Add more DataCite metadata and update error handling #24 and #2917

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

@@ -54,10 +54,14 @@ public void close(){
         client.close();
     }
 
-    public String createIdentifier(String identifier, HashMap<String, String> metadata) {
+    public String createIdentifier(String identifier, HashMap<String, String> metadata, Dataset dataset) {
         DataCiteMetadataTemplate metadataTemplate = new DataCiteMetadataTemplate();
         metadataTemplate.setIdentifier(identifier.substring(identifier.indexOf(':')+1));
         metadataTemplate.setCreators(Util.getListFromStr(metadata.get("datacite.creator")));
+        metadataTemplate.setAuthors(dataset.getLatestVersion().getDatasetAuthors());
+        metadataTemplate.setDescription(dataset.getLatestVersion().getDescription());
+        metadataTemplate.setContacts(dataset.getLatestVersion().getDatasetContacts());
+        metadataTemplate.setProducers(dataset.getLatestVersion().getDatasetProducers());
         metadataTemplate.setTitle(metadata.get("datacite.title"));
         metadataTemplate.setPublisher(metadata.get("datacite.publisher"));
         metadataTemplate.setPublisherYear(metadata.get("datacite.publicationyear"));
@@ -180,6 +184,42 @@ class DataCiteMetadataTemplate {
     private String title;
     private String publisher;
     private String publisherYear;
+    private List<DatasetAuthor> authors;
+    private String description;
+    private List<String[]> contacts;
+    private List<String[]> producers;
+
+    public List<String[]> getProducers() {
+        return producers;
+    }
+
+    public void setProducers(List<String[]> producers) {
+        this.producers = producers;
+    }
+
+    public List<String[]> getContacts() {
+        return contacts;
+    }
+
+    public void setContacts(List<String[]> contacts) {
+        this.contacts = contacts;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+
+    public void setDescription(String description) {
+        this.description = description;
+    }
+
+    public List<DatasetAuthor> getAuthors() {
+        return authors;
+    }
+
+    public void setAuthors(List<DatasetAuthor> authors) {
+        this.authors = authors;
+    }
 
     public DataCiteMetadataTemplate(){
     }
@@ -207,21 +247,56 @@ public DataCiteMetadataTemplate(String xmlMetaData){
     }
 
     public String generateXML() {
-        System.out.print("in generate xml...");
         xmlMetadata = template.replace("${identifier}", this.identifier.trim())
                 .replace("${title}", this.title)
                 .replace("${publisher}", this.publisher)
-                .replace("${publisherYear}", this.publisherYear);
+                .replace("${publisherYear}", this.publisherYear)
+                .replace("${description}", this.description);
         StringBuilder creatorsElement = new StringBuilder();
-        for (String creator : creators) {
-            creator = creator.trim();
-            if (creator.length() > 0) {
-                creatorsElement.append("<creator><creatorName>");
-                creatorsElement.append(creator);
-                creatorsElement.append("</creatorName></creator>");
+        for (DatasetAuthor author : authors) {
+            creatorsElement.append("<creator><creatorName>");
+            creatorsElement.append(author.getName().getDisplayValue());
+            creatorsElement.append("</creatorName>");
+
+            if (author.getIdType() != null && author.getIdValue() != null && !author.getIdType().isEmpty() && !author.getIdValue().isEmpty() && author.getAffiliation() != null && !author.getAffiliation().getDisplayValue().isEmpty()) {
+
+                if (author.getIdType().equals("ORCID")) {   
+                    System.out.print("orcid " + author.getIdType());
+                    creatorsElement.append("<nameIdentifier schemeURI=\"http://orcid.org/\" nameIdentifierScheme=\"ORCID\">" + author.getIdValue() + "</nameIdentifier>");
+                }
+                if (author.getIdType().equals("ISNI")) {   
+                    System.out.print("isni " + author.getIdType());
+                    creatorsElement.append("<nameIdentifier schemeURI=\"http://isni.org/isni/\" nameIdentifierScheme=\"ISNI\">" + author.getIdValue() + "</nameIdentifier>");
+                }
+                if (author.getIdType().equals("LCNA")) {   
+                    System.out.print("lcna " + author.getIdType());
+                    creatorsElement.append("<nameIdentifier schemeURI=\"http://id.loc.gov/authorities/names/\" nameIdentifierScheme=\"LCNA\">" + author.getIdValue() + "</nameIdentifier>");
+                }
+            }
+            if (author.getAffiliation() != null && !author.getAffiliation().getDisplayValue().isEmpty()) {
+                creatorsElement.append("<affiliation>" + author.getAffiliation().getDisplayValue() + "</affiliation>");
             }
+            creatorsElement.append("</creator>");
         }
         xmlMetadata = xmlMetadata.replace("${creators}", creatorsElement.toString());
+
+        StringBuilder contributorsElement = new StringBuilder();
+        for (String[] contact: this.getContacts()){
+            contributorsElement.append("<contributor contributorType=\"ContactPerson\"><contributorName>" + contact[0] + "</contributorName>");
+            if (!contact[1].isEmpty()){
+                contributorsElement.append("<affiliation>" + contact[1] + "</affiliation>");
+            }
+            contributorsElement.append("</contributor>");
+        }
+        for (String[] producer: this.getProducers()){
+            contributorsElement.append("<contributor contributorType=\"Producer\"><contributorName>" + producer[0] + "</contributorName>");
+            if (!producer[1].isEmpty()){
+                contributorsElement.append("<affiliation>" + producer[1] + "</affiliation>");
+            }
+            contributorsElement.append("</contributor>");
+        }
+        System.out.print("Contributors element: " + contributorsElement.toString());
+        xmlMetadata = xmlMetadata.replace("{$contributors}", contributorsElement.toString());
         return xmlMetadata;
     }
 

