@jbrowse/plugin-data-management 1.6.7 → 1.7.0

package/dist/AddTrackWidget/components/AddTrackWidget.js

@@ -0,0 +1,215 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _react = _interopRequireWildcard(require("react"));
+
+var _core = require("@material-ui/core");
+
+var _util = require("@jbrowse/core/util");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _mobxReact = require("mobx-react");
+
+var _lab = require("@material-ui/lab");
+
+var _ConfirmTrack = _interopRequireDefault(require("./ConfirmTrack"));
+
+var _TrackSourceSelect = _interopRequireDefault(require("./TrackSourceSelect"));
+
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+
+var useStyles = (0, _core.makeStyles)(function (theme) {
+  return {
+    root: {
+      marginTop: theme.spacing(1)
+    },
+    stepper: {
+      backgroundColor: theme.palette.background["default"]
+    },
+    button: {
+      marginTop: theme.spacing(1),
+      marginRight: theme.spacing(1)
+    },
+    actionsContainer: {
+      marginBottom: theme.spacing(2)
+    },
+    stepContent: {
+      margin: theme.spacing(1)
+    },
+    alertContainer: {
+      padding: "".concat(theme.spacing(2), "px 0px ").concat(theme.spacing(2), "px 0px")
+    }
+  };
+});
+var steps = ['Enter track data', 'Confirm track type'];
+
+function AddTrackWidget(_ref) {
+  var model = _ref.model;
+
+  var _useState = (0, _react.useState)(0),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      activeStep = _useState2[0],
+      setActiveStep = _useState2[1];
+
+  var classes = useStyles();
+  var session = (0, _util.getSession)(model);
+  var assembly = model.assembly,
+      trackAdapter = model.trackAdapter,
+      trackData = model.trackData,
+      trackName = model.trackName,
+      trackType = model.trackType;
+
+  var _useState3 = (0, _react.useState)(),
+      _useState4 = (0, _slicedToArray2["default"])(_useState3, 2),
+      trackErrorMessage = _useState4[0],
+      setTrackErrorMessage = _useState4[1];
+
+  function getStepContent(step) {
+    switch (step) {
+      case 0:
+        return /*#__PURE__*/_react["default"].createElement(_TrackSourceSelect["default"], {
+          model: model
+        });
+
+      case 1:
+        return /*#__PURE__*/_react["default"].createElement(_ConfirmTrack["default"], {
+          model: model
+        });
+
+      default:
+        return /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Unknown step");
+    }
+  }
+
+  function handleNext() {
+    return _handleNext.apply(this, arguments);
+  }
+
+  function _handleNext() {
+    _handleNext = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+      var trackId, assemblyInstance;
+      return _regenerator["default"].wrap(function _callee$(_context) {
+        while (1) {
+          switch (_context.prev = _context.next) {
+            case 0:
+              if (!(activeStep !== steps.length - 1)) {
+                _context.next = 3;
+                break;
+              }
+
+              setActiveStep(activeStep + 1);
+              return _context.abrupt("return");
+
+            case 3:
+              trackId = "".concat(trackName.toLowerCase().replace(/ /g, '_'), "-").concat(Date.now()).concat(session.adminMode ? '' : '-sessionTrack');
+              assemblyInstance = session.assemblyManager.get(assembly);
+
+              if (trackAdapter && trackAdapter.type !== 'UNKNOWN') {
+                // @ts-ignore
+                session.addTrackConf({
+                  trackId: trackId,
+                  type: trackType,
+                  name: trackName,
+                  assemblyNames: [assembly],
+                  adapter: _objectSpread(_objectSpread({}, trackAdapter), {}, {
+                    sequenceAdapter: (0, _configuration.getConf)(assemblyInstance, ['sequence', 'adapter'])
+                  })
+                });
+
+                if (model.view) {
+                  model.view.showTrack(trackId);
+                } else {
+                  session.notify('Open a new view, or use the track selector in an existing view, to view this track', 'info');
+                }
+
+                model.clearData(); // @ts-ignore
+
+                session.hideWidget(model);
+              } else {
+                setTrackErrorMessage('Failed to add track.\nThe configuration of this file is not currently supported.');
+              }
+
+            case 6:
+            case "end":
+              return _context.stop();
+          }
+        }
+      }, _callee);
+    }));
+    return _handleNext.apply(this, arguments);
+  }
+
