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 index 31d1c757700..ff4d1cda0d9 100644 --- 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 2015-2024-01-30 OpenCB +* Copyright 2015-2024-02-02 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 index fe013c129cd..b783ac8c631 100644 --- 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 2015-2024-01-30 OpenCB +* Copyright 2015-2024-02-02 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/executors/MetaCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java index 0d8987f61d6..3a674a32c68 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/MetaCommandExecutor.java @@ -106,7 +106,11 @@ private RestResponse model() throws Exception { logger.debug("Executing model in Meta command line"); MetaCommandOptions.ModelCommandOptions commandOptions = metaCommandOptions.modelCommandOptions; - return openCGAClient.getMetaClient().model(); + + ObjectMap queryParams = new ObjectMap(); + queryParams.putIfNotEmpty("model", commandOptions.model); + + return openCGAClient.getMetaClient().model(queryParams); } private RestResponse ping() throws Exception { diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/MetaCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/MetaCommandOptions.java index 4cb695c9e32..c72e4325362 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/MetaCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/MetaCommandOptions.java @@ -87,6 +87,9 @@ public class ModelCommandOptions { @ParametersDelegate public CommonCommandOptions commonOptions = commonCommandOptions; + @Parameter(names = {"--model"}, description = "Model description", required = false, arity = 1) + public String model; + } @Parameters(commandNames = {"ping"}, commandDescription ="Ping Opencga webservices.") diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index cd6c1bd235a..16934e37c0a 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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 index a3110d0b076..6cf06517077 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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 index 177a61e827a..3b8fbf19e0a 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -5,17 +5,17 @@ setGeneric("userClient", function(OpencgaR, user, users, filterId, endpointName, # ############################################################################## ## ProjectClient -setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...) +setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...) standardGeneric("projectClient")) # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, studies, members, templateId, study, variableSet, group, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, members, study, group, variableSet, templateId, studies, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, members, folder, file, files, annotationSet, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, members, folder, file, annotationSet, files, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## @@ -30,17 +30,17 @@ setGeneric("sampleClient", function(OpencgaR, annotationSet, members, sample, sa # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, individual, annotationSet, members, individuals, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, members, annotationSet, families, family, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, families, annotationSet, members, family, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, cohort, annotationSet, members, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, members, interpretations, clinicalAnalysis, interpretation, annotationSet, clinicalAnalyses, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, annotationSet, 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 index 9184f341a42..6bcb2f2b22b 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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, interpretations, clinicalAnalysis, interpretation, annotationSet, clinicalAnalyses, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, annotationSet, 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 index ff52e896b22..c18e887d317 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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, cohort, annotationSet, members, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, members, cohort, 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 index a0ae9ced80d..9320d10c540 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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, members, annotationSet, families, family, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, families, annotationSet, members, 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 index aa5d9a763a1..132fa43c0dd 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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, members, folder, file, files, annotationSet, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, file, annotationSet, files, 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 index 0a240e6d6a3..5a37a5dc5c4 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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 index 0c81ab901f7..85433cf5129 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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, members, annotationSet, individuals, individual, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, annotationSet, 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 index 44abcff66ef..d17aaa553a7 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index d8fa6d73da6..94a18107431 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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. @@ -23,7 +23,7 @@ #' | about | /{apiVersion}/meta/about | | #' | api | /{apiVersion}/meta/api | category | #' | fail | /{apiVersion}/meta/fail | | -#' | model | /{apiVersion}/meta/model | | +#' | model | /{apiVersion}/meta/model | model | #' | ping | /{apiVersion}/meta/ping | | #' | status | /{apiVersion}/meta/status | | #' @@ -56,7 +56,7 @@ setMethod("metaClient", "OpencgaR", function(OpencgaR, endpointName, params=NULL #' @section Endpoint /{apiVersion}/meta/model: #' Opencga model webservices. - + #' @param model Model description. model=fetchOpenCGA(object=OpencgaR, category="meta", categoryId=NULL, subcategory=NULL, subcategoryId=NULL, action="model", params=params, httpMethod="GET", as.queryParam=NULL, ...), diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 5347a1eca81..6b7ce28a8c6 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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 index cd408e39313..ec0aba4e3df 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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 index 4af959c7597..fc4593e0459 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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. @@ -34,7 +34,7 @@ #' [*]: Required parameter #' @export -setMethod("projectClient", "OpencgaR", function(OpencgaR, project, projects, endpointName, params=NULL, ...) { +setMethod("projectClient", "OpencgaR", function(OpencgaR, projects, project, 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 index dac7f36ccbd..1ef209a32ec 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index cbce8be6beb..c2b9b912241 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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, studies, members, templateId, study, variableSet, group, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, members, study, group, variableSet, templateId, studies, 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 index 3505c6cffc5..17acf92aff0 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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 index 71116af6b8c..f2dc429c877 100644 --- 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: 2024-01-30 +# Autogenerated on: 2024-02-02 # # 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 index 226785e12de..df91987ff7f 100644 --- 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: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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 index 9f1fe0c3762..1a3cbd6e61c 100644 --- 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: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index 2a536a0200b..f98b6d7c58e 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -54,7 +54,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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 index e70f528ead2..fb16691423c 100644 --- 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: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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 index ddbc803466a..2cf832703f8 100644 --- 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: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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 index bbd0ece17d3..129b4b14705 100644 --- 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: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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 index d180259c267..06ae8e4b9c7 100644 --- 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: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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 index 792bd4512cf..2af3d0c9e28 100644 --- 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: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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 index 39d0f05a7c5..0f1413db069 100644 --- 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: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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 index 93cc6bd33b5..c15fa77699f 100644 --- 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: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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 index c00a5087087..baadc9f1b8a 100644 --- 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: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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. @@ -80,11 +80,13 @@ public RestResponse fail() throws ClientException { /** * Opencga model webservices. + * @param params Map containing any of the following optional parameters. + * model: Model description. * @return a RestResponse object. * @throws ClientException ClientException if there is any server error. */ - public RestResponse model() throws ClientException { - ObjectMap params = new ObjectMap(); + public RestResponse model(ObjectMap params) throws ClientException { + params = params != null ? params : new ObjectMap(); return execute("meta", null, null, null, "model", params, GET, String.class); } diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index d3f6a379f3a..9a2f3b27f1b 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -32,7 +32,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index fd4789a4dc4..7387954d23c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index c537f9b4227..eccd24ddd6a 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -45,7 +45,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index 0a6620159a8..509de9c2944 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index bb2741388d7..a7a369dcd46 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index 66d77561bba..594a79f83bf 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-01-30 +* Autogenerated on: 2024-02-02 * * 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/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index d533d8eb0ba..05a71e5ced1 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index b4847e1dac0..1075d6d854c 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/Clinical.js b/opencga-client/src/main/javascript/Clinical.js deleted file mode 100644 index 2c695aacd91..00000000000 --- a/opencga-client/src/main/javascript/Clinical.js +++ /dev/null @@ -1,807 +0,0 @@ -/** - * Copyright 2015-2020 OpenCB - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * http://www.apache.org/licenses/LICENSE-2.0 - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * WARNING: AUTOGENERATED CODE - * - * This code was generated by a tool. - * Autogenerated on: 2022-08-02 08:25:32 ->>>>>>> develop ->>>>>>> release-2.4.x ->>>>>>> release-2.4.x - * - * 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. - * -**/ - -import OpenCGAParentClass from "./../opencga-parent-class.js"; - - -/** - * This class contains the methods for the "Clinical" resource - */ - -export default class Clinical extends OpenCGAParentClass { - - constructor(config) { - super(config); - } - - /** Update the set of permissions granted for the member - * @param {String} members - Comma separated list of user or group IDs. - * @param {Object} data - JSON containing the parameters to add ACLs. - * @param {String} action = "ADD" - Action to be performed [ADD, SET, REMOVE or RESET]. The default value is ADD. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {Boolean} [params.propagate = "false"] - Propagate permissions to related families, individuals, samples and files. The default - * value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - updateAcl(members, action, data, params) { - return this._post("analysis", null, "clinical/acl", members, "update", data, {action, ...params}); - } - - /** Update Clinical Analysis configuration. - * @param {Object} [data] - Configuration params to update. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - updateClinicalConfiguration(data, params) { - return this._post("analysis", null, "clinical/clinical/configuration", null, "update", data, params); - } - - /** Create a new clinical analysis - * @param {Object} data - JSON containing clinical analysis information. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {Boolean} [params.skipCreateDefaultInterpretation] - Flag to skip creating and initialise an empty default primary - * interpretation (Id will be '{clinicalAnalysisId}.1'). This flag is only considered if no Interpretation object is passed. - * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. - * The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - create(data, params) { - return this._post("analysis", null, "clinical", null, "create", data, params); - } - - /** Clinical Analysis distinct method - * @param {String} field - Field for which to obtain the distinct values. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. - * @param {String} [params.uuid] - Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. - * @param {String} [params.type] - Clinical Analysis type. - * @param {String} [params.disorder] - Clinical Analysis disorder. - * @param {String} [params.files] - Clinical Analysis files. - * @param {String} [params.sample] - Sample associated to the proband or any member of a family. - * @param {String} [params.individual] - Proband or any member of a family. - * @param {String} [params.proband] - Clinical Analysis proband. - * @param {String} [params.probandSamples] - Clinical Analysis proband samples. - * @param {String} [params.family] - Clinical Analysis family. - * @param {String} [params.familyMembers] - Clinical Analysis family members. - * @param {String} [params.familyMemberSamples] - Clinical Analysis family members samples. - * @param {String} [params.panels] - Clinical Analysis panels. - * @param {Boolean} [params.locked] - Locked Clinical Analyses. - * @param {String} [params.analystId] - Clinical Analysis analyst id. - * @param {String} [params.priority] - Clinical Analysis priority. - * @param {String} [params.flags] - Clinical Analysis flags. - * @param {String} [params.creationDate] - Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.modificationDate] - Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, - * <201805. - * @param {String} [params.dueDate] - Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.qualityControlSummary] - Clinical Analysis quality control summary. - * @param {String} [params.release] - Release when it was created. - * @param {String} [params.status] - Filter by status. - * @param {String} [params.internalStatus] - Filter by internal status. - * @param {Boolean} [params.deleted] - Boolean to retrieve deleted entries. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - distinct(field, params) { - return this._get("analysis", null, "clinical", null, "distinct", {field, ...params}); - } - - /** Interpretation distinct method - * @param {String} field - Field for which to obtain the distinct values. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. - * @param {String} [params.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. - * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. - * @param {String} [params.analystId] - Analyst ID. - * @param {String} [params.methodName] - Interpretation method name. - * @param {String} [params.panels] - Interpretation panels. - * @param {String} [params.primaryFindings] - Interpretation primary findings. - * @param {String} [params.secondaryFindings] - Interpretation secondary findings. - * @param {String} [params.creationDate] - Interpretation Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.modificationDate] - Interpretation Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, - * <201805. - * @param {String} [params.status] - Filter by status. - * @param {String} [params.internalStatus] - Filter by internal status. - * @param {String} [params.release] - Release when it was created. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - distinctInterpretation(field, params) { - return this._get("analysis", null, "clinical/interpretation", null, "distinct", {field, ...params}); - } - - /** Search clinical interpretations - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.sort] - Sort the results. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. - * @param {String} [params.