4499 - dataset version pids

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

@@ -1,5 +1,7 @@
 package edu.harvard.iq.dataverse;
 
+import edu.harvard.iq.dataverse.pidproviders.VersionPidMode.GenStyle;
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import edu.harvard.iq.dataverse.util.SystemConfig;
 import java.io.InputStream;
@@ -155,6 +157,50 @@ public DvObject generateIdentifier(DvObject dvObject) {
         return dvObject;
     }
 
+    /**
+     * Generate an identifier for a given dataset version, depending on the chosen (configured) generation style.
+     * (See also {@link GenStyle} for available styles.)
+     *
+     * @param datasetVersion The version of a dataset to create a PID for
+     * @return The identifier (will never be null)
+     * @throws IllegalArgumentException If the style configured is not supported by this generator, the version is
+     *                                  already released or a minor version, or if the owning dataset has no identifier
+     *                                  while creating a suffix style identifier.
+     */
+    @Override
+    public String generateDatasetVersionIdentifier(final DatasetVersion datasetVersion) throws IllegalArgumentException {
+        if (datasetVersion == null || datasetVersion.isReleased()) {
+            throw new IllegalArgumentException("Version may not be null or released");
+        }
+
+        // If this is a minor version update, reuse the identifier of the last released version
+        if (datasetVersion.getMinorVersionNumber() > 0) {
+            return datasetVersion.getDataset().getReleasedVersion().getPersistentIdentifier();
+        }
+
+        try {
+            GenStyle style = JvmSettings.PID_VERSIONS_STYLE.lookup(GenStyle.class);
+
+            if (style == GenStyle.DATASET) {
+                return generateDatasetIdentifier(datasetVersion.getDataset());
+
+            } else if (style == GenStyle.SUFFIX) {
+                String datasetIdentifier = datasetVersion.getDataset().getIdentifier();
+                if (datasetIdentifier == null || datasetIdentifier.isEmpty()) {
+                    throw new IllegalArgumentException("Dataset must not have empty identifier when creating dataset version identifier by suffix");
+                }
+
+                return datasetIdentifier + getVersionSuffixDelimiter() + datasetVersion.getVersionNumber();
+
+            // Nothing appropriate found - bail out
+            } else {
+                throw new IllegalArgumentException("No supported version PID generation style configured");
+            }
+        } catch (NoSuchElementException e) {
+            throw new IllegalArgumentException("No supported version PID generation style configured", e);
+        }
+    }
+
     //ToDo just send the DvObject.DType
     public String generateDatasetIdentifier(Dataset dataset) {
         //ToDo - track these in the bean

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

@@ -63,7 +63,7 @@ public boolean alreadyExists(GlobalId pid) {
 
 
     @Override
-    public String createIdentifier(DvObject dvObject) throws Exception {
+    public String createIdentifier(DvObject dvObject) throws IOException {
         logger.log(Level.FINE,"createIdentifier");
         if(dvObject.getIdentifier() == null || dvObject.getIdentifier().isEmpty() ){
             dvObject = generateIdentifier(dvObject);

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

@@ -3,6 +3,8 @@
 import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.ucsb.nceas.ezid.EZIDException;
 import edu.ucsb.nceas.ezid.EZIDService;
+
+import java.io.IOException;
 import java.util.*;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -240,7 +242,7 @@ public List<String> getProviderInformation(){
     }
 
     @Override
-    public String createIdentifier(DvObject dvObject) throws Throwable {
+    public String createIdentifier(DvObject dvObject) throws IOException {
         logger.log(Level.FINE, "createIdentifier");
         if(dvObject.getIdentifier() == null || dvObject.getIdentifier().isEmpty() ){
             dvObject = generateIdentifier(dvObject);
@@ -265,7 +267,7 @@ public String createIdentifier(DvObject dvObject) throws Throwable {
             logger.log(Level.WARNING, "cause", e.getCause());
             logger.log(Level.WARNING, "message {0}", e.getMessage());
             logger.log(Level.WARNING, "identifier: ", identifier);
-            throw e;
+            throw new IOException(e);
         }
     }
 

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

@@ -129,6 +129,33 @@ public enum VersionState {
     @Column(length = VERSION_NOTE_MAX_LENGTH)
     private String versionNote;
 
