@jbrowse/plugin-sequence 1.7.9 → 2.0.0

package/dist/DivSequenceRenderer/components/DivSequenceRendering.test.js

@@ -1,245 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-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 _react = _interopRequireDefault(require("react"));
-
-var _propTypes = _interopRequireDefault(require("prop-types"));
-
-var _react2 = require("@testing-library/react");
-
-var _ui = require("@jbrowse/core/ui");
-
-var _PrecomputedLayout = _interopRequireDefault(require("@jbrowse/core/util/layouts/PrecomputedLayout"));
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _core = require("@material-ui/core");
-
-var _DivSequenceRendering = _interopRequireDefault(require("./DivSequenceRendering"));
-
-var _configSchema = _interopRequireDefault(require("../configSchema"));
-
-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; } }
-
-function Rendering(props) {
-  return /*#__PURE__*/_react.default.createElement(_core.ThemeProvider, {
-    theme: (0, _ui.createJBrowseTheme)()
-  }, /*#__PURE__*/_react.default.createElement(_DivSequenceRendering.default, props));
-}
-
-var ErrorCatcher = /*#__PURE__*/function (_React$Component) {
-  (0, _inherits2.default)(ErrorCatcher, _React$Component);
-
-  var _super = _createSuper(ErrorCatcher);
-
-  function ErrorCatcher(props) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, ErrorCatcher);
-    _this = _super.call(this, props);
-    _this.state = {
-      hasError: false,
-      errorText: ''
-    };
-    return _this;
-  }
-
-  (0, _createClass2.default)(ErrorCatcher, [{
-    key: "render",
-    value: function render() {
-      var _this$state = this.state,
-          hasError = _this$state.hasError,
-          errorText = _this$state.errorText;
-
-      if (hasError) {
-        // You can render any custom fallback UI
-        return /*#__PURE__*/_react.default.createElement("h1", {
-          className: "error"
-        }, errorText);
-      }
-
-      var children = this.props.children;
-      return children;
-    }
-  }], [{
-    key: "getDerivedStateFromError",
-    value: function getDerivedStateFromError(error) {
-      // Update state so the next render will show the fallback UI.
-      return {
-        hasError: true,
-        errorText: String(error)
-      };
-    }
-  }]);
-  return ErrorCatcher;
-}(_react.default.Component);
-
-ErrorCatcher.propTypes = {
-  children: _propTypes.default.node.isRequired
-};
-describe('<DivSequenceRendering />', function () {
-  // This just keeps our testing logs clean by not displaying `console.error`s
-  // from errors we intentionally throw in our tests. Hopefully React will
-  // someday provide a way for error boundaries to prevent error logging so we
-  // won't have to do this: https://github.com/facebook/react/issues/15069
-  var originalError = console.error;
-  beforeAll(function () {
-    console.error = function () {
-      for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-        args[_key] = arguments[_key];
-      }
-
-      if (args[0].includes('feature one did not contain a valid `seq` attribute') || args[0].includes('The above error occurred in the <SequenceDivs> component')) {
-        return;
-      }
-
-      originalError.call.apply(originalError, [console].concat(args));
-    };
-  });
-  afterAll(function () {
-    console.error = originalError;
-  });
-  it('renders with no features', function () {
-    var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(Rendering, {
-      width: 500,
-      height: 500,
-      regions: [{
-        refName: 'zonk',
-        start: 0,
-        end: 300
-      }],
