@jbrowse/plugin-config 1.7.9 → 2.0.0

package/src/ConfigurationEditorWidget/index.js

@@ -5,13 +5,13 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration'
 export { default as stateModelFactory } from './model'
 export const configSchema = ConfigurationSchema('ConfigurationEditorWidget', {})
 export const HeadingComponent = observer(({ model }) => {
-  if (model && model.target) {
+  if (model?.target) {
     if (model.target.type) {
       return `${model.target.type} settings`
     }
     if (isStateTreeNode(model.target)) {
       const type = getType(model.target)
-      if (type && type.name) {
+      if (type?.name) {
         return `${type.name.replace('ConfigurationSchema', '')} settings`
       }
     }

package/src/RefNameAliasAdapter/RefNameAliasAdapter.ts

@@ -23,7 +23,7 @@ export default class RefNameAliasAdapter
       .map(row => {
         const aliases = row.split('\t')
         const [refName] = aliases.splice(refColumn, 1)
-        return { refName, aliases }
+        return { refName, aliases: aliases.filter(f => !!f.trim()) }
       })
   }
 

package/src/index.ts

@@ -9,19 +9,13 @@ import {
   stateModelFactory as ConfigurationEditorStateModelFactory,
 } from './ConfigurationEditorWidget'
 import {
-  AdapterClass as FromConfigAdapterClass,
-  RegionsAdapterClass as FromConfigRegionsAdapterClass,
-  SequenceAdapterClass as FromConfigSequenceAdapterClass,
   configSchema as fromConfigAdapterConfigSchema,
   regionsConfigSchema as fromConfigRegionsAdapterConfigSchema,
   sequenceConfigSchema as fromConfigSequenceAdapterConfigSchema,
 } from './FromConfigAdapter'
-import {
-  AdapterClass as RefNameAliasAdapterClass,
-  configSchema as refNameAliasAdapterConfigSchema,
-} from './RefNameAliasAdapter'
+import { configSchema as refNameAliasAdapterConfigSchema } from './RefNameAliasAdapter'
 
-const ConfigurationEditorComponent = lazy(
+const LazyConfigurationEditorComponent = lazy(
   () => import('./ConfigurationEditorWidget/components/ConfigurationEditor'),
 )
 
@@ -34,7 +28,10 @@ export default class extends Plugin {
         new AdapterType({
           name: 'FromConfigAdapter',
           configSchema: fromConfigAdapterConfigSchema,
-          AdapterClass: FromConfigAdapterClass,
+          getAdapterClass: () =>
+            import('./FromConfigAdapter/FromConfigAdapter').then(
+              r => r.default,
+            ),
           adapterMetadata: {
             category: null,
             hiddenFromGUI: true,
@@ -48,7 +45,10 @@ export default class extends Plugin {
         new AdapterType({
           name: 'FromConfigRegionsAdapter',
           configSchema: fromConfigRegionsAdapterConfigSchema,
-          AdapterClass: FromConfigRegionsAdapterClass,
+          getAdapterClass: () =>
+            import('./FromConfigAdapter/FromConfigRegionsAdapter').then(
+              r => r.default,
+            ),
           adapterMetadata: {
             category: null,
             hiddenFromGUI: true,
@@ -62,7 +62,10 @@ export default class extends Plugin {
         new AdapterType({
           name: 'FromConfigSequenceAdapter',
           configSchema: fromConfigSequenceAdapterConfigSchema,
-          AdapterClass: FromConfigSequenceAdapterClass,
+          getAdapterClass: () =>
+            import('./FromConfigAdapter/FromConfigSequenceAdapter').then(
+              r => r.default,
+            ),
           adapterMetadata: {
             category: null,
             hiddenFromGUI: true,
@@ -76,7 +79,10 @@ export default class extends Plugin {
         new AdapterType({
           name: 'RefNameAliasAdapter',
           configSchema: refNameAliasAdapterConfigSchema,
-          AdapterClass: RefNameAliasAdapterClass,
+          getAdapterClass: () =>
+            import('./RefNameAliasAdapter/RefNameAliasAdapter').then(
+              r => r.default,
+            ),
           adapterMetadata: {
             category: null,
             hiddenFromGUI: true,
@@ -92,7 +98,7 @@ export default class extends Plugin {
         HeadingComponent: ConfigurationEditorHeadingComponent,
         configSchema: ConfigurationEditorConfigSchema,
         stateModel: ConfigurationEditorStateModelFactory(pluginManager),
-        ReactComponent: ConfigurationEditorComponent,
+        ReactComponent: LazyConfigurationEditorComponent,
       })
     })
   }
@@ -100,4 +106,4 @@ export default class extends Plugin {
 
 export { default as JsonEditor } from './ConfigurationEditorWidget/components/JsonEditor'
 
