Merge branch 'hotfix-4.1.7'

LICENSE.txt

@@ -1,5 +1,5 @@
 JBEI Registry of Parts (JBEIR), JBEI Inventory of Composable Parts (ICE)
-Copyright (c) 2009, The Regents of the University of California,
+Copyright (c) 2009 - 2015, The Regents of the University of California,
 through Lawrence Berkeley National Laboratory (subject to receipt of
 any required approvals from the U.S. Dept. of Energy).  All rights
 reserved.

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>4.1.6</version>
+    <version>4.1.7</version>
     <name>ice</name>
     <description>Inventory of Composable Elements (ICE) for Synthetic Biology</description>
     <repositories>

src/main/java/org/jbei/ice/lib/account/AccountController.java

@@ -82,26 +82,26 @@ public Account get(long id) {
     }
 
     /**
-     * Changes user's password
+     * Reset a user's password
      *
-     * @param email       optional unique account identifier for user making request. If valid and an administrator
-     *                    then the newly created password is also sent
-     * @param targetEmail email address of user account to be changeds
+     * @param targetEmail email address of user account to be changed
+     * @return true if the user account is found with email specified in the parameter and password for it is
+     *         successfully reset, false otherwise
      */
-    public AccountTransfer resetPassword(String email, String targetEmail) {
+    public boolean resetPassword(String targetEmail) {
         Account account = getByEmail(targetEmail);
         if (account == null)
-            throw new IllegalArgumentException("Cannot retrieve account for " + targetEmail);
+            return false;
 
-        String newPassword = Utils.generateUUID().substring(24);
-        String encryptedNewPassword = AccountUtils.encryptNewUserPassword(newPassword, account.getSalt());
-        account.setPassword(encryptedNewPassword);
+        try {
+            String newPassword = Utils.generateUUID().substring(24);
+            String encryptedNewPassword = AccountUtils.encryptNewUserPassword(newPassword, account.getSalt());
+            account.setPassword(encryptedNewPassword);
 
-        account = dao.update(account);
-        AccountTransfer transfer = account.toDataTransferObject();
-        transfer.setPassword(newPassword);
+            account = dao.update(account);
+            AccountTransfer transfer = account.toDataTransferObject();
+            transfer.setPassword(newPassword);
 
-        if (email == null || !isAdministrator(email)) {
             String url = Utils.getConfigValue(ConfigurationKey.URI_PREFIX);
             String projectName = Utils.getConfigValue(ConfigurationKey.PROJECT_NAME);
             if (StringUtils.isEmpty(projectName))
@@ -110,8 +110,6 @@ public AccountTransfer resetPassword(String email, String targetEmail) {
             String name = account.getFirstName();
             if (StringUtils.isBlank(name)) {
                 name = account.getLastName();
-                if (StringUtils.isBlank(name))
-                    name = email;
             }
 
             SimpleDateFormat dateFormat = new SimpleDateFormat("EEE, MMM d, yyyy 'at' HH:mm aaa, z");
@@ -127,9 +125,11 @@ public AccountTransfer resetPassword(String email, String targetEmail) {
                    .append("\n\nThank you.");
 
             Emailer.send(account.getEmail(), subject, builder.toString());
-            return null;
+        } catch (Exception ex) {
+            Logger.error(ex);
+            return false;
         }
-        return transfer;
+        return true;
     }
 
     /**

src/main/java/org/jbei/ice/lib/entry/filter/EntrySecurityFilterFactory.java

@@ -57,9 +57,12 @@ public SecurityFilter(String id, HashSet<String> uuids) {
         @Override
         public DocIdSet getDocIdSet(IndexReader reader) throws IOException {
             OpenBitSet bitSet = new OpenBitSet(reader.maxDoc());
-            TermDocs docs = reader.termDocs(new Term("canRead", accountId));
-            while (docs.next()) {
-                bitSet.set(docs.doc());
+            TermDocs docs;
+            if (accountId != null) {
+                docs = reader.termDocs(new Term("canRead", accountId));
+                while (docs.next()) {
+                    bitSet.set(docs.doc());
+                }
             }
 
             if (uuids != null) {

src/main/java/org/jbei/ice/lib/entry/sample/SampleController.java

@@ -40,6 +40,7 @@ public SampleController() {
     // mainly used by the api to create a strain sample record
     public Sample createStrainSample(Account account, String recordId, String rack, String location, String barcode,
             String label, String strainNamePrefix) {
+
         entryAuthorization.expectAdmin(account.getEmail());
 
         // check if there is an existing sample with barcode
@@ -124,6 +125,10 @@ public PartSample createSample(String userId, long entryId, PartSample partSampl
                     currentStorage = storageDAO.create(currentStorage);
                     break;
 
