pacht v6.3+10797+10820

IQSS#10797
IQSS#10820

doc/release-notes/10797-update-current-version-bug-fix.md

@@ -0,0 +1,11 @@
+A significant bug in the superuser-only "Update-Current-Version" publication was found and fixed in this release. If the Update-Current-Version option was used when changes were made to the dataset Terms (rather than to dataset metadata), or if the PID provider service was down/returned an error, the update would fail and render the dataset unusable and require restoration from a backup. The fix in this release allows the update to succeed in both of these cases and redesigns the functionality such that any unknown issues should not make the dataset unusable (i.e. the error would be reported and the dataset would remain in its current state with the last-published version as it was and changes still in the draft version.)
+
+Users of earlier Dataverse releases are encouraged to alert their superusers to this issue. Those who wish to disable this functionality have two options:
+* Change the dataset.updateRelease entry in the Bundle.properties file (or local language version) to "Do Not Use" or similar (doesn't disable but alerts superusers to the issue), or
+* Edit the dataset.xhtml file to remove the lines
+
+<c:if test="#{dataverseSession.user.isSuperuser()}">
+  <f:selectItem rendered="#" itemLabel="#{bundle['dataset.updateRelease']}" itemValue="3" />
+</c:if>
+
+, delete the contents of the generated and osgi-cache directories in the Dataverse Payara domain, and restart the Payara server.

doc/release-notes/10819-publish-thumbnail-bug.md

@@ -0,0 +1,5 @@
+The initial release of the Dataverse v6.3 introduced a bug where publishing would break the dataset thumbnail, which in turn broke the rendering of the parent Collection ("dataverse") page. This problem was fixed in the PR 10820.
+
+This bug fix will prevent this from happening in the future, but does not fix any existing broken links. To restore any broken thumbnails caused by this bug, you can call the http://localhost:8080/api/admin/clearThumbnailFailureFlag API, which will attempt to clear the flag on all files (regardless of whether caused by this bug or some other problem with the file) or the http://localhost:8080/api/admin/clearThumbnailFailureFlag/id to clear the flag for individual files. Calling the former, batch API is recommended. 
+
+Additionally, the same PR made it possible to turn off the feature that automatically selects of one of the image datafiles to serve as the thumbnail of the parent dataset. An admin can turn it off by raising the feature flag `<jvm-options>-Ddataverse.feature.disable-dataset-thumbnail-autoselect=true</jvm-options>`. When the feature is disabled, a user can still manually pick a thumbnail image, or upload a dedicated thumbnail image.

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

@@ -6,6 +6,7 @@
 import edu.harvard.iq.dataverse.license.License;
 import edu.harvard.iq.dataverse.makedatacount.DatasetExternalCitations;
 import edu.harvard.iq.dataverse.makedatacount.DatasetMetrics;
+import edu.harvard.iq.dataverse.settings.FeatureFlags;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.sql.Timestamp;
@@ -206,6 +207,10 @@ public Dataset(boolean isHarvested) {
             StorageUse storageUse = new StorageUse(this); 
             this.setStorageUse(storageUse);
         }
+
+        if (FeatureFlags.DISABLE_DATASET_THUMBNAIL_AUTOSELECT.enabled()) {
+            this.setUseGenericThumbnail(true);
+        }
     }
 
     /**
@@ -969,4 +974,4 @@ public DatasetThumbnail getDatasetThumbnail(DatasetVersion datasetVersion, int s
     public String getTargetUrl() {
         return Dataset.TARGET_URL;
     }
-}
+}

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

@@ -9,6 +9,7 @@
 import static edu.harvard.iq.dataverse.batch.jobs.importer.filesystem.FileRecordJobListener.SEP;
 import edu.harvard.iq.dataverse.batch.util.LoggingUtil;
 import edu.harvard.iq.dataverse.search.SolrSearchResult;
+import edu.harvard.iq.dataverse.settings.FeatureFlags;
 import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import edu.harvard.iq.dataverse.util.MarkupChecker;
@@ -315,6 +316,23 @@ private void msg(String s){
         //logger.fine(s);
     }
 
