@jbrowse/plugin-linear-genome-view 1.7.11 → 2.0.0

package/src/LinearGenomeView/index.test.ts

@@ -88,6 +88,7 @@ function initialize() {
       assemblyManager: types.optional(AssemblyManager, {
         assemblies: {
           volvox: {
+            // @ts-ignore
             regions: volvoxDisplayedRegions,
           },
         },

package/src/LinearGenomeView/index.tsx

@@ -39,13 +39,13 @@ import { saveAs } from 'file-saver'
 
 // icons
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons'
-import SyncAltIcon from '@material-ui/icons/SyncAlt'
-import VisibilityIcon from '@material-ui/icons/Visibility'
-import LabelIcon from '@material-ui/icons/Label'
-import FolderOpenIcon from '@material-ui/icons/FolderOpen'
-import PhotoCameraIcon from '@material-ui/icons/PhotoCamera'
-import ZoomInIcon from '@material-ui/icons/ZoomIn'
-import MenuOpenIcon from '@material-ui/icons/MenuOpen'
+import SyncAltIcon from '@mui/icons-material/SyncAlt'
+import VisibilityIcon from '@mui/icons-material/Visibility'
+import LabelIcon from '@mui/icons-material/Label'
+import FolderOpenIcon from '@mui/icons-material/FolderOpen'
+import PhotoCameraIcon from '@mui/icons-material/PhotoCamera'
+import ZoomInIcon from '@mui/icons-material/ZoomIn'
+import MenuOpenIcon from '@mui/icons-material/MenuOpen'
 
 // locals
 import { renderToSvg } from './components/LinearGenomeViewSvg'
@@ -311,8 +311,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
         if (bp < 0) {
           const region = self.displayedRegions[0]
           const offset = bp
+          const snap = getSnapshot(region)
           return {
-            ...getSnapshot(region),
+            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+            ...(snap as Omit<typeof snap, symbol>),
             oob: true,
             coord: region.reversed
               ? Math.floor(region.end - offset) + 1
@@ -330,8 +332,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
           const len = region.end - region.start
           const offset = bp - bpSoFar
           if (len + bpSoFar > bp && bpSoFar <= bp) {
+            const snap = getSnapshot(region)
             return {
-              ...getSnapshot(region),
+              // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+              ...(snap as Omit<typeof snap, symbol>),
               oob: false,
               offset,
               coord: region.reversed
@@ -358,8 +362,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
           const region = self.displayedRegions[n - 1]
           const len = region.end - region.start
           const offset = bp - bpSoFar + len
+          const snap = getSnapshot(region)
           return {
-            ...getSnapshot(region),
+            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+            ...(snap as Omit<typeof snap, symbol>),
             oob: true,
             offset,
             coord: region.reversed
@@ -529,26 +535,19 @@ export function stateModelFactory(pluginManager: PluginManager) {
         initialSnapshot = {},
         displayInitialSnapshot = {},
       ) {
-        const trackConfigSchema =
-          pluginManager.pluggableConfigSchemaType('track')
-        const configuration = resolveIdentifier(
-          trackConfigSchema,
-          getRoot(self),
-          trackId,
-        )
-        if (!configuration) {
+        const schema = pluginManager.pluggableConfigSchemaType('track')
+        const conf = resolveIdentifier(schema, getRoot(self), trackId)
+        if (!conf) {
           throw new Error(`Could not resolve identifier "${trackId}"`)
         }
-        const trackType = pluginManager.getTrackType(configuration?.type)
+        const trackType = pluginManager.getTrackType(conf?.type)
         if (!trackType) {
-          throw new Error(`Unknown track type ${configuration.type}`)
+          throw new Error(`Unknown track type ${conf.type}`)
         }
         const viewType = pluginManager.getViewType(self.type)
-        const supportedDisplays = viewType.displayTypes.map(
-          displayType => displayType.name,
-        )
-        const displayConf = configuration.displays.find(
-          (d: AnyConfigurationModel) => supportedDisplays.includes(d.type),
+        const supportedDisplays = viewType.displayTypes.map(d => d.name)
+        const displayConf = conf.displays.find((d: AnyConfigurationModel) =>
+          supportedDisplays.includes(d.type),
         )
         if (!displayConf) {
           throw new Error(
@@ -556,14 +555,12 @@ export function stateModelFactory(pluginManager: PluginManager) {
           )
         }
 
-        const shownTracks = self.tracks.filter(
-          t => t.configuration === configuration,
-        )
-        if (shownTracks.length === 0) {
+        const t = self.tracks.filter(t => t.configuration === conf)
+        if (t.length === 0) {
           const track = trackType.stateModel.create({
             ...initialSnapshot,
-            type: configuration.type,
-            configuration,
+            type: conf.type,
+            configuration: conf,
             displays: [
               {
                 type: displayConf.type,
@@ -575,38 +572,26 @@ export function stateModelFactory(pluginManager: PluginManager) {
           self.tracks.push(track)
           return track
         }
-        return shownTracks[0]
+        return t[0]
       },
 
       hideTrack(trackId: string) {
-        const trackConfigSchema =
-          pluginManager.pluggableConfigSchemaType('track')
-        const configuration = resolveIdentifier(
-          trackConfigSchema,
-          getRoot(self),
-          trackId,
-        )
-        // if we have any tracks with that configuration, turn them off
-        const shownTracks = self.tracks.filter(
-          t => t.configuration === configuration,
-        )
-        transaction(() => shownTracks.forEach(t => self.tracks.remove(t)))
-        return shownTracks.length
+        const schema = pluginManager.pluggableConfigSchemaType('track')
+        const conf = resolveIdentifier(schema, getRoot(self), trackId)
+        const t = self.tracks.filter(t => t.configuration === conf)
+        transaction(() => t.forEach(t => self.tracks.remove(t)))
+        return t.length
       },
     }))
     .actions(self => ({
-      moveTrack(movingTrackId: string, targetTrackId: string) {
-        const oldIndex = self.tracks.findIndex(
-          track => track.id === movingTrackId,
-        )
+      moveTrack(movingId: string, targetId: string) {
+        const oldIndex = self.tracks.findIndex(track => track.id === movingId)
         if (oldIndex === -1) {
-          throw new Error(`Track ID ${movingTrackId} not found`)
+          throw new Error(`Track ID ${movingId} not found`)
         }
-        const newIndex = self.tracks.findIndex(
-          track => track.id === targetTrackId,
-        )
+        const newIndex = self.tracks.findIndex(track => track.id === targetId)
         if (newIndex === -1) {
-          throw new Error(`Track ID ${targetTrackId} not found`)
+          throw new Error(`Track ID ${targetId} not found`)
         }
         const track = getSnapshot(self.tracks[oldIndex])
         self.tracks.splice(oldIndex, 1)
@@ -953,21 +938,21 @@ export function stateModelFactory(pluginManager: PluginManager) {
         leftOffset: BpOffset | undefined,
         rightOffset: BpOffset | undefined,
       ) {
+        const snap = getSnapshot(self)
         const simView = Base1DView.create({
-          ...getSnapshot(self),
+          // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+          ...(snap as Omit<typeof self, symbol>),
           interRegionPaddingWidth: self.interRegionPaddingWidth,
         })
 
         simView.setVolatileWidth(self.width)
         simView.zoomToDisplayedRegions(leftOffset, rightOffset)
 
-        return simView.dynamicBlocks.contentBlocks.map(region => {
-          return {
-            ...region,
-            start: Math.floor(region.start),
-            end: Math.ceil(region.end),
-          }
-        })
+        return simView.dynamicBlocks.contentBlocks.map(region => ({
+          ...region,
+          start: Math.floor(region.start),
+          end: Math.ceil(region.end),
+        }))
       },
 
