Merge branch 'hotfix-4.1.6'

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>4.1.5</version>
+    <version>4.1.6</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

@@ -277,15 +277,10 @@ public Account getByEmail(String email) {
         return dao.getByEmail(email);
     }
 
-    public long getAccountId(String email) throws ControllerException {
-        Account account;
-        try {
-            account = dao.getByEmail(email);
-        } catch (DAOException e) {
-            throw new ControllerException(e);
-        }
+    public long getAccountId(String email) {
+        Account account = dao.getByEmail(email);
         if (account == null)
-            throw new ControllerException("Could not retrieve account for " + email);
+            throw new IllegalArgumentException("No account found with email " + email);
         return account.getId();
     }
 

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

@@ -225,6 +225,11 @@ public BulkUploadInfo updateStatus(String userId, long id, BulkUploadStatus stat
                 if (new BulkUploadController().approveBulkImport(account, id))
                     return upload.toDataTransferObject();
                 return null;
+
+            case BULK_EDIT:
+                upload.getContents().clear();
+                dao.delete(upload);
+                return upload.toDataTransferObject();
         }
     }
 

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

@@ -76,7 +76,11 @@ public BulkUploadInfo create(String userId, BulkUploadInfo info) {
         upload.setAccount(account);
         upload.setCreationTime(new Date());
         upload.setLastUpdateTime(upload.getCreationTime());
-        upload.setStatus(BulkUploadStatus.IN_PROGRESS);
+        if (info.getStatus() == BulkUploadStatus.BULK_EDIT)
+            upload.setStatus(BulkUploadStatus.BULK_EDIT);
+        else
+            upload.setStatus(BulkUploadStatus.IN_PROGRESS);
+
         upload.setImportType(info.getType());
         upload = dao.create(upload);
 

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

@@ -12,5 +12,6 @@ public enum BulkUploadStatus implements IDataTransferModel {
 
     APPROVED,
     PENDING_APPROVAL,
+    BULK_EDIT,
     IN_PROGRESS
 }

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

@@ -192,7 +192,7 @@ public boolean removeFolderContents(String userId, long folderId, ArrayList<Long
     /**
      * Retrieves the folder specified in the parameter and contents
      *
-     * @param userId   unique identifier for user making request
+     * @param userId   unique identifier for user making request. If null, folder must have public read privs
      * @param folderId unique identifier for folder to be retrieved
      * @param sort     sort order for folder content retrieval
      * @param asc      sort order for folder content retrieval; ascending if true
@@ -213,8 +213,11 @@ public FolderDetails retrieveFolderContents(String userId, long folderId, Column
         FolderDetails details = folder.toDataTransferObject();
         long folderSize = dao.getFolderSize(folderId);
         details.setCount(folderSize);
-        ArrayList<AccessPermission> permissions = getAndFilterFolderPermissions(userId, folder);
-        details.setAccessPermissions(permissions);
+
+        if (userId != null) {
+            ArrayList<AccessPermission> permissions = getAndFilterFolderPermissions(userId, folder);
+            details.setAccessPermissions(permissions);
+        }
 
         details.setPublicReadAccess(permissionsController.isPublicVisible(folder));
         Account owner = accountController.getByEmail(folder.getOwnerEmail());

src/main/webapp/index.html

@@ -130,7 +130,7 @@
                                             <a href="http://public-registry.jbei.org/manual">Help</a>
                                         </td>
                                         <td align="left" style="vertical-align: top;">
-                                            <div>&nbsp; | &nbsp; v4.1.5</div>
+                                            <div>&nbsp; | &nbsp; v4.1.6</div>
                                         </td>
                                     </tr>
                                 </table>

src/main/webapp/scripts/controllers.js

@@ -127,7 +127,7 @@ iceControllers.controller('ActionMenuController', function ($scope, $window, $ro
             }
 
             // first create bulk upload
-            upload.create({name:"Bulk Edit", type:type, entryList:selectedEntries}, function (result) {
+            upload.create({name:"Bulk Edit", type:type, status:'BULK_EDIT', entryList:selectedEntries}, function (result) {
                 console.log(result);
                 $location.path("/upload/" + result.id);
             }, function (error) {

src/main/webapp/scripts/entry/entryService.js

@@ -87,7 +87,7 @@ angular.module('ice.entry.service', [])
             },
 
             canDelete:function () {
-                return ($rootScope.user.isAdmin || canDelete) && selectedSearchResultsCount > 0;
+                return (($rootScope.user && $rootScope.user.isAdmin) || canDelete) && selectedSearchResultsCount > 0;
             },
 