+    public boolean isVersionDefaultCustomTerms(DatasetVersion datasetVersion) {
+        //SEK - belt and suspenders here, but this is where the bug 10719 first manifested
+        if (datasetVersion != null && datasetVersion.getId() != null) {
+            try {
+                TermsOfUseAndAccess toua = (TermsOfUseAndAccess) em.createNamedQuery("TermsOfUseAndAccess.findByDatasetVersionIdAndDefaultTerms")
+                        .setParameter("id", datasetVersion.getId()).setParameter("defaultTerms", TermsOfUseAndAccess.DEFAULT_NOTERMS).getSingleResult();
+                if (toua != null && datasetVersion.getTermsOfUseAndAccess().getLicense() == null) {
+                    return true;
+                }
+
+            } catch (NoResultException e) {
+                return false;
+            }
+        }
+        return false;
+    }
+
     /**
      * Does the version identifier in the URL ask for a "DRAFT"?
      * 
@@ -790,100 +808,101 @@ public Long getThumbnailByVersionId(Long versionId) {
             return null;
         }
 
-        Long thumbnailFileId;
-
-        // First, let's see if there are thumbnails that have already been 
-        // generated:
-        try {
-            thumbnailFileId = (Long) em.createNativeQuery("SELECT df.id "
-                    + "FROM datafile df, filemetadata fm, datasetversion dv, dvobject o "
-                    + "WHERE dv.id = " + versionId + " "
-                    + "AND df.id = o.id "
-                    + "AND fm.datasetversion_id = dv.id "
-                    + "AND fm.datafile_id = df.id "
-                    + "AND df.restricted = false "
-                    + "AND df.embargo_id is null "
-                    + "AND df.retention_id is null "
-                    + "AND o.previewImageAvailable = true "
-                    + "ORDER BY df.id LIMIT 1;").getSingleResult();
-        } catch (Exception ex) {
-            thumbnailFileId = null;
-        }
-
-        if (thumbnailFileId != null) {
-            logger.fine("DatasetVersionService,getThumbnailByVersionid(): found already generated thumbnail for version " + versionId + ": " + thumbnailFileId);
-            assignDatasetThumbnailByNativeQuery(versionId, thumbnailFileId);
-            return thumbnailFileId;
-        }
-
-        if (!systemConfig.isThumbnailGenerationDisabledForImages()) {
-            // OK, let's try and generate an image thumbnail!
-            long imageThumbnailSizeLimit = systemConfig.getThumbnailSizeLimitImage();
+        if (!FeatureFlags.DISABLE_DATASET_THUMBNAIL_AUTOSELECT.enabled()) {
+            Long thumbnailFileId;
 
+            // First, let's see if there are thumbnails that have already been 
+            // generated:
             try {
                 thumbnailFileId = (Long) em.createNativeQuery("SELECT df.id "
                         + "FROM datafile df, filemetadata fm, datasetversion dv, dvobject o "
                         + "WHERE dv.id = " + versionId + " "
                         + "AND df.id = o.id "
                         + "AND fm.datasetversion_id = dv.id "
                         + "AND fm.datafile_id = df.id "
-                        + "AND o.previewimagefail = false "
                         + "AND df.restricted = false "
                         + "AND df.embargo_id is null "
                         + "AND df.retention_id is null "
-                        + "AND df.contenttype LIKE 'image/%' "
-                        + "AND NOT df.contenttype = 'image/fits' "
-                        + "AND df.filesize < " + imageThumbnailSizeLimit + " "
-                        + "ORDER BY df.filesize ASC LIMIT 1;").getSingleResult();
+                        + "AND o.previewImageAvailable = true "
+                        + "ORDER BY df.id LIMIT 1;").getSingleResult();
             } catch (Exception ex) {
                 thumbnailFileId = null;
             }
 
