Merge pull request #1042 from parklab/jkmarx/add-file-download-data-set2

Jkmarx/add file download data set2

refinery/data_set_manager/tests.py

@@ -646,15 +646,17 @@ def test_hide_fields_from_list(self):
                          {'solr_field': 'SubAnalysis'}]
 
         filtered_list = hide_fields_from_list(weighted_list)
-        self.assertListEqual(filtered_list, [{'solr_field': 'SubAnalysis'}])
+        self.assertListEqual(filtered_list, [
+            {'solr_field': 'uuid'},
+            {'solr_field': 'SubAnalysis'}])
 
     def test_is_field_in_hidden_list(self):
-        list_of_hidden_field = ['uuid', 'id', 'django_id', 'file_uuid',
+        list_of_hidden_field = ['id', 'django_id', 'file_uuid',
                                 'study_uuid', 'assay_uuid', 'type',
                                 'is_annotation', 'species', 'genome_build',
                                 'name', 'django_ct']
-        list_not_hidden_field = ['Analysis', 'Cell Type', '', 'Cell Line',
-                                 'Group Name', 'Character Title']
+        list_not_hidden_field = ['uuid', 'Analysis', 'Cell Type', '',
+                                 'Cell Line', 'Group Name', 'Character Title']
 
         for field in list_of_hidden_field:
             self.assertEqual(is_field_in_hidden_list(field), True)

refinery/data_set_manager/utils.py

@@ -642,7 +642,7 @@ def hide_fields_from_list(facet_obj):
 
 
 def is_field_in_hidden_list(field):
-    hidden_fields = ['uuid', 'id', 'django_id', 'file_uuid', 'study_uuid',
+    hidden_fields = ['id', 'django_id', 'file_uuid', 'study_uuid',
                      'assay_uuid', 'type', 'is_annotation', 'species',
                      'genome_build', 'name', 'django_ct']
 
@@ -773,7 +773,9 @@ def customize_attribute_response(facet_fields):
         customized_field = {'internal_name': field}
 
         field_name = field.split('_')
-        customized_field['file_ext'] = field_name[-1]
+        # For uuid fields
+        if len(field_name) > 1:
+            customized_field['file_ext'] = field_name[-1]
 
         if 'REFINERY_SUBANALYSIS' in field:
             customized_field['display_name'] = 'Analysis Group'
@@ -802,6 +804,10 @@ def customize_attribute_response(facet_fields):
             field_name = ' '.join(field_name[0:index])
             customized_field['display_name'] = field_name.title()
             customized_field['attribute_type'] = 'Characteristics'
+        # For uuid fields
+        elif len(field_name) == 1:
+            customized_field['display_name'] = \
+                customized_field['internal_name']
         else:
             customized_field['display_name'] = ' '.join(
                     field_name[0:-3]).title()

refinery/ui/source/js/commons/services/assay-attribute.js

@@ -0,0 +1,25 @@
+'use strict';
+
+angular
+  .module('refineryApp')
+  .factory('assayAttributeService', ['$resource', 'settings',
+    function ($resource, settings) {
+      var assayAttribute = $resource(
+        settings.appRoot + settings.refineryApiV2 + '/assays/:uuid/attributes/',
+        {
+          uuid: '@uuid'
+        },
+        {
+          query: {
+            method: 'GET',
+            isArray: true
+          },
+
+          update: {
+            method: 'PUT'
+          }
+        }
+      );
+      return assayAttribute;
+    }
+  ]);