       // schedule something to be run after the next time displayedRegions is set

package/src/index.ts

@@ -11,7 +11,7 @@ import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
-import LineStyleIcon from '@material-ui/icons/LineStyle'
+import LineStyleIcon from '@mui/icons-material/LineStyle'
 import {
   BaseLinearDisplay,
   BaseLinearDisplayComponent,

package/dist/LinearBareDisplay/index.test.js

@@ -1,33 +0,0 @@
-"use strict";
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _ = require(".");
-
-test('config schema renderer type', function () {
-  var stubPluginManager = {
-    pluggableConfigSchemaType: function pluggableConfigSchemaType(type) {
-      var one = (0, _configuration.ConfigurationSchema)("".concat(type, "_TypeOne"), {}, {
-        explicitlyTyped: true
-      });
-      var two = (0, _configuration.ConfigurationSchema)("".concat(type, "_TypeTwo"), {}, {
-        explicitlyTyped: true
-      });
-      var three = (0, _configuration.ConfigurationSchema)("".concat(type, "_TypeThree"), {}, {
-        explicitlyTyped: true
-      });
-      return _mobxStateTree.types.union(one, two, three);
-    }
-  };
-  var configSchema = (0, _.configSchemaFactory)(stubPluginManager);
-  var instance = configSchema.create({
-    type: 'LinearBareDisplay',
-    displayId: 'displayId0',
-    renderer: {
-      type: 'renderer_TypeTwo'
-    }
-  });
-  expect(instance.renderer.type).toBe('renderer_TypeTwo');
-});

