Merge branch 'develop' into 8184-preview-url-changes

Author: sekmiller

.github/PULL_REQUEST_TEMPLATE.md

@@ -2,7 +2,7 @@
 
 **Which issue(s) this PR closes**:
 
-Closes #
+- Closes #
 
 **Special notes for your reviewer**:
 

doc/release-notes/10697-improve-permission-indexing.md

@@ -0,0 +1,7 @@
+### Reindexing after a role assignment is less memory intensive
+
+Adding/removing a user from a role on a collection, particularly the root collection, could lead to a significant increase in memory use resulting in Dataverse itself failing with an out-of-memory condition. Such changes now consume much less memory.
+
+If you have experienced out-of-memory failures in Dataverse in the past that could have been caused by this problem, you may wish to run a [reindex in place](https://guides.dataverse.org/en/latest/admin/solr-search-index.html#reindex-in-place) to update any out-of-date information.
+
+For more information, see #10697 and #10698.

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

@@ -18,8 +18,8 @@
 @Named
 public class WidgetWrapper implements java.io.Serializable {
 
-    private final static String WIDGET_PARAMETER = "widget";
-    private final static char WIDGET_SEPARATOR = '@';
+    private static final String WIDGET_PARAMETER = "widget";
+    private static final char WIDGET_SEPARATOR = '@';
 
     private Boolean widgetView;
     private String widgetHome;

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

@@ -30,7 +30,7 @@
  */
 public abstract class AbstractOAuth2AuthenticationProvider implements AuthenticationProvider {
 
-    final static Logger logger = Logger.getLogger(AbstractOAuth2AuthenticationProvider.class.getName());
+    static final Logger logger = Logger.getLogger(AbstractOAuth2AuthenticationProvider.class.getName());
 
     protected static class ParsedUserResponse {
         public final AuthenticatedUserDisplayInfo displayInfo;

src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/AbstractOAuth2AuthenticationProvider.java

@@ -49,7 +49,7 @@
  */
 public class OrcidOAuth2AP extends AbstractOAuth2AuthenticationProvider {
 
-    final static Logger logger = Logger.getLogger(OrcidOAuth2AP.class.getName());
+    static final Logger logger = Logger.getLogger(OrcidOAuth2AP.class.getName());
 
     public static final String PROVIDER_ID_PRODUCTION = "orcid";
     public static final String PROVIDER_ID_SANDBOX = "orcid-sandbox";

src/main/java/edu/harvard/iq/dataverse/authorization/providers/oauth2/impl/OrcidOAuth2AP.java

@@ -26,9 +26,9 @@ public class DataverseRequest {
     private final String invocationId;
     private final HttpServletRequest httpServletRequest;
 
-    private final static String undefined = "0.0.0.0";
+    private static final String undefined = "0.0.0.0";
 
-    private final static String MDKEY_PREFIX="mdkey.";
+    private static final String MDKEY_PREFIX="mdkey.";
 
     private static final Logger logger = Logger.getLogger(DataverseRequest.class.getName());
 

src/main/java/edu/harvard/iq/dataverse/engine/command/DataverseRequest.java

@@ -34,7 +34,7 @@
 public class SolrIndexServiceBean {
 
     private static final Logger logger = Logger.getLogger(SolrIndexServiceBean.class.getCanonicalName());
-    
+
     @EJB
     DvObjectServiceBean dvObjectService;
     @EJB
@@ -149,7 +149,7 @@ private List<DvObjectSolrDoc> constructDatasetSolrDocs(Dataset dataset) {
         return solrDocs;
     }
 
