Jkmarx/add tools list landing page

refinery/tool_manager/serializers.py

@@ -68,6 +68,11 @@ class Meta:
 class ToolDefinitionSerializer(serializers.ModelSerializer):
     file_relationship = FileRelationshipSerializer()
     parameters = ParameterSerializer(many=True, allow_null=True)
+    workflow = serializers.SerializerMethodField()
+
+    def get_workflow(self, tool):
+        if tool.workflow is not None:
+            return tool.workflow.uuid
 
     class Meta:
         model = ToolDefinition

refinery/tool_manager/tests.py

@@ -670,6 +670,23 @@ def test_unallowed_http_verbs(self):
             self.delete_response.data['detail'], 'Method "DELETE" not '
                                                  'allowed.')
 
+    def test_request_without_any_params_returns_all(self):
+        get_request = self.factory.get(self.tool_defs_url_root)
+        force_authenticate(get_request, self.user)
+        get_response = self.tool_defs_view(get_request)
+        serialized_data = ToolDefinitionSerializer(
+            ToolDefinition.objects.all(), many=True
+        ).data
+        self.assertEqual(get_response.status_code, 200)
+        self.assertEqual(get_response.data, serialized_data)
+
+    def test_request_without_data_set_uuid_returns_all(self):
+        serialized_data = ToolDefinitionSerializer(
+            ToolDefinition.objects.all(), many=True
+        ).data
+        self.assertEqual(self.get_response.status_code, 200)
+        self.assertEqual(self.get_response.data, serialized_data)
+
     def test_for_proper_parameters_in_response(self):
         """ToolDefinitions for Workflows will have an extra field on their
          parameter objects
@@ -710,25 +727,6 @@ def test_request_from_public_dataset_shows_vis_tools_only(self):
                 )
             )
 
-    def test_no_query_params_in_get_yields_bad_request(self):
-        get_request = self.factory.get(self.tool_defs_url_root)
-        force_authenticate(get_request, self.user)
-        get_response = self.tool_defs_view(get_request)
-        self.assertEqual(get_response.status_code, 400)
-        self.assertIn("Must specify a DataSet UUID", get_response.content)
-
-    def test_bad_query_params_in_get_yields_bad_request(self):
-        get_request = self.factory.get(
-            "{}?coffee={}".format(
-                self.tool_defs_url_root,
-                self.dataset.uuid
-            )
-        )
-        force_authenticate(get_request, self.user)
-        get_response = self.tool_defs_view(get_request)
-        self.assertEqual(get_response.status_code, 400)
-        self.assertIn("Must specify a DataSet UUID", get_response.content)
-
     def test_missing_dataset_in_get_yields_bad_request(self):
         dataset_uuid = str(uuid.uuid4())
 

refinery/tool_manager/views.py

@@ -11,6 +11,7 @@
 from django_docker_engine.proxy import Proxy
 from rest_framework.decorators import detail_route
 from rest_framework.generics import get_object_or_404
+from rest_framework.response import Response
 from rest_framework.viewsets import ModelViewSet
 
 from core.models import DataSet
@@ -56,6 +57,14 @@ class ToolDefinitionsViewSet(ToolManagerViewSetBase):
     lookup_field = 'uuid'
     http_method_names = ['get']
 
+    def list(self, request):
+        if request.query_params.get('data_set_uuid'):
+            return super(ToolDefinitionsViewSet, self).list(request)
+
+        serializer = ToolDefinitionSerializer(ToolDefinition.objects.all(),
+                                              many=True)
+        return Response(serializer.data)
+
     def get_queryset(self):
         if self.request.user.has_perm('core.change_dataset', self.data_set):
             return ToolDefinition.objects.all()

refinery/ui/Gruntfile.js

@@ -647,6 +647,8 @@ module.exports = function (grunt) {
             '<%= cfg.basePath.ui.src %>/styles/treemap.less',
           '<%= cfg.basePath.ui.compile %>/styles/dashboard.css':
             '<%= cfg.basePath.ui.src %>/styles/dashboard.less',
+          '<%= cfg.basePath.ui.compile %>/styles/home.css':
+            '<%= cfg.basePath.ui.src %>/styles/home.less',
           '<%= cfg.basePath.ui.compile %>/styles/provenance-visualization.css':
             '<%= cfg.basePath.ui.src %>/styles/provenance-visualization.less',
           '<%= cfg.basePath.ui.compile %>/styles/file-browser.css':

