAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/family/qc/run")); @@ -665,7 +660,6 @@ private RestResponse runGatk() throws Exception { GatkWrapperParams gatkWrapperParams = null; if (commandOptions.jsonDataModel) { - gatkWrapperParams = new GatkWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/gatk/run")); @@ -704,7 +698,6 @@ private RestResponse runGenomePlot() throws Exception { GenomePlotAnalysisParams genomePlotAnalysisParams = null; if (commandOptions.jsonDataModel) { - genomePlotAnalysisParams = new GenomePlotAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/genomePlot/run")); @@ -745,7 +738,6 @@ private RestResponse runGwas() throws Exception { GwasAnalysisParams gwasAnalysisParams = null; if (commandOptions.jsonDataModel) { - gwasAnalysisParams = new GwasAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/gwas/run")); @@ -793,7 +785,6 @@ private RestResponse runHrDetect() throws Exception { HRDetectAnalysisParams hRDetectAnalysisParams = null; if (commandOptions.jsonDataModel) { - hRDetectAnalysisParams = new HRDetectAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/hrDetect/run")); @@ -842,7 +833,6 @@ private RestResponse runIndex() throws Exception { VariantIndexParams variantIndexParams = null; if (commandOptions.jsonDataModel) { - variantIndexParams = new VariantIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/index/run")); @@ -907,7 +897,6 @@ private RestResponse runIndividualQc() throws Exception { IndividualQcAnalysisParams individualQcAnalysisParams = null; if (commandOptions.jsonDataModel) { - individualQcAnalysisParams = new IndividualQcAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/individual/qc/run")); @@ -947,7 +936,6 @@ private RestResponse runInferredSex() throws Exception { InferredSexAnalysisParams inferredSexAnalysisParams = null; if (commandOptions.jsonDataModel) { - inferredSexAnalysisParams = new InferredSexAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/inferredSex/run")); @@ -1020,7 +1008,6 @@ private RestResponse runKnockout() throws Exception { KnockoutAnalysisParams knockoutAnalysisParams = null; if (commandOptions.jsonDataModel) { - knockoutAnalysisParams = new KnockoutAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/knockout/run")); @@ -1066,7 +1053,6 @@ private RestResponse runMendelianError() throws Exception { MendelianErrorAnalysisParams mendelianErrorAnalysisParams = null; if (commandOptions.jsonDataModel) { - mendelianErrorAnalysisParams = new MendelianErrorAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/mendelianError/run")); @@ -1159,7 +1145,6 @@ private RestResponse runMutationalSignature() throws Exception { MutationalSignatureAnalysisParams mutationalSignatureAnalysisParams = null; if (commandOptions.jsonDataModel) { - mutationalSignatureAnalysisParams = new MutationalSignatureAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/mutationalSignature/run")); @@ -1211,7 +1196,6 @@ private RestResponse runPlink() throws Exception { PlinkWrapperParams plinkWrapperParams = null; if (commandOptions.jsonDataModel) { - plinkWrapperParams = new PlinkWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/plink/run")); @@ -1339,7 +1323,6 @@ private RestResponse runRelatedness() throws Exception { RelatednessAnalysisParams relatednessAnalysisParams = null; if (commandOptions.jsonDataModel) { - relatednessAnalysisParams = new RelatednessAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/relatedness/run")); @@ -1380,7 +1363,6 @@ private RestResponse runRvtests() throws Exception { RvtestsWrapperParams rvtestsWrapperParams = null; if (commandOptions.jsonDataModel) { - rvtestsWrapperParams = new RvtestsWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/rvtests/run")); @@ -1454,7 +1436,6 @@ private RestResponse runSampleEligibility() throws Exception { SampleEligibilityAnalysisParams sampleEligibilityAnalysisParams = null; if (commandOptions.jsonDataModel) { - sampleEligibilityAnalysisParams = new SampleEligibilityAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/eligibility/run")); @@ -1493,7 +1474,6 @@ private RestResponse runSampleQc() throws Exception { SampleQcAnalysisParams sampleQcAnalysisParams = null; if (commandOptions.jsonDataModel) { - sampleQcAnalysisParams = new SampleQcAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/qc/run")); @@ -1594,7 +1574,6 @@ private RestResponse runSample() throws Exception { SampleVariantFilterParams sampleVariantFilterParams = null; if (commandOptions.jsonDataModel) { - sampleVariantFilterParams = new SampleVariantFilterParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/run")); @@ -1688,7 +1667,6 @@ private RestResponse runSampleStats() throws Exception { SampleVariantStatsAnalysisParams sampleVariantStatsAnalysisParams = null; if (commandOptions.jsonDataModel) { - sampleVariantStatsAnalysisParams = new SampleVariantStatsAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/stats/run")); @@ -1761,7 +1739,6 @@ private RestResponse runStatsExport() throws Exception { VariantStatsExportParams variantStatsExportParams = null; if (commandOptions.jsonDataModel) { - variantStatsExportParams = new VariantStatsExportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/stats/export/run")); @@ -1802,7 +1779,6 @@ private RestResponse runStats() throws Exception { VariantStatsAnalysisParams variantStatsAnalysisParams = null; if (commandOptions.jsonDataModel) { - variantStatsAnalysisParams = new VariantStatsAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/stats/run")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java index 4767a83173c..d2ed4126cd3 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java @@ -127,7 +127,6 @@ private RestResponse updateAcl() throws Exception { CohortAclUpdateParams cohortAclUpdateParams = null; if (commandOptions.jsonDataModel) { - cohortAclUpdateParams = new CohortAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/acl/{members}/update")); @@ -188,7 +187,6 @@ private RestResponse loadAnnotationSets() throws Exception { TsvAnnotationParams tsvAnnotationParams = null; if (commandOptions.jsonDataModel) { - tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/annotationSets/load")); @@ -226,7 +224,6 @@ private RestResponse create() throws Exception { CohortCreateParams cohortCreateParams = null; if (commandOptions.jsonDataModel) { - cohortCreateParams = new CohortCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/create")); @@ -312,7 +309,6 @@ private RestResponse generate() throws Exception { CohortGenerateParams cohortGenerateParams = null; if (commandOptions.jsonDataModel) { - cohortGenerateParams = new CohortGenerateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/generate")); @@ -439,7 +435,6 @@ private RestResponse update() throws Exception { CohortUpdateParams cohortUpdateParams = null; if (commandOptions.jsonDataModel) { - cohortUpdateParams = new CohortUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/{cohorts}/update")); @@ -482,7 +477,6 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception ObjectMap objectMap = null; if (commandOptions.jsonDataModel) { - objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/{cohort}/annotationSets/{annotationSet}/annotations/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java index 29e5e25e4b9..7079d284db3 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java @@ -112,7 +112,6 @@ private RestResponse updateAcl() throws