Merge tag 'v2.8.2' of https://github.com/genepi/cloudgene into releas…

…e/2.8.2-tis

.github/workflows/maven-test.yml

@@ -18,6 +18,6 @@ jobs:
         java-version: '12'
         distribution: 'adopt'
     - name: Run JUnit Tests
-      run: mvn install
+      run: mvn -B install
     - name: Upload coverage report to Codecov
       uses: codecov/codecov-action@v2 

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>cloudgene</groupId>
 	<artifactId>cloudgene</artifactId>
-	<version>2.7.0</version>
+	<version>2.8.2</version>
 
 	<name>Cloudgene</name>
 	<url>http://www.cloudgene.io</url>

src/main/html/webapp/components/admin/app/list/list.js

@@ -228,40 +228,48 @@ export default Control.extend({
 
     Group.findAll({},
       function(groups) {
-        var selection = new canMap();
-        selection.attr('group', application.attr('permission'));
-        selection.attr('name', '');
-
-        bootbox.confirm(templatePermission({
-            selection: selection,
-            application: application,
-            groups: groups
-          }),
+
+        var roles = application.attr('permission').split(',');
+
+        var options = '';
+        groups.forEach(function(group, index) {
+          if ($.inArray(group.attr('name'), roles) >= 0) {
+            options = options + '<label class="checkbox"><input type="checkbox" name="role-select" value="' + group.attr('name') + '" checked />';
+            //options = options + '<option selected>' + group.attr('name') + '</option>';
+          } else {
+            //options = options + '<option>' + group.attr('name') + '</option>';
+            options = options + '<label class="checkbox"><input type="checkbox" name="role-select" value="' + group.attr('name') + '" />';
+          }
+          options = options + ' <b>' + group.attr('name') + '</b></label><br>';
+        });
+
+        bootbox.confirm(
+          '<h4>Edit permission of ' + application.attr('name') + '</h4><hr><form id="role-form">' + options + '</form>',
           function(result) {
             if (result) {
-              var group = selection.attr('group');
-              if (group !== '') {
-                application.attr('permission', group);
-                application.save(function(data) {},
-                  function(response) {
-                    showErrorDialog("Operation failed", response);
-                  });
-              } else {
-                var name = selection.attr('name');
-                if (name !== '') {
-                  application.attr('permission', name);
-                  application.save(function(data) {},
-                    function(response) {
-                      showErrorDialog("Operation failed", response);
-                    });
-
-                } else {
-                  bootbox.alert("Error: Please enter a name for the new group.")
+
+              var boxes = $('#role-form input:checkbox');
+              var checked = [];
+              for (var i = 0; boxes[i]; ++i) {
+                if (boxes[i].checked) {
+                  checked.push(boxes[i].value);
                 }
               }
 
+              var text = checked.join(',');
+              application.attr('permission', text);
+              application.save(function(data) {},
+                function(response) {
+                  showErrorDialog("Operation failed", response);
+                });
+
             }
-          });
+          }
+        );
+
+      },
+      function(response) {
+        new ErrorPage(element, response);
       });
 
   },

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

@@ -16,19 +16,37 @@ import templateNewTokenDialog from './dialogs/new.stache'
 export default Control.extend({
 
   "init": function(element, options) {
-
+    this.emailRequired = options.appState.attr('emailRequired');
     $(element).hide();
     User.findOne({
       user: 'me'
     }, function(user) {
       $(element).html(template({
-        user: user
+        user: user,
+        anonymousAccount: (!options.appState.attr('emailRequired')),
+        emailProvided: (user.attr('mail') != "" && user.attr('mail') != undefined),
+        userEmailDescription: options.appState.attr('userEmailDescription'),
+        userWithoutEmailDescription: options.appState.attr('userWithoutEmailDescription')
       }));
       options.user = user;
       $(element).fadeIn();
     });
   },
 
