Merge pull request #2360 from opencb/TASK-5279

TASK-5279 - Port Patch 1.6.6 -> 1.10.1

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-11-13 OpenCB
+* Copyright 2015-2023-11-21 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-11-13 OpenCB
+* Copyright 2015-2023-11-21 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/io/TextOutputWriter.java

@@ -88,22 +88,14 @@ public void print(RestResponse queryResponse) {
             throw new RuntimeException(e);
         }
 
-     /*   //   if (queryResponse != null && queryResponse.getType().equals(QueryType.VOID)) {
-        if (queryResponse.getEvents() != null) {
-            for (Event event : ((RestResponse<Object>)queryResponse.getResponses().get(0)).getEvents()) {
-                if (StringUtils.isNotEmpty(event.getMessage())) {
-                    if (event.getType().equals(Event.Type.ERROR)) {
-                        PrintUtils.printError(event.getMessage());
-                    } else {
-                        PrintUtils.printInfo(event.getMessage());
-                    }
-                } else {
-                    PrintUtils.printError(event.getMessage());
-                }
+        if (queryResponse != null && queryResponse.getType().equals(QueryType.VOID)) {
+            if (queryResponse.getResponses() != null && queryResponse.getResponses().size() > 0) {
+                manageEvents(((RestResponse<Object>) queryResponse.getResponses().get(0)).getEvents());
+            } else if (queryResponse.getEvents() != null && queryResponse.getEvents().size() > 0) {
+                manageEvents(queryResponse.getEvents());
             }
+            return;
         }
-        // return;
-        //  }
         if (checkErrors(queryResponse) && queryResponse.allResultsSize() == 0) {
             return;
         }
@@ -112,11 +104,9 @@ public void print(RestResponse queryResponse) {
             return;
         }
 
-
         ps.print(printMetadata(queryResponse));
-*/
-        List<DataResult> queryResultList = queryResponse.getResponses();
 
+        List<DataResult> queryResultList = queryResponse.getResponses();
 
         if (CollectionUtils.isNotEmpty(queryResultList) && ((OpenCGAResult) queryResultList.get(0)) != null
                 && ((OpenCGAResult) queryResultList.get(0)).getNumMatches() > -1 && !isEdition(queryResultList) && isNotAnIdOrMessage(queryResultList)) {
@@ -183,6 +173,20 @@ public void print(RestResponse queryResponse) {
         }
     }
 
+    private void manageEvents(final List<Event> events) {
+        for (Event event : events) {
+            if (StringUtils.isNotEmpty(event.getMessage())) {
+                if (event.getType().equals(Event.Type.ERROR)) {
+                    PrintUtils.printError(event.getMessage());
+                } else {
+                    PrintUtils.printInfo(event.getMessage());
+                }
+            } else {
+                PrintUtils.printError(event.getMessage());
+            }
+        }
+    }
+
     private boolean isNotAnIdOrMessage(List<DataResult> queryResultList) {
         return !(queryResultList.get(0).getResultType().equals("java.lang.String") &&
                 ((OpenCGAResult) queryResultList.get(0)).getNumMatches() == 1);

opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/FileManager.java

@@ -3712,16 +3712,23 @@ OpenCGAResult<File> registerFile(Study study, String filePath, URI fileUri, Stri
 
         File.Type type = filePath.endsWith("/") ? File.Type.DIRECTORY : File.Type.FILE;
 
-        File subfile = new File(Paths.get(filePath).getFileName().toString(), type, File.Format.UNKNOWN,
-                File.Bioformat.NONE, fileUri, filePath, "", TimeUtils.getTime(), TimeUtils.getTime(),
-                "", isExternal(study, filePath, fileUri), size, new Software(), new FileExperiment(), Collections.emptyList(),
-                Collections.emptyList(), jobId, studyManager.getCurrentRelease(study), Collections.emptyList(), Collections.emptyList(),
-                new FileQualityControl(), Collections.emptyMap(), new Status(), FileInternal.init(), Collections.emptyMap());
+        File.Format format = org.opencb.opencga.catalog.managers.FileUtils.detectFormat(fileUri);
+        File.Bioformat bioformat = org.opencb.opencga.catalog.managers.FileUtils.detectBioformat(fileUri);
+        File subfile = new File(Paths.get(filePath).getFileName().toString(), type, format, bioformat, fileUri, filePath, "",
+                TimeUtils.getTime(), TimeUtils.getTime(), "", isExternal(study, filePath, fileUri), size, new Software(),
+                new FileExperiment(), Collections.emptyList(), Collections.emptyList(), jobId, studyManager.getCurrentRelease(study),
+                Collections.emptyList(), Collections.emptyList(), new FileQualityControl(), Collections.emptyMap(), new Status(),
+                FileInternal.init(), Collections.emptyMap());
         subfile.setUuid(UuidUtils.generateOpenCgaUuid(UuidUtils.Entity.FILE));
         checkHooks(subfile, study.getFqn(), HookConfiguration.Stage.CREATE);
 
