server app: Autogenerated classes

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2022-07-29 OpenCB
+* Copyright 2015-2022-08-01 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -32,12 +32,12 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.
 *    Command line version: 2.4.2-SNAPSHOT
-*    Command line commit: 2cf51b8ad4bf1b394b0162d81a7e4da82fd12ae4
+*    Command line commit: 1107fd8d544e2788500aa3075ff4476e798d1251
 */
 
 public abstract class OpenCgaCompleter implements Completer {

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2022-07-29 OpenCB
+* Copyright 2015-2022-08-01 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -26,12 +26,12 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.
 *    Command line version: 2.4.2-SNAPSHOT
-*    Command line commit: 2cf51b8ad4bf1b394b0162d81a7e4da82fd12ae4
+*    Command line commit: 1107fd8d544e2788500aa3075ff4476e798d1251
 */
 
 public class OpencgaCliOptionsParser extends ParentCliOptionsParser {

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java

@@ -36,7 +36,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java

@@ -18,6 +18,7 @@
 import org.opencb.opencga.app.cli.main.options.AnalysisClinicalCommandOptions;
 
 import java.util.Map;
+import org.opencb.biodata.models.clinical.ClinicalDiscussion;
 import org.opencb.biodata.models.clinical.ClinicalProperty;
 import org.opencb.biodata.models.clinical.interpretation.ClinicalVariant;
 import org.opencb.biodata.models.clinical.interpretation.InterpretationMethod;
@@ -67,7 +68,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.
@@ -304,7 +305,6 @@ private RestResponse<ClinicalAnalysis> create() throws Exception {
             putNestedIfNotEmpty(beanParams, "analyst.id",commandOptions.analystId, true);
             putNestedIfNotEmpty(beanParams, "report.title",commandOptions.reportTitle, true);
             putNestedIfNotEmpty(beanParams, "report.overview",commandOptions.reportOverview, true);
-            putNestedIfNotEmpty(beanParams, "report.discussion",commandOptions.reportDiscussion, true);
             putNestedIfNotEmpty(beanParams, "report.logo",commandOptions.reportLogo, true);
             putNestedIfNotEmpty(beanParams, "report.signedBy",commandOptions.reportSignedBy, true);
             putNestedIfNotEmpty(beanParams, "report.signature",commandOptions.reportSignature, true);
@@ -1213,7 +1213,6 @@ private RestResponse<ClinicalAnalysis> update() throws Exception {
             putNestedIfNotEmpty(beanParams, "analyst.id",commandOptions.analystId, true);
             putNestedIfNotEmpty(beanParams, "report.title",commandOptions.reportTitle, true);
             putNestedIfNotEmpty(beanParams, "report.overview",commandOptions.reportOverview, true);
-            putNestedIfNotEmpty(beanParams, "report.discussion",commandOptions.reportDiscussion, true);
             putNestedIfNotEmpty(beanParams, "report.logo",commandOptions.reportLogo, true);
             putNestedIfNotEmpty(beanParams, "report.signedBy",commandOptions.reportSignedBy, true);
             putNestedIfNotEmpty(beanParams, "report.signature",commandOptions.reportSignature, true);

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisVariantCommandExecutor.java

@@ -64,7 +64,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/CohortsCommandExecutor.java

@@ -38,7 +38,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/DiseasePanelsCommandExecutor.java

@@ -32,7 +32,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FamiliesCommandExecutor.java

@@ -37,7 +37,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/FilesCommandExecutor.java

@@ -57,7 +57,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/IndividualsCommandExecutor.java

@@ -43,7 +43,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/JobsCommandExecutor.java

@@ -43,7 +43,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java

@@ -25,7 +25,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java

@@ -50,7 +50,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java

@@ -31,7 +31,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java

@@ -42,7 +42,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/StudiesCommandExecutor.java

@@ -58,7 +58,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/UsersCommandExecutor.java

@@ -40,7 +40,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisAlignmentCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.
@@ -214,9 +214,6 @@ public class CreateCommandOptions {
         @Parameter(names = {"--report-overview"}, description = "Report overview.", required = false, arity = 1)
         public String reportOverview;
 
-        @Parameter(names = {"--report-discussion"}, description = "Report discussion.", required = false, arity = 1)
-        public String reportDiscussion;
-
         @Parameter(names = {"--report-logo"}, description = "Report logo.", required = false, arity = 1)
         public String reportLogo;
 
@@ -1865,9 +1862,6 @@ public class UpdateCommandOptions {
         @Parameter(names = {"--report-overview"}, description = "Report overview.", required = false, arity = 1)
         public String reportOverview;
 
-        @Parameter(names = {"--report-discussion"}, description = "Report discussion.", required = false, arity = 1)
-        public String reportDiscussion;
-
         @Parameter(names = {"--report-logo"}, description = "Report logo.", required = false, arity = 1)
         public String reportLogo;
 

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java

@@ -19,7 +19,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java

@@ -19,7 +19,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/MetaCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/OperationsVariantStorageCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/ProjectsCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java

@@ -17,7 +17,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/StudiesCommandOptions.java

@@ -19,7 +19,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/UsersCommandOptions.java

@@ -19,7 +19,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2022-07-29
+* Autogenerated on: 2022-08-01
 *
 * 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.

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: 2022-07-29 14:04:06
+#    Autogenerated on: 2022-08-01 16:35:36
 #    
 #    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.

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: 2022-07-29 14:04:06
+#    Autogenerated on: 2022-08-01 16:35:36
 #    
 #    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.