Merge branch '4.2.0'

.gitignore

@@ -5,3 +5,4 @@ war/
 *.class
 data/
 ice.iml
+*.pem

README.rst

@@ -0,0 +1,86 @@
+ICE
+===
+
+Inventory of Composable Elements (ICE) is an open source registry
+software for biological parts developed by the `Joint
+BioEnergy Institute <http://www.jbei.org/>`__. It is a Web application used by laboratories to track and search their
+constructs.
+
+ICE is distributed under the Modified BSD license. See LICENSE.txt and LIBRARY_LICENSES.txt for details.
+
+You can try out the software at our `Public
+Registry <http://public-registry.jbei.org>`__.
+
+Documentation for ICE Users
+-------------
+
+Read the `Manual <https://jbei.github.io/ice/>`__ for installation and usage instructions.
+
+
+Documentation for ICE developers
+--------------------------------
+
+Requirements
+~~~~~~~~~~~~
+To set up a development environment for ICE you will need to install:
+
+* `BLAST+ <http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download>`__ ≥ 2.2.28
+* `Java JDK 7 <http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html>`__
+* `Maven <https://maven.apache.org/download.cgi>`__  ≥ 3.0
+
+If you use a Debian-like operating system, the following command will install all the requirements
+
+::
+
+  sudo apt-get install ncbi-blast+ default-jdk maven
+
+
+Set Up
+~~~~~~
+1. Checkout the code and enter the repository
+
+::
+
+  git checkout https://github.com/JBEI/ice.git
+  cd ice
+
+2. Since the application requires an SSL certificate, generate one that the Jetty Web server can use this command. When prompted for a password, enter **changeit**
+
+::
+
+  keytool -genkey -alias tomcat -keyalg RSA -keystore ./.keystore
+
+3. Start Jetty
+
+::
+
+  mvn jetty:run
+
+4. Point your browser to https://localhost:8443/ to access the application
+
+Testing
+~~~~~~~
+To run the unit test suite
+
+::
+
+  mvn test
+
+Links
+-----
+
+* `ICE Google Group <http://groups.google.com/group/gd-ice>`__
+* `Releases <https://github.com/JBEI/ice/releases>`__: Download the war file associated with the latest release
+* `REST API WADL <https://public-registry.jbei.org/rest/application.wadl>`__
+
+Related Projects
+----------------
+
+`The VectorEditor project <https://github.com/JBEI/vectoreditor/>`__ is
+used in ICE to display and edit sequences. It also contains other
+modules such as sequence checker.
+
+|Build Status|
+
+.. |Build Status| image:: https://travis-ci.org/JBEI/ice.svg?branch=dev
+   :target: https://travis-ci.org/JBEI/ice

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>4.1.18</version>
+    <version>4.2.0</version>
     <name>ice</name>
     <description>Inventory of Composable Elements (ICE) for Synthetic Biology</description>
     <repositories>
@@ -187,6 +187,18 @@
                 <configuration>
                 </configuration>
             </plugin>
+            <plugin>
+              <groupId>org.apache.maven.plugins</groupId>
+              <artifactId>maven-war-plugin</artifactId>
+              <version>2.6</version>
+              <configuration>
+                <webResources>
+                  <resource>
+                    <directory>src/main/resources/aws</directory>
+                  </resource>
+                </webResources>
+              </configuration>
+            </plugin>
         </plugins>
     </build>
     <properties>

src/main/java/org/jbei/ice/lib/account/PasswordUtil.java → src/main/java/org/jbei/ice/lib/account/TokenHash.java

@@ -1,28 +1,27 @@
 package org.jbei.ice.lib.account;
 
-import org.jbei.ice.lib.utils.UtilityException;
-
 import javax.crypto.SecretKeyFactory;
 import javax.crypto.spec.PBEKeySpec;
 import javax.xml.bind.DatatypeConverter;
 import java.security.NoSuchAlgorithmException;
 import java.security.SecureRandom;
 import java.security.spec.InvalidKeySpecException;
 import java.security.spec.KeySpec;
-import java.util.UUID;
 
 /**
- * Utility class for handling account passwords
  *
  * @author Hector Plahar
  */
-public class PasswordUtil {
+public class TokenHash {
 
     private static final int HASH_BYTE_SIZE = 160;
     private static final int SALT_BYTE_SIZE = 32;
     private static final int PBKDF2_ITERATIONS = 20000;
 
-    public static String encryptPassword(String password, String salt) throws UtilityException {
+    public TokenHash() {
+    }
+
+    public String encryptPassword(String password, String salt) {
         if (password == null || password.trim().isEmpty() || salt == null || salt.trim().isEmpty())
             throw new NullPointerException("Password and/or salt cannot be empty");
 