Exception { PanelAclUpdateParams panelAclUpdateParams = null; if (commandOptions.jsonDataModel) { - panelAclUpdateParams = new PanelAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/acl/{members}/update")); @@ -149,7 +148,6 @@ private RestResponse create() throws Exception { PanelCreateParams panelCreateParams = null; if (commandOptions.jsonDataModel) { - panelCreateParams = new PanelCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/create")); @@ -228,7 +226,6 @@ private RestResponse importPanels() throws Exception { PanelImportParams panelImportParams = null; if (commandOptions.jsonDataModel) { - panelImportParams = new PanelImportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/import")); @@ -350,7 +347,6 @@ private RestResponse update() throws Exception { PanelUpdateParams panelUpdateParams = null; if (commandOptions.jsonDataModel) { - panelUpdateParams = new PanelUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/{panels}/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java index 60a56535f4a..5d43691e059 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java @@ -125,7 +125,6 @@ private RestResponse updateAcl() throws Exception { FamilyAclUpdateParams familyAclUpdateParams = null; if (commandOptions.jsonDataModel) { - familyAclUpdateParams = new FamilyAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/acl/{members}/update")); @@ -190,7 +189,6 @@ private RestResponse loadAnnotationSets() throws Exception { TsvAnnotationParams tsvAnnotationParams = null; if (commandOptions.jsonDataModel) { - tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/annotationSets/load")); @@ -227,7 +225,6 @@ private RestResponse create() throws Exception { FamilyCreateParams familyCreateParams = null; if (commandOptions.jsonDataModel) { - familyCreateParams = new FamilyCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/create")); @@ -391,7 +388,6 @@ private RestResponse update() throws Exception { FamilyUpdateParams familyUpdateParams = null; if (commandOptions.jsonDataModel) { - familyUpdateParams = new FamilyUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/{families}/update")); @@ -435,7 +431,6 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception ObjectMap objectMap = null; if (commandOptions.jsonDataModel) { - objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/{family}/annotationSets/{annotationSet}/annotations/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java index b4cfc6fdb9f..403df36ac0d 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java @@ -218,7 +218,6 @@ private RestResponse updateAcl() throws Exception { FileAclUpdateParams fileAclUpdateParams = null; if (commandOptions.jsonDataModel) { - fileAclUpdateParams = new FileAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/acl/{members}/update")); @@ -288,7 +287,6 @@ private RestResponse loadAnnotationSets() throws Exception { TsvAnnotationParams tsvAnnotationParams = null; if (commandOptions.jsonDataModel) { - tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/annotationSets/load")); @@ -329,7 +327,6 @@ private RestResponse create() throws Exception { FileCreateParams fileCreateParams = null; if (commandOptions.jsonDataModel) { - fileCreateParams = new FileCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/create")); @@ -425,7 +422,6 @@ private RestResponse fetch() throws Exception { FileFetch fileFetch = null; if (commandOptions.jsonDataModel) { - fileFetch = new FileFetch(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/fetch")); @@ -467,7 +463,6 @@ private RestResponse link() throws Exception { FileLinkParams fileLinkParams = null; if (commandOptions.jsonDataModel) { - fileLinkParams = new FileLinkParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/link")); @@ -513,7 +508,6 @@ private RestResponse runLink() throws Exception { FileLinkToolParams fileLinkToolParams = null; if (commandOptions.jsonDataModel) { - fileLinkToolParams = new FileLinkToolParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/link/run")); @@ -555,7 +549,6 @@ private RestResponse runPostlink() throws Exception { PostLinkToolParams postLinkToolParams = null; if (commandOptions.jsonDataModel) { - postLinkToolParams = new PostLinkToolParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/postlink/run")); @@ -721,7 +714,6 @@ private RestResponse update() throws Exception { FileUpdateParams fileUpdateParams = null; if (commandOptions.jsonDataModel) { - fileUpdateParams = new FileUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/{files}/update")); @@ -788,7 +780,6 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception { ObjectMap objectMap = null; if (commandOptions.jsonDataModel) { - objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/{file}/annotationSets/{annotationSet}/annotations/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java index 0675de1255f..1ced6389e2c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java @@ -134,7 +134,6 @@ private RestResponse updateAcl() throws Exception { IndividualAclUpdateParams individualAclUpdateParams = null; if (commandOptions.jsonDataModel) { - individualAclUpdateParams = new IndividualAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/acl/{members}/update")); @@ -205,7 +204,6 @@ private RestResponse loadAnnotationSets() throws Exception { TsvAnnotationParams tsvAnnotationParams = null; if (commandOptions.jsonDataModel) { - tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/annotationSets/load")); @@ -242,7 +240,6 @@ private RestResponse create() throws Exception { IndividualCreateParams individualCreateParams = null; if (commandOptions.jsonDataModel) { - individualCreateParams = new IndividualCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/create")); @@ -447,7 +444,6 @@ private RestResponse update() throws Exception { IndividualUpdateParams individualUpdateParams = null; if (commandOptions.jsonDataModel) { - individualUpdateParams = new IndividualUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/{individuals}/update")); @@ -517,7 +513,6 @@ private RestResponse updateAnnotationSetsAnnotations() throws Except ObjectMap objectMap = null; if (commandOptions.jsonDataModel) { - objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/{individual}/annotationSets/{annotationSet}/annotations/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java index 846c568724e..03b344a434f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java @@ -140,7 +140,6 @@ private RestResponse updateAcl() throws Exception { JobAclUpdateParams jobAclUpdateParams = null; if (commandOptions.jsonDataModel) { - jobAclUpdateParams = new JobAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/acl/{members}/update")); @@ -205,7 +204,6 @@ private RestResponse create() throws Exception { JobCreateParams jobCreateParams = null; if (commandOptions.jsonDataModel) { - jobCreateParams = new JobCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/create")); @@ -292,7 +290,6 @@ private RestResponse retry() throws Exception { JobRetryParams jobRetryParams = null; if (commandOptions.jsonDataModel) { - jobRetryParams = new JobRetryParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/retry")); @@ -428,7 +425,6 @@ private RestResponse update() throws Exception { JobUpdateParams jobUpdateParams = null; if (commandOptions.jsonDataModel) { - jobUpdateParams = new JobUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/{jobs}/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java