Merged Jims PR

DANS-KNAW · Dec 13, 2024 · 07e4d1d · 07e4d1d
1 parent 4fec5ea
commit 07e4d1d
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Showing 24 changed files with 1,113 additions and 579 deletions.
diff --git a/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValue.java b/src/main/java/edu/harvard/iq/dataverse/ControlledVocabularyValue.java
@@ -34,7 +34,7 @@
  */
 @Entity
 @Table(indexes = {@Index(columnList="datasetfieldtype_id"), @Index(columnList="displayorder")})
-public class ControlledVocabularyValue implements Serializable  {
+public class ControlledVocabularyValue implements Serializable, Comparable<ControlledVocabularyValue> {
 
     private static final Logger logger = Logger.getLogger(ControlledVocabularyValue.class.getCanonicalName());
 
@@ -167,7 +167,13 @@ public boolean equals(Object object) {
         }
         ControlledVocabularyValue other = (ControlledVocabularyValue) object;
         return Objects.equals(getId(), other.getId());
-    }    
+    } 
+
+    @Override
+    public int compareTo(ControlledVocabularyValue o) {
+        //Display order may be better but the raw return from the db is by id, so for now we use id.
+        return Long.compare(this.getId(), o.getId());
+    }
 
     @Override
     public String toString() {

diff --git a/src/main/java/edu/harvard/iq/dataverse/Dataset.java b/src/main/java/edu/harvard/iq/dataverse/Dataset.java
@@ -348,6 +348,8 @@ public void setVersions(List<DatasetVersion> versions) {
     private DatasetVersion createNewDatasetVersion(Template template, FileMetadata fmVarMet) {
 
         DatasetVersion dsv = new DatasetVersion();
+        DatasetVersionModifiedDate date = new DatasetVersionModifiedDate();
+        dsv.setModifiedDate(date);
         dsv.setVersionState(DatasetVersion.VersionState.DRAFT);
         dsv.setFileMetadatas(new ArrayList<>());
         DatasetVersion latestVersion;

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetFieldServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetFieldServiceBean.java
@@ -276,9 +276,11 @@ public ControlledVocabAlternate save(ControlledVocabAlternate alt) {
      * @return - a map of JsonObjects containing configuration information keyed by the DatasetFieldType id (Long)
      */
     public Map<Long, JsonObject> getCVocConf(boolean byTermUriField){
-
+        return getCVocConf(byTermUriField, settingsService.getValueForKey(SettingsServiceBean.Key.CVocConf));
+    }
+
+    public Map<Long, JsonObject> getCVocConf(boolean byTermUriField, String cvocSetting) {
         //ToDo - change to an API call to be able to provide feedback if the json is invalid?
-        String cvocSetting = settingsService.getValueForKey(SettingsServiceBean.Key.CVocConf);
         if (cvocSetting == null || cvocSetting.isEmpty()) {
             oldHash=null;
             //Release old maps
@@ -356,11 +358,11 @@ public Set<Long> getCvocFieldSet() {
     /**
      * Adds information about the external vocabulary term being used in this DatasetField to the ExternalVocabularyValue table if it doesn't already exist.
      * @param df - the primitive/parent compound field containing a newly saved value
+     * @param cvocEntry 
      */
-    public void registerExternalVocabValues(DatasetField df) {
+    public void registerExternalVocabValues(DatasetField df, JsonObject cvocEntry) {
         DatasetFieldType dft = df.getDatasetFieldType();
         logger.fine("Registering for field: " + dft.getName());
-        JsonObject cvocEntry = getCVocConf(true).get(dft.getId());
         if (dft.isPrimitive()) {
             List<DatasetField> siblingsDatasetFields = new ArrayList<>();
             if(dft.getParentDatasetFieldType()!=null) {

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java b/src/main/java/edu/harvard/iq/dataverse/DatasetPage.java
@@ -37,6 +37,7 @@
 import edu.harvard.iq.dataverse.engine.command.impl.PublishDatasetCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.PublishDataverseCommand;
 import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand;
+import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionMetadataCommand;
 import edu.harvard.iq.dataverse.export.ExportService;
 import edu.harvard.iq.dataverse.util.cache.CacheFactoryBean;
 import io.gdcc.spi.export.ExportException;
@@ -101,6 +102,7 @@
 import jakarta.faces.view.ViewScoped;
 import jakarta.inject.Inject;
 import jakarta.inject.Named;
+import jakarta.persistence.OptimisticLockException;
 
 import org.apache.commons.lang3.StringUtils;
 import org.primefaces.event.FileUploadEvent;
@@ -182,7 +184,7 @@ public class DatasetPage implements java.io.Serializable {
 
     public enum EditMode {
 
-        CREATE, INFO, FILE, METADATA, LICENSE
+        CREATE, INFO, FILE, METADATA, LICENSE, DEFAULT
     };
 
     public enum DisplayMode {
@@ -2887,6 +2889,9 @@ private String releaseDataset(boolean minor) {
                     // the lock info system.
                     JsfHelper.addErrorMessage(ex.getLocalizedMessage());
                 }
+                if(ex.getCause()!=null && ex.getCause() instanceof OptimisticLockException) {
+                    JsfHelper.addErrorMessage(BundleUtil.getStringFromBundle("dataset.message.parallelPublishError"));
+                }
                 logger.severe(ex.getMessage());
             }
 
@@ -2896,21 +2901,6 @@ private String releaseDataset(boolean minor) {
         return returnToDraftVersion();
     }
 
-    @Deprecated
-    public String registerDataset() {
-        try {
-            UpdateDatasetVersionCommand cmd = new UpdateDatasetVersionCommand(dataset, dvRequestService.getDataverseRequest());
-            cmd.setValidateLenient(true);
-            dataset = commandEngine.submit(cmd);
-        } catch (CommandException ex) {
-            FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_WARN,BundleUtil.getStringFromBundle( "dataset.registration.failed"), " - " + ex.toString()));
-            logger.severe(ex.getMessage());
-        }
-        FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_INFO, BundleUtil.getStringFromBundle("dataset.registered"), BundleUtil.getStringFromBundle("dataset.registered.msg"));
-        FacesContext.getCurrentInstance().addMessage(null, message);
-        return returnToDatasetOnly();
-    }
-
     public String updateCurrentVersion() {
         /*
          * Note: The code here mirrors that in the
@@ -3918,8 +3908,10 @@ public String save() {
         Map<Long, String> deleteStorageLocations = null;
 
         try {
-            if (editMode == EditMode.CREATE) {
-                //Lock the metadataLanguage once created
+            EditMode currentMode = (editMode == null? EditMode.DEFAULT : editMode);
+            switch (currentMode) {
+            case CREATE:
+              //Lock the metadataLanguage once created
                 dataset.setMetadataLanguage(getEffectiveMetadataLanguage());
                 //ToDo - could drop use of selectedTemplate and just use the persistent dataset.getTemplate() 
                 if ( selectedTemplate != null ) {
@@ -3932,8 +3924,9 @@ public String save() {
                 } else {
                    cmd = new CreateNewDatasetCommand(dataset, dvRequestService.getDataverseRequest());
                 }
-
-            } else {
+                break;
+            case METADATA:
+            case LICENSE:
                 //Precheck - also checking db copy of dataset to catch edits in progress that would cause update command transaction to fail
                 if (dataset.getId() != null) {
                     Dataset lockTest = datasetService.find(dataset.getId());
@@ -3944,6 +3937,21 @@ public String save() {
                         return returnToDraftVersion();
                     }
                 }
+
+                cmd = new UpdateDatasetVersionMetadataCommand(dataset, dvRequestService.getDataverseRequest(), clone );
+                ((UpdateDatasetVersionMetadataCommand) cmd).setValidateLenient(true);
+                break;
+            default:
+              //Precheck - also checking db copy of dataset to catch edits in progress that would cause update command transaction to fail
+                if (dataset.getId() != null) {
+                    Dataset lockTest = datasetService.find(dataset.getId());
+                    if (dataset.isLockedFor(DatasetLock.Reason.EditInProgress) || lockTest.isLockedFor(DatasetLock.Reason.EditInProgress)) {
+                        logger.log(Level.INFO, "Couldn''t save dataset: {0}", "It is locked."
+                                + "");
+                        JH.addMessage(FacesMessage.SEVERITY_FATAL, BundleUtil.getStringFromBundle("dataset.locked.editInProgress.message"),BundleUtil.getStringFromBundle("dataset.locked.editInProgress.message.details", Arrays.asList(BrandingUtil.getSupportTeamName(null))));
+                        return returnToDraftVersion();
+                    }
+                }
                 if (!filesToBeDeleted.isEmpty()) {
                     deleteStorageLocations = datafileService.getPhysicalFilesToDelete(filesToBeDeleted);
                 }
@@ -3964,6 +3972,10 @@ public String save() {
             Throwable cause = ex;
             while (cause.getCause()!= null) {
                 cause = cause.getCause();
+                if (cause != null && cause instanceof OptimisticLockException) {
+                    JsfHelper.addErrorMessage(BundleUtil.getStringFromBundle("dataset.message.parallelUpdateError"));
+                    return null;
+                }
                 error.append(cause).append(" ");
                 error.append(cause.getMessage()).append(" ");
             }
@@ -3973,6 +3985,15 @@ public String save() {
         } catch (CommandException ex) {
             //FacesContext.getCurrentInstance().addMessage(null, new FacesMessage(FacesMessage.SEVERITY_ERROR, "Dataset Save Failed", " - " + ex.toString()));
             logger.log(Level.SEVERE, "CommandException, when attempting to update the dataset: " + ex.getMessage(), ex);
+            Throwable cause = ex;
+            while (cause.getCause()!= null) {
+                cause = cause.getCause();
+                logger.info("Cause is: " + cause.getClass().getName() + ", Message: " + cause.getMessage());
+                if (cause != null && cause instanceof OptimisticLockException) {
+                    JsfHelper.addErrorMessage(BundleUtil.getStringFromBundle("dataset.message.parallelUpdateError"));
+                    return null;
+                }
+            }
             populateDatasetUpdateFailureMessage();
             return returnToDraftVersion();
         }