         // Improve metadata information and extract samples if any
-        new FileMetadataReader(catalogManager).addMetadataInformation(study.getFqn(), subfile);
+        try {
+            new FileMetadataReader(catalogManager).addMetadataInformation(study.getFqn(), subfile);
+        } catch (CatalogException e) {
+            subfile.getInternal().setStatus(new FileStatus(FileStatus.ERROR, "Could not extract metadata information: " + e.getMessage()));
+            logger.warn("Could not extract metadata information from file {}: {}", fileUri, e.getMessage(), e);
+        }
         List<Sample> existingSamples = new LinkedList<>();
         List<Sample> nonExistingSamples = new LinkedList<>();
         validateNewSamples(study, subfile, existingSamples, nonExistingSamples, token);

opencga-catalog/src/main/java/org/opencb/opencga/catalog/utils/FileMetadataReader.java

@@ -181,7 +181,7 @@ private FileUpdateParams extractMetadataInformation(String studyId, File file) t
                 VariantFileMetadata fileMetadata;
                 try {
                     fileMetadata = readVariantFileMetadata(file, file.getUri());
-                } catch (IOException e) {
+                } catch (Exception e) {
                     throw new CatalogIOException("Unable to read VariantSource", e);
                 }
                 if (fileMetadata != null) {

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: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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

@@ -1,46 +1,46 @@
 # ##############################################################################
 ## UserClient
-setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...)
+setGeneric("userClient", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...)
     standardGeneric("userClient"))
 
 # ##############################################################################
 ## ProjectClient
-setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...)
+setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...)
     standardGeneric("projectClient"))
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, templateId, group, members, variableSet, studies, study, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, templateId, members, studies, variableSet, study, group, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, file, members, folder, files, annotationSet, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, folder, members, file, annotationSet, files, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
 ## JobClient
-setGeneric("jobClient", function(OpencgaR, job, jobs, members, endpointName, params=NULL, ...)
+setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...)
     standardGeneric("jobClient"))
 
 # ##############################################################################
 ## SampleClient
-setGeneric("sampleClient", function(OpencgaR, sample, annotationSet, members, samples, endpointName, params=NULL, ...)
+setGeneric("sampleClient", function(OpencgaR, annotationSet, members, samples, sample, endpointName, params=NULL, ...)
     standardGeneric("sampleClient"))
 
 # ##############################################################################
 ## IndividualClient
-setGeneric("individualClient", function(OpencgaR, individual, annotationSet, individuals, members, endpointName, params=NULL, ...)
+setGeneric("individualClient", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("individualClient"))
 
 # ##############################################################################
 ## FamilyClient
-setGeneric("familyClient", function(OpencgaR, families, annotationSet, members, family, endpointName, params=NULL, ...)
+setGeneric("familyClient", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
 ## CohortClient
-setGeneric("cohortClient", function(OpencgaR, cohort, annotationSet, members, cohorts, endpointName, params=NULL, ...)
+setGeneric("cohortClient", function(OpencgaR, cohorts, members, cohort, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("cohortClient"))
 
 # ##############################################################################
@@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, clinicalAnalyses, interpretations, clinicalAnalysis, members, interpretation, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, members, interpretation, interpretations, 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: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -58,7 +58,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalyses, interpretations, clinicalAnalysis, members, interpretation, endpointName, params=NULL, ...) {
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, members, interpretation, interpretations, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:

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: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, annotationSet, members, cohorts, endpointName, params=NULL, ...) {
+setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohorts, members, cohort, annotationSet, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update:

opencga-client/src/main/R/R/Family-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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, families, annotationSet, members, family, endpointName, params=NULL, ...) {
+setMethod("familyClient", "OpencgaR", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/families/acl/{members}/update:

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: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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, file, members, folder, files, annotationSet, endpointName, params=NULL, ...) {
+setMethod("fileClient", "OpencgaR", function(OpencgaR, folder, members, file, annotationSet, files, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/files/acl/{members}/update:

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: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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/Individual-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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, individual, annotationSet, individuals, members, endpointName, params=NULL, ...) {
+setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, members, individuals, annotationSet, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update:

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: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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, job, jobs, members, endpointName, params=NULL, ...) {
+setMethod("jobClient", "OpencgaR", function(OpencgaR, jobs, members, job, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update:

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: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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/Operation-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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/Panel-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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/Project-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -34,7 +34,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("projectClient", "OpencgaR", function(OpencgaR, project, projects, endpointName, params=NULL, ...) {
+setMethod("projectClient", "OpencgaR", function(OpencgaR, projects, project, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/projects/create:

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: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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, sample, annotationSet, members, samples, endpointName, params=NULL, ...) {
+setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, members, samples, sample, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/samples/acl/{members}/update:

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: 2023-11-13
+#    Autogenerated on: 2023-11-21
 #    
 #    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, templateId, group, members, variableSet, studies, study, endpointName, params=NULL, ...) {
+setMethod("studyClient", "OpencgaR", function(OpencgaR, templateId, members, studies, variableSet, study, group, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: