DANS/Local PermaLink PID Provider

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

@@ -5,6 +5,7 @@
  */
 package edu.harvard.iq.dataverse;
 
+import edu.harvard.iq.dataverse.pidproviders.PidUtil;
 import edu.harvard.iq.dataverse.util.StringUtil;
 import java.io.IOException;
 import java.io.PrintWriter;
@@ -21,7 +22,7 @@
 public class CitationServlet extends HttpServlet {
 
     @EJB
-    DatasetServiceBean datasetService;    
+    DvObjectServiceBean dvObjectService;
 
     /**
      * Processes requests for both HTTP <code>GET</code> and <code>POST</code>
@@ -37,10 +38,14 @@ protected void processRequest(HttpServletRequest request, HttpServletResponse re
 
         String persistentId = request.getParameter("persistentId");
         if (persistentId != null) {
-            Dataset ds = datasetService.findByGlobalId(persistentId);        
-            if (ds != null) {
-                response.sendRedirect("dataset.xhtml?persistentId=" + persistentId);
-                return;        
+            DvObject dob = dvObjectService.findByGlobalId(PidUtil.parseAsGlobalID(persistentId));
+            if (dob != null) {
+                if (dob instanceof Dataset) {
+                    response.sendRedirect("dataset.xhtml?persistentId=" + persistentId);
+                } else if (dob instanceof DataFile) {
+                    response.sendRedirect("file.xhtml?persistentId=" + persistentId);
+                }
+                return;
             }
         }
         response.sendError(HttpServletResponse.SC_NOT_FOUND);

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

@@ -45,7 +45,7 @@ public class DOIDataCiteRegisterService {
     DataverseServiceBean dataverseService;
 
     @EJB
-    DOIDataCiteServiceBean doiDataCiteServiceBean;
+    AbstractGlobalIdServiceBean doiDataCiteServiceBean;
 
 
     //A singleton since it, and the httpClient in it can be reused.

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

@@ -10,19 +10,23 @@
 import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
+import javax.annotation.PostConstruct;
 import javax.ejb.EJB;
 import javax.ejb.Stateless;
 
 import org.apache.commons.httpclient.HttpException;
 import org.apache.commons.httpclient.HttpStatus;
 
+import edu.harvard.iq.dataverse.settings.SettingsServiceBean.Key;
+
 
 /**
  *
  * @author luopc
  */
 @Stateless
-public class DOIDataCiteServiceBean extends AbstractGlobalIdServiceBean {
+public class DOIDataCiteServiceBean extends DOIServiceBean {
 
     private static final Logger logger = Logger.getLogger(DOIDataCiteServiceBean.class.getCanonicalName());
 
@@ -34,22 +38,20 @@ public class DOIDataCiteServiceBean extends AbstractGlobalIdServiceBean {
     @EJB
     DOIDataCiteRegisterService doiDataCiteRegisterService;
 
-    public DOIDataCiteServiceBean() {
+    @PostConstruct
+    private void init() {
+        String doiProvider = settingsService.getValueForKey(Key.DoiProvider, "");
+        if("DataCite".equals(doiProvider)) {
+            isConfigured=true;
+        }
     }
 
     @Override
     public boolean registerWhenPublished() {
         return false;
     }
 
-    @Override
-    public boolean alreadyExists(DvObject dvObject) {
-        if(dvObject==null) {
-            logger.severe("Null DvObject sent to alreadyExists().");
-            return false;
-        }
-        return alreadyExists(dvObject.getGlobalId());
-    }
+
 
     @Override
     public boolean alreadyExists(GlobalId pid) {
@@ -103,29 +105,6 @@ public HashMap getIdentifierMetadata(DvObject dvObject) {
     }
 
 
-    /**
-     * Looks up the metadata for a Global Identifier
-     * @param protocol the identifier system, e.g. "doi"
-     * @param authority the namespace that the authority manages in the identifier system
-     * @param identifier the local identifier part
-     * @return a Map of metadata. It is empty when the lookup failed, e.g. when
-     * the identifier does not exist.
-     */
-    @Override
-    public HashMap<String, String> lookupMetadataFromIdentifier(String protocol, String authority, String identifier) {
-        logger.log(Level.FINE,"lookupMetadataFromIdentifier");
-        String identifierOut = getIdentifierForLookup(protocol, authority, identifier);
-        HashMap<String, String> metadata = new HashMap<>();
-        try {
-            metadata = doiDataCiteRegisterService.getMetadata(identifierOut);
-        } catch (Exception e) {
-            logger.log(Level.WARNING, "None existing so we can use this identifier");
-            logger.log(Level.WARNING, "identifier: {0}", identifierOut);
-        }
-        return metadata;
-    }
-
-
     /**
      * Modifies the DOI metadata for a Dataset
      * @param dvObject the dvObject whose metadata needs to be modified
@@ -277,5 +256,7 @@ public List<String> getProviderInformation(){
         return providerInfo;
     }
 
