Clients for release 2.12.2 #TASK-5445

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<Candidate> 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<Candidate> 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());

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);

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<Interpretation> updateInterpretation() throws Exception {
         }
         return openCGAClient.getClinicalAnalysisClient().updateInterpretation(commandOptions.clinicalAnalysis, commandOptions.interpretation, interpretationUpdateParams, queryParams);
     }
+
+    private RestResponse<ClinicalReport> 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<ClinicalReport> 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);
+    }
 }

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;
+
+    }
+
 }

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.

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.

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"))
 
 # ##############################################################################

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.
@@ -53,14 +53,15 @@
 #' | 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
 #' \url{http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/}
 #' [*]: 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, ...),
     )
 })