CLI: getObjetcJson method params are now category and path

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.

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.

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<ObjectMap> installCatalog() throws Exception {
             installationParams = new InstallationParams();
             RestResponse<ObjectMap> 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<ObjectMap> jwtCatalog() throws Exception {
             jWTParams = new JWTParams();
             RestResponse<ObjectMap> 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<User> createUsers() throws Exception {
             userCreateParams = new UserCreateParams();
             RestResponse<User> 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<User> importUsers() throws Exception {
             userImportParams = new UserImportParams();
             RestResponse<User> 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<Group> syncUsers() throws Exception {
             groupSyncParams = new GroupSyncParams();
             RestResponse<Group> 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<Group> usersUpdateGroups() throws Exception {
             userUpdateGroup = new UserUpdateGroup();
             RestResponse<Group> 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()

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<Job> runBwa() throws Exception {
             bwaWrapperParams = new BwaWrapperParams();
             RestResponse<Job> 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<Job> runCoverageIndex() throws Exception {
             coverageIndexParams = new CoverageIndexParams();
             RestResponse<Job> 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<Job> coverageQcGeneCoverageStatsRun() throws Exception {
             alignmentGeneCoverageStatsParams = new AlignmentGeneCoverageStatsParams();
             RestResponse<Job> 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<Job> runDeeptools() throws Exception {
             deeptoolsWrapperParams = new DeeptoolsWrapperParams();
             RestResponse<Job> 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<Job> runFastqc() throws Exception {
             fastqcWrapperParams = new FastqcWrapperParams();
             RestResponse<Job> 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<Job> runIndex() throws Exception {
             alignmentIndexParams = new AlignmentIndexParams();
             RestResponse<Job> 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<Job> runPicard() throws Exception {
             picardWrapperParams = new PicardWrapperParams();
             RestResponse<Job> 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<Job> runQc() throws Exception {
             alignmentQcParams = new AlignmentQcParams();
             RestResponse<Job> 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<Job> runSamtools() throws Exception {
             samtoolsWrapperParams = new SamtoolsWrapperParams();
             RestResponse<Job> 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()

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<ClinicalAnalysisAclEntryList> updateAcl() throws Exception
             clinicalAnalysisAclUpdateParams = new ClinicalAnalysisAclUpdateParams();
             RestResponse<ClinicalAnalysisAclEntryList> 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<ObjectMap> updateClinicalConfiguration() throws Exception {
             clinicalAnalysisStudyConfiguration = new ClinicalAnalysisStudyConfiguration();
             RestResponse<ObjectMap> 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<ClinicalAnalysis> create() throws Exception {
             clinicalAnalysisCreateParams = new ClinicalAnalysisCreateParams();
             RestResponse<ClinicalAnalysis> 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<Job> runInterpreterCancerTiering() throws Exception {
             cancerTieringInterpretationAnalysisParams = new CancerTieringInterpretationAnalysisParams();
             RestResponse<Job> 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<Job> runInterpreterExomiser() throws Exception {
             exomiserInterpretationAnalysisParams = new ExomiserInterpretationAnalysisParams();
             RestResponse<Job> 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<Job> runInterpreterTeam() throws Exception {
             teamInterpretationAnalysisParams = new TeamInterpretationAnalysisParams();
             RestResponse<Job> 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<Job> runInterpreterTiering() throws Exception {
             tieringInterpretationAnalysisParams = new TieringInterpretationAnalysisParams();
             RestResponse<Job> 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<Job> runInterpreterZetta() throws Exception {
             zettaInterpretationAnalysisParams = new ZettaInterpretationAnalysisParams();
             RestResponse<Job> 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<Job> runRgaIndex() throws Exception {
             rgaAnalysisParams = new RgaAnalysisParams();
             RestResponse<Job> 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<ClinicalAnalysis> update() throws Exception {
             clinicalAnalysisUpdateParams = new ClinicalAnalysisUpdateParams();
             RestResponse<ClinicalAnalysis> 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<Interpretation> createInterpretation() throws Exception {
             interpretationCreateParams = new InterpretationCreateParams();
             RestResponse<Interpretation> 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<Interpretation> updateInterpretation() throws Exception {
             interpretationUpdateParams = new InterpretationUpdateParams();
             RestResponse<Interpretation> 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()