@jbrowse/core 2.0.1 → 2.1.0

package/data_adapters/CytobandAdapter.js

@@ -1,128 +1,42 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.configSchema = exports.DataAdapter = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
-
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _simpleFeature = _interopRequireDefault(require("../util/simpleFeature"));
-
-var _configuration = require("../configuration");
-
-var _io = require("../util/io");
-
-var _BaseAdapter2 = require("./BaseAdapter");
-
-function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
-
-function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
-
-var configSchema = (0, _configuration.ConfigurationSchema)('CytobandAdapter', {
-  cytobandLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/cytoband.txt.gz'
-    }
-  }
-}, {
-  explicitlyTyped: true
-});
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DataAdapter = exports.configSchema = void 0;
+const simpleFeature_1 = __importDefault(require("../util/simpleFeature"));
+const configuration_1 = require("../configuration");
+const io_1 = require("../util/io");
+const BaseAdapter_1 = require("./BaseAdapter");
+const configSchema = (0, configuration_1.ConfigurationSchema)('CytobandAdapter', {
+    cytobandLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/cytoband.txt.gz' },
+    },
+}, { explicitlyTyped: true });
 exports.configSchema = configSchema;
-
-var CytobandAdapter = /*#__PURE__*/function (_BaseAdapter) {
-  (0, _inherits2.default)(CytobandAdapter, _BaseAdapter);
-
-  var _super = _createSuper(CytobandAdapter);
-
-  function CytobandAdapter() {
-    (0, _classCallCheck2.default)(this, CytobandAdapter);
-    return _super.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(CytobandAdapter, [{
-    key: "getData",
-    value: function () {
-      var _getData = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var loc, data;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                loc = (0, _configuration.readConfObject)(this.config, 'cytobandLocation');
-
-                if (!(loc.uri === '' || loc.uri === '/path/to/cytoband.txt.gz')) {
-                  _context.next = 3;
-                  break;
-                }
-
-                return _context.abrupt("return", []);
-
-              case 3:
-                _context.next = 5;
-                return (0, _io.openLocation)(loc).readFile('utf8');
-
-              case 5:
-                data = _context.sent;
-                return _context.abrupt("return", data.split('\n').filter(function (f) {
-                  return !!f.trim();
-                }).map(function (line) {
-                  var _line$split = line.split('\t'),
-                      _line$split2 = (0, _slicedToArray2.default)(_line$split, 5),
-                      refName = _line$split2[0],
-                      start = _line$split2[1],
-                      end = _line$split2[2],
-                      name = _line$split2[3],
-                      type = _line$split2[4];
-
-                  return new _simpleFeature.default({
-                    uniqueId: line,
-                    refName: refName,
-                    start: +start,
-                    end: +end,
-                    name: name,
-                    type: type
-                  });
-                }));
-
-              case 7:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getData() {
-        return _getData.apply(this, arguments);
-      }
-
-      return getData;
-    }()
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }]);
-  return CytobandAdapter;
-}(_BaseAdapter2.BaseAdapter);
-
-exports.DataAdapter = CytobandAdapter;
+class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
+    async getData() {
+        const loc = (0, configuration_1.readConfObject)(this.config, 'cytobandLocation');
+        if (loc.uri === '' || loc.uri === '/path/to/cytoband.txt.gz') {
+            return [];
+        }
+        const data = await (0, io_1.openLocation)(loc).readFile('utf8');
+        return data
+            .split('\n')
+            .filter(f => !!f.trim())
+            .map(line => {
+            const [refName, start, end, name, type] = line.split('\t');
+            return new simpleFeature_1.default({
+                uniqueId: line,
+                refName,
+                start: +start,
+                end: +end,
+                name,
+                type,
+            });
+        });
+    }
+    freeResources( /* { region } */) { }
+}
+exports.DataAdapter = CytobandAdapter;

