Merge branch '5.2.1'

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>5.2.0</version>
+    <version>5.2.1</version>
     <name>ice</name>
     <description>Inventory of Composable Elements (ICE) for Synthetic Biology</description>
     <repositories>

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

@@ -198,7 +198,7 @@ protected PartData doUpdate(String userId, Entry entry, PartData data) {
             }
         } else {
             // linking to existing
-            EntryLinks entryLinks = new EntryLinks(userId, entry.getId());
+            EntryLinks entryLinks = new EntryLinks(userId, Long.toString(entry.getId()));
             entryLinks.addLink(linkedPartData, LinkType.CHILD);
         }
 
@@ -515,7 +515,7 @@ public boolean createEntries(String userId, long draftId, List<PartWithSample> d
                 if (linked.getId() != 0) {
                     Entry linkedEntry = entryDAO.get(linked.getId());
                     if (linkedEntry != null && entryAuthorization.canWriteThoroughCheck(userId, entry)) {
-                        EntryLinks links = new EntryLinks(userId, entry.getId());
+                        EntryLinks links = new EntryLinks(userId, Long.toString(entry.getId()));
                         links.addLink(linked, LinkType.CHILD);
                     }
                 }
@@ -548,7 +548,7 @@ public boolean createEntries(String userId, long draftId, List<PartWithSample> d
             if (partSample == null)
                 continue;
 
-            sampleService.createSample(userId, entry.getId(), partSample, null);
+            sampleService.createSample(userId, Long.toString(entry.getId()), partSample, null);
         }
 
         return true;

src/main/java/org/jbei/ice/lib/config/SiteSettings.java

@@ -9,7 +9,7 @@
  */
 public class SiteSettings implements IDataTransferModel {
 
-    private String version = "5.2.0";
+    private String version = "5.2.1";
     private String assetName;
     private boolean hasLogo;
     private boolean hasLoginMessage;

src/main/java/org/jbei/ice/lib/entry/EntryController.java

@@ -1,13 +1,11 @@
 package org.jbei.ice.lib.entry;
 
-import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.jbei.ice.lib.access.PermissionException;
 import org.jbei.ice.lib.access.PermissionsController;
 import org.jbei.ice.lib.account.AccountController;
 import org.jbei.ice.lib.account.TokenHash;
 import org.jbei.ice.lib.common.logging.Logger;
-import org.jbei.ice.lib.dto.DNASequence;
 import org.jbei.ice.lib.dto.access.AccessPermission;
 import org.jbei.ice.lib.dto.comment.UserComment;
 import org.jbei.ice.lib.dto.entry.*;
@@ -21,10 +19,7 @@
 import org.jbei.ice.storage.hibernate.dao.*;
 import org.jbei.ice.storage.model.*;
 
-import java.io.*;
 import java.util.*;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
 
 /**
  * ABI to manipulate {@link Entry}s.
@@ -39,13 +34,11 @@ public class EntryController extends HasEntry {
     private PermissionsController permissionsController;
     private AccountController accountController;
     private final EntryAuthorization authorization;
-    private final SequenceAnalysisController sequenceAnalysisController;
 
     public EntryController() {
         dao = DAOFactory.getEntryDAO();
         commentDAO = DAOFactory.getCommentDAO();
         permissionsController = new PermissionsController();
-        sequenceAnalysisController = new SequenceAnalysisController();
         accountController = new AccountController();
         authorization = new EntryAuthorization();
         sequenceDAO = DAOFactory.getSequenceDAO();
@@ -426,92 +419,4 @@ protected PartData retrieveEntryDetails(String userId, Entry entry) throws Permi
 
