cli: Regenerate client and command line #TASK-6111

Author: juanfeSanahuja

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2024-04-17 OpenCB
+* Copyright 2015-2024-04-25 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2024-04-17 OpenCB
+* Copyright 2015-2024-04-25 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

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

@@ -1687,7 +1687,7 @@ public class QueryVariantCommandOptions {
         @Parameter(names = {"--include-interpretation"}, description = "Interpretation ID to include the fields related to this interpretation", required = false, arity = 1)
         public String includeInterpretation; 
 
-        @Parameter(names = {"--id"}, description = "List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. rs116600158,19:7177679:C:T", required = false, arity = 1)
+        @Parameter(names = {"--id"}, description = "List of variant IDs in the format chrom:start:ref:alt, e.g. 19:7177679:C:T", required = false, arity = 1)
         public String id; 
 
         @Parameter(names = {"--region"}, description = "List of regions, these can be just a single chromosome name or regions in the format chr:start-end, e.g.: 2,3:100000-200000", required = false, arity = 1)
@@ -1768,7 +1768,7 @@ public class QueryVariantCommandOptions {
         @Parameter(names = {"--ct"}, description = "List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and 'protein_altering'", required = false, arity = 1)
         public String ct; 
 
-        @Parameter(names = {"--xref"}, description = "List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ...", required = false, arity = 1)
+        @Parameter(names = {"--xref"}, description = "List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, HGVS ...", required = false, arity = 1)
         public String xref; 
 
         @Parameter(names = {"--biotype"}, description = "List of biotypes, e.g. protein_coding", required = false, arity = 1)

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

@@ -177,7 +177,7 @@ public class AggregationStatsCommandOptions {
         @Parameter(names = {"--ct"}, description = "List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and 'protein_altering'", required = false, arity = 1)
         public String ct; 
 
-        @Parameter(names = {"--xref"}, description = "List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ...", required = false, arity = 1)
+        @Parameter(names = {"--xref"}, description = "List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, HGVS ...", required = false, arity = 1)
         public String xref; 
 
         @Parameter(names = {"--biotype"}, description = "List of biotypes, e.g. protein_coding", required = false, arity = 1)
@@ -259,7 +259,7 @@ public class QueryAnnotationCommandOptions {
         @ParametersDelegate
         public CommonCommandOptions commonOptions = commonCommandOptions;
 
-        @Parameter(names = {"--id"}, description = "List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. rs116600158,19:7177679:C:T", required = false, arity = 1)
+        @Parameter(names = {"--id"}, description = "List of variant IDs in the format chrom:start:ref:alt, e.g. 19:7177679:C:T", required = false, arity = 1)
         public String id; 
 
         @Parameter(names = {"--region"}, description = "List of regions, these can be just a single chromosome name or regions in the format chr:start-end, e.g.: 2,3:100000-200000", required = false, arity = 1)
@@ -1614,7 +1614,7 @@ public class QueryCommandOptions {
         @Parameter(names = {"--saved-filter"}, description = "Use a saved filter at User level", required = false, arity = 1)
         public String savedFilter; 
 
-        @Parameter(names = {"--id"}, description = "List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. rs116600158,19:7177679:C:T", required = false, arity = 1)
+        @Parameter(names = {"--id"}, description = "List of variant IDs in the format chrom:start:ref:alt, e.g. 19:7177679:C:T", required = false, arity = 1)
         public String id; 
 
         @Parameter(names = {"--region"}, description = "List of regions, these can be just a single chromosome name or regions in the format chr:start-end, e.g.: 2,3:100000-200000", required = false, arity = 1)
@@ -1740,7 +1740,7 @@ public class QueryCommandOptions {
         @Parameter(names = {"--ct"}, description = "List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and 'protein_altering'", required = false, arity = 1)
         public String ct; 
 
-        @Parameter(names = {"--xref"}, description = "List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ...", required = false, arity = 1)
+        @Parameter(names = {"--xref"}, description = "List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, HGVS ...", required = false, arity = 1)
         public String xref; 
 
         @Parameter(names = {"--biotype"}, description = "List of biotypes, e.g. protein_coding", required = false, arity = 1)

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: 2024-04-17
+#    Autogenerated on: 2024-04-25
 #    
 #    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: 2024-04-17
+#    Autogenerated on: 2024-04-25
 #    
 #    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/AllGenerics.R

@@ -1,6 +1,6 @@
 # ##############################################################################
 ## UserClient
-setGeneric("userClient", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...)
+setGeneric("userClient", function(OpencgaR, users, user, filterId, endpointName, params=NULL, ...)
     standardGeneric("userClient"))
 
