@jbrowse/plugin-config 1.7.9 → 2.0.0

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/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/ConfigurationEditor.js

@@ -1,154 +0,0 @@
-import React from 'react'
-import {
-  readConfObject,
-  getTypeNamesFromExplicitlyTypedUnion,
-  isConfigurationSchemaType,
-  isConfigurationSlotType,
-} from '@jbrowse/core/configuration'
-import {
-  FormGroup,
-  Accordion,
-  AccordionDetails,
-  AccordionSummary,
-  Typography,
-  makeStyles,
-} from '@material-ui/core'
-import { observer } from 'mobx-react'
-import { getMembers } from 'mobx-state-tree'
-import { singular } from 'pluralize'
-
-// icons
-import ExpandMoreIcon from '@material-ui/icons/ExpandMore'
-
-// locals
-import SlotEditor from './SlotEditor'
-import TypeSelector from './TypeSelector'
-
-const useStyles = makeStyles(theme => ({
-  expandIcon: {
-    color: '#fff',
-  },
-  root: {
-    padding: theme.spacing(1, 3, 1, 1),
-  },
-  expansionPanelDetails: {
-    display: 'block',
-    padding: theme.spacing(1),
-  },
-
-  accordion: {
-    border: `1px solid ${theme.palette.text.primary}`,
-  },
-}))
-
-const Member = observer(props => {
-  const classes = useStyles()
-  const {
-    slotName,
-    slotSchema,
-    schema,
-    slot = schema[slotName],
-    path = [],
-  } = props
-  let typeSelector
-  if (isConfigurationSchemaType(slotSchema)) {
-    if (slot.length) {
-      return slot.map((subslot, slotIndex) => {
-        const key = `${singular(slotName)} ${slotIndex + 1}`
-        return <Member {...props} key={key} slot={subslot} slotName={key} />
-      })
-    }
-    // if this is an explicitly typed schema, make a type-selecting dropdown
-    // that can be used to change its type
-    const typeNameChoices = getTypeNamesFromExplicitlyTypedUnion(slotSchema)
-    if (typeNameChoices.length) {
-      typeSelector = (
-        <TypeSelector
-          typeNameChoices={typeNameChoices}
-          slotName={slotName}
-          slot={slot}
-          onChange={evt => {
-            if (evt.target.value !== slot.type) {
-              schema.setSubschema(slotName, { type: evt.target.value })
-            }
-          }}
-        />
-      )
-    }
-    return (
-      <Accordion
-        defaultExpanded
-        className={classes.accordion}
-        TransitionProps={{ unmountOnExit: true, timeout: 150 }}
-      >
-        <AccordionSummary
-          expandIcon={<ExpandMoreIcon className={classes.expandIcon} />}
-        >
-          <Typography>{[...path, slotName].join('🡒')}</Typography>
-        </AccordionSummary>
-        <AccordionDetails className={classes.expansionPanelDetails}>
-          {typeSelector}
-          <FormGroup>
-            <Schema schema={slot} path={[...path, slotName]} />
-          </FormGroup>
-        </AccordionDetails>
-      </Accordion>
-    )
-  }
-
-  if (isConfigurationSlotType(slotSchema)) {
-    // this is a regular config slot
-    return <SlotEditor key={slotName} slot={slot} slotSchema={slotSchema} />
-  }
-
-  return null
-})
-
-const Schema = observer(({ schema, path = [] }) => {
-  const properties = getMembers(schema).properties
-  return Object.entries(properties).map(([slotName, slotSchema]) => (
-    <Member
-      key={slotName}
-      slotName={slotName}
-      slotSchema={slotSchema}
-      path={path}
-      schema={schema}
-    />
-  ))
-})
-
-const ConfigurationEditor = observer(({ model }) => {
-  const classes = useStyles()
-  // key forces a re-render, otherwise the same field can end up being used
-  // for different tracks since only the backing model changes for example
-  // see pr #804
-  const key = model.target && readConfObject(model.target, 'trackId')
-  const name = model.target && readConfObject(model.target, 'name')
-  return (
-    <>
-      <Accordion
-        key={key}
-        defaultExpanded
-        className={classes.accordion}
-        TransitionProps={{ unmountOnExit: true, timeout: 150 }}
-      >
-        <AccordionSummary
-          expandIcon={<ExpandMoreIcon className={classes.expandIcon} />}
-        >
-          <Typography>{name ? name : 'Configuration'}</Typography>
-        </AccordionSummary>
-        <AccordionDetails
-          className={classes.expansionPanelDetails}
-          data-testid="configEditor"
-        >
-          {!model.target ? 'no target set' : <Schema schema={model.target} />}
-        </AccordionDetails>
-      </Accordion>
-
-      {/* blank space at the bottom of screen allows scroll */}
-      <div style={{ height: 300 }} />
-    </>
-  )
-})
-
-export default ConfigurationEditor