Merge branch 'master' into clostridium

* master:
  Removing measurements route
  Edit characteristic
  'Select All' in compare.
  Fixed sort order in strains list
  genbank url for whole genome sequences

app/models/characteristic.js

@@ -12,4 +12,5 @@ export default DS.Model.extend({
   updatedBy             : DS.attr('number'),
   deletedBy             : DS.attr('number'),
   sortOrder             : DS.attr('number'),
+  canEdit               : DS.attr('boolean'),
 });

app/pods/components/x-application/template.hbs

@@ -5,9 +5,6 @@
       {{#link-to 'protected.compare' tagName='li' href=false}}
         {{link-to 'Compare' 'protected.compare'}}
       {{/link-to}}
-      {{#link-to 'protected.measurements' tagName='li' href=false}}
-        {{link-to 'Measurements' 'protected.measurements'}}
-      {{/link-to}}
       {{#link-to 'protected.characteristics' tagName='li' href=false}}
         {{link-to 'Characteristics' 'protected.characteristics'}}
       {{/link-to}}

app/pods/protected/characteristics/controller.js

@@ -1,6 +1,6 @@
 import Ember from 'ember';
 
 export default Ember.Controller.extend({
-  sortParams: ['characteristicTypeName', 'sortOrder'],
+  sortParams: ['characteristicTypeName', 'sortOrder', 'characteristicName'],
   sortedCharacteristics: Ember.computed.sort('model', 'sortParams'),
 });

app/pods/protected/characteristics/editable-row/component.js

@@ -0,0 +1,28 @@
+import Ember from 'ember';
+
+export default Ember.Component.extend({
+  tagName: 'tr',
+
+  actions: {
+    edit: function() {
+      this.set('characteristicName', this.get('row.characteristicName'));
+      this.set('characteristicTypeName', this.get('row.characteristicTypeName'));
+      this.set('sortOrder', this.get('row.sortOrder'));
+      this.toggleProperty('isEditing');
+    },
+
+    save: function() {
+      if (this.get('characteristicName') !== this.get('row.characteristicName') ||
+          this.get('characteristicTypeName') !== this.get('row.characteristicTypeName') ||
+          this.get('sortOrder') !== this.get('row.sortOrder')) {
+        this.set('row.characteristicName', this.get('characteristicName'));
+        this.set('row.characteristicTypeName', this.get('characteristicTypeName'));
+        this.set('row.sortOrder', this.get('sortOrder'));
+        this.get('row').save();
+      }
+      this.toggleProperty('isEditing');
+    },
+
+  }
+
+});

app/pods/protected/characteristics/editable-row/template.hbs

@@ -0,0 +1,15 @@
+{{#if isEditing}}
+  <td>{{input value=characteristicName}}</td>
+  <td>{{input value=characteristicTypeName}}</td>
+  <td>{{input value=sortOrder}}</td>
+  <td {{action 'save'}}>Save</td>
+{{else}}
+  <td>{{row.characteristicName}}</td>
+  <td>{{row.characteristicTypeName}}</td>
+  <td>{{row.sortOrder}}</td>
+  {{#if row.canEdit}}
+    <td {{action 'edit'}}>Edit</td>
+  {{else}}
+    <td></td>
+  {{/if}}
+{{/if}}

app/pods/protected/characteristics/template.hbs

@@ -7,15 +7,12 @@
       <th>Name</th>
       <th>Type</th>
       <th>Sort Order</th>
+      <th></th>
     </tr>
   </thead>
   <tbody>
     {{#each sortedCharacteristics as |row|}}
-      <tr>
-        <td>{{row.characteristicName}}</td>
-        <td>{{row.characteristicTypeName}}</td>
-        <td>{{row.sortOrder}}</td>
-      </tr>
+      {{protected/characteristics/editable-row row=row}}
     {{/each}}
   </tbody>
 </table>

app/pods/protected/compare/controller.js

@@ -9,6 +9,33 @@ export default Ember.Controller.extend({
       };
 
       this.transitionToRoute('protected.compare.results', {queryParams: query});
-    }
+    },
+
+    selectAllStrains: function() {
+      let strains = this.get('strains');
+      let strain_ids = [];
+      strains.forEach((strain) => {
+        strain_ids.push(strain.id);
+      });
+      this.set('selectedStrains', strain_ids.join(","));
+    },
+
+    deselectAllStrains: function() {
+      this.set('selectedStrains', '');
+    },
+
+    selectAllCharacteristics: function() {
+      let chars = this.get('characteristics');
+      let char_ids = [];
+      chars.forEach((char) => {
+        char_ids.push(char.id);
+      });
+      this.set('selectedCharacteristics', char_ids.join(","));
+    },
+
+    deselectAllCharacteristics: function() {
+      this.set('selectedCharacteristics', '');
+    },
+
   }
 });

app/pods/protected/compare/template.hbs

@@ -16,6 +16,14 @@
             placeholder="Select one or more strains"
           }}
         </li>
+        <li>
+          <button class="action button-green smaller right" {{action 'selectAllStrains'}}>
+            Select All
+          </button>
+          <button class="action button-red smaller right" {{action 'deselectAllStrains'}}>
+            Deselect All
+          </button>
+        </li>
         <li>
           <label>Characteristics</label>
           {{
@@ -28,6 +36,14 @@
             placeholder="Select one or more characteristics"
           }}
         </li>
+        <li>
+          <button class="action button-green smaller right" {{action 'selectAllCharacteristics'}}>
+            Select All
+          </button>
+          <button class="action button-red smaller right" {{action 'deselectAllCharacteristics'}}>
+            Deselect All
+          </button>
+        </li>
         <li>
           <button type="submit" class="action button-gray smaller right">
             Search

app/pods/protected/measurements/route.js

@@ -1,3 +0,0 @@
-import Ember from 'ember';
-
-export default Ember.Route.extend({});

app/pods/protected/measurements/template.hbs

@@ -1,3 +0,0 @@
-<h2>{{genus-name}} Measurements</h2>
-
-Be back soon

app/pods/protected/strains/index/controller.js

@@ -1,6 +1,6 @@
 import Ember from 'ember';
 
 export default Ember.Controller.extend({
-  sortParams: ['fullNameMU', 'totalMeasurements'],
+  sortParams: ['sortOrder'],
   sortedStrains: Ember.computed.sort('model', 'sortParams'),
 });

app/pods/protected/strains/show/template.hbs

@@ -39,7 +39,7 @@
       <dl class="span-1">
         <dt>Whole Genome Sequence</dt>
         <dd>
-          {{model.wholeGenomeSequence}}
+          {{genbank-url genbank=model.wholeGenomeSequence}}
         </dd>
       </dl>
     </div>

app/serializers/characteristic.js

@@ -0,0 +1,18 @@
+import DS from 'ember-data';
+import Ember from 'ember';
+
+export default DS.RESTSerializer.extend({
+  isNewSerializerAPI: true,
+
+  serializeHasMany: function(snapshot, json, relationship) {
+    var key = relationship.key;
+    var hasMany = snapshot.hasMany(key);
+    key = this.keyForRelationship ? this.keyForRelationship(key, "hasMany", "serialize") : key;
+
+    json[key] = [];
+    hasMany.forEach((item) => {
+      json[key].push(+item.get('id'));
+    });
+  }
+
+});