client: generate clients, #TASK-4158

opencb · Nov 17, 2023 · 41f3ca0 · 41f3ca0
1 parent 7757fab
commit 41f3ca0
Show file tree

Hide file tree

Showing 11 changed files with 20 additions and 20 deletions.
diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R
@@ -5,42 +5,42 @@ setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName,
 
 # ##############################################################################
 ## ProjectClient
-setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...)
+setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...)
     standardGeneric("projectClient"))
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, group, members, templateId, studies, study, variableSet, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, study, variableSet, templateId, studies, group, members, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, members, files, file, annotationSet, folder, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, annotationSet, file, files, folder, members, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
 ## JobClient
-setGeneric("jobClient", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...)
+setGeneric("jobClient", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...)
     standardGeneric("jobClient"))
 
 # ##############################################################################
 ## SampleClient
-setGeneric("sampleClient", function(OpencgaR, annotationSet, sample, samples, members, endpointName, params=NULL, ...)
+setGeneric("sampleClient", function(OpencgaR, members, annotationSet, samples, sample, endpointName, params=NULL, ...)
     standardGeneric("sampleClient"))
 
 # ##############################################################################
 ## IndividualClient
-setGeneric("individualClient", function(OpencgaR, individuals, individual, annotationSet, members, endpointName, params=NULL, ...)
+setGeneric("individualClient", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
 ## FamilyClient
-setGeneric("familyClient", function(OpencgaR, annotationSet, family, families, members, endpointName, params=NULL, ...)
+setGeneric("familyClient", function(OpencgaR, members, annotationSet, families, family, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
 ## CohortClient
-setGeneric("cohortClient", function(OpencgaR, annotationSet, cohort, cohorts, members, endpointName, params=NULL, ...)
+setGeneric("cohortClient", function(OpencgaR, cohort, members, annotationSet, cohorts, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
@@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, interpretations, clinicalAnalyses, interpretation, members, clinicalAnalysis, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretation, interpretations, members, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################
@@ -75,7 +75,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## GA4GHClient
-setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...)
+setGeneric("ga4ghClient", function(OpencgaR, file, study, 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
@@ -59,7 +59,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, clinicalAnalyses, interpretation, members, clinicalAnalysis, endpointName, params=NULL, ...) {
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretation, interpretations, members, 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
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohort, cohorts, members, endpointName, params=NULL, ...) {
+setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, members, annotationSet, 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
@@ -38,7 +38,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, family, families, members, endpointName, params=NULL, ...) {
+setMethod("familyClient", "OpencgaR", function(OpencgaR, members, annotationSet, 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
@@ -54,7 +54,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("fileClient", "OpencgaR", function(OpencgaR, members, files, file, annotationSet, folder, endpointName, params=NULL, ...) {
+setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, file, files, folder, members, 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
@@ -31,7 +31,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, study, file, endpointName, params=NULL, ...) {
+setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, 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
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("individualClient", "OpencgaR", function(OpencgaR, individuals, individual, annotationSet, members, endpointName, params=NULL, ...) {
+setMethod("individualClient", "OpencgaR", function(OpencgaR, members, annotationSet, individuals, individual, 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
@@ -40,7 +40,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("jobClient", "OpencgaR", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...) {
+setMethod("jobClient", "OpencgaR", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update:

diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R
@@ -34,7 +34,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("projectClient", "OpencgaR", function(OpencgaR, projects, project, endpointName, params=NULL, ...) {
+setMethod("projectClient", "OpencgaR", function(OpencgaR, project, projects, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/projects/create:

diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, sample, samples, members, endpointName, params=NULL, ...) {
+setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, annotationSet, samples, sample, 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
@@ -46,7 +46,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("studyClient", "OpencgaR", function(OpencgaR, group, members, templateId, studies, study, variableSet, endpointName, params=NULL, ...) {
+setMethod("studyClient", "OpencgaR", function(OpencgaR, study, variableSet, templateId, studies, group, members, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: