From a3fcda03a8e4aaa425669ac912ee637167567496 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 30 Jan 2024 16:59:55 +0100 Subject: [PATCH] Clients for release 2.12.2 #TASK-5445 --- .../app/cli/main/OpenCgaCompleter.java | 4 +- .../app/cli/main/OpencgaCliOptionsParser.java | 3 +- .../AnalysisClinicalCommandExecutor.java | 47 ++++++++++++++ .../AnalysisClinicalCommandOptions.java | 61 +++++++++++++++++++ opencga-client/src/main/R/R/Admin-methods.R | 2 +- .../src/main/R/R/Alignment-methods.R | 2 +- opencga-client/src/main/R/R/AllGenerics.R | 22 +++---- .../src/main/R/R/Clinical-methods.R | 20 +++++- opencga-client/src/main/R/R/Cohort-methods.R | 4 +- opencga-client/src/main/R/R/Family-methods.R | 4 +- opencga-client/src/main/R/R/File-methods.R | 4 +- opencga-client/src/main/R/R/GA4GH-methods.R | 2 +- .../src/main/R/R/Individual-methods.R | 4 +- opencga-client/src/main/R/R/Job-methods.R | 4 +- opencga-client/src/main/R/R/Meta-methods.R | 2 +- .../src/main/R/R/Operation-methods.R | 2 +- opencga-client/src/main/R/R/Panel-methods.R | 4 +- opencga-client/src/main/R/R/Project-methods.R | 4 +- opencga-client/src/main/R/R/Sample-methods.R | 4 +- opencga-client/src/main/R/R/Study-methods.R | 4 +- opencga-client/src/main/R/R/User-methods.R | 4 +- opencga-client/src/main/R/R/Variant-methods.R | 2 +- .../client/rest/clients/AdminClient.java | 6 +- .../client/rest/clients/AlignmentClient.java | 6 +- .../rest/clients/ClinicalAnalysisClient.java | 29 ++++++++- .../client/rest/clients/CohortClient.java | 6 +- .../rest/clients/DiseasePanelClient.java | 6 +- .../client/rest/clients/FamilyClient.java | 6 +- .../client/rest/clients/FileClient.java | 6 +- .../client/rest/clients/GA4GHClient.java | 6 +- .../client/rest/clients/IndividualClient.java | 6 +- .../client/rest/clients/JobClient.java | 6 +- .../client/rest/clients/MetaClient.java | 6 +- .../client/rest/clients/ProjectClient.java | 6 +- .../client/rest/clients/SampleClient.java | 6 +- .../client/rest/clients/StudyClient.java | 6 +- .../client/rest/clients/UserClient.java | 6 +- .../client/rest/clients/VariantClient.java | 6 +- .../rest/clients/VariantOperationClient.java | 6 +- opencga-client/src/main/javascript/Admin.js | 2 +- .../src/main/javascript/Alignment.js | 2 +- .../src/main/javascript/ClinicalAnalysis.js | 23 ++++++- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- opencga-client/src/main/javascript/Study.js | 2 +- opencga-client/src/main/javascript/User.js | 2 +- opencga-client/src/main/javascript/Variant.js | 2 +- .../src/main/javascript/VariantOperation.js | 2 +- .../pyopencga/rest_clients/admin_client.py | 4 +- .../rest_clients/alignment_client.py | 4 +- .../rest_clients/clinical_analysis_client.py | 31 +++++++++- .../pyopencga/rest_clients/cohort_client.py | 4 +- .../rest_clients/disease_panel_client.py | 4 +- .../pyopencga/rest_clients/family_client.py | 4 +- .../pyopencga/rest_clients/file_client.py | 4 +- .../pyopencga/rest_clients/ga4gh_client.py | 4 +- .../rest_clients/individual_client.py | 4 +- .../pyopencga/rest_clients/job_client.py | 4 +- .../pyopencga/rest_clients/meta_client.py | 4 +- .../pyopencga/rest_clients/project_client.py | 4 +- .../pyopencga/rest_clients/sample_client.py | 4 +- .../pyopencga/rest_clients/study_client.py | 4 +- .../pyopencga/rest_clients/user_client.py | 4 +- .../pyopencga/rest_clients/variant_client.py | 4 +- .../rest_clients/variant_operation_client.py | 4 +- 73 files changed, 340 insertions(+), 144 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index 154dd0010dd..31d1c757700 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 2015-2023-12-15 OpenCB +* Copyright 2015-2024-01-30 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -60,7 +60,7 @@ public abstract class OpenCgaCompleter implements Completer { .map(Candidate::new) .collect(toList()); - private List clinicalList = asList( "acl-update","annotation-sets-load","clinical-configuration-update","create","distinct","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","annotation-sets-annotations-update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update") + private List clinicalList = asList( "acl-update","annotation-sets-load","clinical-configuration-update","create","distinct","interpretation-distinct","interpretation-search","interpretation-info","interpreter-cancer-tiering-run","interpreter-exomiser-run","interpreter-team-run","interpreter-tiering-run","interpreter-zetta-run","rga-aggregation-stats","rga-gene-query","rga-gene-summary","rga-index-run","rga-individual-query","rga-individual-summary","rga-variant-query","rga-variant-summary","search","variant-query","acl","delete","update","annotation-sets-annotations-update","info","interpretation-create","interpretation-clear","interpretation-delete","interpretation-revert","interpretation-update","report-update") .stream() .map(Candidate::new) .collect(toList()); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index a88d83dac78..fe013c129cd 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 2015-2023-12-15 OpenCB +* Copyright 2015-2024-01-30 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -160,6 +160,7 @@ public OpencgaCliOptionsParser() { analysisClinicalSubCommands.addCommand("interpretation-delete", analysisClinicalCommandOptions.deleteInterpretationCommandOptions); analysisClinicalSubCommands.addCommand("interpretation-revert", analysisClinicalCommandOptions.revertInterpretationCommandOptions); analysisClinicalSubCommands.addCommand("interpretation-update", analysisClinicalCommandOptions.updateInterpretationCommandOptions); + analysisClinicalSubCommands.addCommand("report-update", analysisClinicalCommandOptions.updateReportCommandOptions); jobsCommandOptions = new JobsCommandOptions(commonCommandOptions, jCommander); jCommander.addCommand("jobs", jobsCommandOptions); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java index 490e6ca3166..22df7f71de9 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java @@ -198,6 +198,9 @@ public void execute() throws Exception { case "interpretation-update": queryResponse = updateInterpretation(); break; + case "report-update": + queryResponse = updateReport(); + break; default: logger.error("Subcommand not valid"); break; @@ -1445,4 +1448,48 @@ private RestResponse updateInterpretation() throws Exception { } return openCGAClient.getClinicalAnalysisClient().updateInterpretation(commandOptions.clinicalAnalysis, commandOptions.interpretation, interpretationUpdateParams, queryParams); } + + private RestResponse updateReport() throws Exception { + logger.debug("Executing updateReport in Analysis - Clinical command line"); + + AnalysisClinicalCommandOptions.UpdateReportCommandOptions commandOptions = analysisClinicalCommandOptions.updateReportCommandOptions; + + ObjectMap queryParams = new ObjectMap(); + queryParams.putIfNotEmpty("include", commandOptions.include); + queryParams.putIfNotEmpty("exclude", commandOptions.exclude); + queryParams.putIfNotEmpty("study", commandOptions.study); + queryParams.putIfNotNull("supportingEvidencesAction", commandOptions.supportingEvidencesAction); + queryParams.putIfNotNull("includeResult", commandOptions.includeResult); + if (queryParams.get("study") == null && OpencgaMain.isShellMode()) { + queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy()); + } + + + ClinicalReport clinicalReport = null; + if (commandOptions.jsonDataModel) { + RestResponse res = new RestResponse<>(); + res.setType(QueryType.VOID); + PrintUtils.println(getObjectAsJSON(categoryName,"/{apiVersion}/analysis/clinical/{clinicalAnalysis}/report/update")); + return res; + } else if (commandOptions.jsonFile != null) { + clinicalReport = JacksonUtils.getDefaultObjectMapper() + .readValue(new java.io.File(commandOptions.jsonFile), ClinicalReport.class); + } else { + ObjectMap beanParams = new ObjectMap(); + putNestedIfNotEmpty(beanParams, "title",commandOptions.title, true); + putNestedIfNotEmpty(beanParams, "overview",commandOptions.overview, true); + putNestedIfNotEmpty(beanParams, "discussion.author",commandOptions.discussionAuthor, true); + putNestedIfNotEmpty(beanParams, "discussion.date",commandOptions.discussionDate, true); + putNestedIfNotEmpty(beanParams, "discussion.text",commandOptions.discussionText, true); + putNestedIfNotEmpty(beanParams, "logo",commandOptions.logo, true); + putNestedIfNotEmpty(beanParams, "signedBy",commandOptions.signedBy, true); + putNestedIfNotEmpty(beanParams, "signature",commandOptions.signature, true); + putNestedIfNotEmpty(beanParams, "date",commandOptions.date, true); + + clinicalReport = JacksonUtils.getDefaultObjectMapper().copy() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true) + .readValue(beanParams.toJson(), ClinicalReport.class); + } + return openCGAClient.getClinicalAnalysisClient().updateReport(commandOptions.clinicalAnalysis, clinicalReport, queryParams); + } } \ No newline at end of file diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java index 11d6220ddef..3a7ccffd4bd 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java @@ -66,6 +66,7 @@ public class AnalysisClinicalCommandOptions { public DeleteInterpretationCommandOptions deleteInterpretationCommandOptions; public RevertInterpretationCommandOptions revertInterpretationCommandOptions; public UpdateInterpretationCommandOptions updateInterpretationCommandOptions; + public UpdateReportCommandOptions updateReportCommandOptions; public AnalysisClinicalCommandOptions(CommonCommandOptions commonCommandOptions, JCommander jCommander) { @@ -105,6 +106,7 @@ public AnalysisClinicalCommandOptions(CommonCommandOptions commonCommandOptions, this.deleteInterpretationCommandOptions = new DeleteInterpretationCommandOptions(); this.revertInterpretationCommandOptions = new RevertInterpretationCommandOptions(); this.updateInterpretationCommandOptions = new UpdateInterpretationCommandOptions(); + this.updateReportCommandOptions = new UpdateReportCommandOptions(); } @@ -2274,4 +2276,63 @@ public class UpdateInterpretationCommandOptions { } + @Parameters(commandNames = {"report-update"}, commandDescription ="Update clinical analysis report") + public class UpdateReportCommandOptions { + + @ParametersDelegate + public CommonCommandOptions commonOptions = commonCommandOptions; + + @Parameter(names = {"--json-file"}, description = "File with the body data in JSON format. Note, that using this parameter will ignore all the other parameters.", required = false, arity = 1) + public String jsonFile; + + @Parameter(names = {"--json-data-model"}, description = "Show example of file structure for body data.", help = true, arity = 0) + public Boolean jsonDataModel = false; + + @Parameter(names = {"--include", "-I"}, description = "Fields included in the response, whole JSON path must be provided", required = false, arity = 1) + public String include; + + @Parameter(names = {"--exclude", "-E"}, description = "Fields excluded in the response, whole JSON path must be provided", required = false, arity = 1) + public String exclude; + + @Parameter(names = {"--clinical-analysis"}, description = "Clinical analysis ID", required = true, arity = 1) + public String clinicalAnalysis; + + @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) + public String study; + + @Parameter(names = {"--supporting-evidences-action"}, description = "Action to be performed if the array of supporting evidences is being updated.", required = false, arity = 1) + public String supportingEvidencesAction = "ADD"; + + @Parameter(names = {"--include-result"}, description = "Flag indicating to include the created or updated document result in the response", required = false, help = true, arity = 0) + public boolean includeResult = false; + + @Parameter(names = {"--title"}, description = "Report title.", required = false, arity = 1) + public String title; + + @Parameter(names = {"--overview"}, description = "Report overview.", required = false, arity = 1) + public String overview; + + @Parameter(names = {"--discussion-author"}, description = "The body web service author parameter", required = false, arity = 1) + public String discussionAuthor; + + @Parameter(names = {"--discussion-date"}, description = "The body web service date parameter", required = false, arity = 1) + public String discussionDate; + + @Parameter(names = {"--discussion-text"}, description = "The body web service text parameter", required = false, arity = 1) + public String discussionText; + + @Parameter(names = {"--logo"}, description = "Report logo.", required = false, arity = 1) + public String logo; + + @Parameter(names = {"--signed-by"}, description = "Indicates who has signed the report.", required = false, arity = 1) + public String signedBy; + + @Parameter(names = {"--signature"}, description = "Report signature.", required = false, arity = 1) + public String signature; + + @Parameter(names = {"--date"}, description = "Report date.", required = false, arity = 1) + public String date; + + } + } \ No newline at end of file diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 82c35928a09..cd6c1bd235a 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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 5f7dd5ccb76..a3110d0b076 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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 e617555c2fe..177a61e827a 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,51 +1,51 @@ # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, user, users, filterId, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## ## ProjectClient -setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...) +setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...) standardGeneric("projectClient")) # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, members, templateId, group, studies, variableSet, study, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, studies, members, templateId, study, variableSet, group, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, members, annotationSet, files, folder, file, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, members, folder, file, files, annotationSet, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, annotationSet, members, sample, samples, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, annotationSet, members, individual, individuals, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, family, members, annotationSet, families, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, members, annotationSet, families, family, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, members, cohort, annotationSet, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, cohort, annotationSet, members, cohorts, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## ## PanelClient -setGeneric("panelClient", function(OpencgaR, members, panels, endpointName, params=NULL, ...) +setGeneric("panelClient", function(OpencgaR, panels, members, endpointName, params=NULL, ...) standardGeneric("panelClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, members, annotationSet, interpretation, clinicalAnalyses, clinicalAnalysis, interpretations, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, members, interpretations, clinicalAnalysis, interpretation, 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 a65b13dc3c0..9184f341a42 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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. @@ -53,6 +53,7 @@ #' | deleteInterpretation | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/delete | study, clinicalAnalysis[*], interpretations[*], setAsPrimary | #' | revertInterpretation | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/revert | study, clinicalAnalysis[*], interpretation[*], version[*] | #' | updateInterpretation | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update | include, exclude, study, primaryFindingsAction, methodsAction, secondaryFindingsAction, commentsAction, panelsAction, setAs, clinicalAnalysis[*], interpretation[*], includeResult, body[*] | +#' | updateReport | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/report/update | include, exclude, clinicalAnalysis[*], study, commentsAction, supportingEvidencesAction, filesAction, includeResult, body[*] | #' #' @md #' @seealso \url{http://docs.opencb.org/display/opencga/Using+OpenCGA} and the RESTful API documentation @@ -60,7 +61,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, annotationSet, interpretation, clinicalAnalyses, clinicalAnalysis, interpretations, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, interpretations, clinicalAnalysis, interpretation, annotationSet, clinicalAnalyses, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: @@ -715,5 +716,20 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, members, annotationSe updateInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis/clinical", categoryId=clinicalAnalysis, subcategory="interpretation", subcategoryId=interpretation, action="update", params=params, httpMethod="POST", as.queryParam=NULL, ...), + + #' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/report/update: + #' Update clinical analysis report. + #' @param include Fields included in the response, whole JSON path must be provided. + #' @param exclude Fields excluded in the response, whole JSON path must be provided. + #' @param clinicalAnalysis Clinical analysis ID. + #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. + #' @param commentsAction Action to be performed if the array of comments is being updated. Allowed values: ['ADD REMOVE REPLACE'] + #' @param supportingEvidencesAction Action to be performed if the array of supporting evidences is being updated. Allowed values: ['ADD SET REMOVE'] + #' @param filesAction Action to be performed if the array of files is being updated. Allowed values: ['ADD SET REMOVE'] + #' @param includeResult Flag indicating to include the created or updated document result in the response. + #' @param data JSON containing clinical report information. + updateReport=fetchOpenCGA(object=OpencgaR, category="analysis/clinical", categoryId=clinicalAnalysis, + subcategory="report", subcategoryId=NULL, action="update", params=params, httpMethod="POST", + as.queryParam=NULL, ...), ) }) \ No newline at end of file diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 5ae80da7c28..ff52e896b22 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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, members, cohort, annotationSet, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, annotationSet, members, cohorts, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index 12a05627674..a0ae9ced80d 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, family, members, annotationSet, families, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, members, annotationSet, families, family, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index f99abec5c6a..aa5d9a763a1 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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, annotationSet, files, folder, file, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, file, files, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index 6c33f10e805..0a240e6d6a3 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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 8425d762354..0c81ab901f7 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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, annotationSet, members, individual, individuals, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index eecb9ef55ee..44abcff66ef 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -40,7 +40,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index dc99ac4767f..d8fa6d73da6 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index c5e5da6eb2f..5347a1eca81 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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 6c3328e544c..cd408e39313 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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. @@ -36,7 +36,7 @@ #' [*]: Required parameter #' @export -setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpointName, params=NULL, ...) { +setMethod("panelClient", "OpencgaR", function(OpencgaR, panels, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/panels/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index f4126c3670d..4af959c7597 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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, projects, project, endpointName, params=NULL, ...) { +setMethod("projectClient", "OpencgaR", function(OpencgaR, project, projects, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/projects/create: diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index 055fb46a729..dac7f36ccbd 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("sampleClient", "OpencgaR", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, members, sample, samples, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index e816b97a05f..cbce8be6beb 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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, members, templateId, group, studies, variableSet, study, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, studies, members, templateId, study, variableSet, group, 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 908e172768b..3505c6cffc5 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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("userClient", "OpencgaR", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, user, users, filterId, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/login: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 86b24f1e3d2..71116af6b8c 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: 2023-12-15 +# Autogenerated on: 2024-01-30 # # 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 5861b2857e5..226785e12de 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -45,7 +45,7 @@ /** * This class contains methods for the Admin webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: admin */ public class AdminClient extends AbstractParentClient { 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 c9c840941a1..9f1fe0c3762 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -40,7 +40,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -49,7 +49,7 @@ /** * This class contains methods for the Alignment webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: analysis/alignment */ public class AlignmentClient extends AbstractParentClient { 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 600f937bb50..2a536a0200b 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -34,6 +34,7 @@ import org.opencb.opencga.core.models.clinical.ClinicalAnalysisAclUpdateParams; import org.opencb.opencga.core.models.clinical.ClinicalAnalysisCreateParams; import org.opencb.opencga.core.models.clinical.ClinicalAnalysisUpdateParams; +import org.opencb.opencga.core.models.clinical.ClinicalReport; import org.opencb.opencga.core.models.clinical.ExomiserInterpretationAnalysisParams; import org.opencb.opencga.core.models.clinical.Interpretation; import org.opencb.opencga.core.models.clinical.InterpretationCreateParams; @@ -53,7 +54,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -62,7 +63,7 @@ /** * This class contains methods for the ClinicalAnalysis webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: analysis/clinical */ public class ClinicalAnalysisClient extends AbstractParentClient { @@ -978,4 +979,26 @@ public RestResponse updateInterpretation(String clinicalAnalysis return execute("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "update", params, POST, Interpretation.class); } + + /** + * Update clinical analysis report. + * @param clinicalAnalysis Clinical analysis ID. + * @param data JSON containing clinical report information. + * @param params Map containing any of the following optional parameters. + * include: Fields included in the response, whole JSON path must be provided. + * exclude: Fields excluded in the response, whole JSON path must be provided. + * study: Study [[user@]project:]study where study and project can be either the ID or UUID. + * commentsAction: Action to be performed if the array of comments is being updated. + * supportingEvidencesAction: Action to be performed if the array of supporting evidences is being updated. + * filesAction: Action to be performed if the array of files is being updated. + * includeResult: Flag indicating to include the created or updated document result in the response. + * @return a RestResponse object. + * @throws ClientException ClientException if there is any server error. + */ + public RestResponse updateReport(String clinicalAnalysis, ClinicalReport data, ObjectMap params) + throws ClientException { + params = params != null ? params : new ObjectMap(); + params.put("body", data); + return execute("analysis/clinical", clinicalAnalysis, "report", null, "update", params, POST, ClinicalReport.class); + } } 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 7551de54734..e70f528ead2 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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 @@ /** * This class contains methods for the Cohort webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: cohorts */ public class CohortClient extends AbstractParentClient { 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 a2d2294288f..ddbc803466a 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -44,7 +44,7 @@ /** * This class contains methods for the DiseasePanel webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: panels */ public class DiseasePanelClient extends AbstractParentClient { 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 3864e673c1c..bbd0ece17d3 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -45,7 +45,7 @@ /** * This class contains methods for the Family webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: families */ public class FamilyClient extends AbstractParentClient { 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 e31b21892cf..d180259c267 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -43,7 +43,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -52,7 +52,7 @@ /** * This class contains methods for the File webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: files */ public class FileClient extends AbstractParentClient { 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 8ed457c91fa..792bd4512cf 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -27,7 +27,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -36,7 +36,7 @@ /** * This class contains methods for the GA4GH webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: ga4gh */ public class GA4GHClient extends AbstractParentClient { 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 2d62e0d63c9..39d0f05a7c5 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -45,7 +45,7 @@ /** * This class contains methods for the Individual webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: individuals */ public class IndividualClient extends AbstractParentClient { 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 0847486e2f3..93cc6bd33b5 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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 @@ /** * This class contains methods for the Job webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: jobs */ public class JobClient extends AbstractParentClient { 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 00f596604e2..c00a5087087 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -28,7 +28,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -37,7 +37,7 @@ /** * This class contains methods for the Meta webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: meta */ public class MetaClient extends AbstractParentClient { 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 93ff43c9374..d3f6a379f3a 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -32,7 +32,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -41,7 +41,7 @@ /** * This class contains methods