package/data_adapters/dataAdapterCache.js

@@ -1,27 +1,14 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.clearAdapterCache = clearAdapterCache;
-exports.freeAdapterResources = freeAdapterResources;
-exports.getAdapter = getAdapter;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _idMaker = _interopRequireDefault(require("../util/idMaker"));
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.clearAdapterCache = exports.freeAdapterResources = exports.getAdapter = void 0;
+const idMaker_1 = __importDefault(require("../util/idMaker"));
 function adapterConfigCacheKey(adapterConfig) {
-  return "".concat((0, _idMaker.default)(adapterConfig));
+    return `${(0, idMaker_1.default)(adapterConfig)}`;
 }
-
-var adapterCache = {};
+let adapterCache = {};
 /**
  * instantiate a data adapter, or return an already-instantiated one if we have one with the same
  * configuration
@@ -31,149 +18,81 @@ var adapterCache = {};
  *   used for reference counting
  * @param adapterConfigSnapshot - plain-JS configuration snapshot for the adapter
  */
-
-function getAdapter(_x, _x2, _x3) {
-  return _getAdapter.apply(this, arguments);
-}
-/**
- * this is a callback that is passed to adapters that
- * allows them to get any sub-adapters that they need
- * internally, staying with the same worker session ID
- */
-
-
-function _getAdapter() {
-  _getAdapter = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(pluginManager, sessionId, adapterConfigSnapshot) {
-    var cacheKey, adapterType, dataAdapterType, adapterConfig, getSubAdapter, AdapterClass, getAdapterClass, CLASS, dataAdapter, cacheEntry;
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            // cache the adapter object
-            cacheKey = adapterConfigCacheKey(adapterConfigSnapshot);
-
-            if (adapterCache[cacheKey]) {
-              _context.next = 21;
-              break;
-            }
-
-            adapterType = (adapterConfigSnapshot || {}).type;
-
-            if (adapterType) {
-              _context.next = 5;
-              break;
-            }
-
+async function getAdapter(pluginManager, sessionId, adapterConfigSnapshot) {
+    // cache the adapter object
+    const cacheKey = adapterConfigCacheKey(adapterConfigSnapshot);
+    if (!adapterCache[cacheKey]) {
+        const adapterType = (adapterConfigSnapshot || {}).type;
+        if (!adapterType) {
             throw new Error('could not determine adapter type from adapter config snapshot');
-
-          case 5:
-            dataAdapterType = pluginManager.getAdapterType(adapterType);
-
-            if (dataAdapterType) {
-              _context.next = 8;
-              break;
-            }
-
-            throw new Error("unknown data adapter type ".concat(adapterType));
-
-          case 8:
-            // instantiate the data adapter's config schema so it gets its defaults,
-            // callbacks, etc
-            adapterConfig = dataAdapterType.configSchema.create(adapterConfigSnapshot, {
-              pluginManager: pluginManager
-            });
-            getSubAdapter = getAdapter.bind(null, pluginManager, sessionId); // instantiate the adapter itself with its config schema, and a bound
-            // func that it can use to get any inner adapters
-            // (such as sequence adapters or wrapped subadapters) that it needs
-            //
-
-            AdapterClass = dataAdapterType.AdapterClass, getAdapterClass = dataAdapterType.getAdapterClass; // @ts-ignore
-
-            _context.t0 = AdapterClass;
-
-            if (_context.t0) {
-              _context.next = 16;
-              break;
-            }
-
-            _context.next = 15;
-            return getAdapterClass();
-
-          case 15:
-            _context.t0 = _context.sent;
-
-          case 16:
-            CLASS = _context.t0;
-
-            if (CLASS) {
-              _context.next = 19;
-              break;
-            }
-
+        }
+        const dataAdapterType = pluginManager.getAdapterType(adapterType);
+        if (!dataAdapterType) {
+            throw new Error(`unknown data adapter type ${adapterType}`);
+        }
+        // instantiate the data adapter's config schema so it gets its defaults,
+        // callbacks, etc
+        const adapterConfig = dataAdapterType.configSchema.create(adapterConfigSnapshot, { pluginManager });
+        const getSubAdapter = getAdapter.bind(null, pluginManager, sessionId);
+        // instantiate the adapter itself with its config schema, and a bound
+        // func that it can use to get any inner adapters
+        // (such as sequence adapters or wrapped subadapters) that it needs
+        //
+        const { AdapterClass, getAdapterClass } = dataAdapterType;
+        // @ts-ignore
+        const CLASS = AdapterClass || (await getAdapterClass());
+        if (!CLASS) {
             throw new Error('Failed to get adapter');
-
-          case 19:
-            dataAdapter = new CLASS(adapterConfig, getSubAdapter, pluginManager); // store it in our cache
-
-            adapterCache[cacheKey] = {
-              dataAdapter: dataAdapter,
-              sessionIds: new Set([sessionId])
-            };
-
-          case 21:
-            cacheEntry = adapterCache[cacheKey];
-            cacheEntry.sessionIds.add(sessionId);
-            return _context.abrupt("return", cacheEntry);
-
-          case 24:
-          case "end":
-            return _context.stop();
         }
-      }
-    }, _callee);
-  }));
-  return _getAdapter.apply(this, arguments);
+        const dataAdapter = new CLASS(adapterConfig, getSubAdapter, pluginManager);
+        // store it in our cache
+        adapterCache[cacheKey] = {
+            dataAdapter,
+            sessionIds: new Set([sessionId]),
+        };
+    }
+    const cacheEntry = adapterCache[cacheKey];
+    cacheEntry.sessionIds.add(sessionId);
+    return cacheEntry;
 }
-
+exports.getAdapter = getAdapter;
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function freeAdapterResources(specification) {
-  var deleteCount = 0;
-  var specKeys = Object.keys(specification); // if we don't specify a range, delete any adapters that are
-  // only associated with that session
-
-  if (specKeys.length === 1 && specKeys[0] === 'sessionId') {
-    var sessionId = specification.sessionId;
-    Object.entries(adapterCache).forEach(function (_ref) {
-      var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-          cacheKey = _ref2[0],
-          cacheEntry = _ref2[1];
-
-      cacheEntry.sessionIds.delete(sessionId);
-
-      if (cacheEntry.sessionIds.size === 0) {
-        deleteCount += 1;
-        delete adapterCache[cacheKey];
-      }
-    });
-  } else {
-    // otherwise call freeResources on all the cached data adapters
-    Object.values(adapterCache).forEach(function (cacheEntry) {
-      if (!cacheEntry.dataAdapter.freeResources) {
-        console.warn(cacheEntry.dataAdapter, 'does not implement freeResources');
-      } else {
-        var regions = specification.regions || (specification.region ? [specification.region] : []);
-        regions.forEach(function (region) {
-          if (region.refName !== undefined) {
-            cacheEntry.dataAdapter.freeResources(region);
-          }
+    let deleteCount = 0;
+    const specKeys = Object.keys(specification);
+    // if we don't specify a range, delete any adapters that are
+    // only associated with that session
+    if (specKeys.length === 1 && specKeys[0] === 'sessionId') {
+        const { sessionId } = specification;
+        Object.entries(adapterCache).forEach(([cacheKey, cacheEntry]) => {
+            cacheEntry.sessionIds.delete(sessionId);
+            if (cacheEntry.sessionIds.size === 0) {
+                deleteCount += 1;
+                delete adapterCache[cacheKey];
+            }
+        });
+    }
+    else {
+        // otherwise call freeResources on all the cached data adapters
+        Object.values(adapterCache).forEach(cacheEntry => {
+            if (!cacheEntry.dataAdapter.freeResources) {
+                console.warn(cacheEntry.dataAdapter, 'does not implement freeResources');
+            }
+            else {
+                const regions = specification.regions ||
+                    (specification.region ? [specification.region] : []);
+                regions.forEach((region) => {
+                    if (region.refName !== undefined) {
+                        cacheEntry.dataAdapter.freeResources(region);
+                    }
+                });
+            }
         });
-      }
-    });
-  }
-
-  return deleteCount;
+    }
+    return deleteCount;
 }
-
+exports.freeAdapterResources = freeAdapterResources;
 function clearAdapterCache() {
-  adapterCache = {};
-}
+    adapterCache = {};
+}
+exports.clearAdapterCache = clearAdapterCache;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.0.1",
+  "version": "2.1.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -25,8 +25,7 @@
     "clean": "rimraf dist tsconfig.build.tsbuildinfo",
     "prebuild": "yarn clean",
     "prepack": "yarn build",
-    "build": "babel . --root-mode upward --out-dir dist --extensions '.ts,.js,.tsx,.jsx' && cp package.json README.md ../../LICENSE dist/",
-    "postbuild": "tsc -b tsconfig.build.json"
+    "build": "tsc -b tsconfig.build.json && cp package.json README.md ../../LICENSE dist/"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
@@ -43,7 +42,7 @@
     "dompurify": "^2.3.4",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
-    "generic-filehandle": "^2.2.2",
+    "generic-filehandle": "^3.0.0",
     "http-range-fetcher": "^1.4.0",
     "is-object": "^1.0.1",
     "jexl": "^2.3.0",
@@ -74,5 +73,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "ed935bf5612af3818abdc8ef52d100d5d81d33a2"
+  "gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
 }

