Merge branch

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>4.4.0</version>
+    <version>4.4.1</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

@@ -1,6 +1,7 @@
 package org.jbei.ice.lib.account;
 
 import org.apache.commons.lang3.StringUtils;
+import org.jbei.ice.lib.access.PermissionException;
 import org.jbei.ice.lib.account.authentication.AuthenticationException;
 import org.jbei.ice.lib.account.authentication.IAuthentication;
 import org.jbei.ice.lib.account.authentication.LocalAuthentication;
@@ -53,7 +54,8 @@ public AccountController() {
     public AccountTransfer updateAccount(final String requester, final long userId,
                                          final AccountTransfer transfer) {
         final Account account = dao.get(userId);
-        if (!account.getEmail().equalsIgnoreCase(requester) && !isAdministrator(requester)) {
+        boolean requesterIsAdmin = isAdministrator(requester);
+        if (!account.getEmail().equalsIgnoreCase(requester) && !requesterIsAdmin) {
             return null;
         }
 
@@ -74,7 +76,16 @@ public AccountTransfer updateAccount(final String requester, final long userId,
             account.setInstitution(transfer.getInstitution());
         }
 
-        return dao.update(account).toDataTransferObject();
+        if (transfer.getAccountType() != null) {
+            if (transfer.getAccountType() != account.getType() && !requesterIsAdmin)
+                throw new PermissionException("Only admins can change account type");
+
+            account.setType(transfer.getAccountType());
+        }
+
+        AccountTransfer result = dao.update(account).toDataTransferObject();
+        result.setAdmin(isAdministrator(account.getEmail()));
+        return result;
     }
 
     /**
@@ -357,14 +368,6 @@ public Account save(final Account account) {
         return dao.create(account);
     }
 
-    /**
-     * @param account
-     * @return {@code true} if an administrator account
-     */
-    public boolean isAdministrator(final Account account) {
-        return isAdministrator(account.getEmail());
-    }
-
     /**
      * Check in the database if an account is a moderator.
      *

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

@@ -27,7 +27,6 @@ public class SampleResource extends RestResource {
     private SampleService sampleService = new SampleService();
 
     /**
-     * @param token
      * @return Response with matching part sample
      */
     @GET
@@ -46,24 +45,20 @@ public Response getSampleByToken(@PathParam("token") String token,
     }
 
     /**
-     * @param offset
-     * @param limit
-     * @param sort
-     * @param asc
-     * @param filter
-     * @param status
      * @return Response with matching samples
      */
     @GET
     @Produces(MediaType.APPLICATION_JSON)
     @Path("/requests")
-    public Response getRequests(@DefaultValue("0") @QueryParam("offset") final int offset,
+    public Response getRequests(
+            @HeaderParam(value = "X-ICE-Authentication-SessionId") String userAgentHeader,
+            @DefaultValue("0") @QueryParam("offset") final int offset,
             @DefaultValue("15") @QueryParam("limit") final int limit,
             @DefaultValue("requested") @QueryParam("sort") final String sort,
             @DefaultValue("false") @QueryParam("asc") final boolean asc,
             @QueryParam("filter") final String filter,
             @QueryParam("status") final SampleRequestStatus status) {
-        final String userId = getUserId();
+        final String userId = getUserId(userAgentHeader);
         Logger.info(userId + ": retrieving sample requests");
         final UserSamples samples = requestRetriever.getRequests(userId, offset, limit, sort, asc,
                 status, filter);
@@ -74,14 +69,12 @@ public Response getRequests(@DefaultValue("0") @QueryParam("offset") final int o
      * Sets the status of sample requests. Must have admin privs to set the sample for others This
      * is intended for requesting samples
      *
-     * @param status
-     * @param requestIds
      * @return Response success or failure
      */
     @PUT
     @Path("/requests")
     public Response setRequestStatus(@QueryParam("status") final SampleRequestStatus status,
-            final ArrayList<Long> requestIds) {
+                                     final ArrayList<Long> requestIds) {
         final String userId = getUserId();
         try {
             if (requestIds == null || requestIds.isEmpty()) {
@@ -102,71 +95,61 @@ public Response setRequestStatus(@QueryParam("status") final SampleRequestStatus
         }
     }
 
-    /**
-     * @param requestId
-     * @return Response with the removed sample
-     */
     @DELETE
     @Path("/requests/{id}")
-    public Response deleteSampleRequest(@PathParam("id") final long requestId) {
-        final String userId = getUserId();
+    public Response deleteSampleRequest(@HeaderParam(value = "X-ICE-Authentication-SessionId") String sessionId,
+                                        @PathParam("id") final long requestId) {
+        final String userId = getUserId(sessionId);
         return respond(Response.Status.OK, requestRetriever.removeSampleFromCart(userId, requestId));
     }
 
     /**
-     * @param requestId
-     * @param status
      * @return Response with the updated sample request
      */
     @PUT
     @Path("/requests/{id}")
-    public Response updateSampleRequest(@PathParam("id") final long requestId,
-            @QueryParam("status") final SampleRequestStatus status) {
-        final String userId = getUserId();
+    public Response updateSampleRequest(@HeaderParam(value = "X-ICE-Authentication-SessionId") String sessionId,
+                                        @PathParam("id") final long requestId,
+                                        @QueryParam("status") final SampleRequestStatus status) {
+        final String userId = getUserId(sessionId);
         final SampleRequest request = requestRetriever.updateStatus(userId, requestId, status);
         return respond(Response.Status.OK, request);
     }
 
     /**
-     * @param offset
-     * @param limit
-     * @param sort
-     * @param asc
-     * @param uid
-     * @param status
      * @return response with the matching sample requests
      */
     @GET
     @Produces(MediaType.APPLICATION_JSON)
     @Path("/requests/{userId}")
-    public Response getUserRequests(@DefaultValue("0") @QueryParam("offset") final int offset,
-            @DefaultValue("15") @QueryParam("limit") final int limit,
-            @DefaultValue("requested") @QueryParam("sort") final String sort,
-            @DefaultValue("false") @QueryParam("asc") final boolean asc,
-            @PathParam("userId") final long uid,
-            @DefaultValue("IN_CART") @QueryParam("status") final SampleRequestStatus status) {
-        final String userId = getUserId();
+    public Response getUserRequests(@HeaderParam(value = "X-ICE-Authentication-SessionId") String sessionId,
+                                    @DefaultValue("0") @QueryParam("offset") final int offset,
+                                    @DefaultValue("15") @QueryParam("limit") final int limit,
+                                    @DefaultValue("requested") @QueryParam("sort") final String sort,
+                                    @DefaultValue("false") @QueryParam("asc") final boolean asc,
+                                    @PathParam("userId") final long uid,
+                                    @DefaultValue("IN_CART") @QueryParam("status") final SampleRequestStatus status) {
+        final String userId = getUserId(sessionId);
         Logger.info(userId + ": retrieving sample requests for user");
         final UserSamples userSamples = requestRetriever.getUserSamples(userId, status, offset,
                 limit, sort, asc);
         return super.respond(Response.Status.OK, userSamples);
     }
 
     /**
-     * @param request
      * @return Response with the added sample requests
      */
     @POST
     @Produces(MediaType.APPLICATION_JSON)
     @Path("/requests")
-    public ArrayList<SampleRequest> addRequest(final SampleRequest request) {
-        final String userId = getUserId();
+    public ArrayList<SampleRequest> addRequest(@HeaderParam(value = "X-ICE-Authentication-SessionId") String sessionId,
+                                               final SampleRequest request) {
+        final String userId = getUserId(sessionId);
         log(userId, "add sample request to cart for " + request.getPartData().getId());
         return requestRetriever.placeSampleInCart(userId, request);
     }
 
     /**
-     * @param type
      * @return Response with the current sample requests
      */
     @GET

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

@@ -66,7 +66,7 @@ private void getSBOLVisualType(String userId, String entryId, HttpServletRespons
             if (uri != null) {
                 try {
                     IOUtils.copy(uri.toURL().openStream(),
-                                 new FileOutputStream(tmpDir + File.separatorChar + hash + ".png"));
+                            new FileOutputStream(tmpDir + File.separatorChar + hash + ".png"));
                     fileId = hash + ".png";
                 } catch (IOException e) {
                     Logger.error(e);
@@ -76,6 +76,9 @@ private void getSBOLVisualType(String userId, String entryId, HttpServletRespons
         }
 
         response.setContentType("image/png");
+        if (fileId == null)
+            return;
+
         File file = Paths.get(tmpDir, fileId).toFile();
         if (file.exists() && file.canRead()) {
             response.setContentLength((int) file.length());

src/main/resources/logback.xml

@@ -16,8 +16,8 @@
         </encoder>
     </appender>
 
-    <logger name="org.jbei.ice" level="DEBUG"/>
-    <logger name="org.jbei.auth" level="DEBUG" additivity="false">
+    <logger name="org.jbei.ice" level="INFO"/>
+    <logger name="org.jbei.auth" level="INFO" additivity="false">
         <appender-ref ref="STDOUT"/>
     </logger>
 

src/main/webapp/index.jsp

@@ -19,14 +19,14 @@
     <script src="scripts/lib/angular/angular-touch.min.js"></script>
 
