cli: Autogenerated CLI and clients for release 2.12.1

opencb · Nov 28, 2023 · 67fe7a2 · 67fe7a2
1 parent 1392ecf
commit 67fe7a2
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Showing 71 changed files with 86 additions and 86 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/opencga-client/src/main/R/R/Admin-methods.R b/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: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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
@@ -10,37 +10,37 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName,
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, templateId, members, studies, variableSet, study, group, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, members, variableSet, group, studies, templateId, study, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, folder, members, file, annotationSet, files, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, annotationSet, members, folder, files, file, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
 ## JobClient
-setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...)
+setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...)
     standardGeneric("jobClient"))
 
 # ##############################################################################
 ## SampleClient
-setGeneric("sampleClient", function(OpencgaR, annotationSet, members, samples, sample, endpointName, params=NULL, ...)
+setGeneric("sampleClient", function(OpencgaR, annotationSet, sample, members, samples, endpointName, params=NULL, ...)
     standardGeneric("sampleClient"))
 
 # ##############################################################################
 ## IndividualClient
-setGeneric("individualClient", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...)
+setGeneric("individualClient", function(OpencgaR, annotationSet, individual, members, individuals, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
 ## FamilyClient
-setGeneric("familyClient", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...)
+setGeneric("familyClient", function(OpencgaR, annotationSet, members, families, family, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
 ## CohortClient
-setGeneric("cohortClient", function(OpencgaR, cohorts, members, cohort, annotationSet, endpointName, params=NULL, ...)
+setGeneric("cohortClient", function(OpencgaR, annotationSet, cohort, members, cohorts, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
@@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, members, interpretation, interpretations, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################

diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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.
@@ -58,7 +58,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, members, interpretation, interpretations, endpointName, params=NULL, ...) {
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:

diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohorts, members, cohort, annotationSet, endpointName, params=NULL, ...) {
+setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohort, members, cohorts, 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
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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.
@@ -38,7 +38,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("familyClient", "OpencgaR", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...) {
+setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, members, families, family, 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
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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.
@@ -54,7 +54,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("fileClient", "OpencgaR", function(OpencgaR, folder, members, file, annotationSet, files, endpointName, params=NULL, ...) {
+setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, members, folder, files, file, 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
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) {
+setMethod("individualClient", "OpencgaR", function(OpencgaR, annotationSet, individual, members, individuals, 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
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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.
@@ -40,7 +40,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("jobClient", "OpencgaR", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) {
+setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, 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
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, members, samples, sample, endpointName, params=NULL, ...) {
+setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, sample, members, samples, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/samples/acl/{members}/update:

diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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.
@@ -46,7 +46,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("studyClient", "OpencgaR", function(OpencgaR, templateId, members, studies, variableSet, study, group, endpointName, params=NULL, ...) {
+setMethod("studyClient", "OpencgaR", function(OpencgaR, members, variableSet, group, studies, templateId, study, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/studies/acl/{members}/update:

diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R
@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-21
+#    Autogenerated on: 2023-11-28
 #    
 #    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/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java
@@ -36,7 +36,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java
@@ -40,7 +40,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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/...a-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/...a-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java
@@ -51,7 +51,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java
@@ -37,7 +37,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java
@@ -35,7 +35,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java
@@ -36,7 +36,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java
@@ -43,7 +43,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java
@@ -27,7 +27,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java
@@ -36,7 +36,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java
@@ -37,7 +37,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java
@@ -28,7 +28,7 @@
 * WARNING: AUTOGENERATED CODE
 *
 * This code was generated by a tool.
-* Autogenerated on: 2023-11-21
+* Autogenerated on: 2023-11-28
 *
 * 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.