IQSS/5043 streaming and new exporters

scripts/database/5043-update.sql

@@ -0,0 +1,2 @@
+ALTER TABLE datasetfieldtype ADD COLUMN uri text;
+ALTER TABLE metadatablock ADD COLUMN namespaceuri text;

src/main/java/Bundle.properties

@@ -149,6 +149,7 @@ contact.context.support.intro={0},\n\nThe following message was sent from {1}.\n
 contact.context.support.ending=\n\n---\n\nMessage sent from Support contact form.
 
 # dataverseuser.xhtml
+institution.name=A Dataverse Instance
 account.info=Account Information
 account.edit=Edit Account
 account.apiToken=API Token
@@ -1158,7 +1159,9 @@ dataset.exportBtn=Export Metadata
 dataset.exportBtn.itemLabel.ddi=DDI
 dataset.exportBtn.itemLabel.dublinCore=Dublin Core
 dataset.exportBtn.itemLabel.schemaDotOrg=Schema.org JSON-LD
+dataset.exportBtn.itemLabel.datacite=DataCite
 dataset.exportBtn.itemLabel.json=JSON
+dataset.exportBtn.itemLabel.oai_ore=OAI_ORE
 metrics.title=Metrics
 metrics.title.tip=View more metrics information
 metrics.comingsoon=Coming soon...

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

@@ -38,9 +38,6 @@ public class DOIDataCiteRegisterService {
     @PersistenceContext(unitName = "VDCNet-ejbPU")
     private EntityManager em;
 
-    @EJB
-    DataverseServiceBean dataverseService;
-
     private DataCiteRESTfullClient openClient() throws IOException {
         return new DataCiteRESTfullClient(System.getProperty("doi.baseurlstring"), System.getProperty("doi.username"), System.getProperty("doi.password"));
     }
@@ -115,7 +112,7 @@ public String deactivateIdentifier(String identifier, HashMap<String, String> me
         return retString;
     }
 
-    private String getMetadataFromDvObject(String identifier, Map<String, String> metadata, DvObject dvObject) {
+    public static String getMetadataFromDvObject(String identifier, Map<String, String> metadata, DvObject dvObject) {
 
         Dataset dataset = null;
 
@@ -145,7 +142,7 @@ private String getMetadataFromDvObject(String identifier, Map<String, String> me
         metadataTemplate.setContacts(dataset.getLatestVersion().getDatasetContacts());
         metadataTemplate.setProducers(dataset.getLatestVersion().getDatasetProducers());
         metadataTemplate.setTitle(dvObject.getDisplayName());
-        String producerString = dataverseService.findRootDataverse().getName();
+        String producerString = dataset.getLatestVersion().getRootDataverseNameforCitation();
         if (producerString.isEmpty()) {
             producerString = ":unav";
         }

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

@@ -17,7 +17,9 @@
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Date;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.util.regex.Matcher;
@@ -201,7 +203,6 @@ public String toString(boolean html) {
         citationList.add(version);
 
         StringBuilder citation = new StringBuilder(citationList.stream().filter(value -> !StringUtils.isEmpty(value))
-                // QDRCustom: Use period to join values, not comma
                 .collect(Collectors.joining(separator)));
 
         if ((fileTitle != null) && !isDirect()) {
@@ -592,9 +593,30 @@ private void createEndNoteXML(XMLStreamWriter xmlw) throws XMLStreamException {
 
         xmlw.writeEndElement(); // records
         xmlw.writeEndElement(); // xml
+
+    }
+
+	public Map<String, String> getDataCiteMetadata() {
+        Map<String, String> metadata = new HashMap<>();
+        String authorString = getAuthorsString();
+
+        if (authorString.isEmpty()) {
+            authorString = ":unav";
     }
+        String producerString = getPublisher();
+
+        if (producerString.isEmpty()) {
+            producerString = ":unav";
+        }
 
+        metadata.put("datacite.creator", authorString);
+        metadata.put("datacite.title", getTitle());
+        metadata.put("datacite.publisher", producerString);
+        metadata.put("datacite.publicationyear", getYear());
+        return metadata;
+	}
 
+
     // helper methods   
     private String formatString(String value, boolean escapeHtml) {
         return formatString(value, escapeHtml, "");

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

@@ -335,7 +335,8 @@ public boolean isEmptyForDisplay() {
 
     private boolean isEmpty(boolean forDisplay) {
         if (datasetFieldType.isPrimitive()) { // primitive
-            for (String value : getValues()) {
+        	List<String> values = forDisplay ? getValues() : getValues_nondisplay();
+            for (String value : values) {
                 if (!StringUtils.isBlank(value) && !(forDisplay && DatasetField.NA_VALUE.equals(value))) {
                     return false;
                 }

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

@@ -294,6 +294,20 @@ public void setMetadataBlock(MetadataBlock metadataBlock) {
         this.metadataBlock = metadataBlock;
     }
 
+    /**
+     * A formal URI for the field used in json-ld exports
+     */
+    @Column(name = "uri", columnDefinition = "TEXT")
+    private String uri;
+
+    public String getUri() {
+    	return uri;
+    }
+
+    public void setUri(String uri) {
+    	this.uri=uri;
+    }
+
     /**
      * The list of controlled vocabulary terms that may be used as values for
      * fields of this field type.

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

@@ -43,6 +43,9 @@ public class MetadataBlock implements Serializable {
     @Column( nullable = false )
     private String displayName;
 
+    @Column( name = "namespaceuri", columnDefinition = "TEXT")
+    private String namespaceUri;
+
     public Long getId() {
         return id;
     }
@@ -56,7 +59,14 @@ public String getName() {
     public void setName(String name) {
         this.name = name;
     }
-
+
+    public String getNamespaceUri() {
+        return namespaceUri;
+    }
+    public void setNamespaceUri(String namespaceUri) {
+        this.namespaceUri = namespaceUri;
+    }
+
     @OneToMany(mappedBy = "metadataBlock", cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
     @OrderBy("displayOrder")
     private List<DatasetFieldType> datasetFieldTypes;

src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java

@@ -55,6 +55,8 @@ public class DatasetFieldServiceApi extends AbstractApiBean {
     @EJB
     ControlledVocabularyValueServiceBean controlledVocabularyValueService;
 
+    private static final Logger logger = Logger.getLogger(DatasetFieldServiceApi.class.getName());
+
     @GET
     public Response getAll() {
         try {
@@ -277,7 +279,7 @@ public Response loadDatasetFields(File file) {
             return error(Status.EXPECTATION_FAILED, "File not found");
 
         } catch (Exception e) {
-            Logger.getLogger(DatasetFieldServiceApi.class.getName()).log(Level.WARNING, "Error parsing dataset fields:" + e.getMessage(), e);
+            logger.log(Level.WARNING, "Error parsing dataset fields:" + e.getMessage(), e);
             alr.setActionResult(ActionLogRecord.Result.InternalError);
             alr.setInfo( alr.getInfo() + "// " + e.getMessage());
             return error(Status.INTERNAL_SERVER_ERROR, e.getMessage());
@@ -287,8 +289,7 @@ public Response loadDatasetFields(File file) {
                 try {
                     br.close();
                 } catch (IOException e) {
-                    Logger.getLogger(DatasetFieldServiceApi.class.getName())
-                            .log(Level.WARNING, "Error closing the reader while importing Dataset Fields.");
+                    logger.log(Level.WARNING, "Error closing the reader while importing Dataset Fields.");
                 }
             }
             actionLogSvc.log(alr);
@@ -308,6 +309,9 @@ private String parseMetadataBlock(String[] values) {
             mdb.setOwner(dataverseService.findByAlias(values[2]));
         }
         mdb.setDisplayName(values[3]);
+        if (values.length>4 && !StringUtils.isEmpty(values[4])) {
+            mdb.setNamespaceUri(values[4]);
+        }
 
         metadataBlockService.save(mdb);
         return mdb.getName();
@@ -337,8 +341,13 @@ private String parseDatasetField(String[] values) {
         dsf.setRequired(Boolean.parseBoolean(values[13]));
         if (!StringUtils.isEmpty(values[14])) {
             dsf.setParentDatasetFieldType(datasetFieldService.findByName(values[14]));
+        } else {
+            dsf.setParentDatasetFieldType(null);
         }
         dsf.setMetadataBlock(dataverseService.findMDBByName(values[15]));
+        if(values.length>16 && !StringUtils.isEmpty(values[16])) {
+          dsf.setUri(values[16]);
+        }
         datasetFieldService.save(dsf);
         return dsf.getName();
     }