+    //PID recognition
+
 
 }

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

@@ -1,19 +1,23 @@
 package edu.harvard.iq.dataverse;
 
+import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
+import edu.harvard.iq.dataverse.settings.SettingsServiceBean.Key;
 import edu.ucsb.nceas.ezid.EZIDException;
 import edu.ucsb.nceas.ezid.EZIDService;
 import edu.ucsb.nceas.ezid.EZIDServiceRequest;
 import java.util.*;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
+import javax.ejb.EJB;
 import javax.ejb.Stateless;
 
 /**
  *
  * @author skraffmiller
  */
 @Stateless
-public class DOIEZIdServiceBean extends AbstractGlobalIdServiceBean {
+public class DOIEZIdServiceBean extends DOIServiceBean {
 
     EZIDService ezidService;
     EZIDServiceRequest ezidServiceRequest;
@@ -23,16 +27,20 @@ public class DOIEZIdServiceBean extends AbstractGlobalIdServiceBean {
     // get username and password from system properties
     private String USERNAME = "";
     private String PASSWORD = "";
-
     public DOIEZIdServiceBean() {
         logger.log(Level.FINE,"Constructor");
-        baseURLString = System.getProperty("doi.baseurlstring");
-        ezidService = new EZIDService(baseURLString);
-        USERNAME = System.getProperty("doi.username");
-        PASSWORD = System.getProperty("doi.password");
-        logger.log(Level.FINE, "Using baseURLString {0}", baseURLString);
+       logger.log(Level.FINE, "Using baseURLString {0}", baseURLString);
         try {
-            ezidService.login(USERNAME, PASSWORD);
+            String doiProvider = settingsService.getValueForKey(Key.DoiProvider, "");
+            if ("EZID".equals(doiProvider)) {
+                //Guessing these are SYstem.getProperty rather than using settingsService because this is a constructir rather than a @PostConstruct method
+                baseURLString = System.getProperty("doi.baseurlstring");
+                ezidService = new EZIDService(baseURLString);
+                USERNAME = System.getProperty("doi.username");
+                PASSWORD = System.getProperty("doi.password");
+                ezidService.login(USERNAME, PASSWORD);
+                isConfigured = true;
+            }
         } catch (EZIDException e) {
             logger.log(Level.WARNING, "login failed ");
             logger.log(Level.WARNING, "Exception String: {0}", e.toString());
@@ -102,32 +110,6 @@ public Map<String, String> getIdentifierMetadata(DvObject dvObject) {
         return metadata;
     }
 
-    /**
-     * Looks up the metadata for a Global Identifier
-     *
-     * @param protocol the identifier system, e.g. "doi"
-     * @param authority the namespace that the authority manages in the
-     * identifier system
-     * identifier part
-     * @param identifier the local identifier part
-     * @return a Map of metadata. It is empty when the lookup failed, e.g. when
-     * the identifier does not exist.
-     */
-    @Override
-    public HashMap<String, String> lookupMetadataFromIdentifier(String protocol, String authority, String identifier) {
-        logger.log(Level.FINE,"lookupMetadataFromIdentifier");
-        String identifierOut = getIdentifierForLookup(protocol, authority, identifier);
-        HashMap<String, String> metadata = new HashMap<>();
-        try {
-            metadata = ezidService.getMetadata(identifierOut);
-        } catch (EZIDException e) {
-            logger.log(Level.FINE, "None existing so we can use this identifier");
-            logger.log(Level.FINE, "identifier: {0}", identifierOut);
-            return metadata;
-        }
-        return metadata;
-    }
-
     /**
      * Modifies the EZID metadata for a Dataset
      *

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

@@ -0,0 +1,51 @@
+package edu.harvard.iq.dataverse;
+
+public abstract class DOIServiceBean extends AbstractGlobalIdServiceBean {
+
+    public static final String DOI_PROTOCOL = "doi";
+    public static final String DOI_RESOLVER_URL = "https://doi.org/";
+    public static final String HTTP_DOI_RESOLVER_URL = "http://doi.org/";
+    public static final String DXDOI_RESOLVER_URL = "https://dx.doi.org/";
+    public static final String HTTP_DXDOI_RESOLVER_URL = "http://dx.doi.org/";
+    public DOIServiceBean() {
+        super();
+    }
+
+    @Override
+    public GlobalId parsePersistentId(String pidString) {
+        if (pidString.startsWith(DOI_RESOLVER_URL)) {
+            pidString = pidString.replace(DOI_RESOLVER_URL,
+                    (DOI_PROTOCOL + ":"));
+        } else if (pidString.startsWith(HTTP_DOI_RESOLVER_URL)) {
+            pidString = pidString.replace(HTTP_DOI_RESOLVER_URL,
+                    (DOI_PROTOCOL + ":"));
+        } else if (pidString.startsWith(DXDOI_RESOLVER_URL)) {
+            pidString = pidString.replace(DXDOI_RESOLVER_URL,
+                    (DOI_PROTOCOL + ":"));
+        }
+        return super.parsePersistentId(pidString);
+    }
+
+    public GlobalId parsePersistentId(String protocol, String identifierString) {
+        if (!DOI_PROTOCOL.equals(protocol)) {
+            return null;
+        }
+        GlobalId globalId = super.parsePersistentId(protocol, identifierString);
+        if (globalId!=null && !GlobalIdServiceBean.checkDOIAuthority(globalId.getAuthority())) {
+            return null;
+        }
+        return globalId;
+    }
+
+    public GlobalId parsePersistentId(String protocol, String authority, String identifier) {
+        if (!DOI_PROTOCOL.equals(protocol)) {
+            return null;
+        }
+        return super.parsePersistentId(protocol, authority, identifier);
+    }
+
+    public String getUrlPrefix() {
+        return DOI_RESOLVER_URL;
+    }
+
+}

