@jbrowse/plugin-data-management 1.7.0 → 1.7.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (52) hide show
  1. package/dist/AddConnectionWidget/components/AddConnectionWidget.d.ts +9 -9
  2. package/dist/AddConnectionWidget/components/ConfigureConnection.d.ts +2 -2
  3. package/dist/AddConnectionWidget/components/ConnectionTypeSelect.d.ts +8 -8
  4. package/dist/AddConnectionWidget/index.d.ts +2 -2
  5. package/dist/AddConnectionWidget/model.d.ts +5 -5
  6. package/dist/AddTrackWidget/components/AddTrackWidget.d.ts +7 -7
  7. package/dist/AddTrackWidget/components/ConfirmTrack.d.ts +7 -7
  8. package/dist/AddTrackWidget/components/TrackSourceSelect.d.ts +7 -7
  9. package/dist/AddTrackWidget/index.d.ts +2 -2
  10. package/dist/AddTrackWidget/model.d.ts +42 -42
  11. package/dist/AssemblyManager/AssemblyAddForm.d.ts +6 -6
  12. package/dist/AssemblyManager/AssemblyEditor.d.ts +5 -5
  13. package/dist/AssemblyManager/AssemblyManager.d.ts +6 -6
  14. package/dist/AssemblyManager/AssemblyTable.d.ts +13 -13
  15. package/dist/AssemblyManager/index.d.ts +1 -1
  16. package/dist/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.d.ts +7 -7
  17. package/dist/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.d.ts +13 -13
  18. package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts +6 -6
  19. package/dist/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.d.ts +9 -9
  20. package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.d.ts +10 -10
  21. package/dist/HierarchicalTrackSelectorWidget/index.d.ts +2 -2
  22. package/dist/HierarchicalTrackSelectorWidget/model.d.ts +37 -37
  23. package/dist/PluginStoreWidget/components/CustomPluginForm.d.ts +9 -9
  24. package/dist/PluginStoreWidget/components/InstalledPlugin.d.ts +11 -11
  25. package/dist/PluginStoreWidget/components/InstalledPluginsList.d.ts +9 -9
  26. package/dist/PluginStoreWidget/components/PluginCard.d.ts +10 -10
  27. package/dist/PluginStoreWidget/components/PluginStoreWidget.d.ts +7 -7
  28. package/dist/PluginStoreWidget/index.d.ts +3 -3
  29. package/dist/PluginStoreWidget/model.d.ts +13 -13
  30. package/dist/SetDefaultSession/SetDefaultSession.d.ts +6 -6
  31. package/dist/SetDefaultSession/index.d.ts +1 -1
  32. package/dist/index.d.ts +27 -27
  33. package/dist/ucsc-trackhub/configSchema.d.ts +2 -2
  34. package/dist/ucsc-trackhub/index.d.ts +2 -2
  35. package/dist/ucsc-trackhub/model.d.ts +15 -4
  36. package/dist/ucsc-trackhub/ucscAssemblies.d.ts +2 -2
  37. package/dist/ucsc-trackhub/ucscTrackHub.d.ts +6 -6
  38. package/package.json +4 -3
  39. package/dist/AddConnectionWidget/components/AddConnectionWidget.test.d.ts +0 -1
  40. package/dist/AddTrackWidget/components/AddTrackWidget.test.d.ts +0 -1
  41. package/dist/AddTrackWidget/index.test.d.ts +0 -1
  42. package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.d.ts +0 -1
  43. package/dist/HierarchicalTrackSelectorWidget/model.test.d.ts +0 -1
  44. package/dist/PluginStoreWidget/components/PluginStoreWidget.test.d.ts +0 -1
  45. package/dist/PluginStoreWidget/model.test.d.ts +0 -1
  46. package/dist/index.test.d.ts +0 -1
  47. package/dist/plugin-data-management.cjs.development.js +0 -4856
  48. package/dist/plugin-data-management.cjs.development.js.map +0 -1
  49. package/dist/plugin-data-management.cjs.production.min.js +0 -2
  50. package/dist/plugin-data-management.cjs.production.min.js.map +0 -1
  51. package/dist/plugin-data-management.esm.js +0 -4829
  52. package/dist/plugin-data-management.esm.js.map +0 -1
@@ -1,4829 +0,0 @@
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- import React, { useState, useEffect, lazy, Suspense, useRef, useMemo, useCallback } from 'react';
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- import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType';
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- import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
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- import Plugin from '@jbrowse/core/Plugin';
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- import { baseConnectionConfig, BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
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- import { ConfigurationSchema, ConfigurationReference, getConf, readConfObject } from '@jbrowse/core/configuration';
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- import { objectHash, getSession, isElectron } from '@jbrowse/core/util';
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- import { types, getParent, getEnv, getRoot } from 'mobx-state-tree';
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- import { openLocation } from '@jbrowse/core/util/io';
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- import { generateUnknownTrackConf, generateUnsupportedTrackConf, guessAdapter, getFileName, UNSUPPORTED, guessTrackType, UNKNOWN } from '@jbrowse/core/util/tracks';
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- import { ElementId } from '@jbrowse/core/util/types/mst';
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- import { observer, PropTypes } from 'mobx-react';
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- import { ListItem, IconButton, Typography, Tooltip, Dialog, DialogTitle, DialogContent, DialogActions, Button, makeStyles, List, Card, CardContent, Link, CardActions, DialogContentText, TextField, Collapse, InputAdornment, Accordion, AccordionSummary, TableRow, TableCell, TableContainer, Paper, Table, TableHead, TableBody, Grid, MenuItem, Fab, Menu, FormControlLabel, Checkbox, ListSubheader, Stepper, Step, StepLabel, StepContent } from '@material-ui/core';
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- import ExpandMoreIcon from '@material-ui/icons/ExpandMore';
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- import ClearIcon from '@material-ui/icons/Clear';
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- import InfoOutlinedIcon from '@material-ui/icons/InfoOutlined';
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- import CloseIcon from '@material-ui/icons/Close';
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- import LockIcon from '@material-ui/icons/Lock';
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- import { isSessionWithSessionPlugins } from '@jbrowse/core/util/types';
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- import PersonIcon from '@material-ui/icons/Person';
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- import AddIcon from '@material-ui/icons/Add';
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- import CheckIcon from '@material-ui/icons/Check';
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- import clsx from 'clsx';
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- import IconButton$1 from '@material-ui/core/IconButton';
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- import { makeStyles as makeStyles$1 } from '@material-ui/core/styles';
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- import ArrowBackIosIcon from '@material-ui/icons/ArrowBackIos';
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- import CreateIcon from '@material-ui/icons/Create';
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- import DeleteIcon from '@material-ui/icons/Delete';
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- import FileSelector from '@jbrowse/core/ui/FileSelector';
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- import { ConfigurationEditor } from '@jbrowse/plugin-config';
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- import ArrowDropDownIcon from '@material-ui/icons/ArrowDropDown';
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- import ArrowRightIcon from '@material-ui/icons/ArrowRight';
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- import MenuIcon from '@material-ui/icons/Menu';
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- import MoreIcon from '@material-ui/icons/MoreHoriz';
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- import { Cable } from '@jbrowse/core/ui/Icons';
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- import AutoSizer from 'react-virtualized-auto-sizer';
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- import JBrowseMenu from '@jbrowse/core/ui/Menu';
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- import { VariableSizeTree } from 'react-vtree';
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- import { Alert } from '@material-ui/lab';
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- import { FileSelector as FileSelector$1 } from '@jbrowse/core/ui';
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- import Button$1 from '@material-ui/core/Button';
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- import Step$1 from '@material-ui/core/Step';
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- import StepContent$1 from '@material-ui/core/StepContent';
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- import StepLabel$1 from '@material-ui/core/StepLabel';
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- import Stepper$1 from '@material-ui/core/Stepper';
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- import Typography$1 from '@material-ui/core/Typography';
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- import MenuItem$1 from '@material-ui/core/MenuItem';
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- import TextField$1 from '@material-ui/core/TextField';
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- function _createClass(Constructor, protoProps, staticProps) {
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- if (protoProps) _defineProperties(Constructor.prototype, protoProps);
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- if (key in obj) {
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- if (typeof superClass !== "function" && superClass !== null) {
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- throw new TypeError("Super expression must either be null or a function");
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- }
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-
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- subClass.prototype = Object.create(superClass && superClass.prototype, {
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- constructor: {
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- value: subClass,
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- writable: true,
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- configurable: true
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- }
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- });
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- Object.defineProperty(subClass, "prototype", {
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- writable: false
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- });
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- if (superClass) _setPrototypeOf(subClass, superClass);
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- }
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-
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- function _getPrototypeOf(o) {
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- _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) {
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- return o.__proto__ || Object.getPrototypeOf(o);
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- };
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- return _getPrototypeOf(o);
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- }
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-
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- function _setPrototypeOf(o, p) {
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- _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) {
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- o.__proto__ = p;
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- return o;
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- };
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-
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- return _setPrototypeOf(o, p);
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- }
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-
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- function _isNativeReflectConstruct() {
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- if (typeof Reflect === "undefined" || !Reflect.construct) return false;
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- if (typeof Proxy === "function") return true;
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-
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- Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {}));
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- return true;
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- } catch (e) {
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- return false;
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- }
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-
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- function _assertThisInitialized(self) {
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- if (self === void 0) {
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- throw new ReferenceError("this hasn't been initialised - super() hasn't been called");
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- }
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-
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- return self;
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- }
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- function _possibleConstructorReturn(self, call) {
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- if (call && (typeof call === "object" || typeof call === "function")) {
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- return call;
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- } else if (call !== void 0) {
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- throw new TypeError("Derived constructors may only return object or undefined");
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- }
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- return _assertThisInitialized(self);
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- }
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- function _createSuper(Derived) {
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- var hasNativeReflectConstruct = _isNativeReflectConstruct();
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- return function _createSuperInternal() {
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- result;
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- if (hasNativeReflectConstruct) {
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- var NewTarget = _getPrototypeOf(this).constructor;
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-
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- result = Reflect.construct(Super, arguments, NewTarget);
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- } else {
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- result = Super.apply(this, arguments);
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- }
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- return _possibleConstructorReturn(this, result);
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- };
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- }
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-
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- function _slicedToArray(arr, i) {
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- return _arrayWithHoles(arr) || _iterableToArrayLimit(arr, i) || _unsupportedIterableToArray(arr, i) || _nonIterableRest();
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- }
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-
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- function _toConsumableArray(arr) {
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- return _arrayWithoutHoles(arr) || _iterableToArray(arr) || _unsupportedIterableToArray(arr) || _nonIterableSpread();
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- }
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-
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- function _arrayWithoutHoles(arr) {
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- if (Array.isArray(arr)) return _arrayLikeToArray(arr);
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- }
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- function _arrayWithHoles(arr) {
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- if (Array.isArray(arr)) return arr;
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- }
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- function _iterableToArray(iter) {
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- if (typeof Symbol !== "undefined" && iter[Symbol.iterator] != null || iter["@@iterator"] != null) return Array.from(iter);
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- }
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-
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- function _iterableToArrayLimit(arr, i) {
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-
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- if (_i == null) return;
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- var _arr = [];
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- var _n = true;
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- var _d = false;
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-
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- var _s, _e;
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-
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- try {
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- for (_i = _i.call(arr); !(_n = (_s = _i.next()).done); _n = true) {
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- _arr.push(_s.value);
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-
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- if (i && _arr.length === i) break;
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- }
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- } catch (err) {
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- _d = true;
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- _e = err;
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- } finally {
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- try {
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- if (!_n && _i["return"] != null) _i["return"]();
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- } finally {
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- if (_d) throw _e;
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- }
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- }
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- return _arr;
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- }
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- function _unsupportedIterableToArray(o, minLen) {
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- if (!o) return;
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- if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen);
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- }
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- function _arrayLikeToArray(arr, len) {
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- if (len == null || len > arr.length) len = arr.length;
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- throw new TypeError("Invalid attempt to spread non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.");
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- }
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-
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- var ucscConfigSchema = /*#__PURE__*/ConfigurationSchema('UCSCTrackHubConnection', {
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- hubTxtLocation: {
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- defaultValue: {
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- uri: 'http://mysite.com/path/to/hub.txt',
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- },
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- description: 'location of the hub file (usually called hub.txt)'
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- },
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- assemblyNames: {
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- baseConfiguration: baseConnectionConfig
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- /**
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- * Copyright (c) 2014-present, Facebook, Inc.
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- *
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- * This source code is licensed under the MIT license found in the
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- */
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- var runtime = function (exports) {
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- // record like context.tryEntries[i].completion. This interface could
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- // invoked without arguments, but in all the cases we care about we
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- // only additional allocation required is the completion record, which
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- arg: fn.call(obj, arg)
465
- };
466
- } catch (err) {
467
- return {
468
- type: "throw",
469
- arg: err
470
- };
471
- }
472
- }
473
-
474
- var GenStateSuspendedStart = "suspendedStart";
475
- var GenStateSuspendedYield = "suspendedYield";
476
- var GenStateExecuting = "executing";
477
- var GenStateCompleted = "completed"; // Returning this object from the innerFn has the same effect as
478
- // breaking out of the dispatch switch statement.
479
-
480
- var ContinueSentinel = {}; // Dummy constructor functions that we use as the .constructor and
481
- // .constructor.prototype properties for functions that return Generator
482
- // objects. For full spec compliance, you may wish to configure your
483
- // minifier not to mangle the names of these two functions.
484
-
485
- function Generator() {}
486
-
487
- function GeneratorFunction() {}
488
-
489
- function GeneratorFunctionPrototype() {} // This is a polyfill for %IteratorPrototype% for environments that
490
- // don't natively support it.
491
-
492
-
493
- var IteratorPrototype = {};
494
- define(IteratorPrototype, iteratorSymbol, function () {
495
- return this;
496
- });
497
- var getProto = Object.getPrototypeOf;
498
- var NativeIteratorPrototype = getProto && getProto(getProto(values([])));
499
-
500
- if (NativeIteratorPrototype && NativeIteratorPrototype !== Op && hasOwn.call(NativeIteratorPrototype, iteratorSymbol)) {
501
- // This environment has a native %IteratorPrototype%; use it instead
502
- // of the polyfill.