-//    private List<DvObjectSolrDoc> constructDatafileSolrDocs(DataFile dataFile) {
+    // private List<DvObjectSolrDoc> constructDatafileSolrDocs(DataFile dataFile) {
     private List<DvObjectSolrDoc> constructDatafileSolrDocs(DataFile dataFile, Map<Long, List<String>> permStringByDatasetVersion) {
         List<DvObjectSolrDoc> datafileSolrDocs = new ArrayList<>();
         Map<DatasetVersion.VersionState, Boolean> desiredCards = searchPermissionsService.getDesiredCards(dataFile.getOwner());
@@ -166,14 +166,14 @@ private List<DvObjectSolrDoc> constructDatafileSolrDocs(DataFile dataFile, Map<L
                         cachedPerms = permStringByDatasetVersion.get(datasetVersionFileIsAttachedTo.getId());
                     }
                     if (cachedPerms != null) {
-                        logger.fine("reusing cached perms for file " + dataFile.getId());
+                        logger.finest("reusing cached perms for file " + dataFile.getId());
                         perms = cachedPerms;
                     } else if (datasetVersionFileIsAttachedTo.isReleased()) {
-                        logger.fine("no cached perms, file is public/discoverable/searchable for file " + dataFile.getId());
+                        logger.finest("no cached perms, file is public/discoverable/searchable for file " + dataFile.getId());
                         perms.add(IndexServiceBean.getPublicGroupString());
                     } else {
                         // go to the well (slow)
-                        logger.fine("no cached perms, file is not public, finding perms for file " + dataFile.getId());
+                        logger.finest("no cached perms, file is not public, finding perms for file " + dataFile.getId());
                         perms = searchPermissionsService.findDatasetVersionPerms(datasetVersionFileIsAttachedTo);
                     }
                 } else {
@@ -204,13 +204,14 @@ private List<DvObjectSolrDoc> constructDatafileSolrDocsFromDataset(Dataset datas
                 } else {
                     perms = searchPermissionsService.findDatasetVersionPerms(datasetVersionFileIsAttachedTo);
                 }
+
                 for (FileMetadata fileMetadata : datasetVersionFileIsAttachedTo.getFileMetadatas()) {
                     Long fileId = fileMetadata.getDataFile().getId();
                     String solrIdStart = IndexServiceBean.solrDocIdentifierFile + fileId;
                     String solrIdEnd = getDatasetOrDataFileSolrEnding(datasetVersionFileIsAttachedTo.getVersionState());
                     String solrId = solrIdStart + solrIdEnd;
                     DvObjectSolrDoc dataFileSolrDoc = new DvObjectSolrDoc(fileId.toString(), solrId, datasetVersionFileIsAttachedTo.getId(), fileMetadata.getLabel(), perms);
-                    logger.fine("adding fileid " + fileId);
+                    logger.finest("adding fileid " + fileId);
                     datafileSolrDocs.add(dataFileSolrDoc);
                 }
             }
@@ -361,20 +362,19 @@ private void persistToSolr(Collection<SolrInputDocument> docs) throws SolrServer
 
     public IndexResponse indexPermissionsOnSelfAndChildren(long definitionPointId) {
         DvObject definitionPoint = dvObjectService.findDvObject(definitionPointId);
-        if ( definitionPoint == null ) {
+        if (definitionPoint == null) {
             logger.log(Level.WARNING, "Cannot find a DvOpbject with id of {0}", definitionPointId);
             return null;
         } else {
             return indexPermissionsOnSelfAndChildren(definitionPoint);
         }
     }
-    
+
     /**
      * We use the database to determine direct children since there is no
      * inheritance
      */
     public IndexResponse indexPermissionsOnSelfAndChildren(DvObject definitionPoint) {
-        List<DvObject> dvObjectsToReindexPermissionsFor = new ArrayList<>();
         List<DataFile> filesToReindexAsBatch = new ArrayList<>();
         /**
          * @todo Re-indexing the definition point itself seems to be necessary
@@ -383,27 +383,47 @@ public IndexResponse indexPermissionsOnSelfAndChildren(DvObject definitionPoint)
 
