Merge branch 'master' of https://github.com/genepi/cloudgene into rel…

…ease-2.6.3-tis

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.5.7</version>
+	<version>2.6.3</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>

src/main/html/webapp/components/core/user/profile/dialogs/new.stache

@@ -0,0 +1,3 @@
+<h4>API Token</h4>
+Make sure to copy your personal access token now. <b>You won’t be able to see it again</b>:<br><br>
+<textarea style="width:100%;height:100px;">{{token}}</textarea>

src/main/html/webapp/components/core/user/profile/profile.js

@@ -11,7 +11,7 @@ import UserProfile from 'models/user-profile';
 
 import template from './profile.stache';
 import templateDeleteDialog from './dialogs/delete.stache';
-
+import templateNewTokenDialog from './dialogs/new.stache'
 
 export default Control.extend({
 
@@ -99,17 +99,25 @@ export default Control.extend({
         callback: function(result) {
           if (result) {
 
+            var token_expiration = $('#token_expiration').val();
 
             var user = that.options.user;
 
             var userToken = new UserToken();
             userToken.attr('user', user.attr('username'));
+            userToken.attr('expiration', token_expiration);
 
             userToken.save(function(responseText) {
               user.attr('hasApiToken', true);
               user.attr('apiTokenValid', true);
               user.attr('apiTokenMessage', "");
-              bootbox.alert('<h4>API Token</h4>Your token for this service is:<br><textarea style="width:100%;height:100px;">' + responseText.token + '</textarea>');
+
+              bootbox.alert({
+                message: templateNewTokenDialog({
+                  token: responseText.token
+                })
+              });
+
             }, function(message) {
               bootbox.alert('<h4>API Token</h4>Error: ' + message);
             });
@@ -210,4 +218,4 @@ export default Control.extend({
 
   }
 
-});
+});

src/main/html/webapp/components/core/user/profile/profile.stache

@@ -50,18 +50,19 @@ Please fill out the form below to change your account settings or your password.
 <p>You need a access token to use the API. <a href="https://imputationbot.readthedocs.io/en/latest/getting-started/">Learn more</a>.</p>
 
 {{#user.hasApiToken}}
-
 	<div class="control-group">
 		<div class="controls">
-			<button class="btn btn-primary" id="show_token">Show API Token</button>
 			<button class="btn btn-danger" id="revoke_token">Revoke API Token</button>
 		</div>
 	</div>
   <small class="{{#is(../user.apiTokenValid, false)}}text-danger{{#is}}">{{../user.apiTokenMessage}}</small>
 	{{else}}
-		<button class="btn btn-primary" id="create_token">Create API Token
-	</button>
-
+		<button class="btn btn-primary" id="create_token">Create API Token</button>
+		Expires in 
+		<select  id="token_expiration">
+			<option value="30">30 days</option>
+			<option value="60">60 days</option>
+		</select>
 
 
 {{/user.hasApiToken}}
@@ -76,4 +77,4 @@ Please fill out the form below to change your account settings or your password.
 	<div class="controls">
 		<button class="btn btn-danger" id="delete_account">Delete Account</button>
 	</div>
-</div>
+</div>

src/main/html/webapp/models/user-token.js

@@ -2,6 +2,6 @@ import Model from 'can-connect/can/model/model';
 
 export default Model.extend({
   findOne: 'GET /api/v2/users/{user}/api-token',
-  create: 'POST /api/v2/users/{user}/api-token',
+  create: 'POST /api/v2/users/{user}/api-token?expiration={expiration}',
   destroy: 'DELETE /api/v2/users/{user}/api-token',
 }, {});

src/main/html/webapp/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cloudgene",
-  "version": "2.5.6",
+  "version": "2.6.3",
   "description": "Cloudgene web client",
   "homepage": "http://www.cloudgene.io",
   "author": "Lukas Forer <[email protected] (http://www.forer.it)",

src/main/java/cloudgene/mapred/Main.java

@@ -36,7 +36,7 @@
 
 public class Main {
 
-	public static final String VERSION = "2.5.7";
+	public static final String VERSION = "2.6.3";
 
 	private Database database;
 

src/main/java/cloudgene/mapred/api/v2/admin/GetAllJobs.java

@@ -65,13 +65,6 @@ public Representation getJobs() {
 		case "current":
 
 			jobs = dao.findAllNotRetiredJobs();
-			List<AbstractJob> toRemove = new Vector<AbstractJob>();
-			for (AbstractJob job : jobs) {
-				if (engine.isInQueue(job)) {
-					toRemove.add(job);
-				}
-			}
-			jobs.removeAll(toRemove);
 			break;
 
 		case "retired":
@@ -99,15 +92,15 @@ public Representation getJobs() {
 		int running = 0;
 
 		for (AbstractJob job : jobs) {
-			
+
 			String workspace = getSettings().getLocalWorkspace();
 			String folder = FileUtil.path(workspace, job.getId());
 			File file = new File(folder);
 			if (file.exists()) {
 				long size = FileUtils.sizeOfDirectory(file);
 				job.setWorkspaceSize(FileUtils.byteCountToDisplaySize(size));
 			}
-			
+
 			if (job.getState() == AbstractJob.STATE_EXPORTING || job.getState() == AbstractJob.STATE_RUNNING) {
 				running++;
 			}