             // resets all selected and send notifications

src/main/webapp/scripts/search/search-results.html

@@ -136,7 +136,7 @@ <h4 ng-if="isWebSearch()">
                    popover-placement="right">{{result.entryInfo.partId}}</a>
             </td>
             <td>{{result.entryInfo.name}}</td>
-            <td title="{{result.entryInfo.shortDescription}}">
+            <td tooltip="{{result.entryInfo.shortDescription}}">
                 <div style="width: 400px; white-space: nowrap; overflow: hidden; text-overflow: ellipsis">
                     {{result.entryInfo.shortDescription}}
                 </div>

src/main/webapp/scripts/services.js

@@ -808,7 +808,7 @@ iceServices.factory('Authentication',
             },
 
             // todo : use a parameter in isSessionValid to check
-            isAdmin:function (User) {
+            isAdmin:function () {
                 this.isSessionValid().then(function (result) {
                     if (!result || !result.data || !result.data.isAdmin) {
                         $location.path("/folders/personal");

src/main/webapp/scripts/upload/import.html

@@ -29,25 +29,28 @@ <h4>
                         </h4>
                     </td>
                     <td style="padding-left: 40px">
-                        <span class="opacity_hover edit_icon font-90em" ng-click="fileUploadModal()">
-                            <i style="font-size: 14px; color: #555" class="fa fa-cloud-upload"></i> File Upload
-                        </span>
+                        <span ng-if="!bulkUpload||bulkUpload.status!='BULK_EDIT'">
+                            <span class="opacity_hover edit_icon font-90em" ng-click="fileUploadModal()">
+                                <i style="font-size: 14px; color: #555" class="fa fa-cloud-upload"></i> File Upload
+                            </span>
 
-                        <span style="font-weight: normal; color: #ccc">&nbsp;|&nbsp;</span>
+                            <span style="font-weight: normal; color: #ccc">&nbsp;|&nbsp;</span>
 
-                        <div class="dropdown display-inline">
-                        <span class="opacity_hover edit_icon font-90em dropdown-toggle">
-                            <i style="font-size: 14px; color: #555" class="fa fa-link"></i> Link To
-                            <span class="caret"></span>
+                            <div class="dropdown display-inline">
+                            <span class="opacity_hover edit_icon font-90em dropdown-toggle">
+                                <i style="font-size: 14px; color: #555" class="fa fa-link"></i> Link To
+                                <span class="caret"></span>
+                            </span>
+                                <ul class="dropdown-menu">
+                                    <li class="cursor_pointer font-80em"><a ng-click="addExisting=true">Existing
+                                        Entry</a>
+                                    </li>
+                                    <li class="cursor_pointer font-80em" ng-repeat="option in linkOptions">
+                                        <a ng-click="addNewPartLink(option.type)"><i>New {{option.display}}</i></a>
+                                    </li>
+                                </ul>
+                            </div>
                         </span>
-                            <ul class="dropdown-menu">
-                                <li class="cursor_pointer font-80em"><a ng-click="addExisting=true">Existing Entry</a>
-                                </li>
-                                <li class="cursor_pointer font-80em" ng-repeat="option in linkOptions">
-                                    <a ng-click="addNewPartLink(option.type)"><i>New {{option.display}}</i></a>
-                                </li>
-                            </ul>
-                        </div>
                     </td>
                 </tr>
             </table>
@@ -58,6 +61,7 @@ <h4>
                     ng-click="submitImportForApproval()">
                 <span ng-if="bulkUpload.status==undefined || bulkUpload.status=='IN_PROGRESS'">Submit</span>
                 <span ng-if="bulkUpload.status=='PENDING_APPROVAL'">Approve</span>
+                <span ng-if="bulkUpload.status=='BULK_EDIT'">Done</span>
             </button>
             <button ng-if="bulkUpload.status==undefined || bulkUpload.status=='IN_PROGRESS'"
                     type="button" class="btn btn-xs btn-default" ng-click="confirmResetFormModal()">

src/main/webapp/scripts/upload/uploadController.js

@@ -591,10 +591,10 @@ angular.module('ice.upload.controller', [])
                 var requiresApproval = $scope.bulkUpload.status && $scope.bulkUpload.status == 'PENDING_APPROVAL';
 
                 // validate the contents;
-                var tmp = {id:$scope.bulkUpload.id};
+                var tmp = {id:$scope.bulkUpload.id, status:$scope.bulkUpload.status};
                 if (requiresApproval)
                     tmp.status = 'APPROVED';
-                else
+                else if ($scope.bulkUpload.status != "BULK_EDIT")
                     tmp.status = 'PENDING_APPROVAL';
                 $scope.requestError = undefined;
 

src/main/webapp/views/folder/folder-contents.html

@@ -138,7 +138,7 @@ <h4>
                     <div title="{{entry.name}}" class="ellipsis" style="width: 150px">{{entry.name}}</div>
                 </td>
                 <td>
-                    <div title="{{entry.shortDescription}}"
+                    <div tooltip="{{entry.shortDescription}}"
                          style="width: 500px; white-space: nowrap; overflow: hidden; text-overflow: ellipsis;">
                         {{entry.shortDescription}}
                     </div>

src/test/java/org/jbei/ice/lib/folder/FolderControllerTest.java

@@ -77,6 +77,9 @@ public void testCreateNewFolder() throws Exception {
 
     @Test
     public void testRetrieveFolderContents() throws Exception {
+        // test with null id
+        controller.retrieveFolderContents(null, 0, ColumnField.PART_ID, false, 0, 10);
+
         Account account = AccountCreator.createTestAccount("testRetrieveFolderContents", false);
         String userId = account.getEmail();