cli:Deleted unused object in executors #TASK-5160

opencb · Nov 3, 2023 · 98d42e3 · 98d42e3
1 parent 5226ae7
commit 98d42e3
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Showing 87 changed files with 88 additions and 216 deletions.
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java
@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-11-02 OpenCB
+* Copyright 2015-2023-11-03 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-11-02 OpenCB
+* Copyright 2015-2023-11-03 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

diff --git a/...cga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java b/...cga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java
@@ -136,7 +136,6 @@ private RestResponse<ObjectMap> installCatalog() throws Exception {
 
         InstallationParams installationParams = null;
         if (commandOptions.jsonDataModel) {
-            installationParams = new InstallationParams();
             RestResponse<ObjectMap> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/install"));
@@ -165,7 +164,6 @@ private RestResponse<ObjectMap> jwtCatalog() throws Exception {
 
         JWTParams jWTParams = null;
         if (commandOptions.jsonDataModel) {
-            jWTParams = new JWTParams();
             RestResponse<ObjectMap> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/jwt"));
@@ -191,7 +189,6 @@ private RestResponse<User> createUsers() throws Exception {
 
         UserCreateParams userCreateParams = null;
         if (commandOptions.jsonDataModel) {
-            userCreateParams = new UserCreateParams();
             RestResponse<User> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/create"));
@@ -222,7 +219,6 @@ private RestResponse<User> importUsers() throws Exception {
 
         UserImportParams userImportParams = null;
         if (commandOptions.jsonDataModel) {
-            userImportParams = new UserImportParams();
             RestResponse<User> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/import"));
@@ -270,7 +266,6 @@ private RestResponse<Group> syncUsers() throws Exception {
 
         GroupSyncParams groupSyncParams = null;
         if (commandOptions.jsonDataModel) {
-            groupSyncParams = new GroupSyncParams();
             RestResponse<Group> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/sync"));
@@ -306,7 +301,6 @@ private RestResponse<Group> usersUpdateGroups() throws Exception {
 
         UserUpdateGroup userUpdateGroup = null;
         if (commandOptions.jsonDataModel) {
-            userUpdateGroup = new UserUpdateGroup();
             RestResponse<Group> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/{user}/groups/update"));

diff --git a/...main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java b/...main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java
@@ -132,7 +132,6 @@ private RestResponse<Job> runBwa() throws Exception {
 
         BwaWrapperParams bwaWrapperParams = null;
         if (commandOptions.jsonDataModel) {
-            bwaWrapperParams = new BwaWrapperParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/bwa/run"));
@@ -174,7 +173,6 @@ private RestResponse<Job> runCoverageIndex() throws Exception {
 
         CoverageIndexParams coverageIndexParams = null;
         if (commandOptions.jsonDataModel) {
-            coverageIndexParams = new CoverageIndexParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/coverage/index/run"));
@@ -213,7 +211,6 @@ private RestResponse<Job> coverageQcGeneCoverageStatsRun() throws Exception {
 
         AlignmentGeneCoverageStatsParams alignmentGeneCoverageStatsParams = null;
         if (commandOptions.jsonDataModel) {
-            alignmentGeneCoverageStatsParams = new AlignmentGeneCoverageStatsParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/coverage/qc/geneCoverageStats/run"));
@@ -309,7 +306,6 @@ private RestResponse<Job> runDeeptools() throws Exception {
 
         DeeptoolsWrapperParams deeptoolsWrapperParams = null;
         if (commandOptions.jsonDataModel) {
-            deeptoolsWrapperParams = new DeeptoolsWrapperParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/deeptools/run"));
@@ -348,7 +344,6 @@ private RestResponse<Job> runFastqc() throws Exception {
 
         FastqcWrapperParams fastqcWrapperParams = null;
         if (commandOptions.jsonDataModel) {
-            fastqcWrapperParams = new FastqcWrapperParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/fastqc/run"));
@@ -387,7 +382,6 @@ private RestResponse<Job> runIndex() throws Exception {
 
         AlignmentIndexParams alignmentIndexParams = null;
         if (commandOptions.jsonDataModel) {
-            alignmentIndexParams = new AlignmentIndexParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/index/run"));
@@ -425,7 +419,6 @@ private RestResponse<Job> runPicard() throws Exception {
 
         PicardWrapperParams picardWrapperParams = null;
         if (commandOptions.jsonDataModel) {
-            picardWrapperParams = new PicardWrapperParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/picard/run"));
@@ -464,7 +457,6 @@ private RestResponse<Job> runQc() throws Exception {
 
         AlignmentQcParams alignmentQcParams = null;
         if (commandOptions.jsonDataModel) {
-            alignmentQcParams = new AlignmentQcParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/qc/run"));
@@ -536,7 +528,6 @@ private RestResponse<Job> runSamtools() throws Exception {
 