@@ -31,20 +30,23 @@ public static String encryptPassword(String password, String salt) throws Utilit
         try {
             SecretKeyFactory keyFactory = SecretKeyFactory.getInstance("PBKDF2WithHmacSHA1");
             byte[] hash = keyFactory.generateSecret(spec).getEncoded();
-            return DatatypeConverter.printHexBinary(hash);
+            return DatatypeConverter.printBase64Binary(hash);
         } catch (NoSuchAlgorithmException | InvalidKeySpecException e) {
-            throw new UtilityException(e);
+            return null;
         }
     }
 
-    public static String generateSalt() {
+    public String generateSalt() {
         SecureRandom random = new SecureRandom();
         byte[] salt = new byte[SALT_BYTE_SIZE];
         random.nextBytes(salt);
-        return DatatypeConverter.printHexBinary(salt);
+        return DatatypeConverter.printBase64Binary(salt);
     }
 
-    public static String generateTemporaryPassword() {
-        return UUID.randomUUID().toString().substring(24);
+    public String generateRandomToken() {
+        SecureRandom random = new SecureRandom();
+        byte[] salt = new byte[256];
+        random.nextBytes(salt);
+        return DatatypeConverter.printBase64Binary(salt);
     }
 }

src/main/java/org/jbei/ice/lib/account/authentication/LocalAuthentication.java

@@ -1,6 +1,5 @@
 package org.jbei.ice.lib.account.authentication;
 
-import org.jbei.ice.lib.account.AccountController;
 import org.jbei.ice.lib.account.AccountUtils;
 import org.jbei.ice.lib.account.model.Account;
 import org.jbei.ice.lib.common.logging.Logger;
@@ -22,8 +21,7 @@ public String authenticates(String userId, String password) throws Authenticatio
         if (userId == null || password == null)
             throw new AuthenticationException("Invalid username and password");
 
-        AccountController controller = new AccountController();
-        Account account = controller.getByEmail(userId);
+        Account account = DAOFactory.getAccountDAO().getByEmail(userId);
         if (account == null || !isValidPassword(account, password))
             return null;
         return account.getEmail();

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

@@ -92,24 +92,35 @@ protected PartData createEntryForUpload(String userId, PartData data, BulkUpload
         entry.setOwner(account.getFullName());
         entry.setOwnerEmail(account.getEmail());
 
-        // check if there is any linked parts. create if so (expect a max of 1)
+        // check if there is any linked parts.
         if (data.getLinkedParts() != null && data.getLinkedParts().size() > 0) {
-            // create linked
             PartData linked = data.getLinkedParts().get(0);
-            Entry linkedEntry = InfoToModelFactory.infoToEntry(linked);
-            if (linkedEntry != null) {
-                linkedEntry.setVisibility(Visibility.DRAFT.getValue());
-                linkedEntry.setOwner(account.getFullName());
-                linkedEntry.setOwnerEmail(account.getEmail());
-                linkedEntry = entryDAO.create(linkedEntry);
-
-                linked.setId(linkedEntry.getId());
-                linked.setModificationTime(linkedEntry.getModificationTime().getTime());
-                data.getLinkedParts().clear();
-                data.getLinkedParts().add(linked);
-
-                // link to main entry in the database
-                entry.getLinkedEntries().add(linkedEntry);
+
+            // check if linking to existing
+            if (StringUtils.isEmpty(linked.getPartId())) {
+                // create new
+
+                Entry linkedEntry = InfoToModelFactory.infoToEntry(linked);
+                if (linkedEntry != null) {
+                    linkedEntry.setVisibility(Visibility.DRAFT.getValue());
+                    linkedEntry.setOwner(account.getFullName());
+                    linkedEntry.setOwnerEmail(account.getEmail());
+                    linkedEntry = entryDAO.create(linkedEntry);
+
+                    linked.setId(linkedEntry.getId());
+                    linked.setModificationTime(linkedEntry.getModificationTime().getTime());
+                    data.getLinkedParts().clear();
+                    data.getLinkedParts().add(linked);
+
+                    // link to main entry in the database
+                    entry.getLinkedEntries().add(linkedEntry);
+                }
+            } else {
+                // link existing
+                Entry linkedEntry = entryDAO.getByPartNumber(linked.getPartId());
+                if (!entry.getLinkedEntries().contains(linkedEntry)) {
+                    entry.getLinkedEntries().add(linkedEntry);
+                }
             }
         }
 