index 6197d5eb410..b06ef4b655c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java @@ -185,7 +185,6 @@ private RestResponse configureCellbase() throws Exception { CellBaseConfiguration cellBaseConfiguration = null; if (commandOptions.jsonDataModel) { - cellBaseConfiguration = new CellBaseConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/cellbase/configure")); @@ -225,7 +224,6 @@ private RestResponse aggregateVariant() throws Exception { VariantAggregateParams variantAggregateParams = null; if (commandOptions.jsonDataModel) { - variantAggregateParams = new VariantAggregateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/aggregate")); @@ -280,7 +278,6 @@ private RestResponse indexVariantAnnotation() throws Exception { VariantAnnotationIndexParams variantAnnotationIndexParams = null; if (commandOptions.jsonDataModel) { - variantAnnotationIndexParams = new VariantAnnotationIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/annotation/index")); @@ -322,7 +319,6 @@ private RestResponse saveVariantAnnotation() throws Exception { VariantAnnotationSaveParams variantAnnotationSaveParams = null; if (commandOptions.jsonDataModel) { - variantAnnotationSaveParams = new VariantAnnotationSaveParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/annotation/save")); @@ -356,7 +352,6 @@ private RestResponse configureVariant() throws Exception { VariantConfigureParams variantConfigureParams = null; if (commandOptions.jsonDataModel) { - variantConfigureParams = new VariantConfigureParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/configure")); @@ -393,7 +388,6 @@ private RestResponse deleteVariant() throws Exception { VariantFileDeleteParams variantFileDeleteParams = null; if (commandOptions.jsonDataModel) { - variantFileDeleteParams = new VariantFileDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/delete")); @@ -431,7 +425,6 @@ private RestResponse aggregateVariantFamily() throws Exception { VariantAggregateFamilyParams variantAggregateFamilyParams = null; if (commandOptions.jsonDataModel) { - variantAggregateFamilyParams = new VariantAggregateFamilyParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/family/aggregate")); @@ -470,7 +463,6 @@ private RestResponse indexVariantFamily() throws Exception { VariantFamilyIndexParams variantFamilyIndexParams = null; if (commandOptions.jsonDataModel) { - variantFamilyIndexParams = new VariantFamilyIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/family/index")); @@ -510,7 +502,6 @@ private RestResponse indexVariant() throws Exception { VariantIndexParams variantIndexParams = null; if (commandOptions.jsonDataModel) { - variantIndexParams = new VariantIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/index")); @@ -575,7 +566,6 @@ private RestResponse launcherVariantIndex() throws Exception { VariantFileIndexJobLauncherParams variantFileIndexJobLauncherParams = null; if (commandOptions.jsonDataModel) { - variantFileIndexJobLauncherParams = new VariantFileIndexJobLauncherParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/index/launcher")); @@ -642,7 +632,6 @@ private RestResponse runVariantJulie() throws Exception { JulieParams julieParams = null; if (commandOptions.jsonDataModel) { - julieParams = new JulieParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/julie/run")); @@ -677,7 +666,6 @@ private RestResponse repairVariantMetadata() throws Exception { VariantStorageMetadataRepairToolParams variantStorageMetadataRepairToolParams = null; if (commandOptions.jsonDataModel) { - variantStorageMetadataRepairToolParams = new VariantStorageMetadataRepairToolParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/metadata/repair")); @@ -715,7 +703,6 @@ private RestResponse synchronizeVariantMetadata() throws Exception { VariantStorageMetadataSynchronizeParams variantStorageMetadataSynchronizeParams = null; if (commandOptions.jsonDataModel) { - variantStorageMetadataSynchronizeParams = new VariantStorageMetadataSynchronizeParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/metadata/synchronize")); @@ -749,7 +736,6 @@ private RestResponse pruneVariant() throws Exception { VariantPruneParams variantPruneParams = null; if (commandOptions.jsonDataModel) { - variantPruneParams = new VariantPruneParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/prune")); @@ -788,7 +774,6 @@ private RestResponse deleteVariantSample() throws Exception { VariantSampleDeleteParams variantSampleDeleteParams = null; if (commandOptions.jsonDataModel) { - variantSampleDeleteParams = new VariantSampleDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/sample/delete")); @@ -827,7 +812,6 @@ private RestResponse indexVariantSample() throws Exception { VariantSecondarySampleIndexParams variantSecondarySampleIndexParams = null; if (commandOptions.jsonDataModel) { - variantSecondarySampleIndexParams = new VariantSecondarySampleIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/sample/index")); @@ -865,7 +849,6 @@ private RestResponse variantSampleIndexConfigure() throws Exception { SampleIndexConfiguration sampleIndexConfiguration = null; if (commandOptions.jsonDataModel) { - sampleIndexConfiguration = new SampleIndexConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/sample/index/configure")); @@ -916,7 +899,6 @@ private RestResponse indexVariantScore() throws Exception { VariantScoreIndexParams variantScoreIndexParams = null; if (commandOptions.jsonDataModel) { - variantScoreIndexParams = new VariantScoreIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/score/index")); @@ -959,7 +941,6 @@ private RestResponse variantSecondaryAnnotationIndex() throws Exception { VariantSecondaryAnnotationIndexParams variantSecondaryAnnotationIndexParams = null; if (commandOptions.jsonDataModel) { - variantSecondaryAnnotationIndexParams = new VariantSecondaryAnnotationIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondary/annotation/index")); @@ -998,7 +979,6 @@ private RestResponse variantSecondarySampleIndex() throws Exception { VariantSecondarySampleIndexParams variantSecondarySampleIndexParams = null; if (commandOptions.jsonDataModel) { - variantSecondarySampleIndexParams = new VariantSecondarySampleIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondary/sample/index")); @@ -1036,7 +1016,6 @@ private RestResponse configureVariantSecondarySampleIndex() throws Exceptio SampleIndexConfiguration sampleIndexConfiguration = null; if (commandOptions.jsonDataModel) { - sampleIndexConfiguration = new SampleIndexConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondary/sample/index/configure")); @@ -1067,7 +1046,6 @@ private RestResponse secondaryIndexVariant() throws Exception { VariantSecondaryAnnotationIndexParams variantSecondaryAnnotationIndexParams = null; if (commandOptions.jsonDataModel) { - variantSecondaryAnnotationIndexParams = new VariantSecondaryAnnotationIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondaryIndex")); @@ -1125,7 +1103,6 @@ private RestResponse deleteVariantStats() throws Exception { VariantStatsDeleteParams variantStatsDeleteParams = null; if (commandOptions.jsonDataModel) { - variantStatsDeleteParams = new VariantStatsDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/stats/delete")); @@ -1163,7 +1140,6 @@ private RestResponse indexVariantStats() throws Exception { VariantStatsIndexParams variantStatsIndexParams = null; if (commandOptions.jsonDataModel) { - variantStatsIndexParams = new VariantStatsIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/stats/index")); @@ -1205,7 +1181,6 @@ private RestResponse deleteVariantStudy() throws Exception { VariantStudyDeleteParams variantStudyDeleteParams = null; if (commandOptions.jsonDataModel) { - variantStudyDeleteParams = new VariantStudyDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/study/delete")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java index 98bb7eb2814..e1f4f665965 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java @@ -103,7 +103,6 @@ private RestResponse create() throws Exception { ProjectCreateParams projectCreateParams = null; if (commandOptions.jsonDataModel) { - projectCreateParams = new ProjectCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/projects/create")); @@ -225,7 +224,6 @@ private RestResponse update() throws Exception { ProjectUpdateParams projectUpdateParams = null; if (commandOptions.jsonDataModel) { - projectUpdateParams = new ProjectUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/projects/{project}/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java index 7d0ebf47cc8..7b7041d8979 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java @@ -132,7 +132,6 @@ private RestResponse updateAcl() throws Exception { SampleAclUpdateParams sampleAclUpdateParams = null; if (commandOptions.jsonDataModel) { - sampleAclUpdateParams = new SampleAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/acl/{members}/update")); @@ -200,7 +199,6 @@ private RestResponse loadAnnotationSets() throws Exception { TsvAnnotationParams tsvAnnotationParams = null; if (commandOptions.jsonDataModel) { - tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/annotationSets/load")); @@ -236,7 +234,6 @@ private RestResponse create() throws Exception { SampleCreateParams sampleCreateParams = null; if (commandOptions.jsonDataModel) { - sampleCreateParams = new SampleCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/create")); @@ -474,7 +471,6 @@ private RestResponse update() throws Exception { SampleUpdateParams sampleUpdateParams = null; if (commandOptions.jsonDataModel) { - sampleUpdateParams = new SampleUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/{samples}/update")); @@ -534,7 +530,6 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception ObjectMap objectMap = null; if (commandOptions.jsonDataModel) { - objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/{sample}/annotationSets/{annotationSet}/annotations/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java index fef8f85a042..3ede6e70bfd 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java @@ -181,7 +181,6 @@ private RestResponse updateAcl() throws Exception { StudyAclUpdateParams studyAclUpdateParams = null; if (commandOptions.jsonDataModel) { - studyAclUpdateParams = new StudyAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/acl/{members}/update")); @@ -216,7 +215,6 @@ private RestResponse create() throws Exception { StudyCreateParams studyCreateParams = null; if (commandOptions.jsonDataModel) { - studyCreateParams = new StudyCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/create")); @@ -358,7 +356,6 @@ private RestResponse updateGroups() throws Exception { GroupCreateParams groupCreateParams = null; if (commandOptions.jsonDataModel) { - groupCreateParams = new GroupCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/groups/update")); @@ -389,7 +386,6 @@ private RestResponse updateGroupsUsers() throws Exception { GroupUpdateParams groupUpdateParams = null; if (commandOptions.jsonDataModel) { - groupUpdateParams = new GroupUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/groups/{group}/users/update")); @@ -426,7 +422,6 @@ private RestResponse updatePermissionRules() throws Exception { PermissionRule permissionRule = null; if (commandOptions.jsonDataModel) { - permissionRule = new PermissionRule(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/permissionRules/update")); @@ -509,7 +504,6 @@ private RestResponse update() throws Exception { StudyUpdateParams studyUpdateParams = null; if (commandOptions.jsonDataModel) { - studyUpdateParams = new StudyUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/update")); @@ -560,7 +554,6 @@ private RestResponse updateVariableSets() throws Exception { VariableSetCreateParams variableSetCreateParams = null; if (commandOptions.jsonDataModel) { - variableSetCreateParams = new VariableSetCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/variableSets/update")); @@ -594,7 +587,6 @@ private RestResponse updateVariableSetsVariables() throws Exception Variable variable = null; if (commandOptions.jsonDataModel) { - variable = new Variable(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/variableSets/{variableSet}/variables/update")); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java index f44e3449cc5..c2480761b0f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java @@ -134,7 +134,6 @@ private RestResponse password() throws Exception { PasswordChangeParams passwordChangeParams = null; if (commandOptions.jsonDataModel) { - passwordChangeParams = new PasswordChangeParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/users/password")); @@ -190,7 +189,6 @@ private RestResponse updateConfigs() throws Exception { ConfigUpdateParams configUpdateParams = null; if (commandOptions.jsonDataModel) { - configUpdateParams = new ConfigUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/users/{user}/configs/update")); @@ -255,7 +253,6 @@ private RestResponse update() throws Exception { UserUpdateParams userUpdateParams = null; if (commandOptions.jsonDataModel) { - userUpdateParams = new UserUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/users/{user}/update")); diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 1c4a4479bb0..21b9e768143 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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 5c97d7f69d1..8a5cd0de53b 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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 85629266564..d9e358e4632 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, filterId, user, users, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -10,37 +10,37 @@ setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, group, members, studies, study, templateId, variableSet, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, variableSet, group, templateId, studies, study, members, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, files, file, members, annotationSet, folder, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, annotationSet, folder, file, files, members, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, sample, annotationSet, members, samples, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, individuals, annotationSet, members, individual, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, members, family, families, annotationSet, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, family, families, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, cohort, members, cohorts, annotationSet, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, cohort, cohorts, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, members, interpretation, interpretations, clinicalAnalyses, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, clinicalAnalyses, interpretations, interpretation, members, clinicalAnalysis, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index 