-export { ConfigurationEditorComponent as ConfigurationEditor }
+export { LazyConfigurationEditorComponent as ConfigurationEditor }

package/dist/ConfigurationEditorWidget/components/ColorEditor.test.js

@@ -1,31 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-var _ColorEditor = require("./ColorEditor");
-
-describe('ColorPicker widget', function () {
-  it('can change value via the text field', function () {
-    var myfn = jest.fn();
-
-    var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_ColorEditor.ColorSlot, {
-      value: "green",
-      onChange: myfn
-    })),
-        getByDisplayValue = _render.getByDisplayValue;
-
-    var ret = getByDisplayValue('green');
-
-    _react2.fireEvent.change(ret, {
-      target: {
-        value: 'red'
-      }
-    });
-
-    expect(myfn).toHaveBeenCalledWith('red');
-  });
-});

package/dist/ConfigurationEditorWidget/components/ConfigurationEditor.test.js

@@ -1,121 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _pluginAlignments = _interopRequireDefault(require("@jbrowse/plugin-alignments"));
-
-var _pluginSvg = _interopRequireDefault(require("@jbrowse/plugin-svg"));
-
-var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
-
-var _ConfigurationEditor = _interopRequireDefault(require("./ConfigurationEditor"));
-
-describe('ConfigurationEditor widget', function () {
-  it('renders with just the required model elements', function () {
-    var TestSchema = (0, _configuration.ConfigurationSchema)('TestThing', {
-      foo: {
-        type: 'string',
-        defaultValue: 'bar'
-      }
-    });
-
-    var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_ConfigurationEditor.default, {
-      model: {
-        target: TestSchema.create()
-      }
-    })),
-        container = _render.container;
-
-    expect(container.firstChild).toMatchSnapshot();
-  });
-  it('renders all the different types of built-in slots', function () {
-    var TestSchema = (0, _configuration.ConfigurationSchema)('TestThing', {
-      stringTest: {
-        name: 'stringTest',
-        description: 'stringTest',
-        type: 'string',
-        defaultValue: 'string1'
-      },
-      fileLocationTest: {
-        name: 'fileLocationTest',
-        description: 'fileLocationTest',
-        type: 'fileLocation',
-        defaultValue: {
-          uri: '/path/to/my.file',
-          locationType: 'UriLocation'
-        }
-      },
-      stringArrayTest: {
-        name: 'stringArrayTest',
-        description: 'stringArrayTest',
-        type: 'stringArray',
-        defaultValue: ['string1', 'string2']
-      },
-      stringArrayMapTest: {
-        name: 'stringArrayMapTest',
-        description: 'stringArrayMapTest',
-        type: 'stringArrayMap',
-        defaultValue: {
-          key1: ['string1', 'string2']
-        }
-      },
-      numberTest: {
-        name: 'numberTest',
-        description: 'numberTest',
-        type: 'number',
-        defaultValue: 88.5
-      },
-      integerTest: {
-        name: 'integerTest',
-        description: 'integerTest',
-        type: 'integer',
-        defaultValue: 42
-      },
-      colorTest: {
-        name: 'colorTest',
-        description: 'colorTest',
-        type: 'color',
-        defaultValue: '#396494'
-      },
-      booleanTest: {
-        name: 'booleanTest',
-        description: 'booleanTest',
-        type: 'boolean',
-        defaultValue: true
-      }
-    });
-
-    var _render2 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_ConfigurationEditor.default, {
-      model: {
-        target: TestSchema.create()
-      }
-    })),
-        container = _render2.container;
-
-    expect(container.firstChild).toMatchSnapshot();
-  });
-  it('renders with defaults of the PileupTrack schema', function () {
-    console.warn = jest.fn();
-    var pluginManager = new _PluginManager.default([new _pluginAlignments.default(), new _pluginSvg.default()]);
-    pluginManager.createPluggableElements();
-    pluginManager.configure();
-    var PileupDisplaySchema = (0, _pluginLinearGenomeView.linearBasicDisplayConfigSchemaFactory)(pluginManager);
-
-    var _render3 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_ConfigurationEditor.default, {
-      model: {
-        target: PileupDisplaySchema.create()
-      }
-    })),
-        container = _render3.container;
-
-    expect(container.firstChild).toMatchSnapshot();
-  });
-});

package/dist/FromConfigAdapter/FromConfigAdapter.test.js

@@ -1,100 +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 _FromConfigAdapter = _interopRequireDefault(require("./FromConfigAdapter"));
-
-var _configSchema = require("./configSchema");
-
-test('adapter can fetch features', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var features, adapter, result, featuresArray;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          features = [{
-            uniqueId: 'one',
-            refName: 'ctgA',
-            start: 20,
-            end: 40
-          }, {
-            uniqueId: 'two',
-            refName: 'ctgB',
-            start: 50,
-            end: 60
-          }];
-          adapter = new _FromConfigAdapter.default(_configSchema.configSchema.create({
-            features: features
-          }));
-          result = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context.next = 5;
-          return result.pipe((0, _operators.toArray)()).toPromise();
-
-        case 5:
-          featuresArray = _context.sent;
-          expect(featuresArray.length).toBe(1);
-          expect(featuresArray[0].toJSON()).toEqual(features[0]);
-
-        case 8:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));
-test('adapter can fetch features with subfeatures', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var features, adapter, result, featuresArray;
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          features = [{
-            refName: 'ctgA',
-            uniqueId: 'feat1',
-            start: 200,
-            end: 750,
-            name: 'Feature1',
-            subfeatures: [{
-              uniqueId: 'feat2',
-              start: 225,
-              end: 300,
-              name: 'Feature2'
-            }, {
-              uniqueId: 'feat3',
-              start: 400,
-              end: 600,
-              name: 'Feature3'
-            }]
-          }];
-          adapter = new _FromConfigAdapter.default(_configSchema.configSchema.create({
-            features: features
-          }));
-          result = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _context2.next = 5;
-          return result.pipe((0, _operators.toArray)()).toPromise();
-
-        case 5:
-          featuresArray = _context2.sent;
-          expect(featuresArray.length).toBe(1);
-
-        case 7:
-        case "end":
-          return _context2.stop();
-      }
-    }
-  }, _callee2);
-})));

package/dist/FromConfigAdapter/FromConfigRegionsAdapter.test.js

@@ -1,200 +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 _FromConfigRegionsAdapter = _interopRequireDefault(require("./FromConfigRegionsAdapter"));
-
-var _configSchema = require("./configSchema");
-
-test('adapter can fetch regions 1', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var features, adapter, result;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          features = [{
-            uniqueId: 'one',
-            refName: 'ctgA',
-            start: 250,
-            end: 400
-          }, {
-            uniqueId: 'two',
-            refName: 'ctgA',
-            start: 150,
-            end: 300
-          }, {
-            uniqueId: 'three',
-            refName: 'ctgB',
-            start: 50,
-            end: 60
-          }];
-          adapter = new _FromConfigRegionsAdapter.default(_configSchema.regionsConfigSchema.create({
-            features: features
-          }));
-          _context.next = 4;
-          return adapter.getRegions();
-
-        case 4:
-          result = _context.sent;
-          expect(result).toEqual([{
-            refName: 'ctgA',
-            start: 150,
-            end: 400
-          }, {
-            refName: 'ctgB',
-            start: 50,
-            end: 60
-          }]);
-
-        case 6:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));
-test('adapter can fetch regions 2', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var features, adapter, result;
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          features = [{
-            uniqueId: 'three',
-            refName: 'ctgB',
-            start: 50,
-            end: 60
-          }, {
-            uniqueId: 'two',
-            refName: 'ctgA',
-            start: 150,
-            end: 300
-          }, {
-            uniqueId: 'one',
-            refName: 'ctgA',
-            start: 250,
-            end: 400
-          }];
-          adapter = new _FromConfigRegionsAdapter.default(_configSchema.regionsConfigSchema.create({
-            features: features
-          }));
-          _context2.next = 4;
-          return adapter.getRegions();
-
-        case 4:
-          result = _context2.sent;
-          expect(result).toEqual([{
-            refName: 'ctgA',
-            start: 150,
-            end: 400
-          }, {
-            refName: 'ctgB',
-            start: 50,
-            end: 60
-          }]);
-
-        case 6:
-        case "end":
-          return _context2.stop();
-      }
-    }
-  }, _callee2);
-})));
-test('adapter can fetch regions 3', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-  var features, adapter, result;
-  return _regenerator.default.wrap(function _callee3$(_context3) {
-    while (1) {
-      switch (_context3.prev = _context3.next) {
-        case 0:
-          features = [{
-            uniqueId: 'two',
-            refName: 'ctgA',
-            start: 150,
-            end: 300
-          }, {
-            uniqueId: 'one',
-            refName: 'ctgA',
-            start: 250,
-            end: 400
-          }, {
-            uniqueId: 'three',
-            refName: 'ctgB',
-            start: 50,
-            end: 60
-          }];
-          adapter = new _FromConfigRegionsAdapter.default(_configSchema.regionsConfigSchema.create({
-            features: features
-          }));
-          _context3.next = 4;
-          return adapter.getRegions();
-
-        case 4:
-          result = _context3.sent;
-          expect(result).toEqual([{
-            refName: 'ctgA',
-            start: 150,
-            end: 400
-          }, {
-            refName: 'ctgB',
-            start: 50,
-            end: 60
-          }]);
-
-        case 6:
-        case "end":
-          return _context3.stop();
-      }
-    }
-  }, _callee3);
-})));
-test('adapter can fetch regions 4', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
-  var features, adapter, result;
-  return _regenerator.default.wrap(function _callee4$(_context4) {
-    while (1) {
-      switch (_context4.prev = _context4.next) {
-        case 0:
-          features = [{
-            uniqueId: 'two',
-            refName: 'ctgA',
-            start: 150,
-            end: 300
-          }, {
-            uniqueId: 'onePrime',
-            refName: 'ctgA',
-            start: 300,
-            end: 400
-          }, {
-            uniqueId: 'three',
-            refName: 'ctgB',
-            start: 50,
-            end: 60
-          }];
-          adapter = new _FromConfigRegionsAdapter.default(_configSchema.regionsConfigSchema.create({
-            features: features
-          }));
-          _context4.next = 4;
-          return adapter.getRegions();
-
-        case 4:
-          result = _context4.sent;
-          expect(result).toEqual([{
-            refName: 'ctgA',
-            start: 150,
-            end: 400
-          }, {
-            refName: 'ctgB',
-            start: 50,
-            end: 60
-          }]);
-
-        case 6:
-        case "end":
-          return _context4.stop();
-      }
-    }
-  }, _callee4);
-})));

