@jbrowse/plugin-data-management 1.7.11 → 2.1.0

package/dist/HierarchicalTrackSelectorWidget/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/HierarchicalTrackSelectorWidget/index.ts"],"names":[],"mappings":";;;;;;AAAA,kDAA2E;AAGlE,4BAHF,eAAiB,CAGE;AAF1B,gEAAyC;AAEb,uBAFrB,sBAAY,CAEqB"}

package/dist/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,7 +1,6 @@
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { AbstractView } from 'react';
 export declare type TreeNode = {
     name: string;
     id: string;
@@ -20,7 +19,16 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     filterText: import("mobx-state-tree").IType<string | undefined, string, string>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
-    setView(view: AbstractView): void;
+    selection: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+} & {
+    addToSelection(elt: AnyConfigurationModel[]): void;
+    removeFromSelection(elt: AnyConfigurationModel[]): void;
+    clearSelection(): void;
+    setView(view: unknown): void;
     toggleCategory(pathName: string): void;
     clearFilterText(): void;
     setFilterText(newText: string): void;
@@ -31,7 +39,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     readonly assemblyNames: string[];
     connectionTrackConfigurations(assemblyName: string, connection: {
         tracks: AnyConfigurationModel[];
-    }): (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+    }): ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
 } & {

package/dist/HierarchicalTrackSelectorWidget/model.js

@@ -1,298 +1,264 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = stateTreeFactory;
-exports.generateHierarchy = generateHierarchy;
-
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _util = require("@jbrowse/core/util");
-
-var _mst = require("@jbrowse/core/util/types/mst");
-
-function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
-
-function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
-
-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; }
-
-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);
-  });
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+var __values = (this && this.__values) || function(o) {
+    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
+    if (m) return m.call(o);
+    if (o && typeof o.length === "number") return {
+        next: function () {
+            if (o && i >= o.length) o = void 0;
+            return { value: o && o[i++], done: !o };
+        }
+    };
+    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.generateHierarchy = void 0;
+var mobx_state_tree_1 = require("mobx-state-tree");
+var configuration_1 = require("@jbrowse/core/configuration");
+var util_1 = require("@jbrowse/core/util");
+var mst_1 = require("@jbrowse/core/util/types/mst");
+function hasAnyOverlap(a1, a2) {
+    if (a1 === void 0) { a1 = []; }
+    if (a2 === void 0) { a2 = []; }
+    return !!a1.find(function (value) { return a2.includes(value); });
 }
-
 function passesFilter(filter, config) {
-  var categories = (0, _configuration.readConfObject)(config, 'category');
-  var filterLower = filter.toLowerCase();
-  return getTrackName(config).toLowerCase().includes(filterLower) || (categories === null || categories === void 0 ? void 0 : categories.filter(function (c) {
-    return c.toLowerCase().includes(filterLower);
-  }).length);
+    var categories = (0, configuration_1.readConfObject)(config, 'category');
+    var filterLower = filter.toLowerCase();
+    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) {
-  if (!config.trackId) {
-    throw new Error('not a track');
-  }
-
-  return (0, _configuration.readConfObject)(config, 'name') || "Reference sequence (".concat((0, _configuration.readConfObject)((0, _mobxStateTree.getParent)(config), 'name'), ")");
-}
-
-function generateHierarchy(model, trackConfigurations, collapsed) {
-  var hierarchy = {
-    children: []
-  };
-  var filterText = model.filterText,
-      view = model.view;
-  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)(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 (conf.trackId.endsWith('sessionTrack')) {
-      categories.unshift(' Session tracks');
+    if (!config.trackId) {
+        throw new Error('not a track');
     }
-
-    var currLevel = hierarchy; // find existing category to put track into or create it
-
-    var _loop = function _loop(i) {
-      var category = categories[i];
-      var ret = currLevel.children.find(function (c) {
-        return c.name === category;
-      });
-      var id = categories.slice(0, i + 1).join(',');
-
-      if (!ret) {
-        var n = {
-          children: [],
-          name: category,
-          id: id,
-          isOpenByDefault: !collapsed.get(id)
-        };
-        currLevel.children.push(n);
-        currLevel = n;
-      } else {
-        currLevel = ret;
-      }
-    };
-
-    for (var i = 0; i < categories.length; i++) {
-      _loop(i);
+    return ((0, configuration_1.readConfObject)(config, 'name') ||
+        "Reference sequence (".concat((0, configuration_1.readConfObject)((0, mobx_state_tree_1.getParent)(config), 'name'), ")"));
+}
+function filterTracks(tracks, self, assemblyName) {
+    var assemblyManager = (0, util_1.getSession)(self).assemblyManager;
+    var pluginManager = (0, mobx_state_tree_1.getEnv)(self).pluginManager;
+    var assembly = assemblyManager.get(assemblyName);
+    if (!assembly) {
+        return [];
     }
-
-    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: conf.trackId,
-      name: getTrackName(conf),
-      conf: conf,
-      checked: !!tracks.find(function (f) {
-        return f.configuration === conf;
-      }),
-      children: []
+    return tracks
+        .filter(function (c) {
+        var trackConfAssemblies = (0, configuration_1.readConfObject)(c, 'assemblyNames');
+        var allAliases = assembly.allAliases;
+        return hasAnyOverlap(allAliases, trackConfAssemblies);
+    })
+        .filter(function (c) {
+        var displayTypes = pluginManager.getViewType(self.view.type).displayTypes;
+        var compatDisplays = displayTypes.map(function (d) { return d.name; });
+        var trackDisplays = c.displays.map(function (d) { return d.type; });
+        return hasAnyOverlap(compatDisplays, trackDisplays);
     });
-  });
-  return hierarchy.children;
 }
-
-function stateTreeFactory(pluginManager) {
-  return _mobxStateTree.types.model('HierarchicalTrackSelectorWidget', {
-    id: _mst.ElementId,
-    type: _mobxStateTree.types.literal('HierarchicalTrackSelectorWidget'),
-    collapsed: _mobxStateTree.types.map(_mobxStateTree.types.boolean),
-    filterText: '',
-    view: _mobxStateTree.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel'))
-  }).actions(function (self) {
-    return {
-      setView: function setView(view) {
-        self.view = view;
-      },
-      toggleCategory: function toggleCategory(pathName) {
-        self.collapsed.set(pathName, !self.collapsed.get(pathName));
-      },
-      clearFilterText: function clearFilterText() {
-        self.filterText = '';
-      },
-      setFilterText: function setFilterText(newText) {
-        self.filterText = newText;
-      }
-    };
-  }).views(function (self) {
-    return {
-      getRefSeqTrackConf: function getRefSeqTrackConf(assemblyName) {
-        var _getSession = (0, _util.getSession)(self),
-            assemblyManager = _getSession.assemblyManager;
-
-        var assembly = assemblyManager.get(assemblyName);
-        var trackConf = assembly === null || assembly === void 0 ? void 0 : assembly.configuration.sequence;
-        var viewType = pluginManager.getViewType(self.view.type);
-
-        if (!trackConf) {
-          return undefined;
+function generateHierarchy(model, trackConfigurations, collapsed) {
+    var hierarchy = { children: [] };
+    var filterText = model.filterText, view = model.view;
+    trackConfigurations
+        .filter(function (conf) { return passesFilter(filterText, conf); })
+        .forEach(function (conf) {
+        // copy the categories since this array can be mutated downstream
+        var categories = __spreadArray([], __read(((0, configuration_1.readConfObject)(conf, 'category') || [])), false);
+        // 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 (conf.trackId.endsWith('sessionTrack')) {
+            categories.unshift(' Session tracks');
         }
-
-        var _iterator = _createForOfIteratorHelper(trackConf.displays),
-            _step;
-
-        try {
-          var _loop2 = function _loop2() {
-            var display = _step.value;
-
-            if (viewType.displayTypes.find(function (d) {
-              return d.name === display.type;
-            })) {
-              return {
-                v: trackConf
-              };
+        var currLevel = hierarchy;
+        var _loop_1 = function (i) {
+            var category = categories[i];
+            var ret = currLevel.children.find(function (c) { return c.name === category; });
+            var id = categories.slice(0, i + 1).join(',');
+            if (!ret) {
+                var n = {
+                    children: [],
+                    name: category,
+                    id: id,
+                    isOpenByDefault: !collapsed.get(id),
+                };
+                currLevel.children.push(n);
+                currLevel = n;
             }
-          };
-
-          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();
-        }
-      }
-    };
-  }).views(function (self) {
-    return {
-      trackConfigurations: function trackConfigurations(assemblyName) {
-        if (!self.view) {
-          return [];
-        }
-
-        var _getSession2 = (0, _util.getSession)(self),
-            tracks = _getSession2.tracks,
-            assemblyManager = _getSession2.assemblyManager;
-
-        var assembly = assemblyManager.get(assemblyName);
-
-        if (!assembly) {
-          return [];
-        }
-
-        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)(tracks.filter(function (c) {
-          var trackConfAssemblies = (0, _configuration.readConfObject)(c, 'assemblyNames');
-          var allAliases = assembly.allAliases;
-          return hasAnyOverlap(allAliases, trackConfAssemblies);
-        }).filter(function (c) {
-          var _pluginManager$getVie = pluginManager.getViewType(self.view.type),
-              displayTypes = _pluginManager$getVie.displayTypes;
-
-          var compatibleDisplays = displayTypes.map(function (d) {
-            return d.name;
-          });
-          var trackDisplays = c.displays.map(function (d) {
-            return d.type;
-          });
-          return hasAnyOverlap(compatibleDisplays, trackDisplays);
-        })));
-      },
-
-      get assemblyNames() {
-        var _self$view;
-
-        return ((_self$view = self.view) === null || _self$view === void 0 ? void 0 : _self$view.assemblyNames) || [];
-      },
-
-      connectionTrackConfigurations: function connectionTrackConfigurations(assemblyName, connection) {
-        if (!self.view) {
-          return [];
+            else {
+                currLevel = ret;
+            }
+        };
+        // find existing category to put track into or create it
+        for (var i = 0; i < categories.length; i++) {
+            _loop_1(i);
         }
-
-        var trackConfigurations = connection.tracks;
-
-        var _getSession3 = (0, _util.getSession)(self),
-            assemblyManager = _getSession3.assemblyManager;
-
-        var assembly = assemblyManager.get(assemblyName);
-
-        if (!(assembly && assembly.initialized)) {
-          return [];
-        } // filter out tracks that don't match the current display types
-
-
-        return trackConfigurations.filter(function (c) {
-          var trackConfAssemblies = (0, _configuration.readConfObject)(c, 'assemblyNames');
-          var allAliases = assembly.allAliases;
-          return hasAnyOverlap(allAliases, trackConfAssemblies);
-        }).filter(function (c) {
-          var _pluginManager$getVie2 = pluginManager.getViewType(self.view.type),
-              displayTypes = _pluginManager$getVie2.displayTypes;
-
-          var compatibleDisplays = displayTypes.map(function (d) {
-            return d.name;
-          });
-          var trackDisplays = c.displays.map(function (d) {
-            return d.type;
-          });
-          return hasAnyOverlap(compatibleDisplays, trackDisplays);
+        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: conf.trackId,
+            name: getTrackName(conf),
+            conf: conf,
+            checked: !!tracks.find(function (f) { return f.configuration === conf; }),
+            children: [],
         });
-      }
-    };
-  }).views(function (self) {
-    return {
-      hierarchy: function hierarchy(assemblyName) {
-        var _this = this;
-
-        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 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 = connections[index];
-          return {
-            id: c.connectionId,
-            name: (0, _configuration.readConfObject)(c, 'name'),
-            children: _this.connectionHierarchy(assemblyName, conn),
-            state: {
-              expanded: true
+    });
+    return hierarchy.children;
+}
+exports.generateHierarchy = generateHierarchy;
+function stateTreeFactory(pluginManager) {
+    return mobx_state_tree_1.types
+        .model('HierarchicalTrackSelectorWidget', {
+        id: mst_1.ElementId,
+        type: mobx_state_tree_1.types.literal('HierarchicalTrackSelectorWidget'),
+        collapsed: mobx_state_tree_1.types.map(mobx_state_tree_1.types.boolean),
+        filterText: '',
+        view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
+    })
+        .volatile(function () { return ({
+        selection: [],
+    }); })
+        .actions(function (self) { return ({
+        addToSelection: function (elt) {
+            self.selection = __spreadArray(__spreadArray([], __read(self.selection), false), __read(elt), false);
+        },
+        removeFromSelection: function (elt) {
+            self.selection = self.selection.filter(function (f) { return !elt.includes(f); });
+        },
+        clearSelection: function () {
+            self.selection = [];
+        },
+        setView: function (view) {
+            self.view = view;
+        },
+        toggleCategory: function (pathName) {
+            self.collapsed.set(pathName, !self.collapsed.get(pathName));
+        },
+        clearFilterText: function () {
+            self.filterText = '';
+        },
+        setFilterText: function (newText) {
+            self.filterText = newText;
+        },
+    }); })
+        .views(function (self) { return ({