refinery/ui/source/js/home/ctrls/tool-list-ctrl.js

@@ -0,0 +1,35 @@
+/**
+ * Tool List Ctrl
+ * @namespace ToolListCtrl
+ * @desc Component controller for the tool list partial.
+ * @memberOf refineryApp.refineryHome
+ */
+(function () {
+  'use strict';
+  angular
+    .module('refineryHome')
+    .controller('ToolListCtrl', ToolListCtrl);
+
+  ToolListCtrl.$inject = ['toolListService'];
+
+  function ToolListCtrl (toolListService) {
+    var vm = this;
+    vm.toolList = toolListService.toolList;
+
+    activate();
+    /*
+     * -----------------------------------------------------------------------------
+     * Methods
+     * -----------------------------------------------------------------------------
+    */
+    function activate () {
+      // tool list won't be updated often, so no need for api call
+      // if list is already populated
+      if (!vm.toolList.length) {
+        toolListService.getTools().then(function () {
+          vm.toolList = toolListService.toolList;
+        });
+      }
+    }
+  }
+})();

refinery/ui/source/js/home/ctrls/tool-list-ctrl.spec.js

@@ -0,0 +1,65 @@
+(function () {
+  'use strict';
+
+  describe('Controller: Tool List Ctrl', function () {
+    var ctrl;
+    var genCtrl;
+    var mockService;
+    var mockServiceResponse = false;
+    var scope;
+    var service;
+    var rootScope;
+
+    beforeEach(module('refineryApp'));
+    beforeEach(module('refineryHome'));
+    beforeEach(inject(function (
+      $rootScope,
+      $controller,
+      $httpBackend,
+      settings,
+      toolListService
+    ) {
+      service = toolListService;
+      mockService = spyOn(service, 'getTools').and.callFake(function () {
+        return {
+          then: function () {
+            mockServiceResponse = true;
+          }
+        };
+      });
+      rootScope = $rootScope;
+      scope = rootScope.$new();
+      genCtrl = $controller;
+      ctrl = $controller('ToolListCtrl', {
+        $scope: scope
+      });
+    }));
+
+    it('Tool List Ctrl ctrl should exist', function () {
+      expect(ctrl).toBeDefined();
+    });
+
+    it('data variables should exist for views', function () {
+      expect(ctrl.toolList).toEqual([]);
+    });
+
+    it('should call service when initalized', function () {
+      scope.$apply();
+      expect(mockService).toHaveBeenCalled();
+      expect(mockServiceResponse).toEqual(true);
+    });
+
+    it('should not call service when list exists', function () {
+      mockServiceResponse = false;
+      mockService.calls.reset();
+      angular.copy([{ name: 'FastQC' }], service.toolList);
+      var newScope = rootScope.$new();
+      genCtrl('ToolListCtrl', {
+        $scope: newScope
+      });
+      newScope.$apply();
+      expect(mockService).not.toHaveBeenCalled();
+      expect(mockServiceResponse).toEqual(false);
+    });
+  });
+})();

refinery/ui/source/js/home/directives/home.spec.js

@@ -13,14 +13,12 @@
       $templateCache,
       $window
     ) {
-      // Parent component contains the input-group (child) component
       $templateCache.put(
         $window.getStaticUrl('partials/home/views/home.html'),
         '<div id="home-main">/div>'
       );
 
       var scope = $rootScope.$new();
-      // Parent component
       var template = '<rp-home></rp-home>';
       directiveElement = $compile(template)(scope);
       scope.$digest();

