Merge branch 'IQSS:develop' into develop

Author: ErykKul

.github/workflows/deploy_beta_testing.yml

@@ -45,7 +45,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Download war artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4.1.7
         with:
           name: built-app
           path: ./

.github/workflows/maven_unit_test.yml

@@ -107,7 +107,7 @@ jobs:
                   cache: maven
 
             # Get the build output from the unit test job
-            - uses: actions/download-artifact@v3
+            - uses: actions/download-artifact@v4.1.7
               with:
                   name: java-artifacts
             - run: |
@@ -140,7 +140,7 @@ jobs:
                 cache: maven
 
           # Get the build output from the integration test job
-          - uses: actions/download-artifact@v3
+          - uses: actions/download-artifact@v4.1.7
             with:
                 name: java-reportdir
           - run: tar -xvf java-reportdir.tar

doc/release-notes/10708 - MDC Citation and DOI parsing improvements.md

@@ -0,0 +1,3 @@
+MDC Citation retrieval with the PID settings has been fixed.
+DOI parsing in Dataverse is case insensitive, improving interaction with services that may change the case.
+Warnings related to managed/excluded PID lists for PID providers have been reduced

src/main/java/edu/harvard/iq/dataverse/api/MakeDataCountApi.java

@@ -19,6 +19,9 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.util.Iterator;
 import java.util.List;
@@ -152,10 +155,17 @@ public Response updateCitationsForDataset(@PathParam("id") String id) throws IOE
             // DataCite wants "doi=", not "doi:".
             String authorityPlusIdentifier = persistentId.replaceFirst("doi:", "");
             // Request max page size and then loop to handle multiple pages
-            URL url = new URL(JvmSettings.DATACITE_REST_API_URL.lookup() +
+            URL url = null;
+            try {
+                url = new URI(JvmSettings.DATACITE_REST_API_URL.lookup(pidProvider.getId()) +
                               "/events?doi=" +
                               authorityPlusIdentifier +
-                              "&source=crossref&page[size]=1000");
+                              "&source=crossref&page[size]=1000").toURL();
+            } catch (URISyntaxException e) {
+                //Nominally this means a config error/ bad DATACITE_REST_API_URL for this provider
+                logger.warning("Unable to create URL for " + persistentId + ", pidProvider " + pidProvider.getId());
+                return error(Status.INTERNAL_SERVER_ERROR, "Unable to create DataCite URL to retrieve citations.");
+            }
             logger.fine("Retrieving Citations from " + url.toString());
             boolean nextPage = true;
             JsonArrayBuilder dataBuilder = Json.createArrayBuilder();
@@ -178,7 +188,12 @@ public Response updateCitationsForDataset(@PathParam("id") String id) throws IOE
                     dataBuilder.add(iter.next());
                 }
                 if (links.containsKey("next")) {
-                    url = new URL(links.getString("next"));
+                    try {
+                        url = new URI(links.getString("next")).toURL();
+                    } catch (URISyntaxException e) {
+                        logger.warning("Unable to create URL from DataCite response: " + links.getString("next"));
+                        return error(Status.INTERNAL_SERVER_ERROR, "Unable to retrieve all results from DataCite");
+                    }
                 } else {
                     nextPage = false;
                 }
@@ -187,7 +202,7 @@ public Response updateCitationsForDataset(@PathParam("id") String id) throws IOE
             JsonArray allData = dataBuilder.build();
             List<DatasetExternalCitations> datasetExternalCitations = datasetExternalCitationsService.parseCitations(allData);
             /*
-             * ToDo: If this is the only source of citations, we should remove all the existing ones for the dataset and repopuate them.
+             * ToDo: If this is the only source of citations, we should remove all the existing ones for the dataset and repopulate them.
              * As is, this call doesn't remove old citations if there are now none (legacy issue if we decide to stop counting certain types of citation
              * as we've done for 'hasPart').
              * If there are some, this call individually checks each one and if a matching item exists, it removes it and adds it back. Faster and better to delete all and

src/main/java/edu/harvard/iq/dataverse/makedatacount/DatasetExternalCitationsServiceBean.java