503
- IteratorPrototype = NativeIteratorPrototype;
504
- }
505
-
506
- var Gp = GeneratorFunctionPrototype.prototype = Generator.prototype = Object.create(IteratorPrototype);
507
- GeneratorFunction.prototype = GeneratorFunctionPrototype;
508
- define(Gp, "constructor", GeneratorFunctionPrototype);
509
- define(GeneratorFunctionPrototype, "constructor", GeneratorFunction);
510
- GeneratorFunction.displayName = define(GeneratorFunctionPrototype, toStringTagSymbol, "GeneratorFunction"); // Helper for defining the .next, .throw, and .return methods of the
511
- // Iterator interface in terms of a single ._invoke method.
512
-
513
- function defineIteratorMethods(prototype) {
514
- ["next", "throw", "return"].forEach(function (method) {
515
- define(prototype, method, function (arg) {
516
- return this._invoke(method, arg);
517
- });
518
- });
519
- }
520
-
521
- exports.isGeneratorFunction = function (genFun) {
522
- var ctor = typeof genFun === "function" && genFun.constructor;
523
- return ctor ? ctor === GeneratorFunction || // For the native GeneratorFunction constructor, the best we can
524
- // do is to check its .name property.
525
- (ctor.displayName || ctor.name) === "GeneratorFunction" : false;
526
- };
527
-
528
- exports.mark = function (genFun) {
529
- if (Object.setPrototypeOf) {
530
- Object.setPrototypeOf(genFun, GeneratorFunctionPrototype);
531
- } else {
532
- genFun.__proto__ = GeneratorFunctionPrototype;
533
- define(genFun, toStringTagSymbol, "GeneratorFunction");
534
- }
535
-
536
- genFun.prototype = Object.create(Gp);
537
- return genFun;
538
- }; // Within the body of any async function, `await x` is transformed to
539
- // `yield regeneratorRuntime.awrap(x)`, so that the runtime can test
540
- // `hasOwn.call(value, "__await")` to determine if the yielded value is
541
- // meant to be awaited.
542
-
543
-
544
- exports.awrap = function (arg) {
545
- return {
546
- __await: arg
547
- };
548
- };
549
-
550
- function AsyncIterator(generator, PromiseImpl) {
551
- function invoke(method, arg, resolve, reject) {
552
- var record = tryCatch(generator[method], generator, arg);
553
-
554
- if (record.type === "throw") {
555
- reject(record.arg);
556
- } else {
557
- var result = record.arg;
558
- var value = result.value;
559
-
560
- if (value && typeof value === "object" && hasOwn.call(value, "__await")) {
561
- return PromiseImpl.resolve(value.__await).then(function (value) {
562
- invoke("next", value, resolve, reject);
563
- }, function (err) {
564
- invoke("throw", err, resolve, reject);
565
- });
566
- }
567
-
568
- return PromiseImpl.resolve(value).then(function (unwrapped) {
569
- // When a yielded Promise is resolved, its final value becomes
570
- // the .value of the Promise<{value,done}> result for the
571
- // current iteration.
572
- result.value = unwrapped;
573
- resolve(result);
574
- }, function (error) {
575
- // If a rejected Promise was yielded, throw the rejection back
576
- // into the async generator function so it can be handled there.
577
- return invoke("throw", error, resolve, reject);
578
- });
579
- }
580
- }
581
-
582
- var previousPromise;
583
-
584
- function enqueue(method, arg) {
585
- function callInvokeWithMethodAndArg() {
586
- return new PromiseImpl(function (resolve, reject) {
587
- invoke(method, arg, resolve, reject);
588
- });
589
- }
590
-
591
- return previousPromise = // If enqueue has been called before, then we want to wait until
592
- // all previous Promises have been resolved before calling invoke,
593
- // so that results are always delivered in the correct order. If
594
- // enqueue has not been called before, then it is important to
595
- // call invoke immediately, without waiting on a callback to fire,
596
- // so that the async generator function has the opportunity to do
597
- // any necessary setup in a predictable way. This predictability
598
- // is why the Promise constructor synchronously invokes its
599
- // executor callback, and why async functions synchronously
600
- // execute code before the first await. Since we implement simple
601
- // async functions in terms of async generators, it is especially
602
- // important to get this right, even though it requires care.
603
- previousPromise ? previousPromise.then(callInvokeWithMethodAndArg, // Avoid propagating failures to Promises returned by later
604
- // invocations of the iterator.
605
- callInvokeWithMethodAndArg) : callInvokeWithMethodAndArg();
606
- } // Define the unified helper method that is used to implement .next,
607
- // .throw, and .return (see defineIteratorMethods).
608
-
609
-
610
- this._invoke = enqueue;
611
- }
612
-
613
- defineIteratorMethods(AsyncIterator.prototype);
614
- define(AsyncIterator.prototype, asyncIteratorSymbol, function () {
615
- return this;
616
- });
617
- exports.AsyncIterator = AsyncIterator; // Note that simple async functions are implemented on top of
618
- // AsyncIterator objects; they just return a Promise for the value of
619
- // the final result produced by the iterator.
620
-
621
- exports.async = function (innerFn, outerFn, self, tryLocsList, PromiseImpl) {
622
- if (PromiseImpl === void 0) PromiseImpl = Promise;
623
- var iter = new AsyncIterator(wrap(innerFn, outerFn, self, tryLocsList), PromiseImpl);
624
- return exports.isGeneratorFunction(outerFn) ? iter // If outerFn is a generator, return the full iterator.
625
- : iter.next().then(function (result) {
626
- return result.done ? result.value : iter.next();
627
- });
628
- };
629
-
630
- function makeInvokeMethod(innerFn, self, context) {
631
- var state = GenStateSuspendedStart;
632
- return function invoke(method, arg) {
633
- if (state === GenStateExecuting) {
634
- throw new Error("Generator is already running");
635
- }
636
-
637
- if (state === GenStateCompleted) {
638
- if (method === "throw") {
639
- throw arg;
640
- } // Be forgiving, per 25.3.3.3.3 of the spec:
641
- // https://people.mozilla.org/~jorendorff/es6-draft.html#sec-generatorresume
642
-
643
-
644
- return doneResult();
645
- }
646
-
647
- context.method = method;
648
- context.arg = arg;
649
-
650
- while (true) {
651
- var delegate = context.delegate;
652
-
653
- if (delegate) {
654
- var delegateResult = maybeInvokeDelegate(delegate, context);
655
-
656
- if (delegateResult) {
657
- if (delegateResult === ContinueSentinel) continue;
658
- return delegateResult;
659
- }
660
- }
661
-
662
- if (context.method === "next") {
663
- // Setting context._sent for legacy support of Babel's
664
- // function.sent implementation.
665
- context.sent = context._sent = context.arg;
666
- } else if (context.method === "throw") {
667
- if (state === GenStateSuspendedStart) {
668
- state = GenStateCompleted;
669
- throw context.arg;
670
- }
671
-
672
- context.dispatchException(context.arg);
673
- } else if (context.method === "return") {
674
- context.abrupt("return", context.arg);
675
- }
676
-
677
- state = GenStateExecuting;
678
- var record = tryCatch(innerFn, self, context);
679
-
680
- if (record.type === "normal") {
681
- // If an exception is thrown from innerFn, we leave state ===
682
- // GenStateExecuting and loop back for another invocation.
683
- state = context.done ? GenStateCompleted : GenStateSuspendedYield;
684
-
685
- if (record.arg === ContinueSentinel) {
686
- continue;
687
- }
688
-
689
- return {
690
- value: record.arg,
691
- done: context.done
692
- };
693
- } else if (record.type === "throw") {
694
- state = GenStateCompleted; // Dispatch the exception by looping back around to the
695
- // context.dispatchException(context.arg) call above.
696
-
697
- context.method = "throw";
698
- context.arg = record.arg;
699
- }
700
- }
701
- };
702
- } // Call delegate.iterator[context.method](context.arg) and handle the
703
- // result, either by returning a { value, done } result from the
704
- // delegate iterator, or by modifying context.method and context.arg,
705
- // setting context.delegate to null, and returning the ContinueSentinel.
706
-
707
-
708
- function maybeInvokeDelegate(delegate, context) {
709
- var method = delegate.iterator[context.method];
710
-
711
- if (method === undefined$1) {
712
- // A .throw or .return when the delegate iterator has no .throw
713
- // method always terminates the yield* loop.
714
- context.delegate = null;
715
-
716
- if (context.method === "throw") {
717
- // Note: ["return"] must be used for ES3 parsing compatibility.
718
- if (delegate.iterator["return"]) {
719
- // If the delegate iterator has a return method, give it a
720
- // chance to clean up.
721
- context.method = "return";
722
- context.arg = undefined$1;
723
- maybeInvokeDelegate(delegate, context);
724
-
725
- if (context.method === "throw") {
726
- // If maybeInvokeDelegate(context) changed context.method from
727
- // "return" to "throw", let that override the TypeError below.
728
- return ContinueSentinel;
729
- }
730
- }
731
-
732
- context.method = "throw";
733
- context.arg = new TypeError("The iterator does not provide a 'throw' method");
734
- }
735
-
736
- return ContinueSentinel;
737
- }
738
-
739
- var record = tryCatch(method, delegate.iterator, context.arg);
740
-
741
- if (record.type === "throw") {
742
- context.method = "throw";
743
- context.arg = record.arg;
744
- context.delegate = null;
745
- return ContinueSentinel;
746
- }
747
-
748
- var info = record.arg;
749
-
750
- if (!info) {
751
- context.method = "throw";
752
- context.arg = new TypeError("iterator result is not an object");
753
- context.delegate = null;
754
- return ContinueSentinel;
755
- }
756
-
757
- if (info.done) {
758
- // Assign the result of the finished delegate to the temporary
759
- // variable specified by delegate.resultName (see delegateYield).
760
- context[delegate.resultName] = info.value; // Resume execution at the desired location (see delegateYield).
761
-
762
- context.next = delegate.nextLoc; // If context.method was "throw" but the delegate handled the
763
- // exception, let the outer generator proceed normally. If
764
- // context.method was "next", forget context.arg since it has been
765
- // "consumed" by the delegate iterator. If context.method was
766
- // "return", allow the original .return call to continue in the
767
- // outer generator.
768
-
769
- if (context.method !== "return") {
770
- context.method = "next";
771
- context.arg = undefined$1;
772
- }
773
- } else {
774
- // Re-yield the result returned by the delegate method.
775
- return info;
776
- } // The delegate iterator is finished, so forget it and continue with
777
- // the outer generator.
778
-
779
-
780
- context.delegate = null;
781
- return ContinueSentinel;
782
- } // Define Generator.prototype.{next,throw,return} in terms of the
783
- // unified ._invoke helper method.
784
-
785
-
786
- defineIteratorMethods(Gp);
787
- define(Gp, toStringTagSymbol, "Generator"); // A Generator should always return itself as the iterator object when the
788
- // @@iterator function is called on it. Some browsers' implementations of the
789
- // iterator prototype chain incorrectly implement this, causing the Generator
790
- // object to not be returned from this call. This ensures that doesn't happen.
791
- // See https://github.com/facebook/regenerator/issues/274 for more details.
792
-
793
- define(Gp, iteratorSymbol, function () {
794
- return this;
795
- });
796
- define(Gp, "toString", function () {
797
- return "[object Generator]";
798
- });
799
-
800
- function pushTryEntry(locs) {
801
- var entry = {
802
- tryLoc: locs[0]
803
- };
804
-
805
- if (1 in locs) {
806
- entry.catchLoc = locs[1];
807
- }
808
-
809
- if (2 in locs) {
810
- entry.finallyLoc = locs[2];
811
- entry.afterLoc = locs[3];
812
- }
813
-
814
- this.tryEntries.push(entry);
815
- }
816
-
817
- function resetTryEntry(entry) {
818
- var record = entry.completion || {};
819
- record.type = "normal";
820
- delete record.arg;
821
- entry.completion = record;
822
- }
823
-
824
- function Context(tryLocsList) {
825
- // The root entry object (effectively a try statement without a catch
826
- // or a finally block) gives us a place to store values thrown from
827
- // locations where there is no enclosing try statement.
828
- this.tryEntries = [{
829
- tryLoc: "root"
830
- }];
831
- tryLocsList.forEach(pushTryEntry, this);
832
- this.reset(true);
833
- }
834
-
835
- exports.keys = function (object) {
836
- var keys = [];
837
-
838
- for (var key in object) {
839
- keys.push(key);
840
- }
841
-
842
- keys.reverse(); // Rather than returning an object with a next method, we keep
843
- // things simple and return the next function itself.
844
-
845
- return function next() {
846
- while (keys.length) {
847
- var key = keys.pop();
848
-
849
- if (key in object) {
850
- next.value = key;
851
- next.done = false;
852
- return next;
853
- }
854
- } // To avoid creating an additional object, we just hang the .value
855
- // and .done properties off the next function object itself. This
856
- // also ensures that the minifier will not anonymize the function.
857
-
858
-
859
- next.done = true;
860
- return next;
861
- };
862
- };
863
-
864
- function values(iterable) {
865
- if (iterable) {
866
- var iteratorMethod = iterable[iteratorSymbol];
867
-
868
- if (iteratorMethod) {
869
- return iteratorMethod.call(iterable);
870
- }
871
-
872
- if (typeof iterable.next === "function") {
873
- return iterable;
874
- }
875
-
876
- if (!isNaN(iterable.length)) {
877
- var i = -1,
878
- next = function next() {
879
- while (++i < iterable.length) {
880
- if (hasOwn.call(iterable, i)) {
881
- next.value = iterable[i];
882
- next.done = false;
883
- return next;
884
- }
885
- }
886
-
887
- next.value = undefined$1;
888
- next.done = true;
889
- return next;
890
- };
891
-
892
- return next.next = next;
893
- }
894
- } // Return an iterator with no values.
