diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index ee9f603f739..7d088edef53 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-09-12 OpenCB +* Copyright 2015-2023-10-27 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index 832d5638d49..279ccd36197 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-09-12 OpenCB +* Copyright 2015-2023-10-27 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java index a16efb4df47..0ab7c6405dc 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java @@ -48,6 +48,7 @@ */ public class AdminCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "admin"; public AdminCommandOptions adminCommandOptions; public AdminCommandExecutor(AdminCommandOptions adminCommandOptions) throws CatalogAuthenticationException { @@ -138,7 +139,7 @@ private RestResponse installCatalog() throws Exception { installationParams = new InstallationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(installationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/install")); return res; } else if (commandOptions.jsonFile != null) { installationParams = JacksonUtils.getDefaultObjectMapper() @@ -167,7 +168,7 @@ private RestResponse jwtCatalog() throws Exception { jWTParams = new JWTParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(jWTParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/jwt")); return res; } else if (commandOptions.jsonFile != null) { jWTParams = JacksonUtils.getDefaultObjectMapper() @@ -193,7 +194,7 @@ private RestResponse createUsers() throws Exception { userCreateParams = new UserCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(userCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/create")); return res; } else if (commandOptions.jsonFile != null) { userCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -224,7 +225,7 @@ private RestResponse importUsers() throws Exception { userImportParams = new UserImportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(userImportParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/import")); return res; } else if (commandOptions.jsonFile != null) { userImportParams = JacksonUtils.getDefaultObjectMapper() @@ -272,7 +273,7 @@ private RestResponse syncUsers() throws Exception { groupSyncParams = new GroupSyncParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(groupSyncParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/sync")); return res; } else if (commandOptions.jsonFile != null) { groupSyncParams = JacksonUtils.getDefaultObjectMapper() @@ -308,7 +309,7 @@ private RestResponse usersUpdateGroups() throws Exception { userUpdateGroup = new UserUpdateGroup(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(userUpdateGroup)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/{user}/groups/update")); return res; } else if (commandOptions.jsonFile != null) { userUpdateGroup = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java index 328a83daeb4..60c7752ddbe 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java @@ -48,6 +48,7 @@ */ public class AnalysisAlignmentCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "analysisAlignment"; public AnalysisAlignmentCommandOptions analysisAlignmentCommandOptions; public AnalysisAlignmentCommandExecutor(AnalysisAlignmentCommandOptions analysisAlignmentCommandOptions) throws CatalogAuthenticationException { @@ -134,7 +135,7 @@ private RestResponse runBwa() throws Exception { bwaWrapperParams = new BwaWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(bwaWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/bwa/run")); return res; } else if (commandOptions.jsonFile != null) { bwaWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -176,7 +177,7 @@ private RestResponse runCoverageIndex() throws Exception { coverageIndexParams = new CoverageIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(coverageIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/coverage/index/run")); return res; } else if (commandOptions.jsonFile != null) { coverageIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -215,7 +216,7 @@ private RestResponse coverageQcGeneCoverageStatsRun() throws Exception { alignmentGeneCoverageStatsParams = new AlignmentGeneCoverageStatsParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(alignmentGeneCoverageStatsParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/coverage/qc/geneCoverageStats/run")); return res; } else if (commandOptions.jsonFile != null) { alignmentGeneCoverageStatsParams = JacksonUtils.getDefaultObjectMapper() @@ -311,7 +312,7 @@ private RestResponse runDeeptools() throws Exception { deeptoolsWrapperParams = new DeeptoolsWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(deeptoolsWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/deeptools/run")); return res; } else if (commandOptions.jsonFile != null) { deeptoolsWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -350,7 +351,7 @@ private RestResponse runFastqc() throws Exception { fastqcWrapperParams = new FastqcWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fastqcWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/fastqc/run")); return res; } else if (commandOptions.jsonFile != null) { fastqcWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -389,7 +390,7 @@ private RestResponse runIndex() throws Exception { alignmentIndexParams = new AlignmentIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(alignmentIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/index/run")); return res; } else if (commandOptions.jsonFile != null) { alignmentIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -427,7 +428,7 @@ private RestResponse runPicard() throws Exception { picardWrapperParams = new PicardWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(picardWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/picard/run")); return res; } else if (commandOptions.jsonFile != null) { picardWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -466,7 +467,7 @@ private RestResponse runQc() throws Exception { alignmentQcParams = new AlignmentQcParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(alignmentQcParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/qc/run")); return res; } else if (commandOptions.jsonFile != null) { alignmentQcParams = JacksonUtils.getDefaultObjectMapper() @@ -538,7 +539,7 @@ private RestResponse runSamtools() throws Exception { samtoolsWrapperParams = new SamtoolsWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(samtoolsWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/samtools/run")); return res; } else if (commandOptions.jsonFile != null) { samtoolsWrapperParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java index 3039ab1cc68..0bd8b87285e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java @@ -80,6 +80,7 @@ */ public class AnalysisClinicalCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "analysisClinical"; public AnalysisClinicalCommandOptions analysisClinicalCommandOptions; public AnalysisClinicalCommandExecutor(AnalysisClinicalCommandOptions analysisClinicalCommandOptions) throws CatalogAuthenticationException { @@ -217,7 +218,7 @@ private RestResponse updateAcl() throws Exception clinicalAnalysisAclUpdateParams = new ClinicalAnalysisAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(clinicalAnalysisAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { clinicalAnalysisAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -251,7 +252,7 @@ private RestResponse updateClinicalConfiguration() throws Exception { clinicalAnalysisStudyConfiguration = new ClinicalAnalysisStudyConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(clinicalAnalysisStudyConfiguration)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/clinical/configuration/update")); return res; } else if (commandOptions.jsonFile != null) { clinicalAnalysisStudyConfiguration = JacksonUtils.getDefaultObjectMapper() @@ -288,7 +289,7 @@ private RestResponse create() throws Exception { clinicalAnalysisCreateParams = new ClinicalAnalysisCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(clinicalAnalysisCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/create")); return res; } else if (commandOptions.jsonFile != null) { clinicalAnalysisCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -467,7 +468,7 @@ private RestResponse runInterpreterCancerTiering() throws Exception { cancerTieringInterpretationAnalysisParams = new CancerTieringInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cancerTieringInterpretationAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/cancerTiering/run")); return res; } else if (commandOptions.jsonFile != null) { cancerTieringInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -506,7 +507,7 @@ private RestResponse runInterpreterExomiser() throws Exception { exomiserInterpretationAnalysisParams = new ExomiserInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(exomiserInterpretationAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/exomiser/run")); return res; } else if (commandOptions.jsonFile != null) { exomiserInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -543,7 +544,7 @@ private RestResponse runInterpreterTeam() throws Exception { teamInterpretationAnalysisParams = new TeamInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(teamInterpretationAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/team/run")); return res; } else if (commandOptions.jsonFile != null) { teamInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -583,7 +584,7 @@ private RestResponse runInterpreterTiering() throws Exception { tieringInterpretationAnalysisParams = new TieringInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tieringInterpretationAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/tiering/run")); return res; } else if (commandOptions.jsonFile != null) { tieringInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -623,7 +624,7 @@ private RestResponse runInterpreterZetta() throws Exception { zettaInterpretationAnalysisParams = new ZettaInterpretationAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(zettaInterpretationAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/zetta/run")); return res; } else if (commandOptions.jsonFile != null) { zettaInterpretationAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -826,7 +827,7 @@ private RestResponse runRgaIndex() throws Exception { rgaAnalysisParams = new RgaAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(rgaAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/rga/index/run")); return res; } else if (commandOptions.jsonFile != null) { rgaAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1166,7 +1167,7 @@ private RestResponse update() throws Exception { clinicalAnalysisUpdateParams = new ClinicalAnalysisUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(clinicalAnalysisUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalyses}/update")); return res; } else if (commandOptions.jsonFile != null) { clinicalAnalysisUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -1241,7 +1242,7 @@ private RestResponse createInterpretation() throws Exception { interpretationCreateParams = new InterpretationCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(interpretationCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create")); return res; } else if (commandOptions.jsonFile != null) { interpretationCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -1331,7 +1332,7 @@ private RestResponse updateInterpretation() throws Exception { interpretationUpdateParams = new InterpretationUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(interpretationUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update")); return res; } else if (commandOptions.jsonFile != null) { interpretationUpdateParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java index 601ea3739bf..418b0c3ac40 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java @@ -76,6 +76,7 @@ */ public class AnalysisVariantCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "analysisVariant"; public AnalysisVariantCommandOptions analysisVariantCommandOptions; public AnalysisVariantCommandExecutor(AnalysisVariantCommandOptions analysisVariantCommandOptions) throws CatalogAuthenticationException { @@ -315,7 +316,7 @@ private RestResponse runCircos() throws Exception { circosAnalysisParams = new CircosAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(circosAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/circos/run")); return res; } else if (commandOptions.jsonFile != null) { circosAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -384,7 +385,7 @@ private RestResponse runCohortStats() throws Exception { cohortVariantStatsAnalysisParams = new CohortVariantStatsAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cohortVariantStatsAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/cohort/stats/run")); return res; } else if (commandOptions.jsonFile != null) { cohortVariantStatsAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -425,7 +426,7 @@ private RestResponse runExomiser() throws Exception { exomiserWrapperParams = new ExomiserWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(exomiserWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/exomiser/run")); return res; } else if (commandOptions.jsonFile != null) { exomiserWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -466,7 +467,7 @@ private RestResponse runExport() throws Exception { variantExportParams = new VariantExportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantExportParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/export/run")); return res; } else if (commandOptions.jsonFile != null) { variantExportParams = JacksonUtils.getDefaultObjectMapper() @@ -607,7 +608,7 @@ private RestResponse runFamilyQc() throws Exception { familyQcAnalysisParams = new FamilyQcAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(familyQcAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/family/qc/run")); return res; } else if (commandOptions.jsonFile != null) { familyQcAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -667,7 +668,7 @@ private RestResponse runGatk() throws Exception { gatkWrapperParams = new GatkWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(gatkWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/gatk/run")); return res; } else if (commandOptions.jsonFile != null) { gatkWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -706,7 +707,7 @@ private RestResponse runGenomePlot() throws Exception { genomePlotAnalysisParams = new GenomePlotAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(genomePlotAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/genomePlot/run")); return res; } else if (commandOptions.jsonFile != null) { genomePlotAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -747,7 +748,7 @@ private RestResponse runGwas() throws Exception { gwasAnalysisParams = new GwasAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(gwasAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/gwas/run")); return res; } else if (commandOptions.jsonFile != null) { gwasAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -795,7 +796,7 @@ private RestResponse runHrDetect() throws Exception { hRDetectAnalysisParams = new HRDetectAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(hRDetectAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/hrDetect/run")); return res; } else if (commandOptions.jsonFile != null) { hRDetectAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -844,7 +845,7 @@ private RestResponse runIndex() throws Exception { variantIndexParams = new VariantIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/index/run")); return res; } else if (commandOptions.jsonFile != null) { variantIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -909,7 +910,7 @@ private RestResponse runIndividualQc() throws Exception { individualQcAnalysisParams = new IndividualQcAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(individualQcAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/individual/qc/run")); return res; } else if (commandOptions.jsonFile != null) { individualQcAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -949,7 +950,7 @@ private RestResponse runInferredSex() throws Exception { inferredSexAnalysisParams = new InferredSexAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(inferredSexAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/inferredSex/run")); return res; } else if (commandOptions.jsonFile != null) { inferredSexAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1022,7 +1023,7 @@ private RestResponse runKnockout() throws Exception { knockoutAnalysisParams = new KnockoutAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(knockoutAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/knockout/run")); return res; } else if (commandOptions.jsonFile != null) { knockoutAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1068,7 +1069,7 @@ private RestResponse runMendelianError() throws Exception { mendelianErrorAnalysisParams = new MendelianErrorAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(mendelianErrorAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/mendelianError/run")); return res; } else if (commandOptions.jsonFile != null) { mendelianErrorAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1161,7 +1162,7 @@ private RestResponse runMutationalSignature() throws Exception { mutationalSignatureAnalysisParams = new MutationalSignatureAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(mutationalSignatureAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/mutationalSignature/run")); return res; } else if (commandOptions.jsonFile != null) { mutationalSignatureAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1213,7 +1214,7 @@ private RestResponse runPlink() throws Exception { plinkWrapperParams = new PlinkWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(plinkWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/plink/run")); return res; } else if (commandOptions.jsonFile != null) { plinkWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -1341,7 +1342,7 @@ private RestResponse runRelatedness() throws Exception { relatednessAnalysisParams = new RelatednessAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(relatednessAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/relatedness/run")); return res; } else if (commandOptions.jsonFile != null) { relatednessAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1382,7 +1383,7 @@ private RestResponse runRvtests() throws Exception { rvtestsWrapperParams = new RvtestsWrapperParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(rvtestsWrapperParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/rvtests/run")); return res; } else if (commandOptions.jsonFile != null) { rvtestsWrapperParams = JacksonUtils.getDefaultObjectMapper() @@ -1456,7 +1457,7 @@ private RestResponse runSampleEligibility() throws Exception { sampleEligibilityAnalysisParams = new SampleEligibilityAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleEligibilityAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/eligibility/run")); return res; } else if (commandOptions.jsonFile != null) { sampleEligibilityAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1495,7 +1496,7 @@ private RestResponse runSampleQc() throws Exception { sampleQcAnalysisParams = new SampleQcAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleQcAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/qc/run")); return res; } else if (commandOptions.jsonFile != null) { sampleQcAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1596,7 +1597,7 @@ private RestResponse runSample() throws Exception { sampleVariantFilterParams = new SampleVariantFilterParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleVariantFilterParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/run")); return res; } else if (commandOptions.jsonFile != null) { sampleVariantFilterParams = JacksonUtils.getDefaultObjectMapper() @@ -1690,7 +1691,7 @@ private RestResponse runSampleStats() throws Exception { sampleVariantStatsAnalysisParams = new SampleVariantStatsAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleVariantStatsAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/sample/stats/run")); return res; } else if (commandOptions.jsonFile != null) { sampleVariantStatsAnalysisParams = JacksonUtils.getDefaultObjectMapper() @@ -1763,7 +1764,7 @@ private RestResponse runStatsExport() throws Exception { variantStatsExportParams = new VariantStatsExportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStatsExportParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/stats/export/run")); return res; } else if (commandOptions.jsonFile != null) { variantStatsExportParams = JacksonUtils.getDefaultObjectMapper() @@ -1804,7 +1805,7 @@ private RestResponse runStats() throws Exception { variantStatsAnalysisParams = new VariantStatsAnalysisParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStatsAnalysisParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/variant/stats/run")); return res; } else if (commandOptions.jsonFile != null) { variantStatsAnalysisParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java index 92677f27fa4..4767a83173c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java @@ -50,6 +50,7 @@ */ public class CohortsCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "cohorts"; public CohortsCommandOptions cohortsCommandOptions; public CohortsCommandExecutor(CohortsCommandOptions cohortsCommandOptions) throws CatalogAuthenticationException { @@ -129,7 +130,7 @@ private RestResponse updateAcl() throws Exception { cohortAclUpdateParams = new CohortAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cohortAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { cohortAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -190,7 +191,7 @@ private RestResponse loadAnnotationSets() throws Exception { tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tsvAnnotationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/annotationSets/load")); return res; } else if (commandOptions.jsonFile != null) { tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper() @@ -228,7 +229,7 @@ private RestResponse create() throws Exception { cohortCreateParams = new CohortCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cohortCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/create")); return res; } else if (commandOptions.jsonFile != null) { cohortCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -314,7 +315,7 @@ private RestResponse generate() throws Exception { cohortGenerateParams = new CohortGenerateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cohortGenerateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/generate")); return res; } else if (commandOptions.jsonFile != null) { cohortGenerateParams = JacksonUtils.getDefaultObjectMapper() @@ -441,7 +442,7 @@ private RestResponse update() throws Exception { cohortUpdateParams = new CohortUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cohortUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/{cohorts}/update")); return res; } else if (commandOptions.jsonFile != null) { cohortUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -484,7 +485,7 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(objectMap)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/cohorts/{cohort}/annotationSets/{annotationSet}/annotations/update")); return res; } else if (commandOptions.jsonFile != null) { objectMap = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java index 3e05c22aa5f..5c6446b45e4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java @@ -44,6 +44,7 @@ */ public class DiseasePanelsCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "diseasePanels"; public DiseasePanelsCommandOptions diseasePanelsCommandOptions; public DiseasePanelsCommandExecutor(DiseasePanelsCommandOptions diseasePanelsCommandOptions) throws CatalogAuthenticationException { @@ -114,7 +115,7 @@ private RestResponse updateAcl() throws Exception { panelAclUpdateParams = new PanelAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(panelAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { panelAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -151,7 +152,7 @@ private RestResponse create() throws Exception { panelCreateParams = new PanelCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(panelCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/create")); return res; } else if (commandOptions.jsonFile != null) { panelCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -230,7 +231,7 @@ private RestResponse importPanels() throws Exception { panelImportParams = new PanelImportParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(panelImportParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/import")); return res; } else if (commandOptions.jsonFile != null) { panelImportParams = JacksonUtils.getDefaultObjectMapper() @@ -352,7 +353,7 @@ private RestResponse update() throws Exception { panelUpdateParams = new PanelUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(panelUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/panels/{panels}/update")); return res; } else if (commandOptions.jsonFile != null) { panelUpdateParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java index 35e1596aba4..60a56535f4a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java @@ -50,6 +50,7 @@ */ public class FamiliesCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "families"; public FamiliesCommandOptions familiesCommandOptions; public FamiliesCommandExecutor(FamiliesCommandOptions familiesCommandOptions) throws CatalogAuthenticationException { @@ -127,7 +128,7 @@ private RestResponse updateAcl() throws Exception { familyAclUpdateParams = new FamilyAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(familyAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { familyAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -192,7 +193,7 @@ private RestResponse loadAnnotationSets() throws Exception { tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tsvAnnotationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/annotationSets/load")); return res; } else if (commandOptions.jsonFile != null) { tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper() @@ -229,7 +230,7 @@ private RestResponse create() throws Exception { familyCreateParams = new FamilyCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(familyCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/create")); return res; } else if (commandOptions.jsonFile != null) { familyCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -393,7 +394,7 @@ private RestResponse update() throws Exception { familyUpdateParams = new FamilyUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(familyUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/{families}/update")); return res; } else if (commandOptions.jsonFile != null) { familyUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -437,7 +438,7 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(objectMap)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/families/{family}/annotationSets/{annotationSet}/annotations/update")); return res; } else if (commandOptions.jsonFile != null) { objectMap = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java index 039e0d536e3..b4cfc6fdb9f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java @@ -96,6 +96,7 @@ */ public class FilesCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "files"; public