package/dist/FromConfigAdapter/FromConfigSequenceAdapter.test.js

@@ -1,110 +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 _FromConfigSequenceAdapter = _interopRequireDefault(require("./FromConfigSequenceAdapter"));
-
-var _configSchema = require("./configSchema");
-
-test('adapter can fetch sequences when there is just one feature representing whole refseq', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var features, adapter, result, featuresArray, result2, featuresArray2;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          features = [{
-            uniqueId: 'one',
-            refName: 'ctgA',
-            start: 0,
-            end: 150,
-            seq: 'ccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctc'
-          }];
-          adapter = new _FromConfigSequenceAdapter.default(_configSchema.sequenceConfigSchema.create({
-            features: features
-          }));
-          result = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 50
-          });
-          _context.next = 5;
-          return result.pipe((0, _operators.toArray)()).toPromise();
-
-        case 5:
-          featuresArray = _context.sent;
-          expect(featuresArray.length).toBe(1);
-          expect(featuresArray[0].get('seq')).toBe(features[0].seq.slice(0, 50));
-          result2 = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 100,
-            end: 150
-          });
-          _context.next = 11;
-          return result2.pipe((0, _operators.toArray)()).toPromise();
-
-        case 11:
-          featuresArray2 = _context.sent;
-          expect(featuresArray2.length).toBe(1);
-          expect(featuresArray2[0].get('seq')).toBe(features[0].seq.slice(100, 150));
-
-        case 14:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));
-test("adapter can fetch sequences when the config's sequence doesn't start at 0", /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var features, adapter, result, featuresArray, result2, featuresArray2;
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          features = [{
-            uniqueId: 'one',
-            refName: 'ctgA',
-            start: 5000,
-            end: 5150,
-            seq: 'ccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctc'
-          }];
-          adapter = new _FromConfigSequenceAdapter.default(_configSchema.sequenceConfigSchema.create({
-            features: features
-          }));
-          result = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 4950,
-            end: 5050
-          });
-          _context2.next = 5;
-          return result.pipe((0, _operators.toArray)()).toPromise();
-
-        case 5:
-          featuresArray = _context2.sent;
-          expect(featuresArray.length).toBe(1);
-          expect(featuresArray[0].get('seq')).toBe(features[0].seq.slice(0, 50));
-          result2 = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 5050,
-            end: 5150
-          });
-          _context2.next = 11;
-          return result2.pipe((0, _operators.toArray)()).toPromise();
-
-        case 11:
-          featuresArray2 = _context2.sent;
-          expect(featuresArray2.length).toBe(1);
-          expect(featuresArray2[0].get('seq')).toBe(features[0].seq.slice(50, 150));
-
-        case 14:
-        case "end":
-          return _context2.stop();
-      }
-    }
-  }, _callee2);
-})));