Merge branch '4.2.1'

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>4.2.0</version>
+    <version>4.2.1</version>
     <name>ice</name>
     <description>Inventory of Composable Elements (ICE) for Synthetic Biology</description>
     <repositories>
@@ -60,12 +60,12 @@
         <dependency>
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-core</artifactId>
-            <version>4.3.9.Final</version>
+            <version>4.3.10.Final</version>
         </dependency>
         <dependency>
             <groupId>org.hibernate</groupId>
-            <artifactId>hibernate-search</artifactId>
-            <version>5.2.0.Final</version>
+            <artifactId>hibernate-search-orm</artifactId>
+            <version>5.3.0.Final</version>
         </dependency>
         <dependency>
             <groupId>org.hibernate</groupId>
@@ -75,7 +75,7 @@
         <dependency>
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-c3p0</artifactId>
-            <version>4.3.8.Final</version>
+            <version>4.3.10.Final</version>
         </dependency>
         <dependency>
             <groupId>commons-cli</groupId>

src/main/java/org/jbei/ice/lib/bulkupload/BulkEntryCreator.java

@@ -3,6 +3,7 @@
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringUtils;
 import org.jbei.ice.ApplicationController;
+import org.jbei.ice.lib.access.Permission;
 import org.jbei.ice.lib.account.AccountController;
 import org.jbei.ice.lib.account.model.Account;
 import org.jbei.ice.lib.common.logging.Logger;
@@ -125,6 +126,20 @@ protected PartData createEntryForUpload(String userId, PartData data, BulkUpload
         }
 
         entry = entryDAO.create(entry);
+
+        // check for pi
+        String piEmail = entry.getPrincipalInvestigatorEmail();
+        if (StringUtils.isNotEmpty(piEmail)) {
+            Account pi = DAOFactory.getAccountDAO().getByEmail(piEmail);
+            if (pi != null) {
+                // add write permission for the PI
+                addWritePermission(pi, entry);
+            }
+        }
+
+        // add write permissions for owner
+        addWritePermission(account, entry);
+
         upload.getContents().add(entry);
 
         dao.update(upload);
@@ -385,6 +400,15 @@ public BulkUploadInfo createOrUpdateEntries(String userId, long draftId, List<Pa
         return uploadInfo;
     }
 
+    protected void addWritePermission(Account account, Entry entry) {
+        Permission permission = new Permission();
+        permission.setCanWrite(true);
+        permission.setEntry(entry);
+        entry.getPermissions().add(permission); // triggers the permission class bridge
+        permission.setAccount(account);
+        DAOFactory.getPermissionDAO().create(permission);
+    }
+
     public boolean createEntries(String userId, long draftId, List<PartData> data, HashMap<String, InputStream> files) {
         BulkUpload draft = dao.get(draftId);
         if (draft == null)
@@ -420,6 +444,8 @@ public boolean createEntries(String userId, long draftId, List<PartData> data, H
                     linked.setId(linkedEntry.getId());
                     linked.setModificationTime(linkedEntry.getModificationTime().getTime());
 
+                    addWritePermission(account, linkedEntry);
+
                     // check for attachments and sequences for linked entry
                     saveFiles(linked, linkedEntry, files);
 
@@ -429,6 +455,19 @@ public boolean createEntries(String userId, long draftId, List<PartData> data, H
             }
 
             entry = entryDAO.create(entry);
+            // check for pi
+            String piEmail = entry.getPrincipalInvestigatorEmail();
+            if (StringUtils.isNotEmpty(piEmail)) {
+                Account pi = DAOFactory.getAccountDAO().getByEmail(piEmail);
+                if (pi != null) {
+                    // add write permission for the PI
+                    addWritePermission(pi, entry);
+                }
+            }
+
+            // add write permissions for owner
+            addWritePermission(account, entry);
+
             draft.getContents().add(entry);
 
             dao.update(draft);

src/main/java/org/jbei/ice/lib/bulkupload/BulkUploadController.java

@@ -22,6 +22,7 @@
 import org.jbei.ice.lib.entry.attachment.AttachmentController;
 import org.jbei.ice.lib.entry.model.Entry;
 import org.jbei.ice.lib.entry.sequence.SequenceController;
+import org.jbei.ice.lib.executor.IceExecutorService;
 import org.jbei.ice.lib.group.Group;
 import org.jbei.ice.lib.group.GroupController;
 import org.jbei.ice.lib.models.Sequence;
@@ -77,9 +78,11 @@ public BulkUploadInfo create(String userId, BulkUploadInfo info) {
         upload.setAccount(account);
         upload.setCreationTime(new Date());
         upload.setLastUpdateTime(upload.getCreationTime());
-        if (info.getStatus() == BulkUploadStatus.BULK_EDIT)
+        if (info.getStatus() == BulkUploadStatus.BULK_EDIT) {
+            // only one instance of bulk edit is allowed to remain
+            clearBulkEdits(userId);
             upload.setStatus(BulkUploadStatus.BULK_EDIT);
-        else
+        } else
             upload.setStatus(BulkUploadStatus.IN_PROGRESS);
 
         upload.setImportType(info.getType());
@@ -113,6 +116,28 @@ public BulkUploadInfo create(String userId, BulkUploadInfo info) {
         return upload.toDataTransferObject();
     }
 