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. - * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. - * @param {String} [params.analystId] - Analyst ID. - * @param {String} [params.methodName] - Interpretation method name. - * @param {String} [params.panels] - Interpretation panels. - * @param {String} [params.primaryFindings] - Interpretation primary findings. - * @param {String} [params.secondaryFindings] - Interpretation secondary findings. - * @param {String} [params.creationDate] - Interpretation Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.modificationDate] - Interpretation Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, - * <201805. - * @param {String} [params.status] - Filter by status. - * @param {String} [params.internalStatus] - Filter by internal status. - * @param {String} [params.release] - Release when it was created. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - searchInterpretation(params) { - return this._get("analysis", null, "clinical/interpretation", null, "search", params); - } - - /** Clinical interpretation information - * @param {String} interpretations - Comma separated list of clinical interpretation IDs up to a maximum of 100. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.version] - Comma separated list of interpretation versions. 'all' to get all the interpretation versions. Not - * supported if multiple interpretation ids are provided. - * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - infoInterpretation(interpretations, params) { - return this._get("analysis", null, "clinical/interpretation", interpretations, "info", params); - } - - /** Run cancer tiering interpretation analysis - * @param {Object} data - Cancer tiering interpretation analysis params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runInterpreterCancerTiering(data, params) { - return this._post("analysis", null, "clinical/interpreter/cancerTiering", null, "run", data, params); - } - - /** Run exomiser interpretation analysis - * @param {Object} data - Exomizer interpretation analysis params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runInterpreterExomiser(data, params) { - return this._post("analysis", null, "clinical/interpreter/exomiser", null, "run", data, params); - } - - /** Run TEAM interpretation analysis - * @param {Object} data - TEAM interpretation analysis params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runInterpreterTeam(data, params) { - return this._post("analysis", null, "clinical/interpreter/team", null, "run", data, params); - } - - /** Run tiering interpretation analysis - * @param {Object} data - Tiering interpretation analysis params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runInterpreterTiering(data, params) { - return this._post("analysis", null, "clinical/interpreter/tiering", null, "run", data, params); - } - - /** Run Zetta interpretation analysis - * @param {Object} data - Zetta interpretation analysis params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runInterpreterZetta(data, params) { - return this._post("analysis", null, "clinical/interpreter/zetta", null, "run", data, params); - } - - /** RGA aggregation stats - * @param {String} field - List of fields separated by semicolons, e.g.: clinicalSignificances;type. For nested fields use >>, e.g.: - * type>>clinicalSignificances;knockoutType. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - aggregationStatsRga(field, params) { - return this._get("analysis", null, "clinical/rga", null, "aggregationStats", {field, ...params}); - } - - /** Query gene RGA - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.includeIndividual] - Include only the comma separated list of individuals to the response. - * @param {Number} [params.skipIndividual] - Number of individuals to skip. - * @param {Number} [params.limitIndividual] - Limit number of individuals returned (default: 1000). - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - queryRgaGene(params) { - return this._get("analysis", null, "clinical/rga/gene", null, "query", params); - } - - /** RGA gene summary stats - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - summaryRgaGene(params) { - return this._get("analysis", null, "clinical/rga/gene", null, "summary", params); - } - - /** Generate Recessive Gene Analysis secondary index - * @param {Object} data - Recessive Gene Analysis index params. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.jobId] - Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not - * provided. - * @param {String} [params.jobDescription] - Job description. - * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on. - * @param {String} [params.jobTags] - Job tags. - * @param {Boolean} [params.auxiliarIndex = "false"] - Index auxiliar collection to improve performance assuming RGA is completely - * indexed. The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - runRgaIndex(data, params) { - return this._post("analysis", null, "clinical/rga/index", null, "run", data, params); - } - - /** Query individual RGA - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - queryRgaIndividual(params) { - return this._get("analysis", null, "clinical/rga/individual", null, "query", params); - } - - /** RGA individual summary stats - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - summaryRgaIndividual(params) { - return this._get("analysis", null, "clinical/rga/individual", null, "summary", params); - } - - /** Query variant RGA - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.includeIndividual] - Include only the comma separated list of individuals to the response. - * @param {Number} [params.skipIndividual] - Number of individuals to skip. - * @param {Number} [params.limitIndividual] - Limit number of individuals returned (default: 1000). - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - queryRgaVariant(params) { - return this._get("analysis", null, "clinical/rga/variant", null, "query", params); - } - - /** RGA