@@ -7,6 +7,9 @@
 
 import edu.harvard.iq.dataverse.Dataset;
 import edu.harvard.iq.dataverse.DatasetServiceBean;
+import edu.harvard.iq.dataverse.GlobalId;
+import edu.harvard.iq.dataverse.pidproviders.PidUtil;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -40,7 +43,8 @@ public class DatasetExternalCitationsServiceBean implements java.io.Serializable
           Arrays.asList(
           "cites",
           "references",
-          "supplements"));
+          "supplements",
+          "is-supplement-to"));
   static ArrayList<String> outboundRelationships = new ArrayList<String>( 
           Arrays.asList(
           "is-cited-by",
@@ -59,22 +63,21 @@ public List<DatasetExternalCitations> parseCitations(JsonArray citations) {
             if (inboundRelationships.contains(relationship)) {
                 Dataset localDs = null;
                 if (objectUri.contains("doi")) {
-                    String globalId = objectUri.replace("https://", "").replace("doi.org/", "doi:").toUpperCase().replace("DOI:", "doi:");
-                    localDs = datasetService.findByGlobalId(globalId);
+                    localDs = datasetService.findByGlobalId(objectUri);
                     exCit.setDataset(localDs);
                 }
                 exCit.setCitedByUrl(subjectUri);
-                
+
                 if (localDs != null && !exCit.getCitedByUrl().isEmpty()) {
                     datasetExternalCitations.add(exCit);
                 }
             }
             if (outboundRelationships.contains(relationship)) {
                 Dataset localDs = null;
                 if (subjectUri.contains("doi")) {
-                    String globalId = subjectUri.replace("https://", "").replace("doi.org/", "doi:").toUpperCase().replace("DOI:", "doi:");
-                    localDs = datasetService.findByGlobalId(globalId);
+                    localDs = datasetService.findByGlobalId(subjectUri);
                     exCit.setDataset(localDs);
+
                 }
                 exCit.setCitedByUrl(objectUri);
 

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

@@ -36,9 +36,9 @@ public abstract class AbstractPidProvider implements PidProvider {
 
     private String datafilePidFormat = null;
 
-    private HashSet<String> managedSet;
+    protected HashSet<String> managedSet = new HashSet<String>();
 
-    private HashSet<String> excludedSet;
+    protected HashSet<String> excludedSet = new HashSet<String>();
 
     private String id;
     private String label;
@@ -47,8 +47,6 @@ protected AbstractPidProvider(String id, String label, String protocol) {
         this.id = id;
         this.label = label;
         this.protocol = protocol;
-        this.managedSet = new HashSet<String>();
-        this.excludedSet = new HashSet<String>();
     }
 
     protected AbstractPidProvider(String id, String label, String protocol, String authority, String shoulder,
@@ -60,8 +58,12 @@ protected AbstractPidProvider(String id, String label, String protocol, String a
         this.shoulder = shoulder;
         this.identifierGenerationStyle = identifierGenerationStyle;
         this.datafilePidFormat = datafilePidFormat;
-        this.managedSet = new HashSet<String>(Arrays.asList(managedList.split(",\\s")));
-        this.excludedSet = new HashSet<String>(Arrays.asList(excludedList.split(",\\s")));
+        if(!managedList.isEmpty()) {
+            this.managedSet.addAll(Arrays.asList(managedList.split(",\\s")));
+        }
+        if(!excludedList.isEmpty()) {
+            this.excludedSet.addAll(Arrays.asList(excludedList.split(",\\s")));
+        }
         if (logger.isLoggable(Level.FINE)) {
             Iterator<String> iter = managedSet.iterator();
             while (iter.hasNext()) {
@@ -313,10 +315,17 @@ protected GlobalId parsePersistentId(String protocol, String identifierString) {
     }
 
     public GlobalId parsePersistentId(String protocol, String authority, String identifier) {
+        return parsePersistentId(protocol, authority, identifier, false);
+    }
+    
+    public GlobalId parsePersistentId(String protocol, String authority, String identifier, boolean isCaseInsensitive) {
         logger.fine("Parsing: " + protocol + ":" + authority + getSeparator() + identifier + " in " + getId());
         if (!PidProvider.isValidGlobalId(protocol, authority, identifier)) {
             return null;
         }
+        if(isCaseInsensitive) {
+            identifier = identifier.toUpperCase();
+        }
         // Check authority/identifier if this is a provider that manages specific
         // identifiers
         // /is not one of the unmanaged providers that has null authority
@@ -333,7 +342,7 @@ public GlobalId parsePersistentId(String protocol, String authority, String iden
             logger.fine("managed in " + getId() + ": " + getManagedSet().contains(cleanIdentifier));
             logger.fine("excluded from " + getId() + ": " + getExcludedSet().contains(cleanIdentifier));
 