+    /**
+     * Removes any bulk edits belonging to the specified user
+     *
+     * @param userId unique identifier for user whose bulk edits are to be removed
+     */
+    protected void clearBulkEdits(String userId) {
+        Account account = DAOFactory.getAccountDAO().getByEmail(userId);
+        if (account == null)
+            return;
+
+        List<BulkUpload> userEdits = dao.retrieveByAccount(account);
+        if (userEdits == null || userEdits.isEmpty())
+            return;
+
+        for (BulkUpload upload : userEdits) {
+            if (upload.getStatus() != BulkUploadStatus.BULK_EDIT)
+                continue;
+            upload.getContents().clear();
+            dao.delete(upload);
+        }
+    }
+
     /**
      * Retrieves list of bulk imports that are owned by the system. System ownership is assigned to
      * all bulk imports that are submitted by non-admins and indicates that it is pending approval.
@@ -283,19 +308,8 @@ public BulkUploadInfo deleteDraftById(String userId, long draftId) throws Permis
         if (!userId.equals(draftAccount.getEmail()) && !accountController.isAdministrator(userId))
             throw new PermissionException("No permissions to delete draft " + draftId);
 
-        // delete all associated entries. for strain with plasmids both are returned
-        // todo : use task to speed up process and also check for status
-
-        ArrayList<Long> entryIds = dao.getEntryIds(draft);
-        for (long entryId : entryIds) {
-            try {
-                entryController.delete(userId, entryId);
-            } catch (PermissionException pe) {
-                Logger.warn(userId + " does not have permission to delete" + entryId + " for bulk upload " + draftId);
-            }
-        }
-
-        dao.delete(draft);
+        BulkUploadDeleteTask task = new BulkUploadDeleteTask(userId, draftId);
+        IceExecutorService.getInstance().runTask(task);
 
         BulkUploadInfo draftInfo = draft.toDataTransferObject();
         AccountTransfer accountTransfer = draft.getAccount().toDataTransferObject();

src/main/java/org/jbei/ice/lib/bulkupload/BulkUploadDeleteTask.java

@@ -0,0 +1,60 @@
+package org.jbei.ice.lib.bulkupload;
+
+import org.jbei.ice.lib.common.logging.Logger;
+import org.jbei.ice.lib.dao.DAOFactory;
+import org.jbei.ice.lib.dao.hibernate.BulkUploadDAO;
+import org.jbei.ice.lib.dto.entry.Visibility;
+import org.jbei.ice.lib.entry.model.Entry;
+import org.jbei.ice.lib.executor.Task;
+
+
+/**
+ * Task to delete bulk uploads with a status of draft and their contents.
+ *
+ * @author Hector Plahar
+ */
+public class BulkUploadDeleteTask extends Task {
+
+    private final long bulkUploadId;
+    private final String userId;
+
+    public BulkUploadDeleteTask(final String userId, final long id) {
+        this.bulkUploadId = id;
+        this.userId = userId;
+    }
+
+    @Override
+    public void execute() {
+        BulkUploadDAO dao = DAOFactory.getBulkUploadDAO();
+
+        BulkUpload upload = dao.get(bulkUploadId);
+        if (upload == null) {
+            Logger.error("Could not locate bulk upload " + bulkUploadId + " for deletion");
+            return;
+        }
+
+        BulkUploadAuthorization authorization = new BulkUploadAuthorization();
+        authorization.expectWrite(userId, upload);
+
+        if (upload.getStatus() != BulkUploadStatus.IN_PROGRESS)
+            return;
+
+        // delete all associated entries that have a status of draft
+        for (Entry entry : upload.getContents()) {
+            for (Entry linkedEntry : entry.getLinkedEntries()) {
+                if (linkedEntry.getVisibility() != Visibility.DRAFT.getValue())
+                    continue;
+
+                DAOFactory.getEntryDAO().fullDelete(linkedEntry);
+//                entryController.fullDelete(userId, linkedEntry.getId());
+            }
+
+            if (entry.getVisibility() == Visibility.DRAFT.getValue()) {
+                DAOFactory.getEntryDAO().fullDelete(entry);
+//                entryController.fullDelete(userId, entry.getId());
+            }
+        }
+
+        dao.delete(upload);
+    }
+}