package/dist/LinearGenomeView/components/LinearGenomeView.test.js

@@ -1,234 +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");
-
-require("@testing-library/jest-dom/extend-expect");
-
-var _rootModel = require("@jbrowse/web/src/rootModel");
-
-require("requestidlecallback-polyfill");
-
-var _LinearGenomeView = _interopRequireDefault(require("./LinearGenomeView"));
-
-jest.mock('@jbrowse/web/src/makeWorkerInstance', function () {
-  return function () {};
-});
-var assemblyConf = {
-  name: 'volMyt1',
-  sequence: {
-    trackId: 'sequenceConfigId',
-    type: 'ReferenceSequenceTrack',
-    adapter: {
-      type: 'FromConfigSequenceAdapter',
-      features: [{
-        refName: 'ctgA',
-        uniqueId: 'firstId',
-        start: 0,
-        end: 10,
-        seq: 'cattgttgcg'
-      }]
-    }
-  }
-};
-describe('<LinearGenomeView />', function () {
-  it('renders setup wizard', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    var session, model, _render, findByText;
-
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            session = (0, _rootModel.createTestSession)();
-            session.addAssemblyConf(assemblyConf);
-            session.addView('LinearGenomeView', {
-              id: 'lgv'
-            });
-            model = session.views[0];
-            model.setWidth(800);
-            _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_LinearGenomeView.default, {
-              model: model
-            })), findByText = _render.findByText;
-            expect(model.displayedRegions.length).toEqual(0);
-            _context.t0 = _react2.fireEvent;
-            _context.next = 10;
-            return findByText('Open');
-
-          case 10:
-            _context.t1 = _context.sent;
-
-            _context.t0.click.call(_context.t0, _context.t1);
-
-            _context.next = 14;
-            return (0, _react2.waitFor)(function () {
-              expect(model.displayedRegions.length).toEqual(1);
-            });
-
-          case 14:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  })));
-  it('renders one track, one region', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-    var session, model, _render2, container, findByText;
-
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            session = (0, _rootModel.createTestSession)();
-            session.addAssemblyConf(assemblyConf);
-            session.addTrackConf({
-              trackId: 'testConfig',
-              assemblyNames: ['volMyt1'],
-              name: 'Foo Track',
-              type: 'BasicTrack',
-              adapter: {
-                type: 'FromConfigAdapter',
-                features: []
-              }
-            });
-            session.addView('LinearGenomeView', {
-              type: 'LinearGenomeView',
-              id: 'lgv',
-              offsetPx: 0,
-              bpPerPx: 1,
-              tracks: [{
-                id: 'foo',
-                type: 'BasicTrack',
-                height: 20,
-                configuration: 'testConfig',
-                displays: [{
-                  type: 'LinearBareDisplay',
-                  configuration: 'testConfig-LinearBareDisplay'
-                }]
-              }],
-              displayedRegions: [{
-                assemblyName: 'volMyt1',
-                refName: 'ctgA',
-                start: 0,
-                end: 100
-              }]
-            });
-            model = session.views[0];
-            model.setWidth(800);
-            _render2 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_LinearGenomeView.default, {
-              model: model
-            })), container = _render2.container, findByText = _render2.findByText;
-            _context2.next = 9;
-            return findByText('Foo Track');
-
-          case 9:
-            _context2.next = 11;
-            return findByText('100bp');
-
-          case 11:
-            expect(container.firstChild).toMatchSnapshot();
-
-          case 12:
-          case "end":
-            return _context2.stop();
-        }
-      }
-    }, _callee2);
-  })));
-  it('renders two tracks, two regions', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-    var session, model, _render3, container, findByText, findAllByTestId;
-
-    return _regenerator.default.wrap(function _callee3$(_context3) {
-      while (1) {
-        switch (_context3.prev = _context3.next) {
-          case 0:
-            session = (0, _rootModel.createTestSession)();
-            session.addAssemblyConf(assemblyConf);
-            session.addTrackConf({
-              trackId: 'testConfig',
-              name: 'Foo Track',
-              assemblyNames: ['volMyt1'],
-              type: 'BasicTrack',
-              adapter: {
-                type: 'FromConfigAdapter',
-                features: []
-              }
-            });
-            session.addTrackConf({
-              trackId: 'testConfig2',
-              name: 'Bar Track',
-              assemblyNames: ['volMyt1'],
-              type: 'BasicTrack',
-              adapter: {
-                type: 'FromConfigAdapter',
-                features: []
-              }
-            });
-            session.addView('LinearGenomeView', {
-              id: 'lgv',
-              offsetPx: 0,
-              bpPerPx: 1,
-              displayedRegions: [{
-                assemblyName: 'volMyt1',
-                refName: 'ctgA',
-                start: 0,
-                end: 100
-              }, {
-                assemblyName: 'volMyt1',
-                refName: 'ctgB',
-                start: 1000,
-                end: 2000
-              }],
-              tracks: [{
-                id: 'foo',
-                type: 'BasicTrack',
-                height: 20,
-                configuration: 'testConfig',
-                displays: [{
-                  type: 'LinearBareDisplay',
-                  configuration: 'testConfig-LinearBareDisplay'
-                }]
-              }, {
-                id: 'bar',
-                type: 'BasicTrack',
-                height: 20,
-                configuration: 'testConfig2',
-                displays: [{
-                  type: 'LinearBareDisplay',
-                  configuration: 'testConfig2-LinearBareDisplay'
-                }]
-              }]
-            });
-            model = session.views[0];
-            model.setWidth(800);
-            _render3 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_LinearGenomeView.default, {
-              model: model
-            })), container = _render3.container, findByText = _render3.findByText, findAllByTestId = _render3.findAllByTestId;
-            _context3.next = 10;
-            return findByText('Foo Track');
-
-          case 10:
-            _context3.next = 12;
-            return findByText('798bp');
-
-          case 12:
-            _context3.next = 14;
-            return findAllByTestId('svgfeatures');
-
-          case 14:
-            expect(container.firstChild).toMatchSnapshot();
-
-          case 15:
-          case "end":
-            return _context3.stop();
-        }
-      }
-    }, _callee3);
-  })));
-});