         SamtoolsWrapperParams samtoolsWrapperParams = null;
         if (commandOptions.jsonDataModel) {
-            samtoolsWrapperParams = new SamtoolsWrapperParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/samtools/run"));

diff --git a/.../main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java b/.../main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java
@@ -215,7 +215,6 @@ private RestResponse<ClinicalAnalysisAclEntryList> updateAcl() throws Exception
 
         ClinicalAnalysisAclUpdateParams clinicalAnalysisAclUpdateParams = null;
         if (commandOptions.jsonDataModel) {
-            clinicalAnalysisAclUpdateParams = new ClinicalAnalysisAclUpdateParams();
             RestResponse<ClinicalAnalysisAclEntryList> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/acl/{members}/update"));
@@ -249,7 +248,6 @@ private RestResponse<ObjectMap> updateClinicalConfiguration() throws Exception {
 
         ClinicalAnalysisStudyConfiguration clinicalAnalysisStudyConfiguration = null;
         if (commandOptions.jsonDataModel) {
-            clinicalAnalysisStudyConfiguration = new ClinicalAnalysisStudyConfiguration();
             RestResponse<ObjectMap> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/clinical/configuration/update"));
@@ -286,7 +284,6 @@ private RestResponse<ClinicalAnalysis> create() throws Exception {
 
         ClinicalAnalysisCreateParams clinicalAnalysisCreateParams = null;
         if (commandOptions.jsonDataModel) {
-            clinicalAnalysisCreateParams = new ClinicalAnalysisCreateParams();
             RestResponse<ClinicalAnalysis> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/create"));
@@ -465,7 +462,6 @@ private RestResponse<Job> runInterpreterCancerTiering() throws Exception {
 
         CancerTieringInterpretationAnalysisParams cancerTieringInterpretationAnalysisParams = null;
         if (commandOptions.jsonDataModel) {
-            cancerTieringInterpretationAnalysisParams = new CancerTieringInterpretationAnalysisParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/cancerTiering/run"));
@@ -504,7 +500,6 @@ private RestResponse<Job> runInterpreterExomiser() throws Exception {
 
         ExomiserInterpretationAnalysisParams exomiserInterpretationAnalysisParams = null;
         if (commandOptions.jsonDataModel) {
-            exomiserInterpretationAnalysisParams = new ExomiserInterpretationAnalysisParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/exomiser/run"));
@@ -541,7 +536,6 @@ private RestResponse<Job> runInterpreterTeam() throws Exception {
 
         TeamInterpretationAnalysisParams teamInterpretationAnalysisParams = null;
         if (commandOptions.jsonDataModel) {
-            teamInterpretationAnalysisParams = new TeamInterpretationAnalysisParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/team/run"));
@@ -581,7 +575,6 @@ private RestResponse<Job> runInterpreterTiering() throws Exception {
 
         TieringInterpretationAnalysisParams tieringInterpretationAnalysisParams = null;
         if (commandOptions.jsonDataModel) {
-            tieringInterpretationAnalysisParams = new TieringInterpretationAnalysisParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/tiering/run"));
@@ -621,7 +614,6 @@ private RestResponse<Job> runInterpreterZetta() throws Exception {
 
         ZettaInterpretationAnalysisParams zettaInterpretationAnalysisParams = null;
         if (commandOptions.jsonDataModel) {
-            zettaInterpretationAnalysisParams = new ZettaInterpretationAnalysisParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/interpreter/zetta/run"));
@@ -824,7 +816,6 @@ private RestResponse<Job> runRgaIndex() throws Exception {
 
         RgaAnalysisParams rgaAnalysisParams = null;
         if (commandOptions.jsonDataModel) {
-            rgaAnalysisParams = new RgaAnalysisParams();
             RestResponse<Job> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/rga/index/run"));
@@ -1164,7 +1155,6 @@ private RestResponse<ClinicalAnalysis> update() throws Exception {
 
         ClinicalAnalysisUpdateParams clinicalAnalysisUpdateParams = null;
         if (commandOptions.jsonDataModel) {
-            clinicalAnalysisUpdateParams = new ClinicalAnalysisUpdateParams();
             RestResponse<ClinicalAnalysis> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalyses}/update"));
@@ -1239,7 +1229,6 @@ private RestResponse<Interpretation> createInterpretation() throws Exception {
 
         InterpretationCreateParams interpretationCreateParams = null;
         if (commandOptions.jsonDataModel) {
-            interpretationCreateParams = new InterpretationCreateParams();
             RestResponse<Interpretation> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create"));
@@ -1329,7 +1318,6 @@ private RestResponse<Interpretation> updateInterpretation() throws Exception {
 
         InterpretationUpdateParams interpretationUpdateParams = null;
         if (commandOptions.jsonDataModel) {
-            interpretationUpdateParams = new InterpretationUpdateParams();
             RestResponse<Interpretation> res = new RestResponse<>();
             res.setType(QueryType.VOID);
             PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update"));