895
-
896
-
897
- return {
898
- next: doneResult
899
- };
900
- }
901
-
902
- exports.values = values;
903
-
904
- function doneResult() {
905
- return {
906
- value: undefined$1,
907
- done: true
908
- };
909
- }
910
-
911
- Context.prototype = {
912
- constructor: Context,
913
- reset: function reset(skipTempReset) {
914
- this.prev = 0;
915
- this.next = 0; // Resetting context._sent for legacy support of Babel's
916
- // function.sent implementation.
917
-
918
- this.sent = this._sent = undefined$1;
919
- this.done = false;
920
- this.delegate = null;
921
- this.method = "next";
922
- this.arg = undefined$1;
923
- this.tryEntries.forEach(resetTryEntry);
924
-
925
- if (!skipTempReset) {
926
- for (var name in this) {
927
- // Not sure about the optimal order of these conditions:
928
- if (name.charAt(0) === "t" && hasOwn.call(this, name) && !isNaN(+name.slice(1))) {
929
- this[name] = undefined$1;
930
- }
931
- }
932
- }
933
- },
934
- stop: function stop() {
935
- this.done = true;
936
- var rootEntry = this.tryEntries[0];
937
- var rootRecord = rootEntry.completion;
938
-
939
- if (rootRecord.type === "throw") {
940
- throw rootRecord.arg;
941
- }
942
-
943
- return this.rval;
944
- },
945
- dispatchException: function dispatchException(exception) {
946
- if (this.done) {
947
- throw exception;
948
- }
949
-
950
- var context = this;
951
-
952
- function handle(loc, caught) {
953
- record.type = "throw";
954
- record.arg = exception;
955
- context.next = loc;
956
-
957
- if (caught) {
958
- // If the dispatched exception was caught by a catch block,
959
- // then let that catch block handle the exception normally.
960
- context.method = "next";
961
- context.arg = undefined$1;
962
- }
963
-
964
- return !!caught;
965
- }
966
-
967
- for (var i = this.tryEntries.length - 1; i >= 0; --i) {
968
- var entry = this.tryEntries[i];
969
- var record = entry.completion;
970
-
971
- if (entry.tryLoc === "root") {
972
- // Exception thrown outside of any try block that could handle
973
- // it, so set the completion value of the entire function to
974
- // throw the exception.
975
- return handle("end");
976
- }
977
-
978
- if (entry.tryLoc <= this.prev) {
979
- var hasCatch = hasOwn.call(entry, "catchLoc");
980
- var hasFinally = hasOwn.call(entry, "finallyLoc");
981
-
982
- if (hasCatch && hasFinally) {
983
- if (this.prev < entry.catchLoc) {
984
- return handle(entry.catchLoc, true);
985
- } else if (this.prev < entry.finallyLoc) {
986
- return handle(entry.finallyLoc);
987
- }
988
- } else if (hasCatch) {
989
- if (this.prev < entry.catchLoc) {
990
- return handle(entry.catchLoc, true);
991
- }
992
- } else if (hasFinally) {
993
- if (this.prev < entry.finallyLoc) {
994
- return handle(entry.finallyLoc);
995
- }
996
- } else {
997
- throw new Error("try statement without catch or finally");
998
- }
999
- }
1000
- }
1001
- },
1002
- abrupt: function abrupt(type, arg) {
1003
- for (var i = this.tryEntries.length - 1; i >= 0; --i) {
1004
- var entry = this.tryEntries[i];
1005
-
1006
- if (entry.tryLoc <= this.prev && hasOwn.call(entry, "finallyLoc") && this.prev < entry.finallyLoc) {
1007
- var finallyEntry = entry;
1008
- break;
1009
- }
1010
- }
1011
-
1012
- if (finallyEntry && (type === "break" || type === "continue") && finallyEntry.tryLoc <= arg && arg <= finallyEntry.finallyLoc) {
1013
- // Ignore the finally entry if control is not jumping to a
1014
- // location outside the try/catch block.
1015
- finallyEntry = null;
1016
- }
1017
-
1018
- var record = finallyEntry ? finallyEntry.completion : {};
1019
- record.type = type;
1020
- record.arg = arg;
1021
-
1022
- if (finallyEntry) {
1023
- this.method = "next";
1024
- this.next = finallyEntry.finallyLoc;
1025
- return ContinueSentinel;
1026
- }
1027
-
1028
- return this.complete(record);
1029
- },
1030
- complete: function complete(record, afterLoc) {
1031
- if (record.type === "throw") {
1032
- throw record.arg;
1033
- }
1034
-
1035
- if (record.type === "break" || record.type === "continue") {
1036
- this.next = record.arg;
1037
- } else if (record.type === "return") {
1038
- this.rval = this.arg = record.arg;
1039
- this.method = "return";
1040
- this.next = "end";
1041
- } else if (record.type === "normal" && afterLoc) {
1042
- this.next = afterLoc;
1043
- }
1044
-
1045
- return ContinueSentinel;
1046
- },
1047
- finish: function finish(finallyLoc) {
1048
- for (var i = this.tryEntries.length - 1; i >= 0; --i) {
1049
- var entry = this.tryEntries[i];
1050
-
1051
- if (entry.finallyLoc === finallyLoc) {
1052
- this.complete(entry.completion, entry.afterLoc);
1053
- resetTryEntry(entry);
1054
- return ContinueSentinel;
1055
- }
1056
- }
1057
- },
1058
- "catch": function _catch(tryLoc) {
1059
- for (var i = this.tryEntries.length - 1; i >= 0; --i) {
1060
- var entry = this.tryEntries[i];
1061
-
1062
- if (entry.tryLoc === tryLoc) {
1063
- var record = entry.completion;
1064
-
1065
- if (record.type === "throw") {
1066
- var thrown = record.arg;
1067
- resetTryEntry(entry);
1068
- }
1069
-
1070
- return thrown;
1071
- }
1072
- } // The context.catch method must only be called with a location
1073
- // argument that corresponds to a known catch block.
1074
-
1075
-
1076
- throw new Error("illegal catch attempt");
1077
- },
1078
- delegateYield: function delegateYield(iterable, resultName, nextLoc) {
1079
- this.delegate = {
1080
- iterator: values(iterable),
1081
- resultName: resultName,
1082
- nextLoc: nextLoc
1083
- };
1084
-
1085
- if (this.method === "next") {
1086
- // Deliberately forget the last sent value so that we don't
1087
- // accidentally pass it on to the delegate.
1088
- this.arg = undefined$1;
1089
- }
1090
-
1091
- return ContinueSentinel;
1092
- }
1093
- }; // Regardless of whether this script is executing as a CommonJS module
1094
- // or not, return the runtime object so that we can declare the variable
1095
- // regeneratorRuntime in the outer scope, which allows this module to be
1096
- // injected easily by `bin/regenerator --include-runtime script.js`.
1097
-
1098
- return exports;
1099
- }( // If this script is executing as a CommonJS module, use module.exports
1100
- // as the regeneratorRuntime namespace. Otherwise create a new empty
1101
- // object. Either way, the resulting object will be used to initialize
1102
- // the regeneratorRuntime variable at the top of this file.
1103
- module.exports );
1104
-
1105
- try {
1106
- regeneratorRuntime = runtime;
1107
- } catch (accidentalStrictMode) {
1108
- // This module should not be running in strict mode, so the above
1109
- // assignment should always work unless something is misconfigured. Just
1110
- // in case runtime.js accidentally runs in strict mode, in modern engines
1111
- // we can explicitly access globalThis. In older engines we can escape
1112
- // strict mode using a global Function call. This could conceivably fail
1113
- // if a Content Security Policy forbids using Function, but in that case
1114
- // the proper solution is to fix the accidental strict mode problem. If
1115
- // you've misconfigured your bundler to force strict mode and applied a
1116
- // CSP to forbid Function, and you're not willing to fix either of those
1117
- // problems, please detail your unique predicament in a GitHub issue.
1118
- if (typeof globalThis === "object") {
1119
- globalThis.regeneratorRuntime = runtime;
1120
- } else {
1121
- Function("r", "regeneratorRuntime = r")(runtime);
1122
- }
1123
- }
1124
- });
1125
-
1126
- function fetchHubFile(_x) {
1127
- return _fetchHubFile.apply(this, arguments);
1128
- }
1129
-
1130
- function _fetchHubFile() {
1131
- _fetchHubFile = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee(hubFileLocation) {
1132
- var hubFileText, _yield$import, HubFile;
1133
-
1134
- return runtime_1.wrap(function _callee$(_context) {
1135
- while (1) {
1136
- switch (_context.prev = _context.next) {
1137
- case 0:
1138
- _context.prev = 0;
1139
- _context.next = 3;
1140
- return openLocation(hubFileLocation).readFile('utf8');
1141
-
1142
- case 3:
1143
- hubFileText = _context.sent;
1144
- _context.next = 6;
1145
- return import('@gmod/ucsc-hub');
1146
-
1147
- case 6:
1148
- _yield$import = _context.sent;
1149
- HubFile = _yield$import.HubFile;
1150
- return _context.abrupt("return", new HubFile(hubFileText));
1151
-
1152
- case 11:
1153
- _context.prev = 11;
1154
- _context.t0 = _context["catch"](0);
1155
- throw new Error("Not a valid hub.txt file, got error: '".concat(_context.t0, "'"));
1156
-
1157
- case 14:
1158
- case "end":
1159
- return _context.stop();
1160
- }
1161
- }
1162
- }, _callee, null, [[0, 11]]);
1163
- }));
1164
- return _fetchHubFile.apply(this, arguments);
1165
- }
1166
-
1167
- function fetchGenomesFile(_x2) {
1168
- return _fetchGenomesFile.apply(this, arguments);
1169
- }
1170
-
1171
- function _fetchGenomesFile() {
1172
- _fetchGenomesFile = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee2(genomesFileLocation) {
1173
- var genomesFileText, _yield$import2, GenomesFile;
1174
-
1175
- return runtime_1.wrap(function _callee2$(_context2) {
1176
- while (1) {
1177
- switch (_context2.prev = _context2.next) {
1178
- case 0:
1179
- _context2.next = 2;
1180
- return openLocation(genomesFileLocation).readFile('utf8');
1181
-
1182
- case 2:
1183
- genomesFileText = _context2.sent;
1184
- _context2.next = 5;
1185
- return import('@gmod/ucsc-hub');
1186
-
1187
- case 5:
1188
- _yield$import2 = _context2.sent;
1189
- GenomesFile = _yield$import2.GenomesFile;
1190
- return _context2.abrupt("return", new GenomesFile(genomesFileText));
1191
-
1192
- case 8:
1193
- case "end":
1194
- return _context2.stop();
1195
- }
1196
- }
1197
- }, _callee2);
1198
- }));
1199
- return _fetchGenomesFile.apply(this, arguments);
1200
- }
1201
-
1202
- function fetchTrackDbFile(_x3) {
1203
- return _fetchTrackDbFile.apply(this, arguments);
1204
- }
1205
-
1206
- function _fetchTrackDbFile() {
1207
- _fetchTrackDbFile = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3(trackDbFileLocation) {
1208
- var text, _yield$import3, TrackDbFile;
1209
-
1210
- return runtime_1.wrap(function _callee3$(_context3) {
1211
- while (1) {
1212
- switch (_context3.prev = _context3.next) {
1213
- case 0:
1214
- _context3.next = 2;
1215
- return openLocation(trackDbFileLocation).readFile('utf8');
1216
-
1217
- case 2:
1218
- text = _context3.sent;
1219
- _context3.next = 5;
1220
- return import('@gmod/ucsc-hub');
1221
-
1222
- case 5:
1223
- _yield$import3 = _context3.sent;
1224
- TrackDbFile = _yield$import3.TrackDbFile;
1225
- return _context3.abrupt("return", new TrackDbFile(text));
1226
-
1227
- case 8:
1228
- case "end":
1229
- return _context3.stop();
1230
- }
1231
- }
1232
- }, _callee3);
1233
- }));
1234
- return _fetchTrackDbFile.apply(this, arguments);
1235
- }
1236
-
1237
- function generateTracks(trackDb, trackDbFileLocation, assemblyName, sequenceAdapter) {
1238
- var tracks = [];
1239
- trackDb.forEach(function (track, trackName) {
1240
- var trackKeys = Array.from(track.keys());
1241
- var parentTrackKeys = ['superTrack', 'compositeTrack', 'container', 'view'];
1242
-
1243
- if (trackKeys.some(function (key) {
1244
- return parentTrackKeys.includes(key);
1245
- })) {
1246
- return;
1247
- }
1248
-
1249
- var parentTracks = [];
1250
- var currentTrackName = trackName;
1251
-
1252
- do {
1253
- currentTrackName = trackDb.get(currentTrackName).get('parent');
1254
-
1255
- if (currentTrackName) {
1256
-
1257
- var _currentTrackName$spl = currentTrackName.split(' ');
1258
-
1259
- var _currentTrackName$spl2 = _slicedToArray(_currentTrackName$spl, 1);
1260
-
1261
- currentTrackName = _currentTrackName$spl2[0];
1262
- parentTracks.push(trackDb.get(currentTrackName));
1263
- }
1264
- } while (currentTrackName);
1265
-
1266
- parentTracks.reverse();
1267
- var categories = parentTracks.map(function (parentTrack) {
1268
- return parentTrack.get('shortLabel');
1269
- });
1270
- var res = makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter);
1271
- res.trackId = "ucsc-trackhub-".concat(objectHash(res));
1272
- res.assemblyNames = [assemblyName];
1273
- tracks.push(res);
1274
- });
1275
- return tracks;
1276
- }
1277
-
1278
- function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter) {
1279
- var trackType = track.get('type');
1280
-
1281
- if (!trackType) {
1282
- trackType = trackDb.get(track.get('parent')).get('type');
1283
- }
1284
-
1285
- var baseTrackType = trackType.split(' ')[0];
1286
-
1287
- if (baseTrackType === 'bam' && track.get('bigDataUrl').toLowerCase().endsWith('cram')) {
1288
- baseTrackType = 'cram';
1289
- }
1290
-
1291
- var bigDataLocation;
1292
-
1293
- if (trackDbFileLocation.uri) {
1294
- bigDataLocation = {
1295
- uri: new URL(track.get('bigDataUrl'), trackDbFileLocation.uri).href,
1296
- locationType: 'UriLocation'
1297
- };
1298
- } else {
1299
- bigDataLocation = {
1300
- localPath: track.get('bigDataUrl'),
1301
- locationType: 'LocalPathLocation'
1302
- };
1303
- }
1304
-
1305
- var bigDataIndexLocation;
1306
-
1307
- switch (baseTrackType) {
1308
- case 'bam':
1309
- if (trackDbFileLocation.uri) {
1310
- bigDataIndexLocation = track.get('bigDataIndex') ? {
1311
- uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri).href,
1312
- locationType: 'UriLocation'
1313
- } : {
1314
- uri: new URL("".concat(track.get('bigDataUrl'), ".bai"), trackDbFileLocation.uri).href,
1315
- locationType: 'UriLocation'
1316
- };
1317
- } else {
1318
- bigDataIndexLocation = track.get('bigDataIndex') ? {
1319
- localPath: track.get('bigDataIndex'),
1320
- locationType: 'LocalPathLocation'
1321
- } : {
1322
- localPath: "".concat(track.get('bigDataUrl'), ".bai"),
1323
- locationType: 'LocalPathLocation'
1324
- };
1325
- }
1326
-
1327
- return {
1328
- type: 'AlignmentsTrack',
1329
- name: track.get('shortLabel'),
1330
- description: track.get('longLabel'),
1331
- category: categories,
1332
- adapter: {
1333
- type: 'BamAdapter',
1334
- bamLocation: bigDataLocation,
1335
- index: {
1336
- location: bigDataIndexLocation
1337
- }
1338
- }
1339
- };
1340
-
1341
- case 'bed':
1342
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1343
-
1344
- case 'bed5FloatScore':
1345
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1346
-
1347
- case 'bedGraph':
1348
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1349
-
1350
- case 'bedRnaElements':
1351
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1352
-
1353
- case 'bigBarChart':
1354
- return {
1355
- type: 'FeatureTrack',
1356
- name: track.get('shortLabel'),
1357
- description: track.get('longLabel'),
1358
- category: categories,
1359
- adapter: {
1360
- type: 'BigBedAdapter',
1361
- bigBedLocation: bigDataLocation
1362
- },
1363
- renderer: {
1364
- type: 'SvgFeatureRenderer'
1365
- }
1366
- };
1367
-
1368
- case 'bigBed':
1369
- return {
1370
- type: 'FeatureTrack',
1371
- name: track.get('shortLabel'),
1372
- description: track.get('longLabel'),
1373
- category: categories,
1374
- adapter: {
1375
- type: 'BigBedAdapter',
1376
- bigBedLocation: bigDataLocation
1377
- }
1378
- };
1379
-
1380
- case 'bigGenePred':
1381
- return {
1382
- type: 'FeatureTrack',
1383
- name: track.get('shortLabel'),
1384
- description: track.get('longLabel'),
1385
- category: categories,
1386
- adapter: {
1387
- type: 'BigBedAdapter',
1388
- bigBedLocation: bigDataLocation
1389
- }
1390
- };
1391
-
1392
- case 'bigChain':
1393
- return {
1394
- type: 'FeatureTrack',
1395
- name: track.get('shortLabel'),
1396
- description: track.get('longLabel'),
1397
- category: categories,
1398