         return partData;
     }
-
-    public boolean addTraceSequence(String userId, long partId, File file, String uploadFileName) {
-        Entry entry = dao.get(partId);
-        if (entry == null)
-            return false;
-
-        authorization.expectRead(userId, entry);
-
-        FileInputStream inputStream;
-        try {
-            inputStream = new FileInputStream(file);
-        } catch (FileNotFoundException e) {
-            Logger.error(e);
-            return false;
-        }
-
-        if (uploadFileName.toLowerCase().endsWith(".zip")) {
-            try (ZipInputStream zis = new ZipInputStream(inputStream)) {
-                ZipEntry zipEntry;
-                while (true) {
-                    zipEntry = zis.getNextEntry();
-
-                    if (zipEntry != null) {
-                        if (!zipEntry.isDirectory() && !zipEntry.getName().startsWith("__MACOSX")) {
-                            ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
-                            int c;
-                            while ((c = zis.read()) != -1) {
-                                byteArrayOutputStream.write(c);
-                            }
-
-                            boolean parsed = parseTraceSequence(userId, entry, zipEntry.getName(),
-                                    byteArrayOutputStream.toByteArray());
-                            if (!parsed) {
-                                String errMsg = ("Could not parse \"" + zipEntry.getName()
-                                        + "\". Only Fasta, GenBank & ABI files are supported.");
-                                Logger.error(errMsg);
-                                return false;
-                            }
-                        }
-                    } else {
-                        break;
-                    }
-                }
-            } catch (IOException e) {
-                String errMsg = ("Could not parse zip file.");
-                Logger.error(errMsg);
-                return false;
-            }
-        } else {
-            try {
-                boolean parsed = parseTraceSequence(userId, entry, uploadFileName, IOUtils.toByteArray(inputStream));
-                if (!parsed) {
-                    String errMsg = ("Could not parse \"" + uploadFileName
-                            + "\". Only Fasta, GenBank & ABI files are supported.");
-                    Logger.error(errMsg);
-                    return false;
-                }
-            } catch (IOException e) {
-                Logger.error(e);
-                return false;
-            }
-        }
-
-        return true;
-    }
-
-    // uploads trace sequence file and builds or rebuilds alignment
-    private boolean parseTraceSequence(String userId, Entry entry, String fileName, byte[] bytes) {
-        DNASequence dnaSequence = sequenceAnalysisController.parse(bytes);
-        if (dnaSequence == null || dnaSequence.getSequence() == null) {
-            String errMsg = ("Could not parse \"" + fileName
-                    + "\". Only Fasta, GenBank & ABI files are supported.");
-            Logger.error(errMsg);
-            return false;
-        }
-
-        TraceSequence traceSequence = sequenceAnalysisController.uploadTraceSequence(
-                entry, fileName, userId, dnaSequence.getSequence().toLowerCase(), new ByteArrayInputStream(bytes));
-
-        if (traceSequence == null)
-            return false;
-
-        Sequence sequence = DAOFactory.getSequenceDAO().getByEntry(entry);
-        if (sequence == null)
-            return true;
-        sequenceAnalysisController.buildOrRebuildAlignment(traceSequence, sequence);
-        return true;
-    }
 }

src/main/java/org/jbei/ice/lib/entry/EntryLinks.java

@@ -5,7 +5,6 @@
 import org.jbei.ice.lib.dto.entry.EntryType;
 import org.jbei.ice.lib.dto.entry.PartData;
 import org.jbei.ice.storage.DAOFactory;
-import org.jbei.ice.storage.hibernate.dao.EntryDAO;
 import org.jbei.ice.storage.hibernate.dao.SequenceDAO;
 import org.jbei.ice.storage.model.Entry;
 
@@ -19,17 +18,15 @@
  *
  * @author Hector Plahar
  */
-public class EntryLinks {
+public class EntryLinks extends HasEntry {
 
-    private final EntryDAO entryDAO;
     private final SequenceDAO sequenceDAO;
     private final Entry entry;
     private final EntryAuthorization entryAuthorization;
     private final String userId;
 
-    public EntryLinks(String userId, long partId) {
-        this.entryDAO = DAOFactory.getEntryDAO();
-        this.entry = this.entryDAO.get(partId);
+    public EntryLinks(String userId, String partId) {
+        this.entry = super.getEntry(partId);
         if (this.entry == null)
             throw new IllegalArgumentException("Could not retrieve part with id " + partId);
         this.userId = userId;