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java b/src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java
@@ -442,7 +442,8 @@ public DatasetLock addDatasetLock(Long datasetId, DatasetLock.Reason reason, Lon
         // (to prevent multiple, duplicate locks on the dataset!)
         DatasetLock lock = dataset.getLockFor(reason);
         if (lock != null) {
-            return lock;
+            //return lock;
+            return null;
         }
 
         // Create new:

diff --git a/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java b/src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java
@@ -83,6 +83,12 @@
 @ValidateVersionNote(versionNote = "versionNote", versionState = "versionState")
 public class DatasetVersion implements Serializable {
 
+    public DatasetVersion() {
+        super();
+        this.modifiedDate = new DatasetVersionModifiedDate();
+
+    }
+
     private static final Logger logger = Logger.getLogger(DatasetVersion.class.getCanonicalName());
     private static final Validator validator = Validation.buildDefaultValidatorFactory().getValidator();
 
@@ -127,8 +133,17 @@ public enum VersionState {
 
     private String UNF;
 
-    @Version
-    private Long version;
+
+    @OneToOne(cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
+    private DatasetVersionModifiedDate modifiedDate;
+
+    public void setModifiedDate(DatasetVersionModifiedDate modifiedDate) {
+        this.modifiedDate = modifiedDate;
+    }
+
+    public DatasetVersionModifiedDate getModifiedDate() {
+        return modifiedDate;
+    }
 
     private Long versionNumber;
     private Long minorVersionNumber;
@@ -163,10 +178,6 @@ public enum VersionState {
     @Column( nullable=false )
     private Date createTime;
 
-    @Temporal(value = TemporalType.TIMESTAMP)
-    @Column( nullable=false )
-    private Date lastUpdateTime;
-
     @Temporal(value = TemporalType.TIMESTAMP)
     private Date releaseTime;
 
@@ -231,17 +242,6 @@ public void setUNF(String UNF) {
         this.UNF = UNF;
     }
 
-    /**
-     * This is JPA's optimistic locking mechanism, and has no semantic meaning in the DV object model.
-     * @return the object db version
-     */
-    public Long getVersion() {
-        return this.version;
-    }
-
-    public void setVersion(Long version) {
-    }
-
     public String getDataverseSiteUrl() {
         return dataverseSiteUrl;
     }
@@ -429,25 +429,25 @@ public void setCreateTime(Date createTime) {
     }
 
     public Date getLastUpdateTime() {
-        return lastUpdateTime;
+        return modifiedDate.getLastUpdateTime();
     }
 
     public void setLastUpdateTime(Date lastUpdateTime) {
         if (createTime == null) {
             createTime = lastUpdateTime;
         }
-        this.lastUpdateTime = lastUpdateTime;
+        modifiedDate.setLastUpdateTime(lastUpdateTime);
     }
 
     public String getVersionDate() {
-        if (this.lastUpdateTime == null){
+        if (modifiedDate.getLastUpdateTime() == null){
             return null; 
         }
-        return DateUtil.formatDate(lastUpdateTime);
+        return DateUtil.formatDate(modifiedDate.getLastUpdateTime());
     }
 
     public String getVersionYear() {
-        return new SimpleDateFormat("yyyy").format(lastUpdateTime);
+        return new SimpleDateFormat("yyyy").format(modifiedDate.getLastUpdateTime());
     }
 
     public Date getReleaseTime() {
@@ -672,7 +672,7 @@ public void updateDefaultValuesFromTemplate(Template template) {
 
     public DatasetVersion cloneDatasetVersion(){
         DatasetVersion dsv = new DatasetVersion();
-        dsv.setVersionState(this.getPriorVersionState());
+        dsv.setVersionState(this.getVersionState());
         dsv.setFileMetadatas(new ArrayList<>());
 
            if (this.getUNF() != null){
@@ -2122,7 +2122,7 @@ public String getJsonLd() {
     }
 
     public String getLocaleLastUpdateTime() {
-        return DateUtil.formatDate(new Timestamp(lastUpdateTime.getTime()));
+        return DateUtil.formatDate(new Timestamp(modifiedDate.getLastUpdateTime().getTime()));
     }
 
     public String getExternalStatusLabel() {