- adapter: {
1399
- type: 'BigBedAdapter',
1400
- bigBedLocation: bigDataLocation
1401
- },
1402
- renderer: {
1403
- type: 'SvgFeatureRenderer'
1404
- }
1405
- };
1406
-
1407
- case 'bigInteract':
1408
- return {
1409
- type: 'FeatureTrack',
1410
- name: track.get('shortLabel'),
1411
- description: track.get('longLabel'),
1412
- category: categories,
1413
- adapter: {
1414
- type: 'BigBedAdapter',
1415
- bigBedLocation: bigDataLocation
1416
- },
1417
- renderer: {
1418
- type: 'SvgFeatureRenderer'
1419
- }
1420
- };
1421
-
1422
- case 'bigMaf':
1423
- return {
1424
- type: 'FeatureTrack',
1425
- name: track.get('shortLabel'),
1426
- description: track.get('longLabel'),
1427
- category: categories,
1428
- adapter: {
1429
- type: 'BigBedAdapter',
1430
- bigBedLocation: bigDataLocation
1431
- },
1432
- renderer: {
1433
- type: 'SvgFeatureRenderer'
1434
- }
1435
- };
1436
-
1437
- case 'bigPsl':
1438
- return {
1439
- type: 'FeatureTrack',
1440
- name: track.get('shortLabel'),
1441
- description: track.get('longLabel'),
1442
- category: categories,
1443
- adapter: {
1444
- type: 'BigBedAdapter',
1445
- bigBedLocation: bigDataLocation
1446
- },
1447
- renderer: {
1448
- type: 'SvgFeatureRenderer'
1449
- }
1450
- };
1451
-
1452
- case 'bigWig':
1453
- return {
1454
- type: 'QuantitativeTrack',
1455
- name: track.get('shortLabel'),
1456
- description: track.get('longLabel'),
1457
- category: categories,
1458
- adapter: {
1459
- type: 'BigWigAdapter',
1460
- bigWigLocation: bigDataLocation
1461
- }
1462
- };
1463
-
1464
- case 'broadPeak':
1465
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1466
-
1467
- case 'coloredExon':
1468
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1469
-
1470
- case 'cram':
1471
- if (trackDbFileLocation.uri) {
1472
- bigDataIndexLocation = track.get('bigDataIndex') ? {
1473
- uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri).href,
1474
- locationType: 'UriLocation'
1475
- } : {
1476
- uri: new URL("".concat(track.get('bigDataUrl'), ".crai"), trackDbFileLocation.uri).href,
1477
- locationType: 'UriLocation'
1478
- };
1479
- } else {
1480
- bigDataIndexLocation = track.get('bigDataIndex') ? {
1481
- localPath: track.get('bigDataIndex'),
1482
- locationType: 'LocalPathLocation'
1483
- } : {
1484
- localPath: "".concat(track.get('bigDataUrl'), ".crai"),
1485
- locationType: 'LocalPathLocation'
1486
- };
1487
- }
1488
-
1489
- return {
1490
- type: 'AlignmentsTrack',
1491
- name: track.get('shortLabel'),
1492
- description: track.get('longLabel'),
1493
- category: categories,
1494
- adapter: {
1495
- type: 'CramAdapter',
1496
- cramLocation: bigDataLocation,
1497
- craiLocation: bigDataIndexLocation,
1498
- sequenceAdapter: sequenceAdapter
1499
- }
1500
- };
1501
-
1502
- case 'gvf':
1503
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1504
-
1505
- case 'ld2':
1506
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1507
-
1508
- case 'narrowPeak':
1509
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1510
-
1511
- case 'bigNarrowPeak':
1512
- return {
1513
- type: 'FeatureTrack',
1514
- name: track.get('shortLabel'),
1515
- description: track.get('longLabel'),
1516
- category: categories,
1517
- adapter: {
1518
- type: 'BigBedAdapter',
1519
- bigBedLocation: bigDataLocation
1520
- }
1521
- };
1522
-
1523
- case 'peptideMapping':
1524
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1525
-
1526
- case 'vcfTabix':
1527
- if (trackDbFileLocation.uri) {
1528
- bigDataIndexLocation = track.get('bigDataIndex') ? {
1529
- uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri).href,
1530
- locationType: 'UriLocation'
1531
- } : {
1532
- uri: new URL("".concat(track.get('bigDataUrl'), ".tbi"), trackDbFileLocation.uri).href,
1533
- locationType: 'UriLocation'
1534
- };
1535
- } else {
1536
- bigDataIndexLocation = track.get('bigDataIndex') ? {
1537
- localPath: track.get('bigDataIndex'),
1538
- locationType: 'LocalPathLocation'
1539
- } : {
1540
- localPath: "".concat(track.get('bigDataUrl'), ".tbi"),
1541
- locationType: 'LocalPathLocation'
1542
- };
1543
- }
1544
-
1545
- return {
1546
- type: 'VariantTrack',
1547
- name: track.get('shortLabel'),
1548
- description: track.get('longLabel'),
1549
- category: categories,
1550
- adapter: {
1551
- type: 'VcfTabixAdapter',
1552
- vcfGzLocation: bigDataLocation,
1553
- index: {
1554
- location: bigDataIndexLocation
1555
- }
1556
- }
1557
- };
1558
-
1559
- case 'wig':
1560
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1561
-
1562
- case 'wigMaf':
1563
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1564
-
1565
- case 'hic':
1566
- return {
1567
- type: 'HicTrack',
1568
- name: track.get('shortLabel'),
1569
- description: track.get('longLabel'),
1570
- category: categories,
1571
- adapter: {
1572
- type: 'HicAdapter',
1573
- hicLocation: bigDataLocation
1574
- }
1575
- };
1576
-
1577
- case 'halSnake':
1578
- return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
1579
-
1580
- default:
1581
- return generateUnknownTrackConf(track.get('shortLabel'), baseTrackType, categories);
1582
- }
1583
- }
1584
-
1585
- function UCSCTrackHubConnection(pluginManager) {
1586
- return types.compose('UCSCTrackHubConnection', BaseConnectionModelFactory(pluginManager), types.model({
1587
- configuration: ConfigurationReference(ucscConfigSchema),
1588
- type: types.literal('UCSCTrackHubConnection')
1589
- }).actions(function (self) {
1590
- return {
1591
- connect: function connect() {
1592
- var connectionName = getConf(self, 'name');
1593
- var hubFileLocation = getConf(self, 'hubTxtLocation');
1594
- var session = getSession(self);
1595
- fetchHubFile(hubFileLocation).then(function (hubFile) {
1596
- var genomesFileLocation = hubFileLocation.uri ? {
1597
- uri: new URL(hubFile.get('genomesFile'), hubFileLocation.uri).href,
1598
- locationType: 'UriLocation'
1599
- } : {
1600
- localPath: hubFile.get('genomesFile'),
1601
- locationType: 'LocalPathLocation'
1602
- };
1603
- return Promise.all([hubFile, fetchGenomesFile(genomesFileLocation)]);
1604
- }).then(function (_ref) {
1605
- var _ref2 = _slicedToArray(_ref, 2),
1606
- hubFile = _ref2[0],
1607
- genomesFile = _ref2[1];
1608
-
1609
- var trackDbData = [];
1610
-
1611
- var _iterator = _createForOfIteratorHelper(genomesFile),
1612
- _step;
1613
-
1614
- try {
1615
- var _loop = function _loop() {
1616
- var _step$value = _slicedToArray(_step.value, 2),
1617
- genomeName = _step$value[0],
1618
- genome = _step$value[1];
1619
-
1620
- var assemblyNames = getConf(self, 'assemblyNames');
1621
-
1622
- if (assemblyNames.length > 0 && !assemblyNames.includes(genomeName)) {
1623
- return "break";
1624
- }
1625
-
1626
- var assemblyConf = session.assemblies.find(function (assembly) {
1627
- return readConfObject(assembly, 'name') === genomeName;
1628
- });
1629
-
1630
- if (!assemblyConf) {
1631
- throw new Error("Cannot find assembly for \"".concat(genomeName, "\" from the genomes file for connection \"").concat(connectionName, "\""));
1632
- }
1633
-
1634
- var trackDbFileLocation = hubFileLocation.uri ? {
1635
- uri: new URL(genome.get('trackDb'), new URL(hubFile.get('genomesFile'), hubFileLocation.uri)).href,
1636
- locationType: 'UriLocation'
1637
- } : {
1638
- localPath: genome.get('trackDb'),
1639
- locationType: 'LocalPathLocation'
1640
- };
1641
- trackDbData.push(Promise.all([trackDbFileLocation, fetchTrackDbFile(trackDbFileLocation), genomeName, assemblyConf]));
1642
- };
1643
-
1644
- for (_iterator.s(); !(_step = _iterator.n()).done;) {
1645
- var _ret = _loop();
1646
-
1647
- if (_ret === "break") break;
1648
- }
1649
- } catch (err) {
1650
- _iterator.e(err);
1651
- } finally {
1652
- _iterator.f();
1653
- }
1654
-
1655
- return Promise.all([].concat(trackDbData));
1656
- }).then(function (trackDbData) {
1657
- var _iterator2 = _createForOfIteratorHelper(trackDbData),
1658
- _step2;
1659
-
1660
- try {
1661
- for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
1662
- var _step2$value = _slicedToArray(_step2.value, 4),
1663
- trackDbFileLocation = _step2$value[0],
1664
- trackDbFile = _step2$value[1],
1665
- genomeName = _step2$value[2],
1666
- assemblyConf = _step2$value[3];
1667
-
1668
- var sequenceAdapter = readConfObject(assemblyConf, ['sequence', 'adapter']);
1669
- var tracks = generateTracks(trackDbFile, trackDbFileLocation, genomeName, sequenceAdapter);
1670
- self.addTrackConfs(tracks);
1671
- }
1672
- } catch (err) {
1673
- _iterator2.e(err);
1674
- } finally {
1675
- _iterator2.f();
1676
- }
1677
- })["catch"](function (error) {
1678
- console.error(error);
1679
- session.notify("There was a problem connecting to the UCSC Track Hub \"".concat(self.name, "\". Please make sure you have entered a valid hub.txt file. The error that was thrown is: \"").concat(error, "\""), 'error');
1680
- session.breakConnection(self.configuration);
1681
- });
1682
- }
1683
- };
1684
- }));
1685
- }
1686
-
1687
- function isAbsoluteUrl() {
1688
- var url = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : '';
1689
-
1690
- try {
1691
- new URL(url);
1692
- return true;
1693
- } catch (error) {
1694
- return url.startsWith('/');
1695
- }
1696
- }
1697
-
1698
- function f(pluginManager) {
1699
- return types.model('AddTrackModel', {
1700
- id: ElementId,
1701
- type: types.literal('AddTrackWidget'),
1702
- view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel'))
1703
- })["volatile"](function () {
1704
- return {
1705
- trackSource: 'fromFile',
1706
- trackData: undefined,
1707
- indexTrackData: undefined,
1708
- // alts
1709
- altAssemblyName: '',
1710
- altTrackName: '',
1711
- altTrackType: '',
1712
- adapterHint: ''
1713
- };
1714
- }).actions(function (self) {
1715
- return {
1716
- setAdapterHint: function setAdapterHint(obj) {
1717
- self.adapterHint = obj;
1718
- },
1719
- setTrackSource: function setTrackSource(str) {
1720
- self.trackSource = str;
1721
- },
1722
- setTrackData: function setTrackData(obj) {
1723
- self.trackData = obj;
1724
- },
1725
- setIndexTrackData: function setIndexTrackData(obj) {
1726
- self.indexTrackData = obj;
1727
- },
1728
- setAssembly: function setAssembly(str) {
1729
- self.altAssemblyName = str;
1730
- },
1731
- setTrackName: function setTrackName(str) {
1732
- self.altTrackName = str;
1733
- },
1734
- setTrackType: function setTrackType(str) {
1735
- self.altTrackType = str;
1736
- },
1737
- clearData: function clearData() {
1738
- self.trackSource = '';
1739
- self.altTrackName = '';
1740
- self.altTrackType = '';
1741
- self.altAssemblyName = '';
1742
- self.adapterHint = '';
1743
- self.indexTrackData = undefined;
1744
- self.trackData = undefined;
1745
- }
1746
- };
1747
- }).views(function (self) {
1748
- return {
1749
- get trackAdapter() {
1750
- var trackData = self.trackData,
1751
- indexTrackData = self.indexTrackData,
1752
- adapterHint = self.adapterHint;
1753
- return trackData ? guessAdapter(trackData, indexTrackData, adapterHint, self) : undefined;
1754
- },
1755
-
1756
- get trackName() {
1757
- return self.altTrackName || (self.trackData ? getFileName(self.trackData) : '');
1758
- },
1759
-
1760
- get isFtp() {
1761
- var _index$uri, _track$uri;
1762
-
1763
- var track = self.trackData,
1764
- index = self.indexTrackData;
1765
- return !!( // @ts-ignore
1766
- index !== null && index !== void 0 && (_index$uri = index.uri) !== null && _index$uri !== void 0 && _index$uri.startsWith('ftp://') || track !== null && track !== void 0 && (_track$uri = track.uri) !== null && _track$uri !== void 0 && _track$uri.startsWith('ftp://'));
1767
- },
1768
-
1769
- get isRelativeTrackUrl() {
1770
- var _self$trackData;
1771
-
1772
- // @ts-ignore
1773
- var uri = (_self$trackData = self.trackData) === null || _self$trackData === void 0 ? void 0 : _self$trackData.uri;
1774
- return uri ? !isAbsoluteUrl(uri) : false;
1775
- },
1776
-
1777
- get isRelativeIndexUrl() {
1778
- var _self$indexTrackData;
1779
-
1780
- // @ts-ignore
1781
- var uri = (_self$indexTrackData = self.indexTrackData) === null || _self$indexTrackData === void 0 ? void 0 : _self$indexTrackData.uri;
1782
- return uri ? !isAbsoluteUrl(uri) : false;
1783
- },
1784
-
1785
- get isRelativeUrl() {
1786
- return this.isRelativeIndexUrl || this.isRelativeTrackUrl;
1787
- },
1788
-
1789
- get trackHttp() {
1790
- var _self$trackData2, _self$trackData2$uri;
1791
-
1792
- // @ts-ignore
1793
- return (_self$trackData2 = self.trackData) === null || _self$trackData2 === void 0 ? void 0 : (_self$trackData2$uri = _self$trackData2.uri) === null || _self$trackData2$uri === void 0 ? void 0 : _self$trackData2$uri.startsWith('http://');
1794
- },
1795
-
1796
- get indexHttp() {
1797
- var _self$indexTrackData2, _self$indexTrackData3;
1798
-
1799
- // @ts-ignore
1800
- return (_self$indexTrackData2 = self.indexTrackData) === null || _self$indexTrackData2 === void 0 ? void 0 : (_self$indexTrackData3 = _self$indexTrackData2.uri) === null || _self$indexTrackData3 === void 0 ? void 0 : _self$indexTrackData3.startsWith('http://');
1801
- },
1802
-
1803
- get wrongProtocol() {
1804
- return window.location.protocol === 'https:' && (this.trackHttp || this.indexHttp);
1805
- },
1806
-
1807
- get unsupported() {
1808
- var _this$trackAdapter;
1809
-
1810
- return ((_this$trackAdapter = this.trackAdapter) === null || _this$trackAdapter === void 0 ? void 0 : _this$trackAdapter.type) === UNSUPPORTED;
1811
- },
1812
-
1813
- get assembly() {
1814
- var _self$view$assemblyNa;
1815
-
1816
- return self.altAssemblyName || ((_self$view$assemblyNa = self.view.assemblyNames) === null || _self$view$assemblyNa === void 0 ? void 0 : _self$view$assemblyNa[0]);
1817
- },
1818
-
1819
- get trackType() {
1820
- return self.altTrackType || (this.trackAdapter ? guessTrackType(this.trackAdapter.type, self) : '');
1821
- }
1822
-
1823
- };
1824
- }).views(function (self) {
1825
- return {
1826
- get warningMessage() {
1827
- if (self.isFtp) {
1828
- return "Warning: JBrowse cannot access files using the ftp protocol";
1829
- } else if (self.isRelativeUrl) {
1830
- return "Warning: one or more of your files do not provide the protocol e.g.\n https://, please provide an absolute URL unless you are sure a\n relative URL is intended.";
1831
- } else if (self.wrongProtocol) {
1832
- return "Warning: You entered a http:// resources but we cannot access HTTP\n resources from JBrowse when it is running on https. Please use an\n https URL for your track, or access the JBrowse app from the http\n protocol";
1833
- }
1834
-
1835
- return '';
1836
- }
1837
-
1838
- };
1839
- });
1840
- }
1841
-
1842
- var configSchema = /*#__PURE__*/ConfigurationSchema('AddTrackWidget', {});
1843
-
1844
- var AddConnectionStateModel = /*#__PURE__*/types.model('AddConnectionModel', {
1845
- id: ElementId,
1846
- type: /*#__PURE__*/types.literal('AddConnectionWidget')
1847
- });
1848
-
1849
- var configSchema$1 = /*#__PURE__*/ConfigurationSchema('AddConnectionWidget', {});
1850
-
1851
- var hasAnyOverlap = function hasAnyOverlap() {
1852
- var a1 = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : [];
1853
- var a2 = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : [];
1854
- return !!a1.find(function (value) {
1855
- return a2.includes(value);
1856
- });
1857
- };
1858
-
1859
- function passesFilter(filter, config) {
1860
- var name = getTrackName(config);
1861
- var categories = readConfObject(config, 'category') || [];
1862
- var filterLower = filter.toLowerCase();
1863
- return !!name.toLowerCase().includes(filterLower) || categories.filter(function (cat) {
1864
- return !!cat.toLowerCase().includes(filterLower);