@@ -157,6 +168,11 @@ protected PartData doUpdate(String userId, Entry entry, PartData data) {
         // retrieve the entry (this is the only time you can create another entry on update)
         PartData linkedPartData = data.getLinkedParts().get(0); // bulk upload can only link 1
         Entry linkedEntry = entryDAO.get(linkedPartData.getId());
+        if (linkedEntry == null && !StringUtils.isEmpty(linkedPartData.getPartId())) {
+            // try partId
+            linkedEntry = entryDAO.getByPartNumber(linkedPartData.getPartId());
+        }
+
         if (linkedEntry == null && (linkedEntry = InfoToModelFactory.infoToEntry(linkedPartData)) != null) {
             linkedEntry.setVisibility(Visibility.DRAFT.getValue());
             Account account = accountController.getByEmail(userId);

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

@@ -3,7 +3,6 @@
 import org.jbei.ice.lib.access.Permission;
 import org.jbei.ice.lib.account.AccountTransfer;
 import org.jbei.ice.lib.account.model.Account;
-import org.jbei.ice.lib.account.model.Preference;
 import org.jbei.ice.lib.dao.IDataModel;
 import org.jbei.ice.lib.entry.model.Entry;
 
@@ -58,12 +57,6 @@ public class BulkUpload implements IDataModel {
             inverseJoinColumns = {@JoinColumn(name = "entry_id", nullable = false)})
     private Set<Entry> contents = new HashSet<>();
 
-    @OneToMany(fetch = FetchType.LAZY, cascade = {CascadeType.REMOVE, CascadeType.MERGE, CascadeType.PERSIST})
-    @JoinTable(name = "bulk_upload_preferences",
-            joinColumns = {@JoinColumn(name = "bulk_upload_id", nullable = false)},
-            inverseJoinColumns = {@JoinColumn(name = "preference_id", nullable = false)})
-    private Set<Preference> preferences = new HashSet<>();
-
     @OneToMany(cascade = {CascadeType.PERSIST, CascadeType.REMOVE, CascadeType.MERGE})
     @JoinTable(name = "bulk_upload_permissions",
             joinColumns = {@JoinColumn(name = "bulk_upload_id", nullable = false)},
@@ -125,10 +118,6 @@ public void setImportType(String importType) {
         this.importType = importType;
     }
 
-    public Set<Preference> getPreferences() {
-        return preferences;
-    }
-
     public BulkUploadStatus getStatus() {
         return status;
     }

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

@@ -529,6 +529,19 @@ public boolean deleteAttachment(String userId, long bulkUploadId, long entryId)
         return true;
     }
 
+    public boolean deleteEntry(String userId, long uploadId, long entryId) {
+        try {
+            BulkUpload upload = dao.get(uploadId);
+            Entry entry = new EntryDAO().get(entryId);
+            authorization.expectWrite(userId, upload);
+            upload.getContents().remove(entry);
+            return true;
+        } catch (Exception e) {
+            Logger.error(e);
+            return false;
+        }
+    }
+
     public List<AccessPermission> getUploadPermissions(String userId, long uploadId) {
         List<AccessPermission> permissions = new ArrayList<>();
         BulkUpload upload = dao.get(uploadId);
@@ -599,4 +612,32 @@ public boolean deletePermission(String userId, long uploadId, long permissionId)
         DAOFactory.getPermissionDAO().delete(toDelete);
         return dao.update(upload) != null;
     }
+
+    /**
+     * Retrieves part numbers that match the token passed in the parameter, that are compatible with the type
+     * in the parameter. Two entry types are compatible if they can be associated with specific entries (as descendants)
+     * in a hierarchical relationship
+     *
+     * @param type  type of entry the part numbers must be compatible with
+     * @param token part number token to match
+     * @param limit maximum number of matches to return
+     * @return list of part numbers that can be linked to the type of entry
+     */
+    public ArrayList<String> getMatchingPartNumbersForLinks(EntryType type, String token, int limit) {
+        ArrayList<String> dataList = new ArrayList<>();
+        if (token == null)
+            return dataList;
+
+        Set<String> compatibleTypes = new HashSet<>();
+        compatibleTypes.add(type.getName());
+        compatibleTypes.add(EntryType.PART.getName());
+        if (type == EntryType.STRAIN)
+            compatibleTypes.add(EntryType.PLASMID.getName());
+
+        token = token.replaceAll("'", "");
+        for (Entry entry : DAOFactory.getEntryDAO().getMatchingEntryPartNumbers(token, limit, compatibleTypes)) {
+            dataList.add(entry.getPartNumber());
+        }
+        return dataList;
+    }
 }