Clariah submission

dspace-api/src/main/java/cz/cuni/mff/ufal/curation/RequiredMetadata.java

@@ -147,11 +147,7 @@ public int perform(DSpaceObject dso) throws IOException
                 	colhandle = item.getOwningCollection().getHandle();
                 	checkExtra = checkExtraIds.contains(Integer.toString(item.getOwningCollection().getID()));
                 }
-                Metadatum[] itemTypeDCV = item.getMetadata("dc", "type", null, Item.ANY);
-                String itemType = null;
-                if(itemTypeDCV != null && itemTypeDCV.length >0){
-                	itemType = itemTypeDCV[0].value;
-                }
+                Metadatum[] itemTypes = item.getMetadata(Item.ANY, "type", Item.ANY, Item.ANY);
                 for (DCInput input : getReqList(colhandle,checkExtra))
                 {
                 	StringBuilder reqsb = new StringBuilder();
@@ -177,7 +173,7 @@ public int perform(DSpaceObject dso) throws IOException
 
                     if (!mdPatFound) {
                         Metadatum[] vals = item.getMetadataByMetadataString(req);
-                        if ((itemType == null || input.isAllowedFor(itemType)) && vals.length == 0)
+                        if ((itemTypes == null || itemTypes.length == 0 || input.isAllowedFor(itemTypes)) && vals.length == 0)
                         {
                             boolean issue_warning = true;
                         	if (mdEquivalenceMap.containsKey(req)) {

dspace-api/src/main/java/cz/cuni/mff/ufal/dspace/app/itemimport/ItemImportReplacingMetadata.java

@@ -0,0 +1,99 @@
+package cz.cuni.mff.ufal.dspace.app.itemimport;
+
+import cz.cuni.mff.ufal.DSpaceApi;
+import cz.cuni.mff.ufal.lindat.utilities.hibernate.LicenseDefinition;
+import cz.cuni.mff.ufal.lindat.utilities.interfaces.IFunctionalities;
+import org.dspace.app.itemimport.ItemImport;
+import org.dspace.content.*;
+import org.dspace.core.Context;
+import org.dspace.handle.HandleManager;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+public class ItemImportReplacingMetadata extends ItemImport {
+
+    private java.nio.file.FileSystem fs = java.nio.file.FileSystems.getDefault();
+    IFunctionalities functionalities = DSpaceApi.getFunctionalityManager();
+
+    @Override
+    protected void replaceItems(Context c, Collection[] mycollections, String sourceDir, String mapFile,
+                            boolean template) throws Exception {
+        // verify the source directory
+        File d = new java.io.File(sourceDir);
+        List<Item> processedItems = new ArrayList<>();
+
+        if (d == null || !d.isDirectory())
+        {
+            throw new Exception("Error, cannot open source directory "
+                    + sourceDir);
+        }
+
+        // read in HashMap first, to get list of handles & source dirs
+        Map<String, String> myHash = readMapFile(mapFile);
+
+        for (Map.Entry<String, String> mapEntry : myHash.entrySet())
+        {
+            String itemName = mapEntry.getKey();
+            String handle = mapEntry.getValue();
+            Item item;
+
+            if (handle.indexOf('/') != -1)
+            {
+                System.out.println("\tReplacing:  " + handle);
+
+                // add new item, locate old one
+                item = (Item) HandleManager.resolveToObject(c, handle);
+            }
+            else
+            {
+                item = Item.find(c, Integer.parseInt(handle));
+            }
+
+            final Metadatum[] provenance = item.getMetadataByMetadataString("dc.description.provenance");
+            final Metadatum[] accessioned = item.getMetadataByMetadataString("dc.date.accessioned");
+            final Metadatum[] available = item.getMetadataByMetadataString("dc.date.available");
+            final Metadatum[] branding = item.getMetadataByMetadataString("local.branding");
+
+            item.clearMetadata(Item.ANY, Item.ANY, Item.ANY, Item.ANY);
+            loadMetadata(c, item, java.nio.file.Paths.get(sourceDir, itemName).toString() + fs.getSeparator());
+            for (Metadatum[] mds : new Metadatum[][]{provenance, accessioned, available, branding}){
+                for(Metadatum md : mds){
+                    item.addMetadatum(md);
+                }
+            }
+            processedItems.add(item);
+        }
+
+        //attempt at saving all changes or none;
+        for(Item i : processedItems){
+            i.update();
+        }
+        c.commit();
+        c.clearCache();
+
+        // attach license, license label requires an update
+        functionalities.openSession();
+        for(Item i : processedItems){
+            final String licenseURI = i.getMetadata("dc.rights.uri");
+            if(licenseURI != null) {
+                final LicenseDefinition license = functionalities.getLicenseByDefinition(licenseURI);
+                final int licenseId = license.getLicenseId();
+                for(Bundle bundle : i.getBundles("ORIGINAL")){
+                    for(Bitstream b : bundle.getBitstreams()){
+                        functionalities.detachLicenses(b.getID());
+                        functionalities.attachLicense(licenseId, b.getID());
+                    }
+                }
+                i.clearMetadata("dc", "rights", "label", Item.ANY);
+                i.addMetadata("dc", "rights", "label", Item.ANY, license.getLicenseLabel().getLabel());
+                i.update();
+            }
+        }
+        c.commit();
+        c.clearCache();
+        functionalities.closeSession();
+    }
+}

dspace-api/src/main/java/cz/cuni/mff/ufal/dspace/submit/step/UFALExtraMetadataStep.java