+    /**
+     * A (globally) unique persistent identifier for this version.
+     * The version PID will always be dependent on the protocol and authority of the containing dataset.
+     * This identifier may contain {@link edu.harvard.iq.dataverse.settings.SettingsServiceBean.Key#Shoulder} if
+     * configured and some more unique characters, also depending on the admin's choice to make version PIDs dependent
+     * on the dataset PID.
+     *
+     * The PID may be null (feature disabled, old entry, etc.). It might not be unique, as minor versions by default
+     * carry the identifier of their adjacent major version.
+     */
+    @Column
+    private String persistentIdentifier;
+
+    /**
+     * Caching the {@link GlobalId} in a transient field saves retrievals and reformatting. Its value will
+     * be based on {@link #persistentIdentifier}, and details from {@link #dataset} like protocol, authority and
+     * shoulder.
+     */
+    @Transient
+    private GlobalId globalId;
+
+    /**
+     * Saving in the database if this identifier has been registered before to avoid
+     * re-registration (which would probably fail) and switch to modification
+     */
+    private boolean identifierRegistered = false;
+
     /*
      * @todo versionState should never be null so when we are ready, uncomment
      * the `nullable = false` below.
@@ -233,6 +260,56 @@ public Long getVersion() {
 
     public void setVersion(Long version) {
     }
+
+    public String getPersistentIdentifier() {
+        return this.persistentIdentifier;
+    }
+
+    public void setPersistentIdentifier(String identifier) {
+        this.persistentIdentifier = identifier;
+    }
+
+    /**
+     * Create a {@link GlobalId} from {@link #persistentIdentifier} and the owning {@link #dataset}
+     * details of protocol and authority. This method is not free of side effects: it will cache
+     * the generated value in a transient instance variable if not yet initialized.
+     *
+     * @return The global id for this version or null if no PID, protocol or authority present.
+     */
+    public GlobalId getGlobalId() {
+        if (this.globalId == null && this.getPersistentIdentifier() != null &&
+            this.dataset.getProtocol() != null && this.dataset.getAuthority() != null) {
+            this.globalId = PidUtil.parseAsGlobalID(
+                this.dataset.getProtocol(),
+                this.dataset.getAuthority(),
+                this.getPersistentIdentifier());
+        }
+        return this.globalId;
+    }
+
+    /**
+     * Check the status of the version identifier - has it been registered?
+     * @return True if registered, false otherwise.
+     */
+    public boolean isIdentifierRegistered() {
+        return this.identifierRegistered;
+    }
+
+    /**
+     * Set registration as done.
+     */
+    public void setIdentifierRegistered() {
+        this.identifierRegistered = true;
+    }
+
+    /**
+     * Overwrite the registration status with a specific value
+     * @param status The new status of the registration
+     */
+    public void setIdentifierRegistered(boolean status) {
+        this.identifierRegistered = status;
+    }
+
 
     public String getDataverseSiteUrl() {
         return dataverseSiteUrl;

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

@@ -2,7 +2,7 @@
 
 import edu.harvard.iq.dataverse.harvest.client.HarvestingClient;
 import edu.harvard.iq.dataverse.authorization.DataverseRole;
-import edu.harvard.iq.dataverse.dataaccess.DataAccess;
+import edu.harvard.iq.dataverse.pidproviders.VersionPidMode.CollectionConduct;
 import edu.harvard.iq.dataverse.search.savedsearch.SavedSearch;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import edu.harvard.iq.dataverse.util.SystemConfig;
@@ -30,14 +30,13 @@
 import javax.persistence.OneToOne;
 import javax.persistence.OrderBy;
 import javax.persistence.Table;
-import javax.persistence.Transient;
+import javax.validation.constraints.NotBlank;
+import javax.validation.constraints.NotEmpty;
 import javax.validation.constraints.NotNull;
 import javax.validation.constraints.Pattern;
 import javax.validation.constraints.Size;
 
 import org.apache.commons.lang3.StringUtils;
-import org.hibernate.validator.constraints.NotBlank;
-import org.hibernate.validator.constraints.NotEmpty;
 
 /**
  *
@@ -182,8 +181,7 @@ public void setDefaultContributorRole(DataverseRole defaultContributorRole) {
     private boolean facetRoot;
     // By default, themeRoot should be true, as new dataverses should start with the default theme
     private boolean themeRoot = true;
-    private boolean templateRoot;    
-
+    private boolean templateRoot;
 
     @OneToOne(mappedBy = "dataverse",cascade={ CascadeType.REMOVE, CascadeType.MERGE,CascadeType.PERSIST}, orphanRemoval=true)
       private DataverseTheme dataverseTheme;
@@ -591,6 +589,31 @@ public void setCitationDatasetFieldTypes(List<DatasetFieldType> citationDatasetF
     }
 
