IQSS · kcondon · Jul 27, 2018 · Jun 28, 2018 · Jul 13, 2018 · Jul 23, 2018
diff --git a/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java b/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java
@@ -37,15 +37,16 @@ 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"));
     }
-    
+
     public String createIdentifierLocal(String identifier, Map<String, String> metadata, DvObject dvObject) {
+
         String xmlMetadata = getMetadataFromDvObject(identifier, metadata, dvObject);
         String status = metadata.get("_status").trim();
         String target = metadata.get("_target");
@@ -65,9 +66,10 @@ public String createIdentifierLocal(String identifier, Map<String, String> metad
             rc.setUrl(target);
         }
         retString = "success to reserved " + identifier;
+
         return retString;
     }
-    
+
     public String registerIdentifier(String identifier, Map<String, String> metadata, DvObject dvObject) throws IOException {
         String retString = "";
         String xmlMetadata = getMetadataFromDvObject(identifier, metadata, dvObject);
@@ -88,63 +90,69 @@ public String registerIdentifier(String identifier, Map<String, String> metadata
             } catch (UnsupportedEncodingException ex) {
                 Logger.getLogger(DOIDataCiteRegisterService.class.getName()).log(Level.SEVERE, null, ex);
             }
-        } else{
+        } else {
             try (DataCiteRESTfullClient client = openClient()) {
                 retString = client.postMetadata(xmlMetadata);
                 client.postUrl(identifier.substring(identifier.indexOf(":") + 1), target);
             } catch (UnsupportedEncodingException ex) {
                 Logger.getLogger(DOIDataCiteRegisterService.class.getName()).log(Level.SEVERE, null, ex);
-            }           
+            }
         }
         return retString;
     }
-
-    public String deactivateIdentifier (String identifier, HashMap<String, String> metadata, DvObject dvObject){
-        String retString = "";
-                    DOIDataCiteRegisterCache rc = findByDOI(identifier);
-            try (DataCiteRESTfullClient client = openClient()) {
-                if (rc != null) {
-                    rc.setStatus("unavailable");
-                    retString = client.inactiveDataset(identifier.substring(identifier.indexOf(":") + 1));
-                }
-            } catch (IOException io) {
 
+    public String deactivateIdentifier(String identifier, HashMap<String, String> metadata, DvObject dvObject) {
+        String retString = "";
+        DOIDataCiteRegisterCache rc = findByDOI(identifier);
+        try (DataCiteRESTfullClient client = openClient()) {
+            if (rc != null) {
+                rc.setStatus("unavailable");
+                retString = client.inactiveDataset(identifier.substring(identifier.indexOf(":") + 1));
             }
-            return retString;
+        } catch (IOException io) {
+
+        }
+        return retString;
     }
-     
-    private String getMetadataFromDvObject(String identifier, Map<String, String> metadata,DvObject dvObject) {
-        
+
+    private String getMetadataFromDvObject(String identifier, Map<String, String> metadata, DvObject dvObject) {
+
         Dataset dataset = null;
-        
-        if (dvObject instanceof Dataset){
+
+        if (dvObject instanceof Dataset) {
             dataset = (Dataset) dvObject;
         } else {
             dataset = (Dataset) dvObject.getOwner();
-        }        
-        
+        }
+
         DataCiteMetadataTemplate metadataTemplate = new DataCiteMetadataTemplate();
-        metadataTemplate.setIdentifier(identifier.substring(identifier.indexOf(':') + 1));       
+        metadataTemplate.setIdentifier(identifier.substring(identifier.indexOf(':') + 1));
         metadataTemplate.setCreators(Util.getListFromStr(metadata.get("datacite.creator")));
         metadataTemplate.setAuthors(dataset.getLatestVersion().getDatasetAuthors());
         if (dvObject.isInstanceofDataset()) {
             metadataTemplate.setDescription(dataset.getLatestVersion().getDescriptionPlainText());
         }
         if (dvObject.isInstanceofDataFile()) {
             DataFile df = (DataFile) dvObject;
-            String fileDescription =df.getDescription();
-            metadataTemplate.setDescription(fileDescription == null ? "" :fileDescription );
+            String fileDescription = df.getDescription();
+            metadataTemplate.setDescription(fileDescription == null ? "" : fileDescription);
+            String datasetPid = df.getOwner().getGlobalId().asString();
+            metadataTemplate.setDatasetIdentifier(datasetPid);
+        } else {
+            metadataTemplate.setDatasetIdentifier("");
         }
+
         metadataTemplate.setContacts(dataset.getLatestVersion().getDatasetContacts());
         metadataTemplate.setProducers(dataset.getLatestVersion().getDatasetProducers());
         metadataTemplate.setTitle(dvObject.getDisplayName());
-        String producerString =  dataverseService.findRootDataverse().getName();
+        String producerString = dataverseService.findRootDataverse().getName();
         if (producerString.isEmpty()) {
             producerString = ":unav";
         }
         metadataTemplate.setPublisher(producerString);
         metadataTemplate.setPublisherYear(metadata.get("datacite.publicationyear"));
-        String xmlMetadata = metadataTemplate.generateXML();
+
+        String xmlMetadata = metadataTemplate.generateXML(dvObject);
         logger.log(Level.FINE, "XML to send to DataCite: {0}", xmlMetadata);
         return xmlMetadata;
     }
@@ -188,14 +196,14 @@ public String modifyIdentifier(String identifier, HashMap<String, String> metada
                 try (DataCiteRESTfullClient client = openClient()) {
                     retString = client.postMetadata(xmlMetadata);
                     client.postUrl(identifier.substring(identifier.indexOf(":") + 1), target);
-                    
+
                 } catch (UnsupportedEncodingException ex) {
                     logger.log(Level.SEVERE, null, ex);
-                    
-                } catch ( RuntimeException rte ) {
+
+                } catch (RuntimeException rte) {
                     logger.log(Level.SEVERE, "Error creating DOI at DataCite: {0}", rte.getMessage());
                     logger.log(Level.SEVERE, "Exception", rte);
-                    
+
                 }
             }
         } else if (status.equals("unavailable")) {
@@ -281,6 +289,8 @@ class DataCiteMetadataTemplate {
 