1865
- }).length;
1866
- }
1867
-
1868
- function getTrackName(config) {
1869
- if (!config.trackId) {
1870
- throw new Error('not a track');
1871
- }
1872
-
1873
- return readConfObject(config, 'name') || "Reference sequence (".concat(readConfObject(getParent(config), 'name'), ")");
1874
- }
1875
-
1876
- function generateHierarchy(model, trackConfigurations, collapsed) {
1877
- var hierarchy = {
1878
- children: []
1879
- };
1880
- var filterText = model.filterText,
1881
- view = model.view;
1882
- trackConfigurations.filter(function (trackConf) {
1883
- return passesFilter(filterText, trackConf);
1884
- }).forEach(function (trackConf) {
1885
- // copy the categories since this array can be mutated downstream
1886
- var categories = _toConsumableArray(readConfObject(trackConf, 'category') || []); // silly thing where if trackId ends with sessionTrack, then push it to
1887
- // a category that starts with a space to force sort to the top...
1888
- // double whammy hackyness
1889
-
1890
-
1891
- if (trackConf.trackId.endsWith('sessionTrack')) {
1892
- categories.unshift(' Session tracks');
1893
- }
1894
-
1895
- var currLevel = hierarchy; // find existing category to put track into or create it
1896
-
1897
- var _loop = function _loop(i) {
1898
- var category = categories[i];
1899
- var ret = currLevel.children.find(function (c) {
1900
- return c.name === category;
1901
- });
1902
- var id = categories.slice(0, i + 1).join(',');
1903
-
1904
- if (!ret) {
1905
- var n = {
1906
- children: [],
1907
- name: category,
1908
- id: id,
1909
- isOpenByDefault: !collapsed.get(id)
1910
- };
1911
- currLevel.children.push(n);
1912
- currLevel = n;
1913
- } else {
1914
- currLevel = ret;
1915
- }
1916
- };
1917
-
1918
- for (var i = 0; i < categories.length; i++) {
1919
- _loop(i);
1920
- } // using splice here tries to group leaf nodes above hierarchical nodes
1921
-
1922
-
1923
- currLevel.children.splice(currLevel.children.findIndex(function (elt) {
1924
- return elt.children.length;
1925
- }), 0, {
1926
- id: trackConf.trackId,
1927
- name: getTrackName(trackConf),
1928
- conf: trackConf,
1929
- checked: !!view.tracks.find(function (f) {
1930
- return f.configuration === trackConf;
1931
- }),
1932
- children: []
1933
- });
1934
- });
1935
- return hierarchy.children;
1936
- }
1937
- var HierarchicalTrackSelectorStateModelFactory = (function (pluginManager) {
1938
- return types.model('HierarchicalTrackSelectorWidget', {
1939
- id: ElementId,
1940
- type: types.literal('HierarchicalTrackSelectorWidget'),
1941
- collapsed: types.map(types["boolean"]),
1942
- filterText: '',
1943
- view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel'))
1944
- }).actions(function (self) {
1945
- return {
1946
- setView: function setView(view) {
1947
- self.view = view;
1948
- },
1949
- toggleCategory: function toggleCategory(pathName) {
1950
- self.collapsed.set(pathName, !self.collapsed.get(pathName));
1951
- },
1952
- clearFilterText: function clearFilterText() {
1953
- self.filterText = '';
1954
- },
1955
- setFilterText: function setFilterText(newText) {
1956
- self.filterText = newText;
1957
- }
1958
- };
1959
- }).views(function (self) {
1960
- return {
1961
- getRefSeqTrackConf: function getRefSeqTrackConf(assemblyName) {
1962
- var _getSession = getSession(self),
1963
- assemblyManager = _getSession.assemblyManager;
1964
-
1965
- var assembly = assemblyManager.get(assemblyName);
1966
- var trackConf = assembly === null || assembly === void 0 ? void 0 : assembly.configuration.sequence;
1967
- var viewType = pluginManager.getViewType(self.view.type);
1968
-
1969
- if (trackConf) {
1970
- var _iterator = _createForOfIteratorHelper(trackConf.displays),
1971
- _step;
1972
-
1973
- try {
1974
- var _loop2 = function _loop2() {
1975
- var display = _step.value;
1976
-
1977
- if (viewType.displayTypes.find(function (displayType) {
1978
- return displayType.name === display.type;
1979
- })) {
1980
- return {
1981
- v: trackConf
1982
- };
1983
- }
1984
- };
1985
-
1986
- for (_iterator.s(); !(_step = _iterator.n()).done;) {
1987
- var _ret = _loop2();
1988
-
1989
- if (_typeof(_ret) === "object") return _ret.v;
1990
- }
1991
- } catch (err) {
1992
- _iterator.e(err);
1993
- } finally {
1994
- _iterator.f();
1995
- }
1996
- }
1997
-
1998
- return undefined;
1999
- },
2000
- trackConfigurations: function trackConfigurations(assemblyName) {
2001
- if (!self.view) {
2002
- return [];
2003
- }
2004
-
2005
- var session = getSession(self);
2006
- var trackConfigurations = session.tracks,
2007
- assemblyManager = session.assemblyManager;
2008
- var assembly = assemblyManager.get(assemblyName);
2009
-
2010
- if (!assembly) {
2011
- return [];
2012
- }
2013
-
2014
- var refseq = self.getRefSeqTrackConf(assemblyName); // filter out tracks that don't match the current assembly (check all
2015
- // assembly aliases) and display types
2016
-
2017
- return (refseq ? [refseq] : []).concat(_toConsumableArray(trackConfigurations.filter(function (conf) {
2018
- var trackConfAssemblies = readConfObject(conf, 'assemblyNames');
2019
- var allAliases = assembly.allAliases;
2020
- return hasAnyOverlap(allAliases, trackConfAssemblies);
2021
- }).filter(function (conf) {
2022
- var _pluginManager$getVie = pluginManager.getViewType(self.view.type),
2023
- displayTypes = _pluginManager$getVie.displayTypes;
2024
-
2025
- var compatibleDisplays = displayTypes.map(function (display) {
2026
- return display.name;
2027
- });
2028
- var trackDisplays = conf.displays.map(function (display) {
2029
- return display.type;
2030
- });
2031
- return hasAnyOverlap(compatibleDisplays, trackDisplays);
2032
- })));
2033
- },
2034
-
2035
- get assemblyNames() {
2036
- return self.view ? self.view.assemblyNames : [];
2037
- },
2038
-
2039
- connectionTrackConfigurations: function connectionTrackConfigurations(assemblyName, connection) {
2040
- if (!self.view) {
2041
- return [];
2042
- }
2043
-
2044
- var trackConfigurations = connection.tracks;
2045
- var session = getSession(self);
2046
- var assemblyManager = session.assemblyManager;
2047
- var assembly = assemblyManager.get(assemblyName);
2048
-
2049
- if (!(assembly && assembly.initialized)) {
2050
- return [];
2051
- } // filter out tracks that don't match the current display types
2052
-
2053
-
2054
- return trackConfigurations.filter(function (conf) {
2055
- var trackConfAssemblies = readConfObject(conf, 'assemblyNames');
2056
- var allAliases = assembly.allAliases;
2057
- return hasAnyOverlap(allAliases, trackConfAssemblies);
2058
- }).filter(function (conf) {
2059
- var _pluginManager$getVie2 = pluginManager.getViewType(self.view.type),
2060
- displayTypes = _pluginManager$getVie2.displayTypes;
2061
-
2062
- var compatibleDisplays = displayTypes.map(function (display) {
2063
- return display.name;
2064
- });
2065
- var trackDisplays = conf.displays.map(function (display) {
2066
- return display.type;
2067
- });
2068
- return hasAnyOverlap(compatibleDisplays, trackDisplays);
2069
- });
2070
- },
2071
- hierarchy: function hierarchy(assemblyName) {
2072
- var _this = this;
2073
-
2074
- var hier = generateHierarchy(self, self.trackConfigurations(assemblyName), self.collapsed);
2075
- var session = getSession(self);
2076
- var conns = session.connectionInstances.filter(function (conn) {
2077
- var configAssemblyNames = readConfObject(conn.configuration, 'assemblyNames');
2078
-
2079
- if (configAssemblyNames.length === 0) {
2080
- return true;
2081
- }
2082
-
2083
- return configAssemblyNames.includes(assemblyName);
2084
- }).map(function (conn, index) {
2085
- var c = session.connections[index];
2086
- return {
2087
- id: c.connectionId,
2088
- name: readConfObject(c, 'name'),
2089
- children: _this.connectionHierarchy(assemblyName, conn),
2090
- state: {
2091
- expanded: true
2092
- }
2093
- };
2094
- });
2095
- return {
2096
- name: 'Root',
2097
- id: 'Root',
2098
- children: [{
2099
- name: 'Tracks',
2100
- id: 'Tracks',
2101
- children: hier
2102
- }].concat(_toConsumableArray(conns))
2103
- };
2104
- },
2105
- connectionHierarchy: function connectionHierarchy(assemblyName, connection) {
2106
- return generateHierarchy(self, self.connectionTrackConfigurations(assemblyName, connection), self.collapsed);
2107
- },
2108
- // This recursively gets tracks from lower paths
2109
- allTracksInCategoryPath: function allTracksInCategoryPath(path, connection, assemblyName) {
2110
- var currentHier = connection ? self.connectionHierarchy(connection) : self.hierarchy(assemblyName);
2111
- path.forEach(function (pathItem) {
2112
- currentHier = currentHier.get(pathItem) || new Map();
2113
- });
2114
- var tracks = {};
2115
- currentHier.forEach(function (contents, name) {
2116
- if (contents.trackId) {
2117
- tracks[contents.trackId] = contents;
2118
- } else {
2119
- tracks = Object.assign(tracks, self.allTracksInCategoryPath(path.concat([name])));
2120
- }
2121
- });
2122
- return tracks;
2123
- }
2124
- };
2125
- });
2126
- });
2127
-
2128
- var configSchema$2 = /*#__PURE__*/ConfigurationSchema('HierarchicalTrackSelectorWidget', {});
2129
-
2130
- var useStyles = /*#__PURE__*/makeStyles(function () {
2131
- return {
2132
- closeDialog: {
2133
- position: 'absolute',
2134
- right: 0,
2135
- top: 0
2136
- },
2137
- dialogContainer: {
2138
- margin: 15
2139
- },
2140
- lockedPluginTooltip: {
2141
- marginRight: '0.5rem'
2142
- }
2143
- };
2144
- });
2145
-
2146
- function LockedPlugin() {
2147
- var classes = useStyles();
2148
- return /*#__PURE__*/React.createElement(Tooltip, {
2149
- className: classes.lockedPluginTooltip,
2150
- title: "This plugin was installed by an administrator, you cannot remove it."
2151
- }, /*#__PURE__*/React.createElement(LockIcon, null));
2152
- }
2153
-
2154
- function PluginDialog(_ref) {
2155
- var _onClose = _ref.onClose,
2156
- plugin = _ref.plugin;
2157
- var classes = useStyles();
2158
- return /*#__PURE__*/React.createElement(Dialog, {
2159
- open: true,
2160
- onClose: function onClose() {
2161
- return _onClose();
2162
- }
2163
- }, /*#__PURE__*/React.createElement(DialogTitle, null, /*#__PURE__*/React.createElement(IconButton, {
2164
- className: classes.closeDialog,
2165
- "aria-label": "close-dialog",
2166
- onClick: function onClick() {
2167
- return _onClose();
2168
- }
2169
- }, /*#__PURE__*/React.createElement(CloseIcon, null))), /*#__PURE__*/React.createElement(DialogContent, null, /*#__PURE__*/React.createElement(Typography, null, "Please confirm that you want to remove ", plugin, ". Note: if any resources in this session still use this plugin, it may cause your session to crash"), /*#__PURE__*/React.createElement(DialogActions, null, /*#__PURE__*/React.createElement(Button, {
2170
- variant: "contained",
2171
- color: "primary",
2172
- onClick: function onClick() {
2173
- // avoid showing runtime plugin warning
2174
- window.setTimeout(function () {
2175
- _onClose(plugin);
2176
- }, 500);
2177
- }
2178
- }, "Confirm"), /*#__PURE__*/React.createElement(Button, {
2179
- variant: "contained",
2180
- color: "secondary",
2181
- onClick: function onClick() {
2182
- _onClose();
2183
- }
2184
- }, "Cancel"))));
2185
- }
2186
-
2187
- function InstalledPlugin(_ref2) {
2188
- var plugin = _ref2.plugin,
2189
- model = _ref2.model,
2190
- pluginManager = _ref2.pluginManager;
2191
-
2192
- var _useState = useState(),
2193
- _useState2 = _slicedToArray(_useState, 2),
2194
- dialogPlugin = _useState2[0],
2195
- setDialogPlugin = _useState2[1];
2196
-
2197
- var session = getSession(model);
2198
- var sessionPlugins = session.sessionPlugins;
2199
- var isSessionPlugin = sessionPlugins === null || sessionPlugins === void 0 ? void 0 : sessionPlugins.some(function (p) {
2200
- return pluginManager.pluginMetadata[plugin.name].url === p.url;
2201
- });
2202
- var rootModel = getParent(model, 3);
2203
- var jbrowse = rootModel.jbrowse,
2204
- adminMode = rootModel.adminMode;
2205
- return /*#__PURE__*/React.createElement(React.Fragment, null, dialogPlugin ? /*#__PURE__*/React.createElement(PluginDialog, {
2206
- plugin: dialogPlugin,
2207
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2208
- if (name) {
2209
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2210
-
2211
- if (adminMode) {
2212
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2213
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2214
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2215
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2216
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2217
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2218
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2219
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2220
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2221
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2222
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2223
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2224
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2225
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2226
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2227
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2228
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2229
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2230
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2231
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2232
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2233
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2234
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2235
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2236
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2237
- var corePlugins = plugins.filter(function (p) {
2238
- var _pluginManager$plugin;
2239
-
2240
- return (_pluginManager$plugin = pluginManager.pluginMetadata[p.name]) === null || _pluginManager$plugin === void 0 ? void 0 : _pluginManager$plugin.isCore;
2241
- }).map(function (p) {
2242
- return p.name;
2243
- });
2244
- var externalPlugins = plugins.filter(function (plugin) {
2245
- return !corePlugins.includes(plugin.name);
2246
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2247
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2248
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2249
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2250
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2251
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2252
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2253
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2254
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2255
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2256
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2257
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2258
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2259
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2260
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2261
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2262
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2263
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2264
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2265
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2266
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2267
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2268
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2269
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2270
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2271
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2272
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2273
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2274
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2275
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2276
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2277
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2278
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2279
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2280
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2281
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2282
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2283
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2284
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2285
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2286
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2287
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2288
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2289
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2290
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2291
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2292
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2293
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2294
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2295
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2296
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2297
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2298
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2299
-
2300
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2301
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2302
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2303
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2304
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2305
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2306
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2307
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2308
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2309
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2310
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2311
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2312
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2313
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2314
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2315
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2316
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2317
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2318
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2319
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2320
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2321
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2322
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2323
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2324
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2325
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2326
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2327
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2328
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2329
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2330
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2331
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2332
- url: plugin.url
2333
- });
2334
- } else if (isSessionWithSessionPlugins(session)) {
2335
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2336
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2337
-
2338
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2339
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2340
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2342
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2343
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2344
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2345
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2346
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2347
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2348
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2349
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2350
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2351
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2352
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2353
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2354
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2355
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2356
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2357
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2358
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2359
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2360
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2361
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2362
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2363
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2364
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2365
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2366
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2367
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2368
-
2369
- function CustomPluginForm(_ref) {
2370
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2371
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2372
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2373
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2374
-
2375
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2376
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2377
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2378
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2379
-
2380
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2381
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2382
- umdPluginUrl = _useState4[0],
2383
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2384
-
2385
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2386
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2387
- esmPluginUrl = _useState6[0],
2388
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2389
-
2390
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2391
- _useState8 = _slicedToArray(_useState7, 2),
2392
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2393
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2394
-
2395
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2396
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2397
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2398
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2399
-
2400
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2401
- var _event$target = event.target,
2402
- name = _event$target.name,
2403
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2404
-
2405
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2406
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2407
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2408
-
2409
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2410
- setUMDPluginUrl(value);
2411
- }
2412
-
2413
- if (name === 'esmUrl') {
2414
- setESMPluginUrl(value);
2415
- }
2416
-
2417
- if (name === 'cjsUrl') {
2418
- setCJSPluginUrl(value);
2419
- }
2420
- }
2421
-
2422
- function handleOpenAdvancedOptions() {
2423
- setAdvancedOptionsOpen(!advancedOptionsOpen);
2424
- }
2425
-
2426
- var rootModel = getRoot(model);
2427
- var jbrowse = rootModel.jbrowse;
2428
- var ready = Boolean(umdPluginName && umdPluginUrl || esmPluginUrl || cjsPluginUrl);
2429
-
2430
- function handleSubmit() {
2431
- if (!ready) {
2432
- return;
2433
- }
2434
-
2435
- var pluginDefinition = {};
2436
-
2437
- if (umdPluginName && umdPluginUrl) {
2438
- pluginDefinition.name = umdPluginName;
2439
- pluginDefinition.umdUrl = umdPluginUrl;
2440
- }
2441
-
2442
- if (esmPluginUrl) {
2443
- pluginDefinition.esmUrl = esmPluginUrl;
2444
- }
2445
-
2446
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2447
- pluginDefinition.cjsUrl = cjsPluginUrl;
2448
- }
2449
-
2450
- jbrowse.addPlugin(pluginDefinition);
2451
- }
2452
-
2453
- function handleClose() {
2454
- setUMDPluginName('');
2455
- setUMDPluginUrl('');
2456
- setESMPluginUrl('');
2457
- setCJSPluginUrl('');
2458
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2459
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2460
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2461
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2462
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2463
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2464
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2465
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2466
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2467
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2468
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2469
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2470
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2471
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2472
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2473
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2474
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2475
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2476
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2477
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2478
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2479
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2480
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2481
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2482
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2483
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2484
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2485
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2486
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2487
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2488
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2489
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2490
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2491
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2492
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2493
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2494
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2495
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2496
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2497
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2498
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2499
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2500
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2501
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2502
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2503
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2504
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2505
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2506
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2507
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2508
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2509
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2510
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2511
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2512
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2513
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2514
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2515
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2516
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2517
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2518
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2519
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2520
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2521
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2522
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2523
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2524
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2525
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2526
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2527
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2528
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2529
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2530
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2531
- color: '#fff'
2532
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2533
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2534
- margin: '0.5em',
2535
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2536
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2537
- backgroundColor: '#FFB11D',
2538
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2539
- display: 'flex',
2540
- alignContent: 'center'
2541
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2542
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2543
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2544
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2545
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2546
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2547
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2548
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2549
-
2550
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2551
- var model = _ref.model;
2552
- var classes = useStyles$3();
2553
-
2554
- var _useState = useState(),
2555
- _useState2 = _slicedToArray(_useState, 2),
2556
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2557
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2558
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2559
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2560
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2561
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2562
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2563
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2564
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2565
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2566
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2567
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2568
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2569
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2570
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2571
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2572
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2573
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2574
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2575
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2576
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2577
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2578
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2579
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2580
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2581
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2582
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2583
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2584
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2585
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2586
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2587