-      layout: new _PrecomputedLayout.default({
-        rectangles: {},
-        totalHeight: 20
-      }),
-      config: _configSchema.default.create(),
-      bpPerPx: 3
-    })),
-        container = _render.container;
-
-    expect(container).toMatchSnapshot();
-  });
-  it('renders with one, zoomed way out', function () {
-    var _render2 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(Rendering, {
-      width: 500,
-      height: 500,
-      regions: [{
-        refName: 'zonk',
-        start: 0,
-        end: 1000
-      }],
-      features: new Map([['one', new _simpleFeature.default({
-        uniqueId: 'one',
-        start: 1,
-        end: 3,
-        seq: 'AB'
-      })]]),
-      config: _configSchema.default.create({}),
-      bpPerPx: 3
-    })),
-        container = _render2.container;
-
-    expect(container).toMatchSnapshot();
-  });
-  it('renders with one feature with no seq, zoomed in, should throw', function () {
-    var _render3 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(ErrorCatcher, null, /*#__PURE__*/_react.default.createElement(Rendering, {
-      width: 500,
-      height: 500,
-      regions: [{
-        refName: 'zonk',
-        start: 0,
-        end: 1000
-      }],
-      features: new Map([['one', new _simpleFeature.default({
-        uniqueId: 'one',
-        start: 1,
-        end: 3
-      })]]),
-      config: _configSchema.default.create({}),
-      bpPerPx: 0.05
-    }))),
-        container = _render3.container;
-
-    expect(container).toMatchSnapshot();
-  });
-  it('renders with one feature with an incorrect seq, zoomed in, should throw', function () {
-    var _render4 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(ErrorCatcher, null, /*#__PURE__*/_react.default.createElement(Rendering, {
-      width: 500,
-      height: 500,
-      regions: [{
-        refName: 'zonk',
-        start: 0,
-        end: 1000
-      }],
-      features: new Map([['one', new _simpleFeature.default({
-        uniqueId: 'one',
-        start: 1,
-        end: 3,
-        seq: 'ABC'
-      })]]),
-      config: _configSchema.default.create({}),
-      bpPerPx: 0.05
-    }))),
-        container = _render4.container;
-
-    expect(container).toMatchSnapshot();
-  });
-  it('renders with one feature with a correct seq, zoomed in, should render nicely', function () {
-    var _render5 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(Rendering, {
-      width: 500,
-      height: 500,
-      regions: [{
-        refName: 'zonk',
-        start: 0,
-        end: 1000
-      }],
-      features: new Map([['one', new _simpleFeature.default({
-        uniqueId: 'one',
-        start: 1,
-        end: 10,
-        seq: 'ABCDEFGHI'
-      })]]),
-      config: _configSchema.default.create({}),
-      bpPerPx: 0.05
-    })),
-        container = _render5.container;
-
-    expect(container).toMatchSnapshot();
-  });
-  it('renders with one feature reversed with a correct seq, zoomed in, should render nicely', function () {
-    var _render6 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(Rendering, {
-      width: 500,
-      height: 500,
-      regions: [{
-        refName: 'zonk',
-        start: 0,
-        end: 1000,
-        reversed: true
-      }],
-      features: new Map([['one', new _simpleFeature.default({
-        uniqueId: 'one',
-        start: 1,
-        end: 10,
-        seq: 'ABCDEFGHI'
-      })]]),
-      config: _configSchema.default.create({}),
-      bpPerPx: 0.05
-    })),
-        container = _render6.container;
-
-    expect(container).toMatchSnapshot();
-  });
-});

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.test.js

@@ -1,81 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _operators = require("rxjs/operators");
-
-var _IndexedFastaAdapter = _interopRequireDefault(require("./IndexedFastaAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch sequence from volvox.fa', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, features, featuresArray, features2, featuresArray2, features3, data, featuresArray3;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          adapter = new _IndexedFastaAdapter.default(_configSchema.default.create({
-            fastaLocation: {
-              localPath: require.resolve('../../test_data/volvox.fa'),
-              locationType: 'LocalPathLocation'
-            },
-            faiLocation: {
-              localPath: require.resolve('../../test_data/volvox.fa.fai'),
-              locationType: 'LocalPathLocation'
-            },
-            metadataLocation: {
-              localPath: require.resolve('../../test_data/hello.txt'),
-              locationType: 'LocalPathLocation'
-            }
-          }));
-          features = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context.sent;
-          expect(featuresArray).toMatchSnapshot();
-          features2 = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 45000,
-            end: 55000
-          });
-          _context.next = 9;
-          return features2.pipe((0, _operators.toArray)()).toPromise();
-
-        case 9:
-          featuresArray2 = _context.sent;
-          expect(featuresArray2[0].get('end')).toBe(50001);
-          features3 = adapter.getFeatures({
-            refName: 'ctgC',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 14;
-          return adapter.getHeader();
-
-        case 14:
-          data = _context.sent;
-          expect(data === null || data === void 0 ? void 0 : data.trim()).toBe('hello world');
-          _context.next = 18;
-          return features3.pipe((0, _operators.toArray)()).toPromise();
-
-        case 18:
-          featuresArray3 = _context.sent;
-          expect(featuresArray3).toMatchSnapshot();
-
-        case 20:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/TwoBitAdapter/TwoBitAdapter.test.js

@@ -1,94 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _operators = require("rxjs/operators");
-
-var _TwoBitAdapter = _interopRequireDefault(require("./TwoBitAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch features from volvox.2bit', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, features, featuresArray, features2, featuresArray2, features3, featuresArray3;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          adapter = new _TwoBitAdapter.default(_configSchema.default.create({
-            twoBitLocation: {
-              localPath: require.resolve('../../test_data/volvox.2bit'),
-              locationType: 'LocalPathLocation'
-            }
-          }));
-          features = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context.sent;
-          expect(featuresArray).toMatchSnapshot();
-          features2 = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 45000,
-            end: 55000
-          });
-          _context.next = 9;
-          return features2.pipe((0, _operators.toArray)()).toPromise();
-
-        case 9:
-          featuresArray2 = _context.sent;
-          expect(featuresArray2[0].get('end')).toBe(50001);
-          features3 = adapter.getFeatures({
-            refName: 'ctgC',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 14;
-          return features3.pipe((0, _operators.toArray)()).toPromise();
-
-        case 14:
-          featuresArray3 = _context.sent;
-          expect(featuresArray3).toMatchSnapshot();
-
-        case 16:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));
-test('adapter can fetch regions from with chrom.sizes', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var adapter;
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          adapter = new _TwoBitAdapter.default(_configSchema.default.create({
-            chromSizesLocation: {
-              localPath: require.resolve('../../test_data/volvox.chrom.sizes'),
-              locationType: 'LocalPathLocation'
-            }
-          }));
-          _context2.t0 = expect;
-          _context2.next = 4;
-          return adapter.getRegions();
-
-        case 4:
-          _context2.t1 = _context2.sent;
-          (0, _context2.t0)(_context2.t1).toMatchSnapshot();
-
-        case 6:
-        case "end":
-          return _context2.stop();
-      }
-    }
-  }, _callee2);
-})));

package/dist/declare.d.js

@@ -1 +0,0 @@
-"use strict";

package/dist/index.test.js

@@ -1,29 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _ = _interopRequireDefault(require("."));
-
-test('plugin in a stock JBrowse', function () {
-  console.warn = jest.fn();
-  var pluginManager = new _PluginManager.default([new _.default()]);
-  pluginManager.createPluggableElements();
-  pluginManager.configure();
-  expect(function () {
-    return pluginManager.addPlugin(new _.default());
-  }).toThrow(/JBrowse already configured, cannot add plugins/);
-  var TwoBitAdapter = pluginManager.getAdapterType('TwoBitAdapter');
-  var config = TwoBitAdapter.configSchema.create({
-    type: 'TwoBitAdapter'
-  });
-  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
-  var IndexedFastaAdapter = pluginManager.getAdapterType('IndexedFastaAdapter');
-  var config2 = IndexedFastaAdapter.configSchema.create({
-    type: 'IndexedFastaAdapter'
-  });
-  expect((0, _mobxStateTree.getSnapshot)(config2)).toMatchSnapshot();
-});