@jbrowse/plugin-data-management 1.7.8 → 1.7.11

package/dist/HierarchicalTrackSelectorWidget/model.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = void 0;
+exports.default = stateTreeFactory;
 exports.generateHierarchy = generateHierarchy;
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
@@ -26,21 +26,20 @@ function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o =
 
 function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
 
-var hasAnyOverlap = function hasAnyOverlap() {
+function hasAnyOverlap() {
   var a1 = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : [];
   var a2 = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : [];
   return !!a1.find(function (value) {
     return a2.includes(value);
   });
-};
+}
 
 function passesFilter(filter, config) {
-  var name = getTrackName(config);
-  var categories = (0, _configuration.readConfObject)(config, 'category') || [];
+  var categories = (0, _configuration.readConfObject)(config, 'category');
   var filterLower = filter.toLowerCase();
-  return !!name.toLowerCase().includes(filterLower) || categories.filter(function (cat) {
-    return !!cat.toLowerCase().includes(filterLower);
-  }).length;
+  return getTrackName(config).toLowerCase().includes(filterLower) || (categories === null || categories === void 0 ? void 0 : categories.filter(function (c) {
+    return c.toLowerCase().includes(filterLower);
+  }).length);
 }
 
 function getTrackName(config) {
@@ -57,15 +56,15 @@ function generateHierarchy(model, trackConfigurations, collapsed) {
   };
   var filterText = model.filterText,
       view = model.view;
-  trackConfigurations.filter(function (trackConf) {
-    return passesFilter(filterText, trackConf);
-  }).forEach(function (trackConf) {
+  trackConfigurations.filter(function (conf) {
+    return passesFilter(filterText, conf);
+  }).forEach(function (conf) {
     // copy the categories since this array can be mutated downstream
-    var categories = (0, _toConsumableArray2.default)((0, _configuration.readConfObject)(trackConf, 'category') || []); // silly thing where if trackId ends with sessionTrack, then push it to
+    var categories = (0, _toConsumableArray2.default)((0, _configuration.readConfObject)(conf, 'category') || []); // silly thing where if trackId ends with sessionTrack, then push it to
     // a category that starts with a space to force sort to the top...
     // double whammy hackyness
 
-    if (trackConf.trackId.endsWith('sessionTrack')) {
+    if (conf.trackId.endsWith('sessionTrack')) {
       categories.unshift(' Session tracks');
     }
 
@@ -94,17 +93,18 @@ function generateHierarchy(model, trackConfigurations, collapsed) {
 
     for (var i = 0; i < categories.length; i++) {
       _loop(i);
-    } // using splice here tries to group leaf nodes above hierarchical nodes
+    }
 
+    var tracks = view.tracks; // using splice here tries to group leaf nodes above hierarchical nodes
 
     currLevel.children.splice(currLevel.children.findIndex(function (elt) {
       return elt.children.length;
     }), 0, {
-      id: trackConf.trackId,
-      name: getTrackName(trackConf),
-      conf: trackConf,
-      checked: !!view.tracks.find(function (f) {
-        return f.configuration === trackConf;
+      id: conf.trackId,
+      name: getTrackName(conf),
+      conf: conf,
+      checked: !!tracks.find(function (f) {
+        return f.configuration === conf;
       }),
       children: []
     });
@@ -112,7 +112,7 @@ function generateHierarchy(model, trackConfigurations, collapsed) {
   return hierarchy.children;
 }
 
-var _default = function _default(pluginManager) {
+function stateTreeFactory(pluginManager) {
   return _mobxStateTree.types.model('HierarchicalTrackSelectorWidget', {
     id: _mst.ElementId,
     type: _mobxStateTree.types.literal('HierarchicalTrackSelectorWidget'),
@@ -144,45 +144,49 @@ var _default = function _default(pluginManager) {
         var trackConf = assembly === null || assembly === void 0 ? void 0 : assembly.configuration.sequence;
         var viewType = pluginManager.getViewType(self.view.type);
 
-        if (trackConf) {
-          var _iterator = _createForOfIteratorHelper(trackConf.displays),
-              _step;
-
-          try {
-            var _loop2 = function _loop2() {
-              var display = _step.value;
+        if (!trackConf) {
+          return undefined;
+        }
 
-              if (viewType.displayTypes.find(function (displayType) {
-                return displayType.name === display.type;
-              })) {
-                return {
-                  v: trackConf
-                };
-              }
-            };
+        var _iterator = _createForOfIteratorHelper(trackConf.displays),
+            _step;
 
-            for (_iterator.s(); !(_step = _iterator.n()).done;) {
-              var _ret = _loop2();
+        try {
+          var _loop2 = function _loop2() {
+            var display = _step.value;
 