     private String xmlMetadata;
     private String identifier;
+    private String datasetIdentifier;
+    private List<String> datafileIdentifiers;
     private List<String> creators;
     private String title;
     private String publisher;
@@ -325,6 +335,14 @@ public void setAuthors(List<DatasetAuthor> authors) {
     public DataCiteMetadataTemplate() {
     }
 
+    public List<String> getDatafileIdentifiers() {
+        return datafileIdentifiers;
+    }
+
+    public void setDatafileIdentifiers(List<String> datafileIdentifiers) {
+        this.datafileIdentifiers = datafileIdentifiers;
+    }
+
     public DataCiteMetadataTemplate(String xmlMetaData) {
         this.xmlMetadata = xmlMetaData;
         Document doc = Jsoup.parseBodyFragment(xmlMetaData);
@@ -351,7 +369,7 @@ public DataCiteMetadataTemplate(String xmlMetaData) {
         }
     }
 
-    public String generateXML() {
+    public String generateXML(DvObject dvObject) {
         // Can't use "UNKNOWN" here because DataCite will respond with "[facet 'pattern'] the value 'unknown' is not accepted by the pattern '[\d]{4}'"
         String publisherYearFinal = "9999";
         // FIXME: Investigate why this.publisherYear is sometimes null now that pull request #4606 has been merged.
@@ -406,10 +424,69 @@ public String generateXML() {
             }
             contributorsElement.append("</contributor>");
         }
+
+        String relIdentifiers = generateRelatedIdentifiers(dvObject);
+
+        xmlMetadata = xmlMetadata.replace("${relatedIdentifiers}", relIdentifiers);
+
         xmlMetadata = xmlMetadata.replace("{$contributors}", contributorsElement.toString());
         return xmlMetadata;
     }
 
+    private String generateRelatedIdentifiers(DvObject dvObject) {
+
+        StringBuilder sb = new StringBuilder();
+        if (dvObject.isInstanceofDataset()) {
+            Dataset dataset = (Dataset) dvObject;
+            if (!dataset.getFiles().isEmpty() && !(dataset.getFiles().get(0).getIdentifier() == null)) {
+
+                datafileIdentifiers = new ArrayList<>();
+                for (DataFile dataFile : dataset.getFiles()) {
+                    if (!dataFile.getGlobalId().asString().isEmpty()) {
+                        if (sb.toString().isEmpty()) {
+                            sb.append("<relatedIdentifiers>");
+                        }
+                        sb.append("<relatedIdentifier relatedIdentifierType=\"DOI\" relationType=\"HasPart\">" + dataFile.getGlobalId() + "</relatedIdentifier>");
+                    }
+                }
+
+                if (!sb.toString().isEmpty()) {
+                    sb.append("</relatedIdentifiers>");
+                }
+            }
+        } else if (dvObject.isInstanceofDataFile()) {
+            DataFile df = (DataFile) dvObject;
+            sb.append("<relatedIdentifiers>");
+            sb.append("<relatedIdentifier relatedIdentifierType=\"DOI\" relationType=\"IsPartOf\""
+                    + ">" + df.getOwner().getGlobalId() + "</relatedIdentifier>");
+            sb.append("</relatedIdentifiers>");
+        }
+        return sb.toString();
+    }
+
+    public void generateFileIdentifiers(DvObject dvObject) {
+
+        if (dvObject.isInstanceofDataset()) {
+            Dataset dataset = (Dataset) dvObject;
+
+            if (!dataset.getFiles().isEmpty() && !(dataset.getFiles().get(0).getIdentifier() == null)) {
+
+                datafileIdentifiers = new ArrayList<>();
+                for (DataFile dataFile : dataset.getFiles()) {
+                    datafileIdentifiers.add(dataFile.getIdentifier());
+                    int x = xmlMetadata.indexOf("</relatedIdentifiers>") - 1;
+                    xmlMetadata = xmlMetadata.replace("{relatedIdentifier}", dataFile.getIdentifier());
+                    xmlMetadata = xmlMetadata.substring(0, x) + "<relatedIdentifier relatedIdentifierType=\"hasPart\" "
+                            + "relationType=\"doi\">${relatedIdentifier}</relatedIdentifier>" + template.substring(x, template.length() - 1);
+
+                }
+
+            } else {
+                xmlMetadata = xmlMetadata.replace("<relatedIdentifier relatedIdentifierType=\"hasPart\" relationType=\"doi\">${relatedIdentifier}</relatedIdentifier>", "");
+            }
+        }
+    }
+
     public static String getTemplate() {
         return template;
     }
@@ -426,6 +503,10 @@ public void setIdentifier(String identifier) {
         this.identifier = identifier;
     }
 