         // We don't create a Solr "primary/content" doc for the root dataverse
         // so don't create a Solr "permission" doc either.
+        int i = 0;
+        int numObjects = 0;
         if (definitionPoint.isInstanceofDataverse()) {
             Dataverse selfDataverse = (Dataverse) definitionPoint;
             if (!selfDataverse.equals(dataverseService.findRootDataverse())) {
-                dvObjectsToReindexPermissionsFor.add(definitionPoint);
+                indexPermissionsForOneDvObject(definitionPoint);
+                numObjects++;
             }
             List<Dataset> directChildDatasetsOfDvDefPoint = datasetService.findByOwnerId(selfDataverse.getId());
             for (Dataset dataset : directChildDatasetsOfDvDefPoint) {
-                dvObjectsToReindexPermissionsFor.add(dataset);
+                indexPermissionsForOneDvObject(dataset);
+                numObjects++;
                 for (DataFile datafile : filesToReIndexPermissionsFor(dataset)) {
                     filesToReindexAsBatch.add(datafile);
+                    i++;
+                    if (i % 100 == 0) {
+                        reindexFilesInBatches(filesToReindexAsBatch);
+                        filesToReindexAsBatch.clear();
+                    }
+                    if (i % 1000 == 0) {
+                        logger.fine("Progress: " +i + " files permissions reindexed");
+                    }
                 }
+                logger.fine("Progress : dataset " + dataset.getId() + " permissions reindexed");
             }
         } else if (definitionPoint.isInstanceofDataset()) {
-            dvObjectsToReindexPermissionsFor.add(definitionPoint);
+            indexPermissionsForOneDvObject(definitionPoint);
+            numObjects++;
             // index files
             Dataset dataset = (Dataset) definitionPoint;
             for (DataFile datafile : filesToReIndexPermissionsFor(dataset)) {
                 filesToReindexAsBatch.add(datafile);
+                i++;
+                if (i % 100 == 0) {
+                    reindexFilesInBatches(filesToReindexAsBatch);
+                    filesToReindexAsBatch.clear();
+                }
             }
         } else {
-            dvObjectsToReindexPermissionsFor.add(definitionPoint);
+            indexPermissionsForOneDvObject(definitionPoint);
+            numObjects++;
         }
 
         /**
@@ -412,64 +432,64 @@ public IndexResponse indexPermissionsOnSelfAndChildren(DvObject definitionPoint)
          * @todo Should update timestamps, probably, even thought these are
          * files, see https://github.com/IQSS/dataverse/issues/2421
          */
-        String response = reindexFilesInBatches(filesToReindexAsBatch);
-
-        for (DvObject dvObject : dvObjectsToReindexPermissionsFor) {
-            /**
-             * @todo do something with this response
-             */
-            IndexResponse indexResponse = indexPermissionsForOneDvObject(dvObject);
-        }
-        
+        reindexFilesInBatches(filesToReindexAsBatch);
+        logger.fine("Reindexed permissions for " + i + " files and " + numObjects + " datasets/collections");
         return new IndexResponse("Number of dvObject permissions indexed for " + definitionPoint
-                + ": " + dvObjectsToReindexPermissionsFor.size()
-        );
+                + ": " + numObjects);
     }
 
