Jkmarx/dataset2 igv (#1433)

* Remove tab buttons.

* Remove other orange button references.

* Refactor, remove style.

* Remove style tag.

* Remove unused states.

* Remove hanging div.

* Add conditional for dataset 2.

* Move analysis tab to it's own partial.

* Move details tab to own partial.

* Move files to own partial.

* Tab views.

* Fix unit test.

* Move display into own component.

* Set default to files.

* Add unit test.

* Remove unused code.

* Render pivotMatrixView call from within directive.

* Unwrap provenance-view-tab watcher.

* Add watchers to directive.

* Remove console.log.

* Correct description.

* Update label.

* New launch analysis component.

* Add disable button conditionals.

* Add unit test.

* Add save directive.

* Move save and reset buttons.

* Add unit tests.

* Move selected nodes text.

* Move file display and config to new layout.

* Add view and remove partial.

* Add comments.

* Adjust popover location.

* Move save funtion to node_group partial.

* Rename reset to better reflect purpose.

* Rename partial.

* Move analyses tab into own feature.

* Column adjustments.

* Parent controller.

* Move file to view folder.

* Keep only table view.

* Fix typo in address.

* Change buttons size.

* Fix hidden popover.

* Add css styling.

* Fix padding.

* Fix padding

* Fix unit test.

* Fix reset button.

* Remove console.

* Fix reset selection count.

* Fix scoping issue.

* Remove console.log

* Fix run analysis ui.

* Update color scheme.

* Add IGV directory.

* Add directive.

* Include partial in tab.

* Add css.

* Disable if no nodes are selected.

* Add error handling and code to accomodate data set2.

* Fix unit test and adjust css.

* Add modal for launching igv

* Add modal script.

* Add visualization directory.

* Add module.

* Update partials.

* Remove unused code.

* Add script to partial and launch modal when igv selected.

* Remove inline script.

* Restructure modals to launch when visualization is selected.

* Remove unused service.

* Remove ununeccessary ctrl.

* Clean up responsibilities.

* Add conditions to launching igv.

* Add factory.

* Add comments.

* Controller unit test.

* Add visualization ctrl test.

* Add directive unit tests.

* Add factory unit test.

* Comments.

* Fix filter bug.

* Fix description.

* Remove duplicate id.

* Add method comment.

* Fix unit test.

* Remove unused dependency.

* Fix logger error message.

* Clafity variable name.

refinery/core/views.py

@@ -33,6 +33,7 @@
 )
 
 from data_set_manager.models import Node
+from data_set_manager.utils import generate_solr_params
 from visualization_manager.views import igv_multi_species
 from annotation_server.models import GenomeBuild
 from file_store.models import FileStoreItem
@@ -746,6 +747,14 @@ def solr_igv(request):
         logger.debug('IGV data query: ' + str(igv_config['query']))
         logger.debug('IGV annotation query: ' + str(igv_config['annotation']))
 
+        if igv_config['query'] is None:
+            # generate solr_query method
+            # assay uuid
+            solr_query = generate_solr_params({}, igv_config['assay_uuid'])
+            url_path = '/'.join(["data_set_manager", "select"])
+            url = urljoin(settings.REFINERY_SOLR_BASE_URL, url_path)
+            igv_config['query'] = ''.join([url, '/?', solr_query])
+
         # attributes associated with node selection from interface
         node_selection_blacklist_mode = igv_config[
             'node_selection_blacklist_mode']

refinery/templates/base.html

@@ -301,7 +301,9 @@
   <script src="{% static "js/dashboard.js" %}"></script>
   <script src="{% static "js/collaboration.js" %}"></script>
   <script src="{% static "js/chart.js"%}"></script>
-   <script src="{% static "js/data-set-about.js" %}"></script>
+  <script src="{% static "js/data-set-about.js" %}"></script>
+  <script src="{% static "js/visualization.js" %}"></script>
+  <script src="{% static "js/igv.js" %}"></script>
 
   <script src="{% static "vendor/ng-file-upload/angular-file-upload.min.js" %}"></script>
   <script src="{% static "vendor/angular-ui-grid/ui-grid.min.js" %}"></script>

refinery/templates/core/data_set2.html

@@ -193,7 +193,6 @@ <h1>Data Set <small>{{ data_set.name }}</small></h1>
     <rp-assay-files-util-modal-detail></rp-assay-files-util-modal-detail>
    </script>
 
-
   <script type="application/javascript">
     setTimeout(function() {
           sizing();

refinery/ui/config.json

@@ -29,11 +29,13 @@
       "file-browser",
       "data-set-about",
       "globals",
+      "igv",
       "metadata-table-import",
       "node-mapping",
       "node-relationship",
       "statistics",
-      "workflows"
+      "workflows",
+      "visualization"
     ],
     "vendor": {
       "css": [

refinery/ui/source/js/analysis-monitor/filters/offset.js

@@ -3,7 +3,10 @@
 function analysisMonitorOffset () {
   return function (input, _start_) {
     var start = parseInt(_start_, 10);
-    return input.slice(start);
+    if (start) {
+      return input.slice(start);
+    }
+    return input;
   };
 }
 

refinery/ui/source/js/file-browser/module.js

@@ -7,6 +7,5 @@ angular
     'ui.grid.infiniteScroll',
     'ui.grid.resizeColumns',
     'dndLists',
-    'ui.select',
-    'ngSanitize'
+    'ui.select'
   ]);

refinery/ui/source/js/file-browser/views/files-tab.html

@@ -19,7 +19,7 @@
         </a>
       </span>
     </div>
-    <div class="col-md-6">
+    <div class="col-md-4">
       <span class="align-bottom p-r-1-3">
         {{ FBCtrl.selectNodesCount }} of
         {{ FBCtrl.assayFilesTotal }} files selected.
@@ -39,7 +39,10 @@
       </a>
       <rp-file-browser-node-group></rp-file-browser-node-group>
     </div>
-    <div class="col-md-offset-1 col-md-3 text-right">
+    <div class="col-md-3 text-right">
+      <rp-visualization></rp-visualization>
+    </div>
+    <div class="col-md-3 text-right">
       <rp-select-workflow></rp-select-workflow>
       <rp-analysis-launch></rp-analysis-launch>
     </div>

refinery/ui/source/js/igv/ctrls/ctrl.js

@@ -0,0 +1,103 @@
+'use strict';
+
+function IGVCtrl (
+  $scope,
+  $window,
+  $log,
+  $resource,
+  $httpParamSerializer,
+  $uibModalInstance,
+  selectedNodesService,
+  IGVFactory
+) {
+  var vm = this;
+  // includes unused fields to accomodate current igv backend
+  vm.igvConfig = {
+    query: null,
+    annotation: null,
+    node_selection: [],
+    node_selection_blacklist_mode: true
+  };
+  vm.speciesList = [];
+  vm.selectedSpecies = { select: vm.speciesList[0] };
+  vm.message = null;
+  vm.messageType = 'info';
+  vm.isLoadingSpecies = true;
+
+  // Helper method to set alert message in modal
+  var generateAlertMessage = function (infoType) {
+    vm.messageType = infoType;
+    if (infoType === 'error') {
+      vm.message = 'Sorry! Unable to configure IGV for the selected file set.';
+    } else if (vm.speciesList.length === 0) {
+      vm.message = 'Please select the correct genome and launch IGV.';
+    } else if (vm.speciesList.length === 1) {
+      vm.message = null;
+      vm.selectedSpecies.select = vm.speciesList[0];
+    } else {
+      vm.message = 'Multiple species detected. Please select a ' +
+          'genome and launch IGV. You may repeat this step multiple times.';
+    }
+  };
+
+  // Helper method set igvConfig based on selected nodes
+  var setIGVConfig = function () {
+    if (selectedNodesService.selectedAllFlag) {
+      vm.igvConfig.node_selection = selectedNodesService.complementSelectedNodesUuids;
+      vm.igvConfig.node_selection_blacklist_mode = true;
+      vm.igvConfig.assay_uuid = $window.externalAssayUuid;
+    } else {
+      vm.igvConfig.node_selection = selectedNodesService.selectedNodesUuids;
+      vm.igvConfig.node_selection_blacklist_mode = false;
+      vm.igvConfig.assay_uuid = $window.externalAssayUuid;
+    }
+  };
+
+  // Upon launch modal, method retrives species list
+  vm.retrieveSpecies = function () {
+    setIGVConfig();
+
+    IGVFactory.getSpeciesList(vm.igvConfig).then(function () {
+      vm.isLoadingSpecies = false;
+      // update species list
+      vm.speciesList = IGVFactory.speciesList;
+      generateAlertMessage('info');
+    }, function () {
+      vm.isLoadingSpecies = false;
+      generateAlertMessage('error');
+      $log.error('Error creating IGV session URLs.');
+    });
+  };
+
+  // Launches web based IGV and dismissed modal
+  vm.launchIgvJs = function () {
+    var params = $httpParamSerializer({
+      species: vm.selectedSpecies.select.name,
+      node_ids: vm.igvConfig.node_selection
+    });
+    // close modal
+    $uibModalInstance.dismiss();
+    $window.open('/visualize/genome?' + params);
+  };
+
+  // Modal method to cancel
+  vm.cancel = function () {
+    $uibModalInstance.dismiss('cancel');
+  };
+
+  vm.retrieveSpecies();
+}
+
+angular
+  .module('refineryIGV')
+  .controller('IGVCtrl', [
+    '$scope',
+    '$window',
+    '$log',
+    '$resource',
+    '$httpParamSerializer',
+    '$uibModalInstance',
+    'selectedNodesService',
+    'IGVFactory',
+    IGVCtrl
+  ]);