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

@@ -5,6 +5,8 @@
  */
 package edu.harvard.iq.dataverse;
 
+import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
+import edu.harvard.iq.dataverse.engine.command.impl.PublishDatasetCommand;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import java.net.InetAddress;
 import java.net.UnknownHostException;
@@ -49,7 +51,7 @@ public String createIdentifier(Dataset dataset) {
         metadata.put("_status", "reserved");
         try {
             logger.log(Level.INFO, "doiDataCiteRegisterService.toString : " + doiDataCiteRegisterService.toString());
-            retString = doiDataCiteRegisterService.createIdentifier(identifier, metadata);
+            retString = doiDataCiteRegisterService.createIdentifier(identifier, metadata, dataset);
             logger.log(Level.INFO, "create DOI identifier retString : " + retString);
         } catch (Exception e) {
             logger.log(Level.INFO, "Identifier not created: create failed");
@@ -99,7 +101,7 @@ public String getIdentifierForLookup(String protocol, String authority, String s
     public String modifyIdentifier(Dataset dataset, HashMap metadata) {
         String identifier = getIdentifierFromDataset(dataset);
         try {
-            doiDataCiteRegisterService.createIdentifier(identifier, metadata);
+            doiDataCiteRegisterService.createIdentifier(identifier, metadata, dataset);
         } catch (Exception e) {
             logger.log(Level.INFO, "modifyMetadata failed");
             logger.log(Level.INFO, "String " + e.toString());
@@ -111,7 +113,7 @@ public String modifyIdentifier(Dataset dataset, HashMap metadata) {
         return identifier;
     }
 
-    public void deleteIdentifier(Dataset datasetIn) {
+    public void deleteIdentifier(Dataset datasetIn) throws RuntimeException {
         String identifier = getIdentifierFromDataset(datasetIn);
         HashMap doiMetadata = new HashMap();
         try {
@@ -240,16 +242,16 @@ private String getIdentifierFromDataset(Dataset dataset) {
         return dataset.getGlobalId();
     }
 
-    public void publicizeIdentifier(Dataset studyIn) {
+    public void publicizeIdentifier(Dataset studyIn) throws IllegalCommandException {
         updateIdentifierStatus(studyIn, "public");
     }
 
-    private void updateIdentifierStatus(Dataset dataset, String statusIn) {
+    private void updateIdentifierStatus(Dataset dataset, String statusIn) throws RuntimeException {
         String identifier = getIdentifierFromDataset(dataset);
         HashMap metadata = getUpdateMetadataFromDataset(dataset);
         metadata.put("_status", statusIn);
         try {
-            doiDataCiteRegisterService.createIdentifier(identifier, metadata);
+            doiDataCiteRegisterService.createIdentifier(identifier, metadata, dataset);
         } catch (Exception e) {
             logger.log(Level.INFO, "modifyMetadata failed");
             logger.log(Level.INFO, "String " + e.toString());