+    public void setDatasetIdentifier(String datasetIdentifier) {
+        this.datasetIdentifier = datasetIdentifier;
+    }
+
     public List<String> getCreators() {
         return creators;
     }

diff --git a/src/main/java/edu/harvard/iq/dataverse/DataFile.java b/src/main/java/edu/harvard/iq/dataverse/DataFile.java
@@ -401,14 +401,6 @@ public void setOwner(Dataset dataset) {
         super.setOwner(dataset);
     }
 
-//    public String getStorageIdentifier() {
-//        return this.fileSystemName;
-//    }
-//
-//    public void setStorageIdentifier(String storageIdentifier) {
-//        this.fileSystemName = storageIdentifier;
-//    }
-
     public String getDescription() {
         FileMetadata fmd = getLatestFileMetadata();
 

diff --git a/.../java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java b/.../java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java
@@ -182,15 +182,15 @@ private void publicizeExternalIdentifier(Dataset dataset, CommandContext ctxt) t
         GlobalIdServiceBean idServiceBean = GlobalIdServiceBean.getBean(protocol, ctxt);
         if ( idServiceBean != null ){
             try {
-                idServiceBean.publicizeIdentifier(dataset);
-                dataset.setGlobalIdCreateTime(new Date()); // TODO these two methods should be in the responsibility of the idServiceBean.
-                dataset.setIdentifierRegistered(true);
                 for (DataFile df : dataset.getFiles()) {
                     logger.log(Level.FINE, "registering global id for file {0}", df.getId());
                     idServiceBean.publicizeIdentifier(df);
                     df.setGlobalIdCreateTime(getTimestamp());
                     df.setIdentifierRegistered(true);
                 }
+                idServiceBean.publicizeIdentifier(dataset);
+                dataset.setGlobalIdCreateTime(new Date()); // TODO these two methods should be in the responsibility of the idServiceBean.
+                dataset.setIdentifierRegistered(true);
             } catch (Throwable e) {
                 ctxt.datasets().removeDatasetLocks(dataset, DatasetLock.Reason.pidRegister);
                 throw new CommandException(BundleUtil.getStringFromBundle("dataset.publish.error", idServiceBean.getProviderInformation()),this); 

diff --git a/src/main/resources/edu/harvard/iq/dataverse/datacite_metadata_template.xml b/src/main/resources/edu/harvard/iq/dataverse/datacite_metadata_template.xml
@@ -10,6 +10,7 @@
     <publisher>${publisher}</publisher>
     <publicationYear>${publisherYear}</publicationYear>
     <resourceType resourceTypeGeneral="Dataset"/>
+    ${relatedIdentifiers}
     <descriptions>
         <description descriptionType="Abstract">${description}</description>
     </descriptions>

diff --git a/src/test/java/edu/harvard/iq/dataverse/api/DataCiteIT.java b/src/test/java/edu/harvard/iq/dataverse/api/DataCiteIT.java
@@ -10,7 +10,8 @@
  * These tests will only work if you are using "DataCite" rather than "EZID" for
  * your :DoiProvider and have done all the other related setup to switch from
  * EZID, including setting JVM options. Look for DataCite in the dev guide for
- * more tips.
+ * more tips. You should switch away from EZID for dev anyway because it's going
+ * away: https://www.cdlib.org/cdlinfo/2017/08/04/ezid-doi-service-is-evolving/
  */
 public class DataCiteIT {
 
@@ -35,6 +36,10 @@ public void testCreateAndPublishDataset() {
         createDataset.prettyPrint();
         String datasetPersistentId = UtilIT.getDatasetPersistentIdFromResponse(createDataset);
 
+        Response uploadFile = UtilIT.uploadRandomFile(datasetPersistentId, apiToken);
+        uploadFile.then().assertThat()
+                .statusCode(201);
+
         Response publishDataverse = UtilIT.publishDataverseViaSword(dataverseAlias, apiToken);
         assertEquals(200, publishDataverse.getStatusCode());
 

diff --git a/workingDataCiteMetadataTemplate-Files.xml b/workingDataCiteMetadataTemplate-Files.xml