refinery/ui/source/js/igv/ctrls/ctrl.spec.js

@@ -0,0 +1,63 @@
+'use strict';
+
+describe('Controller: IGV Ctrl', function () {
+  var ctrl;
+  var scope;
+  var factory;
+  var $controller;
+  var $uibModalInstance = { open: function () {}, dismiss: function () {} };
+
+  beforeEach(module('refineryApp'));
+  beforeEach(module('refineryIGV'));
+  beforeEach(inject(function (
+    $rootScope,
+    _$controller_,
+    _IGVFactory_
+  ) {
+    scope = $rootScope.$new();
+    $controller = _$controller_;
+    ctrl = $controller('IGVCtrl', {
+      $scope: scope,
+      $uibModalInstance: $uibModalInstance
+    });
+    factory = _IGVFactory_;
+  }));
+
+  it('IGVCtrl ctrl should exist', function () {
+    expect(ctrl).toBeDefined();
+  });
+
+  it('Data & UI displays variables should exist for views', function () {
+    expect(ctrl.igvConfig.node_selection).toEqual([]);
+    expect(ctrl.speciesList).toEqual([]);
+    expect(ctrl.selectedSpecies.select).toEqual();
+    expect(ctrl.message).toEqual(null);
+    expect(ctrl.messageType).toEqual('info');
+    expect(ctrl.isLoadingSpecies).toEqual(true);
+  });
+
+  it('Helper Methods exist', function () {
+    expect(angular.isFunction(ctrl.launchIgvJs)).toBe(true);
+    expect(angular.isFunction(ctrl.cancel)).toBe(true);
+  });
+
+  describe('Test RetrieveSpecies', function () {
+    it('refreshNodeGroupList is method', function () {
+      expect(angular.isFunction(ctrl.retrieveSpecies)).toBe(true);
+    });
+
+    it('getSpeciesList calls on correct factory method', function () {
+      var mockResponse = false;
+      spyOn(factory, 'getSpeciesList').and.callFake(function () {
+        return {
+          then: function () {
+            mockResponse = true;
+          }
+        };
+      });
+      expect(mockResponse).toEqual(false);
+      ctrl.retrieveSpecies();
+      expect(mockResponse).toEqual(true);
+    });
+  });
+});

refinery/ui/source/js/igv/directives/modal-detail.js

@@ -0,0 +1,14 @@
+'use strict';
+
+function rpIGVLaunchModalDetail () {
+  return {
+    restrict: 'AE',
+    templateUrl: '/static/partials/igv/partials/modal-detail.html'
+  };
+}
+
+angular
+  .module('refineryIGV')
+  .directive('rpIGVLaunchModalDetail', [
+    rpIGVLaunchModalDetail
+  ]);

refinery/ui/source/js/igv/directives/modal-detail.spec.js

@@ -0,0 +1,35 @@
+// Unit test for visualization spec
+'use strict';
+
+describe('rpIGVLaunchModalDetail directive unit test', function () {
+  beforeEach(module('refineryApp'));
+  beforeEach(module('refineryVisualization'));
+
+  var compile;
+  var rootScope;
+  var scope;
+  var template;
+  var directiveElement;
+
+  beforeEach(inject(function (
+    _$compile_,
+    _$rootScope_,
+    $templateCache
+  ) {
+    $templateCache.put(
+      '/static/partials/igv/partials/modal-detail.html',
+      '<div id="modal-header">igv</div>'
+    );
+    compile = _$compile_;
+    rootScope = _$rootScope_;
+    scope = rootScope.$new();
+    template = '<rp-i-g-v-launch-modal-detail></rp-i-g-v-launch-modal-detail>';
+    directiveElement = compile(template)(scope);
+    scope.$digest();
+  }));
+
+  it('generates the appropriate HTML', function () {
+    expect(directiveElement.html()).toContain('modal-header');
+    expect(directiveElement.html()).toContain('igv');
+  });
+});

refinery/ui/source/js/igv/module.js

@@ -0,0 +1,4 @@
+'use strict';
+
+angular
+  .module('refineryIGV', ['ui.select']);

refinery/ui/source/js/igv/module.spec.js

@@ -0,0 +1,30 @@
+'use strict';
+
+describe('RefineryIGV.module: unit tests', function () {
+  var module;
+
+  beforeEach(function () {
+    module = angular.module('refineryIGV');
+  });
+
+  describe('Module', function () {
+    it('should be registered', function () {
+      expect(!!module).toEqual(true);
+    });
+  });
+
+  describe('Dependencies:', function () {
+    var deps;
+    var hasModule = function (m) {
+      return deps.indexOf(m) >= 0;
+    };
+
+    beforeEach(function () {
+      deps = module.value('refineryIGV').requires;
+    });
+
+    it('should have "ui-select" as a dependency', function () {
+      expect(hasModule('ui.select')).toEqual(true);
+    });
+  });
+});