@@ -76,13 +76,9 @@ public int doProcessing(Context context, HttpServletRequest request,
         }
 
         // Fetch the document type (dc.type)
-        String documentType = "";
-        if( (item.getMetadataByMetadataString("dc.type") != null) && (item.getMetadataByMetadataString("dc.type").length >0) )
-        {
-            documentType = item.getMetadataByMetadataString("dc.type")[0].value;
-        }
-
-
+        Metadatum[] documentTypes = item.getMetadata(Item.ANY, "type", Item.ANY, Item.ANY);
+
+
 
         // Step 1:
         // clear out all item metadata defined on this page
@@ -115,7 +111,7 @@ public int doProcessing(Context context, HttpServletRequest request,
         for (int j = 0; j < inputs.length; j++)
         {
         	// Omit fields not allowed for this document type
-            if(!inputs[j].isAllowedFor(documentType))
+            if(!inputs[j].isAllowedFor(documentTypes))
             {
             	continue;
             }
@@ -249,7 +245,7 @@ else if (buttonPressed.equals("submit_" + fieldName + "_delete"))
             {
                	// Do not check the required attribute if it is not visible or not allowed for the document type
             	String scope = subInfo.isInWorkflow() ? DCInput.WORKFLOW_SCOPE : DCInput.SUBMISSION_SCOPE;
-                if ( !( inputs[i].isVisible(scope) && inputs[i].isAllowedFor(documentType) ) )
+                if ( !( inputs[i].isVisible(scope) && inputs[i].isAllowedFor(documentTypes) ) )
                 {
                 	continue;
                 }

dspace-api/src/main/java/org/dspace/app/itemimport/ItemImport.java

@@ -789,7 +789,7 @@ public void addItems(Context c, Collection[] mycollections,
         }
     }
 
-    private void replaceItems(Context c, Collection[] mycollections,
+    protected void replaceItems(Context c, Collection[] mycollections,
             String sourceDir, String mapFile, boolean template) throws Exception
     {
         // verify the source directory
@@ -1048,7 +1048,7 @@ private void deleteItem(Context c, String myhandle) throws Exception
     // utility methods
     ////////////////////////////////////
     // read in the map file and generate a hashmap of (file,handle) pairs
-    private Map<String, String> readMapFile(String filename) throws Exception
+    protected Map<String, String> readMapFile(String filename) throws Exception
     {
         Map<String, String> myHash = new HashMap<String, String>();
 
@@ -1100,7 +1100,7 @@ private Map<String, String> readMapFile(String filename) throws Exception
     }
 
     // Load all metadata schemas into the item.
-    private void loadMetadata(Context c, Item myitem, String path)
+    protected void loadMetadata(Context c, Item myitem, String path)
             throws SQLException, IOException, ParserConfigurationException,
             SAXException, TransformerException, AuthorizeException
     {

dspace-api/src/main/java/org/dspace/app/util/DCInput.java

@@ -11,6 +11,7 @@
 
 import org.apache.commons.lang.StringUtils;
 import org.dspace.content.MetadataSchema;
+import org.dspace.content.Metadatum;
 import org.dspace.core.Context;
 import org.xml.sax.SAXException;
 
@@ -110,7 +111,7 @@ public class DCInput
     private boolean closedVocabulary = false;
 
     /** allowed document types */
-    private List<String> typeBind = null;
+    private Map<String, List<String>> typeBind = new HashMap<>();
 
 	private ComplexDefinition complexDefinition = null;   
 
@@ -199,13 +200,21 @@ public DCInput(Map<String, String> fieldMap,
                             || "yes".equalsIgnoreCase(closedVocabularyStr);
 
         // parsing of the <type-bind> element (using the colon as split separator)
-        typeBind = new ArrayList<String>();
         String typeBindDef = fieldMap.get("type-bind");
         if(typeBindDef != null && typeBindDef.trim().length() > 0) {
         	String[] types = typeBindDef.split(",");
+        	List<String> boundTypes = new ArrayList<>();
         	for(String type : types) {
-        		typeBind.add( type.trim() );
+        		boundTypes.add( type.trim() );
         	}
+            String typeBindField = fieldMap.get(DCInputsReader.TYPE_BIND_FIELD_ATTRIBUTE);
+        	List<String> existingTypes = typeBind.get(typeBindField);
+        	if(existingTypes == null){
+        	    typeBind.put(typeBindField, boundTypes);
+            }else{
+        	    existingTypes.addAll(boundTypes);
+            }
+
         }
 
