@jbrowse/core 1.4.1 → 1.5.2

package/data_adapters/BaseAdapter.test.js

@@ -24,6 +24,8 @@ var _rxjs = require("../util/rxjs");
 
 var _simpleFeature = _interopRequireDefault(require("../util/simpleFeature"));
 
+var _configurationSchema = require("../configuration/configurationSchema");
+
 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; } }
@@ -83,7 +85,7 @@ describe('base data adapter', function () {
               return Adapter;
             }(_BaseAdapter.BaseFeatureDataAdapter);
 
-            adapter = new Adapter();
+            adapter = new Adapter((0, _configurationSchema.ConfigurationSchema)('empty', {}).create());
             features = adapter.getFeatures({
               assemblyName: 'volvox',
               refName: 'ctgA',
@@ -162,7 +164,7 @@ describe('base data adapter', function () {
               return Adapter;
             }(_BaseAdapter.BaseFeatureDataAdapter);
 
-            adapter = new Adapter();
+            adapter = new Adapter((0, _configurationSchema.ConfigurationSchema)('empty', {}).create());
             features = adapter.getFeatures({
               assemblyName: 'volvox',
               refName: 'ctgA',

package/data_adapters/CytobandAdapter.d.ts

@@ -0,0 +1,8 @@
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { BaseAdapter } from './BaseAdapter';
+declare const configSchema: import("../configuration/configurationSchema").AnyConfigurationSchemaType;
+declare class CytobandAdapter extends BaseAdapter {
+    getData(): Promise<SimpleFeature[]>;
+    freeResources(): void;
+}
+export { configSchema, CytobandAdapter as DataAdapter };

package/data_adapters/CytobandAdapter.js

@@ -0,0 +1,128 @@
+"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("@jbrowse/core/util/simpleFeature"));
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _io = require("@jbrowse/core/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
+});
+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;

package/data_adapters/dataAdapterCache.js

@@ -5,9 +5,9 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.getAdapter = getAdapter;
-exports.freeAdapterResources = freeAdapterResources;
 exports.clearAdapterCache = clearAdapterCache;
+exports.freeAdapterResources = freeAdapterResources;
+exports.getAdapter = getAdapter;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -113,7 +113,7 @@ function _getAdapter() {
             throw new Error('Failed to get adapter');
 
           case 19:
-            dataAdapter = new CLASS(adapterConfig, getSubAdapter); // store it in our cache
+            dataAdapter = new CLASS(adapterConfig, getSubAdapter, pluginManager); // store it in our cache
 
             adapterCache[cacheKey] = {
               dataAdapter: dataAdapter,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.4.1",
+  "version": "1.5.2",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -31,7 +31,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.15.3",
-    "@material-ui/icons": "^4.0.0",
+    "@material-ui/icons": "^4.0.1",
     "abortable-promise-cache": "^1.1.3",
     "base64-js": "^1.3.0",
     "canvas": "^2.8.0",
@@ -44,18 +44,19 @@
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
     "file-uri-to-path": "^1.0.0",
-    "generic-filehandle": "^2.0.1",
+    "generic-filehandle": "^2.2.2",
     "http-range-fetcher": "^1.2.2",
     "is-object": "^1.0.1",
     "jexl": "^2.3.0",
     "json-stable-stringify": "^1.0.1",
+    "librpc-web-mod": "^1.1.4",
     "load-script2": "^2.0.5",
     "object.fromentries": "^2.0.0",
-    "pako": "^1.0.10",
     "rbush": "^3.0.1",
     "react-error-boundary": "^3.0.0",
     "react-intersection-observer": "^8.31.0",
     "react-measure": "^2.3.0",
+    "sanitize-filename": "^1.6.3",
     "shortid": "^2.2.13",
     "svg-path-generator": "^1.1.0",
     "tenacious-fetch": "^2.1.0",
@@ -63,8 +64,8 @@
   },
   "peerDependencies": {
     "@material-ui/core": "^4.12.2",
-    "@material-ui/data-grid": "^4.0.0-alpha.37",
     "@material-ui/lab": "^4.0.0-alpha.45",
+    "@mui/x-data-grid": "^4.0.0",
     "mobx": "^5.0.0",
     "mobx-react": "^6.0.0",
     "mobx-state-tree": "^3.14.1",
@@ -77,5 +78,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "42c7e1b98bb0d16fa440a8a8f500a1030607f16c"
+  "gitHead": "94fdfbc34787ab8f12a87e00038da74b247b42fa"
 }

package/pluggableElementTypes/AdapterType.d.ts

@@ -1,15 +1,23 @@
 import PluggableElementBase from './PluggableElementBase';
 import { AnyConfigurationSchemaType } from '../configuration/configurationSchema';
 import { AnyAdapter } from '../data_adapters/BaseAdapter';
+export declare type AdapterMetadata = {
+    category: string | null;
+    hiddenFromGUI: boolean | null;
+    displayName: string | null;
+    description: string | null;
+};
 export default class AdapterType extends PluggableElementBase {
     AdapterClass?: AnyAdapter;
-    getAdapterClass?: () => Promise<AnyAdapter>;
+    getAdapterClass: () => Promise<AnyAdapter>;
     configSchema: AnyConfigurationSchemaType;
     adapterCapabilities: string[];
+    adapterMetadata?: AdapterMetadata;
     constructor(stuff: {
         name: string;
         configSchema: AnyConfigurationSchemaType;
         adapterCapabilities?: string[];
+        adapterMetadata?: AdapterMetadata;
     } & ({
         AdapterClass: AnyAdapter;
     } | {

package/pluggableElementTypes/AdapterType.js

@@ -7,6 +7,10 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -39,9 +43,24 @@ var AdapterType = /*#__PURE__*/function (_PluggableElementBase) {
     (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 {
@@ -50,6 +69,7 @@ var AdapterType = /*#__PURE__*/function (_PluggableElementBase) {
 
     _this.configSchema = stuff.configSchema;
     _this.adapterCapabilities = stuff.adapterCapabilities || [];
+    _this.adapterMetadata = stuff.adapterMetadata;
     return _this;
   }
 

package/pluggableElementTypes/InternetAccountType.d.ts

@@ -0,0 +1,12 @@
+import { IAnyModelType } from 'mobx-state-tree';
+import PluggableElementBase from './PluggableElementBase';
+import { AnyConfigurationSchemaType } from '../configuration/configurationSchema';
+export default class InternetAccountType extends PluggableElementBase {
+    stateModel: IAnyModelType;
+    configSchema: AnyConfigurationSchemaType;
+    constructor(stuff: {
+        name: string;
+        stateModel: IAnyModelType;
+        configSchema: AnyConfigurationSchemaType;
+    });
+}

package/pluggableElementTypes/InternetAccountType.js

@@ -0,0 +1,64 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.default = void 0;
+
+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"));
+
+var _mstReflection = require("../util/mst-reflection");
+
+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 InternetAccountType = /*#__PURE__*/function (_PluggableElementBase) {
+  (0, _inherits2.default)(InternetAccountType, _PluggableElementBase);
+
+  var _super = _createSuper(InternetAccountType);
+
+  function InternetAccountType(stuff) {
+    var _this;
+
+    (0, _classCallCheck2.default)(this, InternetAccountType);
+    _this = _super.call(this, stuff);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "stateModel", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "configSchema", void 0);
+    _this.stateModel = stuff.stateModel;
+    _this.configSchema = stuff.configSchema;
+
+    if (!_this.stateModel) {
+      throw new Error("no stateModel defined for internet account type ".concat(_this.name));
+    }
+
+    if (!_this.configSchema) {
+      throw new Error("no configSchema provided for internet account type ".concat(_this.name));
+    }
+
+    if (!(0, _mstReflection.getDefaultValue)(_this.configSchema).type) {
+      var name = _this.configSchema ? _this.configSchema.name : 'UNKNOWN';
+      throw new Error("".concat(name, " is not explicitlyTyped"));
+    }
+
+    return _this;
+  }
+
+  return InternetAccountType;
+}(_PluggableElementBase2.default);
+
+exports.default = InternetAccountType;

package/pluggableElementTypes/PluggableElementBase.d.ts

@@ -1,7 +1,6 @@
 export default abstract class PluggableElementBase {
-    [key: string]: unknown;
     name: string;
-    constructor({ name }: {
+    constructor(args: {
         name: string;
     });
 }

package/pluggableElementTypes/PluggableElementBase.js

@@ -11,11 +11,10 @@ var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/cl
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
-var PluggableElementBase = function PluggableElementBase(_ref) {
-  var name = _ref.name;
+var PluggableElementBase = function PluggableElementBase(args) {
   (0, _classCallCheck2.default)(this, PluggableElementBase);
   (0, _defineProperty2.default)(this, "name", '');
-  this.name = name;
+  this.name = args.name;
 };
 
 exports.default = PluggableElementBase;

package/pluggableElementTypes/RpcMethodType.d.ts

@@ -1,5 +1,6 @@
 import PluginManager from '../PluginManager';
 import PluggableElementBase from './PluggableElementBase';
+import { UriLocation } from '../util/types';
 import { RemoteAbortSignal } from '../rpc/remoteAbortSignals';
 export declare type RpcMethodConstructor = new (pm: PluginManager) => RpcMethodType;
 export default abstract class RpcMethodType extends PluggableElementBase {
@@ -7,6 +8,7 @@ export default abstract class RpcMethodType extends PluggableElementBase {
     name: string;
     constructor(pluginManager: PluginManager);
     serializeArguments(args: {}, _rpcDriverClassName: string): Promise<{}>;
+    serializeNewAuthArguments(location: UriLocation): Promise<UriLocation>;
     deserializeArguments<SERIALIZED extends {
         signal?: RemoteAbortSignal;
         blobMap?: Record<string, File>;
@@ -18,4 +20,5 @@ export default abstract class RpcMethodType extends PluggableElementBase {
     abstract execute(serializedArgs: unknown, rpcDriverClassName: string): Promise<unknown>;
     serializeReturn(originalReturn: unknown, _args: unknown, _rpcDriverClassName: string): Promise<unknown>;
     deserializeReturn(serializedReturn: unknown, _args: unknown, _rpcDriverClassName: string): Promise<unknown>;
+    private augmentLocationObjects;
 }