Merge branch 'develop' into 11912-edit-template-api

sekmiller · sekmiller · commit 1bba8766f8b3 · 2026-04-08T09:13:05.000-04:00
diff --git a/doc/release-notes/12070-datacite-getmetadata.md b/doc/release-notes/12070-datacite-getmetadata.md
@@ -0,0 +1,11 @@
+Incremental improvements have been made to the process of registering dataset metadata with DataCite. If your instance is using DataCite, please make sure you have a valid DataCite REST API url configured, since it is now required.
+
+The JVM option(s) in question are `dataverse.pid.*.datacite.rest-api-url` if the recommended, new-style pid configuration is used, or `doi.dataciterestapiurlstring` if the legacy settings are in place. In the latter case however, this may be a good occasion to switch to the new configuration setup.
+
+For instances using registered DataCite authorities in production the url should be:
+
+```<jvm-options>-Ddataverse.pid.<providername>.datacite.rest-api-url=https://api.datacite.org</jvm-options>```
+
+Or, for test and development instances:
+
+```<jvm-options>-Ddataverse.pid.<providername>.datacite.rest-api-url=https://api.test.datacite.org</jvm-options>```
diff --git a/doc/release-notes/12112-get-default-contributor-role.md b/doc/release-notes/12112-get-default-contributor-role.md
@@ -0,0 +1 @@
+A new API endpoint for getting the default contributor role of a collection (`GET /api/dataverses/$ID/defaultContributorRole`) was added.
diff --git a/doc/release-notes/360-modify-notvalid-deaccession-reason.md b/doc/release-notes/360-modify-notvalid-deaccession-reason.md
@@ -0,0 +1,16 @@
+# Language change for file.deaccessionDialog.reason.selectItem.notValid
+
+"Not a valid dataset." is being changed to "Not valid. This dataset does not comply with repository policies."
+This is the default English language version. For installations using customized languages, replacing the Bundle.properties file, please follow these manual instructions to make this modification, if desired.
+
+Make the change to the Bundle_##.properties file with the new verbiage. Either locally or as an update to [dataverse-language-packs Repo](https://github.com/GlobalDataverseCommunityConsortium/dataverse-language-packs/tree/develop)
+
+The SQL statements to modify the datasets is:
+
+- `UPDATE dvobject SET indextime=null WHERE id in (SELECT dataset_id FROM datasetversion WHERE deaccessionnote='Not a valid dataset.');`
+
+- `UPDATE datasetversion SET deaccessionnote='Not valid. This dataset does not comply with repository policies.' WHERE deaccessionnote='Not a valid dataset.';`
+
+Once the database is updated the Solr indexes need to be rebuilt using the following Admin API:
+
+- `curl http://localhost:8080/api/admin/index`
diff --git a/doc/sphinx-guides/source/api/native-api.rst b/doc/sphinx-guides/source/api/native-api.rst
@@ -525,7 +525,7 @@ The fully expanded example above (without environment variables) looks like this
 Assign Default Role to User Creating a Dataset in a Dataverse Collection
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Assign a default role to a user creating a dataset in a Dataverse collection ``id`` where ``roleAlias`` is the database alias of the role to be assigned:
+Assign a default role to a user creating a dataset in a Dataverse collection ``id`` where ``roleAlias`` is the database alias of the role to be assigned (requires ``ManageDataversePermissions``):
 
 .. code-block:: bash
 
@@ -544,6 +544,27 @@ The fully expanded example above (without environment variables) looks like this
 
 Note: You may use "none" as the ``ROLE_ALIAS``. This will prevent a user who creates a dataset from having any role on that dataset. It is not recommended for Dataverse collections with human contributors.
 