58c38ecb630..dc8d8f8f907 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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, clinicalAnalysis, members, interpretation, interpretations, clinicalAnalyses, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalyses, interpretations, interpretation, members, clinicalAnalysis, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index aeca965c7b2..81cae39da51 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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, cohort, members, cohorts, annotationSet, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, cohorts, annotationSet, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index 747382a2b15..b16d016404b 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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, families, annotationSet, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, family, families, annotationSet, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 89b8034de42..5251f640f97 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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, file, members, annotationSet, folder, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, folder, file, files, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index 98aaad0e987..d02b3cde65e 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index bf6750fc941..d26b4443259 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, individuals, annotationSet, members, individual, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index 37e3a2c9548..2fa40f4bb1a 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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, jobs, members, job, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index 481bae671e6..666c2bc2d65 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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 93934f11fef..84e56923789 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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 4d45393c182..c43aefd4e83 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 570ebfc9cf7..fca55584441 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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 319ded3abbb..1902a9802b9 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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, samples, members, sample, annotationSet, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, sample, annotationSet, members, samples, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 9873110e560..c5a9c65dbc2 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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, group, members, studies, study, templateId, variableSet, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, variableSet, group, templateId, studies, study, members, 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 458947e9b4e..75e1312fd44 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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, filterId, user, 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 1957998638d..20dcf8ed70d 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: 2023-11-02 +# Autogenerated on: 2023-11-03 # # 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 5460d28052e..712a7c20af5 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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 33a9c268320..b44121e5a72 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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 a322c2c9e3b..eb7f743ba10 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 9631f0aacb0..ad36e64ed70 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index 7e60a93d950..cfa9601a978 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index 25e941e8b0b..b524791ca20 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 7abe70688b7..97a97aaa3a2 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index 45eea839db8..624e63f5837 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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 478a20a285a..3d60c1d23aa 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index cf96ffaaf61..c377f59750b 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index 6dd12a34e12..4c127e53014 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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 3db333e8d16..46e60e4ce05 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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 e80e58efb11..abbfcda3ee1 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index df90b1e2153..7501055226c 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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 736744268b5..1662f2637ac 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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 d85feb6f179..00082995e1d 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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 2e20373c6d7..897c7238585 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: 2023-11-02 +* Autogenerated on: 2023-11-03 * * 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 0522ec1c5a9..418a0581e82 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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 6f3df1f5998..beeafc20632 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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 6431faa5cf3..1212831ff4b 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 6a234b6554e..d7c504eb522 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index 21eb1f0422e..d8a09b02b0c 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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/Family.js b/opencga-client/src/main/javascript/Family.js index cae578e4413..de43021a504 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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/File.js b/opencga-client/src/main/javascript/File.js index 63ce3b943da..e755e011718 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index 611b81c5727..f3173a19f88 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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 534e2d3c7ed..3949189d8d8 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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/Job.js b/opencga-client/src/main/javascript/Job.js index be7c71c00e7..85872676aee 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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/Meta.js b/opencga-client/src/main/javascript/Meta.js index 07bd4c5b07c..6c314393866 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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 54dd86064a5..d3df6335892 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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 42cd10689ae..7e6faef19ec 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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/Study.js b/opencga-client/src/main/javascript/Study.js index 4c6931b0c89..f1a64ad76bc 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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 2db00a202b2..b608f4ddf47 