IQSS · kcondon · Jul 22, 2022 · Jul 20, 2022
diff --git a/src/main/java/edu/harvard/iq/dataverse/EditDataFilesPageHelper.java b/src/main/java/edu/harvard/iq/dataverse/EditDataFilesPageHelper.java
@@ -2,9 +2,11 @@
 
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import edu.harvard.iq.dataverse.util.file.CreateDataFileResult;
+import org.apache.commons.text.StringEscapeUtils;
 
 import javax.ejb.Stateless;
 import javax.inject.Inject;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
@@ -22,6 +24,14 @@ public class EditDataFilesPageHelper {
     @Inject
     private SettingsWrapper settingsWrapper;
 
+    public String consolidateHtmlErrorMessages(List<String> errorMessages) {
+        if(errorMessages == null || errorMessages.isEmpty()) {
+            return null;
+        }
+
+        return String.join("</br>", errorMessages);
+    }
+
     public String getHtmlErrorMessage(CreateDataFileResult createDataFileResult) {
         List<String> errors = createDataFileResult.getErrors();
         if(errors == null || errors.isEmpty()) {
@@ -33,8 +43,8 @@ public String getHtmlErrorMessage(CreateDataFileResult createDataFileResult) {
             return null;
         }
 
-        String typeMessage = Optional.ofNullable(BundleUtil.getStringFromBundle(createDataFileResult.getBundleKey())).orElse("Error processing file");
-        String errorsMessage = errors.stream().limit(maxErrorsToShow).map(text -> String.format("<li>%s</li>", text)).collect(Collectors.joining());
-        return String.format("%s:<br /><ul>%s</ul>", typeMessage, errorsMessage);
+        String typeMessage = Optional.ofNullable(BundleUtil.getStringFromBundle(createDataFileResult.getBundleKey(), Arrays.asList(createDataFileResult.getFilename()))).orElse("Error processing file");
+        String errorsMessage = errors.stream().limit(maxErrorsToShow).map(text -> String.format("<li>%s</li>", StringEscapeUtils.escapeHtml4(text))).collect(Collectors.joining());
+        return String.format("%s<br /><ul>%s</ul>", typeMessage, errorsMessage);
     }
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java b/src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java
@@ -51,6 +51,7 @@
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
 import java.util.logging.Logger;
 import javax.ejb.EJB;
 import javax.ejb.EJBException;
@@ -1491,7 +1492,7 @@ public void handleDropBoxUpload(ActionEvent event) {
                 //datafiles = ingestService.createDataFiles(workingVersion, dropBoxStream, fileName, "application/octet-stream");
                 CreateDataFileResult createDataFilesResult = FileUtil.createDataFiles(workingVersion, dropBoxStream, fileName, "application/octet-stream", null, null, systemConfig);
                 datafiles = createDataFilesResult.getDataFiles();
-                errorMessage = editDataFilesPageHelper.getHtmlErrorMessage(createDataFilesResult);
+                Optional.ofNullable(editDataFilesPageHelper.getHtmlErrorMessage(createDataFilesResult)).ifPresent(errorMessage -> errorMessages.add(errorMessage));
 
             } catch (IOException ex) {
                 this.logger.log(Level.SEVERE, "Error during ingest of DropBox file {0} from link {1}", new Object[]{fileName, fileLink});
@@ -1745,12 +1746,13 @@ public void uploadFinished() {
             uploadedFiles.clear();
             uploadInProgress.setValue(false);
         }
-        if(errorMessage != null) {
-            FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, BundleUtil.getStringFromBundle("dataset.file.uploadFailure"), errorMessage));
-            PrimeFaces.current().ajax().update(":messagePanel");
-        }
+
         // refresh the warning message below the upload component, if exists:
         if (uploadComponentId != null) {
+            if(!errorMessages.isEmpty()) {
+                FacesContext.getCurrentInstance().addMessage(uploadComponentId, new FacesMessage(FacesMessage.SEVERITY_ERROR,  BundleUtil.getStringFromBundle("dataset.file.uploadFailure"), editDataFilesPageHelper.consolidateHtmlErrorMessages(errorMessages)));
+            }
+
             if (uploadWarningMessage != null) {
                 if (existingFilesWithDupeContent != null || newlyUploadedFilesWithDupeContent != null) {
                     setWarningMessageForAlreadyExistsPopUp(uploadWarningMessage);
@@ -1797,7 +1799,7 @@ public void uploadFinished() {
         multipleDupesNew = false;
         uploadWarningMessage = null;
         uploadSuccessMessage = null;
-        errorMessage = null;
+        errorMessages = new ArrayList<>();
     }
 