refinery/ui/source/js/commons/services/assay-attribute.spec.js

@@ -0,0 +1,141 @@
+'use strict';
+
+describe('Common.service.assayAttribute: unit tests', function () {
+  var $httpBackend;
+  var $rootScope;
+  var fakeUuid = 'x508x83x-x9xx-4740-x9x7-x7x0x631280x';
+  var service;
+  var settings;
+  var fakeResponse = [
+    {
+      assay: 3,
+      study: 6,
+      solr_field: 'uuid',
+      rank: 1,
+      is_exposed: true,
+      is_facet: false,
+      is_active: false,
+      is_internal: true,
+      id: 43,
+      display_name: 'uuid'
+    },
+    {
+      assay: 3,
+      study: 6,
+      solr_field: 'REFINERY_ANALYSIS_UUID_6_3_s',
+      rank: 2,
+      is_exposed: true,
+      is_facet: true,
+      is_active: false,
+      is_internal: false,
+      id: 42,
+      display_name: 'Analysis'
+    },
+    {
+      assay: 3,
+      study: 6,
+      solr_field: 'REFINERY_NAME_6_3_s',
+      rank: 3,
+      is_exposed: false,
+      is_facet: true,
+      is_active: true,
+      is_internal: false,
+      id: 52,
+      display_name: 'Name'
+    }
+  ];
+
+  var putAttribute = {
+    uuid: fakeUuid,
+    solr_field: 'REFINERY_NAME_6_3_s',
+    rank: 1,
+    is_exposed: false,
+    is_facet: false
+  };
+
+  var putResponse = {
+    assay: 3,
+    study: 6,
+    solr_field: 'REFINERY_NAME_6_3_s',
+    rank: 3,
+    is_exposed: false,
+    is_facet: true,
+    is_active: true,
+    is_internal: false,
+    id: 52,
+    display_name: 'Name'
+  };
+
+  beforeEach(function () {
+    module('refineryApp');
+
+    inject(function ($injector) {
+      settings = $injector.get('settings');
+      $httpBackend = $injector.get('$httpBackend');
+      $rootScope = $injector.get('$rootScope');
+      service = $injector.get('assayAttributeService');
+    });
+  });
+
+  describe('Service', function () {
+    it('should be defined', function () {
+      expect(service).toBeDefined();
+    });
+
+    it('should be a method', function () {
+      expect(typeof service).toEqual('function');
+    });
+
+    it('query should return a resolving promise', function () {
+      $httpBackend
+        .expectGET(
+          settings.appRoot +
+          settings.refineryApiV2 +
+          '/assays/' + fakeUuid + '/attributes/'
+      ).respond(200, fakeResponse);
+
+      var results;
+      var promise = service.query({
+        uuid: fakeUuid
+      }).$promise.then(function (response) {
+        results = response;
+      });
+
+      expect(typeof promise.then).toEqual('function');
+      $httpBackend.flush();
+      $rootScope.$digest();
+      expect(results.length).toEqual(fakeResponse.length);
+      for (var i = 0; i < results.length; i++) {
+        expect(results[i].solr_field).toEqual(fakeResponse[i].solr_field);
+      }
+    });
+
+    it('update should return a resolving promise', function () {
+      $httpBackend
+        .expectPUT(
+          settings.appRoot +
+          settings.refineryApiV2 +
+          '/assays/' + fakeUuid + '/attributes/',
+          putAttribute
+       ).respond(200, putResponse);
+
+      var results;
+      var promise = service.update(putAttribute).$promise.then(function (response) {
+        results = response;
+      });
+
+      expect(typeof promise.then).toEqual('function');
+      $httpBackend.flush();
+      $rootScope.$digest();
+      expect(results).toBeDefined();
+      expect(results.solr_field).toEqual(putResponse.solr_field);
+      expect(results.rank).toEqual(putResponse.rank);
+
+      results = undefined;
+      promise = service.update().$promise.then(function (response) {
+        results = response;
+      });
+      expect(results).not.toBeDefined();
+    });
+  });
+});

refinery/ui/source/js/commons/services/assay-file.spec.js

@@ -182,7 +182,7 @@ describe('Common.service.assayFile: unit tests', function () {
 
     it('should return a resolving promise', function () {
       var results;
-      var promise = service.get({
+      var promise = service.query({
         uuid: fakeUuid
       }).$promise.then(function (response) {
         results = response;

refinery/ui/source/js/commons/services/node.js

@@ -0,0 +1,25 @@
+'use strict';
+
+angular
+  .module('refineryApp')
+  .factory('nodeService', ['$resource', 'settings',
+    function ($resource, settings) {
+      var node = $resource(
+        settings.appRoot + settings.refineryApi + '/node/:uuid/',
+        {
+          uuid: 'uuid',
+          format: 'json',
+        },
+        {
+          query: {
+            method: 'GET',
+            isArray: false
+          }
+        }
+      );
+
+      return node;
+    }
+  ]);
+
+// http://192.168.50.50:8000/api/v1/node/0c2778e8-eed5-4981-9ccb-5f1ff75571d5/?format=json