for the Project webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: projects */ public class ProjectClient extends AbstractParentClient { 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 68cf5b5bd88..fd4789a4dc4 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -45,7 +45,7 @@ /** * This class contains methods for the Sample webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: samples */ public class SampleClient extends AbstractParentClient { 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 29e8f294907..c537f9b4227 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -45,7 +45,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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 @@ /** * This class contains methods for the Study webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: studies */ public class StudyClient extends AbstractParentClient { 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 0494c7c07be..0a6620159a8 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -45,7 +45,7 @@ /** * This class contains methods for the User webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: users */ public class UserClient extends AbstractParentClient { 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 9abf7befe41..bb2741388d7 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -62,7 +62,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -71,7 +71,7 @@ /** * This class contains methods for the Variant webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: analysis/variant */ public class VariantClient extends AbstractParentClient { 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 8928db2a550..66d77561bba 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 @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023 OpenCB +* Copyright 2015-2024 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-12-15 +* Autogenerated on: 2024-01-30 * * 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. @@ -59,7 +59,7 @@ /** * This class contains methods for the VariantOperation webservices. - * Client version: 2.12.1-SNAPSHOT + * Client version: 2.12.2-SNAPSHOT * PATH: operation */ public class VariantOperationClient extends AbstractParentClient { diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 72ee4c5d577..d533d8eb0ba 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 93ee35f4d5d..b4847e1dac0 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 79e9a43e96f..3430f69661a 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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. @@ -845,4 +845,25 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { return this._post("analysis/clinical", clinicalAnalysis, "interpretation", interpretation, "update", data, params); } + /** Update clinical analysis report + * @param {String} clinicalAnalysis - Clinical analysis ID. + * @param {Object} data - JSON containing clinical report 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.supportingEvidencesAction = "ADD"] - Action to be performed if the array of supporting evidences 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 {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. + */ + updateReport(clinicalAnalysis, data, params) { + return this._post("analysis/clinical", clinicalAnalysis, "report", null, "update", data, params); + } + } \ No newline at end of file diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index b08e27f1127..badd624d5ae 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 db336df392c..628b7c44bf2 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 1531a41b607..5488744f8cd 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 660d3f3733c..54ab6b38608 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 7eb8bb8f1ac..fcce4ffa025 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 43f3cd2e2ed..6b8f1ecd931 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 9273b924274..c92fb36da73 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 fb5f1f99602..1fae236ef72 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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/Project.js b/opencga-client/src/main/javascript/Project.js index 61cfe76321a..a1a491cfc74 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 b28d8147fb9..f0e3976fcfd 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 11d0ae3b98e..183cf9ac13a 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 90615f3cca2..533db2eada8 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 9a3df7f9fd1..9bf3047933e 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 30c9ad7bbc0..a64b11f4c83 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: 2023-12-15 + * Autogenerated on: 2024-01-30 * * 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 e976c0681a9..343834c5ef7 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Admin(_ParentRestClient): """ This class contains methods for the 'Admin' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/admin """ 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 a0f056eee50..c400a3b2fd1 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Alignment(_ParentRestClient): """ This class contains methods for the 'Analysis - Alignment' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/analysis/alignment """ 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 feade5634db..f53c3ec76af 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class ClinicalAnalysis(_ParentRestClient): """ This class contains methods for the 'Analysis - Clinical' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/analysis/clinical """ @@ -1069,3 +1069,30 @@ def