Jkmarx/clean up ui grid defaults (#1687)

* Fix spacing

* Update partial to view for clarity.

* Fix typo.

* Swap cart and control panel.

* Display control panel tree.

* Remove temp selected file display.

* Add pair styling.

* Tweak css.

* Add file relationship service and depth.

* Fix counters for each group.

* Display selected nodes.

* Move input group into control directive.

* Fix mapping function.

* Fix currentTypes generation.

* Max pairs length.

* Remove console logs

* Trigger current position change when a new tool is selected.

* Fix scope bug due to factory.

* Add comments.

* Remove cloak.

* Add unit test.

* Move attribute generation to service.

* Put method calls into activate method per style guide.

* Style guide changes.

* Add a popover to the selection grid.

* Close popover when not clicking on row.

* Add popover with custom template.

* Modify template to only open one popover at a time.

* rename method for clarity.

* Use jqlite instead.

* Add template to ui-grid selection.

* Add checkbox selection.

* Grab current uuids from service and dynamically create obj.

* Move input groups to service.

* Add a left float, unstyle list class.

* Show current group.

* Rename variable for clarity.

* Add data object to track current group's nodes.

* Remove buttons for now.

* Refactor according to style guide.

* Change method and variable name for clarity.

* Move selection obj to node-service.

* Fix bug which requires deep copy.

* Fix bug with removing selected nodes.

* Add comments.

* fix button css

* Refactor and added comments.

* Update title.

* Add unit for ctrl.

* Add iffy

* Add directive unit test.

* Add line break for readability.

* Add another directive unit test and remove unused variable.

* Update unit test.

* Fix typo in view location.

* Fix unit test.

* Add comments.

* Fix unit tests.

* Add file relationship test.

* Fix bug due to merge.

* Update directive with static url method.

* Remove unneccessary files.

* Fix formatting.

* Reflect selection in control panel.

* Remove recursive directive and rename for clarity.

* Reorder and used service for control panel.

* Fix indexing.

* Add css.

* Add borders to templates.

* Fix orderby .

* Remove current input group.

* Add unit test.

* Consolidate components.

* Disable remove/removeAll if groups are empty.

* Reorder variable and comment.

* Remove hr to keep styling consistent.

* Delete obj properties when empty.

* Split pair portion.

* Seperate pair/list section.

* Update selectionObj reference.

* Adjust css.

* Fix deselect checkbox when clearing group.

* Add list structure to control panel.

* Fix bug with popover.

* Fix remove and deselect bug.

* Add comments.

* Turn off select all.

* Add comments and unit tests.

* Add comment.

* Remove unused igv and visualization module.

* Remove from refinery app.

* Update api endpoint.

* Remove default stylin for selected rows.

* Remove default selection.

* Remove console.log.

* Remove reference to the ui-grid node selections.

* Update unit test.

* Update name for clarity.

refinery/tool_manager/tests.py

@@ -42,7 +42,7 @@ def setUp(self):
         self.factory = APIRequestFactory()
         self.view = ToolDefinitionsViewSet.as_view({'get': 'list'})
 
-        self.url_root = '/api/v2/tools/definitions/'
+        self.url_root = '/api/v2/tool_definitions/'
 
         self.galaxy_instance = Instance.objects.create()
         self.workflow_engine = WorkflowEngine.objects.create(

refinery/ui/source/js/analysis-launch/partials/analysis-launch.html

@@ -3,7 +3,7 @@
       class="btn btn-primary btn-xs"
       rp-analysis-launch-modal
       ng-click="open()"
-      ng-disabled="isLaunchNodesSelectionEmpty() || !currentWorkflow.isAvailable()">
+      ng-disabled="!currentWorkflow.isAvailable()">
       Run Analysis
     </button>
 </span>

refinery/ui/source/js/commons/services/tools-definitions.js

@@ -8,7 +8,7 @@
 
   function toolsDefinitionsService ($resource, settings) {
     var toolsDefinitions = $resource(
-      settings.appRoot + settings.refineryApiV2 + '/tools/definitions',
+      settings.appRoot + settings.refineryApiV2 + '/tool_definitions',
       {},
       {
         query: {