+  "#anonymous click" : function(){
+    if (!this.emailRequired){
+      var anonymousControl = $(this.element).find("[name='anonymous']");
+      var anonymous = !anonymousControl.is(':checked');
+      var mail = $(this.element).find("[name='mail']");
+      if (anonymous){
+        mail.attr('disabled','disabled');
+      } else {
+        mail.removeAttr('disabled');
+      }
+      mail.val("");
+    }
+  },
+
   'submit': function(element, event) {
     event.preventDefault();
     var user = new User();
@@ -38,10 +56,20 @@ export default Control.extend({
     var fullnameError = user.checkName(fullname.val());
     this.updateControl(fullname, fullnameError);
 
+    var anonymous = false;
+    if (!this.emailRequired){
+      var anonymousControl = $(this.element).find("[name='anonymous']");
+      anonymous = !anonymousControl.is(':checked');
+    }
+
     // mail
     var mail = $(element).find("[name='mail']");
-    var mailError = user.checkMail(mail.val());
-    this.updateControl(mail, mailError);
+    if (!anonymous){
+      var mailError = user.checkMail(mail.val());
+      this.updateControl(mail, mailError);
+    } else {
+      this.updateControl(mail, undefined);
+    }
 
     // password if password is not empty. else no password update on server side
     var newPassword = $(element).find("[name='new-password']");
@@ -218,4 +246,4 @@ export default Control.extend({
 
   }
 
-});
+});

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

@@ -16,12 +16,34 @@ Please fill out the form below to change your account settings or your password.
 		<div class="invalid-feedback"></div>
 	</div>
 
+  {{#is(anonymousAccount, false)}}
+
 	<div class="form-group">
 		<label for="mail" class="control-label">E-Mail:</label>
 		<input id="mail" name="mail" type="text" value="{{user.mail}}" class="form-control col-sm-3">
 		<div class="invalid-feedback"></div>
 	</div>
 
+	{{else}}
+	<hr>
+  <div class="form-group">
+   <input type="checkbox" id="anonymous" name="anonymous" value="0" {{#emailProvided}}checked{{/emailProvided}}> <label for="anonymous" class="control-label">E-Mail Address</label>
+    <div class="form-group" style="margin-left: 30px;">
+      <p>
+     {{userEmailDescription}}
+      </p>
+      <label for="mail" class="control-label">E-Mail:</label>
+      <input id="mail" name="mail" type="text" class="form-control col-sm-3" autocomplete="off" {{#is(emailProvided, false)}}disabled{{/is}} value="{{user.mail}}">
+      <div class="invalid-feedback"></div>
+      <p><br>
+        {{userWithoutEmailDescription}}
+      </p>
+    </div>
+     </div>
+       <hr>
+
+	{{/is}}
+
 	<h4>Change password</h4>
 
 	<div class="form-group">
@@ -41,9 +63,9 @@ Please fill out the form below to change your account settings or your password.
 
 	</div>
 </form>
-
+<br>
 <hr>
-
+<br>
 <h3>API Access</h3>
 
 <p>This service provides a rich RestAPI to submit, monitor and download jobs.</p>
@@ -58,17 +80,17 @@ Please fill out the form below to change your account settings or your password.
   <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>
-		Expires in 
+		Expires in
 		<select  id="token_expiration">
 			<option value="30">30 days</option>
 			<option value="60">60 days</option>
 		</select>
 
 
 {{/user.hasApiToken}}
-
+<br>
 <hr>
-
+<br>
 <h3>Delete Account</h3>
 
 <p>Once you delete your user account, there is no going back. Please be certain.</p>
@@ -77,4 +99,4 @@ 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/components/core/user/signup/signup.js

@@ -9,17 +9,51 @@ import template from './signup.stache';
 export default Control.extend({
 
   "init": function(element, options) {
+    this.emailRequired = options.appState.attr('emailRequired');
     $(element).hide();
-    $(element).html(template());
+    $(element).html(template({
+      emailRequired: options.appState.attr('emailRequired'),
+      userEmailDescription: options.appState.attr('userEmailDescription'),
+      userWithoutEmailDescription: options.appState.attr('userWithoutEmailDescription')
+    }));
     $(element).fadeIn();
   },
 