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

@@ -21,9 +21,7 @@
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.OutputStreamWriter;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
+import java.util.*;
 
 /**
  * Handler for sample requests
@@ -106,7 +104,7 @@ public UserSamples getRequests(String userId, int start, int limit, String sort,
 
         for (Request request : results) {
             SampleRequest sampleRequest = request.toDataTransferObject();
-            ArrayList<PartSample> location = sampleService.retrieveEntrySamples(userId, request.getEntry().getId());
+            ArrayList<PartSample> location = sampleService.retrieveEntrySamples(userId, Long.toString(request.getEntry().getId()));
             sampleRequest.setLocation(location);
             samples.getRequests().add(sampleRequest);
         }
@@ -192,7 +190,8 @@ public ByteArrayOutputStream generateCSVFile(String userId, ArrayList<Long> ids)
         try (CSVWriter writer = new CSVWriter(streamWriter)) {
             SampleService sampleService = new SampleService();
 
-            for (long id : ids) {
+            Set<Long> idSet = new HashSet<>(ids);
+            for (long id : idSet) {
                 Request request = dao.get(id);
                 if (request == null)
                     continue;
@@ -201,7 +200,7 @@ public ByteArrayOutputStream generateCSVFile(String userId, ArrayList<Long> ids)
                 Entry entry = request.getEntry();
                 line[0] = entry.getName();
 
-                ArrayList<PartSample> samples = sampleService.retrieveEntrySamples(userId, request.getEntry().getId());
+                ArrayList<PartSample> samples = sampleService.retrieveEntrySamples(userId, Long.toString(request.getEntry().getId()));
                 String plate = null;
                 String well = null;
 

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

@@ -7,6 +7,7 @@
 import org.jbei.ice.lib.dto.sample.PartSample;
 import org.jbei.ice.lib.dto.sample.SampleType;
 import org.jbei.ice.lib.entry.EntryAuthorization;
+import org.jbei.ice.lib.entry.HasEntry;
 import org.jbei.ice.lib.utils.Utils;
 import org.jbei.ice.storage.DAOException;
 import org.jbei.ice.storage.DAOFactory;
@@ -23,7 +24,7 @@
  *
  * @author Hector Plahar
  */
-public class SampleService {
+public class SampleService extends HasEntry {
 
     private final SampleDAO dao;
     private final StorageDAO storageDAO;
@@ -48,8 +49,8 @@ protected Storage createStorage(String userId, String name, SampleType sampleTyp
         return storage;
     }
 
-    public PartSample createSample(String userId, long entryId, PartSample partSample, String strainNamePrefix) {
-        Entry entry = DAOFactory.getEntryDAO().get(entryId);
+    public PartSample createSample(String userId, String entryId, PartSample partSample, String strainNamePrefix) {
+        Entry entry = super.getEntry(entryId);
         if (entry == null) {
             Logger.error("Could not retrieve entry with id " + entryId + ". Skipping sample creation");
             return null;
@@ -214,8 +215,8 @@ protected Storage createChildrenStorage(StorageLocation currentLocation, Storage
     }
 
 
-    public ArrayList<PartSample> retrieveEntrySamples(String userId, long entryId) {
-        Entry entry = DAOFactory.getEntryDAO().get(entryId);
+    public ArrayList<PartSample> retrieveEntrySamples(String userId, String entryId) {
+        Entry entry = super.getEntry(entryId);
         if (entry == null)
             return null;
 

src/main/java/org/jbei/ice/lib/entry/sequence/SequenceAnalysisController.java

@@ -11,12 +11,11 @@
 import org.jbei.ice.lib.search.blast.BlastPlus;
 import org.jbei.ice.lib.utils.Utils;
 import org.jbei.ice.storage.DAOFactory;
-import org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO;
 import org.jbei.ice.storage.hibernate.dao.ShotgunSequenceDAO;
+import org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO;
 import org.jbei.ice.storage.model.*;
 
 import java.io.File;
-import java.io.InputStream;
 import java.nio.file.Paths;
 import java.util.Date;
 import java.util.List;
@@ -39,56 +38,6 @@ public SequenceAnalysisController() {
         shotgunDao = DAOFactory.getShotgunSequenceDAO();
     }
 