refinery/ui/source/js/commons/services/tools-definitions.spec.js

@@ -115,7 +115,7 @@
           .expectGET(
             settings.appRoot +
             settings.refineryApiV2 +
-            '/tools/definitions'
+            '/tool_definitions'
         ).respond(200, fakeResponse);
       });
     });

refinery/ui/source/js/data-set-nav/partials/data-set-ui-mode-analyze.html

@@ -30,19 +30,6 @@ <h4>Inputs ({{currentWorkflow.getCategory()}})</h4>
       </span>
     </div>
 
-    <div ng-if="dataSet2Flag && currentWorkflow.isSingleInput()">
-      <rp-file-browser-node-group></rp-file-browser-node-group>
-      <div class="p-a-1">
-        <button
-          class="btn btn-warning"
-          rp-analysis-launch-modal
-          ng-click="open()"
-          ng-disabled="isLaunchNodesSelectionEmpty()">
-          Launch Analysis
-        </button>
-      </div>
-    </div>
-
     <div ng-if="!dataSet2Flag">
       <div ng-controller="NodeSetListApiCtrl" ng-if="currentWorkflow.isSingleInput()">
       <ui-select

refinery/ui/source/js/file-browser/ctrls/ctrl.js

@@ -75,12 +75,9 @@
       infiniteScrollUp: true,
       infiniteScrollDown: true,
       useExternalSorting: true,
-      enableRowSelection: true,
-      enableSelectAll: false,
       selectionRowHeaderWidth: 35,
       rowHeight: 35,
       showGridFooter: true,
-      enableSelectionBatchEvent: true,
       multiSelect: true,
       columnDefs: fileBrowserFactory.customColumnNames,
       data: fileBrowserFactory.assayFiles,
@@ -94,9 +91,6 @@
     vm.refreshSelectedFieldFromQuery = refreshSelectedFieldFromQuery;
     vm.reset = reset;
     vm.rowCount = maxFileRequest;
-    vm.selectNodesCount = 0;
-    vm.setGridSelectedRows = setGridSelectedRows;
-    vm.setGridUnselectedRows = setGridUnselectedRows;
     vm.sortChanged = sortChanged;
     vm.totalPages = 1;  // variable supporting ui-grid dynamic scrolling
     /** Used by ui to select/deselect, attributes have an object of filter fields
@@ -111,18 +105,6 @@
      * -----------------------------------------------------------------------------
      */
     function activate () {
-      // custom icon for ui-grid selection
-      $templateCache.put('ui-grid/selectionRowHeaderButtons',
-        '<div>' +
-        '<a rp-node-selection-popover title="Select Tool Input"' +
-        'ng-class="{\'ui-grid-row-selected\': row.isSelected}" ' +
-        'class="ui-grid-selection-row-header-buttons" ' +
-        'ng-click="selectButtonClick(row, $event); ' +
-        'grid.appScope.openSelectionPopover(row.entity.uuid);"' +
-        'id="{{row.entity.uuid}}">' +
-        '<i class="fa fa-arrow-right ui-grid-checks"' +
-        ' aria-hidden="true"></i></a></div>'
-      );
       // Ensure data owner
       checkDataSetOwnership();
       // initialize the dataset and updates ui-grid selection, filters, and url
@@ -252,64 +234,16 @@
         // Sort events
         vm.gridApi.core.on.sortChanged(null, vm.sortChanged);
         vm.sortChanged(vm.gridApi.grid, [vm.gridOptions.columnDefs[1]]);
-
-        // Checkbox selection events
-        vm.gridApi.selection.on.rowSelectionChanged(null, function (row) {
-          angular.copy(row.entity, nodesService.activeNodeRow);
-          // When selected All, watching the deselect events for complement nodes
-          if (nodesService.selectedNodeGroupUuid &&
-            nodesService.selectedNodeGroupUuid !==
-            nodesService.defaultCurrentSelectionUuid) {
-            if (vm.afterNodeGroupUpdate) {
-              vm.afterNodeGroupUpdate = false;
-              nodesService.resetNodeGroupSelection(true);
-            }
-          }
-
-          if (nodesService.selectedAllFlag) {
-            nodesService.setComplementSeletedNodes(row);
-            vm.selectNodesCount = vm.assayFilesTotal -
-              nodesService.complementSelectedNodes.length;
-          } else {
-            // add or remove row to list
-            nodesService.setSelectedNodes(row);
-            vm.selectNodesCount = nodesService.selectedNodes.length;
-          }
-
-          // when not current selection, check if a new row was deselect/selected
-          if (nodesService.selectedNodeGroupUuid !==
-            nodesService.defaultCurrentSelectionUuid &&
-            nodesService.selectedNodesUuidsFromNodeGroup.length !==
-            nodesService.selectedNodes.length) {
-            // Reset the node group selection to current selection
-            nodesService.resetNodeGroupSelection(true);
-          }
-        });
-
-       //  Event only occurs when checkbox is selected/deselected.
-        vm.gridApi.selection.on.rowSelectionChangedBatch(null, function
-         (eventRows) {
-          // When event all occurs, the node group should be current selection
-          nodesService.resetNodeGroupSelection(true);
-          // Checking the first row selected, ensures it's a true select all
-          if (eventRows[0].isSelected) {
-            nodesService.setSelectedAllFlags(true);
-            // Need to manually set vm.selectNodesCount to count of all list
-            vm.selectNodesCount = vm.assayFilesTotal;
-          } else {
-            nodesService.setSelectedAllFlags(false);
-            vm.selectNodesCount = 0;
-          }
-        });
       }
     }
 