package/pluggableElementTypes/AdapterType.js

@@ -1,81 +1,26 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
-
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
-
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _PluggableElementBase2 = _interopRequireDefault(require("./PluggableElementBase"));
-
-function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
-
-function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
-
-var AdapterType = /*#__PURE__*/function (_PluggableElementBase) {
-  (0, _inherits2.default)(AdapterType, _PluggableElementBase);
-
-  var _super = _createSuper(AdapterType);
-
-  function AdapterType(stuff) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, AdapterType);
-    _this = _super.call(this, stuff);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "AdapterClass", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "getAdapterClass", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "configSchema", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "adapterCapabilities", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "adapterMetadata", void 0);
-
-    if ('AdapterClass' in stuff) {
-      _this.AdapterClass = stuff.AdapterClass;
-      _this.getAdapterClass = /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                return _context.abrupt("return", stuff.AdapterClass);
-
-              case 1:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee);
-      }));
-    } else if ('getAdapterClass' in stuff) {
-      _this.getAdapterClass = stuff.getAdapterClass;
-    } else {
-      throw new Error("no AdapterClass or getAdapterClass is defined for adapter type ".concat(_this.name));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint curly:error */
+const PluggableElementBase_1 = __importDefault(require("./PluggableElementBase"));
+class AdapterType extends PluggableElementBase_1.default {
+    constructor(stuff) {
+        super(stuff);
+        if ('AdapterClass' in stuff) {
+            this.AdapterClass = stuff.AdapterClass;
+            this.getAdapterClass = async () => stuff.AdapterClass;
+        }
+        else if ('getAdapterClass' in stuff) {
+            this.getAdapterClass = stuff.getAdapterClass;
+        }
+        else {
+            throw new Error(`no AdapterClass or getAdapterClass is defined for adapter type ${this.name}`);
+        }
+        this.configSchema = stuff.configSchema;
+        this.adapterCapabilities = stuff.adapterCapabilities || [];
+        this.adapterMetadata = stuff.adapterMetadata;
     }
-
-    _this.configSchema = stuff.configSchema;
-    _this.adapterCapabilities = stuff.adapterCapabilities || [];
-    _this.adapterMetadata = stuff.adapterMetadata;
-    return _this;
-  }
-
-  return (0, _createClass2.default)(AdapterType);
-}(_PluggableElementBase2.default);
-
-exports.default = AdapterType;
+}
+exports.default = AdapterType;

package/pluggableElementTypes/AddTrackWorkflowType.d.ts

@@ -0,0 +1,17 @@
+import React from 'react';
+import { IAnyModelType } from 'mobx-state-tree';
+import PluggableElementBase from './PluggableElementBase';
+declare type BasicComponent = React.ComponentType<{
+    model: any;
+}>;
+declare type AddTrackWorkflowComponent = React.LazyExoticComponent<BasicComponent> | BasicComponent;
+export default class AddTrackWorkflow extends PluggableElementBase {
+    ReactComponent: AddTrackWorkflowComponent;
+    stateModel: IAnyModelType;
+    constructor(stuff: {
+        name: string;
+        ReactComponent: AddTrackWorkflowComponent;
+        stateModel: IAnyModelType;
+    });
+}
+export {};

package/pluggableElementTypes/AddTrackWorkflowType.js

@@ -0,0 +1,20 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const PluggableElementBase_1 = __importDefault(require("./PluggableElementBase"));
+class AddTrackWorkflow extends PluggableElementBase_1.default {
+    constructor(stuff) {
+        super(stuff);
+        this.ReactComponent = stuff.ReactComponent;
+        this.stateModel = stuff.stateModel;
+        if (!this.ReactComponent) {
+            throw new Error(`no ReactComponent defined for view ${this.name}`);
+        }
+        if (!this.stateModel) {
+            throw new Error(`no stateModel defined for view ${this.name}`);
+        }
+    }
+}
+exports.default = AddTrackWorkflow;