+.. _get-default-contributor-role-on-a-dataverse-api:
+
+Get Default Role Assigned to User Creating a Dataset in a Dataverse Collection
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Get the default role that is assigned to a user creating a dataset in a Dataverse collection ``id`` (requires ``ManageDataversePermissions``):
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export ID=root
+
+  curl -H "X-Dataverse-key:$API_TOKEN" "$SERVER_URL/api/dataverses/$ID/defaultContributorRole"
+
+The fully expanded example above (without environment variables) looks like this:
+
+.. code-block:: bash
+
+  curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" "https://demo.dataverse.org/api/dataverses/root/defaultContributorRole"
+
 .. _assign-role-on-a-dataverse-api:
 
 Assign a New Role on a Dataverse Collection
diff --git a/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java b/src/main/java/edu/harvard/iq/dataverse/api/Dataverses.java
@@ -1633,6 +1633,21 @@ public Response updateDefaultContributorRole(
 
     }
 
+    @GET
+    @AuthRequired
+    @Path("{identifier}/defaultContributorRole")
+    public Response getDefaultContributorRole(
+            @Context ContainerRequestContext crc,
+            @PathParam("identifier") String dvIdtf) {
+
+        return response(req -> ok(
+                json(
+                        execCommand(
+                                new GetCollectionDefaultContributorRoleCommand(req,
+                                        findDataverseOrDie(dvIdtf))))), getRequestUser(crc));
+
+    }
+
     @DELETE
     @AuthRequired
     @Path("{identifier}/groups/{aliasInOwner}")
diff --git a/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetCollectionDefaultContributorRoleCommand.java b/src/main/java/edu/harvard/iq/dataverse/engine/command/impl/GetCollectionDefaultContributorRoleCommand.java
@@ -0,0 +1,38 @@
+package edu.harvard.iq.dataverse.engine.command.impl;
+
+import edu.harvard.iq.dataverse.Dataverse;
+import edu.harvard.iq.dataverse.authorization.DataverseRole;
+import edu.harvard.iq.dataverse.authorization.Permission;
+import edu.harvard.iq.dataverse.engine.command.AbstractCommand;
+import edu.harvard.iq.dataverse.engine.command.CommandContext;
+import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
+import edu.harvard.iq.dataverse.engine.command.RequiredPermissions;
+import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
+
+/**
+ *
+ * Gets the default contributor role of a collection.
+ * Used by the /api/dataverses/.../defaultContributorRole API.
+ */
+@RequiredPermissions( Permission.ManageDataversePermissions )
+public class GetCollectionDefaultContributorRoleCommand extends AbstractCommand<DataverseRole> {
+
+    private final Dataverse dataverse;
+
+    public GetCollectionDefaultContributorRoleCommand(DataverseRequest aRequest, Dataverse target) {
+        super(aRequest, target);
+        dataverse = target;
+    }
+
+    @Override
+    public DataverseRole execute(CommandContext ctxt) throws CommandException {
+
+        if (dataverse != null) {
+            return dataverse.getDefaultContributorRole();
+        }
+
+        return null;
+    }
+}
+
+
diff --git a/src/main/java/edu/harvard/iq/dataverse/pidproviders/doi/datacite/DOIDataCiteRegisterService.java b/src/main/java/edu/harvard/iq/dataverse/pidproviders/doi/datacite/DOIDataCiteRegisterService.java
@@ -42,8 +42,8 @@ public class DOIDataCiteRegisterService {
     //A singleton since it, and the httpClient in it can be reused.
     private DataCiteRESTfullClient client=null;
 
-    public DOIDataCiteRegisterService(String url, String username, String password) {
-            client = new DataCiteRESTfullClient(url, username, password);
+    public DOIDataCiteRegisterService(String url, String restApiUrl, String username, String password) {
+            client = new DataCiteRESTfullClient(url, restApiUrl, username, password);
     }
 
     /**
@@ -80,13 +80,14 @@ public String registerIdentifier(String identifier, Map<String, String> metadata
     