     private String warningMessageForFileTypeDifferentPopUp;
@@ -1948,7 +1950,7 @@ private void handleReplaceFileUpload(String fullStorageLocation,
     }
 
     private String uploadWarningMessage = null;
-    private String errorMessage = null;
+    private List<String> errorMessages = new ArrayList<>();
     private String uploadSuccessMessage = null;
     private String uploadComponentId = null;
 
@@ -2020,7 +2022,11 @@ public void handleFileUpload(FileUploadEvent event) throws IOException {
             // zip file.
             CreateDataFileResult createDataFilesResult = FileUtil.createDataFiles(workingVersion, uFile.getInputStream(), uFile.getFileName(), uFile.getContentType(), null, null, systemConfig);
             dFileList = createDataFilesResult.getDataFiles();
-            errorMessage = editDataFilesPageHelper.getHtmlErrorMessage(createDataFilesResult);
+            String createDataFilesError = editDataFilesPageHelper.getHtmlErrorMessage(createDataFilesResult);
+            if(createDataFilesError != null) {
+                errorMessages.add(createDataFilesError);
+                uploadComponentId = event.getComponent().getClientId();
+            }
 
         } catch (IOException ioex) {
             logger.warning("Failed to process and/or save the file " + uFile.getFileName() + "; " + ioex.getMessage());
@@ -2127,7 +2133,7 @@ public void handleExternalUpload() {
                     //datafiles = ingestService.createDataFiles(workingVersion, dropBoxStream, fileName, "application/octet-stream");
                     CreateDataFileResult createDataFilesResult = FileUtil.createDataFiles(workingVersion, null, fileName, contentType, fullStorageIdentifier, checksumValue, checksumType, systemConfig);
                     datafiles = createDataFilesResult.getDataFiles();
-                    errorMessage = editDataFilesPageHelper.getHtmlErrorMessage(createDataFilesResult);
+                    Optional.ofNullable(editDataFilesPageHelper.getHtmlErrorMessage(createDataFilesResult)).ifPresent(errorMessage -> errorMessages.add(errorMessage));
                 } catch (IOException ex) {
                     logger.log(Level.SEVERE, "Error during ingest of file {0}", new Object[]{fileName});
                 }

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java b/src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java
@@ -876,7 +876,7 @@ public static CreateDataFileResult createDataFiles(DatasetVersion version, Input
                     }
 
                     datafiles.add(datafile);
-                    return CreateDataFileResult.success(finalType, datafiles);
+                    return CreateDataFileResult.success(fileName, finalType, datafiles);
                 }
 
                 // If it's a ZIP file, we are going to unpack it and create multiple
@@ -1052,7 +1052,7 @@ public static CreateDataFileResult createDataFiles(DatasetVersion version, Input
                         logger.warning("Could not remove temp file " + tempFile.getFileName().toString());
                     }
                     // and return:
-                    return CreateDataFileResult.success(finalType, datafiles);
+                    return CreateDataFileResult.success(fileName, finalType, datafiles);
                 }
 
