Merge pull request #3856 from IQSS/3855-cannot-create-dataset

prevent NullPointerException when creating dataset #3855
IQSS · May 25, 2017 · cb0e38f · cb0e38f
2 parents 2054db2 + 6f28f26
commit cb0e38f
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Showing 9 changed files with 42 additions and 32 deletions.
diff --git a/scripts/database/homebrew/run-post-create-post-deploy b/scripts/database/homebrew/run-post-create-post-deploy
@@ -1,5 +1,7 @@
 #!/bin/sh
 scripts/database/homebrew/run-reference_data.sql > /tmp/run-reference_data.sql
+psql dataverse_db -f doc/sphinx-guides/source/_static/util/createsequence.sql
+psql -c 'ALTER TABLE datasetidentifier_seq OWNER TO "dataverse_app";' dataverse_db
 cd scripts/api
 ./setup-all.sh --insecure > /tmp/setup-all.sh.out 2> /tmp/setup-all.sh.err
 cd ../..
diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
@@ -1259,7 +1259,8 @@ private String init(boolean initFull) {
             dataset.setProtocol(protocol);
             dataset.setAuthority(authority);
             dataset.setDoiSeparator(separator);
-            dataset.setIdentifier(datasetService.generateDatasetIdentifier(protocol, authority, separator));
+            //Wait until the create command before actually getting an identifier  
+            //dataset.setIdentifier(datasetService.generateDatasetIdentifier(protocol, authority, separator));
 
             if (dataset.getOwner() == null) {
                 return permissionsWrapper.notFound();

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
@@ -221,30 +221,30 @@ public Dataset findByGlobalId(String globalId) {
         return foundDataset;
     }
 
-    public String generateDatasetIdentifier(String protocol, String authority, String separator) {
+    public String generateDatasetIdentifier(Dataset dataset, IdServiceBean idServiceBean) {
         String doiIdentifierType = settingsService.getValueForKey(SettingsServiceBean.Key.IdentifierGenerationStyle, "randomString");
         switch (doiIdentifierType) {
             case "randomString":
-                return generateIdentifierAsRandomString(protocol, authority, separator);
+                return generateIdentifierAsRandomString(dataset, idServiceBean);
             case "sequentialNumber":
-                return generateIdentifierAsSequentialNumber(protocol, authority, separator);
+                return generateIdentifierAsSequentialNumber(dataset, idServiceBean);
             default:
                 /* Should we throw an exception instead?? -- L.A. 4.6.2 */
-                return generateIdentifierAsRandomString(protocol, authority, separator);
+                return generateIdentifierAsRandomString(dataset, idServiceBean);
         }
     }
 
-    private String generateIdentifierAsRandomString(String protocol, String authority, String separator) {
+    private String generateIdentifierAsRandomString(Dataset dataset, IdServiceBean idServiceBean) {
 
         String identifier = null;
         do {
             identifier = RandomStringUtils.randomAlphanumeric(6).toUpperCase();  
-        } while (!isIdentifierUniqueInDatabase(identifier, protocol, authority, separator));
+        } while (!isIdentifierUniqueInDatabase(identifier, dataset, idServiceBean));
 
         return identifier;
     }
 
-    private String generateIdentifierAsSequentialNumber(String protocol, String authority, String separator) {
+    private String generateIdentifierAsSequentialNumber(Dataset dataset, IdServiceBean idServiceBean) {
 
         String identifier; 
         do {
@@ -257,7 +257,7 @@ private String generateIdentifierAsSequentialNumber(String protocol, String auth
                 return null; 
             }
             identifier = identifierNumeric.toString();
-        } while (!isIdentifierUniqueInDatabase(identifier, protocol, authority, separator));
+        } while (!isIdentifierUniqueInDatabase(identifier, dataset, idServiceBean));
 