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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 5edd6753b11..d001b9138be 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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 b9f8f029258..f6308428e08 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: 2023-11-02 + * Autogenerated on: 2023-11-03 * * 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 972e456556c..2dd26790249 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: 2023-11-02 + Autogenerated on: 2023-11-03 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 1b598296913..70295d0eed4 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: 2023-11-02 + Autogenerated on: 2023-11-03 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 3bd95f48564..ce670c939a5 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: 2023-11-02 + Autogenerated on: 2023-11-03 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/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index 1eea42c98a3..4494f9564a2 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: 2023-11-02 + Autogenerated on: 2023-11-03 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/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index eb9aea88c65..61b41a907d1 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: 2023-11-02 + Autogenerated on: 2023-11-03 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/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index f78c61e2a5a..ef3ab2d231b 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: 2023-11-02 + Autogenerated on: 2023-11-03 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/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index a65add7cf7e..466f5c46cb0 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: 2023-11-02 + Autogenerated on: 2023-11-03 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/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index f4e96d25df2..8802e16df45 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: 2023-11-02 + Autogenerated on: 2023-11-03 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 fadca48f497..5142cc5132a 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: 2023-11-02 + Autogenerated on: 2023-11-03 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/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index e8f18894ef9..6c24a55fbf0 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: 2023-11-02 + Autogenerated on: 2023-11-03 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/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index dd437e17394..cd7536a5f85 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: 2023-11-02 + Autogenerated on: 2023-11-03 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 dac784edf9a..03c4fde1eda 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: 2023-11-02 + Autogenerated on: 2023-11-03 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 b13fec2f082..9adf7677cb8 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: 2023-11-02 + Autogenerated on: 2023-11-03 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/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index d4312e58800..f4e9db46b1e 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: 2023-11-02 + Autogenerated on: 2023-11-03 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 2d6a136c750..4cae5fc0437 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: 2023-11-02 + Autogenerated on: 2023-11-03 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 c3c298dbbc6..1c71eecfa0b 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: 2023-11-02 + Autogenerated on: 2023-11-03 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 f0357486079..01015fe28d5 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: 2023-11-02 + Autogenerated on: 2023-11-03 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-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java index f9c5c7d0f18..f8daa4e2fe2 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java @@ -371,7 +371,6 @@ private String getBodyParams(RestCategory restCategory, RestEndpoint restEndpoin sb.append("\n " + bodyClassName + " " + variableName + " = null;"); sb.append("\n if (commandOptions.jsonDataModel) {"); - sb.append("\n " + variableName + " = new " + bodyClassName + "();"); sb.append("\n RestResponse<" + getValidResponseNames(restEndpoint.getResponse()) + "> res = new RestResponse<>();"); sb.append("\n res.setType(QueryType.VOID);"); sb.append("\n PrintUtils.println(getObjectAsJSON(categoryName,\""+restEndpoint.getPath()+"\"));"); From f79c126b99d5b8b4b5c5b1665b3b67f6ca8091ec Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 27 Nov 2023 16:57:57 +0100 Subject: [PATCH 4/5] OpencgaCommandExecutor: code refactor #TASK-5160 --- .../app/cli/main/executors/OpencgaCommandExecutor.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java index b46e5f387ab..8f935c36ff8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java @@ -225,7 +225,7 @@ public OpencgaCommandExecutor setOpenCGAClient(OpenCGAClient openCGAClient) { } public String getObjectAsJSON(String objectCategory, String objectPath) throws Exception { - String jsonInString = "\n"; + StringBuilder jsonInString = new StringBuilder("\n"); try { ObjectMap queryParams = new ObjectMap(); queryParams.putIfNotEmpty("category", objectCategory); @@ -241,11 +241,11 @@ public String getObjectAsJSON(String objectCategory, String objectPath) throws E //jsonInString += parameter.getName()+":"+parameter.getAllowedValues()+"\n"; if (parameter.getData() != null) { enc = true; - jsonInString += printBody(parameter.getData(), ""); + jsonInString.append(printBody(parameter.getData(), "")); } } if (!enc) { - jsonInString += "No model available"; + jsonInString.append("No model available"); } // } @@ -253,10 +253,10 @@ public String getObjectAsJSON(String objectCategory, String objectPath) throws E } } } catch (Exception e) { - jsonInString = "Data model not found."; + jsonInString = new StringBuilder("Data model not found."); CommandLineUtils.error(e); } - return jsonInString; + return jsonInString.toString(); } private String printBody(List data, String tabs) { From 67fe7a2b1004fd0ab321e997c02c7b033a1edd24 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 28 Nov 2023 14:21:23 +0100 Subject: [PATCH 5/5] cli: Autogenerated CLI and clients for release 2.12.1 --- .../opencga/app/cli/main/OpenCgaCompleter.java | 2 +- .../app/cli/main/OpencgaCliOptionsParser.java | 2 +- opencga-client/src/main/R/R/Admin-methods.R | 2 +- opencga-client/src/main/R/R/Alignment-methods.R | 2 +- opencga-client/src/main/R/R/AllGenerics.R | 16 ++++++++-------- opencga-client/src/main/R/R/Clinical-methods.R | 4 ++-- opencga-client/src/main/R/R/Cohort-methods.R | 4 ++-- opencga-client/src/main/R/R/Family-methods.R | 4 ++-- opencga-client/src/main/R/R/File-methods.R | 4 ++-- opencga-client/src/main/R/R/GA4GH-methods.R | 2 +- opencga-client/src/main/R/R/Individual-methods.R | 4 ++-- opencga-client/src/main/R/R/Job-methods.R | 4 ++-- opencga-client/src/main/R/R/Meta-methods.R | 2 +- opencga-client/src/main/R/R/Operation-methods.R | 2 +- opencga-client/src/main/R/R/Panel-methods.R | 2 +- opencga-client/src/main/R/R/Project-methods.R | 2 +- opencga-client/src/main/R/R/Sample-methods.R | 4 ++-- opencga-client/src/main/R/R/Study-methods.R | 4 ++-- opencga-client/src/main/R/R/User-methods.R | 2 +- opencga-client/src/main/R/R/Variant-methods.R | 2 +- .../opencga/client/rest/clients/AdminClient.java | 2 +- .../client/rest/clients/AlignmentClient.java | 2 +- .../rest/clients/ClinicalAnalysisClient.java | 2 +- .../client/rest/clients/CohortClient.java | 2 +- .../client/rest/clients/DiseasePanelClient.java | 2 +- .../client/rest/clients/FamilyClient.java | 2 +- .../opencga/client/rest/clients/FileClient.java | 2 +- .../opencga/client/rest/clients/GA4GHClient.java | 2 +- .../client/rest/clients/IndividualClient.java | 2 +- .../opencga/client/rest/clients/JobClient.java | 2 +- .../opencga/client/rest/clients/MetaClient.java | 2 +- .../client/rest/clients/ProjectClient.java | 2 +- .../client/rest/clients/SampleClient.java | 2 +- .../opencga/client/rest/clients/StudyClient.java | 2 +- .../opencga/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 +- opencga-client/src/main/javascript/Alignment.js | 2 +- .../src/main/javascript/ClinicalAnalysis.js | 2 +- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- opencga-client/src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- 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 +- .../pyopencga/rest_clients/alignment_client.py | 2 +- .../rest_clients/clinical_analysis_client.py | 2 +- .../pyopencga/rest_clients/cohort_client.py | 2 +- .../rest_clients/disease_panel_client.py | 2 +- .../pyopencga/rest_clients/family_client.py | 2 +- .../python/pyopencga/rest_clients/file_client.py | 2 +- .../pyopencga/rest_clients/ga4gh_client.py | 2 +- .../pyopencga/rest_clients/individual_client.py | 2 +- .../python/pyopencga/rest_clients/job_client.py | 2 +- .../python/pyopencga/rest_clients/meta_client.py | 2 +- .../pyopencga/rest_clients/project_client.py | 2 +- .../pyopencga/rest_clients/sample_client.py | 2 +- .../pyopencga/rest_clients/study_client.py | 2 +- .../python/pyopencga/rest_clients/user_client.py | 2 +- .../pyopencga/rest_clients/variant_client.py | 2 +- .../rest_clients/variant_operation_client.py | 2 +- 71 files changed, 86 insertions(+), 86 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 b80af90ba5e..4044ac48785 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 2015-2023-11-21 OpenCB +* Copyright 2015-2023-11-28 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 a02dfa83516..cd4539d7081 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 2015-2023-11-21 OpenCB +* Copyright 2015-2023-11-28 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-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index ae477210b1e..7edd463fead 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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 8560a244847..8135945335d 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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 b0068c9950b..80478a6a723 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -10,37 +10,37 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, templateId, members, studies, variableSet, study, group, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, members, variableSet, group, studies, templateId, study, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, folder, members, file, annotationSet, files, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, annotationSet, members, folder, files, file, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, annotationSet, members, samples, sample, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, annotationSet, sample, members, samples, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, annotationSet, individual, members, individuals, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, annotationSet, members, families, family, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, cohorts, members, cohort, annotationSet, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, annotationSet, cohort, members, cohorts, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, members, interpretation, interpretations, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index fab63cdbd0a..497a2a4e445 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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, clinicalAnalysis, clinicalAnalyses, members, interpretation, interpretations, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 81c5bfaf062..6741defa9a8 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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, cohorts, members, cohort, annotationSet, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohort, members, cohorts, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index 82c680e4aa1..0bc8e789cae 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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, family, members, families, annotationSet, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, members, families, family, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 224889cbec9..d8b546b1355 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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, folder, members, file, annotationSet, files, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, members, folder, files, file, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index 26788aad18d..9519d1e4e0d 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index c2b5f47ee01..46cca7764b8 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, annotationSet, individual, members, individuals, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index ed99e482cc8..7f0068090ec 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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, jobs, members, job, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index dd5036d5550..a44217acaf5 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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 dd9eb327ea9..28b608bb78a 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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 541d68f22e9..5e341b9d767 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 14d48a37e54..1509cf6470e 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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 43d03aec39d..2f1eb1494c3 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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, annotationSet, members, samples, sample, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, sample, members, samples, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 5b77ac8bf5c..1121835fa7d 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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, templateId, members, studies, variableSet, study, group, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, members, variableSet, group, studies, templateId, study, 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 0ded200ca86..43a27f93168 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 6d2f29fe872..05d2a81c35f 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: 2023-11-21 +# Autogenerated on: 2023-11-28 # # 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 ea9053acf3e..f91feeafed7 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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 9c00f1476bc..292d2a1d7a7 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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 97d4dc4846c..bee2385969b 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 8991b50f7b8..ee62858466e 