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2588
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2589
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2590
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2591
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2592
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2593
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2594
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2595
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2596
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2597
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2598
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2599
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2600
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2601
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2602
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2603
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2604
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2605
-
2606
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2607
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2608
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2609
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2610
- case 11:
2611
- array = _context.sent;
2612
-
2613
- if (!signal.aborted) {
2614
- setPluginArray(array.plugins);
2615
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2616
-
2617
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2618
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2619
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2620
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2621
- _context.prev = 15;
2622
- _context.t0 = _context["catch"](0);
2623
- console.error(_context.t0);
2624
- setError(_context.t0);
2625
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2626
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2627
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2628
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2629
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2630
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2631
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2632
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2633
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2634
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2635
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2636
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2637
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2638
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2639
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2640
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2641
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2642
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2643
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2644
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2645
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2646
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2647
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2648
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2649
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2650
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2651
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2652
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2653
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2654
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2655
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2656
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2657
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2658
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2659
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2660
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2661
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2662
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2663
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2664
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2665
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2666
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2667
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2668
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2669
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2670
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2671
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2672
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2673
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2674
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2675
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2676
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2677
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2678
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2679
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2680
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2681
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2682
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2683
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2684
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2685
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2686
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2687
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2688
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2689
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2690
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2691
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2692
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2693
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2694
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2695
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2696
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2697
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2700
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2701
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2702
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2703
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2704
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2705
- return false;
2706
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2707
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2708
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2709
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2710
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2711
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2712
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2713
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2714
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2718
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2719
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2720
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2721
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2722
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2723
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2724
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2725
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2726
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2727
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2728
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2729
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2730
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2731
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2732
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2733
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2734
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2735
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2736
- },
2737
- setFilterText: function setFilterText(newText) {
2738
- self.filterText = newText;
2739
- }
2740
- };
2741
- });
2742
- }
2743
-
2744
- var configSchema$3 = /*#__PURE__*/ConfigurationSchema('PluginStoreWidget', {});
2745
-
2746
- var SetDefaultSession = /*#__PURE__*/lazy(function () {
2747
- return Promise.resolve().then(function () { return index; });
2748
- });
2749
- var AssemblyManager = /*#__PURE__*/lazy(function () {
2750
- return Promise.resolve().then(function () { return index$1; });
2751
- });
2752
-
2753
- var _default = /*#__PURE__*/function (_Plugin) {
2754
- _inherits(_default, _Plugin);
2755
-
2756
- var _super = /*#__PURE__*/_createSuper(_default);
2757
-
2758
- function _default() {
2759
- var _this;
2760
-
2761
- _classCallCheck(this, _default);
2762
-
2763
- _this = _super.apply(this, arguments);
2764
- _this.name = 'DataManagementPlugin';
2765
- _this.exports = {
2766
- AssemblyManager: AssemblyManager,
2767
- SetDefaultSession: SetDefaultSession
2768
- };
2769
- return _this;
2770
- }
2771
-
2772
- _createClass(_default, [{
2773
- key: "install",
2774
- value: function install(pluginManager) {
2775
- pluginManager.addConnectionType(function () {
2776
- return new ConnectionType({
2777
- name: 'UCSCTrackHubConnection',
2778
- configSchema: ucscConfigSchema,
2779
- stateModel: UCSCTrackHubConnection(pluginManager),
2780
- displayName: 'UCSC Track Hub',
2781
- description: 'A track or assembly hub in the Track Hub format',
2782
- url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro'
2783
- });
2784
- });
2785
- pluginManager.addWidgetType(function () {
2786
- return new WidgetType({
2787
- name: 'HierarchicalTrackSelectorWidget',
2788
- heading: 'Available tracks',
2789
- configSchema: configSchema$2,
2790
- stateModel: HierarchicalTrackSelectorStateModelFactory(pluginManager),
2791
- ReactComponent: /*#__PURE__*/lazy(function () {
2792
- return Promise.resolve().then(function () { return HierarchicalTrackSelector$1; });
2793
- })
2794
- });
2795
- });
2796
- pluginManager.addWidgetType(function () {
2797
- return new WidgetType({
2798
- name: 'AddTrackWidget',
2799
- heading: 'Add a track',
2800
- configSchema: configSchema,
2801
- stateModel: f(pluginManager),
2802
- ReactComponent: /*#__PURE__*/lazy(function () {
2803
- return Promise.resolve().then(function () { return AddTrackWidget$2; });
2804
- })
2805
- });
2806
- });
2807
- pluginManager.addWidgetType(function () {
2808
- return new WidgetType({
2809
- name: 'AddConnectionWidget',
2810
- heading: 'Add a connection',
2811
- configSchema: configSchema$1,
2812
- stateModel: AddConnectionStateModel,
2813
- ReactComponent: /*#__PURE__*/lazy(function () {
2814
- return Promise.resolve().then(function () { return AddConnectionWidget$2; });
2815
- })
2816
- });
2817
- });
2818
- pluginManager.addWidgetType(function () {
2819
- return new WidgetType({
2820
- name: 'PluginStoreWidget',
2821
- heading: 'Plugin store',
2822
- configSchema: configSchema$3,
2823
- stateModel: f$1(pluginManager),
2824
- ReactComponent: /*#__PURE__*/lazy(function () {
2825
- return Promise.resolve().then(function () { return PluginStoreWidget$2; });
2826
- })
2827
- });
2828
- });
2829
- }
2830
- }, {
2831
- key: "configure",
2832
- value: function configure(pluginManager) {}
2833
- }]);
2834
-
2835
- return _default;
2836
- }(Plugin);
2837
-
2838
- function canSetDefaultSession(obj) {
2839
- return _typeof(obj) === 'object' && !!obj && 'jbrowse' in obj;
2840
- }
2841
-
2842
- var SetDefaultSession$1 = /*#__PURE__*/observer(function (_ref) {
2843
- var rootModel = _ref.rootModel,
2844
- onClose = _ref.onClose;
2845
-
2846
- if (!rootModel) {
2847
- return null;
2848
- }
2849
-
2850
- if (!canSetDefaultSession(rootModel)) {
2851
- console.error('Incorrect rootmodel');
2852
- return null;
2853
- }
2854
-
2855
- var jbrowse = rootModel.jbrowse,
2856
- session = rootModel.session;
2857
- return /*#__PURE__*/React.createElement(Dialog, {
2858
- open: true,
2859
- onClose: onClose
2860
- }, /*#__PURE__*/React.createElement(DialogTitle, null, "Set default session"), /*#__PURE__*/React.createElement(DialogContent, null, /*#__PURE__*/React.createElement(Typography, null, "Select \"Set current session as default\" to make your current session saved to the config file. You can also hit \"Clear default session\", which would remove the default session from the config.")), /*#__PURE__*/React.createElement(DialogActions, null, /*#__PURE__*/React.createElement(Button, {
2861
- variant: "contained",
2862
- onClick: function onClick() {
2863
- jbrowse.setDefaultSessionConf({
2864
- name: "New session"
2865
- });
2866
- onClose();
2867
- }
2868
- }, "Clear default session"), /*#__PURE__*/React.createElement(Button, {
2869
- color: "secondary",
2870
- variant: "contained",
2871
- onClick: function onClick() {
2872
- return onClose();
2873
- }
2874
- }, "Cancel"), /*#__PURE__*/React.createElement(Button, {
2875
- color: "primary",
2876
- variant: "contained",
2877
- onClick: function onClick() {
2878
- jbrowse.setDefaultSessionConf(session);
2879
- onClose();
2880
- }
2881
- }, "Set current session as default")));
2882
- });
2883
-
2884
-
2885
-
2886
- var index = {
2887
- __proto__: null,
2888
- 'default': SetDefaultSession$1
2889
- };
2890
-
2891
- var useStyles$4 = /*#__PURE__*/makeStyles(function () {
2892
- return {
2893
- table: {
2894
- minWidth: 500,
2895
- minHeight: 150
2896
- },
2897
- buttonCell: {
2898
- padding: 3
2899
- },
2900
- button: {
2901
- display: 'inline-block',
2902
- padding: 3,
2903
- minHeight: 0,
2904
- minWidth: 0
2905
- }
2906
- };
2907
- });
2908
- var AssemblyTable = /*#__PURE__*/observer(function (_ref) {
2909
- var rootModel = _ref.rootModel,
2910
- setIsAssemblyBeingEdited = _ref.setIsAssemblyBeingEdited,
2911
- setAssemblyBeingEdited = _ref.setAssemblyBeingEdited;
2912
- var classes = useStyles$4();
2913
-
2914
- function removeAssembly(name) {
2915
- rootModel.jbrowse.removeAssemblyConf(name);
2916
- }
2917
-
2918
- var rows = rootModel.jbrowse.assemblies.map(function (assembly) {
2919
- var name = readConfObject(assembly, 'name');
2920
- var displayName = readConfObject(assembly, 'displayName');
2921
- var aliases = readConfObject(assembly, 'aliases');
2922
- return /*#__PURE__*/React.createElement(TableRow, {
2923
- key: name
2924
- }, /*#__PURE__*/React.createElement(TableCell, null, name), /*#__PURE__*/React.createElement(TableCell, null, displayName), /*#__PURE__*/React.createElement(TableCell, null, aliases ? aliases.toString() : ''), /*#__PURE__*/React.createElement(TableCell, {
2925
- className: classes.buttonCell
2926
- }, /*#__PURE__*/React.createElement(IconButton, {
2927
- "data-testid": "".concat(name, "-edit"),
2928
- className: classes.button,
2929
- onClick: function onClick() {
2930
- setIsAssemblyBeingEdited(true);
2931
- setAssemblyBeingEdited(assembly);
2932
- }
2933
- }, /*#__PURE__*/React.createElement(CreateIcon, {
2934
- color: "primary"
2935
- })), /*#__PURE__*/React.createElement(IconButton, {
2936
- "data-testid": "".concat(name, "-delete"),
2937
- className: classes.button,
2938
- onClick: function onClick() {
2939
- removeAssembly(name);
2940
- }
2941
- }, /*#__PURE__*/React.createElement(DeleteIcon, {
2942
- color: "error"
2943
- }))));
2944
- });
2945
- return /*#__PURE__*/React.createElement(TableContainer, {
2946
- component: Paper
2947
- }, /*#__PURE__*/React.createElement(Table, {
2948
- className: classes.table
2949
- }, /*#__PURE__*/React.createElement(TableHead, null, /*#__PURE__*/React.createElement(TableRow, null, /*#__PURE__*/React.createElement(TableCell, null, /*#__PURE__*/React.createElement(Typography, {
