IQSS/9544 - Migrate API fixes

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

@@ -113,18 +113,20 @@ public Map<String, String> getMetadataForTargetURL(DvObject dvObject) {
     }
 
     @Override
-    public boolean alreadyExists(DvObject dvo) throws Exception {
+    public boolean alreadyRegistered(DvObject dvo) throws Exception {
         if(dvo==null) {
-            logger.severe("Null DvObject sent to alreadyExists().");
+            logger.severe("Null DvObject sent to alreadyRegistered().");
             return false;
         }
         GlobalId globalId = dvo.getGlobalId();
         if(globalId == null) {
             return false;
         }
-        return alreadyExists(globalId);
+        return alreadyRegistered(globalId, false);
     }
 
+    public abstract boolean alreadyRegistered(GlobalId globalId, boolean noProviderDefault) throws Exception;
+
     /*
      * ToDo: the DvObject being sent in provides partial support for the case where
      * it has a different authority/protocol than what is configured (i.e. a legacy
@@ -188,7 +190,7 @@ public boolean isGlobalIdUnique(GlobalId globalId) {
 
         // not in local DB, look in the persistent identifier service
         try {
-            return ! alreadyExists(globalId);
+            return ! alreadyRegistered(globalId, false);
         } catch (Exception e){
             //we can live with failure - means identifier not found remotely
         }

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

@@ -44,23 +44,22 @@ public boolean registerWhenPublished() {
 
 
     @Override
-    public boolean alreadyExists(GlobalId pid) {
-        logger.log(Level.FINE,"alreadyExists");
+    public boolean alreadyRegistered(GlobalId pid, boolean noProviderDefault) {
+        logger.log(Level.FINE,"alreadyRegistered");
         if(pid==null || pid.asString().isEmpty()) {
             logger.fine("No identifier sent.");
             return false;
         }
-        boolean alreadyExists;
+        boolean alreadyRegistered;
         String identifier = pid.asString();
         try{
-            alreadyExists = doiDataCiteRegisterService.testDOIExists(identifier); 
+            alreadyRegistered = doiDataCiteRegisterService.testDOIExists(identifier); 
         } catch (Exception e){
-            logger.log(Level.WARNING, "alreadyExists failed");
+            logger.log(Level.WARNING, "alreadyRegistered failed");
             return false;
         }
-        return  alreadyExists;
+        return  alreadyRegistered;
     }
-
 
     @Override
     public String createIdentifier(DvObject dvObject) throws Exception {

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

@@ -63,19 +63,10 @@ public boolean registerWhenPublished() {
     }
 
     @Override
-    public boolean alreadyExists(DvObject dvObject) throws Exception {
-        if(dvObject==null) {
-            logger.severe("Null DvObject sent to alreadyExists().");
-            return false;
-        }
-        return alreadyExists(dvObject.getGlobalId());
-    }
-
-    @Override
-    public boolean alreadyExists(GlobalId pid) throws Exception {
-        logger.log(Level.FINE,"alreadyExists");
+    public boolean alreadyRegistered(GlobalId pid, boolean noProviderDefault) throws Exception {
+        logger.log(Level.FINE,"alreadyRegistered");
         try {
-            HashMap<String, String> result = ezidService.getMetadata(pid.asString());            
+            HashMap<String, String> result = ezidService.getMetadata(pid.asString());
             return result != null && !result.isEmpty();
             // TODO just check for HTTP status code 200/404, sadly the status code is swept under the carpet
         } catch (EZIDException e ){
@@ -87,7 +78,7 @@ public boolean alreadyExists(GlobalId pid) throws Exception {
             if (e.getLocalizedMessage().contains("no such identifier")){
                 return false;
             }
-            logger.log(Level.WARNING, "alreadyExists failed");
+            logger.log(Level.WARNING, "alreadyRegistered failed");
             logger.log(Level.WARNING, "getIdentifier(dvObject) {0}", pid.asString());
             logger.log(Level.WARNING, "String {0}", e.toString());
             logger.log(Level.WARNING, "localized message {0}", e.getLocalizedMessage());