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index fc3bce5fd21..57f3e8020fc 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index f0b96f0ad27..8bf553d4885 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 26420fe0854..483ec904b76 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index 23247404844..2df19bf3ac2 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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 563387f83f9..4c5291d9592 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index 44c77b3ce80..1591b8722ce 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index ef9f54e6ebe..8da55a76d03 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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 aae1fef2033..2a5f21b3ff5 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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 12346da3ee2..34dd6c9076a 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 59756fd7d52..5e16287a2b2 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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 c90bfd45d6b..0bfcaa59932 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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 ca8635f527a..6ee33c331df 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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 0010eb4f421..2637e2ebeb3 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: 2023-11-21 +* Autogenerated on: 2023-11-28 * * 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 ae4ecad6de0..ef4a5ef42b9 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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 74e50dd5dfc..55672582aa7 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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 ed55809ab52..9359eff7999 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 60b4352621f..1aba25258cd 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index f6bbac654c9..a72675f7fcf 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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/Family.js b/opencga-client/src/main/javascript/Family.js index 0269e3aade4..85170821c51 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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/File.js b/opencga-client/src/main/javascript/File.js index c1bc508be19..a83abdb15f6 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index 24a2b3549b7..1b018b3cad5 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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 e2379cf23c1..ac584fa65a2 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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/Job.js b/opencga-client/src/main/javascript/Job.js index 6ad0b13df0a..02b18815c69 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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/Meta.js b/opencga-client/src/main/javascript/Meta.js index 36ae34309b9..7553b05f43d 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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 b885aa0f47d..fd0de7a20c6 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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 df98105cf52..314c05f5726 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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/Study.js b/opencga-client/src/main/javascript/Study.js index e49505ffb54..39d27e28279 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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 ce5c939d795..6768443952a 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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 c20587da1a2..07963160849 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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 1258093c63a..89fd13f071a 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: 2023-11-21 + * Autogenerated on: 2023-11-28 * * 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 4a5396ee94d..a9fab8bb5ca 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: 2023-11-21 + Autogenerated on: 2023-11-28 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 ddd22c8b5f6..262aa8310fa 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: 2023-11-21 + Autogenerated on: 2023-11-28 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 349eadc2182..eb5c777e105 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: 2023-11-21 + Autogenerated on: 2023-11-28 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/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index 1de3e0ed592..e8dbcb72224 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: 2023-11-21 + Autogenerated on: 2023-11-28 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/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index 60340ec0b23..bd716eec69d 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: 2023-11-21 + Autogenerated on: 2023-11-28 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/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index dc4009aec05..49dc4fda423 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: 2023-11-21 + Autogenerated on: 2023-11-28 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/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 3f5c805c15d..d8d5e48f981 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: 2023-11-21 + Autogenerated on: 2023-11-28 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/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index 5abb3fe6d58..4f12022699d 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: 2023-11-21 + Autogenerated on: 2023-11-28 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 2b1fa810d9a..f93b1b7bc45 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: 2023-11-21 + Autogenerated on: 2023-11-28 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/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index ae188fd17cc..ac1beb600a7 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: 2023-11-21 + Autogenerated on: 2023-11-28 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/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index 6b5eaca3dc0..69a0504d168 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: 2023-11-21 + Autogenerated on: 2023-11-28 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 7a80400e608..6061ee85a37 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: 2023-11-21 + Autogenerated on: 2023-11-28 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 6308e43511f..5158e8e6942 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: 2023-11-21 + Autogenerated on: 2023-11-28 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/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 5eba973d147..ed4f05a5533 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: 2023-11-21 + Autogenerated on: 2023-11-28 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 60d21d9ce9b..01a30231982 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: 2023-11-21 + Autogenerated on: 2023-11-28 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 08c8e1b19fb..b8bcda16371 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: 2023-11-21 + Autogenerated on: 2023-11-28 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 c07754aa34d..0f374b14d97 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: 2023-11-21 + Autogenerated on: 2023-11-28 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.