@jbrowse/core 1.7.11 → 2.1.0

package/assemblyManager/assemblyConfigSchema.js

@@ -1,67 +1,50 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("../configuration");
-
-var _default = function _default(pluginManager) {
-  return (0, _configuration.ConfigurationSchema)('BaseAssembly', {
-    aliases: {
-      type: 'stringArray',
-      defaultValue: [],
-      description: 'Other possible names for the assembly'
-    },
-    sequence: pluginManager.getTrackType('ReferenceSequenceTrack').configSchema,
-    refNameColors: {
-      type: 'stringArray',
-      defaultValue: [],
-      description: 'Define custom colors for each reference sequence. Will cycle through this list if there are not enough colors for every sequence.'
-    },
-    refNameAliases: (0, _configuration.ConfigurationSchema)('RefNameAliases', {
-      adapter: pluginManager.pluggableConfigSchemaType('adapter')
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("../configuration");
+exports.default = (pluginManager) => {
+    return (0, configuration_1.ConfigurationSchema)('BaseAssembly', {
+        aliases: {
+            type: 'stringArray',
+            defaultValue: [],
+            description: 'Other possible names for the assembly',
+        },
+        sequence: pluginManager.getTrackType('ReferenceSequenceTrack')
+            .configSchema,
+        refNameColors: {
+            type: 'stringArray',
+            defaultValue: [],
+            description: 'Define custom colors for each reference sequence. Will cycle through this list if there are not enough colors for every sequence.',
+        },
+        refNameAliases: (0, configuration_1.ConfigurationSchema)('RefNameAliases', {
+            adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+        }, {
+            preProcessSnapshot: snap => {
+                // allow refNameAliases to be unspecified
+                // @ts-ignore
+                if (!snap.adapter) {
+                    return { adapter: { type: 'RefNameAliasAdapter' } };
+                }
+                return snap;
+            },
+        }),
+        cytobands: (0, configuration_1.ConfigurationSchema)('Cytoband', {
+            adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+        }, {
+            preProcessSnapshot: snap => {
+                // allow cytoBand to be unspecified
+                // @ts-ignore
+                if (!snap.adapter) {
+                    return { adapter: { type: 'CytobandAdapter' } };
+                }
+                return snap;
+            },
+        }),
+        displayName: {
+            type: 'string',
+            defaultValue: '',
+            description: 'A human readable display name for the assembly e.g. "Homo sapiens (hg38)" while the assembly name may just be "hg38"',
+        },
     }, {
-      preProcessSnapshot: function preProcessSnapshot(snap) {
-        // allow refNameAliases to be unspecified
-        // @ts-ignore
-        if (!snap.adapter) {
-          return {
-            adapter: {
-              type: 'RefNameAliasAdapter'
-            }
-          };
-        }
-
-        return snap;
-      }
-    }),
-    cytobands: (0, _configuration.ConfigurationSchema)('Cytoband', {
-      adapter: pluginManager.pluggableConfigSchemaType('adapter')
-    }, {
-      preProcessSnapshot: function preProcessSnapshot(snap) {
-        // allow cytoBand to be unspecified
-        // @ts-ignore
-        if (!snap.adapter) {
-          return {
-            adapter: {
-              type: 'CytobandAdapter'
-            }
-          };
-        }
-
-        return snap;
-      }
-    }),
-    displayName: {
-      type: 'string',
-      defaultValue: '',
-      description: 'A human readable display name for the assembly e.g. "Homo sapiens (hg38)" while the assembly name may just be "hg38"'
-    }
-  }, {
-    explicitIdentifier: 'name'
-  });
+        explicitIdentifier: 'name',
+    });
 };
-
-exports.default = _default;

package/assemblyManager/assemblyManager.d.ts

@@ -65,9 +65,9 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
-    get(assemblyName: string): (import("mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }> & {
+    get(assemblyName: string): ({
+        configuration: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
@@ -191,7 +191,9 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     readonly assemblyNamesList: string[];
-    readonly assemblyList: (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
+    readonly assemblyList: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType> & {
         name: string;
@@ -200,9 +202,9 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     readonly pluginManager: any;
     readonly allPossibleRefNames: string[] | undefined;
 } & {
-    waitForAssembly(assemblyName: string): Promise<(import("mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }> & {
+    waitForAssembly(assemblyName: string): Promise<({
+        configuration: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
@@ -339,9 +341,9 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     } | undefined>;
     isValidRefName(refName: string, assemblyName?: string): boolean;
 } & {
-    removeAssembly(asm: import("mobx-state-tree").ModelInstanceTypeProps<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }> & {
+    removeAssembly(asm: {
+        configuration: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         error: Error | undefined;
         regions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {

package/assemblyManager/assemblyManager.js

@@ -1,278 +1,134 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = assemblyManagerFactory;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _mobx = require("mobx");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _util = require("../util");
-
-var _configuration = require("../configuration");
-
-var _assembly = _interopRequireDefault(require("./assembly"));
-
-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$/.test(n)) return _arrayLikeToArray(o, minLen); }
-
-function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_1 = require("../util");
+const configuration_1 = require("../configuration");
+const assembly_1 = __importDefault(require("./assembly"));
 function assemblyManagerFactory(assemblyConfigType, pluginManager) {
-  var Assembly = (0, _assembly.default)(assemblyConfigType, pluginManager);
-  return _mobxStateTree.types.model({
-    assemblies: _mobxStateTree.types.array(Assembly)
-  }).views(function (self) {
-    return {
-      get: function get(assemblyName) {
-        return self.assemblies.find(function (assembly) {
-          return assembly.hasName(assemblyName);
-        });
-      },
-
-      get assemblyNamesList() {
-        return this.assemblyList.map(function (asm) {
-          return asm.name;
-        });
-      },
-
-      get assemblyList() {
-        // name is the explicit identifier and can be accessed without getConf,
-        // hence the union with {name:string}
-        var _getParent = (0, _mobxStateTree.getParent)(self),
-            assemblies = _getParent.jbrowse.assemblies,
-            _getParent$session = _getParent.session;
-
-        _getParent$session = _getParent$session === void 0 ? {} : _getParent$session;
-        var _getParent$session$se = _getParent$session.sessionAssemblies,
-            sessionAssemblies = _getParent$session$se === void 0 ? [] : _getParent$session$se;
-        return [].concat((0, _toConsumableArray2.default)(assemblies), (0, _toConsumableArray2.default)(sessionAssemblies));
-      },
-
-      get rpcManager() {
-        return (0, _mobxStateTree.getParent)(self).rpcManager;
-      },
-
-      get pluginManager() {
-        return (0, _mobxStateTree.getParent)(self).pluginManager;
-      },
-
-      get allPossibleRefNames() {
-        var refNames = [];
-
-        var _iterator = _createForOfIteratorHelper(self.assemblies),
-            _step;
-
-        try {
-          for (_iterator.s(); !(_step = _iterator.n()).done;) {
-            var assembly = _step.value;
-
-            if (!assembly.allRefNames) {
-              return undefined;
+    const Assembly = (0, assembly_1.default)(assemblyConfigType, pluginManager);
+    return mobx_state_tree_1.types
+        .model({
+        assemblies: mobx_state_tree_1.types.array(Assembly),
+    })
+        .views(self => ({
+        get(assemblyName) {
+            return self.assemblies.find(assembly => assembly.hasName(assemblyName));
+        },
+        get assemblyNamesList() {
+            return this.assemblyList.map(asm => asm.name);
+        },
+        get assemblyList() {
+            // name is the explicit identifier and can be accessed without getConf,
+            // hence the union with {name:string}
+            const { jbrowse: { assemblies }, session: { sessionAssemblies = [] } = {},
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+             } = (0, mobx_state_tree_1.getParent)(self);
+            return [
+                ...assemblies,
+                ...sessionAssemblies,
+            ];
+        },
+        get rpcManager() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            return (0, mobx_state_tree_1.getParent)(self).rpcManager;
+        },
+        get pluginManager() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            return (0, mobx_state_tree_1.getParent)(self).pluginManager;
+        },
+        get allPossibleRefNames() {
+            let refNames = [];
+            for (const assembly of self.assemblies) {
+                if (!assembly.allRefNames) {
+                    return undefined;
+                }
+                refNames = refNames.concat(assembly.allRefNames);
             }
-
-            refNames = refNames.concat(assembly.allRefNames);
-          }
-        } catch (err) {
-          _iterator.e(err);
-        } finally {
-          _iterator.f();
-        }
-
-        return refNames;
-      }
-
-    };
-  }).views(function (self) {
-    return {
-      // use this method instead of assemblyManager.get(assemblyName)
-      // get an assembly with regions loaded
-      waitForAssembly: function waitForAssembly(assemblyName) {
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-          var assembly;
-          return _regenerator.default.wrap(function _callee$(_context) {
-            while (1) {
-              switch (_context.prev = _context.next) {
-                case 0:
-                  if (assemblyName) {
-                    _context.next = 2;
-                    break;
-                  }
-
-                  throw new Error('no assembly name supplied to waitForAssembly');
-