     /** vm method to open the selection popover and disable all popovers, so
      * only one shows at a time. Needed in the ctrl due to ui-grid template.
      * @param nodeUuid
      */
-    function openSelectionPopover (nodeUuid) {
-      angular.element('#' + nodeUuid).popover('show');
+    function openSelectionPopover (nodeRow) {
+      angular.copy(nodeRow, nodesService.activeNodeRow);
+      angular.element('#' + nodeRow.uuid).popover('show');
       angular.element('.ui-grid-selection-row-header-buttons').popover('disable');
     }
 
@@ -383,48 +317,11 @@
             // timeout needed allows digest cycle to complete,and grid to ingest the data
             vm.gridApi.infiniteScroll.resetScroll(vm.firstPage > 0, vm.lastPage < vm.totalPages);
             resetGridService.setResetGridFlag(false);
-            // Select rows either from node group lists or previously selected
-            if (nodesService.selectedNodesUuidsFromNodeGroup.length > 0) {
-              nodesService.setSelectedNodesFromNodeGroup(
-                nodesService.selectedNodesUuidsFromNodeGroup
-              );
-              nodesService.selectNodesCount = nodesService
-                .selectedNodesUuidsFromNodeGroup.length;
-              correctRowSelectionInUI();
-              vm.afterNodeGroupUpdate = true;
-            } else if (nodesService.selectedNodes.length > 0) {
-              nodesService.selectNodesCount = nodesService.selectedNodesUuids.length;
-              correctRowSelectionInUI();
-            } else {
-              vm.gridApi.selection.clearSelectedRows();
-              nodesService.selectNodesCount = 0;
-            }
           });
         });
       }
     }
 
-    // Helper function: select rows on the ui-grid
-    function setGridSelectedRows (uuidsList) {
-      // If user scrolls quickly, there could be a delay for selected items
-      angular.forEach(vm.gridApi.grid.rows, function (gridRow) {
-        if (uuidsList.indexOf(gridRow.entity.uuid) > -1) {
-          vm.gridApi.selection.selectRow(gridRow.entity);
-        }
-      });
-    }
-
-    // Helper function: unselect rows on the ui-grid
-    function setGridUnselectedRows (uuidsList) {
-      // If user scrolls quickly, there could be a delay for selected items
-      angular.forEach(vm.gridApi.grid.rows, function (gridRow) {
-        // select rows if not in complement list
-        if (uuidsList.indexOf(gridRow.entity.uuid) === -1) {
-          vm.gridApi.selection.selectRow(gridRow.entity);
-        }
-      });
-    }
-
     /**
      * Generates sort param for api call from ui-grid response and calls grid
      * reset
@@ -481,6 +378,7 @@
         });
     };
 