     }
@@ -520,14 +529,24 @@ public boolean isClosedVocabulary() {
 
 	/**
 	 * Decides if this field is valid for the document type
-	 * @param typeName Document type name
+	 * @param types Document type Metadata
 	 * @return true when there is no type restriction or typeName is allowed
 	 */
-	public boolean isAllowedFor(String typeName) {
+	public boolean isAllowedFor(Metadatum[] types) {
 		if(typeBind.size() == 0)
 			return true;
-
-		return typeBind.contains(typeName);
+
+		if(types != null) {
+            for (Metadatum md : types) {
+                String fieldName = md.getField();
+                List<String> allowedTypes = typeBind.get(fieldName);
+                if(allowedTypes != null && allowedTypes.contains(md.value)){
+                    return true;
+                }
+            }
+        }
+
+		return false;
 	}
 
   /**

dspace-api/src/main/java/org/dspace/app/util/DCInputsReader.java

@@ -55,6 +55,7 @@ public class DCInputsReader
     static final String PAIR_TYPE_NAME = "value-pairs-name";
 
     static final String COMPLEX_DEFINITION_REF = "complex-definition-ref";
+    public static final String TYPE_BIND_FIELD_ATTRIBUTE = "field";
 
     /** The fully qualified pathname of the form definition XML file */
     private String defsFile = ConfigurationManager.getProperty("dspace.dir")
@@ -495,7 +496,13 @@ private void processPageParts(String formName, String page, Node n, Map<String,
 				} else if (tagName.equals("vocabulary")) {
 					String closedVocabularyString = getAttribute(nd, "closed");
 					field.put("closedVocabulary", closedVocabularyString);
-				}
+				} else if (tagName.equals("type-bind")){
+				    String typeField = getAttribute(nd, TYPE_BIND_FIELD_ATTRIBUTE);
+				    if(typeField == null || typeField.trim().isEmpty()){
+				        typeField = "dc.type";
+                    }
+				    field.put(TYPE_BIND_FIELD_ATTRIBUTE, typeField);
+                }
 			}
         }
         String missing = null;

dspace-api/src/main/java/org/dspace/content/DSpaceObject.java

@@ -1223,6 +1223,7 @@ private int getMetadataSchemaID(Metadatum dcv) throws SQLException
         MetadataSchema schema = MetadataSchema.find(ourContext,dcv.schema);
         if (schema == null)
         {
+            log.warn(String.format("Failed to find schema \"%s\" using dc instead.", dcv.schema));
             schemaID = MetadataSchema.DC_SCHEMA_ID;
         }
         else

dspace-api/src/main/java/org/dspace/storage/rdbms/DatabaseRegistryUpdater.java

@@ -70,6 +70,7 @@ private void updateRegistries()
             MetadataImporter.loadRegistry(base + "sword-metadata.xml", true);
             MetadataImporter.loadRegistry(base + "metashareSchema.xml", true);
             MetadataImporter.loadRegistry(base + "local-types.xml", true);
+            MetadataImporter.loadRegistry(base + "edm.xml", true);
 
             // Check if XML Workflow is enabled in workflow.cfg
             if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("xmlworkflow"))

dspace-api/src/main/java/org/dspace/submit/step/DescribeStep.java

@@ -161,10 +161,11 @@ public int doProcessing(Context context, HttpServletRequest request,
         }
 
         // Fetch the document type (dc.type)
-        String documentType = "";
-        if( (item.getMetadataByMetadataString("dc.type") != null) && (item.getMetadataByMetadataString("dc.type").length >0) )
+        Metadatum[] documentTypes = null;
+        if( (item.getMetadata(Item.ANY, "type", Item.ANY, Item.ANY) != null) && (item.getMetadata(Item.ANY, "type",
+                Item.ANY, Item.ANY).length > 0) )
         {
-            documentType = item.getMetadataByMetadataString("dc.type")[0].value;
+            documentTypes = item.getMetadata(Item.ANY, "type", Item.ANY, Item.ANY);
         }
 
         // Step 1:
@@ -208,7 +209,7 @@ public int doProcessing(Context context, HttpServletRequest request,
         for (int j = 0; j < inputs.length; j++)
         {
         	// Omit fields not allowed for this document type
-            if(!inputs[j].isAllowedFor(documentType))
+            if(!inputs[j].isAllowedFor(documentTypes))
             {
             	continue;
             }
@@ -339,7 +340,7 @@ else if (buttonPressed.equals("submit_" + fieldName + "_delete"))
             {
             	// Do not check the required attribute if it is not visible or not allowed for the document type
             	String scope = subInfo.isInWorkflow() ? DCInput.WORKFLOW_SCOPE : DCInput.SUBMISSION_SCOPE;
-                if ( !( inputs[i].isVisible(scope) && inputs[i].isAllowedFor(documentType) ) )
+                if ( !( inputs[i].isVisible(scope) && inputs[i].isAllowedFor(documentTypes) ) )
                 {
                 	continue;
                 }