variant summary stats - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {String} [params.sampleId] - Filter by sample id. - * @param {String} [params.individualId] - Filter by individual id. - * @param {String} [params.sex] - Filter by sex. - * @param {String} [params.phenotypes] - Filter by phenotypes. - * @param {String} [params.disorders] - Filter by disorders. - * @param {String} [params.numParents] - Filter by the number of parents registered. - * @param {String} [params.geneId] - Filter by gene id. - * @param {String} [params.geneName] - Filter by gene name. - * @param {String} [params.chromosome] - Filter by chromosome. - * @param {String} [params.start] - Filter by start position. - * @param {String} [params.end] - Filter by end position. - * @param {String} [params.transcriptId] - Filter by transcript id. - * @param {String} [params.variants] - Filter by variant id. - * @param {String} [params.dbSnps] - Filter by DB_SNP id. - * @param {String} [params.knockoutType] - Filter by knockout type. - * @param {String} [params.filter] - Filter by filter (PASS, NOT_PASS). - * @param {String} [params.type] - Filter by variant type. - * @param {String} [params.clinicalSignificance] - Filter by clinical significance. - * @param {String} [params.populationFrequency] - Filter by population frequency. - * @param {String} [params.consequenceType] - Filter by consequence type. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - summaryRgaVariant(params) { - return this._get("analysis", null, "clinical/rga/variant", null, "summary", params); - } - - /** Clinical analysis search. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count = "false"] - Get the total number of results matching the query. Deactivated by default. The default - * value is false. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. - * @param {String} [params.uuid] - Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. - * @param {String} [params.type] - Clinical Analysis type. - * @param {String} [params.disorder] - Clinical Analysis disorder. - * @param {String} [params.files] - Clinical Analysis files. - * @param {String} [params.sample] - Sample associated to the proband or any member of a family. - * @param {String} [params.individual] - Proband or any member of a family. - * @param {String} [params.proband] - Clinical Analysis proband. - * @param {String} [params.probandSamples] - Clinical Analysis proband samples. - * @param {String} [params.family] - Clinical Analysis family. - * @param {String} [params.familyMembers] - Clinical Analysis family members. - * @param {String} [params.familyMemberSamples] - Clinical Analysis family members samples. - * @param {String} [params.panels] - Clinical Analysis panels. - * @param {Boolean} [params.locked] - Locked Clinical Analyses. - * @param {String} [params.analystId] - Clinical Analysis analyst id. - * @param {String} [params.priority] - Clinical Analysis priority. - * @param {String} [params.flags] - Clinical Analysis flags. - * @param {String} [params.creationDate] - Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.modificationDate] - Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, - * <201805. - * @param {String} [params.dueDate] - Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. - * @param {String} [params.qualityControlSummary] - Clinical Analysis quality control summary. - * @param {String} [params.release] - Release when it was created. - * @param {String} [params.status] - Filter by status. - * @param {String} [params.internalStatus] - Filter by internal status. - * @param {Boolean} [params.deleted] - Boolean to retrieve deleted entries. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - search(params) { - return this._get("analysis", null, "clinical", null, "search", params); - } - - /** Fetch actionable clinical variants - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.sample] - Sample ID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - actionableVariant(params) { - return this._get("analysis", null, "clinical/variant", null, "actionable", params); - } - - /** Fetch clinical variants - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {Number} [params.limit] - Number of results to be returned. - * @param {Number} [params.skip] - Number of results to skip. - * @param {Boolean} [params.count] - Get the total number of results matching the query. Deactivated by default. - * @param {Boolean} [params.approximateCount] - Get an approximate count, instead of an exact total count. Reduces execution time. - * @param {Number} [params.approximateCountSamplingSize] - Sampling size to get the approximate count. Larger values increase accuracy - * but also increase execution time. - * @param {String} [params.savedFilter] - Use a saved filter at User level. - * @param {String} [params.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 {String} [params.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 {String} [params.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 {String} [params.study] - Filter variants from the given studies, these can be either the numeric ID or the alias with the - * format user@project:study. - * @param {String} [params.file] - Filter variants from the files specified. This will set includeFile parameter when not provided. - * @param {String} [params.filter] - Specify the FILTER for any of the files. If 'file' filter is provided, will match the file and the - * filter. e.g.: PASS,LowGQX. - * @param {String} [params.qual] - Specify the QUAL for any of the files. If 'file' filter is provided, will match the file and the qual. - * e.g.: >123.4. - * @param {String} [params.fileData] - Filter by file data (i.e. FILTER, QUAL and INFO columns from VCF file). - * [{file}:]{key}{op}{value}[,;]* . If no file is specified, will use all files from "file" filter. e.g. AN>200 or - * file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined. e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP. - * @param {String} [params.sample] - Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not - * provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) - * operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. - * HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice - * versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with - * genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. - * HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted - * segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, - * mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. . - * @param {String} [params.sampleData] - Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is - * specified, will use all samples from "sample" or "genotype" filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can - * be combined. e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10. - * @param {String} [params.sampleAnnotation] - Selects some samples using metadata information from Catalog. e.g. - * age>20;phenotype=hpo:123,hpo:456;name=smith. - * @param {String} [params.cohort] - Select variants with calculated stats for the selected cohorts. - * @param {String} [params.cohortStatsRef] - Reference Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * @param {String} [params.cohortStatsAlt] - Alternate Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * @param {String} [params.cohortStatsMaf] - Minor Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * @param {String} [params.cohortStatsMgf] - Minor Genotype Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4. - * @param {String} [params.cohortStatsPass] - Filter PASS frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8. - * @param {String} [params.missingAlleles] - Number of missing alleles: [{study:}]{cohort}[<|>|<=|>=]{number}. - * @param {String} [params.missingGenotypes] - Number of missing genotypes: [{study:}]{cohort}[<|>|<=|>=]{number}. - * @param {String} [params.score] - Filter by variant score: [{study:}]{score}[<|>|<=|>=]{number}. - * @param {String} [params.family] - Filter variants where any of the samples from the given family contains the variant (HET or - * HOM_ALT). - * @param {String} [params.familyDisorder] - Specify the disorder to use for the family segregation. - * @param {String} [params.familySegregation] - Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, - * autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ]. - * @param {String} [params.familyMembers] - Sub set of the members of a given family. - * @param {String} [params.familyProband] - Specify the proband child to use for the family segregation. - * @param {String} [params.gene] - List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' - * parameter. - * @param {String} [params.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 {String} [params.xref] - List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, - * Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ... - * @param {String} [params.biotype] - List of biotypes, e.g. protein_coding. - * @param {String} [params.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 {String} [params.conservation] - Filter by conservation score: {conservation_score}[<|>|<=|>=]{number} e.g. - * phastCons>0.5,phylop<0.1,gerp>0.1. - * @param {String} [params.populationFrequencyAlt] - Alternate Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. - * 1000G:ALL<0.01. - * @param {String} [params.populationFrequencyRef] - Reference Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. - * 1000G:ALL<0.01. - * @param {String} [params.populationFrequencyMaf] - Population minor allele frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. - * 1000G:ALL<0.01. - * @param {String} [params.transcriptFlag] - List of transcript flags. e.g. canonical, CCDS, basic, LRG, MANE Select, MANE Plus Clinical, - * EGLH_HaemOnc, TSO500. - * @param {String} [params.geneTraitId] - List of gene trait association id. e.g. "umls:C0007222" , "OMIM:269600". - * @param {String} [params.go] - List of GO (Gene Ontology) terms. e.g. "GO:0002020". - * @param {String} [params.expression] - List of tissues of interest. e.g. "lung". - * @param {String} [params.proteinKeyword] - List of Uniprot protein variant annotation keywords. - * @param {String} [params.drug] - List of drug names. - * @param {String} [params.functionalScore] - Functional score: {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 , - * cadd_raw<=0.3. - * @param {String} [params.clinical] - Clinical source: clinvar, cosmic. - * @param {String} [params.clinicalSignificance] - Clinical significance: benign, likely_benign, likely_pathogenic, pathogenic. - * @param {Boolean} [params.clinicalConfirmedStatus] - Clinical confirmed status. - * @param {String} [params.customAnnotation] - Custom annotation: {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}. - * @param {String} [params.panel] - Filter by genes from the given disease panel. - * @param {String} [params.panelModeOfInheritance] - Filter genes from specific panels that match certain mode of inheritance. Accepted - * values : [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, - * compoundHeterozygous ]. - * @param {String} [params.panelConfidence] - Filter genes from specific panels that match certain confidence. Accepted values : [ high, - * medium, low, rejected ]. - * @param {String} [params.panelRoleInCancer] - Filter genes from specific panels that match certain role in cancer. Accepted values : [ - * both, oncogene, tumorSuppressorGene, fusion ]. - * @param {String} [params.panelFeatureType] - Filter elements from specific panels by type. Accepted values : [ gene, region, str, - * variant ]. - * @param {Boolean} [params.panelIntersection] - Intersect panel genes and regions with given genes and regions from que input query. - * This will prevent returning variants from regions out of the panel. - * @param {String} [params.trait] - List of