Port Patch 1.10.2 -> 2.0.0 #TASK-5618

opencb · Mar 6, 2024 · 1ed3c35 · 1ed3c35
1 parent 730e249
commit 1ed3c35
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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
@@ -1,9 +1,5 @@
 /*
-<<<<<<< HEAD
-* Copyright 2015-2024-02-02 OpenCB
-=======
-* Copyright 2015-2024-03-04 OpenCB
->>>>>>> develop
+* Copyright 2015-2024-03-06 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
@@ -64,11 +60,7 @@ public abstract class OpenCgaCompleter implements Completer {
             .map(Candidate::new)
             .collect(toList());
 
-<<<<<<< HEAD
-    private List<Candidate> clinicalList = asList( "acl-update","annotation-sets-load","clinical-configuration-update","create","distinct","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","annotation-sets-annotations-update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update","report-update")
-=======
-    private List<Candidate> clinicalList = asList( "acl-update","annotation-sets-load","clinical-configuration-update","create","distinct","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","load","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","annotation-sets-annotations-update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update")
->>>>>>> develop
+    private List<Candidate> clinicalList = asList( "acl-update","annotation-sets-load","clinical-configuration-update","create","distinct","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","load","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","annotation-sets-annotations-update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update","report-update")
             .stream()
             .map(Candidate::new)
             .collect(toList());

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
@@ -1,9 +1,5 @@
 /*
-<<<<<<< HEAD
-* Copyright 2015-2024-02-02 OpenCB
-=======
-* Copyright 2015-2024-03-04 OpenCB
->>>>>>> develop
+* Copyright 2015-2024-03-06 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/...src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java b/...src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java
@@ -2331,7 +2331,7 @@ public class UpdateReportCommandOptions {
         @Parameter(names = {"--clinical-analysis"}, description = "Clinical analysis ID", required = true, arity = 1)
         public String clinicalAnalysis; 
 
-        @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
+        @Parameter(names = {"--study", "-s"}, description = "Study [[organization@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1)
         public String study; 
 
         @Parameter(names = {"--supporting-evidences-action"}, description = "Action to be performed if the array of supporting evidences is being updated.", required = false, arity = 1)

diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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
@@ -5,79 +5,47 @@ setGeneric("organizationClient", function(OpencgaR, organization, endpointName,
 
 # ##############################################################################
 ## UserClient
-<<<<<<< HEAD
-setGeneric("userClient", function(OpencgaR, user, users, filterId, endpointName, params=NULL, ...)
-=======
 setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...)
->>>>>>> develop
     standardGeneric("userClient"))
 
 # ##############################################################################
 ## ProjectClient
-setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...)
+setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...)
     standardGeneric("projectClient"))
 
 # ##############################################################################
 ## StudyClient
-<<<<<<< HEAD
-setGeneric("studyClient", function(OpencgaR, members, study, group, variableSet, templateId, studies, endpointName, params=NULL, ...)
-=======
-setGeneric("studyClient", function(OpencgaR, group, members, templateId, studies, study, variableSet, endpointName, params=NULL, ...)
->>>>>>> develop
+setGeneric("studyClient", function(OpencgaR, group, variableSet, studies, templateId, study, members, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-<<<<<<< HEAD
-setGeneric("fileClient", function(OpencgaR, members, folder, file, annotationSet, files, endpointName, params=NULL, ...)
-=======
-setGeneric("fileClient", function(OpencgaR, file, annotationSet, members, files, folder, endpointName, params=NULL, ...)
->>>>>>> develop
+setGeneric("fileClient", function(OpencgaR, files, folder, file, members, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
 ## JobClient
-<<<<<<< HEAD
-setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...)
-=======
-setGeneric("jobClient", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...)
->>>>>>> develop
+setGeneric("jobClient", function(OpencgaR, jobs, job, members, endpointName, params=NULL, ...)
     standardGeneric("jobClient"))
 
 # ##############################################################################
 ## SampleClient
-<<<<<<< HEAD
-setGeneric("sampleClient", function(OpencgaR, annotationSet, members, sample, samples, endpointName, params=NULL, ...)
-=======
-setGeneric("sampleClient", function(OpencgaR, members, annotationSet, sample, samples, endpointName, params=NULL, ...)
->>>>>>> develop
+setGeneric("sampleClient", function(OpencgaR, annotationSet, sample, samples, members, endpointName, params=NULL, ...)
     standardGeneric("sampleClient"))
 
