Merge pull request #7118 from IQSS/6918-locking-improvements

6918 locking improvements

doc/release-notes/6918-publishing-lock.md

@@ -0,0 +1,6 @@
+The setting :PIDAsynchRegFileCount is deprecated as of v5.0. 
+
+It used to specify the number of datafiles in the dataset to warrant
+adding a lock during publishing. As of v5.0 all datasets get
+locked for the duration of the publishing process. The setting will be
+ignored if present.

doc/sphinx-guides/source/installation/config.rst

@@ -186,7 +186,6 @@ Here are the configuration options for DOIs:
 - :ref:`:IdentifierGenerationStyle <:IdentifierGenerationStyle>` (optional)
 - :ref:`:DataFilePIDFormat <:DataFilePIDFormat>` (optional)
 - :ref:`:FilePIDsEnabled <:FilePIDsEnabled>` (optional, defaults to true)
-- :ref:`:PIDAsynchRegFileCount <:PIDAsynchRegFileCount>` (optional, defaults to 10)
 
 Configuring Dataverse for Handles
 +++++++++++++++++++++++++++++++++
@@ -1446,24 +1445,13 @@ Note that in either case, when using the ``sequentialNumber`` option, datasets a
 :FilePIDsEnabled
 ++++++++++++++++
 
-Toggles publishing of file-based PIDs for the entire installation. By default this setting is absent and Dataverse assumes it to be true.
+Toggles publishing of file-based PIDs for the entire installation. By default this setting is absent and Dataverse assumes it to be true. If enabled, the registration will be performed asynchronously (in the background) during publishing of a dataset.
 
 If you don't want to register file-based PIDs for your installation, set:
 
 ``curl -X PUT -d 'false' http://localhost:8080/api/admin/settings/:FilePIDsEnabled``
 
-Note: File-level PID registration was added in 4.9 and is required until version 4.9.3.
-
-Note: The dataset will be locked, and the registration will be performed asynchronously, when there are more than N files in the dataset, where N is configured by the database setting ``:PIDAsynchRegFileCount`` (default: 10). 
-
-.. _:PIDAsynchRegFileCount:
-
-:PIDAsynchRegFileCount
-++++++++++++++++++++++
-
-Configures the number of files in the dataset to warrant performing the registration of persistent identifiers (section above) and/or file validation asynchronously during publishing. The setting is optional, and the default value is 10.
-
-``curl -X PUT -d '100' http://localhost:8080/api/admin/settings/:PIDAsynchRegFileCount``
+Note: File-level PID registration was added in 4.9; it could not be disabled until version 4.9.3.
 
 .. _:IndependentHandleService:
 
@@ -1480,14 +1468,12 @@ By default this setting is absent and Dataverse assumes it to be false.
 :FileValidationOnPublishEnabled
 +++++++++++++++++++++++++++++++
 
-Toggles validation of the physical files in the dataset when it's published, by recalculating the checksums and comparing against the values stored in the DataFile table. By default this setting is absent and Dataverse assumes it to be true.
+Toggles validation of the physical files in the dataset when it's published, by recalculating the checksums and comparing against the values stored in the DataFile table. By default this setting is absent and Dataverse assumes it to be true. If enabled, the validation will be performed asynchronously, similarly to how we handle assigning persistent identifiers to datafiles, with the dataset locked for the duration of the publishing process. 
 
 If you don't want the datafiles to be validated on publish, set:
 
 ``curl -X PUT -d 'false' http://localhost:8080/api/admin/settings/:FileValidationOnPublishEnabled``
 
-Note: The dataset will be locked, and the validation will be performed asynchronously, similarly to how we handle assigning persistend identifiers to datafiles, when there are more than N files in the dataset, where N is configured by the database setting ``:PIDAsynchRegFileCount`` (default: 10). 
-
 
 :ApplicationTermsOfUse
 ++++++++++++++++++++++

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

@@ -2658,7 +2658,7 @@ private String releaseDataset(boolean minor) {
         } else {
             JsfHelper.addErrorMessage(BundleUtil.getStringFromBundle("dataset.message.only.authenticatedUsers"));
         }
-        return returnToDatasetOnly();
+        return returnToDraftVersion();
     }
 
     @Deprecated

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

@@ -481,6 +481,13 @@ public String getMessageTextBasedOnNotification(UserNotification userNotificatio
                     version.getDataset().getOwner().getDisplayName(),  getDataverseLink(version.getDataset().getOwner())};
                 messageText += MessageFormat.format(pattern, paramArrayPublishedDataset);
                 return messageText;
+            case PUBLISHFAILED_PIDREG:
+                version =  (DatasetVersion) targetObject;
+                pattern = BundleUtil.getStringFromBundle("notification.email.publishFailedPidReg");
+                String[] paramArrayPublishFailedDatasetPidReg = {version.getDataset().getDisplayName(), getDatasetLink(version.getDataset()), 
+                    version.getDataset().getOwner().getDisplayName(),  getDataverseLink(version.getDataset().getOwner())};
+                messageText += MessageFormat.format(pattern, paramArrayPublishFailedDatasetPidReg);
+                return messageText;
             case RETURNEDDS:
                 version =  (DatasetVersion) targetObject;
                 pattern = BundleUtil.getStringFromBundle("notification.email.wasReturnedByReviewer");
@@ -597,6 +604,7 @@ private Object getObjectOfNotification (UserNotification userNotification){
             case CREATEDS:
             case SUBMITTEDDS:
             case PUBLISHEDDS:
+            case PUBLISHFAILED_PIDREG:
             case RETURNEDDS:
                 return versionService.find(userNotification.getObjectId());
             case CREATEACC:

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

@@ -27,7 +27,7 @@
 
 public class UserNotification implements Serializable {
     public enum Type {
-        ASSIGNROLE, REVOKEROLE, CREATEDV, CREATEDS, CREATEACC, MAPLAYERUPDATED, MAPLAYERDELETEFAILED, SUBMITTEDDS, RETURNEDDS, PUBLISHEDDS, REQUESTFILEACCESS, GRANTFILEACCESS, REJECTFILEACCESS, FILESYSTEMIMPORT, CHECKSUMIMPORT, CHECKSUMFAIL, CONFIRMEMAIL, APIGENERATED, INGESTCOMPLETED, INGESTCOMPLETEDWITHERRORS
+        ASSIGNROLE, REVOKEROLE, CREATEDV, CREATEDS, CREATEACC, MAPLAYERUPDATED, MAPLAYERDELETEFAILED, SUBMITTEDDS, RETURNEDDS, PUBLISHEDDS, REQUESTFILEACCESS, GRANTFILEACCESS, REJECTFILEACCESS, FILESYSTEMIMPORT, CHECKSUMIMPORT, CHECKSUMFAIL, CONFIRMEMAIL, APIGENERATED, INGESTCOMPLETED, INGESTCOMPLETEDWITHERRORS, PUBLISHFAILED_PIDREG
     };
 
     private static final long serialVersionUID = 1L;

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

@@ -13,6 +13,8 @@
 import java.util.logging.Logger;
 import javax.ejb.EJB;
 import javax.ejb.Stateless;
+import javax.ejb.TransactionAttribute;
+import javax.ejb.TransactionAttributeType;
 import javax.inject.Named;
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
@@ -83,6 +85,11 @@ public void delete(UserNotification userNotification) {
         em.remove(em.merge(userNotification));
     }
 
+    @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW)
+    public void sendNotificationInNewTransaction(AuthenticatedUser dataverseUser, Timestamp sendDate, Type type, Long objectId) {
+        sendNotification(dataverseUser, sendDate, type, objectId, "");
+    }
+
     public void sendNotification(AuthenticatedUser dataverseUser, Timestamp sendDate, Type type, Long objectId) {
         sendNotification(dataverseUser, sendDate, type, objectId, "");
     }
@@ -106,10 +113,9 @@ public void sendNotification(AuthenticatedUser dataverseUser, Timestamp sendDate
         if (mailService.sendNotificationEmail(userNotification, comment, requestor, isHtmlContent)) {
             logger.fine("email was sent");
             userNotification.setEmailed(true);
-            save(userNotification);
         } else {
             logger.fine("email was not sent");
-            save(userNotification);
         }
+        save(userNotification);
     }
 }

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

@@ -72,6 +72,7 @@
 
 import java.util.List;
 import edu.harvard.iq.dataverse.authorization.AuthTestDataServiceBean;
+import edu.harvard.iq.dataverse.authorization.AuthenticationProvidersRegistrationServiceBean;
 import edu.harvard.iq.dataverse.authorization.RoleAssignee;
 import edu.harvard.iq.dataverse.authorization.UserRecordIdentifier;
 import edu.harvard.iq.dataverse.authorization.groups.impl.explicit.ExplicitGroupServiceBean;
@@ -114,6 +115,8 @@ public class Admin extends AbstractApiBean {
 
 	private static final Logger logger = Logger.getLogger(Admin.class.getName());
 
+        @EJB
+        AuthenticationProvidersRegistrationServiceBean authProvidersRegistrationSvc;
 	@EJB
 	BuiltinUserServiceBean builtinUserService;
 	@EJB
@@ -223,9 +226,9 @@ public Response addProvider(AuthenticationProviderRow row) {
 				managed = row;
 			}
 			if (managed.isEnabled()) {
-				AuthenticationProvider provider = authSvc.loadProvider(managed);
-				authSvc.deregisterProvider(provider.getId());
-				authSvc.registerProvider(provider);
+				AuthenticationProvider provider = authProvidersRegistrationSvc.loadProvider(managed);
+				authProvidersRegistrationSvc.deregisterProvider(provider.getId());
+				authProvidersRegistrationSvc.registerProvider(provider);
 			}
 			return created("/api/admin/authenticationProviders/" + managed.getId(), json(managed));
 		} catch (AuthorizationSetupException e) {
@@ -271,7 +274,7 @@ public Response enableAuthenticationProvider(@PathParam("id") String id, String
 				return ok(String.format("Authentication provider '%s' already enabled", id));
 			}
 			try {
-				authSvc.registerProvider(authSvc.loadProvider(row));
+				authProvidersRegistrationSvc.registerProvider(authProvidersRegistrationSvc.loadProvider(row));
 				return ok(String.format("Authentication Provider %s enabled", row.getId()));
 
 			} catch (AuthenticationProviderFactoryNotFoundException ex) {
@@ -285,7 +288,7 @@ public Response enableAuthenticationProvider(@PathParam("id") String id, String
 
 		} else {
 			// disable a provider
-			authSvc.deregisterProvider(id);
+			authProvidersRegistrationSvc.deregisterProvider(id);
 			return ok("Authentication Provider '" + id + "' disabled. "
 					+ (authSvc.getAuthenticationProviderIds().isEmpty()
 							? "WARNING: no enabled authentication providers left."
@@ -309,7 +312,7 @@ public Response checkAuthenticationProviderEnabled(@PathParam("id") String id) {
 	@DELETE
 	@Path("authenticationProviders/{id}/")
 	public Response deleteAuthenticationProvider(@PathParam("id") String id) {
-		authSvc.deregisterProvider(id);
+		authProvidersRegistrationSvc.deregisterProvider(id);
 		AuthenticationProviderRow row = em.find(AuthenticationProviderRow.class, id);
 		if (row != null) {
 			em.remove(row);