more metadata-related changes

IQSS · Sep 11, 2018 · 319c8d9 · 319c8d9
1 parent 61bfb31
commit 319c8d9
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Showing 17 changed files with 262 additions and 19 deletions.
diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java
@@ -115,7 +115,7 @@ public String deactivateIdentifier(String identifier, HashMap<String, String> me
         return retString;
     }
 
-    private String getMetadataFromDvObject(String identifier, Map<String, String> metadata, DvObject dvObject) {
+    public String getMetadataFromDvObject(String identifier, Map<String, String> metadata, DvObject dvObject) {
 
         Dataset dataset = null;
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetField.java b/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;
                 }

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldType.java b/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.

diff --git a/src/main/java/edu/harvard/iq/dataverse/MetadataBlock.java b/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;

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java b/src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java
@@ -309,6 +309,10 @@ private String parseMetadataBlock(String[] values) {
         }
         mdb.setDisplayName(values[3]);
 
+        if (!StringUtils.isEmpty(values[4])) {
+            mdb.setNamespaceUri(values[4]);
+        }
+
         metadataBlockService.save(mdb);
         return mdb.getName();
     }
@@ -339,6 +343,9 @@ private String parseDatasetField(String[] values) {
             dsf.setParentDatasetFieldType(datasetFieldService.findByName(values[14]));
         }
         dsf.setMetadataBlock(dataverseService.findMDBByName(values[15]));
+        if (!StringUtils.isEmpty(values[16])) {
+          dsf.setUri(values[16]);
+        }
         datasetFieldService.save(dsf);
         return dsf.getName();
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java b/src/main/java/edu/harvard/iq/dataverse/api/Datasets.java
@@ -206,15 +206,12 @@ public Response exportDataset(@QueryParam("persistentId") String persistentId, @
 
             ExportService instance = ExportService.getInstance(settingsSvc);
 
-            InputStream xml = instance.getExport(dataset, exporter);
+            InputStream is = instance.getExport(dataset, exporter);
 
-            String mediaType = MediaType.TEXT_PLAIN;//PM - output formats appear to be either JSON or XML, unclear why text/plain is being used as default content-type.
-
-            if (instance.isXMLFormat(exporter)){
-                mediaType = MediaType.APPLICATION_XML;
-            }
+            String mediaType = instance.getMediaType(exporter);
+
             return allowCors(Response.ok()
-                    .entity(xml)
+                    .entity(is)
                     .type(mediaType).
                     build());
         } catch (Exception wr) {

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DCTermsExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DCTermsExporter.java
@@ -8,6 +8,7 @@
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.io.OutputStream;
 import javax.json.JsonObject;
+import javax.ws.rs.core.MediaType;
 import javax.xml.stream.XMLStreamException;
 
 /**

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DDIExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DDIExporter.java
@@ -10,6 +10,7 @@
 import java.io.OutputStream;
 import javax.ejb.EJB;
 import javax.json.JsonObject;
+import javax.ws.rs.core.MediaType;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamWriter;
 import javax.xml.stream.XMLOutputFactory;
@@ -44,9 +45,9 @@ public String getDisplayName() {
     @Override
     public void exportDataset(DatasetVersion version, JsonObject json, OutputStream outputStream) throws ExportException {
         try {
-		XMLStreamWriter xmlw = XMLOutputFactory.newInstance().createXMLStreamWriter(outputStream);
-		xmlw.writeStartDocument();
-		xmlw.flush();
+        XMLStreamWriter xmlw = XMLOutputFactory.newInstance().createXMLStreamWriter(outputStream);
+        xmlw.writeStartDocument();
+        xmlw.flush();
             DdiExportUtil.datasetJson2ddi(json, version, outputStream);
         } catch (XMLStreamException xse) {
             throw new ExportException ("Caught XMLStreamException performing DDI export");
@@ -74,17 +75,17 @@ public Boolean isAvailableToUsers() {
 
     @Override
     public String getXMLNameSpace() throws ExportException {
-        return this.DEFAULT_XML_NAMESPACE;   
+        return DDIExporter.DEFAULT_XML_NAMESPACE;   
     }
 
     @Override
     public String getXMLSchemaLocation() throws ExportException {
-        return this.DEFAULT_XML_SCHEMALOCATION;
+        return DDIExporter.DEFAULT_XML_SCHEMALOCATION;
     }
 
     @Override
     public String getXMLSchemaVersion() throws ExportException {
-        return this.DEFAULT_XML_VERSION;
+        return DDIExporter.DEFAULT_XML_VERSION;
     }
 
     @Override

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DataCiteExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DataCiteExporter.java
@@ -16,6 +16,7 @@
 import java.util.ResourceBundle;
 
 import javax.json.JsonObject;
+import javax.ws.rs.core.MediaType;
 