refinery/ui/source/js/commons/services/node.spec.js

@@ -0,0 +1,70 @@
+'use strict';
+
+describe('Common.service.node: unit tests', function () {
+  var $httpBackend;
+  var $rootScope;
+  var fakeUuid = 'x508x83x-x9xx-4740-x9x7-x7x0x631280x';
+  var service;
+  var fakeResponse = {
+    analysis_uuid: null,
+    assay: '/api/v1/assay/5eff885e-49cb-477a-ad76-f65d74d78f8a/',
+    attributes: [],
+    file_import_status: 'PENDING',
+    file_url: '/media/file_store/c5/d2/rfc174.txt',
+    file_uuid: 'd25467be-3185-45d8-bd62-385dd54dde5a',
+    name: 'http://gehlenborg.com/wp-content/uploads/rfc/rfc174.txt',
+    parents: [
+      '/api/v1/node/2d59008b-5abe-4f35-9199-81b75f7e9eef/'
+    ],
+    resource_uri: '/api/v1/node/63647300-3117-4c7b-9205-706ac4daa7fa/',
+    study: '/api/v1/study/ff657398-30db-4481-bfb9-8b86f46e9000/',
+    subanalysis: null,
+    type: 'Raw Data File',
+    uuid: '63647300-3117-4c7b-9205-706ac4daa7fa'
+  };
+
+  beforeEach(function () {
+    module('refineryApp');
+
+    inject(function ($injector) {
+      var settings = $injector.get('settings');
+      $httpBackend = $injector.get('$httpBackend');
+      $rootScope = $injector.get('$rootScope');
+      service = $injector.get('nodeService');
+
+      $httpBackend
+        .expectGET(
+          settings.appRoot +
+          settings.refineryApi +
+          '/node/' + fakeUuid + '/?format=json'
+      ).respond(200, fakeResponse);
+    });
+  });
+
+  describe('Service', function () {
+    it('should be defined', function () {
+      expect(service).toBeDefined();
+    });
+
+    it('should be a method', function () {
+      expect(typeof service).toEqual('function');
+    });
+
+    it('should return a resolving promise', function () {
+      var results;
+      var promise = service.query({
+        uuid: fakeUuid
+      }).$promise.then(function (response) {
+        results = response;
+      });
+
+      expect(typeof promise.then).toEqual('function');
+      $httpBackend.flush();
+      $rootScope.$digest();
+      expect(results.file_url)
+        .toEqual(fakeResponse.file_url);
+      expect(results.uuid).toEqual(fakeResponse.uuid);
+      expect(results.file_uuid).toEqual(fakeResponse.file_uuid);
+    });
+  });
+});

refinery/ui/source/js/file-browser/assay-files-util-modal-ctrl.js

@@ -4,6 +4,8 @@ function AssayFilesUtilModalCtrl (
   $scope,
   $uibModalInstance,
   $window,
+  $q,
+  $log,
   fileBrowserFactory,
   resetGridService) {
   var vm = this;
@@ -18,10 +20,11 @@ function AssayFilesUtilModalCtrl (
   // Refresh attribute lists when modal opens
   vm.refreshAssayAttributes = function () {
     var assayUuid = $window.externalAssayUuid;
-    return fileBrowserFactory.getAssayAttributeOrder(assayUuid).then(function () {
+
+    fileBrowserFactory.getAssayAttributeOrder(assayUuid).then(function () {
       vm.assayAttributeOrder = fileBrowserFactory.assayAttributeOrder;
     }, function (error) {
-      console.error(error);
+      $log.error(error);
     });
   };
 
@@ -57,6 +60,8 @@ angular
     '$scope',
     '$uibModalInstance',
     '$window',
+    '$q',
+    '$log',
     'fileBrowserFactory',
     'resetGridService',
     AssayFilesUtilModalCtrl