Merge branch 'staging' into dataverse_update_v5.12.1_workflow_patch

src/main/java/edu/harvard/iq/dataverse/FileDownloadServiceBean.java

@@ -462,7 +462,7 @@ public void downloadCitationBibtex(FileMetadata fileMetadata, Dataset dataset, b
         HttpServletResponse response = (HttpServletResponse) ctx.getExternalContext().getResponse();
 
         //Fix for 6029 FireFox was failing to parse it when content type was set to json 
-        response.setContentType("text/plain");
+        response.setContentType("text/plain;charset=utf-8");
 
         String fileNameString;
         if (fileMetadata == null || fileMetadata.getLabel() == null) {

src/main/java/edu/harvard/iq/dataverse/api/dto/DatasetVersionDTO.java

@@ -56,6 +56,9 @@ public void setInReview(boolean inReview) {
     }
 
     public String getTermsOfUse() {
+    	if (termsOfUse != null && termsOfUse.contains("CC0")) {
+    		termsOfUse = termsOfUse.replace("CC0", "CC BY");
+    	}
         return termsOfUse;
     }
 

src/main/java/edu/harvard/iq/dataverse/export/openaire/OpenAireExportUtil.java

@@ -1132,6 +1132,7 @@ public static void writeAccessRightsElement(XMLStreamWriter xmlw, DatasetVersion
         xmlw.writeEndElement(); // </rights>
 
         writeRightsHeader(xmlw, language);
+
         if (datasetVersionDTO.getLicense() != null) {
             xmlw.writeAttribute("rightsURI", datasetVersionDTO.getLicense().getUri());
             xmlw.writeCharacters(datasetVersionDTO.getLicense().getName());

src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java

@@ -207,6 +207,8 @@ public class FileUtil implements java.io.Serializable  {
     private static final String FILE_FACET_CLASS_TEXT = "Text";
     private static final String FILE_FACET_CLASS_OTHER = "Other";
     private static final String FILE_FACET_CLASS_UNKNOWN = "Unknown";
+
+    public static final String OVERWRITE_MIME_TYPE_PREFIX = "force-";
 
     // The file type facets and type-specific thumbnail classes (above) are
     // very similar, but not exactly 1:1; so the following map is for 
@@ -819,24 +821,32 @@ public static CreateDataFileResult createDataFiles(DatasetVersion version, Input
             // than the type supplied:
             // -- L.A.
             String recognizedType = null;
-
-            try {
-                recognizedType = determineFileType(tempFile.toFile(), fileName);
-                logger.fine("File utility recognized the file as " + recognizedType);
-                if (recognizedType != null && !recognizedType.equals("")) {
-                    if (useRecognizedType(suppliedContentType, recognizedType)) {
-                        finalType = recognizedType;
-                    }
-                }
-
-            } catch (Exception ex) {
-                logger.warning("Failed to run the file utility mime type check on file " + fileName);
+
+            // If we detect the dataverse prefix in the supplied mimetype we do no 
+            // further recognition
+            if (suppliedContentType.toLowerCase().startsWith(OVERWRITE_MIME_TYPE_PREFIX)) {
+            	finalType = suppliedContentType.toLowerCase().substring(OVERWRITE_MIME_TYPE_PREFIX.length());
+            	logger.fine("Overwrite prefix detected. Using supplied mime type.");
             }
-
-            if (finalType == null) {
-                finalType = (suppliedContentType == null || suppliedContentType.equals(""))
-                        ? MIME_TYPE_UNDETERMINED_DEFAULT
-                        : suppliedContentType;
+            else {
+	            try {
+	                recognizedType = determineFileType(tempFile.toFile(), fileName);
+	                logger.fine("File utility recognized the file as " + recognizedType);
+	                if (recognizedType != null && !recognizedType.equals("")) {
+	                    if (useRecognizedType(suppliedContentType, recognizedType)) {
+	                        finalType = recognizedType;
+	                    }
+	                }
+
+	            } catch (Exception ex) {
+	                logger.warning("Failed to run the file utility mime type check on file " + fileName);
+	            }
+
+	            if (finalType == null) {
+	                finalType = (suppliedContentType == null || suppliedContentType.equals(""))
+	                        ? MIME_TYPE_UNDETERMINED_DEFAULT
+	                        : suppliedContentType;
+	            }
             }
 