-              if ((0, _typeof2.default)(_ret) === "object") return _ret.v;
+            if (viewType.displayTypes.find(function (d) {
+              return d.name === display.type;
+            })) {
+              return {
+                v: trackConf
+              };
             }
-          } catch (err) {
-            _iterator.e(err);
-          } finally {
-            _iterator.f();
+          };
+
+          for (_iterator.s(); !(_step = _iterator.n()).done;) {
+            var _ret = _loop2();
+
+            if ((0, _typeof2.default)(_ret) === "object") return _ret.v;
           }
+        } catch (err) {
+          _iterator.e(err);
+        } finally {
+          _iterator.f();
         }
-
-        return undefined;
-      },
+      }
+    };
+  }).views(function (self) {
+    return {
       trackConfigurations: function trackConfigurations(assemblyName) {
         if (!self.view) {
           return [];
         }
 
-        var session = (0, _util.getSession)(self);
-        var trackConfigurations = session.tracks,
-            assemblyManager = session.assemblyManager;
+        var _getSession2 = (0, _util.getSession)(self),
+            tracks = _getSession2.tracks,
+            assemblyManager = _getSession2.assemblyManager;
+
         var assembly = assemblyManager.get(assemblyName);
 
         if (!assembly) {
@@ -192,26 +196,28 @@ var _default = function _default(pluginManager) {
         var refseq = self.getRefSeqTrackConf(assemblyName); // filter out tracks that don't match the current assembly (check all
         // assembly aliases) and display types
 
-        return (refseq ? [refseq] : []).concat((0, _toConsumableArray2.default)(trackConfigurations.filter(function (conf) {
-          var trackConfAssemblies = (0, _configuration.readConfObject)(conf, 'assemblyNames');
+        return (refseq ? [refseq] : []).concat((0, _toConsumableArray2.default)(tracks.filter(function (c) {
+          var trackConfAssemblies = (0, _configuration.readConfObject)(c, 'assemblyNames');
           var allAliases = assembly.allAliases;
           return hasAnyOverlap(allAliases, trackConfAssemblies);
-        }).filter(function (conf) {
+        }).filter(function (c) {
           var _pluginManager$getVie = pluginManager.getViewType(self.view.type),
               displayTypes = _pluginManager$getVie.displayTypes;
 
-          var compatibleDisplays = displayTypes.map(function (display) {
-            return display.name;
+          var compatibleDisplays = displayTypes.map(function (d) {
+            return d.name;
           });
-          var trackDisplays = conf.displays.map(function (display) {
-            return display.type;
+          var trackDisplays = c.displays.map(function (d) {
+            return d.type;
           });
           return hasAnyOverlap(compatibleDisplays, trackDisplays);
         })));
       },
 
       get assemblyNames() {
-        return self.view ? self.view.assemblyNames : [];
+        var _self$view;
+
+        return ((_self$view = self.view) === null || _self$view === void 0 ? void 0 : _self$view.assemblyNames) || [];
       },
 
       connectionTrackConfigurations: function connectionTrackConfigurations(assemblyName, connection) {
@@ -220,8 +226,10 @@ var _default = function _default(pluginManager) {
         }
 
         var trackConfigurations = connection.tracks;
-        var session = (0, _util.getSession)(self);
-        var assemblyManager = session.assemblyManager;
+
+        var _getSession3 = (0, _util.getSession)(self),
+            assemblyManager = _getSession3.assemblyManager;
+
         var assembly = assemblyManager.get(assemblyName);
 
         if (!(assembly && assembly.initialized)) {
@@ -229,38 +237,39 @@ var _default = function _default(pluginManager) {
         } // filter out tracks that don't match the current display types
 
 
-        return trackConfigurations.filter(function (conf) {
-          var trackConfAssemblies = (0, _configuration.readConfObject)(conf, 'assemblyNames');
+        return trackConfigurations.filter(function (c) {
+          var trackConfAssemblies = (0, _configuration.readConfObject)(c, 'assemblyNames');
           var allAliases = assembly.allAliases;
           return hasAnyOverlap(allAliases, trackConfAssemblies);
-        }).filter(function (conf) {
+        }).filter(function (c) {
           var _pluginManager$getVie2 = pluginManager.getViewType(self.view.type),
               displayTypes = _pluginManager$getVie2.displayTypes;
 
-          var compatibleDisplays = displayTypes.map(function (display) {
-            return display.name;
+          var compatibleDisplays = displayTypes.map(function (d) {
+            return d.name;
           });
-          var trackDisplays = conf.displays.map(function (display) {
-            return display.type;
+          var trackDisplays = c.displays.map(function (d) {
+            return d.type;
           });
           return hasAnyOverlap(compatibleDisplays, trackDisplays);
         });
-      },
+      }
+    };
+  }).views(function (self) {
+    return {
       hierarchy: function hierarchy(assemblyName) {
         var _this = this;
 
-        var hier = generateHierarchy(self, self.trackConfigurations(assemblyName), self.collapsed);
+        var hier = generateHierarchy( // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        self, self.trackConfigurations(assemblyName), self.collapsed);
         var session = (0, _util.getSession)(self);
-        var conns = session.connectionInstances.filter(function (conn) {
-          var configAssemblyNames = (0, _configuration.readConfObject)(conn.configuration, 'assemblyNames');
-
-          if (configAssemblyNames.length === 0) {
-            return true;
-          }
-
-          return configAssemblyNames.includes(assemblyName);
+        var connections = session.connections,
+            connectionInstances = session.connectionInstances;
+        var conns = (connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.filter(function (c) {
+          var names = (0, _configuration.getConf)(c, 'assemblyNames');
+          return names.length === 0 ? true : names.includes(assemblyName);
         }).map(function (conn, index) {
-          var c = session.connections[index];
+          var c = connections[index];
           return {
             id: c.connectionId,
             name: (0, _configuration.readConfObject)(c, 'name'),
@@ -269,7 +278,7 @@ var _default = function _default(pluginManager) {
               expanded: true
             }
           };
-        });
+        })) || [];
         return {
           name: 'Root',
           id: 'Root',
@@ -281,26 +290,9 @@ var _default = function _default(pluginManager) {
         };
       },
       connectionHierarchy: function connectionHierarchy(assemblyName, connection) {
-        return generateHierarchy(self, self.connectionTrackConfigurations(assemblyName, connection), self.collapsed);
-      },
-      // This recursively gets tracks from lower paths
-      allTracksInCategoryPath: function allTracksInCategoryPath(path, connection, assemblyName) {
-        var currentHier = connection ? self.connectionHierarchy(connection) : self.hierarchy(assemblyName);
-        path.forEach(function (pathItem) {
-          currentHier = currentHier.get(pathItem) || new Map();
-        });
-        var tracks = {};
-        currentHier.forEach(function (contents, name) {
-          if (contents.trackId) {
-            tracks[contents.trackId] = contents;
-          } else {
-            tracks = Object.assign(tracks, self.allTracksInCategoryPath(path.concat([name])));
-          }
-        });
-        return tracks;
+        return generateHierarchy( // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        self, self.connectionTrackConfigurations(assemblyName, connection), self.collapsed);
       }
     };
   });
-};
-
-exports.default = _default;
+}

package/dist/ucsc-trackhub/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare var _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 export default _default;

package/dist/ucsc-trackhub/ucscAssemblies.d.ts

@@ -1,2 +1,2 @@
-declare var _default: string[];
+declare const _default: string[];
 export default _default;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "1.7.8",
+  "version": "1.7.11",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -54,5 +54,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "b429fa2bb5734fc8a5380988f6dfdd3f7a41a39f"
+  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
 }

package/src/AddConnectionWidget/components/AddConnectionWidget.test.js

@@ -104,8 +104,8 @@ type bigWig
     const {
       findByTestId,
       getAllByRole,
-      findByPlaceholderText,
       findByText,
+      findByPlaceholderText,
       findByDisplayValue,
     } = render(<AddConnectionWidget model={model} />)
     expect(session.connections.length).toBe(0)
@@ -121,6 +121,7 @@ type bigWig
         target: { value: 'http://test.com/jbrowse/data/' },
       },
     )
+    fireEvent.click(await findByText('Add item'))
     fireEvent.change(await findByPlaceholderText('add new'), {
       target: { value: 'volMyt1' },
     })

package/src/AddTrackWidget/index.test.jsx

@@ -89,6 +89,7 @@ describe('tests on an LGV type system with view.assemblyNames, using URL', () =>
   })
 
   it('adds relative URL (BAM)', () => {
+    console.warn = jest.fn()
     const { widget } = session
     widget.setTrackData({
       uri: 'volvox-sorted.bam',

package/src/AddTrackWidget/model.ts

@@ -82,7 +82,7 @@ export default function f(pluginManager: PluginManager) {
         self.indexTrackData = undefined
         self.trackData = undefined
         self.textIndexingConf = undefined
-        self.textIndexTrack = false
+        self.textIndexTrack = true
       },
     }))
     .views(self => ({

package/src/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.tsx

@@ -15,8 +15,11 @@ function CloseConnectionDialog({
   modalInfo = {},
   setModalInfo,
 }: {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  modalInfo: any
+  modalInfo?: {
+    name?: string
+    dereferenceTypeCount?: { [key: string]: number }
+    safelyBreakConnection?: Function
+  }
   setModalInfo: Function
 }) {
   const { name, dereferenceTypeCount, safelyBreakConnection } = modalInfo
@@ -41,12 +44,7 @@ function CloseConnectionDialog({
         </DialogContentText>
       </DialogContent>
       <DialogActions>
-        <Button
-          onClick={() => {
-            setModalInfo()
-          }}
-          color="primary"
-        >
+        <Button onClick={() => setModalInfo()} color="primary">
           Cancel
         </Button>
         <Button
@@ -54,9 +52,7 @@ function CloseConnectionDialog({
           onClick={
             modalInfo
               ? () => {
-                  if (safelyBreakConnection) {
-                    safelyBreakConnection()
-                  }
+                  safelyBreakConnection?.()
                   setModalInfo()
                 }
               : () => {}

package/src/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.tsx

@@ -18,7 +18,7 @@ function DeleteConnectionDialog({
 }: {
   deleteDialogDetails: { name: string; connectionConf: AnyConfigurationModel }
   session: AbstractSessionModel
-  handleClose: Function
+  handleClose: () => void
 }) {
   const { connectionConf, name } = deleteDialogDetails
   return (