     public String reRegisterIdentifier(String identifier, Map<String, String> metadata, DvObject dvObject) throws IOException {
         String retString = "";
-        String numericIdentifier = identifier.substring(identifier.indexOf(":") + 1);
+        // "bare identifier" is the canonical pid with the "doi:" prefix stripped
+        String bareIdentifier = identifier.substring(identifier.indexOf(":") + 1);
         String xmlMetadata = getMetadataFromDvObject(identifier, metadata, dvObject);
         String target = metadata.get("_target");
         String currentMetadata = null;
         boolean hasDifferences = false;
         try {
-            currentMetadata = client.getMetadata(numericIdentifier);
+            currentMetadata = client.getMetadata(bareIdentifier);
             Diff myDiff = DiffBuilder.compare(xmlMetadata).withTest(currentMetadata).ignoreWhitespace().checkForSimilar()
                     .build();
             hasDifferences = myDiff.hasDifferences();
@@ -96,7 +97,7 @@ public String reRegisterIdentifier(String identifier, Map<String, String> metada
                 }
             }
         } catch (RuntimeException e) {
-            logger.log(Level.INFO, "DOI " + numericIdentifier + " not registered with DataCite, registering now.");
+            logger.log(Level.INFO, "DOI " + bareIdentifier + " not registered with DataCite, registering now.");
             hasDifferences = true;
         }
 
@@ -106,13 +107,13 @@ public String reRegisterIdentifier(String identifier, Map<String, String> metada
         String currentUrl = null;
         try {
             //May get a 204 if the DOI is still draft
-            currentUrl = client.getUrl(numericIdentifier);
+            currentUrl = client.getUrl(bareIdentifier);
         } catch (RuntimeException ex) {
-            logger.fine("Error getting Url for " + numericIdentifier + ": " + ex.getMessage());
+            logger.fine("Error getting Url for " + bareIdentifier + ": " + ex.getMessage());
         }
         if (!target.equals(currentUrl)) {
             logger.info("Updating target URL to " +  target);
-            client.postUrl(numericIdentifier, target);
+            client.postUrl(bareIdentifier, target);
             retString = retString + "url:\\r" + target;
 
         }
diff --git a/src/main/java/edu/harvard/iq/dataverse/pidproviders/doi/datacite/DataCiteDOIProvider.java b/src/main/java/edu/harvard/iq/dataverse/pidproviders/doi/datacite/DataCiteDOIProvider.java
@@ -59,7 +59,7 @@ public DataCiteDOIProvider(String id, String label, String providerAuthority, St
         this.apiUrl = apiUrl;
         this.username = username;
         this.password = password;
-        doiDataCiteRegisterService = new DOIDataCiteRegisterService(mdsUrl, username, password);
+        doiDataCiteRegisterService = new DOIDataCiteRegisterService(mdsUrl, apiUrl, username, password);
     }
 
     @Override
@@ -349,7 +349,7 @@ public boolean updateIdentifier(DvObject dvObject) {
                 logger.info(identifier + "updated: " + updated );
                 return true;
             } else {
-                logger.info("No updated needed for " + identifier);
+                logger.info("No update needed for " + identifier);
                 return false; //No update needed
             }
         } catch (Exception e) {
diff --git a/src/main/java/edu/harvard/iq/dataverse/pidproviders/doi/datacite/DataCiteRESTfullClient.java b/src/main/java/edu/harvard/iq/dataverse/pidproviders/doi/datacite/DataCiteRESTfullClient.java
@@ -8,6 +8,7 @@
 
 import java.io.Closeable;
 import java.io.IOException;
+import java.util.Base64;
 
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -26,10 +27,9 @@
 import org.apache.http.impl.client.BasicCredentialsProvider;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClients;
-
-
-
 import org.apache.http.util.EntityUtils;
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
+import jakarta.json.JsonObject;
 
 /**
  * DataCiteRESTfullClient
@@ -46,12 +46,14 @@ public class DataCiteRESTfullClient implements Closeable {
     private static final long RETRY_DELAY_MS = 10000; // 10 seconds
     