-                case 2:
-                  assembly = self.get(assemblyName);
-
-                  if (assembly) {
-                    _context.next = 5;
-                    break;
-                  }
-
-                  return _context.abrupt("return", undefined);
-
-                case 5:
-                  _context.next = 7;
-                  return (0, _util.when)(function () {
-                    return Boolean(assembly.regions && assembly.refNameAliases) || !!assembly.error;
-                  });
-
-                case 7:
-                  if (!assembly.error) {
-                    _context.next = 9;
-                    break;
-                  }
-
-                  throw assembly.error;
-
-                case 9:
-                  return _context.abrupt("return", assembly);
-
-                case 10:
-                case "end":
-                  return _context.stop();
-              }
+            return refNames;
+        },
+    }))
+        .views(self => ({
+        // use this method instead of assemblyManager.get(assemblyName)
+        // get an assembly with regions loaded
+        async waitForAssembly(assemblyName) {
+            if (!assemblyName) {
+                throw new Error('no assembly name supplied to waitForAssembly');
             }
-          }, _callee);
-        }))();
-      },
-      getRefNameMapForAdapter: function getRefNameMapForAdapter(adapterConf, assemblyName, opts) {
-        var _this = this;
-
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-          var asm;
-          return _regenerator.default.wrap(function _callee2$(_context2) {
-            while (1) {
-              switch (_context2.prev = _context2.next) {
-                case 0:
-                  if (!assemblyName) {
-                    _context2.next = 5;
-                    break;
-                  }
-
-                  _context2.next = 3;
-                  return _this.waitForAssembly(assemblyName);
-
-                case 3:
-                  asm = _context2.sent;
-                  return _context2.abrupt("return", asm === null || asm === void 0 ? void 0 : asm.getRefNameMapForAdapter(adapterConf, opts));
-
-                case 5:
-                  return _context2.abrupt("return", {});
-
-                case 6:
-                case "end":
-                  return _context2.stop();
-              }
+            const assembly = self.get(assemblyName);
+            if (!assembly) {
+                return undefined;
             }
-          }, _callee2);
-        }))();
-      },
-      getReverseRefNameMapForAdapter: function getReverseRefNameMapForAdapter(adapterConf, assemblyName, opts) {
-        var _this2 = this;
-
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-          var asm;
-          return _regenerator.default.wrap(function _callee3$(_context3) {
-            while (1) {
-              switch (_context3.prev = _context3.next) {
-                case 0:
-                  if (!assemblyName) {
-                    _context3.next = 5;
-                    break;
-                  }
-
-                  _context3.next = 3;
-                  return _this2.waitForAssembly(assemblyName);
-
-                case 3:
-                  asm = _context3.sent;
-                  return _context3.abrupt("return", asm === null || asm === void 0 ? void 0 : asm.getReverseRefNameMapForAdapter(adapterConf, opts));
-
-                case 5:
-                  return _context3.abrupt("return", {});
-
-                case 6:
-                case "end":
-                  return _context3.stop();
-              }
+            await (0, util_1.when)(() => Boolean(assembly.regions && assembly.refNameAliases) ||
+                !!assembly.error);
+            if (assembly.error) {
+                throw assembly.error;
             }
-          }, _callee3);
-        }))();
-      },
-      isValidRefName: function isValidRefName(refName, assemblyName) {
-        if (assemblyName) {
-          var assembly = self.get(assemblyName);
-
-          if (assembly) {
-            return assembly.isValidRefName(refName);
-          }
-
-          throw new Error("isValidRefName for ".concat(assemblyName, " failed, assembly does not exist"));
-        }
-
-        if (!self.allPossibleRefNames) {
-          throw new Error("isValidRefName not available, assemblyManager has not yet finished loading. If you are looking for a refname in a specific assembly, pass assembly argument");
-        }
-
-        return self.allPossibleRefNames.includes(refName);
-      }
-    };
-  }).actions(function (self) {
-    return {
-      removeAssembly: function removeAssembly(asm) {
-        self.assemblies.remove(asm);
-      },
-      afterAttach: function afterAttach() {
-        var _this3 = this;
-
-        (0, _mobxStateTree.addDisposer)(self, (0, _mobx.reaction)( // have to slice it to be properly reacted to
-        function () {
-          return self.assemblyList;
-        }, function (assemblyConfigs) {
-          self.assemblies.forEach(function (asm) {
-            if (!asm.configuration) {
-              _this3.removeAssembly(asm);