         return identifier;
     }
@@ -267,19 +267,21 @@ private String generateIdentifierAsSequentialNumber(String protocol, String auth
      * for any other study in this Dataverse Network) alos check for duplicate
      * in EZID if needed
      */
-    public boolean isIdentifierUniqueInDatabase(String userIdentifier, String protocol, String authority, String separator) {
+    public boolean isIdentifierUniqueInDatabase(String userIdentifier, Dataset dataset, IdServiceBean idServiceBean) {
         String query = "SELECT d FROM Dataset d WHERE d.identifier = '" + userIdentifier + "'";
-        query += " and d.protocol ='" + protocol + "'";
-        query += " and d.authority = '" + authority + "'";
+        query += " and d.protocol ='" + dataset.getProtocol() + "'";
+        query += " and d.authority = '" + dataset.getAuthority() + "'";
         boolean u = em.createQuery(query).getResultList().size() == 0;
-        String nonNullDefaultIfKeyNotFound = "";
-        String doiProvider = settingsService.getValueForKey(SettingsServiceBean.Key.DoiProvider, nonNullDefaultIfKeyNotFound);
-        if (protocol.equals("doi") && doiProvider.equals("EZID")) {
-            // TODO would need CommandContext to use IdServiceBean.getBean, then replace condition above with something like idServiceBean.registerWhenPublished
-            if (!doiEZIdServiceBean.lookupMetadataFromIdentifier(protocol, authority, separator, userIdentifier).isEmpty()) {
+
+        try{
+            if (idServiceBean.alreadyExists(dataset)) {
                 u = false;
             }
+        } catch (Exception e){
+            //we can live with failure - means identifier not found remotely
         }
+
+
         return u;
     }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/IdServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/IdServiceBean.java
@@ -50,7 +50,9 @@ static IdServiceBean getBean(String protocol, CommandContext ctxt) {
         logger.log(Level.FINE,"getting bean, protocol=" + protocol);
         String nonNullDefaultIfKeyNotFound = "";
         String doiProvider = ctxt.settings().getValueForKey(SettingsServiceBean.Key.DoiProvider, nonNullDefaultIfKeyNotFound);
-
+        if (protocol == null){
+            protocol = ctxt.settings().getValueForKey(SettingsServiceBean.Key.Protocol, nonNullDefaultIfKeyNotFound);
+        }
         if ("hdl".equals(protocol))
             return (ctxt.handleNet());
         else if (protocol.equals("doi"))

diff --git a/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java b/src/main/java/edu/harvard/iq/dataverse/api/datadeposit/CollectionDepositManagerImpl.java
@@ -101,7 +101,8 @@ public DepositReceipt createNew(String collectionUri, Deposit deposit, AuthCrede
                     dataset.setProtocol(protocol);
                     dataset.setAuthority(authority);
                     dataset.setDoiSeparator(separator);
-                    dataset.setIdentifier(datasetService.generateDatasetIdentifier(protocol, authority, separator));
+                    //Wait until the create command before actually getting an identifier                    
+                    //dataset.setIdentifier(datasetService.generateDatasetIdentifier(protocol, authority, separator));
                     logger.log(Level.FINE, "DS Deposit identifier: {0}", dataset.getIdentifier());
 
                     CreateDatasetCommand createDatasetCommand = new CreateDatasetCommand(dataset, dvReq, false);

diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateDatasetCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateDatasetCommand.java
@@ -74,8 +74,14 @@ public CreateDatasetCommand(Dataset theDataset, DataverseRequest aRequest, boole
     @Override
     public Dataset execute(CommandContext ctxt) throws CommandException {
         SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd-hh.mm.ss");
-
-        if ( (importType != ImportType.MIGRATION && importType != ImportType.HARVEST) && !ctxt.datasets().isIdentifierUniqueInDatabase(theDataset.getIdentifier(), theDataset.getProtocol(), theDataset.getAuthority(), theDataset.getDoiSeparator()) ) {
+
+
+
+        IdServiceBean idServiceBean = IdServiceBean.getBean(theDataset.getProtocol(), ctxt);
+        if(theDataset.getIdentifier() == null || theDataset.getIdentifier().isEmpty()){
+            theDataset.setIdentifier(ctxt.datasets().generateDatasetIdentifier(theDataset, idServiceBean));
+        }
+        if ( (importType != ImportType.MIGRATION && importType != ImportType.HARVEST) && !ctxt.datasets().isIdentifierUniqueInDatabase(theDataset.getIdentifier(), theDataset, idServiceBean)) {
             throw new IllegalCommandException(String.format("Dataset with identifier '%s', protocol '%s' and authority '%s' already exists",
                                                              theDataset.getIdentifier(), theDataset.getProtocol(), theDataset.getAuthority()),
                                                 this);
@@ -143,15 +149,15 @@ by the Dataset page (in CREATE mode), it already has the persistent
                         -- L.A. 4.6.2
              */
 