     private String url;
+    private String restApiUrl;
     private CloseableHttpClient httpClient;
     private HttpClientContext context;
     private String encoding = "utf-8";
-    
-    public DataCiteRESTfullClient(String url, String username, String password) {
+
+    public DataCiteRESTfullClient(String url, String restApiUrl, String username, String password) {
         this.url = url;
+        this.restApiUrl = restApiUrl;
         context = HttpClientContext.create();
         CredentialsProvider credsProvider = new BasicCredentialsProvider();
         credsProvider.setCredentials(new AuthScope(null, -1), new UsernamePasswordCredentials(username, password));
@@ -192,6 +194,13 @@ public String postUrl(String doi, String url) throws IOException {
      * @return
      */
     public String getMetadata(String doi) {
+        // Try obtaining the metadata using the new, REST API:
+        try {
+            return getMetadataViaRestApi(doi);
+        } catch (RuntimeException rex) {
+            logger.warning("Failed to getMetadata via REST API for doi " + doi +", falling back to MDS");
+        }
+        
         HttpGet httpGet = new HttpGet(this.url + "/metadata/" + doi);
         httpGet.setHeader("Accept", "application/xml");
         try {
@@ -209,6 +218,58 @@ public String getMetadata(String doi) {
         }
     }
     
+    /**
+     * getMetadataViaRestApi
+     * obtains registration metadata utilizing REST API instead of MDS. 
+     * This solves some known issues, see #12070 for details. 
+     *
+     * @param doi
+     * @return
+     */
+    public String getMetadataViaRestApi(String doi) {
+        HttpGet httpGet = new HttpGet(this.restApiUrl + "/dois/" + doi);
+
+        try {
+            HttpResponse response = executeWithRetry(httpGet, "getMetadataViaRestApi");
+            String restApiRawData = EntityUtils.toString(response.getEntity(), encoding);
+            
+            logger.fine("REST API raw data: " + restApiRawData);
+            
+            if (response.getStatusLine().getStatusCode() != 200) {
+                String errMsg = "getMetadataViaRestApi, Response: " + response.getStatusLine().getStatusCode() + ", " + restApiRawData;
+                logger.log(Level.SEVERE, errMsg);
+                throw new RuntimeException(errMsg);
+            }
+
+            JsonObject restApiJson = JsonUtil.getJsonObject(restApiRawData);
+            String xmlEncoded = null; 
+            
+            JsonObject restApiJsonData = restApiJson.getJsonObject("data");
+            if (restApiJsonData != null) {
+                JsonObject restApiJsonAttributes = restApiJsonData.getJsonObject("attributes");
+                if (restApiJsonAttributes != null) {
+                    xmlEncoded = restApiJsonAttributes.getString("xml");
+                }
+            }
+            logger.fine("encoded XML entry: " + xmlEncoded);
+            
+            String metadata = null; // what we want to return, registration metadata in the XML format
+
+            if (xmlEncoded != null) {
+                // Stripping any newlines below may be unnecessary - it is likely
+                // always returned as a continuous string; but shouldn't hurt 
+                // either. 
+                metadata = new String(Base64.getDecoder().decode(xmlEncoded.replaceAll("[\\r\\n]", "")), encoding);
+            }
+            
+            logger.fine("decoded XML metadata: " + metadata);
+            return metadata;
+        } catch (IOException ioe) {
+            logger.log(Level.SEVERE, "IOException in getMetadataViaRestApi", ioe);
+            throw new RuntimeException("IOException in getMetadataViaRestAPi", ioe);
+        }
+    }
+    
     /**
      * testDOIExists
      *
@@ -270,9 +331,16 @@ public String inactiveDataset(String doi) {
         }
     }
 
+    /**
+     * The main() method can be used to test the functionality on the command
+     * line outside of Dataverse.
+     * Un-comment out and modify the code below as needed.
+     * @param args
+     * @throws Exception
+     */
     public static void main(String[] args) throws Exception {
         String doi = "10.5072/DVN/274533";
-        DataCiteRESTfullClient client = new DataCiteRESTfullClient("https://mds.test.datacite.org", "DATACITE_TEST_USERNAME", "DATACITE_TEST_PASSWORD");
+        DataCiteRESTfullClient client = new DataCiteRESTfullClient("https://mds.test.datacite.org", "https://api.test.datacite.org", "DATACITE_TEST_USERNAME", "DATACITE_TEST_PASSWORD");
 //		System.out.println(client.getUrl(doi));
 //		System.out.println(client.getMetadata(doi));
 //        System.out.println(client.postMetadata(readAndClose("C:/Users/luopc/Desktop/datacite.xml", "utf-8")));
diff --git a/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java b/src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java
@@ -246,16 +246,19 @@ public static JsonArrayBuilder jsonDataverseRoles(List<DataverseRole> roles) {
     }
 