+  function handleBack() {
+    setTrackErrorMessage(undefined);
+    setActiveStep(activeStep - 1);
+  }
+
+  function isNextDisabled() {
+    switch (activeStep) {
+      case 0:
+        return !trackData;
+
+      case 1:
+        return !(trackName && trackType && trackAdapter !== null && trackAdapter !== void 0 && trackAdapter.type && assembly);
+
+      default:
+        return true;
+    }
+  }
+
+  return /*#__PURE__*/_react["default"].createElement("div", {
+    className: classes.root
+  }, /*#__PURE__*/_react["default"].createElement(_core.Stepper, {
+    className: classes.stepper,
+    activeStep: activeStep,
+    orientation: "vertical"
+  }, steps.map(function (label, idx) {
+    return /*#__PURE__*/_react["default"].createElement(_core.Step, {
+      key: label
+    }, /*#__PURE__*/_react["default"].createElement(_core.StepLabel, null, label), /*#__PURE__*/_react["default"].createElement(_core.StepContent, null, getStepContent(idx), /*#__PURE__*/_react["default"].createElement("div", {
+      className: classes.actionsContainer
+    }, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+      disabled: activeStep === 0,
+      onClick: handleBack,
+      className: classes.button
+    }, "Back"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+      disabled: isNextDisabled(),
+      variant: "contained",
+      color: "primary",
+      onClick: handleNext,
+      className: classes.button,
+      "data-testid": "addTrackNextButton"
+    }, activeStep === steps.length - 1 ? 'Add' : 'Next')), trackErrorMessage ? /*#__PURE__*/_react["default"].createElement("div", {
+      className: classes.alertContainer
+    }, /*#__PURE__*/_react["default"].createElement(_lab.Alert, {
+      severity: "error"
+    }, trackErrorMessage)) : null));
+  })));
+}
+
+var _default = (0, _mobxReact.observer)(AddTrackWidget);
+
+exports["default"] = _default;

package/dist/AddTrackWidget/components/AddTrackWidget.test.js

@@ -0,0 +1,218 @@
+"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 _react = _interopRequireDefault(require("react"));
+
+var _react2 = require("@testing-library/react");
+
+var _rootModel = require("@jbrowse/web/src/rootModel");
+
+var _AddTrackWidget = _interopRequireDefault(require("./AddTrackWidget"));
+
+jest.mock('@jbrowse/web/src/makeWorkerInstance', function () {
+  return function () {};
+});
+describe('<AddTrackWidget />', function () {
+  var session;
+  var model;
+  beforeAll(function () {
+    session = (0, _rootModel.createTestSession)();
+    session.addAssemblyConf({
+      name: 'volMyt1',
+      sequence: {
+        trackId: 'ref0',
+        type: 'ReferenceSequenceTrack',
+        adapter: {
+          type: 'FromConfigSequenceAdapter',
+          features: [{
+            refName: 'ctgA',
+            uniqueId: 'firstId',
+            start: 0,
+            end: 1000,
+            seq: 'cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgattatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctgaattgagaactcgagcgggggctaggcaaattctgattcagcctgacttctcttggaaccctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagaccaacctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctccttggtcgctccgttgtacccaggctactttgaaagagcgcagaatacttagacggtatcgatcatggtagcatagcattctgataacatgtatggagttcgaacatccgtctggggccggacggtccgtttgaggttggttgatctgggtgatagtcagcaagatagacgttagataacaaattaaaggattttaccttagattgcgactagtacaacggtacatcggtgattcgcgctctactagatcacgctatgggtaccataaacaaacggtggaccttctcaagctggttgacgcctcagcaacataggcttcctcctccacgcatctcagcataaaaggcttataaactgcttctttgtgccagagcaactcaattaagcccttggtaccgtgggcacgcattctgtcacggtgaccaactgttcatcctgaatcgccgaatgggactatttggtacaggaatcaagcggatggcactactgcagcttatttacgacggtattcttaaagtttttaagacaatgtatttcatgggtagttcggtttgttttattgctacacaggctcttgtagacgacctacttagcactacgg'
+          }]
+        }
+      }
+    });
+    session.addTrackConf({
+      trackId: 'i3jUPmrgMOS',
+      type: 'FeatureTrack',
+      name: 'Filter Test',
+      assemblyNames: ['volMyt1'],
+      adapter: {
+        type: 'FromConfigAdapter',
+        features: [{
+          uniqueId: 'one',
+          refName: 'ctgA',
+          start: 100,
+          end: 101,
+          type: 'foo',
+          name: 'Boris',
+          note: 'note for boris'
+        }, {
+          uniqueId: 'two',
+          refName: 'ctgA',
+          start: 110,
+          end: 111,
+          type: 'bar',
+          name: 'Theresa',
+          note: 'note for theresa'
+        }, {
+          uniqueId: 'three',
+          refName: 'ctgA',
+          start: 120,
+          end: 121,
+          type: 'baz',