package/dist/LinearGenomeView/components/ScaleBar.test.js

@@ -1,180 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-var _rootModel = require("@jbrowse/web/src/rootModel");
-
-var _ScaleBar = _interopRequireDefault(require("./ScaleBar"));
-
-/* eslint-disable @typescript-eslint/no-explicit-any */
-jest.mock('@jbrowse/web/src/makeWorkerInstance', function () {
-  return function () {};
-});
-describe('ScaleBar genome view component', function () {
-  it('renders two regions', function () {
-    var session = (0, _rootModel.createTestSession)({
-      views: [{
-        type: 'LinearGenomeView',
-        offsetPx: 0,
-        bpPerPx: 1,
-        displayedRegions: [{
-          assemblyName: 'volvox',
-          refName: 'ctgA',
-          start: 0,
-          end: 100
-        }, {
-          assemblyName: 'volvox',
-          refName: 'ctgB',
-          start: 100,
-          end: 200
-        }],
-        tracks: [],
-        configuration: {}
-      }]
-    });
-    session.addAssemblyConf({
-      name: 'volMyt1',
-      sequence: {
-        trackId: 'ref0',
-        type: 'ReferenceSequenceTrack',
-        adapter: {
-          type: 'FromConfigSequenceAdapter',
-          features: [{
-            refName: 'ctgA',
-            uniqueId: 'firstId',
-            start: 0,
-            end: 10,
-            seq: 'cattgttgcg'
-          }]
-        }
-      }
-    });
-    var model = session.views[0];
-
-    var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_ScaleBar.default, {
-      model: model
-    })),
-        getByTestId = _render.getByTestId;
-
-    var ret1 = getByTestId('refLabel-ctgA');
-    var ret2 = getByTestId('refLabel-ctgB');
-    expect(ret1.style.left).toBe('-1px');
-    expect(ret2.style.left).toBe('101px');
-  });
-  it('renders two regions when scrolled to the left, the label is ctgA to the actual blocks', function () {
-    var session = (0, _rootModel.createTestSession)({
-      views: [{
-        type: 'LinearGenomeView',
-        offsetPx: -100,
-        bpPerPx: 1,
-        displayedRegions: [{
-          assemblyName: 'volvox',
-          refName: 'ctgA',
-          start: 0,
-          end: 100
-        }, {
-          assemblyName: 'volvox',
-          refName: 'ctgB',
-          start: 0,
-          end: 100
-        }],
-        tracks: [],
-        configuration: {}
-      }]
-    });
-    session.addAssemblyConf({
-      name: 'volMyt1',
-      sequence: {
-        trackId: 'ref0',
-        type: 'ReferenceSequenceTrack',
-        adapter: {
-          type: 'FromConfigSequenceAdapter',
-          features: [{
-            refName: 'ctgA',
-            uniqueId: 'firstId',
-            start: 0,
-            end: 10,
-            seq: 'cattgttgcg'
-          }]
-        }
-      }
-    });
-    var model = session.views[0];
-
-    var _render2 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_ScaleBar.default, {
-      model: model
-    })),
-        getByTestId = _render2.getByTestId;
-
-    var ret1 = getByTestId('refLabel-ctgA');
-    var ret2 = getByTestId('refLabel-ctgB');
-    expect(ret1.style.left).toBe('99px');
-    expect(ret2.style.left).toBe('201px');
-  });
-  it('renders two regions when scrolled to the left, the label is ctgA to the actual blocks', function () {
-    var session = (0, _rootModel.createTestSession)({
-      views: [{
-        type: 'LinearGenomeView',
-        offsetPx: -100,
-        bpPerPx: 1,
-        displayedRegions: [{
-          assemblyName: 'volvox',
-          refName: 'ctgA',
-          start: 0,
-          end: 1000
-        }, {
-          assemblyName: 'volvox',
-          refName: 'ctgB',
-          start: 0,
-          end: 1
-        }, {
-          assemblyName: 'volvox',
-          refName: 'ctgC',
-          start: 0,
-          end: 1
-        }, {
-          assemblyName: 'volvox',
-          refName: 'ctgD',
-          start: 0,
-          end: 1
-        }],
-        tracks: [],
-        configuration: {}
-      }]
-    });
-    session.addAssemblyConf({
-      name: 'volMyt1',
-      sequence: {
-        trackId: 'ref0',
-        type: 'ReferenceSequenceTrack',
-        adapter: {
-          type: 'FromConfigSequenceAdapter',
-          features: [{
-            refName: 'ctgA',
-            uniqueId: 'firstId',
-            start: 0,
-            end: 10,
-            seq: 'cattgttgcg'
-          }]
-        }
-      }
-    });
-    var model = session.views[0];
-
-    var _render3 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_ScaleBar.default, {
-      model: model
-    })),
-        queryByTestId = _render3.queryByTestId;
-
-    var ret2 = queryByTestId('refLabel-ctgB');
-    var ret3 = queryByTestId('refLabel-ctgC');
-    var ret4 = queryByTestId('refLabel-ctgD');
-    expect(ret2).toBe(null);
-    expect(ret3).toBe(null);
-    expect(ret4).toBe(null);
-  });
-});