             } else if (finalType.equalsIgnoreCase(ShapefileHandler.SHAPEFILE_FILE_TYPE)) {
@@ -1068,7 +1068,7 @@ public static CreateDataFileResult createDataFiles(DatasetVersion version, Input
                 boolean didProcessWork = shpIngestHelper.processFile();
                 if (!(didProcessWork)) {
                     logger.severe("Processing of zipped shapefile failed.");
-                    return CreateDataFileResult.error(finalType);
+                    return CreateDataFileResult.error(fileName, finalType);
                 }
 
                 try {
@@ -1129,11 +1129,11 @@ public static CreateDataFileResult createDataFiles(DatasetVersion version, Input
                         logger.warning("Unable to delete: " + tempFile.toString() + "due to Security Exception: "
                                 + se.getMessage());
                     }
-                    return CreateDataFileResult.success(finalType, datafiles);
+                    return CreateDataFileResult.success(fileName, finalType, datafiles);
                 } else {
                     logger.severe("No files added from directory of rezipped shapefiles");
                 }
-                return CreateDataFileResult.error(finalType);
+                return CreateDataFileResult.error(fileName, finalType);
 
             } else if (finalType.equalsIgnoreCase(BagItFileHandler.FILE_TYPE)) {
                 Optional<BagItFileHandler> bagItFileHandler = CDI.current().select(BagItFileHandlerFactory.class).get().getBagItFileHandler();
@@ -1176,10 +1176,10 @@ public static CreateDataFileResult createDataFiles(DatasetVersion version, Input
             }
             datafiles.add(datafile);
 
-            return CreateDataFileResult.success(finalType, datafiles);
+            return CreateDataFileResult.success(fileName, finalType, datafiles);
         }
 
-        return CreateDataFileResult.error(finalType);
+        return CreateDataFileResult.error(fileName, finalType);
     }   // end createDataFiles
 
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/bagit/BagValidation.java b/src/main/java/edu/harvard/iq/dataverse/util/bagit/BagValidation.java
@@ -3,8 +3,11 @@
 import java.nio.file.Path;
 import java.util.Collections;
 import java.util.LinkedHashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 /**
  *
@@ -16,7 +19,7 @@ public class BagValidation {
     private final Map<Path, FileValidationResult> fileResults;
 
     public BagValidation(Optional<String> errorMessage) {
-        this.errorMessage = errorMessage;
+        this.errorMessage = errorMessage == null ? Optional.empty() : errorMessage;
         this.fileResults = new LinkedHashMap<>();
     }
 
@@ -34,6 +37,12 @@ public Map<Path, FileValidationResult> getFileResults() {
         return Collections.unmodifiableMap(fileResults);
     }
 
+    public List<String> getAllErrors() {
+        Stream<String> mainError = getErrorMessage().stream();
+        Stream<String> fileErrors = getFileResults().values().stream().filter(result -> result.isError()).map(result -> result.getMessage());
+        return Stream.concat(mainError, fileErrors).collect(Collectors.toList());
+    }
+
     public long errors() {
         return fileResults.values().stream().filter(result -> result.isError()).count();
     }
@@ -76,8 +85,9 @@ public void setSuccess() {
             this.status = Status.SUCCESS;
         }
 
-        public void setError() {
+        public void setError(String message) {
             this.status = Status.ERROR;
+            this.message = message;
         }
 
         public boolean isPending() {
@@ -92,10 +102,6 @@ public boolean isError() {
             return status.equals(Status.ERROR);
         }
 
-        public void setMessage(String message) {
-            this.message = message;
-        }
-
         public String getMessage() {
             return message;
         }

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/bagit/BagValidator.java b/src/main/java/edu/harvard/iq/dataverse/util/bagit/BagValidator.java
@@ -118,8 +118,7 @@ private BagValidation validateChecksums(FileDataProvider fileDataProvider, Manif
                 FileChecksumValidationJob validationJob = new FileChecksumValidationJob(inputStreamProvider.get(), filePath, fileChecksum, manifestChecksums.getType(), fileValidationResult);
                 executor.execute(validationJob);
             } else {
-                fileValidationResult.setError();
-                fileValidationResult.setMessage(getMessage("bagit.validation.file.not.found", filePath, fileDataProvider.getName()));
+                fileValidationResult.setError(getMessage("bagit.validation.file.not.found", filePath, fileDataProvider.getName()));
             }
 
         }
@@ -148,7 +147,8 @@ ExecutorService getExecutorService() {
         return Executors.newFixedThreadPool(validatorJobPoolSize);
     }
 