+    // TODO: Update with the new selected rows and the indicator column.
     // Method to select/deselect rows programmically after dynamic
     // scroll adds more data, at reset and per 300 rows
     var correctRowSelectionInUI = function () {
@@ -554,7 +452,6 @@
             });
             selectedFilterService.resetAttributeFilter(fieldsObj);
           });
-          vm.selectNodesCount = 0;
           vm.filesParam.filter_attribute = {};
           vm.reset();
         }

refinery/ui/source/js/file-browser/ctrls/node-group-ctrl.js

@@ -56,10 +56,6 @@ function NodeGroupCtrl (
     resetGridService.setResetGridFlag(true);
   };
 
-  // helper method checking if any nodes are selected
-  vm.isNodeGroupSelectionEmpty = function () {
-    return selectedNodesService.isNodeSelectionEmpty();
-  };
 /*
  * -----------------------------------------------------------------------------
  * Watchers and Method Calls

refinery/ui/source/js/file-browser/partials/assay-files.html

@@ -1,6 +1,5 @@
 <div id="assay-files-table"
   ui-grid="FBCtrl.gridOptions"
-  ui-grid-selection
   ui-grid-infinite-scroll
   ui-grid-resize-columns
   class="grid">

refinery/ui/source/js/file-browser/partials/node-group.html

@@ -24,7 +24,6 @@ <h2>
   </span>
   <div class="p-l-1-3 p-t-1-2 inline">
     <button
-      ng-disabled="FBNGCtrl.isNodeGroupSelectionEmpty()"
       class="btn btn-primary btn-xs p-r-1-3"
       rp-file-browser-node-group-modal
       refinery-tooltip

refinery/ui/source/js/file-browser/services/factory.js

@@ -156,6 +156,7 @@ function fileBrowserFactory (
       angular.copy(culledAttributes, assayAttributes);
       // Add file_download column first
       assayAttributes.unshift({ display_name: 'Url', internal_name: 'Url' });
+      assayAttributes.unshift({ display_name: 'Selection', internal_name: 'Selection' });
       // some attributes will be duplicate in different fields, duplicate
       // column names will throw an error. This prevents duplicates
       for (var ind = 0; ind < assayAttributes.length; ind++) {
@@ -239,6 +240,30 @@ function fileBrowserFactory (
     return internalName;
   };
 
+  var setCustomSelectColumn = function (columnName) {
+    var cellTemplate = '<div class="ngCellText text-align-center">' +
+        '<a rp-node-selection-popover title="Select Tool Input"' +
+        'class="ui-grid-selection-row-header-buttons" ' +
+        'ng-click="selectButtonClick(row, $event); ' +
+        'grid.appScope.openSelectionPopover(row.entity);"' +
+        'id="{{row.entity.uuid}}">' +
+        '<i class="fa fa-arrow-right ui-grid-checks"' +
+        ' aria-hidden="true"></i></a></div>';
+
+    return {
+      name: columnName,
+      field: columnName,
+      cellTooltip: true,
+      width: 4 + '%',
+      displayName: '',
+      enableFiltering: false,
+      enableSorting: false,
+      enableColumnMenu: false,
+      enableColumnResizing: true,
+      cellTemplate: cellTemplate
+    };
+  };
+
    /**
    * Helper method for file download column, requires unique template & fields.
    * @param {string} _columnName - column name
@@ -300,6 +325,8 @@ function fileBrowserFactory (
       if (columnName === 'Url') {
         // Url requires a custom template for downloading links
         tempCustomColumnNames.push(setCustomUrlColumnDef(columnName));
+      } else if (columnName === 'Selection') {
+        tempCustomColumnNames.push(setCustomSelectColumn(columnName));
       } else if (columnName === 'Analysis Group') {
         // Analysis requires a custom template for filtering -1 entries
         var _cellTemplate = '<div class="ngCellText text-align-center"' +