+        getRefSeqTrackConf: function (assemblyName) {
+            var e_1, _a;
+            var assemblyManager = (0, util_1.getSession)(self).assemblyManager;
+            var assembly = assemblyManager.get(assemblyName);
+            var trackConf = assembly === null || assembly === void 0 ? void 0 : assembly.configuration.sequence;
+            var viewType = pluginManager.getViewType(self.view.type);
+            if (!trackConf) {
+                return undefined;
             }
-          };
-        })) || [];
-        return {
-          name: 'Root',
-          id: 'Root',
-          children: [{
-            name: 'Tracks',
-            id: 'Tracks',
-            children: hier
-          }].concat((0, _toConsumableArray2.default)(conns))
-        };
-      },
-      connectionHierarchy: function connectionHierarchy(assemblyName, connection) {
-        return generateHierarchy( // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        self, self.connectionTrackConfigurations(assemblyName, connection), self.collapsed);
-      }
-    };
-  });
-}
+            var _loop_2 = function (display) {
+                if (viewType.displayTypes.find(function (d) { return d.name === display.type; })) {
+                    return { value: trackConf };
+                }
+            };
+            try {
+                for (var _b = __values(trackConf.displays), _c = _b.next(); !_c.done; _c = _b.next()) {
+                    var display = _c.value;
+                    var state_1 = _loop_2(display);
+                    if (typeof state_1 === "object")
+                        return state_1.value;
+                }
+            }
+            catch (e_1_1) { e_1 = { error: e_1_1 }; }
+            finally {
+                try {
+                    if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
+                }
+                finally { if (e_1) throw e_1.error; }
+            }
+        },
+    }); })
+        .views(function (self) { return ({
+        trackConfigurations: function (assemblyName) {
+            if (!self.view) {
+                return [];
+            }
+            var _a = (0, util_1.getSession)(self), tracks = _a.tracks, assemblyManager = _a.assemblyManager;
+            var assembly = assemblyManager.get(assemblyName);
+            if (!assembly) {
+                return [];
+            }
+            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(__spreadArray([], __read(filterTracks(tracks, self, assemblyName)), false));
+        },
+        get assemblyNames() {
+            var _a;
+            return ((_a = self.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
+        },
+        connectionTrackConfigurations: function (assemblyName, connection) {
+            if (!self.view) {
+                return [];
+            }
+            // filter out tracks that don't match the current display types
+            return filterTracks(connection.tracks, self, assemblyName);
+        },
+    }); })
+        .views(function (self) { return ({
+        hierarchy: function (assemblyName) {
+            var _this = this;
+            var hier = generateHierarchy(
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            self, self.trackConfigurations(assemblyName), self.collapsed);
+            var session = (0, util_1.getSession)(self);
+            var connections = session.connections, connectionInstances = session.connectionInstances;
+            var conns = (connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.filter(function (c) {
+                var names = (0, configuration_1.getConf)(c, 'assemblyNames');
+                return names.length === 0 ? true : names.includes(assemblyName);
+            }).map(function (conn, index) {
+                var c = connections[index];
+                return {
+                    id: c.connectionId,
+                    name: (0, configuration_1.readConfObject)(c, 'name'),
+                    children: _this.connectionHierarchy(assemblyName, conn),
+                    state: {
+                        expanded: true,
+                    },
+                };
+            })) || [];
+            return {
+                name: 'Root',
+                id: 'Root',
+                children: __spreadArray([
+                    { name: 'Tracks', id: 'Tracks', children: hier }
+                ], __read(conns), false),
+            };
+        },
+        connectionHierarchy: function (assemblyName, connection) {
+            return generateHierarchy(
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            self, self.connectionTrackConfigurations(assemblyName, connection), self.collapsed);
+        },
+    }); });
+}
+exports.default = stateTreeFactory;
+//# sourceMappingURL=model.js.map

package/dist/HierarchicalTrackSelectorWidget/model.js.map

@@ -0,0 +1 @@
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