refinery/ui/source/js/home/directives/tool-list.js

@@ -0,0 +1,17 @@
+/**
+ * Tool List Component
+ * @namespace rpToolList
+ * @desc Component to show a list of all the tools
+ * @memberOf refineryApp.refineryHome
+ */
+(function () {
+  'use strict';
+  angular
+    .module('refineryHome')
+    .component('rpToolList', {
+      controller: 'ToolListCtrl',
+      templateUrl: ['$window', function ($window) {
+        return $window.getStaticUrl('partials/home/partials/tool-list.html');
+      }]
+    });
+})();

refinery/ui/source/js/home/directives/tool-list.spec.js

@@ -0,0 +1,40 @@
+(function () {
+  'use strict';
+
+  describe('rpToolList component unit test', function () {
+    beforeEach(module('refineryApp'));
+    beforeEach(module('refineryHome'));
+
+    var directiveElement;
+
+    beforeEach(inject(function (
+      $compile,
+      $httpBackend,
+      $rootScope,
+      $templateCache,
+      $window,
+      settings
+    ) {
+      // Mock api call due to ctrl activate method
+      $httpBackend
+        .whenGET(
+          settings.appRoot +
+          settings.refineryApiV2 + '/tool_definitions/?data_set_uuid=').respond(200, []);
+
+      $templateCache.put(
+        $window.getStaticUrl('partials/home/partials/tool-list.html'),
+        '<div id="tool-list">/div>'
+      );
+
+      var scope = $rootScope.$new();
+      var template = '<rp-tool-list></rp-tool-list>';
+      directiveElement = $compile(template)(scope);
+      scope.$digest();
+    }));
+
+    it('generates the appropriate HTML', function () {
+      expect(directiveElement.html()).toContain('tool-list');
+      expect(directiveElement.html()).toContain('</div>');
+    });
+  });
+})();

refinery/ui/source/js/home/partials/data-set-chart.html

@@ -1,20 +1,18 @@
-<div class="row p-t-1">
-  <div class="col-md-4 col-md-offset-7">
-    <ui-select
-      append-to-body="true"
-      ng-model="$ctrl.selectedAttribute.select"
-      on-select="$ctrl.updateAttribute($item)"
-      theme="select2"
-      class="text-left p-l-1 p-b-1">
-       <ui-select-match placeholder="Select an attribute">
-         {{$select.selected.name }}
-       </ui-select-match>
-      <ui-select-choices
-        position="down"
-        repeat="attribute in $ctrl.attributes | orderBy:'name' track by $index">
-        <span ng-bind-html="attribute.name"></span>
-      </ui-select-choices>
-    </ui-select>
-    <canvas id="files-bar-chart"></canvas>
-  </div>
+<div>
+  <ui-select
+    append-to-body="true"
+    ng-model="$ctrl.selectedAttribute.select"
+    on-select="$ctrl.updateAttribute($item)"
+    theme="select2"
+    class="text-left p-l-1 p-b-1">
+     <ui-select-match placeholder="Select an attribute">
+       {{$select.selected.name }}
+     </ui-select-match>
+    <ui-select-choices
+      position="down"
+      repeat="attribute in $ctrl.attributes | orderBy:'name' track by $index">
+      <span ng-bind-html="attribute.name"></span>
+    </ui-select-choices>
+  </ui-select>
+  <canvas id="files-bar-chart"></canvas>
 </div>

refinery/ui/source/js/home/partials/tool-list.html

@@ -0,0 +1,21 @@
+<div>
+  <div class="refinery-header">
+    <h3>
+      Analysis and Visualization Tools
+    </h3>
+  </div>
+  <ul class="list-unstyled">
+    <li ng-repeat="tool in $ctrl.toolList" class="p-b-1-2">
+      <i class="{{tool.tool_type|toolTypeIcon}} p-r-1-4" aria-hidden="true"></i>
+      <span ng-if="tool.tool_type=='WORKFLOW'">
+        <a ng-href="/workflows/{{tool.workflow}}">
+          {{ tool.name }}
+        </a>
+      </span>
+      <span ng-if="tool.tool_type!=='WORKFLOW'">
+         {{ tool.name }}
+      </span>
+       - {{ tool.description }}
+    </li>
+  </ul>
+</div>