FilesCommandOptions filesCommandOptions; public FilesCommandExecutor(FilesCommandOptions filesCommandOptions) throws CatalogAuthenticationException { @@ -220,7 +221,7 @@ private RestResponse updateAcl() throws Exception { fileAclUpdateParams = new FileAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { fileAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -290,7 +291,7 @@ private RestResponse loadAnnotationSets() throws Exception { tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tsvAnnotationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/annotationSets/load")); return res; } else if (commandOptions.jsonFile != null) { tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper() @@ -331,7 +332,7 @@ private RestResponse create() throws Exception { fileCreateParams = new FileCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/create")); return res; } else if (commandOptions.jsonFile != null) { fileCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -427,7 +428,7 @@ private RestResponse fetch() throws Exception { fileFetch = new FileFetch(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileFetch)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/fetch")); return res; } else if (commandOptions.jsonFile != null) { fileFetch = JacksonUtils.getDefaultObjectMapper() @@ -469,7 +470,7 @@ private RestResponse link() throws Exception { fileLinkParams = new FileLinkParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileLinkParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/link")); return res; } else if (commandOptions.jsonFile != null) { fileLinkParams = JacksonUtils.getDefaultObjectMapper() @@ -515,7 +516,7 @@ private RestResponse runLink() throws Exception { fileLinkToolParams = new FileLinkToolParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileLinkToolParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/link/run")); return res; } else if (commandOptions.jsonFile != null) { fileLinkToolParams = JacksonUtils.getDefaultObjectMapper() @@ -557,7 +558,7 @@ private RestResponse runPostlink() throws Exception { postLinkToolParams = new PostLinkToolParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(postLinkToolParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/postlink/run")); return res; } else if (commandOptions.jsonFile != null) { postLinkToolParams = JacksonUtils.getDefaultObjectMapper() @@ -723,7 +724,7 @@ private RestResponse update() throws Exception { fileUpdateParams = new FileUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(fileUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/{files}/update")); return res; } else if (commandOptions.jsonFile != null) { fileUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -790,7 +791,7 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception { objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(objectMap)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/files/{file}/annotationSets/{annotationSet}/annotations/update")); return res; } else if (commandOptions.jsonFile != null) { objectMap = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java index 86fcc2f8d58..0675de1255f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java @@ -56,6 +56,7 @@ */ public class IndividualsCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "individuals"; public IndividualsCommandOptions individualsCommandOptions; public IndividualsCommandExecutor(IndividualsCommandOptions individualsCommandOptions) throws CatalogAuthenticationException { @@ -136,7 +137,7 @@ private RestResponse updateAcl() throws Exception { individualAclUpdateParams = new IndividualAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(individualAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { individualAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -207,7 +208,7 @@ private RestResponse loadAnnotationSets() throws Exception { tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tsvAnnotationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/annotationSets/load")); return res; } else if (commandOptions.jsonFile != null) { tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper() @@ -244,7 +245,7 @@ private RestResponse create() throws Exception { individualCreateParams = new IndividualCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(individualCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/create")); return res; } else if (commandOptions.jsonFile != null) { individualCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -449,7 +450,7 @@ private RestResponse update() throws Exception { individualUpdateParams = new IndividualUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(individualUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/{individuals}/update")); return res; } else if (commandOptions.jsonFile != null) { individualUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -519,7 +520,7 @@ private RestResponse updateAnnotationSetsAnnotations() throws Except objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(objectMap)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/individuals/{individual}/annotationSets/{annotationSet}/annotations/update")); return res; } else if (commandOptions.jsonFile != null) { objectMap = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java index 93723bdc05e..846c568724e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java @@ -67,6 +67,7 @@ */ public class JobsCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "jobs"; public JobsCommandOptions jobsCommandOptions; public JobsCommandExecutor(JobsCommandOptions jobsCommandOptions) throws CatalogAuthenticationException { @@ -142,7 +143,7 @@ private RestResponse updateAcl() throws Exception { jobAclUpdateParams = new JobAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(jobAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { jobAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -207,7 +208,7 @@ private RestResponse create() throws Exception { jobCreateParams = new JobCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(jobCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/create")); return res; } else if (commandOptions.jsonFile != null) { jobCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -294,7 +295,7 @@ private RestResponse retry() throws Exception { jobRetryParams = new JobRetryParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(jobRetryParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/retry")); return res; } else if (commandOptions.jsonFile != null) { jobRetryParams = JacksonUtils.getDefaultObjectMapper() @@ -430,7 +431,7 @@ private RestResponse update() throws Exception { jobUpdateParams = new JobUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(jobUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/jobs/{jobs}/update")); return res; } else if (commandOptions.jsonFile != null) { jobUpdateParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java index 3f8448898be..0cc03b91ef7 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java @@ -37,6 +37,7 @@ */ public class MetaCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "meta"; public MetaCommandOptions metaCommandOptions; public MetaCommandExecutor(MetaCommandOptions metaCommandOptions) throws CatalogAuthenticationException { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java index 8360af46f00..fc2357c14ad 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java @@ -17,11 +17,11 @@ package org.opencb.opencga.app.cli.main.executors; import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.lang3.StringUtils; import org.opencb.commons.datastore.core.ObjectMap; -import org.opencb.commons.utils.DataModelsUtils; import org.opencb.opencga.app.cli.CommandExecutor; import org.opencb.opencga.app.cli.GeneralCliOptions; import org.opencb.opencga.app.cli.main.io.