     public static JsonObjectBuilder json(DataverseRole role) {
-        JsonObjectBuilder bld = jsonObjectBuilder()
-                .add("alias", role.getAlias())
-                .add("name", role.getName())
-                .add("permissions", JsonPrinter.json(role.permissions()))
-                .add("description", role.getDescription());
-        if (role.getId() != null) {
-            bld.add("id", role.getId());
-        }
-        if (role.getOwner() != null && role.getOwner().getId() != null) {
-            bld.add("ownerId", role.getOwner().getId());
+        JsonObjectBuilder bld = jsonObjectBuilder();
+
+        if (role != null) {
+            bld.add("alias", role.getAlias())
+               .add("name", role.getName())
+               .add("permissions", JsonPrinter.json(role.permissions()))
+               .add("description", role.getDescription());
+            if (role.getId() != null) {
+                bld.add("id", role.getId());
+            }
+            if (role.getOwner() != null && role.getOwner().getId() != null) {
+                bld.add("ownerId", role.getOwner().getId());
+            }
         }
 
         return bld;
diff --git a/src/main/java/propertyFiles/Bundle.properties b/src/main/java/propertyFiles/Bundle.properties
@@ -2191,13 +2191,13 @@ file.deaccessionDialog.reason.selectItem.beRetracted=The research article has be
 file.deaccessionDialog.reason.selectItem.beTransferred=The dataset has been transferred to another repository.
 file.deaccessionDialog.reason.selectItem.IRB=IRB request.
 file.deaccessionDialog.reason.selectItem.legalIssue=Legal issue or Data Usage Agreement.
-file.deaccessionDialog.reason.selectItem.notValid=Not a valid dataset.
+file.deaccessionDialog.reason.selectItem.notValid=Not valid. This dataset does not comply with repository policies.
 file.deaccessionDialog.reason.selectItem.other=Other (Please type reason in space provided below)
 file.deaccessionDialog.enterInfo=Please enter additional information about the reason for deaccession.
 file.deaccessionDialog.leaveURL=If applicable, please leave a URL where this dataset can be accessed after deaccessioning.
 file.deaccessionDialog.leaveURL.watermark=Optional dataset site, http://...
 file.deaccessionDialog.deaccession.tip=Are you sure you want to deaccession? This is permanent and the selected version(s) will no longer be viewable by the public.
-file.deaccessionDialog.deaccessionDataset.tip=Are you sure you want to deaccession this dataset? This is permanent an it will no longer be viewable by the public.
+file.deaccessionDialog.deaccessionDataset.tip=Are you sure you want to deaccession this dataset? This is permanent, and it will no longer be viewable by the public.
 file.deaccessionDialog.dialog.selectVersion.error=Please select version(s) for deaccessioning.
 file.deaccessionDialog.dialog.reason.error=Please select reason for deaccessioning.
 file.deaccessionDialog.dialog.url.error=Please enter valid forwarding URL.
diff --git a/src/main/resources/db/migration/V6.10.1.1.sql b/src/main/resources/db/migration/V6.10.1.1.sql
@@ -0,0 +1,3 @@
+-- modify datasetversion.deaccessionnote entries with new Bundle string 'file.deaccessionDialog.reason.selectItem.notValid'
+UPDATE dvobject SET indextime=null WHERE id in (SELECT dataset_id FROM datasetversion WHERE deaccessionnote='Not a valid dataset.');
+UPDATE datasetversion SET deaccessionnote='Not valid. This dataset does not comply with repository policies.' WHERE deaccessionnote='Not a valid dataset.';
diff --git a/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java b/src/test/java/edu/harvard/iq/dataverse/api/DataversesIT.java
diff --git a/src/test/java/edu/harvard/iq/dataverse/api/LDNInboxTest.java b/src/test/java/edu/harvard/iq/dataverse/api/LDNInboxTest.java
diff --git a/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java b/src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	+A new API endpoint for getting the default contributor role of a collection (`GET /api/dataverses/$ID/defaultContributorRole`) was added.