+          name: 'Nigel',
+          note: 'note for nigel'
+        }, {
+          uniqueId: 'four',
+          refName: 'ctgA',
+          start: 130,
+          end: 131,
+          type: 'quux',
+          name: 'Geoffray',
+          note: 'note for geoffray'
+        }]
+      },
+      filterAttributes: ['type', 'start', 'end']
+    });
+    var view = session.addView('LinearGenomeView', {
+      displayedRegions: [{
+        assemblyName: 'volMyt1',
+        refName: 'ctgA',
+        start: 0,
+        end: 1000
+      }]
+    });
+    model = session.addWidget('AddTrackWidget', 'addTrackWidget', {
+      view: view.id
+    });
+  });
+  afterEach(_react2.cleanup);
+  it('renders', function () {
+    var _render = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_AddTrackWidget["default"], {
+      model: model
+    })),
+        container = _render.container;
+
+    expect(container.firstChild).toMatchSnapshot();
+  });
+  it('adds a track', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+    var _render2, getByTestId, getAllByTestId, findByText, findAllByText, bamAdapter, trackTypeSelect, featureTrack, assemblyNameSelect, volMyt1;
+
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            _render2 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_AddTrackWidget["default"], {
+              model: model
+            })), getByTestId = _render2.getByTestId, getAllByTestId = _render2.getAllByTestId, findByText = _render2.findByText, findAllByText = _render2.findAllByText;
+            expect(session.sessionTracks.length).toBe(1);
+
+            _react2.fireEvent.change(getAllByTestId('urlInput')[0], {
+              target: {
+                value: 'test.txt'
+              }
+            });
+
+            _react2.fireEvent.click(getByTestId('addTrackNextButton'));
+
+            _react2.fireEvent.mouseDown(getByTestId('adapterTypeSelect'));
+
+            _context.next = 7;
+            return findByText('BamAdapter');
+
+          case 7:
+            bamAdapter = _context.sent;
+
+            _react2.fireEvent.click(bamAdapter);
+
+            _react2.fireEvent.change(getByTestId('trackNameInput'), {
+              target: {
+                value: 'Test track name'
+              }
+            });
+
+            trackTypeSelect = getByTestId('trackTypeSelect');
+
+            _react2.fireEvent.mouseDown(trackTypeSelect);
+
+            _context.next = 14;
+            return findByText('FeatureTrack');
+
+          case 14:
+            featureTrack = _context.sent;
+
+            _react2.fireEvent.click(featureTrack);
+
+            assemblyNameSelect = getByTestId('assemblyNameSelect');
+
+            _react2.fireEvent.mouseDown(assemblyNameSelect);
+
+            _context.next = 20;
+            return findAllByText('volMyt1');
+
+          case 20:
+            volMyt1 = _context.sent;
+
+            _react2.fireEvent.click(volMyt1[1]);
+
+            _react2.fireEvent.click(getByTestId('addTrackNextButton'));
+
+            expect(session.sessionTracks.length).toBe(2);
+
+          case 24:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  })));
+  xit('fails to add a track', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+    var _render3, getByTestId, getAllByTestId, findByText, chrom;
+
+    return _regenerator["default"].wrap(function _callee2$(_context2) {
+      while (1) {
+        switch (_context2.prev = _context2.next) {
+          case 0:
+            _render3 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_AddTrackWidget["default"], {
+              model: model
+            })), getByTestId = _render3.getByTestId, getAllByTestId = _render3.getAllByTestId, findByText = _render3.findByText;
+            expect(session.sessionTracks.length).toBe(2);
+
+            _react2.fireEvent.change(getAllByTestId('urlInput')[0], {
+              target: {
+                value: 'test.txt'
+              }
+            });
+
+            _react2.fireEvent.click(getByTestId('addTrackNextButton'));
+
+            _react2.fireEvent.mouseDown(getByTestId('adapterTypeSelect'));
+
+            _context2.next = 7;
+            return findByText('ChromSizesAdapter');
+
+          case 7:
+            chrom = _context2.sent;
+
+            _react2.fireEvent.click(chrom);
+
+            _react2.fireEvent.click(getByTestId('addTrackNextButton'));
+
+            expect(session.sessionTracks.length).toBe(2);
+
+          case 11:
+          case "end":
+            return _context2.stop();
+        }
+      }
+    }, _callee2);
+  })));
+});