*; @@ -36,6 +36,9 @@ import org.opencb.opencga.core.models.user.AuthenticationResponse; import org.opencb.opencga.core.response.QueryType; import org.opencb.opencga.core.response.RestResponse; +import org.opencb.opencga.server.generator.models.RestCategory; +import org.opencb.opencga.server.generator.models.RestEndpoint; +import org.opencb.opencga.server.generator.models.RestParameter; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -221,11 +224,30 @@ public OpencgaCommandExecutor setOpenCGAClient(OpenCGAClient openCGAClient) { return this; } - public String getObjectAsJSON(Object o) throws Exception { - String jsonInString = "Data model not found."; + public String getObjectAsJSON(String objectCategory, String objectPath) throws Exception { + String jsonInString = ""; try { - jsonInString = DataModelsUtils.dataModelToJsonString(o.getClass()); + ObjectMap queryParams = new ObjectMap(); + queryParams.putIfNotEmpty("category", String.valueOf(objectCategory)); + RestResponse response = openCGAClient.getMetaClient().api(queryParams); + ObjectMapper jsonObjectMapper = new ObjectMapper(); + for (List list : response.getResponses().get(0).getResults()) { + List categories = jsonObjectMapper.convertValue(list, new TypeReference>() {}); + for (RestCategory category : categories) { + for (RestEndpoint endpoint: category.getEndpoints()){ + if(objectPath.equals(endpoint.getPath())){ + for (RestParameter parameter:endpoint.getParameters()){ + //jsonInString += parameter.getName()+":"+parameter.getAllowedValues()+"\n"; + jsonInString += parameter.toString()+"\n"; + } + // + } + } + } + } + // jsonInString = DataModelsUtils.dataModelToJsonString(o.getClass()); } catch (Exception e) { + jsonInString = "Data model not found."; CommandLineUtils.error(e); } return jsonInString; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java index 78ed32b92dc..7e1faf04dfd 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java @@ -61,6 +61,7 @@ */ public class OperationsVariantStorageCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "operationsVariantStorage"; public OperationsVariantStorageCommandOptions operationsVariantStorageCommandOptions; public OperationsVariantStorageCommandExecutor(OperationsVariantStorageCommandOptions operationsVariantStorageCommandOptions) throws CatalogAuthenticationException { @@ -187,7 +188,7 @@ private RestResponse configureCellbase() throws Exception { cellBaseConfiguration = new CellBaseConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(cellBaseConfiguration)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/cellbase/configure")); return res; } else if (commandOptions.jsonFile != null) { cellBaseConfiguration = JacksonUtils.getDefaultObjectMapper() @@ -227,7 +228,7 @@ private RestResponse aggregateVariant() throws Exception { variantAggregateParams = new VariantAggregateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantAggregateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/aggregate")); return res; } else if (commandOptions.jsonFile != null) { variantAggregateParams = JacksonUtils.getDefaultObjectMapper() @@ -282,7 +283,7 @@ private RestResponse indexVariantAnnotation() throws Exception { variantAnnotationIndexParams = new VariantAnnotationIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantAnnotationIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/annotation/index")); return res; } else if (commandOptions.jsonFile != null) { variantAnnotationIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -324,7 +325,7 @@ private RestResponse saveVariantAnnotation() throws Exception { variantAnnotationSaveParams = new VariantAnnotationSaveParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantAnnotationSaveParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/annotation/save")); return res; } else if (commandOptions.jsonFile != null) { variantAnnotationSaveParams = JacksonUtils.getDefaultObjectMapper() @@ -358,7 +359,7 @@ private RestResponse configureVariant() throws Exception { variantConfigureParams = new VariantConfigureParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantConfigureParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/configure")); return res; } else if (commandOptions.jsonFile != null) { variantConfigureParams = JacksonUtils.getDefaultObjectMapper() @@ -395,7 +396,7 @@ private RestResponse deleteVariant() throws Exception { variantFileDeleteParams = new VariantFileDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantFileDeleteParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/delete")); return res; } else if (commandOptions.jsonFile != null) { variantFileDeleteParams = JacksonUtils.getDefaultObjectMapper() @@ -433,7 +434,7 @@ private RestResponse aggregateVariantFamily() throws Exception { variantAggregateFamilyParams = new VariantAggregateFamilyParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantAggregateFamilyParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/family/aggregate")); return res; } else if (commandOptions.jsonFile != null) { variantAggregateFamilyParams = JacksonUtils.getDefaultObjectMapper() @@ -472,7 +473,7 @@ private RestResponse indexVariantFamily() throws Exception { variantFamilyIndexParams = new VariantFamilyIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantFamilyIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/family/index")); return res; } else if (commandOptions.jsonFile != null) { variantFamilyIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -512,7 +513,7 @@ private RestResponse indexVariant() throws Exception { variantIndexParams = new VariantIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/index")); return res; } else if (commandOptions.jsonFile != null) { variantIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -577,7 +578,7 @@ private RestResponse launcherVariantIndex() throws Exception { variantFileIndexJobLauncherParams = new VariantFileIndexJobLauncherParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantFileIndexJobLauncherParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/index/launcher")); return res; } else if (commandOptions.jsonFile != null) { variantFileIndexJobLauncherParams = JacksonUtils.getDefaultObjectMapper() @@ -644,7 +645,7 @@ private RestResponse runVariantJulie() throws Exception { julieParams = new JulieParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(julieParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/julie/run")); return res; } else if (commandOptions.jsonFile != null) { julieParams = JacksonUtils.getDefaultObjectMapper() @@ -679,7 +680,7 @@ private RestResponse repairVariantMetadata() throws Exception { variantStorageMetadataRepairToolParams = new VariantStorageMetadataRepairToolParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStorageMetadataRepairToolParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/metadata/repair")); return res; } else if (commandOptions.jsonFile != null) { variantStorageMetadataRepairToolParams = JacksonUtils.getDefaultObjectMapper() @@ -717,7 +718,7 @@ private RestResponse synchronizeVariantMetadata() throws Exception { variantStorageMetadataSynchronizeParams = new VariantStorageMetadataSynchronizeParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStorageMetadataSynchronizeParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/metadata/synchronize")); return res; } else if (commandOptions.jsonFile != null) { variantStorageMetadataSynchronizeParams = JacksonUtils.getDefaultObjectMapper() @@ -751,7 +752,7 @@ private RestResponse pruneVariant() throws Exception { variantPruneParams = new VariantPruneParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantPruneParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/prune")); return res; } else if (commandOptions.jsonFile != null) { variantPruneParams = JacksonUtils.getDefaultObjectMapper() @@ -790,7 +791,7 @@ private RestResponse deleteVariantSample() throws Exception { variantSampleDeleteParams = new VariantSampleDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantSampleDeleteParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/sample/delete")); return res; } else if (commandOptions.jsonFile != null) { variantSampleDeleteParams = JacksonUtils.getDefaultObjectMapper() @@ -829,7 +830,7 @@ private RestResponse indexVariantSample() throws Exception { variantSecondarySampleIndexParams = new VariantSecondarySampleIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantSecondarySampleIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/sample/index")); return res; } else if (commandOptions.jsonFile != null) { variantSecondarySampleIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -867,7 +868,7 @@ private RestResponse variantSampleIndexConfigure() throws Exception { sampleIndexConfiguration = new SampleIndexConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleIndexConfiguration)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/sample/index/configure")); return res; } else if (commandOptions.jsonFile != null) { sampleIndexConfiguration = JacksonUtils.getDefaultObjectMapper() @@ -918,7 +919,7 @@ private RestResponse indexVariantScore() throws Exception { variantScoreIndexParams = new VariantScoreIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantScoreIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/score/index")); return res; } else if (commandOptions.jsonFile != null) { variantScoreIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -961,7 +962,7 @@ private RestResponse variantSecondaryAnnotationIndex() throws Exception { variantSecondaryAnnotationIndexParams = new VariantSecondaryAnnotationIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantSecondaryAnnotationIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondary/annotation/index")); return res; } else if (commandOptions.jsonFile != null) { variantSecondaryAnnotationIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -1000,7 +1001,7 @@ private RestResponse variantSecondarySampleIndex() throws Exception { variantSecondarySampleIndexParams = new VariantSecondarySampleIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantSecondarySampleIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondary/sample/index")); return res; } else if (commandOptions.jsonFile != null) { variantSecondarySampleIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -1038,7 +1039,7 @@ private RestResponse configureVariantSecondarySampleIndex() throws Exceptio sampleIndexConfiguration = new