 /**
  *
@@ -45,8 +46,8 @@ public String getDisplayName() {
     public void exportDataset(DatasetVersion version, JsonObject json, OutputStream outputStream)
             throws ExportException {
         try {
-        	DataCitation dc = new DataCitation(version);
-        	
+            DataCitation dc = new DataCitation(version);
+            
             Map<String, String> metadata = dc.getDataCiteMetadata();
             String xml = DOIDataCiteRegisterService.getMetadataFromDvObject(
                     version.getDataset().getGlobalId().asString(), metadata, version.getDataset());
@@ -90,4 +91,5 @@ public String getXMLSchemaVersion() throws ExportException {
     public void setParam(String name, Object value) {
         // this exporter does not uses or supports any parameters as of now.
     }
+
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/DublinCoreExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/DublinCoreExporter.java
@@ -8,6 +8,7 @@
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.io.OutputStream;
 import javax.json.JsonObject;
+import javax.ws.rs.core.MediaType;
 import javax.xml.stream.XMLStreamException;
 
 /**

diff --git a/src/main/java/edu/harvard/iq/dataverse/export/ExportService.java b/src/main/java/edu/harvard/iq/dataverse/export/ExportService.java
@@ -33,6 +33,8 @@
 import java.util.logging.Logger;
 import javax.json.JsonObject;
 import javax.json.JsonObjectBuilder;
+import javax.ws.rs.core.MediaType;
+
 import org.apache.commons.io.IOUtils;
 
 /**
@@ -359,4 +361,19 @@ public Boolean isXMLFormat(String provider) {
         return null;
     }
 
+	public String getMediaType(String provider) {
+		 try {
+	            Iterator<Exporter> exporters = loader.iterator();
+	            while (exporters.hasNext()) {
+	                Exporter e = exporters.next();
+	                if (e.getProviderName().equals(provider)) {
+	                    return e.getMediaType();
+	                }
+	            }
+	        } catch (ServiceConfigurationError serviceError) {
+	            serviceError.printStackTrace();
+	        }
+	        return MediaType.TEXT_PLAIN;
+	}
+
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/JSONExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/JSONExporter.java
@@ -9,6 +9,7 @@
 import java.io.OutputStreamWriter;
 import java.io.Writer;
 import javax.json.JsonObject;
+import javax.ws.rs.core.MediaType;
 
 
 /**
@@ -73,4 +74,9 @@ public void setParam(String name, Object value) {
         // this exporter doesn't need/doesn't currently take any parameters
     }
 
+    @Override
+    public String getMediaType() {
+        return MediaType.APPLICATION_JSON;
+    }
+
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/OAI_OREExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/OAI_OREExporter.java
@@ -12,6 +12,7 @@
 import java.util.logging.Logger;
 
 import javax.json.JsonObject;
+import javax.ws.rs.core.MediaType;
 
 @AutoService(Exporter.class)
 public class OAI_OREExporter implements Exporter {
@@ -80,6 +81,10 @@ public String getXMLSchemaVersion() throws ExportException {
     public void setParam(String name, Object value) {
         // this exporter doesn't need/doesn't currently take any parameters
     }
-
+
+    @Override
+    public String getMediaType() {
+        return MediaType.APPLICATION_JSON;
+    }
 
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporter.java b/src/main/java/edu/harvard/iq/dataverse/export/SchemaDotOrgExporter.java
@@ -11,6 +11,7 @@
 import javax.json.Json;
 import javax.json.JsonObject;
 import javax.json.JsonReader;
+import javax.ws.rs.core.MediaType;
 
 @AutoService(Exporter.class)
 public class SchemaDotOrgExporter implements Exporter {
@@ -82,5 +83,11 @@ public String getXMLSchemaVersion() throws ExportException {
     public void setParam(String name, Object value) {
         // this exporter doesn't need/doesn't currently take any parameters
     }
+
+
+    @Override
+    public String getMediaType() {
+        return MediaType.APPLICATION_JSON;
+    }
 
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/export/spi/Exporter.java b/src/main/java/edu/harvard/iq/dataverse/export/spi/Exporter.java
@@ -9,6 +9,7 @@
 import edu.harvard.iq.dataverse.export.ExportException;
 import java.io.OutputStream;
 import javax.json.JsonObject;
+import javax.ws.rs.core.MediaType;
 
 /**
  *
@@ -43,5 +44,9 @@ but NOT close() it!
     public String getXMLSchemaVersion() throws ExportException; 
 
     public void setParam(String name, Object value);
+
+	public default String getMediaType() {
+	    return MediaType.APPLICATION_XML;
+	};
 
 }
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonLDNamespace.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonLDNamespace.java
@@ -0,0 +1,31 @@
+package edu.harvard.iq.dataverse.util.json;
+
+import edu.harvard.iq.dataverse.util.SystemConfig;
+
+public class JsonLDNamespace {
+
+	String prefix;
+
+
+	String url;
+
+	//FixMe - use a universal Dataverse URL rather than an instance one for Core terms
+	public static JsonLDNamespace dvcore = new JsonLDNamespace("dvcore", SystemConfig.getDataverseSiteUrlStatic() + "/schema/core#");
+	public static JsonLDNamespace dcterms = new JsonLDNamespace("dcterms","http://purl.org/dc/terms/");
+	public static JsonLDNamespace ore = new JsonLDNamespace("ore","http://www.openarchives.org/ore/terms/");
+	public static JsonLDNamespace schema = new JsonLDNamespace("schema","http://schema.org/");
+
+	public JsonLDNamespace(String prefix, String url) {
+		this.prefix = prefix;
+		this.url = url;
+	}
+
+	public String getPrefix() {
+		return prefix;
+	}
+
+	public String getUrl() {
+		return url;
+	}
+
+}