     private String reindexFilesInBatches(List<DataFile> filesToReindexPermissionsFor) {
         List<SolrInputDocument> docs = new ArrayList<>();
         Map<Long, List<Long>> byParentId = new HashMap<>();
         Map<Long, List<String>> permStringByDatasetVersion = new HashMap<>();
-        for (DataFile file : filesToReindexPermissionsFor) {
-            Dataset dataset = (Dataset) file.getOwner();
-            Map<DatasetVersion.VersionState, Boolean> desiredCards = searchPermissionsService.getDesiredCards(dataset);
-            for (DatasetVersion datasetVersionFileIsAttachedTo : datasetVersionsToBuildCardsFor(dataset)) {
-                boolean cardShouldExist = desiredCards.get(datasetVersionFileIsAttachedTo.getVersionState());
-                if (cardShouldExist) {
-                    List<String> cachedPermission = permStringByDatasetVersion.get(datasetVersionFileIsAttachedTo.getId());
-                    if (cachedPermission == null) {
-                        logger.fine("no cached permission! Looking it up...");
-                        List<DvObjectSolrDoc> fileSolrDocs = constructDatafileSolrDocs((DataFile) file, permStringByDatasetVersion);
-                        for (DvObjectSolrDoc fileSolrDoc : fileSolrDocs) {
-                            Long datasetVersionId = fileSolrDoc.getDatasetVersionId();
-                            if (datasetVersionId != null) {
-                                permStringByDatasetVersion.put(datasetVersionId, fileSolrDoc.getPermissions());
+        int i = 0;
+        try {
+            for (DataFile file : filesToReindexPermissionsFor) {
+                Dataset dataset = (Dataset) file.getOwner();
+                Map<DatasetVersion.VersionState, Boolean> desiredCards = searchPermissionsService.getDesiredCards(dataset);
+                for (DatasetVersion datasetVersionFileIsAttachedTo : datasetVersionsToBuildCardsFor(dataset)) {
+                    boolean cardShouldExist = desiredCards.get(datasetVersionFileIsAttachedTo.getVersionState());
+                    if (cardShouldExist) {
+                        List<String> cachedPermission = permStringByDatasetVersion.get(datasetVersionFileIsAttachedTo.getId());
+                        if (cachedPermission == null) {
+                            logger.finest("no cached permission! Looking it up...");
+                            List<DvObjectSolrDoc> fileSolrDocs = constructDatafileSolrDocs((DataFile) file, permStringByDatasetVersion);
+                            for (DvObjectSolrDoc fileSolrDoc : fileSolrDocs) {
+                                Long datasetVersionId = fileSolrDoc.getDatasetVersionId();
+                                if (datasetVersionId != null) {
+                                    permStringByDatasetVersion.put(datasetVersionId, fileSolrDoc.getPermissions());
+                                    SolrInputDocument solrDoc = SearchUtil.createSolrDoc(fileSolrDoc);
+                                    docs.add(solrDoc);
+                                    i++;
+                                }
+                            }
+                        } else {
+                            logger.finest("cached permission is " + cachedPermission);
+                            List<DvObjectSolrDoc> fileSolrDocsBasedOnCachedPermissions = constructDatafileSolrDocs((DataFile) file, permStringByDatasetVersion);
+                            for (DvObjectSolrDoc fileSolrDoc : fileSolrDocsBasedOnCachedPermissions) {
                                 SolrInputDocument solrDoc = SearchUtil.createSolrDoc(fileSolrDoc);
                                 docs.add(solrDoc);
+                                i++;
                             }
                         }
-                    } else {
-                        logger.fine("cached permission is " + cachedPermission);
-                        List<DvObjectSolrDoc> fileSolrDocsBasedOnCachedPermissions = constructDatafileSolrDocs((DataFile) file, permStringByDatasetVersion);
-                        for (DvObjectSolrDoc fileSolrDoc : fileSolrDocsBasedOnCachedPermissions) {
-                            SolrInputDocument solrDoc = SearchUtil.createSolrDoc(fileSolrDoc);
-                            docs.add(solrDoc);
+                        if (i % 20 == 0) {
+                            persistToSolr(docs);
+                            docs = new ArrayList<>();
                         }
                     }
                 }
+                Long parent = file.getOwner().getId();
+                List<Long> existingList = byParentId.get(parent);
+                if (existingList == null) {
+                    List<Long> empty = new ArrayList<>();
+                    byParentId.put(parent, empty);
+                } else {
+                    List<Long> updatedList = existingList;
+                    updatedList.add(file.getId());
+                    byParentId.put(parent, updatedList);
+                }
             }
-            Long parent = file.getOwner().getId();
-            List<Long> existingList = byParentId.get(parent);
-            if (existingList == null) {
-                List<Long> empty = new ArrayList<>();
-                byParentId.put(parent, empty);
-            } else {
-                List<Long> updatedList = existingList;
-                updatedList.add(file.getId());
-                byParentId.put(parent, updatedList);
-            }
-        }
-        try {
+
             persistToSolr(docs);
             return " " + filesToReindexPermissionsFor.size() + " files indexed across " + docs.size() + " Solr documents ";
         } catch (SolrServerException | IOException ex) {
@@ -517,29 +537,26 @@ public JsonObjectBuilder deleteAllFromSolrAndResetIndexTimes() throws SolrServer
     }
 