 # ##############################################################################
@@ -10,42 +10,42 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName,
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, templateId, variableSet, members, study, group, studies, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, studies, members, variableSet, group, templateId, study, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, files, members, folder, file, annotationSet, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, members, file, folder, annotationSet, files, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
 ## JobClient
-setGeneric("jobClient", function(OpencgaR, jobs, job, members, endpointName, params=NULL, ...)
+setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...)
     standardGeneric("jobClient"))
 
 # ##############################################################################
 ## SampleClient
-setGeneric("sampleClient", function(OpencgaR, samples, annotationSet, members, sample, endpointName, params=NULL, ...)
+setGeneric("sampleClient", function(OpencgaR, annotationSet, members, samples, sample, endpointName, params=NULL, ...)
     standardGeneric("sampleClient"))
 
 # ##############################################################################
 ## IndividualClient
-setGeneric("individualClient", function(OpencgaR, annotationSet, individuals, members, individual, endpointName, params=NULL, ...)
+setGeneric("individualClient", function(OpencgaR, annotationSet, individual, members, individuals, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
 ## FamilyClient
-setGeneric("familyClient", function(OpencgaR, family, families, members, annotationSet, endpointName, params=NULL, ...)
+setGeneric("familyClient", function(OpencgaR, family, members, annotationSet, families, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
 ## CohortClient
-setGeneric("cohortClient", function(OpencgaR, cohorts, annotationSet, cohort, members, endpointName, params=NULL, ...)
+setGeneric("cohortClient", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
 ## PanelClient
-setGeneric("panelClient", function(OpencgaR, panels, members, endpointName, params=NULL, ...)
+setGeneric("panelClient", function(OpencgaR, members, panels, endpointName, params=NULL, ...)
     standardGeneric("panelClient"))
 
 # ##############################################################################
@@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, members, clinicalAnalyses, clinicalAnalysis, interpretation, annotationSet, interpretations, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, members, clinicalAnalyses, annotationSet, interpretations, interpretation, clinicalAnalysis, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################
@@ -75,7 +75,7 @@ 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"))
 
 # ##############################################################################

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: 2024-04-17
+#    Autogenerated on: 2024-04-25
 #    
 #    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.
@@ -61,7 +61,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, clinicalAnalyses, clinicalAnalysis, interpretation, annotationSet, interpretations, endpointName, params=NULL, ...) {
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, clinicalAnalyses, annotationSet, interpretations, interpretation, clinicalAnalysis, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:
@@ -541,7 +541,7 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, clinicalAnal
         #' @param approximateCountSamplingSize Sampling size to get the approximate count. Larger values increase accuracy but also increase execution time.
         #' @param savedFilter Use a saved filter at User level.
         #' @param includeInterpretation Interpretation ID to include the fields related to this interpretation.
-        #' @param id List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. rs116600158,19:7177679:C:T.
+        #' @param id List of variant IDs in the format chrom:start:ref:alt, e.g. 19:7177679:C:T.
         #' @param region List of regions, these can be just a single chromosome name or regions in the format chr:start-end, e.g.: 2,3:100000-200000.
         #' @param type List of types, accepted values are SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
         #' @param study Filter variants from the given studies, these can be either the numeric ID or the alias with the format user@project:study.
@@ -568,7 +568,7 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, clinicalAnal
         #' @param familyProband Specify the proband child to use for the family segregation.
         #' @param gene List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' parameter.
         #' @param ct List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and 'protein_altering'.
-        #' @param xref List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ...
+        #' @param xref List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, HGVS ...
         #' @param biotype List of biotypes, e.g. protein_coding.
         #' @param proteinSubstitution Protein substitution scores include SIFT and PolyPhen. You can query using the score {protein_score}[<|>|<=|>=]{number} or the description {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant.
         #' @param conservation Filter by conservation score: {conservation_score}[<|>|<=|>=]{number} e.g. phastCons>0.5,phylop<0.1,gerp>0.1.

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: 2024-04-17
+#    Autogenerated on: 2024-04-25
 #    
 #    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, annotationSet, cohort, members, endpointName, params=NULL, ...) {
+setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update:

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: 2024-04-17
+#    Autogenerated on: 2024-04-25
 #    
 #    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, families, members, annotationSet, endpointName, params=NULL, ...) {
+setMethod("familyClient", "OpencgaR", function(OpencgaR, family, members, annotationSet, families, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/families/acl/{members}/update: