@jbrowse/plugin-config 1.7.11 → 2.1.0

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);
-})));

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.test.js

@@ -1,41 +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 _RefNameAliasAdapter = _interopRequireDefault(require("./RefNameAliasAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch a simple alias file', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, result;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          adapter = new _RefNameAliasAdapter.default(_configSchema.default.create({
-            location: {
-              localPath: require.resolve('./test_data/simple_alias.txt'),
-              locationType: 'LocalPathLocation'
-            }
-          }));
-          _context.next = 3;
-          return adapter.getRefNameAliases();
-
-        case 3:
-          result = _context.sent;
-          expect(result[0].refName).toBe('chr1');
-          expect(result[0].aliases).toEqual(['1', 'NC_000001.10']);
-          expect(result[1].refName).toBe('chr2');
-          expect(result[1].aliases).toEqual(['2', 'NC_000002.11']);
-
-        case 8:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/index.test.js

@@ -1,41 +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("."));
-
-describe('Config editing', function () {
-  var pluginManager;
-  beforeAll(function () {
-    var originalConsoleWarn = console.warn;
-    console.warn = jest.fn();
-    pluginManager = new _PluginManager.default([new _.default()]);
-    pluginManager.createPluggableElements();
-    pluginManager.configure();
-    console.warn = originalConsoleWarn;
-  });
-  it("won't add if already added", function () {
-    expect(function () {
-      return pluginManager.addPlugin(new _.default());
-    }).toThrow(/JBrowse already configured, cannot add plugins/);
-  });
-  it('adds config editor widget', function () {
-    var ConfigurationEditorWidget = pluginManager.getWidgetType('ConfigurationEditorWidget');
-    var config = ConfigurationEditorWidget.configSchema.create({
-      type: 'ConfigurationEditorWidget'
-    });
-    expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
-  });
-  it('creates proper FromConfigAdapter', function () {
-    var adapter = pluginManager.getAdapterType('FromConfigAdapter');
-    var config = adapter.configSchema.create({
-      type: 'FromConfigAdapter',
-      adapterId: 'testFromConfigAdapterId'
-    });
-    expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
-  });
-});

package/src/ConfigurationEditorWidget/components/CallbackEditor.js

@@ -1,112 +0,0 @@
-import React, { useEffect, useState } from 'react'
-import { useDebounce } from '@jbrowse/core/util'
-import { stringToJexlExpression } from '@jbrowse/core/util/jexlStrings'
-import {
-  FormControl,
-  FormHelperText,
-  InputLabel,
-  Tooltip,
-  IconButton,
-  makeStyles,
-} from '@material-ui/core'
-import HelpIcon from '@material-ui/icons/Help'
-import { getEnv } from 'mobx-state-tree'
-import { observer, PropTypes } from 'mobx-react'
-import Editor from 'react-simple-code-editor'
-
-// fontSize and fontFamily have to match between Editor and SyntaxHighlighter
-const fontSize = '12px'
-
-// Optimize by using system default fonts:
-// https://css-tricks.com/snippets/css/font-stacks/
-const fontFamily =
-  'Consolas, "Andale Mono WT", "Andale Mono", "Lucida Console", "Lucida Sans Typewriter", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Liberation Mono", "Nimbus Mono L", Monaco, "Courier New", Courier, monospace'
-
-const useStyles = makeStyles(theme => ({
-  callbackEditor: {
-    marginTop: '16px',
-    borderBottom: `1px solid ${theme.palette.divider}`,
-    fontFamily,
-    fontSize,
-  },
-}))
-
-function CallbackEditor({ slot }) {
-  const classes = useStyles()
-
-  const [code, setCode] = useState(slot.value)
-  const [error, setCodeError] = useState()
-  const debouncedCode = useDebounce(code, 400)
-
-  useEffect(() => {
-    try {
-      const jexlDebouncedCode = debouncedCode.startsWith('jexl:')
-        ? debouncedCode
-        : `jexl:${debouncedCode}`
-      stringToJexlExpression(
-        jexlDebouncedCode,
-        getEnv(slot).pluginManager?.jexl,
-      )
-      slot.set(jexlDebouncedCode)
-      setCodeError(null)
-    } catch (e) {
-      console.error({ e })
-      setCodeError(e)
-    }
-  }, [debouncedCode, slot])
-
-  // if default value is a callback, will have to remove jexl:
-  // do this last
-  return (
-    <>
-      <FormControl>
-        <InputLabel shrink htmlFor="callback-editor">
-          {slot.name}
-        </InputLabel>
-        <Editor
-          className={classes.callbackEditor}
-          value={code.startsWith('jexl:') ? code.split('jexl:')[1] : code}
-          onValueChange={newCode => setCode(newCode)}
-          highlight={newCode => newCode}
-          padding={10}
-          style={{ background: error ? '#fdd' : undefined }}
-        />
-        {error ? (
-          <FormHelperText
-            style={{ color: '#f00' }}
-          >{`${error}`}</FormHelperText>
-        ) : null}
-        <FormHelperText>{slot.description}</FormHelperText>
-      </FormControl>
-      <Tooltip
-        title={
-          <div>
-            Callbacks are written in Jexl format. Click to learn more.
-            <br /> Names of available context items: {slot.contextVariable}
-          </div>
-        }
-        arrow
-      >
-        <IconButton
-          color="primary"
-          onClick={() => {
-            const newWindow = window.open(
-              'https://github.com/TomFrost/Jexl',
-              '_blank',
-              'noopener,noreferrer',
-            )
-            if (newWindow) {
-              newWindow.opener = null
-            }
-          }}
-        >
-          <HelpIcon />
-        </IconButton>
-      </Tooltip>
-    </>
-  )
-}
-CallbackEditor.propTypes = {
-  slot: PropTypes.objectOrObservableObject.isRequired,
-}
-export default observer(CallbackEditor)