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

@@ -60,7 +60,11 @@ public void setAffiliation(DatasetField affiliation) {
     private String idType;
 
     public String getIdType() {
-        return idType;
+        if (this.idType.isEmpty() && !this.idValue.isEmpty()){
+            return ("ORCID");
+        } else {
+            return idType;
+        }        
     }
 
     public void setIdType(String idType) {
@@ -76,11 +80,6 @@ public String getIdValue() {
 
     public void setIdValue(String idValue) {
         this.idValue = idValue;
-        if (!this.idValue.isEmpty()){
-            setIdType("ORCID");
-        } else {
-            setIdType("");
-        }
     }
 
     public boolean isEmpty() {

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

@@ -52,8 +52,8 @@ public class DatasetFieldConstant implements java.io.Serializable  {
     public final static String datasetId = "datasetId";
     public final static String authorName ="authorName";
     public final static String authorAffiliation = "authorAffiliation";
-    public final static String authorIdType = "authorIdType";
-    public final static String authorIdValue = "authorIdValue";
+    public final static String authorIdType = "authorIdentifierScheme";
+    public final static String authorIdValue = "authorIdentifier";
     public final static String otherIdValue="otherIdValue";
     public final static String otherIdAgency= "otherIdAgency";
 

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

@@ -79,6 +79,7 @@
 import java.util.logging.Level;
 import javax.faces.component.UIComponent;
 import javax.faces.component.UIInput;
+import javax.faces.context.ExternalContext;
 import org.primefaces.component.tabview.TabView;
 import org.primefaces.event.TabChangeEvent;
 import org.primefaces.model.LazyDataModel;
@@ -1480,7 +1481,7 @@ public String saveGuestbookResponse(String type) {
             }
             callDownloadServlet(downloadFormat, this.selectedDownloadFile.getId());
         }
-
+        
         if (type.equals("explore")) {
             String retVal = getDataExploreURLComplete(this.selectedDownloadFile.getId());
             try {
@@ -1887,11 +1888,12 @@ private String releaseDataset(boolean minor) {
                     }
                 }
             } catch (CommandException ex) {
-                JH.addMessage(FacesMessage.SEVERITY_FATAL, JH.localize("dataset.message.publishFailure"));
+
+                JsfHelper.addErrorMessage(ex.getLocalizedMessage());
                 logger.severe(ex.getMessage());
             }
         } else {
-            JH.addMessage(FacesMessage.SEVERITY_ERROR, "Only authenticated users can release Datasets.");
+            JsfHelper.addErrorMessage("Only authenticated users can release Datasets.");
         }
         return returnToDatasetOnly();
     }

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

@@ -1,5 +1,6 @@
 package edu.harvard.iq.dataverse;
 