             if (thumbnailFileId != null) {
-                logger.fine("obtained file id: " + thumbnailFileId);
-                DataFile thumbnailFile = datafileService.find(thumbnailFileId);
-                if (thumbnailFile != null) {
-                    if (datafileService.isThumbnailAvailable(thumbnailFile)) {
-                        assignDatasetThumbnailByNativeQuery(versionId, thumbnailFileId);
-                        return thumbnailFileId;
+                logger.fine("DatasetVersionService,getThumbnailByVersionid(): found already generated thumbnail for version " + versionId + ": " + thumbnailFileId);
+                assignDatasetThumbnailByNativeQuery(versionId, thumbnailFileId);
+                return thumbnailFileId;
+            }
+
+            if (!systemConfig.isThumbnailGenerationDisabledForImages()) {
+                // OK, let's try and generate an image thumbnail!
+                long imageThumbnailSizeLimit = systemConfig.getThumbnailSizeLimitImage();
+
+                try {
+                    thumbnailFileId = (Long) em.createNativeQuery("SELECT df.id "
+                            + "FROM datafile df, filemetadata fm, datasetversion dv, dvobject o "
+                            + "WHERE dv.id = " + versionId + " "
+                            + "AND df.id = o.id "
+                            + "AND fm.datasetversion_id = dv.id "
+                            + "AND fm.datafile_id = df.id "
+                            + "AND o.previewimagefail = false "
+                            + "AND df.restricted = false "
+                            + "AND df.embargo_id is null "
+                            + "AND df.retention_id is null "
+                            + "AND df.contenttype LIKE 'image/%' "
+                            + "AND NOT df.contenttype = 'image/fits' "
+                            + "AND df.filesize < " + imageThumbnailSizeLimit + " "
+                            + "ORDER BY df.filesize ASC LIMIT 1;").getSingleResult();
+                } catch (Exception ex) {
+                    thumbnailFileId = null;
+                }
+
+                if (thumbnailFileId != null) {
+                    logger.fine("obtained file id: " + thumbnailFileId);
+                    DataFile thumbnailFile = datafileService.find(thumbnailFileId);
+                    if (thumbnailFile != null) {
+                        if (datafileService.isThumbnailAvailable(thumbnailFile)) {
+                            assignDatasetThumbnailByNativeQuery(versionId, thumbnailFileId);
+                            return thumbnailFileId;
+                        }
                     }
                 }
             }
-        }
 
-        // And if that didn't work, try the same thing for PDFs:
-        if (!systemConfig.isThumbnailGenerationDisabledForPDF()) {
-            // OK, let's try and generate an image thumbnail!
-            long imageThumbnailSizeLimit = systemConfig.getThumbnailSizeLimitPDF();
-            try {
-                thumbnailFileId = (Long) em.createNativeQuery("SELECT df.id "
-                        + "FROM datafile df, filemetadata fm, datasetversion dv, dvobject o "
-                        + "WHERE dv.id = " + versionId + " "
-                        + "AND df.id = o.id "
-                        + "AND fm.datasetversion_id = dv.id "
-                        + "AND fm.datafile_id = df.id "
-                        + "AND o.previewimagefail = false "
-                        + "AND df.restricted = false "
-                        + "AND df.embargo_id is null "
-                        + "AND df.retention_id is null "
-                        + "AND df.contenttype = 'application/pdf' "
-                        + "AND df.filesize < " + imageThumbnailSizeLimit + " "
-                        + "ORDER BY df.filesize ASC LIMIT 1;").getSingleResult();
-            } catch (Exception ex) {
-                thumbnailFileId = null;
-            }
+            // And if that didn't work, try the same thing for PDFs:
+            if (!systemConfig.isThumbnailGenerationDisabledForPDF()) {
+                // OK, let's try and generate an image thumbnail!
+                long imageThumbnailSizeLimit = systemConfig.getThumbnailSizeLimitPDF();
+                try {
+                    thumbnailFileId = (Long) em.createNativeQuery("SELECT df.id "
+                            + "FROM datafile df, filemetadata fm, datasetversion dv, dvobject o "
+                            + "WHERE dv.id = " + versionId + " "
+                            + "AND df.id = o.id "
+                            + "AND fm.datasetversion_id = dv.id "
+                            + "AND fm.datafile_id = df.id "
+                            + "AND o.previewimagefail = false "
+                            + "AND df.restricted = false "
+                            + "AND df.embargo_id is null "
+                            + "AND df.retention_id is null "
+                            + "AND df.contenttype = 'application/pdf' "
+                            + "AND df.filesize < " + imageThumbnailSizeLimit + " "
+                            + "ORDER BY df.filesize ASC LIMIT 1;").getSingleResult();
+                } catch (Exception ex) {
+                    thumbnailFileId = null;
+                }
 
