Merge branch '5.9.0'

Author: hplahar

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>5.8.3</version>
+    <version>5.9.0</version>
     <name>ice</name>
     <description>Inventory of Composable Elements (ICE) for Synthetic Biology</description>
     <repositories>
@@ -18,33 +18,33 @@
         <dependency>
             <groupId>org.glassfish.jersey.containers</groupId>
             <artifactId>jersey-container-servlet-core</artifactId>
-            <version>2.30.1</version>
+            <version>2.32</version>
         </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.media</groupId>
             <artifactId>jersey-media-multipart</artifactId>
-            <version>2.30.1</version>
+            <version>2.32</version>
         </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.inject</groupId>
             <artifactId>jersey-hk2</artifactId>
-            <version>2.30.1</version>
+            <version>2.32</version>
         </dependency>
         <dependency>
             <groupId>javax.servlet</groupId>
             <artifactId>javax.servlet-api</artifactId>
-            <version>3.1.0</version>
+            <version>4.0.1</version>
             <scope>provided</scope>
         </dependency>
         <dependency>
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
-            <version>42.2.6</version>
+            <version>42.2.16</version>
         </dependency>
         <dependency>
             <groupId>com.h2database</groupId>
             <artifactId>h2</artifactId>
-            <version>1.4.199</version>
+            <version>1.4.200</version>
         </dependency>
         <dependency>
             <groupId>junit</groupId>
@@ -55,18 +55,18 @@
         <dependency>
             <groupId>com.google.code.gson</groupId>
             <artifactId>gson</artifactId>
-            <version>2.8.5</version>
+            <version>2.8.6</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-core</artifactId>
-            <version>5.4.14.Final</version>
+            <version>5.4.22.Final</version>
         </dependency>
         <dependency>
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-search-orm</artifactId>
-            <version>5.11.5.Final</version>
+            <version>5.11.8.Final</version>
         </dependency>
         <dependency>
             <groupId>javax.validation</groupId>
@@ -86,7 +86,7 @@
         <dependency>
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-c3p0</artifactId>
-            <version>5.4.14.Final</version>
+            <version>5.4.22.Final</version>
         </dependency>
         <dependency>
             <groupId>commons-io</groupId>
@@ -101,7 +101,7 @@
         <dependency>
             <groupId>com.opencsv</groupId>
             <artifactId>opencsv</artifactId>
-            <version>5.1</version>
+            <version>5.2</version>
         </dependency>
         <dependency>
             <groupId>ch.qos.logback</groupId>
@@ -150,7 +150,7 @@
         <dependency>
             <groupId>io.undertow</groupId>
             <artifactId>undertow-servlet</artifactId>
-            <version>1.4.18.Final</version>
+            <version>2.2.0.Final</version>
         </dependency>
     </dependencies>
     <build>

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

@@ -9,7 +9,7 @@
  */
 public class SiteSettings implements IDataTransferModel {
 
-    private String version = "5.8.3";
+    private String version = "5.9.0";
     private String assetName;
     private boolean hasLogo;
     private boolean hasLoginMessage;

src/main/java/org/jbei/ice/lib/dto/folder/FolderDetails.java

@@ -1,10 +1,14 @@
 package org.jbei.ice.lib.dto.folder;
 
 import org.jbei.ice.lib.account.AccountTransfer;
+import org.jbei.ice.lib.dto.entry.EntryType;
 import org.jbei.ice.lib.dto.sample.SampleRequest;
 import org.jbei.ice.lib.dto.web.RegistryPartner;
 import org.jbei.ice.lib.folder.AbstractFolder;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Folder Transfer Object
  *
@@ -23,14 +27,17 @@ public class FolderDetails extends AbstractFolder {
     private FolderDetails parent;
     private RegistryPartner remotePartner;
     private SampleRequest sampleRequest;
+    private final List<EntryType> contentTypes;         // types of entries contained in this folder
 
     public FolderDetails() {
         super();
+        this.contentTypes = new ArrayList<>();
     }
 
     public FolderDetails(long id, String name) {
         super(id);
         this.folderName = name;
+        this.contentTypes = new ArrayList<>();
     }
 
     public String getName() {
@@ -123,4 +130,8 @@ public SampleRequest getSampleRequest() {
     public void setSampleRequest(SampleRequest sampleRequest) {
         this.sampleRequest = sampleRequest;
     }
+
+    public List<EntryType> getContentTypes() {
+        return this.contentTypes;
+    }
 }

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

@@ -1,5 +1,6 @@
 package org.jbei.ice.lib.folder;
 
+import org.jbei.ice.lib.dto.entry.EntryType;
 import org.jbei.ice.lib.dto.folder.FolderAuthorization;
 import org.jbei.ice.lib.dto.folder.FolderDetails;
 import org.jbei.ice.lib.dto.folder.FolderType;
@@ -43,6 +44,14 @@ public FolderDetails get(long folderId) {
 
         authorization.expectRead(this.userId, folder);
         FolderDetails folderDetails = folder.toDataTransferObject();
+        List<String> types = dao.getContentTypes(folderId);
+        if (!types.isEmpty()) {
+            for (String type : types) {
+                EntryType entryType = EntryType.nameToType(type);
+                if (entryType != null)
+                    folderDetails.getContentTypes().add(entryType);
+            }
+        }
 
         Account owner = accountDAO.getByEmail(folder.getOwnerEmail());
         if (owner != null) {

src/main/java/org/jbei/ice/storage/hibernate/dao/FolderDAO.java

@@ -388,4 +388,25 @@ public long getEntryCountByFolderType(FolderType type, String filter) {
             throw new DAOException(e);
         }
     }
+
+    /**
+     * Retrieves distinct list of types for the entries contained in the folder
+     *
+     * @param folderId unique identifier for folder whose content types are being retrieved
+     * @return list of content types. e.g. if a folder contains 345 Strains, and 23 plasmids, this will return
+     * [STRAIN, PLASMID]. Any empty folder will result in a return of an empty list
+     */
+    public List<String> getContentTypes(long folderId) {
+        try {
+            CriteriaQuery<String> query = getBuilder().createQuery(String.class);
+            Root<Folder> from = query.from(Folder.class);
+            Join<Folder, Entry> entry = from.join("contents");
+            query.select(entry.get("recordType")).distinct(true);
+            query.where(getBuilder().equal(from.get("id"), folderId));
+            return currentSession().createQuery(query).list();
+        } catch (HibernateException e) {
+            Logger.error(e);
+            throw new DAOException(e);
+        }
+    }
 }

src/main/webapp/scripts/controllers.js

@@ -31,7 +31,7 @@ iceControllers.controller('ActionMenuController', function ($stateParams, $uibMo
         }
 
         var i = $scope.selectedFolders.indexOf(folder);
-        if (i == -1) {
+        if (i === -1) {
             $scope.selectedFolders.push(folder);
         } else {
             $scope.selectedFolders.splice(i, 1);
@@ -61,7 +61,7 @@ iceControllers.controller('ActionMenuController', function ($stateParams, $uibMo
         }
 
         var entrySelection = {
-            all: Selection.getSelection().type == 'ALL',
+            all: Selection.getSelection().type === 'ALL',
             folderId: folderSelected,
             selectionType: selectionType,
             entryType: Selection.getSelection().type,