+import edu.harvard.iq.dataverse.util.MarkupChecker;
 import edu.harvard.iq.dataverse.util.StringUtil;
 import java.io.Serializable;
 import java.sql.Timestamp;
@@ -596,14 +597,92 @@ public String getProductionDate() {
         //todo get "Production Date" from datasetfieldvalue table
         return "Production Date";
     }
+
+    public String getDescription() {
+        for (DatasetField dsf : this.getDatasetFields()) {
+            if (dsf.getDatasetFieldType().getName().equals(DatasetFieldConstant.description)) {
+                String descriptionString = "";
+                if (dsf.getDatasetFieldCompoundValues() != null && dsf.getDatasetFieldCompoundValues().get(0) != null) {
+                    DatasetFieldCompoundValue descriptionValue = dsf.getDatasetFieldCompoundValues().get(0);
+                    for (DatasetField subField : descriptionValue.getChildDatasetFields()) {
+                        if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.descriptionText) && !subField.isEmptyForDisplay()) {
+                            descriptionString = subField.getValue();
+                        }
+                    }
+                }
+                return MarkupChecker.sanitizeBasicHTML(descriptionString);
+            }
+        }
+        return "";
+    }
+
+    public List<String[]> getDatasetContacts(){
+        List retList = new ArrayList();
+        for (DatasetField dsf : this.getDatasetFields()) {
+            Boolean addContributor = true;
+            String contributorName = "";
+            String contributorAffiliation = "";
+            if (dsf.getDatasetFieldType().getName().equals(DatasetFieldConstant.datasetContact)) {
+                for (DatasetFieldCompoundValue authorValue : dsf.getDatasetFieldCompoundValues()) {
+                    for (DatasetField subField : authorValue.getChildDatasetFields()) {
+                        if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.datasetContactName)) {
+                            if (subField.isEmptyForDisplay()) {
+                                addContributor = false;
+                            }
+                            contributorName = subField.getDisplayValue();
+                        }
+                        if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.datasetContactAffiliation)) {
+                            contributorAffiliation = subField.getDisplayValue();
+                        }
+
+                    }
+                    if (addContributor) {
+                        String[] datasetContributor = new String[] {contributorName, contributorAffiliation};
+                        retList.add(datasetContributor);
+                    }
+                }
+            }
+        }       
+        return retList;        
+    }
+
+    public List<String[]> getDatasetProducers(){
+        List retList = new ArrayList();
+        for (DatasetField dsf : this.getDatasetFields()) {
+            Boolean addContributor = true;
+            String contributorName = "";
+            String contributorAffiliation = "";
+            if (dsf.getDatasetFieldType().getName().equals(DatasetFieldConstant.producer)) {
+                for (DatasetFieldCompoundValue authorValue : dsf.getDatasetFieldCompoundValues()) {
+                    for (DatasetField subField : authorValue.getChildDatasetFields()) {
+                        if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.producerName)) {
+                            if (subField.isEmptyForDisplay()) {
+                                addContributor = false;
+                            }
+                            contributorName = subField.getDisplayValue();
+                        }
+                        if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.producerAffiliation)) {
+                            contributorAffiliation = subField.getDisplayValue();
+                        }
+
+                    }
+                    if (addContributor) {
+                        String[] datasetContributor = new String[] {contributorName, contributorAffiliation};
+                        retList.add(datasetContributor);
+                    }
+                }
+            }
+        }       
+        return retList;        
+    }
 
     public List<DatasetAuthor> getDatasetAuthors() {
         //todo get "List of Authors" from datasetfieldvalue table
         List retList = new ArrayList();
         for (DatasetField dsf : this.getDatasetFields()) {
             Boolean addAuthor = true;
             if (dsf.getDatasetFieldType().getName().equals(DatasetFieldConstant.author)) {
-                for (DatasetFieldCompoundValue authorValue : dsf.getDatasetFieldCompoundValues()) {
+                for (DatasetFieldCompoundValue authorValue : dsf.getDatasetFieldCompoundValues()) {                   
                     DatasetAuthor datasetAuthor = new DatasetAuthor();
                     for (DatasetField subField : authorValue.getChildDatasetFields()) {
                         if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.authorName)) {
@@ -615,8 +694,14 @@ public List<DatasetAuthor> getDatasetAuthors() {
                         if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.authorAffiliation)) {
                             datasetAuthor.setAffiliation(subField);
                         }
+                        if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.authorIdType)){
+                             datasetAuthor.setIdType(subField.getDisplayValue());
+                        }
+                        if (subField.getDatasetFieldType().getName().equals(DatasetFieldConstant.authorIdValue)){
+                            datasetAuthor.setIdValue(subField.getDisplayValue());
+                        }
                     }
-                    if (addAuthor) {
+                    if (addAuthor) {                       
                         retList.add(datasetAuthor);
                     }
                 }

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/PublishDatasetCommand.java

@@ -209,7 +209,13 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
         }
         if (protocol.equals("doi")
                 && doiProvider.equals("DataCite")) {
-            ctxt.doiDataCite().publicizeIdentifier(savedDataset);
+           try{
+              ctxt.doiDataCite().publicizeIdentifier(savedDataset);
+           } catch (Exception e){
+
+               throw new IllegalCommandException("This dataset may not be published because the DOI update failed. Please contact Dataverse Support for assistance.", this);
+           }
+
         }
 
         return savedDataset;

src/main/resources/edu/harvard/iq/dataverse/datacite_metadata_template.xml

@@ -9,4 +9,9 @@
     </titles>
     <publisher>${publisher}</publisher>
     <publicationYear>${publisherYear}</publicationYear>
+    <resourceType resourceTypeGeneral="Dataset"/>
+    <descriptions>
+        <description descriptionType="Abstract">${description}</description>
+    </descriptions>
+    <contributors>{$contributors}</contributors>
 </resource>