-            if (thumbnailFileId != null) {
-                DataFile thumbnailFile = datafileService.find(thumbnailFileId);
-                if (thumbnailFile != null) {
-                    if (datafileService.isThumbnailAvailable(thumbnailFile)) {
-                        assignDatasetThumbnailByNativeQuery(versionId, thumbnailFileId);
-                        return thumbnailFileId;
+                if (thumbnailFileId != null) {
+                    DataFile thumbnailFile = datafileService.find(thumbnailFileId);
+                    if (thumbnailFile != null) {
+                        if (datafileService.isThumbnailAvailable(thumbnailFile)) {
+                            assignDatasetThumbnailByNativeQuery(versionId, thumbnailFileId);
+                            return thumbnailFileId;
+                        }
                     }
                 }
             }
         }
-
         return null;
     }
 
@@ -1277,4 +1296,4 @@ public List<DatasetVersion> getUnarchivedDatasetVersions(){
             return null;
         }
     } // end getUnarchivedDatasetVersions
-} // end class
+} // end class

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

@@ -17,6 +17,28 @@
 import jakarta.persistence.Transient;
 
 import edu.harvard.iq.dataverse.license.License;
+import jakarta.persistence.NamedQueries;
+import jakarta.persistence.NamedQuery;
+
+@NamedQueries({
+    // TermsOfUseAndAccess.findByDatasetVersionIdAndDefaultTerms 
+    // is used to determine if the dataset terms were set by the multi license support update 
+    // as part of the 5.10 release.
+
+    @NamedQuery(name = "TermsOfUseAndAccess.findByDatasetVersionIdAndDefaultTerms", 
+                query = "SELECT o FROM TermsOfUseAndAccess o, DatasetVersion dv WHERE "
+                        + "dv.id =:id "
+                        + "AND dv.termsOfUseAndAccess.id = o.id "
+                        + "AND o.termsOfUse =:defaultTerms "
+                        + "AND o.confidentialityDeclaration IS null " 
+                        + "AND o.specialPermissions IS null "
+                        + "AND o.restrictions IS null "
+                        + "AND o.citationRequirements IS null "
+                        + "AND o.depositorRequirements IS null "
+                        + "AND o.conditions IS null "
+                        + "AND o.disclaimer IS null "
+    )
+})
 
 /**
  *
@@ -27,6 +49,8 @@
 @ValidateTermsOfUseAndAccess
 public class TermsOfUseAndAccess implements Serializable {
 
+    public static final String DEFAULT_NOTERMS = "This dataset is made available without information on how it can be used. You should communicate with the Contact(s) specified before use.";
+
     @Id
     @GeneratedValue(strategy = GenerationType.IDENTITY)
     private Long id;

src/main/java/edu/harvard/iq/dataverse/dataset/DatasetUtil.java

@@ -114,13 +114,20 @@ public static List<DatasetThumbnail> getThumbnailCandidates(Dataset dataset, boo
      *
      * @param dataset
      * @param datasetVersion
-     * @return
+     * @param size of the requested thumbnail
+     * @return DatasetThumbnail object, or null if not available
      */
     public static DatasetThumbnail getThumbnail(Dataset dataset, DatasetVersion datasetVersion, int size) {
         if (dataset == null) {
             return null;
         }
 
+        if (size == 0) {
+            // Size 0 will fail (and set the failure flag) and should never be sent
+            logger.warning("getThumbnail called with size 0");
+            return null;
+        }   
+
         StorageIO<Dataset> dataAccess = null;
 
         try{