+                case PLATE96:
+                    currentStorage = createPlate96Location(mainLocation);
+                    break;
+
                 default:
                     currentStorage = storageDAO.get(mainLocation.getId());
                     if (currentStorage == null) {
@@ -151,6 +156,19 @@ public PartSample createSample(String userId, long entryId, PartSample partSampl
         return sample.toDataTransferObject();
     }
 
+    /**
+     * Creates location records for a sample contained in a 96 well plate
+     * Provides support for 2-D barcoded systems
+     */
+    protected Storage createPlate96Location(StorageLocation location) {
+//        String name = entry.getName();
+//        if (strainNamePrefix != null && name != null && !name.startsWith(strainNamePrefix)) {
+//            new EntryEditor().updateWithNextStrainName(strainNamePrefix, entry);
+//        }
+//        return sample;
+        return null;
+    }
+
     public ArrayList<PartSample> retrieveEntrySamples(String userId, long entryId) {
         Entry entry = DAOFactory.getEntryDAO().get(entryId);
         if (entry == null)
@@ -180,6 +198,7 @@ public ArrayList<PartSample> retrieveEntrySamples(String userId, long entryId) {
                 location.setType(SampleType.GENERIC);
                 location.setDisplay(sample.getLabel());
                 generic.setLocation(location);
+                generic = setAccountInfo(generic, sample.getDepositor());
                 samples.add(generic);
                 continue;
             }
@@ -204,22 +223,25 @@ public ArrayList<PartSample> retrieveEntrySamples(String userId, long entryId) {
             partSample.setLabel(sample.getLabel());
             partSample.setLocation(storageLocation);
             partSample.setInCart(inCart);
-
-            Account account = DAOFactory.getAccountDAO().getByEmail(sample.getDepositor());
-            if (account != null)
-                partSample.setDepositor(account.toDataTransferObject());
-            else {
-                AccountTransfer accountTransfer = new AccountTransfer();
-                accountTransfer.setEmail(sample.getDepositor());
-                partSample.setDepositor(accountTransfer);
-            }
-
+            partSample = setAccountInfo(partSample, sample.getDepositor());
             samples.add(partSample);
         }
 
         return samples;
     }
 
+    protected PartSample setAccountInfo(PartSample partSample, String email) {
+        Account account = DAOFactory.getAccountDAO().getByEmail(email);
+        if (account != null)
+            partSample.setDepositor(account.toDataTransferObject());
+        else {
+            AccountTransfer accountTransfer = new AccountTransfer();
+            accountTransfer.setEmail(email);
+            partSample.setDepositor(accountTransfer);
+        }
+        return partSample;
+    }
+
     public boolean delete(String userId, long partId, long sampleId) {
         Sample sample = dao.get(sampleId);
         if (sample == null)

src/main/java/org/jbei/ice/lib/folder/FolderController.java

@@ -217,6 +217,8 @@ public FolderDetails retrieveFolderContents(String userId, long folderId, Column
         if (userId != null) {
             ArrayList<AccessPermission> permissions = getAndFilterFolderPermissions(userId, folder);
             details.setAccessPermissions(permissions);
+            boolean canEdit = permissionsController.hasWritePermission(userId, folder);
+            details.setCanEdit(canEdit);
         }
 
         details.setPublicReadAccess(permissionsController.isPublicVisible(folder));

src/main/java/org/jbei/ice/lib/search/SearchController.java

@@ -64,7 +64,7 @@ public SearchResults runWebSearch(SearchQuery query) {
 
         // limit to 50
         query.getParameters().setRetrieveCount(50);
-        query.getParameters().setStart(1);
+        query.getParameters().setStart(0);
 
         LinkedList<SearchResult> resultsList = new LinkedList<>();
         long total = 0;
@@ -112,12 +112,17 @@ public int compare(SearchResult o1, SearchResult o2) {
     /**
      * Executes search using parameters specified in the query.
      *
-     * @param userId
-     * @param query
+     * @param userId unique user identifier making the request. This can be null if the request is via web of
+     *               registries
+     * @param query  wrapper around search query
      * @return wrapper around the list of search results
      */
     public SearchResults runLocalSearch(String userId, SearchQuery query) {
-        String queryString = query.getQueryString();
+        String queryString;
+        if (query.getQueryString() != null)
+            queryString = query.getQueryString().toLowerCase();
+        else
+            queryString = query.getQueryString();
         Account account = null;
         if (userId != null)
             account = DAOFactory.getAccountDAO().getByEmail(userId);