refinery/ui/source/js/file-browser/services/selected-nodes-service.js

@@ -2,12 +2,7 @@
 
 function selectedNodesService ($window, selectedFilterService) {
   var vm = this;
-  vm.selectedNodes = [];
-  vm.selectedNodesUuids = [];
-  vm.selectedNodesUuidsFromNodeGroup = [];
   vm.selectedAllFlag = false;
-  vm.complementSelectedNodes = [];
-  vm.complementSelectedNodesUuids = [];
   vm.selectedNodeGroupUuid = '';
   vm.defaultCurrentSelectionUuid = '';
   vm.resetNodeGroup = false;
@@ -29,29 +24,6 @@ function selectedNodesService ($window, selectedFilterService) {
     });
   };
 
-  /**
-   * Manually keep track of selected nodes which is neccessary due to dynamic
-   * scrolling in the ui-grid
-   * @param {obj} nodeRow - ui-grid row obj
-   * */
-  vm.setSelectedNodes = function (nodeRow) {
-    var ind = vm.selectedNodesUuids.indexOf(nodeRow.entity.uuid);
-    if (nodeRow.isSelected) {
-      if (ind === -1) {
-        vm.selectedNodes.push(nodeRow);
-        vm.selectedNodesUuids.push(nodeRow.entity.uuid);
-      }
-      // Have to set explictly to keep deleted rows from infinite scrolling
-    } else if (nodeRow.isSelected === false) {
-      if (ind > -1) {
-        vm.selectedNodesUuids.splice(ind, 1);
-        vm.selectedNodes.splice(ind, 1);
-      }
-    }
-    // else nothing because it is not in current block of data
-    return vm.selectedNodes;
-  };
-
    /**
    * Deep copy of a list of node uuids to the selected uuids from node group
    * @param {list} nodesUuidsList - list of uuids
@@ -99,28 +71,6 @@ function selectedNodesService ($window, selectedFilterService) {
     }
   };
 
-  /**
-   * These are non-selected nodes uuid, when the select all flag is true
-   * @param {obj} nodeRow - ui-grid row object or ui-grid structured row objects
-   */
-  vm.setComplementSeletedNodes = function (nodeRow) {
-    var ind = vm.complementSelectedNodesUuids.indexOf(nodeRow.entity.uuid);
-    if (nodeRow.isSelected === false) {
-      if (ind === -1) {
-        vm.complementSelectedNodes.push(nodeRow);
-        vm.complementSelectedNodesUuids.push(nodeRow.entity.uuid);
-      }
-      // Have to set explictly to keep deleted rows from infinite scrolling
-    } else if (nodeRow.isSelected === true) {
-      if (ind > -1) {
-        vm.complementSelectedNodes.splice(ind, 1);
-        vm.complementSelectedNodesUuids.splice(ind, 1);
-      }
-    }
-    // else nothing should occur to nodeRow because it is not in assayFiles
-    return vm.complementSelectedNodes;
-  };
-
    /**
    * Resets Node Group UI-Select menu to default Current Selection
    * @param {boolean} flag - resets boolean
@@ -152,17 +102,6 @@ function selectedNodesService ($window, selectedFilterService) {
     }
     return params;
   };
-
-
-  // Used by ctrls for node-group and launch-analysis partials to designate
-  // whether any nodes are selected.
-  vm.isNodeSelectionEmpty = function () {
-    var params = vm.getNodeGroupParams();
-    if (params.nodes.length === 0 && !params.use_complement_nodes) {
-      return true;
-    }
-    return false;
-  };
 }
 
 angular.module('refineryFileBrowser')