-            if (!(((authority.equals(getAuthority()) && identifier.startsWith(getShoulder()))
+            if (!(((authority.equals(getAuthority()) && identifier.startsWith(getShoulder().toUpperCase()))
                     || getManagedSet().contains(cleanIdentifier)) && !getExcludedSet().contains(cleanIdentifier))) {
                 return null;
             }

src/main/java/edu/harvard/iq/dataverse/pidproviders/doi/AbstractDOIProvider.java

@@ -1,6 +1,7 @@
 package edu.harvard.iq.dataverse.pidproviders.doi;
 
 import java.util.Arrays;
+import java.util.HashSet;
 import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -26,9 +27,24 @@ public abstract class AbstractDOIProvider extends AbstractPidProvider {
 
     public AbstractDOIProvider(String id, String label, String providerAuthority, String providerShoulder, String identifierGenerationStyle, String datafilePidFormat, String managedList, String excludedList) {
         super(id, label, DOI_PROTOCOL, providerAuthority, providerShoulder, identifierGenerationStyle, datafilePidFormat, managedList, excludedList);
+        //Create case insensitive (converted toUpperCase) managedSet and excludedSet
+        managedSet = clean(managedSet, "managed");
+        excludedSet = clean(excludedSet, "excluded");
     }
 
-    //For Unmanged provider
+    private HashSet<String> clean(HashSet<String> originalSet, String setName) {
+        HashSet<String> cleanSet = new HashSet<String>();
+        for(String entry: originalSet) {
+            if(entry.startsWith(DOI_PROTOCOL)) {
+                cleanSet.add(DOI_PROTOCOL + entry.substring(DOI_PROTOCOL.length()).toUpperCase());
+            } else {
+                logger.warning("Non-DOI found in " + setName + " set of pidProvider id: " + getId() + ": " + entry + ". Entry is being dropped.");
+            }
+        }
+        return cleanSet;
+    }
+
+    //For Unmanaged provider
     public AbstractDOIProvider(String name, String label) {
         super(name, label, DOI_PROTOCOL);
     }
@@ -67,7 +83,7 @@ public GlobalId parsePersistentId(String protocol, String authority, String iden
         if (!DOI_PROTOCOL.equals(protocol)) {
             return null;
         }
-        return super.parsePersistentId(protocol, authority, identifier);
+        return super.parsePersistentId(protocol, authority, identifier, true);
     }
 
     public String getUrlPrefix() {

src/main/java/edu/harvard/iq/dataverse/pidproviders/doi/datacite/DataCiteDOIProvider.java

@@ -226,8 +226,7 @@ protected String getProviderKeyName() {
 
     @Override
     public String getProviderType() {
-        // TODO Auto-generated method stub
-        return null;
+        return TYPE;
     }
 
     public String getMdsUrl() {

src/test/java/edu/harvard/iq/dataverse/pidproviders/PidUtilTest.java

@@ -250,9 +250,12 @@ public void testDOIParsing() throws IOException {
         assertEquals(pid1String, pid3.asString());
         assertEquals("dc1", pid3.getProviderId());
 
-        String pid4String = "doi:10.5072/FK3ABCDEF";
+        //Also test case insensitive
+        String pid4String = "doi:10.5072/fk3ABCDEF";
         GlobalId pid4 = PidUtil.parseAsGlobalID(pid4String);
-        assertEquals(pid4String, pid4.asString());
+        // Lower case is recognized by converting to upper case internally, so we need to test vs. the upper case identifier
+        // I.e. we are verifying that the lower case string is parsed the same as the upper case string, both give an internal upper case PID representation
+        assertEquals("doi:10.5072/FK3ABCDEF", pid4.asString());
         assertEquals("dc2", pid4.getProviderId());
 
         String pid5String = "doi:10.5072/FK2ABCDEF";