     /**
-     * 
-     *
      * @return A list of dvobject ids that should have their permissions
-     * re-indexed because Solr was down when a permission was added. The permission
-     * should be added to Solr. The id of the permission contains the type of
-     * DvObject and the primary key of the dvObject.
-     * DvObjects of type DataFile are currently skipped because their index
-     * time isn't stored in the database, since they are indexed along 
-     * with their parent dataset (this may change).
+     * re-indexed because Solr was down when a permission was added. The
+     * permission should be added to Solr. The id of the permission contains the
+     * type of DvObject and the primary key of the dvObject. DvObjects of type
+     * DataFile are currently skipped because their index time isn't stored in
+     * the database, since they are indexed along with their parent dataset
+     * (this may change).
      */
     public List<Long> findPermissionsInDatabaseButStaleInOrMissingFromSolr() {
         List<Long> indexingRequired = new ArrayList<>();
         long rootDvId = dataverseService.findRootDataverse().getId();
         List<Long> missingDataversePermissionIds = dataverseService.findIdStalePermission();
         List<Long> missingDatasetPermissionIds = datasetService.findIdStalePermission();
-        for (Long id : missingDataversePermissionIds) {          
+        for (Long id : missingDataversePermissionIds) {
             if (!id.equals(rootDvId)) {
-            indexingRequired.add(id);
+                indexingRequired.add(id);
             }
         }
         indexingRequired.addAll(missingDatasetPermissionIds);
         return indexingRequired;
     }
 
-  
 }

src/main/java/edu/harvard/iq/dataverse/search/SolrIndexServiceBean.java

@@ -68,12 +68,12 @@ public class ShapefileHandler{
     private static final Logger logger = Logger.getLogger(ShapefileHandler.class.getCanonicalName());
 
     // Reference for these extensions: http://en.wikipedia.org/wiki/Shapefile
-    public final static String SHAPEFILE_FILE_TYPE = "application/zipped-shapefile";
-    public final static String SHAPEFILE_FILE_TYPE_FRIENDLY_NAME = "Shapefile as ZIP Archive";
-    public final static List<String> SHAPEFILE_MANDATORY_EXTENSIONS = Arrays.asList("shp", "shx", "dbf", "prj");
-    public final static String SHP_XML_EXTENSION = "shp.xml";
-    public final static String BLANK_EXTENSION = "__PLACEHOLDER-FOR-BLANK-EXTENSION__";
-    public final static List<String> SHAPEFILE_ALL_EXTENSIONS = Arrays.asList("shp", "shx", "dbf", "prj", "sbn", "sbx", "fbn", "fbx", "ain", "aih", "ixs", "mxs", "atx", "cpg", "qpj", "qmd", SHP_XML_EXTENSION);
+    public static final String SHAPEFILE_FILE_TYPE = "application/zipped-shapefile";
+    public static final String SHAPEFILE_FILE_TYPE_FRIENDLY_NAME = "Shapefile as ZIP Archive";
+    public static final List<String> SHAPEFILE_MANDATORY_EXTENSIONS = Arrays.asList("shp", "shx", "dbf", "prj");
+    public static final String SHP_XML_EXTENSION = "shp.xml";
+    public static final String BLANK_EXTENSION = "__PLACEHOLDER-FOR-BLANK-EXTENSION__";
+    public static final List<String> SHAPEFILE_ALL_EXTENSIONS = Arrays.asList("shp", "shx", "dbf", "prj", "sbn", "sbx", "fbn", "fbx", "ain", "aih", "ixs", "mxs", "atx", "cpg", "qpj", "qmd", SHP_XML_EXTENSION);
 
     public boolean DEBUG = false;