-            theDataset.setIdentifier(ctxt.datasets().generateDatasetIdentifier(theDataset.getProtocol(), theDataset.getAuthority(), theDataset.getDoiSeparator()));
+            theDataset.setIdentifier(ctxt.datasets().generateDatasetIdentifier(theDataset, idServiceBean));
 
         }
         logger.log(Level.FINE,"doiProvider={0} protocol={1}  importType={2}  GlobalIdCreateTime=={3}", new Object[]{doiProvider, protocol,  importType, theDataset.getGlobalIdCreateTime()});
         // Attempt the registration if importing dataset through the API, or the app (but not harvest or migrate)
         if ((importType == null || importType.equals(ImportType.NEW))
                 && theDataset.getGlobalIdCreateTime() == null) {
                 String doiRetString = "";
-                IdServiceBean idServiceBean = IdServiceBean.getBean(ctxt);
+                idServiceBean = IdServiceBean.getBean(ctxt);
                 try{
                     logger.log(Level.FINE,"creating identifier");
                     doiRetString = idServiceBean.createIdentifier(theDataset);

diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DestroyDatasetCommand.java
@@ -81,15 +81,11 @@ protected void executeImpl(CommandContext ctxt) throws CommandException {
             ctxt.em().remove(ra);
         }   
 
-        //Register Cache
-        if(ctxt.settings().getValueForKey(SettingsServiceBean.Key.DoiProvider, "").equals("DataCite")){
-            // TODO make ignorant of configured bean
-            ctxt.doiDataCite().deleteRecordFromCache(doomed);
-        }
-
         IdServiceBean idServiceBean = IdServiceBean.getBean(ctxt);
         try{
-            idServiceBean.deleteIdentifier(doomed);
+            if(idServiceBean.alreadyExists(doomed)){
+                idServiceBean.deleteIdentifier(doomed);
+            }
         }  catch (Exception e) {
              logger.log(Level.WARNING, "Identifier deletion was not successfull:",e.getMessage());
         } 

diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/PublishDatasetCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/PublishDatasetCommand.java
@@ -102,7 +102,7 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
                         int attempts = 0;
 
                         while (idServiceBean.alreadyExists(theDataset) && attempts < FOOLPROOF_RETRIAL_ATTEMPTS_LIMIT) {
-                            theDataset.setIdentifier(ctxt.datasets().generateDatasetIdentifier(protocol, authority, theDataset.getDoiSeparator()));
+                            theDataset.setIdentifier(ctxt.datasets().generateDatasetIdentifier(theDataset, idServiceBean));
                             attempts++;
                         }
 

diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDatasetCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/UpdateDatasetCommand.java
@@ -203,7 +203,7 @@ public Dataset save(CommandContext ctxt)  throws CommandException {
                 // enough number of values will be legitimately registered 
                 // by another entity sharing the same authority...)
 
-                    theDataset.setIdentifier(ctxt.datasets().generateDatasetIdentifier(theDataset.getProtocol(), theDataset.getAuthority(), theDataset.getDoiSeparator()));
+                    theDataset.setIdentifier(ctxt.datasets().generateDatasetIdentifier(theDataset, idServiceBean));
                     doiRetString = idServiceBean.createIdentifier(theDataset);
 
                     attempts++;