SampleIndexConfiguration(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleIndexConfiguration)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondary/sample/index/configure")); return res; } else if (commandOptions.jsonFile != null) { sampleIndexConfiguration = JacksonUtils.getDefaultObjectMapper() @@ -1069,7 +1070,7 @@ private RestResponse secondaryIndexVariant() throws Exception { variantSecondaryAnnotationIndexParams = new VariantSecondaryAnnotationIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantSecondaryAnnotationIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/secondaryIndex")); return res; } else if (commandOptions.jsonFile != null) { variantSecondaryAnnotationIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -1127,7 +1128,7 @@ private RestResponse deleteVariantStats() throws Exception { variantStatsDeleteParams = new VariantStatsDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStatsDeleteParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/stats/delete")); return res; } else if (commandOptions.jsonFile != null) { variantStatsDeleteParams = JacksonUtils.getDefaultObjectMapper() @@ -1165,7 +1166,7 @@ private RestResponse indexVariantStats() throws Exception { variantStatsIndexParams = new VariantStatsIndexParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStatsIndexParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/stats/index")); return res; } else if (commandOptions.jsonFile != null) { variantStatsIndexParams = JacksonUtils.getDefaultObjectMapper() @@ -1207,7 +1208,7 @@ private RestResponse deleteVariantStudy() throws Exception { variantStudyDeleteParams = new VariantStudyDeleteParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variantStudyDeleteParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/operation/variant/study/delete")); return res; } else if (commandOptions.jsonFile != null) { variantStudyDeleteParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java index 2ed3593e612..98bb7eb2814 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java @@ -42,6 +42,7 @@ */ public class ProjectsCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "projects"; public ProjectsCommandOptions projectsCommandOptions; public ProjectsCommandExecutor(ProjectsCommandOptions projectsCommandOptions) throws CatalogAuthenticationException { @@ -105,7 +106,7 @@ private RestResponse create() throws Exception { projectCreateParams = new ProjectCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(projectCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/projects/create")); return res; } else if (commandOptions.jsonFile != null) { projectCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -227,7 +228,7 @@ private RestResponse update() throws Exception { projectUpdateParams = new ProjectUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(projectUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/projects/{project}/update")); return res; } else if (commandOptions.jsonFile != null) { projectUpdateParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java index a88c8330a26..7d0ebf47cc8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java @@ -55,6 +55,7 @@ */ public class SamplesCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "samples"; public SamplesCommandOptions samplesCommandOptions; public SamplesCommandExecutor(SamplesCommandOptions samplesCommandOptions) throws CatalogAuthenticationException { @@ -134,7 +135,7 @@ private RestResponse updateAcl() throws Exception { sampleAclUpdateParams = new SampleAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { sampleAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -202,7 +203,7 @@ private RestResponse loadAnnotationSets() throws Exception { tsvAnnotationParams = new TsvAnnotationParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(tsvAnnotationParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/annotationSets/load")); return res; } else if (commandOptions.jsonFile != null) { tsvAnnotationParams = JacksonUtils.getDefaultObjectMapper() @@ -238,7 +239,7 @@ private RestResponse create() throws Exception { sampleCreateParams = new SampleCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/create")); return res; } else if (commandOptions.jsonFile != null) { sampleCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -476,7 +477,7 @@ private RestResponse update() throws Exception { sampleUpdateParams = new SampleUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(sampleUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/{samples}/update")); return res; } else if (commandOptions.jsonFile != null) { sampleUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -536,7 +537,7 @@ private RestResponse updateAnnotationSetsAnnotations() throws Exception objectMap = new ObjectMap(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(objectMap)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/samples/{sample}/annotationSets/{annotationSet}/annotations/update")); return res; } else if (commandOptions.jsonFile != null) { objectMap = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java index 944262e77f1..fef8f85a042 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java @@ -90,6 +90,7 @@ */ public class StudiesCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "studies"; public StudiesCommandOptions studiesCommandOptions; public StudiesCommandExecutor(StudiesCommandOptions studiesCommandOptions) throws CatalogAuthenticationException { @@ -183,7 +184,7 @@ private RestResponse updateAcl() throws Exception { studyAclUpdateParams = new StudyAclUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(studyAclUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/acl/{members}/update")); return res; } else if (commandOptions.jsonFile != null) { studyAclUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -218,7 +219,7 @@ private RestResponse create() throws Exception { studyCreateParams = new StudyCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(studyCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/create")); return res; } else if (commandOptions.jsonFile != null) { studyCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -360,7 +361,7 @@ private RestResponse updateGroups() throws Exception { groupCreateParams = new GroupCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(groupCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/groups/update")); return res; } else if (commandOptions.jsonFile != null) { groupCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -391,7 +392,7 @@ private RestResponse updateGroupsUsers() throws Exception { groupUpdateParams = new GroupUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(groupUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/groups/{group}/users/update")); return res; } else if (commandOptions.jsonFile != null) { groupUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -428,7 +429,7 @@ private RestResponse updatePermissionRules() throws Exception { permissionRule = new PermissionRule(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(permissionRule)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/permissionRules/update")); return res; } else if (commandOptions.jsonFile != null) { permissionRule = JacksonUtils.getDefaultObjectMapper() @@ -511,7 +512,7 @@ private RestResponse update() throws Exception { studyUpdateParams = new StudyUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(studyUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/update")); return res; } else if (commandOptions.jsonFile != null) { studyUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -562,7 +563,7 @@ private RestResponse updateVariableSets() throws Exception { variableSetCreateParams = new VariableSetCreateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variableSetCreateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/variableSets/update")); return res; } else if (commandOptions.jsonFile != null) { variableSetCreateParams = JacksonUtils.getDefaultObjectMapper() @@ -596,7 +597,7 @@ private RestResponse updateVariableSetsVariables() throws Exception variable = new Variable(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(variable)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/studies/{study}/variableSets/{variableSet}/variables/update")); return res; } else if (commandOptions.jsonFile != null) { variable = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java index b2cca1037ba..f44e3449cc5 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java @@ -61,6 +61,7 @@ */ public class UsersCommandExecutor extends OpencgaCommandExecutor { + public String categoryName = "users"; public UsersCommandOptions usersCommandOptions; public UsersCommandExecutor(UsersCommandOptions usersCommandOptions) throws CatalogAuthenticationException { @@ -136,7 +137,7 @@ private RestResponse password() throws Exception { passwordChangeParams = new PasswordChangeParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(passwordChangeParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/users/password")); return res; } else if (commandOptions.jsonFile != null) { passwordChangeParams = JacksonUtils.getDefaultObjectMapper() @@ -192,7 +193,7 @@ private RestResponse updateConfigs() throws Exception { configUpdateParams = new ConfigUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(configUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/users/{user}/configs/update")); return res; } else if (commandOptions.jsonFile != null) { configUpdateParams = JacksonUtils.getDefaultObjectMapper() @@ -257,7 +258,7 @@ private RestResponse update() throws Exception { userUpdateParams = new UserUpdateParams(); RestResponse res = new RestResponse<>(); res.setType(QueryType.VOID); - PrintUtils.println(getObjectAsJSON(userUpdateParams)); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/users/{user}/update")); return res; } else if (commandOptions.jsonFile != null) { userUpdateParams = JacksonUtils.getDefaultObjectMapper() diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index f36ae979df6..ca588e36aec 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index 7f1a6a2d745..42453c4b949 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index 5756f579584..1094354e3de 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,6 +1,6 @@ # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -10,37 +10,37 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, study, group, variableSet, studies, members, templateId, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, templateId, variableSet, study, group, studies, members, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, file, files, folder, members, annotationSet, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, files, file, folder, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, sample, members, annotationSet, samples, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, sample, samples, members, annotationSet, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, families, members, annotationSet, family, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, annotationSet, members, family, families, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, cohort, members, cohorts, annotationSet, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, interpretation, interpretations, clinicalAnalysis, clinicalAnalyses, members, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretations, members, interpretation, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index 5d84fa14614..063b5ca56bf 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -58,7 +58,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretation, interpretations, clinicalAnalysis, clinicalAnalyses, members, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretations, members, interpretation, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index d192d6feec1..86c256ad13c 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, members, cohorts, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index c582b23a93a..f61994486fa 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, families, members, annotationSet, family, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, members, family, families, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index f3eeac80df2..12a692cba71 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +54,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, file, files, folder, members, annotationSet, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, files, file, folder, annotationSet, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index 639683e171c..d03fe839d00 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 1839f2cb8c9..6c6db781f0f 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("individualClient", "OpencgaR", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index ed70e8df6cf..2336177e4e3 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -40,7 +40,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index c278a0c47e4..10888d84a65 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 11621e2cf87..492c6a7c654 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index 20fb425cc31..9ff4ec9416b 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 80d88c4cc79..a0cdf42263b 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index 32e64a3ecc9..e154dbdea1d 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("sampleClient", "OpencgaR", function(OpencgaR, sample, members, annotationSet, samples, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, sample, samples, members, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index a9c9a3c90f8..ec660266b5a 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +46,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, study, group, variableSet, studies, members, templateId, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, templateId, variableSet, study, group, studies, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index 2a1d1bc3e82..65db531b18c 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/login: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index ad760abcd16..70d0f7406a2 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-12 +# Autogenerated on: 2023-10-27 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index 6aad0bc7842..b8650868796 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +45,7 @@ /** * This class contains methods for the Admin webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: admin */ public class AdminClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index 16c679f642f..e979ae69978 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -49,7 +49,7 @@ /** * This class contains methods for the Alignment webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: analysis/alignment */ public class AlignmentClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index 94ab79f677d..8e45768167c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -51,7 +51,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -60,7 +60,7 @@ /** * This class contains methods for the ClinicalAnalysis webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: analysis/clinical */ public class ClinicalAnalysisClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 2320ca7bbcd..a6c7798a94b 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +46,7 @@ /** * This class contains methods for the Cohort webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: cohorts */ public class CohortClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index ad9ef470eaa..979f96e572e 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -44,7 +44,7 @@ /** * This class contains methods for the DiseasePanel webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: panels */ public class DiseasePanelClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index 94b0e7cf66d..60b4ca25d77 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +45,7 @@ /** * This class contains methods for the Family webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: families */ public class FamilyClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 94eeead7197..795aeff6846 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -43,7 +43,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -52,7 +52,7 @@ /** * This class contains methods for the File webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: files */ public class FileClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index 48b4524ea7f..b843ea82794 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -36,7 +36,7 @@ /** * This class contains methods for the GA4GH webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: ga4gh */ public class GA4GHClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index b89c47024df..71a2b12acb5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +45,7 @@ /** * This class contains methods for the Individual webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: individuals */ public class IndividualClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index 7945a8d65cc..a3ba8a9fcd1 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +46,7 @@ /** * This class contains methods for the Job webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: jobs */ public class JobClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index 794c6ad3394..49ec8ae0eed 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -37,7 +37,7 @@ /** * This class contains methods for the Meta webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: meta */ public class MetaClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 317a4af226c..0b92cedd97b 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -32,7 +32,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -41,7 +41,7 @@ /** * This class contains methods for the Project webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: projects */ public class ProjectClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index 5cbb8f10fd4..4dfeecc596d 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +45,7 @@ /** * This class contains methods for the Sample webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: samples */ public class SampleClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 8f018861260..e86ac389d40 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -45,7 +45,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +54,7 @@ /** * This class contains