src/main/java/org/jbei/ice/lib/search/blast/BlastPlus.java

@@ -224,8 +224,12 @@ public static void rebuildDatabase(boolean force) throws BlastException {
         final Path blastFolder = Paths.get(dataDir, BLAST_DB_FOLDER);
         File lockFile = Paths.get(blastFolder.toString(), LOCK_FILE_NAME).toFile();
         if (lockFile.exists()) {
-            Logger.info("Blast db locked (lockfile - " + lockFile.getAbsolutePath() + "). Rebuild aborted!");
-            return;
+            if (lockFile.lastModified() <= (System.currentTimeMillis() - (1000 * 60 * 60 * 24)))
+                lockFile.delete();
+            else {
+                Logger.info("Blast db locked (lockfile - " + lockFile.getAbsolutePath() + "). Rebuild aborted!");
+                return;
+            }
         }
 
         try {
@@ -255,6 +259,7 @@ public static void rebuildDatabase(boolean force) throws BlastException {
         } catch (OverlappingFileLockException l) {
             Logger.warn("Could not obtain lock file for blast at " + blastFolder.toString());
         } catch (IOException eio) {
+            FileUtils.deleteQuietly(lockFile);
             throw new BlastException(eio);
         }
         FileUtils.deleteQuietly(lockFile);

src/main/java/org/jbei/ice/services/rest/FolderResource.java

@@ -165,6 +165,7 @@ public FolderDetails read(@Context UriInfo uriInfo,
 
         try {
             long id = Long.decode(folderId);
+            Logger.info("Retrieving folder " + id + " entries");
             return controller.retrieveFolderContents(userId, id, field, asc, offset, limit);
         } catch (NumberFormatException nfe) {
         }

src/main/java/org/jbei/ice/services/rest/UserResource.java

@@ -11,7 +11,6 @@
 import org.jbei.ice.lib.account.AccountController;
 import org.jbei.ice.lib.account.AccountTransfer;
 import org.jbei.ice.lib.account.PreferencesController;
-import org.jbei.ice.lib.account.SessionHandler;
 import org.jbei.ice.lib.account.model.Account;
 import org.jbei.ice.lib.dao.DAOFactory;
 import org.jbei.ice.lib.dto.AccountResults;
@@ -171,23 +170,15 @@ public AccountTransfer update(@Context UriInfo info, @PathParam("id") long userI
         return controller.updateAccount(user, userId, transfer);
     }
 
-    // reset or validate password (also include current session id for validation pending new method)
     @POST
     @Consumes(MediaType.APPLICATION_JSON)
     @Produces(MediaType.APPLICATION_JSON)
     @Path("/password")
-    public AccountTransfer resetPassword(@HeaderParam(value = "X-ICE-Authentication-SessionId") String sessionId,
-            AccountTransfer transfer) {
-        String userId = SessionHandler.getUserIdBySession(sessionId);
-        if (transfer.getPassword() != null && userId != null) {
-            return controller.authenticate(transfer);
-        }
-
-        // reset
-        AccountTransfer newUpdate = controller.resetPassword(userId, transfer.getEmail());
-        if (newUpdate == null)
-            return transfer;
-        return newUpdate;
+    public Response resetPassword(@Context UriInfo info, AccountTransfer transfer) {
+        boolean success = controller.resetPassword(transfer.getEmail());
+        if (!success)
+            return super.respond(Response.Status.NOT_FOUND);
+        return super.respond(Response.Status.OK);
     }
 
     @PUT

src/main/java/org/jbei/ice/servlet/InfoToModelFactory.java

@@ -197,10 +197,14 @@ private static Entry setCommon(Entry entry, PartData info) {
         if (info.getName() != null)
             entry.setName(info.getName());
 
-        Set<SelectionMarker> markers = getSelectionMarkers(info.getSelectionMarkers(), entry);
-        entry.setSelectionMarkers(markers);
+        if (info.getSelectionMarkers() != null) {
+            Set<SelectionMarker> markers = getSelectionMarkers(info.getSelectionMarkers(), entry);
+            entry.setSelectionMarkers(markers);
+        }
+
+        if (info.getReferences() != null)
+            entry.setReferences(info.getReferences());
 
-        entry.setReferences(info.getReferences());
         if (StringUtils.isBlank(entry.getPartNumber()))
             entry.setPartNumber(info.getPartId());
 
@@ -311,7 +315,8 @@ private static Set<SelectionMarker> getSelectionMarkers(ArrayList<String> marker
                 marker.setEntry(entry);
                 markers.add(marker);
             }
-        }
+        } else
+            return null;
 
         return markers;
     }