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()+"\"));");