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

@@ -207,7 +207,7 @@ public String toString(boolean html, boolean anonymized) {
 
         if (persistentId != null) {
         	// always show url format
-            citationList.add(formatURL(persistentId.toURL().toString(), persistentId.toURL().toString(), html)); 
+            citationList.add(formatURL(persistentId.asURL(), persistentId.asURL(), html)); 
         }
         citationList.add(formatString(publisher, html));
         citationList.add(version);
@@ -298,7 +298,7 @@ public void writeAsBibtexCitation(OutputStream os) throws IOException {
         out.write(persistentId.getIdentifier());
         out.write("},\r\n");
         out.write("url = {");
-        out.write(persistentId.toURL().toString());
+        out.write(persistentId.asURL());
         out.write("}\r\n");
         out.write("}\r\n");
         out.flush();
@@ -387,7 +387,7 @@ public void writeAsRISCitation(OutputStream os) throws IOException {
 
         out.write("SE  - " + date + "\r\n");
 
-        out.write("UR  - " + persistentId.toURL().toString() + "\r\n");
+        out.write("UR  - " + persistentId.asURL() + "\r\n");
         out.write("PB  - " + publisher + "\r\n");
 
         // a DataFile citation also includes filename und UNF, if applicable:
@@ -584,7 +584,7 @@ private void createEndNoteXML(XMLStreamWriter xmlw) throws XMLStreamException {
         xmlw.writeStartElement("urls");
         xmlw.writeStartElement("related-urls");
         xmlw.writeStartElement("url");
-        xmlw.writeCharacters(getPersistentId().toURL().toString());
+        xmlw.writeCharacters(getPersistentId().asURL());
         xmlw.writeEndElement(); // url
         xmlw.writeEndElement(); // related-urls
         xmlw.writeEndElement(); // urls
@@ -781,18 +781,13 @@ private GlobalId getPIDFrom(DatasetVersion dsv, DvObject dv) {
                 || HarvestingClient.HARVEST_STYLE_ICPSR.equals(dsv.getDataset().getHarvestedFrom().getHarvestStyle())
                 || HarvestingClient.HARVEST_STYLE_DATAVERSE
                         .equals(dsv.getDataset().getHarvestedFrom().getHarvestStyle())) {
-                // creating a global id like this:
-                // persistentId = new GlobalId(dv.getGlobalId());
-                // you end up doing new GlobalId((New GlobalId(dv)).toString())
-                // - doing an extra formatting-and-parsing-again
-                // This achieves the same thing:
                 if(!isDirect()) {
                 if (!StringUtils.isEmpty(dsv.getDataset().getIdentifier())) {
-                    return new GlobalId(dsv.getDataset());
+                    return dsv.getDataset().getGlobalId();
                 }
                 } else {
                 if (!StringUtils.isEmpty(dv.getIdentifier())) {
-                    return new GlobalId(dv);
+                    return dv.getGlobalId();
                 }
             }
         }

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

@@ -956,7 +956,7 @@ public JsonObject asGsonObject(boolean prettyPrint){
         // https://github.com/IQSS/dataverse/issues/761, https://github.com/IQSS/dataverse/issues/2110, https://github.com/IQSS/dataverse/issues/3191
         //
         datasetMap.put("title", thisFileMetadata.getDatasetVersion().getTitle());
-        datasetMap.put("persistentId", getOwner().getGlobalIdString());
+        datasetMap.put("persistentId", getOwner().getGlobalId().asString());
         datasetMap.put("url", getOwner().getPersistentURL());
         datasetMap.put("version", thisFileMetadata.getDatasetVersion().getSemanticVersion());
         datasetMap.put("id", getOwner().getId());
@@ -1034,6 +1034,10 @@ public String getCreateDateFormattedYYYYMMDD() {
         return null;
     }
 
+    @Override
+    public String getTargetUrl() {
+        return DataFile.TARGET_URL;
+    }
 
 } // end of class