     <script src="scripts/lib/angular-ui/angular-ui-router.min-0.2.15.js"></script>
-    <script src="scripts/lib/angular-ui/ui-bootstrap-tpls-0.13.4.min.js"></script>
+    <script src="scripts/lib/angular-ui/ui-bootstrap-tpls-0.13.3.min.js"></script>
 
     <script src="scripts/lib/angular-file-upload/angular-file-upload.min.js"></script>
 
-    <script src="scripts/lib/handsontable-0.16.1/handsontable.full.min.js"></script>
-    <script src="scripts/lib/handsontable-0.16.1/pikaday.js"></script>
-    <link rel="stylesheet" href="scripts/lib/handsontable-0.16.1/pikaday.css">
-    <link rel="stylesheet" media="screen" href="scripts/lib/handsontable-0.16.1/handsontable.full.min.css">
+    <script src="scripts/lib/handsontable-0.18.0/handsontable.full.min.js"></script>
+    <script src="scripts/lib/handsontable-0.18.0/pikaday.js"></script>
+    <link rel="stylesheet" href="scripts/lib/handsontable-0.18.0/pikaday.css">
+    <link rel="stylesheet" media="screen" href="scripts/lib/handsontable-0.18.0/handsontable.full.min.css">
 
     <script src="scripts/lib/momentjs/moment.min.js"></script>
     <script src="scripts/lib/angular-moment/angular-moment.min.js"></script>
@@ -90,7 +90,7 @@
             </div>
             <div class="text-right">
                 &copy;&nbsp;<a href="https://github.com/JBEI/ice">JBEI ICE Registry</a> <span
-                    class="label label-primary">v4.4.0</span><br>
+                    class="label label-primary">v4.4.1</span><br>
                 All rights reserved. <br>
                 <a href="https://github.com/JBEI/ice/issues/new">Submit an Issue</a>&nbsp; <span class="text-muted">|</span> &nbsp;<a
                     href="http://public-registry.jbei.org/manual">Help</a>

src/main/webapp/scripts/admin/adminController.js

@@ -250,11 +250,15 @@ angular.module('ice.admin.controller', [])
 
         var samples = Samples($cookieStore.get("sessionId"));
         $scope.maxSize = 5;
-        $scope.params = {sort: 'requested', asc: false, currentPage: 1, status: 'ALL'};
+        $scope.params = {sort: 'requested', asc: false, currentPage: 1, status: undefined};
 
         $scope.requestSamples = function () {
             $scope.loadingPage = true;
-            samples.requests($scope.params, function (result) {
+            var params = angular.copy($scope.params);
+            if (params.status == 'ALL')
+                params.status = undefined;
+
+            samples.requests(params, function (result) {
                 $scope.sampleRequests = result;
                 $scope.loadingPage = false;
                 $scope.indexStart = ($scope.currentPage - 1) * 15;
@@ -340,5 +344,20 @@ angular.module('ice.admin.controller', [])
             }, function (error) {
 
             })
+        };
+
+        $scope.setUserAccountType = function (userItem, accountType) {
+            if (!accountType)
+                accountType = 'NORMAL';
+
+            var userCopy = angular.copy(userItem);
+            userCopy.accountType = accountType;
+
+            user.update({userId: userItem.id}, userCopy, function (result) {
+                userItem.accountType = result.accountType;
+                userItem.isAdmin = result.isAdmin;
+            }, function (error) {
+                console.log(error);
+            });
         }
     });