-    private String getMessage(String propertyKey, Object... parameters){
+    // Visible for testing
+    String getMessage(String propertyKey, Object... parameters){
         List<String> parameterList = Arrays.stream(parameters).map(param -> param.toString()).collect(Collectors.toList());
         return BundleUtil.getStringFromBundle(propertyKey, parameterList);
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/bagit/FileChecksumValidationJob.java b/src/main/java/edu/harvard/iq/dataverse/util/bagit/FileChecksumValidationJob.java
@@ -43,12 +43,10 @@ public void run() {
             if (fileChecksum.equals(calculatedChecksum)) {
                 result.setSuccess();
             } else {
-                result.setError();
-                result.setMessage(getMessage("bagit.checksum.validation.error", filePath, bagChecksumType, fileChecksum, calculatedChecksum));
+                result.setError(getMessage("bagit.checksum.validation.error", filePath, bagChecksumType, fileChecksum, calculatedChecksum));
             }
         } catch (Exception e) {
-            result.setError();
-            result.setMessage(getMessage("bagit.checksum.validation.exception", filePath, bagChecksumType, e.getMessage()));
+            result.setError(getMessage("bagit.checksum.validation.exception", filePath, bagChecksumType, e.getMessage()));
             logger.log(Level.WARNING, String.format("action=validate-checksum result=error filePath=%s type=%s", filePath, bagChecksumType), e);
         } finally {
             IOUtils.closeQuietly(inputStream);

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/file/BagItFileHandler.java b/src/main/java/edu/harvard/iq/dataverse/util/file/BagItFileHandler.java
@@ -21,7 +21,6 @@
 import java.util.List;
 import java.util.Optional;
 import java.util.logging.Logger;
-import java.util.stream.Collectors;
 
 /**
  *
@@ -58,25 +57,25 @@ public CreateDataFileResult handleBagItPackage(SystemConfig systemConfig, Datase
         try {
             List<DataFile> packageDataFiles = processBagItPackage(systemConfig, datasetVersion, uploadedFilename, bagItPackageFile);
             if(packageDataFiles.isEmpty()) {
-                return CreateDataFileResult.error(FILE_TYPE, Collections.emptyList());
+                return CreateDataFileResult.error(uploadedFilename, FILE_TYPE, Collections.emptyList());
             }
 
             BagValidation bagValidation = validateBagItPackage(uploadedFilename, packageDataFiles);
             if(bagValidation.success()) {
                 List<DataFile> finalItems = postProcessor.process(packageDataFiles);
                 logger.info(String.format("action=handleBagItPackage result=success uploadedFilename=%s file=%s", uploadedFilename, bagItPackageFile.getName()));
-                return CreateDataFileResult.success(FILE_TYPE, finalItems);
+                return CreateDataFileResult.success(uploadedFilename, FILE_TYPE, finalItems);
             }
 
             // BagIt package has errors
             // Capture errors and return to caller
-            List<String> errors = bagValidation.getFileResults().values().stream().filter(result -> result.isError()).map(result -> result.getMessage()).collect(Collectors.toList());
+            List<String> errors = bagValidation.getAllErrors();
             logger.info(String.format("action=handleBagItPackage result=errors uploadedFilename=%s file=%s errors=%s", uploadedFilename, bagItPackageFile.getName(), errors.size()));
-            return CreateDataFileResult.error(FILE_TYPE, errors);
+            return CreateDataFileResult.error(uploadedFilename, FILE_TYPE, errors);
 
         } catch (BagItFileHandlerException e) {
             logger.severe(String.format("action=handleBagItPackage result=error uploadedFilename=%s file=%s message=%s", uploadedFilename, bagItPackageFile.getName(), e.getMessage()));
-            return CreateDataFileResult.error(FILE_TYPE, Arrays.asList(e.getMessage()));
+            return CreateDataFileResult.error(uploadedFilename, FILE_TYPE, Arrays.asList(e.getMessage()));
         } finally {
             fileUtil.deleteFile(bagItPackageFile.toPath());
         }