package/src/ConfigurationEditorWidget/components/CodeEditor.js

@@ -1,60 +0,0 @@
-import React, { useEffect } from 'react'
-import Editor from 'react-simple-code-editor'
-import { Light as SyntaxHighlighter } from 'react-syntax-highlighter'
-import json from 'react-syntax-highlighter/dist/cjs/languages/hljs/json'
-import a11yDark from 'react-syntax-highlighter/dist/cjs/styles/hljs/a11y-dark'
-import a11yLight from 'react-syntax-highlighter/dist/cjs/styles/hljs/a11y-light'
-import { useTheme, makeStyles } from '@material-ui/core'
-
-// fontSize and fontFamily have to match between Editor and SyntaxHighlighter
-const fontSize = '12px'
-// Optimize by using system default fonts: https://css-tricks.com/snippets/css/font-stacks/
-const fontFamily =
-  'Consolas, "Andale Mono WT", "Andale Mono", "Lucida Console", "Lucida Sans Typewriter", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Liberation Mono", "Nimbus Mono L", Monaco, "Courier New", Courier, monospace'
-
-const useStyles = makeStyles(theme => ({
-  callbackEditor: {
-    fontFamily,
-    fontSize,
-    background: theme.palette.background.default,
-    overflowX: 'auto',
-    marginTop: '16px',
-    border: '1px solid rgba(0,0,0,0.42)',
-  },
-  syntaxHighlighter: {
-    margin: 0,
-    fontFamily,
-    fontSize,
-  },
-}))
-
-// eslint-disable-next-line react/prop-types
-export default function CodeEditor({ contents, setContents }) {
-  const classes = useStyles()
-  const theme = useTheme()
-  useEffect(() => {
-    SyntaxHighlighter.registerLanguage('json', json)
-  }, [])
-
-  return (
-    <Editor
-      className={classes.callbackEditor}
-      value={contents}
-      onValueChange={setContents}
-      highlight={newCode => (
-        <SyntaxHighlighter
-          language="json"
-          style={theme.palette.type === 'dark' ? a11yDark : a11yLight}
-          className={classes.syntaxHighlighter}
-          // override some inline style stuff that's higher specificity
-          // than className
-          customStyle={{ background: 'none', padding: 0 }}
-        >
-          {newCode}
-        </SyntaxHighlighter>
-      )}
-      padding={10}
-      style={{}}
-    />
-  )
-}

package/src/ConfigurationEditorWidget/components/ColorPicker.tsx

@@ -1,52 +0,0 @@
-import React, { useState } from 'react'
-import { makeStyles } from '@material-ui/core/styles'
-import ReactPropTypes from 'prop-types'
-import { ChromePicker, Color, ColorResult } from 'react-color'
-
-const useStyles = makeStyles({
-  popover: {
-    position: 'absolute',
-    zIndex: 2,
-  },
-  cover: {
-    position: 'fixed',
-    top: 0,
-    right: 0,
-    bottom: 0,
-    left: 0,
-  },
-})
-
-export function ColorPicker(props: {
-  color: Color
-  onChange: (color: ColorResult) => void
-}) {
-  const { color, onChange } = props
-  const classes = useStyles()
-  const [displayColorPicker, setDisplayColorPicker] = useState(true)
-
-  const handleClose = () => {
-    setDisplayColorPicker(false)
-  }
-  return (
-    <div>
-      {displayColorPicker ? (
-        <div className={classes.popover}>
-          <div
-            role="presentation"
-            className={classes.cover}
-            onClick={handleClose}
-          />
-          <ChromePicker color={color} onChange={onChange} />
-        </div>
-      ) : null}
-    </div>
-  )
-}
-
-ColorPicker.propTypes = {
-  color: ReactPropTypes.string.isRequired,
-  onChange: ReactPropTypes.func.isRequired,
-}
-
-export default ColorPicker