src/main/webapp/scripts/admin/users.html

@@ -57,10 +57,8 @@
             </div>
         </form>
     </div>
-
     <div class="pad_top">
-        <table cellspacing="0" class="table table-hover font-95em"
-               ng-class="{'opacity_4':loadingPage}">
+        <table cellspacing="0" class="table table-hover font-95em" ng-class="{'opacity_4':loadingPage}">
             <thead>
             <tr data-ng-show='!userList'>
                 <td colspan="10">Loading...</td>
@@ -82,21 +80,27 @@
             </tr>
             </thead>
             <tbody>
-            <tr data-ng-repeat="user in userList.users">
-                <td class="no_wrap">{{user.firstName}} {{user.lastName}} (<a ng-href="profile/{{user.id}}">{{user.email}}</a>)
-                </td>
-                <td style="width:160px; white-space:nowrap" ng-if="user.isAdmin">
-                    <small class="label label-danger"
-                           style="font-size: 12px; position: relative; top: -4px">{{user.accountType |
-                        capitalize}}
-                    </small>
+            <tr data-ng-repeat="userItem in userList.users">
+                <td class="no_wrap">{{userItem.firstName}} {{userItem.lastName}} (<a ng-href="profile/{{userItem.id}}">{{userItem.email}}</a>)
                 </td>
-                <td style="width:160px; white-space:nowrap" ng-if="!user.isAdmin">{{user.accountType ||
-                    "Normal" | capitalize}}
+                <td style="width:160px; white-space:nowrap">
+                    <!-- Single button -->
+                    <div class="btn-group" dropdown>
+                        <button type="button" class="btn btn-xs dropdown-toggle" dropdown-toggle
+                                ng-class="{'btn-warning':userItem.isAdmin, 'btn-default':!userItem.isAdmin}">
+                            {{userItem.accountType |capitalize}} <span class="caret"></span>
+                        </button>
+                        <ul class="dropdown-menu">
+                            <li ng-if="userItem.accountType != 'ADMIN'"
+                                ng-click="setUserAccountType(userItem, 'ADMIN')"><a href="#">Admin</a></li>
+                            <li ng-if="userItem.accountType != 'NORMAL'"
+                                ng-click="setUserAccountType(userItem, 'NORMAL')"><a href="#">Regular</a></li>
+                        </ul>
+                    </div>
                 </td>
-                <td style="width:90px; white-space:nowrap">{{user.userEntryCount | number}}</td>
-                <td style="width:160px; white-space:nowrap">{{user.registerDate | date:'MMM d, yyyy'}}</td>
-                <td style="width:160px; white-space:nowrap"><span ng-show="user.lastLogin">{{user.lastLogin | date:'MMM d, yyyy'}}</span>
+                <td style="width:90px; white-space:nowrap">{{userItem.userEntryCount | number}}</td>
+                <td style="width:160px; white-space:nowrap">{{userItem.registerDate | date:'MMM d, yyyy'}}</td>
+                <td style="width:160px; white-space:nowrap"><span ng-show="userItem.lastLogin">{{userItem.lastLogin | date:'MMM d, yyyy'}}</span>
                 </td>
             </tr>
             </tbody>

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

@@ -37,7 +37,6 @@ <h4>
                             </span>
 
                             <span style="font-weight: normal; color: #ccc">&nbsp;|&nbsp;</span>
-
                             <div class="dropdown display-inline" dropdown>
                             <span class="opacity_hover edit_icon font-90em dropdown-toggle" dropdown-toggle>
                                 <i style="font-size: 14px; color: #555" class="fa fa-link"></i> Link To
@@ -74,6 +73,7 @@ <h4>
                 <span ng-if="bulkUpload.status=='BULK_EDIT'">Done</span>
             </button>
             <button ng-if="bulkUpload.status==undefined || bulkUpload.status=='IN_PROGRESS'"
+                    ng-disabled="!bulkUpload||!bulkUpload.entryIdData||!bulkUpload.entryIdData.length"
                     type="button" class="btn btn-xs btn-default" ng-click="confirmResetFormModal()">
                 Reset
             </button>

src/main/webapp/scripts/upload/modal/reset-bulk-upload-sheet.html

@@ -12,6 +12,7 @@
 
 <div class="modal-footer">
     <button class="btn btn-default btn-sm" ng-click="cancel()">Cancel</button>
-    <button ng-if="!modalClose && !processing" type="button" ng-click="reset()" class="btn  btn-sm btn-primary"
-            ng-disabled="!importUploader.getNotUploadedItems().length">Reset</button>
+    <button ng-if="!modalClose && !processing" type="button"
+            ng-click="resetBulkUpload()" class="btn  btn-sm btn-primary">Reset
+    </button>
 </div>