show all

index_generator/models.py

@@ -28,6 +28,7 @@ class Pool(DateTimeMixin):
         Library, related_name='pool', blank=True)
     samples = models.ManyToManyField(
         Sample, related_name='pool', blank=True)
+    comment = models.TextField(verbose_name='Comment', blank=True)
 
     # def get_size(self):
     #     size = 0

pooling/models.py

@@ -26,6 +26,8 @@ class Pooling(DateTimeMixin):
         blank=True
     )
 
+    comment = models.TextField(verbose_name='Comment',blank=True)
+
     class Meta:
         verbose_name = 'Pooling'
         verbose_name_plural = 'Pooling'

pooling/serializers.py

@@ -173,10 +173,11 @@ class PoolSerializer(ModelSerializer):
 
     libraries = SerializerMethodField()
     samples = SerializerMethodField()
+    comment = SerializerMethodField()
 
     class Meta:
         model = Pool
-        fields = ('pool', 'pool_name', 'pool_size', 'libraries', 'samples',)
+        fields = ('pool', 'pool_name', 'pool_size', 'libraries', 'samples','comment',)
 
     def get_pool(self, obj):
         return obj.pk
@@ -198,6 +199,10 @@ def get_samples(self, obj):
             obj.samples, many=True, context=self.context)
         return serializer.data
 
+    def get_comment(self,obj):
+        return obj.comment
+
+
     def to_representation(self, instance):
         data = super().to_representation(instance)
         result = []
@@ -215,6 +220,8 @@ def to_representation(self, instance):
                         x['sequencing_depth'] /
                         instance.total_sequencing_depth * 100
                     )),
+
+                    'comment': data['comment']
                 }, **x},
                 data.pop(type),
             )))

static/main-hub/app/model/pooling/Pooling.js

@@ -73,6 +73,10 @@ Ext.define('MainHub.model.pooling.Pooling', {
             name: 'quality_check',
             type: 'string',
             allowNull: true
+        },
+        {
+            name: 'comment',
+            type: 'string'
         }
     ]
 });

static/main-hub/app/view/pooling/Pooling.js

@@ -152,7 +152,20 @@ Ext.define('MainHub.view.pooling.Pooling', {
         tooltip: '% library in Pool',
         dataIndex: 'percentage_library',
         width: 55
-      }
+      },
+      {
+          text: 'Comments',
+          tooltip: 'Comments (facility)',
+          dataIndex: 'comment',
+          width: 150,
+          editor: {
+            xtype: 'textfield'
+          },
+          renderer: function (value, meta) {
+            meta.tdAttr = 'data-qtip="' + value + '"';
+            return value;
+          }
+        }
     ],
 
     features: [{
@@ -162,7 +175,7 @@ Ext.define('MainHub.view.pooling.Pooling', {
       groupHeaderTpl: [
         '<strong class="{children:this.getHeaderClass}">' +
           '{children:this.getName} | Pool Size: {children:this.getRealPoolSize} M reads ' +
-          '{children:this.getPoolSize}' +
+          '{children:this.getPoolSize}| Comment: {children:this.getComment} ' +
         '</strong>',
         {
           getHeaderClass: function (children) {
@@ -181,6 +194,10 @@ Ext.define('MainHub.view.pooling.Pooling', {
 
             return cls;
           },
+          getComment: function(children){
+            return children[0].get('comment')
+
+          },
           getName: function (children) {
             return children[0].get('pool_name');
           },

static/main-hub/app/view/pooling/PoolingController.js

@@ -15,7 +15,7 @@ Ext.define('MainHub.view.pooling.PoolingController', {
         resize: 'resize',
         boxready: 'addToolbarButtons',
         itemcontextmenu: 'showMenu',
-        groupcontextmenu: 'showGroupMenu',
+        groupcontextmenu: 'showPoolingGroupMenu',
         beforeEdit: 'toggleEditors',
         edit: 'editRecord'
       },
@@ -40,6 +40,157 @@ Ext.define('MainHub.view.pooling.PoolingController', {
     }
   },
 