methods for the Study webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: studies */ public class StudyClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index adb4ce85938..e5984ffeff2 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +45,7 @@ /** * This class contains methods for the User webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: users */ public class UserClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index 4801650a0f9..07360eddb66 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -71,7 +71,7 @@ /** * This class contains methods for the Variant webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: analysis/variant */ public class VariantClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index c1ffc952c9d..27222047a76 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-12 +* Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -59,7 +59,7 @@ /** * This class contains methods for the VariantOperation webservices. - * Client version: 2.11.0-SNAPSHOT + * Client version: 2.12.0-SNAPSHOT * PATH: operation */ public class VariantOperationClient extends AbstractParentClient { diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 2466edfccfd..fdfb9de6aa6 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index 446219c5a59..8c967d31de0 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 221fa4a68da..b814ab17d37 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 9d070dc8ec8..8a3379c7348 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index 1d97f0d3b6f..a0967fc19f7 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index 5b11ceacd3a..a1183ca4f60 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index 27d76b733e7..58e1343ad16 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index 2e3f968ab05..e61030ad0e3 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index 160bb589c50..8e5089be7fd 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index 52f5cdde599..21d175e0ca3 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index 0207e95847a..02c96c1dade 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index f43c7394d71..e38753e0c87 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index edefccf3e5a..abbe89cf5ac 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index d153ba9d316..d0eb2bb02fe 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index d8c60b8d409..b65022b6a8b 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index 35617fde07f..d3ced6ac6ad 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index daa6917728a..7044b256894 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-12 + * Autogenerated on: 2023-10-27 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index 28598b602eb..90d868b6533 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Admin(_ParentRestClient): """ This class contains methods for the 'Admin' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/admin """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index d19895d21ba..b3fd66f2f86 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Alignment(_ParentRestClient): """ This class contains methods for the 'Analysis - Alignment' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/analysis/alignment """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index cf8de0798c5..359a1bdcb5b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class ClinicalAnalysis(_ParentRestClient): """ This class contains methods for the 'Analysis - Clinical' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/analysis/clinical """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index f7d6ad80542..021ca07f480 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Cohort(_ParentRestClient): """ This class contains methods for the 'Cohorts' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/cohorts """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index 6d47ea09d3c..e02a70f6560 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class DiseasePanel(_ParentRestClient): """ This class contains methods for the 'Disease Panels' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/panels """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index 65e3a070dce..a321fc45b54 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Family(_ParentRestClient): """ This class contains methods for the 'Families' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/families """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index c6c028d3b3a..7a0f41fcb5a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class File(_ParentRestClient): """ This class contains methods for the 'Files' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/files """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index 48e5b17de75..c9966af7a5e 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class GA4GH(_ParentRestClient): """ This class contains methods for the 'GA4GH' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/ga4gh """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index 07dd3d04b0d..2c811e6c501 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Individual(_ParentRestClient): """ This class contains methods for the 'Individuals' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/individuals """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index d692f8e099c..80078af84e6 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Job(_ParentRestClient): """ This class contains methods for the 'Jobs' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/jobs """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index d43227b33f8..6e7cc082b1f 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Meta(_ParentRestClient): """ This class contains methods for the 'Meta' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/meta """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index bd29b4b1013..1b063026bd1 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Project(_ParentRestClient): """ This class contains methods for the 'Projects' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/projects """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index fcb5c944884..9d4c3d3b56a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Sample(_ParentRestClient): """ This class contains methods for the 'Samples' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/samples """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 40cc9a63c08..0c67bc31819 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Study(_ParentRestClient): """ This class contains methods for the 'Studies' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/studies """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index 3f2ed4eae3e..bfc4b7d4d9a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class User(_ParentRestClient): """ This class contains methods for the 'Users' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/users """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index 80e1746470a..b7e2829b208 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Variant(_ParentRestClient): """ This class contains methods for the 'Analysis - Variant' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/analysis/variant """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index 4297fbf08ae..6736e33528e 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-12 + Autogenerated on: 2023-10-27 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class VariantOperation(_ParentRestClient): """ This class contains methods for the 'Operations - Variant Storage' webservices - Client version: 2.11.0-SNAPSHOT + Client version: 2.12.0-SNAPSHOT PATH: /{apiVersion}/operation """ diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java index f75776a7dfa..9a7c35caa86 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/cli/ExecutorsCliRestApiWriter.java @@ -170,6 +170,7 @@ protected String getClassHeader(String key) { CategoryConfig config = availableCategoryConfigs.get(key); sb.append("public class " + getAsClassName(restCategory.getName()) + "CommandExecutor extends " + getExtendedClass() + " {\n\n"); + sb.append(" public String categoryName = \"" + getAsVariableName(getAsCamelCase(restCategory.getName())) + "\";\n"); sb.append(" public " + getAsClassName(restCategory.getName()) + "CommandOptions " + getAsVariableName(getAsCamelCase(restCategory.getName())) + "CommandOptions;\n\n"); sb.append(" public " + getAsClassName(restCategory.getName()) + "CommandExecutor(" + getAsClassName(restCategory.getName()) @@ -373,7 +374,7 @@ private String getBodyParams(RestCategory restCategory, RestEndpoint restEndpoin sb.append("\n " + variableName + " = new " + bodyClassName + "();"); sb.append("\n RestResponse<" + getValidResponseNames(restEndpoint.getResponse()) + "> res = new RestResponse<>();"); sb.append("\n res.setType(QueryType.VOID);"); - sb.append("\n PrintUtils.println(getObjectAsJSON(" + variableName + "));"); + sb.append("\n PrintUtils.println(getObjectAsJSON(categoryName,\""+restEndpoint.getPath()+"\"));"); sb.append("\n return res;"); sb.append("\n } else if (commandOptions.jsonFile != null) {"); sb.append("\n " + getAsVariableName(bodyClassName) + " = JacksonUtils.getDefaultObjectMapper()");