traits, based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies, descriptions,... - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - queryVariant(params) { - return this._get("analysis", null, "clinical/variant", null, "query", params); - } - - /** Returns the acl of the clinical analyses. If member is provided, it will only return the acl for the member. - * @param {String} clinicalAnalyses - Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.member] - User or group ID. - * @param {Boolean} [params.silent = "false"] - Boolean to retrieve all possible entries that are queried for, false to raise an - * exception whenever one of the entries looked for cannot be shown for whichever reason. The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - acl(clinicalAnalyses, params) { - return this._get("analysis", null, "clinical", clinicalAnalyses, "acl", params); - } - - /** Delete clinical analyses - * @param {String} clinicalAnalyses - Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {Boolean} [params.force = "false"] - Force deletion if the ClinicalAnalysis contains interpretations or is locked. The default - * value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - delete(clinicalAnalyses, params) { - return this._delete("analysis", null, "clinical", clinicalAnalyses, "delete", params); - } - - /** Update clinical analysis attributes - * @param {String} clinicalAnalyses - Comma separated list of clinical analysis IDs. - * @param {Object} data - JSON containing clinical analysis information. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {"ADD"|"REMOVE"|"REPLACE"} [params.commentsAction = "ADD"] - Action to be performed if the array of comments is being updated. - * The default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"} [params.flagsAction = "ADD"] - Action to be performed if the array of flags is being updated. The - * default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"} [params.filesAction = "ADD"] - Action to be performed if the array of files is being updated. The - * default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"} [params.panelsAction = "ADD"] - Action to be performed if the array of panels is being updated. The - * default value is ADD. - * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. - * The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - update(clinicalAnalyses, data, params) { - return this._post("analysis", null, "clinical", clinicalAnalyses, "update", data, params); - } - - /** Clinical analysis info - * @param {String} clinicalAnalysis - Comma separated list of clinical analysis IDs or names up to a maximum of 100. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - info(clinicalAnalysis, params) { - return this._get("analysis", null, "clinical", clinicalAnalysis, "info", params); - } - - /** Create a new Interpretation - * @param {String} clinicalAnalysis - Clinical analysis ID. - * @param {Object} data - JSON containing clinical interpretation information. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - [[user@]project:]study id. - * @param {"PRIMARY"|"SECONDARY"} [params.setAs = "SECONDARY"] - Set interpretation as. The default value is SECONDARY. - * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. - * The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - createInterpretation(clinicalAnalysis, data, params) { - return this._post("analysis/clinical", clinicalAnalysis, "interpretation", null, "create", data, params); - } - - /** Clear the fields of the main interpretation of the Clinical Analysis - * @param {String} interpretations - Interpretation IDs of the Clinical Analysis. - * @param {String} clinicalAnalysis - Clinical analysis ID. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - [[user@]project:]study ID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - clearInterpretation(clinicalAnalysis, interpretations, params) { - return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "clear", params); - } - - /** Delete interpretation - * @param {String} clinicalAnalysis - Clinical analysis ID. - * @param {String} interpretations - Interpretation IDs of the Clinical Analysis. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - [[user@]project:]study ID. - * @param {String} [params.setAsPrimary] - Interpretation id to set as primary from the list of secondaries in case of deleting the - * actual primary one. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - deleteInterpretation(clinicalAnalysis, interpretations, params) { - return this._delete("analysis/clinical", clinicalAnalysis, "interpretation", interpretations, "delete", params); - } - - /** Revert to a previous interpretation version - * @param {String} clinicalAnalysis - Clinical analysis ID. - * @param {String} interpretation - Interpretation ID. - * @param {Number} version - Version to revert to. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.study] - [[user@]project:]study ID. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - revertInterpretation(clinicalAnalysis, interpretation, version, params) { - return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "revert", {version, ...params}); - } - - /** Update interpretation fields - * @param {String} clinicalAnalysis - Clinical analysis ID. - * @param {String} interpretation - Interpretation ID. - * @param {Object} data - JSON containing clinical interpretation information. - * @param {Object} [params] - The Object containing the following optional parameters: - * @param {String} [params.include] - Fields included in the response, whole JSON path must be provided. - * @param {String} [params.exclude] - Fields excluded in the response, whole JSON path must be provided. - * @param {String} [params.study] - [[user@]project:]study ID. - * @param {"ADD"|"SET"|"REMOVE"|"REPLACE"} [params.primaryFindingsAction = "ADD"] - Action to be performed if the array of primary - * findings is being updated. The default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"} [params.methodsAction = "ADD"] - Action to be performed if the array of methods is being updated. The - * default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"|"REPLACE"} [params.secondaryFindingsAction = "ADD"] - Action to be performed if the array of secondary - * findings is being updated. The default value is ADD. - * @param {"ADD"|"REMOVE"|"REPLACE"} [params.commentsAction = "ADD"] - Action to be performed if the array of comments is being updated. - * To REMOVE or REPLACE, the date will need to be provided to identify the comment. The default value is ADD. - * @param {"ADD"|"SET"|"REMOVE"} [params.panelsAction = "ADD"] - Action to be performed if the array of panels is being updated. The - * default value is ADD. - * @param {"PRIMARY"|"SECONDARY"} [params.setAs] - Set interpretation as. - * @param {Boolean} [params.includeResult = "false"] - Flag indicating to include the created or updated document result in the response. - * The default value is false. - * @returns {Promise} Promise object in the form of RestResponse instance. - */ - updateInterpretation(clinicalAnalysis, interpretation, data, params) { - return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "update", data, params); - } - -} \ No newline at end of file diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 3430f69661a..826196fd984 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index badd624d5ae..f11d56a865f 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index 628b7c44bf2..aa4346dce4b 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index 5488744f8cd..51ceba74de6 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/File.js b/opencga-client/src/main/javascript/File.js index 54ab6b38608..7793fe89976 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index fcce4ffa025..a875626c28c 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index 6b8f1ecd931..19ab182bff7 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index c92fb36da73..2ddbc5e5cd8 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index 1fae236ef72..35a8a7bea37 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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. @@ -58,11 +58,12 @@ export default class Meta extends OpenCGAParentClass { } /** Opencga model webservices. - * + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {String} [params.model] - Model description. * @returns {Promise} Promise object in the form of RestResponse instance. */ - model() { - return this._get("meta", null, null, null, "model"); + model(params) { + return this._get("meta", null, null, null, "model", params); } /** Ping Opencga webservices. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index a1a491cfc74..d11f75b8d23 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index f0e3976fcfd..cde2fc56988 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index 183cf9ac13a..89bb9f11141 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/User.js b/opencga-client/src/main/javascript/User.js index 533db2eada8..c7d367f9d91 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index 9bf3047933e..8f80259b632 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index a64b11f4c83..e58c1c5a845 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-01-30 + * Autogenerated on: 2024-02-02 * * 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/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index 343834c5ef7..1e5a18df72c 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index c400a3b2fd1..8068df5192c 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index f53c3ec76af..3c8df26fc32 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index 677706b1e58..0adc73e3160 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index a8ae201e7ef..2252a5bda1e 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index cc9fa767f0f..f117855649f 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index c72e0ffd925..fa9b8715b93 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index 86d7747f04b..11f564a6d50 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index db1015702ce..ae2bae8302c 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index 838451d7ea4..82bf6816596 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index a105a0c620b..17c4fc4a001 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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. @@ -51,6 +51,8 @@ def model(self, **options): """ Opencga model webservices. PATH: /{apiVersion}/meta/model + + :param str model: Model description. """ return self._get(category='meta', resource='model', **options) diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index 610283c05e9..412a3fd08ea 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index 6cece56e1a9..1c4234aaa24 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 594beda62f7..369500ff951 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index cc09130e3a1..60ff5ae333a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index 1709580dcc7..37608000460 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index 56a41020056..21c0eec6ec8 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-01-30 + Autogenerated on: 2024-02-02 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-server/src/main/java/org/opencb/opencga/server/rest/MetaWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/MetaWSServer.java index edb1ab223c1..c416d0474b8 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/MetaWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/MetaWSServer.java @@ -110,7 +110,7 @@ public Response status() { @GET @Path("/model") @ApiOperation(value = "Opencga model webservices.", response = String.class) - public Response model(@QueryParam("model") String modelStr) { + public Response model(@ApiParam(value = "Model description") @QueryParam("model") String modelStr) { return run(() -> new OpenCGAResult<>(0, Collections.emptyList(), 1, Collections.singletonList(DataModelsUtils.dataModelToJsonString(modelStr, false)), 1));