             // A few special cases:

src/main/java/edu/harvard/iq/dataverse/util/MarkupChecker.java

@@ -33,8 +33,8 @@ public static String sanitizeBasicHTML(String unsafe) {
         // basic includes: a, b, blockquote, br, cite, code, dd, dl, dt, em, i, li, ol, p, pre, q, small, span, strike, strong, sub, sup, u, ul
         //Whitelist wl = Whitelist.basic().addTags("img", "h1", "h2", "h3", "kbd", "hr", "s", "del");  
 
-        Safelist sl = Safelist.basicWithImages().addTags("h1", "h2", "h3", "kbd", "hr", "s", "del", "map", "area").addAttributes("img", "usemap")
-                .addAttributes("map", "name").addAttributes("area", "shape", "coords", "href", "title", "alt")
+        Safelist sl = Safelist.basicWithImages().addTags("h1", "h2", "h3", "kbd", "hr", "s", "del", "map", "area").addAttributes("img", "usemap", "style")
+                .addAttributes("map", "name").addAttributes("area", "shape", "coords", "href", "title", "alt").addAttributes("ol", "type")
                 .addEnforcedAttribute("a", "target", "_blank");
 
         return Jsoup.clean(unsafe, sl);

src/main/java/edu/harvard/iq/dataverse/util/json/JsonParser.java

@@ -407,7 +407,7 @@ public DatasetVersion parseDatasetVersion(JsonObject obj, DatasetVersion dsv) th
             throw new JsonParseException(BundleUtil.getStringFromBundle("jsonparser.error.parsing.number", Arrays.asList(ex.getMessage())), ex);
         }
     }
-    
+
     private edu.harvard.iq.dataverse.license.License parseLicense(String licenseNameOrUri) throws JsonParseException {
         if (licenseNameOrUri == null){
             boolean safeDefaultIfKeyNotFound = true;

src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java

@@ -420,6 +420,18 @@ public static JsonObjectBuilder jsonDataFileList(List<DataFile> dataFiles){
         return bld;
     }
 
+    private static String getLicense(DatasetVersion dsv) {
+        if (dsv.getTermsOfUseAndAccess().getLicense() != null) {
+            if (dsv.getTermsOfUseAndAccess().getLicense().equals(TermsOfUseAndAccess.License.CC0)) {
+                return "CC BY";
+            } else {
+                return dsv.getTermsOfUseAndAccess().getLicense().toString();
+            }
+        } else {
+        	return null;
+        }
+    }
+
     /**
      * Export formats such as DDI require the citation to be included. See
      * https://github.com/IQSS/dataverse/issues/2579 for more on DDI export.