-    /**
-     * Create a new {@link TraceSequence} record and associated with the {@link Entry} entry.
-     * <p>
-     * Creates a database record and write the inputStream to disk.
-     *
-     * @param entry
-     * @param filename
-     * @param depositor
-     * @param sequence
-     * @param uuid
-     * @param date
-     * @param inputStream
-     * @return Saved traceSequence
-     */
-    public TraceSequence importTraceSequence(Entry entry, String filename, String depositor, String sequence,
-                                             String uuid, Date date, InputStream inputStream) {
-        if (entry == null) {
-            throw new IllegalArgumentException("Failed to save trace sequence with null entry!");
-        }
-
-        if (filename == null || filename.isEmpty()) {
-            throw new IllegalArgumentException("Failed to save trace sequence without filename!");
-        }
-
-        if (sequence == null || sequence.isEmpty()) {
-            throw new IllegalArgumentException("Failed to save trace sequence without sequence!");
-        }
-
-        TraceSequence traceSequence = new TraceSequence(entry, uuid, filename, depositor, sequence, date);
-        File tracesDir = Paths.get(Utils.getConfigValue(ConfigurationKey.DATA_DIRECTORY), TRACES_DIR_NAME).toFile();
-        return traceDao.create(tracesDir, traceSequence, inputStream);
-    }
-
-    /**
-     * Create a new {@link TraceSequence} record and associated with the {@link Entry} entry.
-     * <p>
-     * Unlike importTraceSequence this method auto generates uuid and timestamp.
-     *
-     * @param entry       entry information
-     * @param filename    name of the file uploaded by the user
-     * @param depositor   email user depositing the information
-     * @param sequence    sequence string
-     * @param inputStream input stream for uploaded file
-     * @return Saved traceSequence
-     */
-    public TraceSequence uploadTraceSequence(Entry entry, String filename, String depositor,
-                                             String sequence, InputStream inputStream) {
-        return importTraceSequence(entry, filename, depositor, sequence, Utils.generateUUID(), new Date(), inputStream);
-    }
-
     /**
      * Remove a {@link TraceSequence} from the database and disk.
      *
@@ -166,7 +115,6 @@ public DNASequence parse(byte[] bytes) {
 
         // Trying to parse as Fasta, Genbank, etc
         DNASequence dnaSequence = GeneralParser.getInstance().parse(bytes);
-
         if (dnaSequence == null) {
             // Trying to parse as ABI
 
@@ -215,7 +163,7 @@ public void buildOrRebuildAlignment(TraceSequence traceSequence, Sequence sequen
         String entrySequenceString = sequence.getSequence();
 
         int entrySequenceLength = entrySequenceString.length();
-        boolean isCircular = (sequence.getEntry() instanceof Plasmid) && ((Plasmid) sequence.getEntry()).getCircular();
+        boolean isCircular = (sequence.getEntry().getRecordType().equalsIgnoreCase("plasmid")) && ((Plasmid) sequence.getEntry()).getCircular();
 
         if (isCircular) {
             entrySequenceString += entrySequenceString;

src/main/java/org/jbei/ice/lib/entry/sequence/SequenceController.java

@@ -88,12 +88,14 @@ public FeaturedDNASequence updateSequence(String userId, long entryId, FeaturedD
         if (!deleteSequence(userId, entryId))
             return null;
 
-//        sequence = update(userId, sequence);
-        BlastPlus.scheduleBlastIndexRebuildTask(true);
         sequence = save(userId, sequence);
-        if (sequence != null)
-            return sequenceToDNASequence(sequence);
-        return null;
+        if (sequence == null)
+            return null;
+
+        BlastPlus.scheduleBlastIndexRebuildTask(true);
+        SequenceAnalysisController sequenceAnalysisController = new SequenceAnalysisController();
+        sequenceAnalysisController.rebuildAllAlignments(entry);
+        return sequenceToDNASequence(sequence);
     }
 
     /**