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

@@ -75,5 +75,4 @@ public boolean isConfigured() {
     protected String getProviderKeyName() {
         return null;
     }
-
 }

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

@@ -1084,38 +1084,6 @@ public List<Long> selectFilesWithMissingOriginalSizes() {
      * @param idServiceBean
      * @return  {@code true} iff the global identifier is unique.
      */
-/*    public boolean isGlobalIdUnique(String userIdentifier, DataFile datafile, GlobalIdServiceBean idServiceBean) {
-        String testProtocol = "";
-        String testAuthority = "";
-        if (datafile.getAuthority() != null){
-            testAuthority = datafile.getAuthority();
-        } else {
-            testAuthority = settingsService.getValueForKey(SettingsServiceBean.Key.Authority);
-        }
-        if (datafile.getProtocol() != null){
-            testProtocol = datafile.getProtocol();
-        } else {
-            testProtocol = settingsService.getValueForKey(SettingsServiceBean.Key.Protocol);
-        }
-
-        boolean u = em.createNamedQuery("DvObject.findByProtocolIdentifierAuthority")
-            .setParameter("protocol", testProtocol)
-            .setParameter("authority", testAuthority)
-            .setParameter("identifier",userIdentifier)
-            .getResultList().isEmpty();
-
-        try{
-            if (idServiceBean.alreadyExists(new GlobalId(testProtocol, testAuthority, userIdentifier))) {
-                u = false;
-            }
-        } catch (Exception e){
-            //we can live with failure - means identifier not found remotely
-        }
-
-
-        return u;
-    }
-*/    
     public void finalizeFileDelete(Long dataFileId, String storageLocation) throws IOException {
         // Verify that the DataFile no longer exists: 
         if (find(dataFileId) != null) {

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

@@ -169,10 +169,14 @@ private Long runFindIdByGlobalId(Query query, GlobalId gid, DvObject.DType dtype
     }
 
     public DvObject findByGlobalId(GlobalId globalId) {
-        return (DvObject) em.createNamedQuery("DvObject.findByProtocolIdentifierAuthority")
-            .setParameter("identifier", globalId.getIdentifier())
-            .setParameter("authority", globalId.getAuthority())
-            .setParameter("protocol", globalId.getProtocol()).getSingleResult();
+        try {
+            return (DvObject) em.createNamedQuery("DvObject.findByProtocolIdentifierAuthority")
+                    .setParameter("identifier", globalId.getIdentifier())
+                    .setParameter("authority", globalId.getAuthority()).setParameter("protocol", globalId.getProtocol())
+                    .getSingleResult();
+        } catch (NoResultException nre) {
+            return null;
+        }
     }
 
     public boolean isGlobalIdLocallyUnique(GlobalId globalId) {

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

@@ -15,10 +15,25 @@ public interface GlobalIdServiceBean {
 
     static final Logger logger = Logger.getLogger(GlobalIdServiceBean.class.getCanonicalName());
 
-    boolean alreadyExists(DvObject dvo) throws Exception;
+    boolean alreadyRegistered(DvObject dvo) throws Exception;
+
+    /**
+     * This call reports whether a PID is registered with the external Provider
+     * service. For providers like DOIs/Handles with an external service, this call
+     * should accurately report whether the PID has been registered in the service.
+     * For providers with no external service, the call should return true if the
+     * PID is defined locally. If it isn't, these no-service providers need to know
+     * whether use case of the caller requires that the returned value should
+     * default to true or false - via the noProviderDefault parameter.
+     * 
+     * @param globalId
+     * @param noProviderDefault - when there is no external service, and no local
+     *                          use of the PID, this should be returned
+     * @return whether the PID should be considered registered or not.
+     * @throws Exception
+     */
+    boolean alreadyRegistered(GlobalId globalId, boolean noProviderDefault) throws Exception;
 