src/main/java/propertyFiles/Bundle.properties

@@ -88,6 +88,7 @@ selectedFiles=Selected Files
 htmlAllowedTitle=Allowed HTML Tags
 htmlAllowedMsg=This field supports only certain <a class="popoverHTML" tabindex="0" role="button">HTML tags</a>.
 htmlAllowedTags=&lt;a&gt;, &lt;b&gt;, &lt;blockquote&gt;, &lt;br&gt;, &lt;code&gt;, &lt;del&gt;, &lt;dd&gt;, &lt;dl&gt;, &lt;dt&gt;, &lt;em&gt;, &lt;hr&gt;, &lt;h1&gt;-&lt;h3&gt;, &lt;i&gt;, &lt;img&gt;, &lt;kbd&gt;, &lt;li&gt;, &lt;ol&gt;, &lt;p&gt;, &lt;pre&gt;, &lt;s&gt;, &lt;sup&gt;, &lt;sub&gt;, &lt;strong&gt;, &lt;strike&gt;, &lt;u&gt;, &lt;ul&gt;
+vocabularyFaqMsg=More information about vocabularies, terms and URLs <a href="https://www.izus.uni-stuttgart.de/en/fokus/darus/#id-22d988a4-3" rel="help" target="_blank">here</a>.
 conditionalRequiredMsg=One or more of these fields may become required if you add to one or more of these optional fields.
 conditionalRequiredMsg.tooltip=This field will become required if you choose to enter values in one or more of these optional fields.
 toggleNavigation=Toggle navigation
@@ -806,7 +807,7 @@ dataverse.enterName=Enter name...
 dataverse.host.title=The dataverse which contains this data.
 dataverse.host.tip=Changing the host dataverse will clear any fields you may have entered data into.
 dataverse.host.autocomplete.nomatches=No matches
-dataverse.identifier.title=Short name used for the URL of this dataverse.
+dataverse.identifier.title=Short name used for the URL of this dataverse. Use your institutional abbreviation as prefix.
 dataverse.affiliation.title=The organization with which this dataverse is affiliated.
 dataverse.storage.title=A storage service to be used for datasets in this dataverse.
 dataverse.metadatalanguage.title=Metadata entered for datasets in this dataverse will be assumed to be in the selected language.
@@ -1417,7 +1418,7 @@ dataset.publish.header=Publish Dataset
 dataset.rejectBtn=Return to Author
 dataset.submitBtn=Submit for Review
 dataset.disabledSubmittedBtn=Submitted for Review
-dataset.submitMessage=You will not be able to make changes to this dataset while it is in review.
+dataset.submitMessage=Please use the publication checklist for authors ( https://www.izus.uni-stuttgart.de/fokus/darus/publication/ ) to ensure publication readiness. You will not be able to make changes to this dataset while it is in review.
 dataset.submit.success=Your dataset has been submitted for review.
 dataset.inreview.infoMessage=The draft version of this dataset is currently under review prior to publication.
 dataset.submit.failure=Dataset Submission Failed - {0}
@@ -1469,7 +1470,7 @@ dataset.share.datasetShare=Share Dataset
 dataset.share.datasetShare.tip=Share this dataset on your favorite social media networks.
 dataset.share.datasetShare.shareText=View this dataset.
 dataset.locked.message=Dataset Locked
-dataset.locked.message.details=This dataset is locked until publication.
+dataset.locked.message.details=This dataset is reviewed prior to publication by the DaRUS-team. You will receive an email with further information in the next days.
 dataset.locked.inReview.message=Submitted for Review
 dataset.locked.ingest.message=The tabular data files uploaded are being processed and converted into the archival format
 dataset.unlocked.ingest.message=The tabular files have been ingested.

src/main/java/propertyFiles/MimeTypeDetectionByFileExtension.properties

@@ -17,6 +17,7 @@ mp3=audio/mp3
 nii=image/nii
 nc=application/netcdf
 ods=application/vnd.oasis.opendocument.spreadsheet
+pdh=text/plain
 png=image/png
 pptx=application/vnd.openxmlformats-officedocument.presentationml.presentation
 prj=application/prj

src/main/webapp/metadataFragment.xhtml

@@ -1,3 +1,4 @@
+
 <ui:composition xmlns="http://www.w3.org/1999/xhtml"
                 xmlns:h="http://java.sun.com/jsf/html"
                 xmlns:f="http://java.sun.com/jsf/core"
@@ -325,6 +326,11 @@
                                                     <h:outputText value="#{bundle.conditionalRequiredMsg}"/>
                                                 </p>
                                             </ui:fragment>
+                                            <ui:fragment rendered="#{dsf.datasetFieldType.name == 'keyword'}">
+                                                <p class="help-block">
+                                                    <h:outputText value="#{bundle.vocabularyFaqMsg}" escape="false"/>
+                                                </p>
+                                            </ui:fragment>
                                             <ui:repeat value="#{dsf.datasetFieldCompoundValues}" var="compoundValue" varStatus="valCount">
                                                 <div class="form-group form-col-container col-sm-9 edit-compound-field"  data-cvoc-parentfield="#{cvocConf.containsKey(dsf.datasetFieldType.id)?cvocConf.get(dsf.datasetFieldType.id).getString('field-name'):''}">
                                                     <!-- Sub Fields -->

src/main/webapp/resources/js/shib/idpselect_config.js

@@ -31,7 +31,7 @@ function IdPSelectUIParms() {
     this.preferredIdP = null;        // Array of entityIds to always show
     this.hiddenIdPs = null;          // Array of entityIds to delete
     this.ignoreKeywords = false;     // Do we ignore the <mdui:Keywords/> when looking for candidates
-    this.showListFirst = true;      // Do we start with a list of IdPs or just the dropdown
+    this.showListFirst = false;      // Do we start with a list of IdPs or just the dropdown
     this.samlIdPCookieTTL = 730;     // in days
     this.setFocusTextBox = true;     // Set to false to supress focus 
     this.testGUI = false;