@jbrowse/plugin-data-management 1.7.11 → 2.0.0

package/src/PluginStoreWidget/index.js

@@ -1,5 +1,4 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export { default as ReactComponent } from './components/PluginStoreWidget'
 export { default as stateModelFactory } from './model'
 export const configSchema = ConfigurationSchema('PluginStoreWidget', {})

package/src/SetDefaultSession/SetDefaultSession.tsx

@@ -7,7 +7,7 @@ import {
   DialogActions,
   Button,
   Typography,
-} from '@material-ui/core'
+} from '@mui/material'
 
 function canSetDefaultSession(obj: unknown): obj is {
   jbrowse: { setDefaultSessionConf: Function }

package/dist/AddConnectionWidget/components/AddConnectionWidget.test.js

@@ -1,279 +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 _react = require("@testing-library/react");
-
-var _react2 = _interopRequireDefault(require("react"));
-
-var _rootModel = require("@jbrowse/web/src/rootModel");
-
-var _AddConnectionWidget = _interopRequireDefault(require("./AddConnectionWidget"));
-
-jest.mock('@jbrowse/web/src/makeWorkerInstance', function () {
-  return function () {};
-});
-window.fetch = jest.fn(function () {
-  return new Promise(function (resolve) {
-    return resolve();
-  });
-});
-describe('<AddConnectionWidget />', function () {
-  var model;
-  var session;
-  beforeEach(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'
-          }]
-        }
-      }
-    });
-    model = session.addWidget('AddConnectionWidget', 'addConnectionWidget');
-  });
-  afterEach(_react.cleanup);
-  it('renders', function () {
-    var _render = (0, _react.render)( /*#__PURE__*/_react2.default.createElement(_AddConnectionWidget.default, {
-      model: model
-    })),
-        container = _render.container;
-
-    expect(container.firstChild).toMatchSnapshot();
-  });
-  it('can handle a custom UCSC trackHub URL', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    var mockFetch, _render2, findByTestId, getAllByRole, findAllByText, findByDisplayValue, ucscTrackHubSelection;
-
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            mockFetch = function mockFetch(url) {
-              var urlText = url.href ? url.href : url;
-              var responseText = '';
-
-              if (urlText.endsWith('hub.txt')) {
-                responseText = "hub TestHub\nshortLabel Test Hub\nlongLabel Test Genome Informatics Hub for human DNase and RNAseq data\ngenomesFile genomes.txt\nemail genome@test.com\ndescriptionUrl test.html\n";
-              } else if (urlText.endsWith('genomes.txt')) {
-                responseText = "genome volMyt1\ntrackDb hg19/trackDb.txt\n";
-              } else if (urlText.endsWith('trackDb.txt')) {
-                responseText = "track dnaseSignal\nbigDataUrl dnaseSignal.bigWig\nshortLabel DNAse Signal\nlongLabel Depth of alignments of DNAse reads\ntype bigWig\n";
-              }
-
-              return Promise.resolve(new Response(responseText, {
-                url: urlText
-              }));
-            };
-
-            jest.spyOn(global, 'fetch').mockImplementation(mockFetch);
-            _render2 = (0, _react.render)( /*#__PURE__*/_react2.default.createElement(_AddConnectionWidget.default, {
-              model: model
-            })), findByTestId = _render2.findByTestId, getAllByRole = _render2.getAllByRole, findAllByText = _render2.findAllByText, findByDisplayValue = _render2.findByDisplayValue;
-            expect(session.connections.length).toBe(0);
-
-            _react.fireEvent.mouseDown(getAllByRole('button')[0]);
-
-            _context.next = 7;
-            return findAllByText('UCSC Track Hub');
-
-          case 7:
-            ucscTrackHubSelection = _context.sent;
-
-            _react.fireEvent.click(ucscTrackHubSelection[ucscTrackHubSelection.length - 1]);
-
-            _context.t0 = _react.fireEvent;
-            _context.next = 12;
-            return findByTestId('addConnectionNext');
-
-          case 12:
-            _context.t1 = _context.sent;
-
-            _context.t0.click.call(_context.t0, _context.t1);
-
-            _context.t2 = _react.fireEvent;
-            _context.next = 17;
-            return findByDisplayValue('nameOfConnection');
-
-          case 17:
-            _context.t3 = _context.sent;
-            _context.t4 = {
-              target: {
-                value: 'Test UCSC connection name'
-              }
-            };
-
-            _context.t2.change.call(_context.t2, _context.t3, _context.t4);
-
-            _context.t5 = _react.fireEvent;
-            _context.next = 23;
-            return findByDisplayValue('http://mysite.com/path/to/hub.txt');
-
-          case 23:
-            _context.t6 = _context.sent;
-            _context.t7 = {
-              target: {
-                value: 'http://test.com/hub.txt'
-              }
-            };
-