-    boolean alreadyExists(GlobalId globalId) throws Exception;
-
     boolean registerWhenPublished();
     boolean canManagePID();
     boolean isConfigured();

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

@@ -314,13 +314,13 @@ private String getAuthenticationHandle(String handlePrefix) {
     }
 
     @Override
-    public boolean alreadyExists(DvObject dvObject) throws Exception {
+    public boolean alreadyRegistered(DvObject dvObject) throws Exception {
         String handle = getDvObjectHandle(dvObject);
         return isHandleRegistered(handle);
     }
 
     @Override
-    public boolean alreadyExists(GlobalId pid) throws Exception {
+    public boolean alreadyRegistered(GlobalId pid, boolean noProviderDefault) throws Exception {
         String handle = pid.getAuthority() + "/" + pid.getIdentifier();
         return isHandleRegistered(handle);
     }

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

@@ -150,19 +150,16 @@ protected void registerExternalIdentifier(Dataset theDataset, CommandContext ctx
         if (!theDataset.isIdentifierRegistered()) {
             GlobalIdServiceBean globalIdServiceBean = GlobalIdServiceBean.getBean(theDataset.getProtocol(), ctxt);
             if ( globalIdServiceBean != null ) {
-                if (globalIdServiceBean instanceof FakePidProviderServiceBean) {
-                    retry=false; //No reason to allow a retry with the FakeProvider, so set false for efficiency
-                }
                 try {
-                    if (globalIdServiceBean.alreadyExists(theDataset)) {
+                    if (globalIdServiceBean.alreadyRegistered(theDataset)) {
                         int attempts = 0;
                         if(retry) {
                             do  {
                                 theDataset.setIdentifier(globalIdServiceBean.generateDatasetIdentifier(theDataset));
                                 logger.log(Level.INFO, "Attempting to register external identifier for dataset {0} (trying: {1}).",
                                     new Object[]{theDataset.getId(), theDataset.getIdentifier()});
                                 attempts++;
-                            } while (globalIdServiceBean.alreadyExists(theDataset) && attempts <= FOOLPROOF_RETRIAL_ATTEMPTS_LIMIT);
+                            } while (globalIdServiceBean.alreadyRegistered(theDataset) && attempts <= FOOLPROOF_RETRIAL_ATTEMPTS_LIMIT);
                         }
                         if(!retry) {
                             logger.warning("Reserving PID for: "  + getDataset().getId() + " during publication failed.");

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

@@ -204,7 +204,7 @@ public FileVisitResult postVisitDirectory(final Path dir, final IOException e)
         }
         GlobalIdServiceBean idServiceBean = GlobalIdServiceBean.getBean(ctxt);
         try {
-            if (idServiceBean.alreadyExists(doomed)) {
+            if (idServiceBean.alreadyRegistered(doomed)) {
                 idServiceBean.deleteIdentifier(doomed);
             }
         } catch (Exception e) {

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

@@ -101,7 +101,7 @@ protected void executeImpl(CommandContext ctxt) throws CommandException {
         if (!doomed.isHarvested()) {
             GlobalIdServiceBean idServiceBean = GlobalIdServiceBean.getBean(ctxt);
             try {
-                if (idServiceBean.alreadyExists(doomed)) {
+                if (idServiceBean.alreadyRegistered(doomed)) {
                     idServiceBean.deleteIdentifier(doomed);
                     for (DataFile df : doomed.getFiles()) {
                         idServiceBean.deleteIdentifier(df);