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/file/CreateDataFileResult.java b/src/main/java/edu/harvard/iq/dataverse/util/file/CreateDataFileResult.java
@@ -13,26 +13,32 @@ public class CreateDataFileResult {
 
     private static final String BUNDLE_KEY_PREFIX = "dataset.file.error";
 
+    private final String filename;
     private final String type;
     private final List<DataFile> dataFiles;
     private final List<String> errors;
 
-    public CreateDataFileResult(String type, List<DataFile> dataFiles, List<String> errors) {
+    public CreateDataFileResult(String filename, String type, List<DataFile> dataFiles, List<String> errors) {
+        this.filename = filename;
         this.type = type;
         this.dataFiles = dataFiles == null ? null : Collections.unmodifiableList(dataFiles);
         this.errors = errors == null ? Collections.emptyList() : Collections.unmodifiableList(errors);
     }
 
-    public static CreateDataFileResult success(String type, List<DataFile> dataFiles) {
-        return new CreateDataFileResult(type, dataFiles, null);
+    public static CreateDataFileResult success(String filename, String type, List<DataFile> dataFiles) {
+        return new CreateDataFileResult(filename, type, dataFiles, null);
     }
 
-    public static CreateDataFileResult error(String type) {
-        return new CreateDataFileResult(type, null, Collections.emptyList());
+    public static CreateDataFileResult error(String filename, String type) {
+        return new CreateDataFileResult(filename, type, null, Collections.emptyList());
     }
 
-    public static CreateDataFileResult error(String type, List<String> errors) {
-        return new CreateDataFileResult(type, null, errors);
+    public static CreateDataFileResult error(String filename, String type, List<String> errors) {
+        return new CreateDataFileResult(filename, type, null, errors);
+    }
+
+    public String getFilename() {
+        return filename;
     }
 
     public String getType() {

diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties
@@ -2270,12 +2270,12 @@ bagit.sourceOrganization=Dataverse Installation (<Site Url>)
 bagit.sourceOrganizationAddress=<Full address>
 bagit.sourceOrganizationEmail=<Email address>
 
-bagit.checksum.validation.error=Invalid checksum. filePath={0} type={1} fileChecksum={2} calculatedChecksum={3}
-bagit.checksum.validation.exception=Error while calculating checksum. filePath={0} type={1} error={2}
-bagit.validation.bag.file.not.found=Invalid bag file: {0}
-bagit.validation.manifest.not.supported=No supported manifest found in: {0} supportedTypes: {1}
-bagit.validation.file.not.found=Manifest declared file: {0} not-found in data provider: {1}
-bagit.validation.exception=Unable to complete checksums for: {0}
+bagit.checksum.validation.error=Invalid checksum for file "{0}". Manifest checksum={2}, calculated checksum={3}, type={1}
+bagit.checksum.validation.exception=Error while calculating checksum for file "{0}". Checksum type={1}, error={2}
+bagit.validation.bag.file.not.found=Invalid BagIt package: "{0}"
+bagit.validation.manifest.not.supported=No supported manifest found in BagIt package. Supported types are: {1}
+bagit.validation.file.not.found=The manifest declared a file, "{0}", that is not found in the BagIt package
+bagit.validation.exception=Unable to complete checksums for BagIt package
 
 #Permission.java
 permission.addDataverseDataverse=Add a dataverse within another dataverse
@@ -2348,7 +2348,7 @@ dataset.file.uploadWarning=upload warning
 dataset.file.uploadWorked=upload worked
 dataset.file.upload.popup.explanation.tip=For more information, please refer to the <a href="{0}/{1}/user/dataset-management.html#duplicate-files" title="Duplicate Files - Dataverse User Guide" target="_blank" rel="noopener">Duplicate Files section of the User Guide</a>.
 
-dataset.file.error.application/zipped-bagit=BagIt package detected, but errors found. These are the errors found until processing stopped
+dataset.file.error.application/zipped-bagit=BagIt package, "{0}", detected but errors found. These are the errors found until processing stopped:
 
 #HarvestingClientsPage.java
 harvest.start.error=Sorry, harvest could not be started for the selected harvesting client configuration (unknown server error).