+  "#anonymous1 click" : function(){
+    this.updateEmailControl();
+  },
+
+  "#anonymous2 click" : function(){
+    this.updateEmailControl();
+  },
+
+  "updateEmailControl": function() {
+      if (!this.emailRequired){
+        var anonymousControl = $(this.element).find("[name='anonymous']:checked");
+        var anonymous = (anonymousControl.val() == "1");
+        var mail = $(this.element).find("[name='mail']");
+        if (anonymous){
+          mail.attr('disabled','disabled');
+        } else {
+          mail.removeAttr('disabled');
+        }
+      }
+   },
+
   'submit': function(element, event) {
     event.preventDefault();
 
     var that = this;
     var user = new User();
 
+    // anonymous radiobutton
+    var anonymous = false;
+
+    if (!this.emailRequired){
+      var anonymousControl = $(element).find("[name='anonymous']:checked");
+      anonymous = (anonymousControl.val() == "1");
+    }
+
     // username
     var username = $(element).find("[name='username']");
     var usernameError = user.checkUsername(username.val());
@@ -32,8 +66,12 @@ export default Control.extend({
 
     // mail
     var mail = $(element).find("[name='mail']");
-    var mailError = user.checkMail(mail.val());
-    this.updateControl(mail, mailError);
+    if (!anonymous){
+      var mailError = user.checkMail(mail.val());
+      this.updateControl(mail, mailError);
+    } else {
+      this.updateControl(mail, undefined);
+    }
 
     // password
     var newPassword = $(element).find("[name='new-password']");
@@ -55,7 +93,16 @@ export default Control.extend({
       success: function(data) {
         if (data.success == true) {
           // shows success
+
+          var message = "";
+          if (!anonymous){
+            message = "Well done!</b> An email including the activation code has been sent to your address."
+          } else {
+            message = "<b>Well done!</b> Your account is now active. <a href=\"/\">Login now</a>."
+          }
+
           $('#signon-form').hide();
+          $('#success-message').html(message);
           $('#success-message').show();
         } else {
           // shows error msg

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

@@ -2,8 +2,6 @@
 <br>
 
 <div class="alert alert-success" id="success-message" style="display: none;">
-  <b>Well done!</b> An email including the activation code has been sent to your address.
-  <br>
 </div>
 
 <form id="signon-form" class="form-horizontal" autocomplete="off">
@@ -21,13 +19,36 @@
     <div class="invalid-feedback"></div>
   </div>
 
+  {{#is(emailRequired, true)}}
 
   <div class="form-group">
     <label for="mail" class="control-label">E-Mail:</label>
     <input id="mail" name="mail" type="text" class="form-control col-sm-3" autocomplete="off">
     <div class="invalid-feedback"></div>
   </div>
 
+  {{else}}
+    <hr>
+  <div class="form-group">
+   <input type="radio" id="anonymous1" name="anonymous" value="0" checked> <label for="anonymous1" class="control-label">E-Mail Address</label>
+    <div class="form-group" style="margin-left: 30px;">
+      <p>
+     {{{userEmailDescription}}}
+      </p>
+      <label for="mail" class="control-label">E-Mail:</label>
+      <input id="mail" name="mail" type="text" class="form-control col-sm-3" autocomplete="off">
+      <div class="invalid-feedback"></div>
+    </div>
+   <input type="radio" id="anonymous2" name="anonymous" value="1"> <label for="anonymous2" class="control-label">I don't want to provide my email address</label>
+   <div class="form-group" style="margin-left: 30px;">
+     <p>
+      {{{userWithoutEmailDescription}}}
+     </p>
+    </div>
+   </div>
+     <hr>
+  {{/is}}
+
   <div class="form-group">
     <label for="new-password" class="control-label">Password:</label>
     <input id="new-password" name="new-password" type="password" class="form-control col-sm-3" autocomplete="off">

src/main/html/webapp/helpers/error-page.stache

@@ -1,4 +1,5 @@
 <br><br><br>
+<div style="margin: 40px">
 <h2 class="text-danger text-center">
   {{error.statusText}}
 </h2>
@@ -22,4 +23,5 @@
     &nbsp;
     {{{error.responseText}}}
 </h5>
+</div>
 <br><br><br><br><br><br><br><br><br>