+    showPoolingGroupMenu: function (gridView, node, groupId, e) {
+    var self = this;
+    var grid = gridView.grid;
+    var customConfig = gridView.grid.initialConfig.customConfig;
+    var qcMenuOptions = [];
+    var menuItems = [
+      {
+        text: 'Select All',
+        margin: '5px 5px 0 5px',
+        handler: function () {
+          self.selectUnselectAll(grid, parseInt(groupId), true);
+        }
+      },
+      {
+        text: 'Unselect All',
+        margin: 5,
+        handler: function () {
+          self.selectUnselectAll(grid, parseInt(groupId), false);
+        }
+      },
+      {
+        text: 'Edit comment',
+        margin: '5px 5px 0 5px',
+        handler: function (){
+            var self = this;
+            var store = grid.getStore();
+            var comment = '';
+            var i = 0;
+            store.each(function (item) {
+
+            if (item.get(store.groupField) === parseInt(groupId)) {
+
+                    comment = item.get('comment')
+                    console.log(comment)
+            }
+            });
+            var editcomment = {
+            xtype: 'container',
+            layout: 'hbox',
+            items: [{
+                xtype: 'textfield',
+                width: 100
+            },
+            {
+                xtype: 'button',
+                text: 'Click Me'
+            }]
+        };
+
+        menuItems.push(editcomment)
+      }
+      }
+    ];
+
+    if (customConfig && customConfig.qualityCheckMenuOptions) {
+      qcMenuOptions = customConfig.qualityCheckMenuOptions;
+    }
+
+    if (
+      qcMenuOptions.length > 0 &&
+      self._getSelectedRecords(grid.getStore(), parseInt(groupId)).length > 0
+    ) {
+      var qcMenu = {
+        xtype: 'container',
+        items: [
+          {
+            xtype: 'container',
+            html: 'Quality Check: Selected',
+            margin: '10px 5px 5px 5px',
+            style: {
+              color: '#000'
+            }
+          },
+          {
+            xtype: 'container',
+            margin: 5,
+            layout: {
+              type: 'hbox',
+              pack: 'center',
+              align: 'middle'
+            },
+            defaults: {
+              xtype: 'button',
+              scale: 'medium',
+              margin: '5px 10px 10px'
+            },
+            items: []
+          }
+        ]
+      };
+
+      if (qcMenuOptions.indexOf('passed') !== -1) {
+        qcMenu.items[1].items.push({
+          ui: 'menu-button-green',
+          tooltip: 'passed',
+          iconCls: 'fa fa-lg fa-check',
+          handler: function () {
+            self.qualityCheckSelected(grid, parseInt(groupId), 'passed');
+            this.up('menu').hide();
+          }
+        });
+      }
+
+      if (qcMenuOptions.indexOf('completed') !== -1) {
+        qcMenu.items[1].items.push({
+          ui: 'menu-button-green',
+          tooltip: 'completed',
+          iconCls: 'fa fa-lg fa-check',
+          handler: function () {
+            self.qualityCheckSelected(grid, parseInt(groupId), 'completed');
+            this.up('menu').hide();
+          }
+        });
+      }
+
+      if (qcMenuOptions.indexOf('compromised') !== -1) {
+        qcMenu.items[1].items.push({
+          ui: 'menu-button-yellow',
+          tooltip: 'compromised',
+          iconCls: 'fa fa-lg fa-exclamation-triangle',
+          handler: function () {
+            self.qualityCheckSelected(grid, parseInt(groupId), 'compromised');
+            this.up('menu').hide();
+          }
+        });
+      }
+
+      if (qcMenuOptions.indexOf('failed') !== -1) {
+        qcMenu.items[1].items.push({
+          ui: 'menu-button-red',
+          tooltip: 'failed',
+          iconCls: 'fa fa-lg fa-times',
+          handler: function () {
+            self.qualityCheckSelected(grid, parseInt(groupId), 'failed');
+            this.up('menu').hide();
+          }
+        });
+      }
+
+      menuItems.push('-');
+      menuItems.push(qcMenu);
+    }
+
+    e.stopEvent();
+    Ext.create('Ext.menu.Menu', {
+      plain: true,
+      items: menuItems
+    }).showAt(e.getXY());
+  },
+
+
   addToolbarButtons: function (grid) {
     var toolbar = grid.down('toolbar[dock="bottom"]');