 
+
+    /**
+     * Indicate if this Dataverse Collection wants to publicize PIDs for each (major) {@link DatasetVersion}
+     * for any {@link Dataset} in it.
+     *
+     * @see edu.harvard.iq.dataverse.pidproviders.VersionPidMode#ALLOW_MAJOR
+     * @see edu.harvard.iq.dataverse.pidproviders.VersionPidMode#ALLOW_MINOR
+     * @see CollectionConduct
+     */
+    @Enumerated(EnumType.STRING)
+    private CollectionConduct datasetVersionPidConduct;
+
+    public void setDatasetVersionPidConduct(CollectionConduct conduct) {
+        this.datasetVersionPidConduct = conduct;
+    }
+
+    /**
+     * Retrieve the version PID conduct mode for this collection
+     * @return One of {@link CollectionConduct}. Never null, defaults to {@link CollectionConduct#INHERIT}.
+     */
+    public CollectionConduct getDatasetVersionPidConduct() {
+        return this.datasetVersionPidConduct != null ? this.datasetVersionPidConduct : CollectionConduct.INHERIT;
+    }
+
+
 
     public List<DataverseFacet> getDataverseFacets() {
         return getDataverseFacets(false);

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

@@ -15,9 +15,11 @@
 import edu.harvard.iq.dataverse.batch.util.LoggingUtil;
 import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter;
 import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
+import edu.harvard.iq.dataverse.pidproviders.VersionPidMode;
 import edu.harvard.iq.dataverse.search.IndexServiceBean;
 import edu.harvard.iq.dataverse.search.SolrIndexServiceBean;
 import edu.harvard.iq.dataverse.search.SolrSearchResult;
+import edu.harvard.iq.dataverse.settings.JvmSettings;
 import edu.harvard.iq.dataverse.util.StringUtil;
 import edu.harvard.iq.dataverse.util.SystemConfig;
 import java.io.File;
@@ -28,9 +30,10 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
+import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.util.Properties;
-import java.util.concurrent.Future;
 import javax.ejb.EJB;
 import javax.ejb.Stateless;
 import javax.inject.Inject;
@@ -927,6 +930,57 @@ public List<Object[]> getDatasetTitlesWithinDataverse(Long dataverseId) {
 
         return em.createNativeQuery(cqString).getResultList();
     }
-
 
+    /**
+     * Check if a given Dataverse Collection has been configured to generate PIDs for a new version of a dataset
+     * contained in it. Will also respect the global version PID settings by an admin via
+     * {@link JvmSettings#PID_VERSIONS_MODE}.
+     *
+     * @param collection The collection to check. May not be null (will throw NPE).
+     * @param willBeMinorVersion Will the {@link DatasetVersion} to receive the PID be a minor version?
+     *
+     * @return true if enabled, false if disabled
+     * @throws java.util.NoSuchElementException When no or invalid configuration for version PID mode is given
+     */
+    public boolean wantsDatasetVersionPids(final Dataverse collection, boolean willBeMinorVersion) {
+        Objects.requireNonNull(collection, "Collection parameter must not be null");
+
+        // Deactivated by admin globally or no PID for minor version allowed?
+        VersionPidMode vpm = JvmSettings.PID_VERSIONS_MODE.lookup(VersionPidMode.class);
+        if (VersionPidMode.OFF.equals(vpm) || ( willBeMinorVersion && VersionPidMode.ALLOW_MAJOR.equals(vpm) )) {
+            return false;
+        }
+
+        // Check the collection itself; and potentially it's ancestors
+        Dataverse c = collection;
+        while (c != null) {
+            // Note: the default behavior is INHERIT for the model class
+            switch (c.getDatasetVersionPidConduct()) {
+                case SKIP:
+                    logger.log(Level.FINE, "Collection {0} makes {1} skip version PIDs", new String[]{c.getAlias(), collection.getAlias()});
+                    return false;
+                case MAJOR:
+                    logger.log(Level.FINE, "Collection {0} allows its sub {1} PIDs for major versions", new String[]{c.getAlias(), collection.getAlias()});
+                    return !willBeMinorVersion;
+                case MINOR:
+                    if (vpm.equals(VersionPidMode.ALLOW_MINOR)) {
+                        logger.log(Level.FINE, "Collection {0} allows its sub {1} PIDs for minor versions", new String[]{c.getAlias(), collection.getAlias()});
+                        return true;
+                    } else {
+                        // In some cases, an admin might have switched the setting after someone already activated it.
+                        // The collection's conduct mode should be updated - we will still cap it as admin says no.
+                        logger.log(Level.INFO, "Collection {0} allows its sub {1} PIDs for minor versions, which is disabled globally. Please update conduct mode of {0}.", new String[]{c.getAlias(), collection.getAlias()});
+                        return !willBeMinorVersion;
+                    }
+                case INHERIT:
+                    // Note: root dataverse has no owner, which will break the loop condition
+                    c = c.getOwner();
+            }
+        }
+
+        // If the root dataverse did also not have a policy set, use what the admin configured.
+        // Note: one could argue we should just return true here, as the below boolean expression is just the
+        //       negation of the one at the top and the collections didn't intervene. But better safe than sorry...
+        return VersionPidMode.ALLOW_MINOR.equals(vpm) || (!willBeMinorVersion && VersionPidMode.ALLOW_MAJOR.equals(vpm));
+    }
 }