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

@@ -79,15 +79,10 @@ protected void additionalParameterTests(CommandContext ctxt) throws CommandExcep
                  * that exist (and accessible in the PID provider account configured in
                  * Dataverse) but aren't findable to be used. That could be the case if, for
                  * example, someone was importing a draft dataset from elsewhere.
-                 * 
-                 * Also note that just replacing the call above with the alreadyExists() call
-                 * here would break import cases where a DOI is public but not managable with
-                 * the currently configured PID provider credentials. If this is not a valid use
-                 * case, the GET above could be removed.
                  */
                 GlobalIdServiceBean globalIdServiceBean = GlobalIdServiceBean.getBean(ds.getProtocol(), ctxt);
                 if (globalIdServiceBean != null) {
-                    if (globalIdServiceBean.alreadyExists(ds)) {
+                    if (globalIdServiceBean.alreadyRegistered(ds.getGlobalId(), true)) {
                         return;
                     }
                 }

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

@@ -70,7 +70,7 @@ protected void executeImpl(CommandContext ctxt) throws CommandException {
                     target.setAuthority(authority);
                 }
             }
-            if (idServiceBean.alreadyExists(target)) {
+            if (idServiceBean.alreadyRegistered(target)) {
                 return;
             }
             String doiRetString = idServiceBean.createIdentifier(target);

src/main/java/edu/harvard/iq/dataverse/pidproviders/FakePidProviderServiceBean.java

@@ -20,16 +20,17 @@ public class FakePidProviderServiceBean extends DOIServiceBean {
     //Only need to check locally
     public boolean isGlobalIdUnique(GlobalId globalId) {
         try {
-            return ! alreadyExists(globalId);
+            return ! alreadyRegistered(globalId, false);
         } catch (Exception e){
             //we can live with failure - means identifier not found remotely
         }
         return true;
     }
 
     @Override
-    public boolean alreadyExists(GlobalId globalId) throws Exception {
-        return ! dvObjectService.isGlobalIdLocallyUnique(globalId);
+    public boolean alreadyRegistered(GlobalId globalId, boolean noProviderDefault) {
+        boolean existsLocally = !dvObjectService.isGlobalIdLocallyUnique(globalId);
+        return existsLocally ? existsLocally : noProviderDefault;
     }
 
     @Override

src/main/java/edu/harvard/iq/dataverse/pidproviders/PermaLinkPidProviderServiceBean.java

@@ -69,10 +69,13 @@ public String getSeparator() {
     }
 
     @Override
-    public boolean alreadyExists(GlobalId globalId) throws Exception {
-        return ! dvObjectService.isGlobalIdLocallyUnique(globalId);
+    public boolean alreadyRegistered(GlobalId globalId, boolean noProviderDefault) {
+        // Perma doesn't manage registration, so we assume all local PIDs can be treated
+        // as registered
+        boolean existsLocally = !dvObjectService.isGlobalIdLocallyUnique(globalId);
+        return existsLocally ? existsLocally : noProviderDefault;
     }
-
+    
     @Override
     public boolean registerWhenPublished() {
         return false;

src/main/java/edu/harvard/iq/dataverse/pidproviders/UnmanagedDOIServiceBean.java

@@ -43,8 +43,8 @@ public boolean registerWhenPublished() {
     }
 
     @Override
-    public boolean alreadyExists(GlobalId pid) {
-        return false;
+    public boolean alreadyRegistered(GlobalId pid, boolean noProviderDefault) {
+        throw new NotImplementedException();
     }
 
     @Override

src/main/java/edu/harvard/iq/dataverse/pidproviders/UnmanagedHandlenetServiceBean.java

@@ -35,7 +35,7 @@ public boolean registerWhenPublished() {
     }
 
     @Override
-    public boolean alreadyExists(GlobalId pid) throws Exception {
+    public boolean alreadyRegistered(GlobalId pid, boolean noProviderDefault) throws Exception {
         throw new NotImplementedException();
     }
 

src/main/java/edu/harvard/iq/dataverse/util/json/JSONLDUtil.java

@@ -240,6 +240,7 @@ else if (key.equals("https://dataverse.org/schema/core#fileRequestAccess")) {
             }
         }
         dsv.setTermsOfUseAndAccess(terms);
+        terms.setDatasetVersion(dsv);
         dsv.setDatasetFields(dsfl);
 
         return dsv;