 # ##############################################################################
 ## IndividualClient
-<<<<<<< HEAD
-setGeneric("individualClient", function(OpencgaR, individual, annotationSet, members, individuals, endpointName, params=NULL, ...)
-=======
-setGeneric("individualClient", function(OpencgaR, individual, members, annotationSet, individuals, endpointName, params=NULL, ...)
->>>>>>> develop
+setGeneric("individualClient", function(OpencgaR, individuals, individual, annotationSet, members, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
 ## FamilyClient
-<<<<<<< HEAD
-setGeneric("familyClient", function(OpencgaR, families, annotationSet, members, family, endpointName, params=NULL, ...)
-=======
-setGeneric("familyClient", function(OpencgaR, members, annotationSet, families, family, endpointName, params=NULL, ...)
->>>>>>> develop
+setGeneric("familyClient", function(OpencgaR, annotationSet, families, family, members, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
 ## CohortClient
-<<<<<<< HEAD
-setGeneric("cohortClient", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...)
-=======
-setGeneric("cohortClient", function(OpencgaR, cohort, members, annotationSet, cohorts, endpointName, params=NULL, ...)
->>>>>>> develop
+setGeneric("cohortClient", function(OpencgaR, annotationSet, cohort, cohorts, members, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
@@ -97,11 +65,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-<<<<<<< HEAD
-setGeneric("clinicalClient", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, annotationSet, clinicalAnalyses, endpointName, params=NULL, ...)
-=======
-setGeneric("clinicalClient", function(OpencgaR, annotationSet, clinicalAnalysis, interpretations, members, clinicalAnalyses, interpretation, endpointName, params=NULL, ...)
->>>>>>> develop
+setGeneric("clinicalClient", function(OpencgaR, interpretation, clinicalAnalyses, interpretations, members, annotationSet, clinicalAnalysis, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################
@@ -116,7 +80,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## GA4GHClient
-setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=NULL, ...)
+setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...)
     standardGeneric("ga4ghClient"))
 
 # ##############################################################################

diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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.
@@ -66,11 +62,7 @@
 #' [*]: Required parameter
 #' @export
 
-<<<<<<< HEAD
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, annotationSet, clinicalAnalyses, endpointName, params=NULL, ...) {
-=======
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, annotationSet, clinicalAnalysis, interpretations, members, clinicalAnalyses, interpretation, endpointName, params=NULL, ...) {
->>>>>>> develop
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretation, clinicalAnalyses, interpretations, members, annotationSet, clinicalAnalysis, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:
@@ -742,7 +734,7 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, annotationSet, clinic
         #' @param include Fields included in the response, whole JSON path must be provided.
         #' @param exclude Fields excluded in the response, whole JSON path must be provided.
         #' @param clinicalAnalysis Clinical analysis ID.
-        #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID.
+        #' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
         #' @param commentsAction Action to be performed if the array of comments is being updated. Allowed values: ['ADD REMOVE REPLACE']
         #' @param supportingEvidencesAction Action to be performed if the array of supporting evidences is being updated. Allowed values: ['ADD SET REMOVE']
         #' @param filesAction Action to be performed if the array of files is being updated. Allowed values: ['ADD SET REMOVE']

diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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.
@@ -42,11 +38,7 @@
 #' [*]: Required parameter
 #' @export
 
-<<<<<<< HEAD
-setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...) {
-=======
-setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, members, annotationSet, cohorts, endpointName, params=NULL, ...) {
->>>>>>> develop
+setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohort, cohorts, members, 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
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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.
@@ -41,11 +37,7 @@
 #' [*]: Required parameter
 #' @export
 
-<<<<<<< HEAD
-setMethod("familyClient", "OpencgaR", function(OpencgaR, families, annotationSet, members, family, endpointName, params=NULL, ...) {
-=======
-setMethod("familyClient", "OpencgaR", function(OpencgaR, members, annotationSet, families, family, endpointName, params=NULL, ...) {
->>>>>>> develop
+setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, families, family, members, 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
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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.
@@ -57,11 +53,7 @@
 #' [*]: Required parameter
 #' @export
 
-<<<<<<< HEAD
-setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, file, annotationSet, files, endpointName, params=NULL, ...) {
-=======
-setMethod("fileClient", "OpencgaR", function(OpencgaR, file, annotationSet, members, files, folder, endpointName, params=NULL, ...) {
->>>>>>> develop
+setMethod("fileClient", "OpencgaR", function(OpencgaR, files, folder, file, members, annotationSet, 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
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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.
@@ -35,7 +31,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, endpointName, params=NULL, ...) {
+setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, study, file, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/ga4gh/reads/search:

diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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.
@@ -42,11 +38,7 @@
 #' [*]: Required parameter
 #' @export
 
-<<<<<<< HEAD
-setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, annotationSet, members, individuals, endpointName, params=NULL, ...) {
-=======
-setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, members, annotationSet, individuals, endpointName, params=NULL, ...) {
->>>>>>> develop
+setMethod("individualClient", "OpencgaR", function(OpencgaR, individuals, individual, annotationSet, members, 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
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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.
@@ -43,11 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-<<<<<<< HEAD
-setMethod("jobClient", "OpencgaR", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) {
-=======
-setMethod("jobClient", "OpencgaR", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) {
->>>>>>> develop
+setMethod("jobClient", "OpencgaR", function(OpencgaR, jobs, job, members, 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
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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
@@ -2,11 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-<<<<<<< HEAD
-#    Autogenerated on: 2024-02-02
-=======
-#    Autogenerated on: 2024-03-04
->>>>>>> develop
+#    Autogenerated on: 2024-03-06
 #    
 #    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.