+            return assembly;
+        },
+        async getRefNameMapForAdapter(adapterConf, assemblyName, opts) {
+            if (assemblyName) {
+                const asm = await this.waitForAssembly(assemblyName);
+                return asm === null || asm === void 0 ? void 0 : asm.getRefNameMapForAdapter(adapterConf, opts);
             }
-          });
-          assemblyConfigs.forEach(function (assemblyConfig) {
-            var existingAssemblyIdx = self.assemblies.findIndex(function (assembly) {
-              return assembly.name === (0, _configuration.readConfObject)(assemblyConfig, 'name');
-            });
-
-            if (existingAssemblyIdx === -1) {
-              _this3.addAssembly(assemblyConfig);
+            return {};
+        },
+        async getReverseRefNameMapForAdapter(adapterConf, assemblyName, opts) {
+            if (assemblyName) {
+                const asm = await this.waitForAssembly(assemblyName);
+                return asm === null || asm === void 0 ? void 0 : asm.getReverseRefNameMapForAdapter(adapterConf, opts);
+            }
+            return {};
+        },
+        isValidRefName(refName, assemblyName) {
+            if (assemblyName) {
+                const assembly = self.get(assemblyName);
+                if (assembly) {
+                    return assembly.isValidRefName(refName);
+                }
+                throw new Error(`isValidRefName for ${assemblyName} failed, assembly does not exist`);
             }
-          });
-        }, {
-          fireImmediately: true,
-          name: 'assemblyManagerAfterAttach'
-        }));
-      },
-      // this can take an active instance of an assembly, in which case it is
-      // referred to, or it can take an identifier e.g. assembly name, which is
-      // used as a reference. snapshots cannot be used
-      addAssembly: function addAssembly(assemblyConfig) {
-        self.assemblies.push({
-          configuration: assemblyConfig
-        });
-      },
-      replaceAssembly: function replaceAssembly(idx, assemblyConfig) {
-        self.assemblies[idx] = (0, _mobxStateTree.cast)({
-          configuration: assemblyConfig
-        });
-      }
-    };
-  });
-}
+            if (!self.allPossibleRefNames) {
+                throw new Error(`isValidRefName not available, assemblyManager has not yet finished loading. If you are looking for a refname in a specific assembly, pass assembly argument`);
+            }
+            return self.allPossibleRefNames.includes(refName);
+        },
+    }))
+        .actions(self => ({
+        removeAssembly(asm) {
+            self.assemblies.remove(asm);
+        },
+        afterAttach() {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(
+            // have to slice it to be properly reacted to
+            () => self.assemblyList, assemblyConfigs => {
+                self.assemblies.forEach(asm => {
+                    if (!asm.configuration) {
+                        this.removeAssembly(asm);
+                    }
+                });
+                assemblyConfigs.forEach(assemblyConfig => {
+                    const existingAssemblyIdx = self.assemblies.findIndex(assembly => assembly.name === (0, configuration_1.readConfObject)(assemblyConfig, 'name'));
+                    if (existingAssemblyIdx === -1) {
+                        this.addAssembly(assemblyConfig);
+                    }
+                });
+            }, { fireImmediately: true, name: 'assemblyManagerAfterAttach' }));
+        },
+        // this can take an active instance of an assembly, in which case it is
+        // referred to, or it can take an identifier e.g. assembly name, which is
+        // used as a reference. snapshots cannot be used
+        addAssembly(assemblyConfig) {
+            self.assemblies.push({ configuration: assemblyConfig });
+        },
+        replaceAssembly(idx, assemblyConfig) {
+            self.assemblies[idx] = (0, mobx_state_tree_1.cast)({
+                configuration: assemblyConfig,
+            });
+        },
+    }));
+}
+exports.default = assemblyManagerFactory;

package/assemblyManager/index.js

@@ -1,23 +1,10 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "assemblyConfigSchemaFactory", {
-  enumerable: true,
-  get: function get() {
-    return _assemblyConfigSchema.default;
-  }
-});
-Object.defineProperty(exports, "default", {
-  enumerable: true,
-  get: function get() {
-    return _assemblyManager.default;
-  }
-});
-
-var _assemblyManager = _interopRequireDefault(require("./assemblyManager"));
-
-var _assemblyConfigSchema = _interopRequireDefault(require("./assemblyConfigSchema"));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.assemblyConfigSchemaFactory = exports.default = void 0;
+var assemblyManager_1 = require("./assemblyManager");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(assemblyManager_1).default; } });
+var assemblyConfigSchema_1 = require("./assemblyConfigSchema");
+Object.defineProperty(exports, "assemblyConfigSchemaFactory", { enumerable: true, get: function () { return __importDefault(assemblyConfigSchema_1).default; } });