update_interpretation(self, clinical_analysis, interpretation, data=None, ** return self._post(category='analysis/clinical', resource='update', query_id=clinical_analysis, subcategory='interpretation', second_query_id=interpretation, data=data, **options) + def update_report(self, clinical_analysis, data=None, **options): + """ + Update clinical analysis report. + PATH: /{apiVersion}/analysis/clinical/{clinicalAnalysis}/report/update + + :param dict data: JSON containing clinical report information. + (REQUIRED) + :param str clinical_analysis: Clinical analysis ID. (REQUIRED) + :param str include: Fields included in the response, whole JSON path + must be provided. + :param str exclude: Fields excluded in the response, whole JSON path + must be provided. + :param str study: Study [[user@]project:]study where study and project + can be either the ID or UUID. + :param str comments_action: Action to be performed if the array of + comments is being updated. Allowed values: ['ADD REMOVE REPLACE'] + :param str supporting_evidences_action: Action to be performed if the + array of supporting evidences is being updated. Allowed values: + ['ADD SET REMOVE'] + :param str files_action: Action to be performed if the array of files + is being updated. Allowed values: ['ADD SET REMOVE'] + :param bool include_result: Flag indicating to include the created or + updated document result in the response. + """ + + return self._post(category='analysis/clinical', resource='update', query_id=clinical_analysis, subcategory='report', data=data, **options) + 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 a9987346408..677706b1e58 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Cohort(_ParentRestClient): """ This class contains methods for the 'Cohorts' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/cohorts """ 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 cbdf3677d81..a8ae201e7ef 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class DiseasePanel(_ParentRestClient): """ This class contains methods for the 'Disease Panels' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/panels """ 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 b2567e84331..cc9fa767f0f 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Family(_ParentRestClient): """ This class contains methods for the 'Families' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/families """ 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 78303d714e9..c72e0ffd925 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class File(_ParentRestClient): """ This class contains methods for the 'Files' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/files """ 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 8225d5bf86f..86d7747f04b 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class GA4GH(_ParentRestClient): """ This class contains methods for the 'GA4GH' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/ga4gh """ 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 36a740bb26b..db1015702ce 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Individual(_ParentRestClient): """ This class contains methods for the 'Individuals' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/individuals """ 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 2fadce8f58f..838451d7ea4 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Job(_ParentRestClient): """ This class contains methods for the 'Jobs' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/jobs """ 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 56b398093e8..a105a0c620b 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Meta(_ParentRestClient): """ This class contains methods for the 'Meta' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/meta """ 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 7e316925332..610283c05e9 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Project(_ParentRestClient): """ This class contains methods for the 'Projects' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/projects """ 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 7cf5749d831..6cece56e1a9 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Sample(_ParentRestClient): """ This class contains methods for the 'Samples' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/samples """ 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 c2ad691a6db..594beda62f7 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Study(_ParentRestClient): """ This class contains methods for the 'Studies' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/studies """ 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 af27dabb31d..cc09130e3a1 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class User(_ParentRestClient): """ This class contains methods for the 'Users' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/users """ 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 d0e7be2e397..1709580dcc7 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class Variant(_ParentRestClient): """ This class contains methods for the 'Analysis - Variant' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/analysis/variant """ 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 c86d4e49b34..56a41020056 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: 2023-12-15 + Autogenerated on: 2024-01-30 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. @@ -14,7 +14,7 @@ class VariantOperation(_ParentRestClient): """ This class contains methods for the 'Operations - Variant Storage' webservices - Client version: 2.12.1-SNAPSHOT + Client version: 2.12.2-SNAPSHOT PATH: /{apiVersion}/operation """