-            _context.t5.change.call(_context.t5, _context.t6, _context.t7);
-
-            _context.t8 = _react.fireEvent;
-            _context.next = 29;
-            return findByTestId('addConnectionNext');
-
-          case 29:
-            _context.t9 = _context.sent;
-
-            _context.t8.click.call(_context.t8, _context.t9);
-
-            expect(session.sessionConnections.length).toBe(1);
-
-          case 32:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  })));
-  it('can handle a custom JBrowse 1 data directory URL', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-    var mockFetch, _render3, findByTestId, getAllByRole, findByText, findByPlaceholderText, findByDisplayValue;
-
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            mockFetch = function mockFetch(url) {
-              var urlText = url.href ? url.href : url;
-              var responseText = '';
-
-              if (urlText.endsWith('trackList.json')) {
-                responseText = '{}';
-              } else if (urlText.endsWith('refSeqs.json')) {
-                responseText = '[]';
-              }
-
-              return Promise.resolve(new Response(responseText, {
-                url: urlText
-              }));
-            };
-
-            jest.spyOn(global, 'fetch').mockImplementation(mockFetch);
-            _render3 = (0, _react.render)( /*#__PURE__*/_react2.default.createElement(_AddConnectionWidget.default, {
-              model: model
-            })), findByTestId = _render3.findByTestId, getAllByRole = _render3.getAllByRole, findByText = _render3.findByText, findByPlaceholderText = _render3.findByPlaceholderText, findByDisplayValue = _render3.findByDisplayValue;
-            expect(session.connections.length).toBe(0);
-
-            _react.fireEvent.mouseDown(getAllByRole('button')[0]);
-
-            _context2.t0 = _react.fireEvent;
-            _context2.next = 8;
-            return findByText('JBrowse 1 Data');
-
-          case 8:
-            _context2.t1 = _context2.sent;
-
-            _context2.t0.click.call(_context2.t0, _context2.t1);
-
-            _context2.t2 = _react.fireEvent;
-            _context2.next = 13;
-            return findByTestId('addConnectionNext');
-
-          case 13:
-            _context2.t3 = _context2.sent;
-
-            _context2.t2.click.call(_context2.t2, _context2.t3);
-
-            _context2.t4 = _react.fireEvent;
-            _context2.next = 18;
-            return findByDisplayValue('nameOfConnection');
-
-          case 18:
-            _context2.t5 = _context2.sent;
-            _context2.t6 = {
-              target: {
-                value: 'Test JBrowse 1 connection name'
-              }
-            };
-
-            _context2.t4.change.call(_context2.t4, _context2.t5, _context2.t6);
-
-            _context2.t7 = _react.fireEvent;
-            _context2.next = 24;
-            return findByDisplayValue('http://mysite.com/jbrowse/data/');
-
-          case 24:
-            _context2.t8 = _context2.sent;
-            _context2.t9 = {
-              target: {
-                value: 'http://test.com/jbrowse/data/'
-              }
-            };
-
-            _context2.t7.change.call(_context2.t7, _context2.t8, _context2.t9);
-
-            _context2.t10 = _react.fireEvent;
-            _context2.next = 30;
-            return findByText('Add item');
-
-          case 30:
-            _context2.t11 = _context2.sent;
-
-            _context2.t10.click.call(_context2.t10, _context2.t11);
-
-            _context2.t12 = _react.fireEvent;
-            _context2.next = 35;
-            return findByPlaceholderText('add new');
-
-          case 35:
-            _context2.t13 = _context2.sent;
-            _context2.t14 = {
-              target: {
-                value: 'volMyt1'
-              }
-            };
-
-            _context2.t12.change.call(_context2.t12, _context2.t13, _context2.t14);
-
-            _context2.t15 = _react.fireEvent;
-            _context2.next = 41;
-            return findByTestId('stringArrayAdd-assemblyNames');
-
-          case 41:
-            _context2.t16 = _context2.sent;
-
-            _context2.t15.click.call(_context2.t15, _context2.t16);
-
-            _context2.t17 = _react.fireEvent;
-            _context2.next = 46;
-            return findByTestId('addConnectionNext');
-
-          case 46:
-            _context2.t18 = _context2.sent;
-
-            _context2.t17.click.call(_context2.t17, _context2.t18);
-
-            expect(session.sessionConnections.length).toBe(1);
-
-          case 49:
-          case "end":
-            return _context2.stop();
-        }
-      }
-    }, _callee2);
-  })));
-});

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

@@ -1,218 +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 _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);
-  })));
-});