Merge branch 'release-2.12.x' into TASK-5300-2.12.x

opencb · Nov 30, 2023 · bff6a64 · bff6a64
2 parents 07d0ece + 6f9d101
commit bff6a64
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Showing 90 changed files with 332 additions and 354 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 2015-2023-11-21 OpenCB
+* Copyright 2015-2023-11-28 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java
@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-11-21 OpenCB
+* Copyright 2015-2023-11-28 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

diff --git a/...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
@@ -44,6 +44,7 @@
  */
 public class AdminCommandExecutor extends OpencgaCommandExecutor {
 
+    public String categoryName = "admin";
     public AdminCommandOptions adminCommandOptions;
 
     public AdminCommandExecutor(AdminCommandOptions adminCommandOptions) throws CatalogAuthenticationException {
@@ -131,10 +132,9 @@ 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(installationParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/install"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             installationParams = JacksonUtils.getDefaultObjectMapper()
@@ -160,10 +160,9 @@ 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(jWTParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/catalog/jwt"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             jWTParams = JacksonUtils.getDefaultObjectMapper()
@@ -186,10 +185,9 @@ 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(userCreateParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/create"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             userCreateParams = JacksonUtils.getDefaultObjectMapper()
@@ -217,10 +215,9 @@ 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(userImportParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/import"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             userImportParams = JacksonUtils.getDefaultObjectMapper()
@@ -265,10 +262,9 @@ 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(groupSyncParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/sync"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             groupSyncParams = JacksonUtils.getDefaultObjectMapper()
@@ -301,10 +297,9 @@ 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(userUpdateGroup));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/admin/users/{user}/groups/update"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             userUpdateGroup = JacksonUtils.getDefaultObjectMapper()

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
@@ -44,6 +44,7 @@
  */
 public class AnalysisAlignmentCommandExecutor extends OpencgaCommandExecutor {
 
+    public String categoryName = "alignment";
     public AnalysisAlignmentCommandOptions analysisAlignmentCommandOptions;
 
     public AnalysisAlignmentCommandExecutor(AnalysisAlignmentCommandOptions analysisAlignmentCommandOptions) throws CatalogAuthenticationException {
@@ -127,10 +128,9 @@ 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(bwaWrapperParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/bwa/run"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             bwaWrapperParams = JacksonUtils.getDefaultObjectMapper()
@@ -169,10 +169,9 @@ 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(coverageIndexParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/coverage/index/run"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             coverageIndexParams = JacksonUtils.getDefaultObjectMapper()
@@ -208,10 +207,9 @@ 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(alignmentGeneCoverageStatsParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/coverage/qc/geneCoverageStats/run"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             alignmentGeneCoverageStatsParams = JacksonUtils.getDefaultObjectMapper()
@@ -304,10 +302,9 @@ 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(deeptoolsWrapperParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/deeptools/run"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             deeptoolsWrapperParams = JacksonUtils.getDefaultObjectMapper()
@@ -343,10 +340,9 @@ 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(fastqcWrapperParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/fastqc/run"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             fastqcWrapperParams = JacksonUtils.getDefaultObjectMapper()
@@ -382,10 +378,9 @@ 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(alignmentIndexParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/index/run"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             alignmentIndexParams = JacksonUtils.getDefaultObjectMapper()
@@ -420,10 +415,9 @@ 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(picardWrapperParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/picard/run"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             picardWrapperParams = JacksonUtils.getDefaultObjectMapper()
@@ -459,10 +453,9 @@ 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(alignmentQcParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/qc/run"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             alignmentQcParams = JacksonUtils.getDefaultObjectMapper()
@@ -531,10 +524,9 @@ 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(samtoolsWrapperParams));
+            PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/alignment/samtools/run"));
             return res;
         } else if (commandOptions.jsonFile != null) {
             samtoolsWrapperParams = JacksonUtils.getDefaultObjectMapper()