2950
- variant: "h5"
2951
- }, "Name")), /*#__PURE__*/React.createElement(TableCell, null, /*#__PURE__*/React.createElement(Typography, {
2952
- variant: "h5"
2953
- }, "Display name")), /*#__PURE__*/React.createElement(TableCell, null, /*#__PURE__*/React.createElement(Typography, {
2954
- variant: "h5"
2955
- }, "Aliases")), /*#__PURE__*/React.createElement(TableCell, null, /*#__PURE__*/React.createElement(Typography, {
2956
- variant: "h5"
2957
- }, "Actions")))), /*#__PURE__*/React.createElement(TableBody, null, rows)));
2958
- });
2959
-
2960
- var useStyles$5 = /*#__PURE__*/makeStyles(function (theme) {
2961
- return {
2962
- root: {
2963
- flexGrow: 1,
2964
- overflow: 'hidden',
2965
- padding: theme.spacing(0, 3)
2966
- },
2967
- paper: {
2968
- margin: "".concat(theme.spacing(1), "px auto"),
2969
- padding: theme.spacing(2)
2970
- },
2971
- createButton: {
2972
- marginTop: '1em',
2973
- justifyContent: 'center'
2974
- },
2975
- paperContent: {
2976
- flex: 'auto',
2977
- margin: "".concat(theme.spacing(1), "px auto"),
2978
- padding: theme.spacing(1),
2979
- overflow: 'auto'
2980
- }
2981
- };
2982
- });
2983
- var AdapterSelector = /*#__PURE__*/observer(function (_ref) {
2984
- var adapterSelection = _ref.adapterSelection,
2985
- setAdapterSelection = _ref.setAdapterSelection,
2986
- adapterTypes = _ref.adapterTypes;
2987
- return /*#__PURE__*/React.createElement(TextField, {
2988
- value: adapterSelection,
2989
- label: "Type",
2990
- select: true,
2991
- helperText: "Type of adapter to use",
2992
- fullWidth: true,
2993
- onChange: function onChange(event) {
2994
- setAdapterSelection(event.target.value);
2995
- }
2996
- }, adapterTypes.map(function (str) {
2997
- return /*#__PURE__*/React.createElement(MenuItem, {
2998
- key: str,
2999
- value: str
3000
- }, str);
3001
- }));
3002
- });
3003
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3004
- var adapterSelection = _ref2.adapterSelection,
3005
- fastaLocation = _ref2.fastaLocation,
3006
- setFastaLocation = _ref2.setFastaLocation,
3007
- faiLocation = _ref2.faiLocation,
3008
- setFaiLocation = _ref2.setFaiLocation,
3009
- gziLocation = _ref2.gziLocation,
3010
- setGziLocation = _ref2.setGziLocation,
3011
- twoBitLocation = _ref2.twoBitLocation,
3012
- setTwoBitLocation = _ref2.setTwoBitLocation,
3013
- chromSizesLocation = _ref2.chromSizesLocation,
3014
- setChromSizesLocation = _ref2.setChromSizesLocation;
3015
-
3016
- if (adapterSelection === 'IndexedFastaAdapter' || adapterSelection === 'BgzipFastaAdapter') {
3017
- return /*#__PURE__*/React.createElement(Grid, {
3018
- container: true,
3019
- spacing: 2
3020
- }, /*#__PURE__*/React.createElement(Grid, {
3021
- item: true
3022
- }, /*#__PURE__*/React.createElement(FileSelector, {
3023
- name: "fastaLocation",
3024
- location: fastaLocation,
3025
- setLocation: function setLocation(loc) {
3026
- return setFastaLocation(loc);
3027
- }
3028
- })), /*#__PURE__*/React.createElement(Grid, {
3029
- item: true
3030
- }, /*#__PURE__*/React.createElement(FileSelector, {
3031
- name: "faiLocation",
3032
- location: faiLocation,
3033
- setLocation: function setLocation(loc) {
3034
- return setFaiLocation(loc);
3035
- }
3036
- })), adapterSelection === 'BgzipFastaAdapter' ? /*#__PURE__*/React.createElement(Grid, {
3037
- item: true
3038
- }, /*#__PURE__*/React.createElement(FileSelector, {
3039
- name: "gziLocation",
3040
- location: gziLocation,
3041
- setLocation: function setLocation(loc) {
3042
- return setGziLocation(loc);
3043
- }
3044
- })) : null);
3045
- }
3046
-
3047
- if (adapterSelection === 'TwoBitAdapter') {
3048
- return /*#__PURE__*/React.createElement(Grid, {
3049
- container: true,
3050
- spacing: 2
3051
- }, /*#__PURE__*/React.createElement(Grid, {
3052
- item: true
3053
- }, /*#__PURE__*/React.createElement(FileSelector, {
3054
- name: "twoBitLocation",
3055
- location: twoBitLocation,
3056
- setLocation: function setLocation(loc) {
3057
- return setTwoBitLocation(loc);
3058
- }
3059
- })), /*#__PURE__*/React.createElement(Grid, {
3060
- item: true
3061
- }, /*#__PURE__*/React.createElement(FileSelector, {
3062
- name: "chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)",
3063
- location: chromSizesLocation,
3064
- setLocation: function setLocation(loc) {
3065
- return setChromSizesLocation(loc);
3066
- }
3067
- })));
3068
- }
3069
-
3070
- return null;
3071
- });
3072
- var blank = {
3073
- uri: ''
3074
- };
3075
- var AssemblyAddForm = /*#__PURE__*/observer(function (_ref3) {
3076
- var rootModel = _ref3.rootModel,
3077
- setFormOpen = _ref3.setFormOpen;
3078
- var classes = useStyles$5();
3079
- var adapterTypes = ['IndexedFastaAdapter', 'BgzipFastaAdapter', 'TwoBitAdapter'];
3080
-
3081
- var _useState = useState(''),
3082
- _useState2 = _slicedToArray(_useState, 2),
3083
- assemblyName = _useState2[0],
3084
- setAssemblyName = _useState2[1];
3085
-
3086
- var _useState3 = useState(''),
3087
- _useState4 = _slicedToArray(_useState3, 2),
3088
- assemblyDisplayName = _useState4[0],
3089
- setAssemblyDisplayName = _useState4[1];
3090
-
3091
- var _useState5 = useState(adapterTypes[0]),
3092
- _useState6 = _slicedToArray(_useState5, 2),
3093
- adapterSelection = _useState6[0],
3094
- setAdapterSelection = _useState6[1];
3095
-
3096
- var _useState7 = useState(blank),
3097
- _useState8 = _slicedToArray(_useState7, 2),
3098
- fastaLocation = _useState8[0],
3099
- setFastaLocation = _useState8[1];
3100
-
3101
- var _useState9 = useState(blank),
3102
- _useState10 = _slicedToArray(_useState9, 2),
3103
- faiLocation = _useState10[0],
3104
- setFaiLocation = _useState10[1];
3105
-
3106
- var _useState11 = useState(blank),
3107
- _useState12 = _slicedToArray(_useState11, 2),
3108
- gziLocation = _useState12[0],
3109
- setGziLocation = _useState12[1];
3110
-
3111
- var _useState13 = useState(blank),
3112
- _useState14 = _slicedToArray(_useState13, 2),
3113
- twoBitLocation = _useState14[0],
3114
- setTwoBitLocation = _useState14[1];
3115
-
3116
- var _useState15 = useState(blank),
3117
- _useState16 = _slicedToArray(_useState15, 2),
3118
- chromSizesLocation = _useState16[0],
3119
- setChromSizesLocation = _useState16[1];
3120
-
3121
- function createAssembly() {
3122
- if (assemblyName === '') {
3123
- rootModel.session.notify("Can't create an assembly without a name");
3124
- } else {
3125
- setFormOpen(false);
3126
- var newAssembly;
3127
-
3128
- if (adapterSelection === 'IndexedFastaAdapter') {
3129
- newAssembly = {
3130
- name: assemblyName,
3131
- displayName: assemblyDisplayName,
3132
- sequence: {
3133
- adapter: {
3134
- type: 'IndexedFastaAdapter',
3135
- fastaLocation: fastaLocation,
3136
- faiLocation: faiLocation
3137
- }
3138
- }
3139
- };
3140
- } else if (adapterSelection === 'BgzipFastaAdapter') {
3141
- newAssembly = {
3142
- name: assemblyName,
3143
- displayName: assemblyDisplayName,
3144
- sequence: {
3145
- adapter: {
3146
- type: 'BgzipFastaAdapter',
3147
- fastaLocation: fastaLocation,
3148
- faiLocation: faiLocation,
3149
- gziLocation: gziLocation
3150
- }
3151
- }
3152
- };
3153
- } else if (adapterSelection === 'TwoBitAdapter') {
3154
- newAssembly = {
3155
- name: assemblyName,
3156
- displayName: assemblyDisplayName,
3157
- sequence: {
3158
- adapter: {
3159
- type: 'TwoBitAdapter',
3160
- twoBitLocation: twoBitLocation,
3161
- chromSizesLocation: chromSizesLocation
3162
- }
3163
- }
3164
- };
3165
- }
3166
-
3167
- rootModel.jbrowse.addAssemblyConf(newAssembly);
3168
- rootModel.session.notify("Successfully added ".concat(assemblyName, " assembly to JBrowse 2"), 'success');
3169
- }
3170
- }
3171
-
3172
- return /*#__PURE__*/React.createElement("div", {
3173
- className: classes.root
3174
- }, /*#__PURE__*/React.createElement(Paper, {
3175
- className: classes.paper
3176
- }, /*#__PURE__*/React.createElement(TextField, {
3177
- id: "assembly-name",
3178
- inputProps: {
3179
- 'data-testid': 'assembly-name'
3180
- },
3181
- label: "Assembly name",
3182
- helperText: "The assembly name e.g. hg38",
3183
- variant: "outlined",
3184
- value: assemblyName,
3185
- onChange: function onChange(event) {
3186
- return setAssemblyName(event.target.value);
3187
- }
3188
- }), /*#__PURE__*/React.createElement(TextField, {
3189
- id: "assembly-name",
3190
- inputProps: {
3191
- 'data-testid': 'assembly-display-name'
3192
- },
3193
- label: "Assembly display name",
3194
- helperText: 'A human readable display name for the assembly e.g. "Homo sapiens (hg38)"',
3195
- variant: "outlined",
3196
- value: assemblyDisplayName,
3197
- onChange: function onChange(event) {
3198
- return setAssemblyDisplayName(event.target.value);
3199
- }
3200
- }), /*#__PURE__*/React.createElement(AdapterSelector, {
3201
- adapterSelection: adapterSelection,
3202
- setAdapterSelection: setAdapterSelection,
3203
- adapterTypes: adapterTypes
3204
- }), /*#__PURE__*/React.createElement("div", {
3205
- className: classes.paperContent
3206
- }, /*#__PURE__*/React.createElement(AdapterInput, {
3207
- adapterSelection: adapterSelection,
3208
- fastaLocation: fastaLocation,
3209
- setFastaLocation: setFastaLocation,
3210
- faiLocation: faiLocation,
3211
- setFaiLocation: setFaiLocation,
3212
- gziLocation: gziLocation,
3213
- setGziLocation: setGziLocation,
3214
- twoBitLocation: twoBitLocation,
3215
- setTwoBitLocation: setTwoBitLocation,
3216
- chromSizesLocation: chromSizesLocation,
3217
- setChromSizesLocation: setChromSizesLocation
3218
- }))), /*#__PURE__*/React.createElement(Grid, {
3219
- container: true,
3220
- className: classes.createButton
3221
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3222
- item: true
3223
- }, /*#__PURE__*/React.createElement(Button, {
3224
- variant: "contained",
3225
- color: "secondary",
3226
- startIcon: /*#__PURE__*/React.createElement(AddIcon, null),
3227
- onClick: createAssembly
3228
- }, "Create new assembly"))));
3229
- });
3230
-
3231
- var AssemblyEditor = /*#__PURE__*/observer(function (_ref) {
3232
- var assembly = _ref.assembly;
3233
- return /*#__PURE__*/React.createElement(ConfigurationEditor, {
3234
- model: {
3235
- target: assembly
3236
- }
3237
- });
3238
- });
3239
-
3240
- var useStyles$6 = /*#__PURE__*/makeStyles$1(function (theme) {
3241
- return {
3242
- titleBox: {
3243
- color: '#fff',
3244
- backgroundColor: theme.palette.primary.main,
3245
- textAlign: 'center'
3246
- },
3247
- dialogContent: {
3248
- width: '100%'
3249
- },
3250
- backButton: {
3251
- color: '#fff',
3252
- position: 'absolute',
3253
- left: theme.spacing(4),
3254
- top: theme.spacing(4)
3255
- },
3256
- closeButton: {
3257
- position: 'absolute',
3258
- right: theme.spacing(1),
3259
- top: theme.spacing(1),
3260
- color: theme.palette.grey[500]
3261
- }
3262
- };
3263
- });
3264
- var AssemblyManager$1 = /*#__PURE__*/observer(function (_ref) {
3265
- var rootModel = _ref.rootModel,
3266
- _onClose = _ref.onClose;
3267
- var classes = useStyles$6();
3268
-
3269
- var _useState = useState(false),
3270
- _useState2 = _slicedToArray(_useState, 2),
3271
- isFormOpen = _useState2[0],
3272
- setFormOpen = _useState2[1];
3273
-
3274
- var _useState3 = useState(false),
3275
- _useState4 = _slicedToArray(_useState3, 2),
3276
- isAssemblyBeingEdited = _useState4[0],
3277
- setIsAssemblyBeingEdited = _useState4[1];
3278
-
3279
- var _useState5 = useState(),
3280
- _useState6 = _slicedToArray(_useState5, 2),
3281
- assemblyBeingEdited = _useState6[0],
3282
- setAssemblyBeingEdited = _useState6[1];
3283
-
3284
- var showAssemblyTable = !isFormOpen && !isAssemblyBeingEdited;
3285
- return /*#__PURE__*/React.createElement(Dialog, {
3286
- open: true,
3287
- onClose: function onClose() {
3288
- return _onClose(false);
3289
- }
3290
- }, /*#__PURE__*/React.createElement(DialogTitle, {
3291
- className: classes.titleBox
3292
- }, showAssemblyTable ? 'Assembly manager' : null, isFormOpen ? /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement(IconButton, {
3293
- "aria-label": "back",
3294
- className: classes.backButton,
3295
- onClick: function onClick() {
3296
- return setFormOpen(false);
3297
- }
3298
- }, /*#__PURE__*/React.createElement(ArrowBackIosIcon, null)), "Add new assembly") : null, isAssemblyBeingEdited ? /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement(IconButton, {
3299
- "aria-label": "back",
3300
- className: classes.backButton,
3301
- onClick: function onClick() {
3302
- return setIsAssemblyBeingEdited(false);
3303
- }
3304
- }, /*#__PURE__*/React.createElement(ArrowBackIosIcon, null)), returnAssemblyName(assemblyBeingEdited)) : null, /*#__PURE__*/React.createElement(IconButton, {
3305
- "aria-label": "close",
3306
- className: classes.closeButton,
3307
- onClick: function onClick() {
3308
- return _onClose(false);
3309
- }
3310
- }, /*#__PURE__*/React.createElement(CloseIcon, null))), /*#__PURE__*/React.createElement(DialogContent, null, /*#__PURE__*/React.createElement("div", {
3311
- className: classes.dialogContent
3312
- }, showAssemblyTable ? /*#__PURE__*/React.createElement(AssemblyTable, {
3313
- rootModel: rootModel,
3314
- setIsAssemblyBeingEdited: setIsAssemblyBeingEdited,
3315
- setAssemblyBeingEdited: setAssemblyBeingEdited
3316
- }) : null, isAssemblyBeingEdited ? /*#__PURE__*/React.createElement(AssemblyEditor, {
3317
- assembly: assemblyBeingEdited
3318
- }) : null, isFormOpen ? /*#__PURE__*/React.createElement(AssemblyAddForm, {
3319
- rootModel: rootModel,
3320
- setFormOpen: setFormOpen
3321
- }) : null)), /*#__PURE__*/React.createElement(DialogActions, null, showAssemblyTable ? /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement(Button, {
3322
- color: "secondary",
3323
- variant: "contained",
3324
- onClick: function onClick() {
3325
- return _onClose(false);
3326
- }
3327
- }, "Close"), /*#__PURE__*/React.createElement(Button, {
3328
- variant: "contained",
3329
- color: "secondary",
3330
- startIcon: /*#__PURE__*/React.createElement(AddIcon, null),
3331
- onClick: function onClick() {
3332
- return setFormOpen(true);
3333
- }
3334
- }, "Add new assembly")) : null));
3335
- }); // eslint-disable-next-line @typescript-eslint/no-explicit-any
3336
-
3337
- function returnAssemblyName(assembly) {
3338
- if (assembly !== undefined) {
3339
- return assembly.name;
3340
- }
3341
-
3342
- return null;
3343
- }
3344
-
3345
-
3346
-
3347
- var index$1 = {
3348
- __proto__: null,
3349
- 'default': AssemblyManager$1
3350
- };
3351
-
3352
- var CloseConnectionDialog = /*#__PURE__*/lazy(function () {
3353
- return Promise.resolve().then(function () { return CloseConnectionDialog$3; });
3354
- });
3355
- var DeleteConnectionDialog = /*#__PURE__*/lazy(function () {
3356
- return Promise.resolve().then(function () { return DeleteConnectionDialog$3; });
3357
- });
3358
- var ManageConnectionsDialog = /*#__PURE__*/lazy(function () {
3359
- return Promise.resolve().then(function () { return ManageConnectionsDialog$2; });
3360
- });
3361
- var ToggleConnectionsDialog = /*#__PURE__*/lazy(function () {
3362
- return Promise.resolve().then(function () { return ToggleConnectionsDialog$2; });
3363
- });
3364
- var useStyles$7 = /*#__PURE__*/makeStyles(function (theme) {
3365
- var _theme$palette$tertia, _theme$palette$tertia2;
3366
-
3367
- return {
3368
- searchBox: {
3369
- margin: theme.spacing(2)
3370
- },
3371
- menuIcon: {
3372
- marginRight: theme.spacing(1),
3373
- marginBottom: 0
3374
- },
3375
- fab: {
3376
- position: 'absolute',
3377
- bottom: theme.spacing(6),
3378
- right: theme.spacing(6)
3379
- },
3380
- compactCheckbox: {
3381
- padding: 0
3382
- },
3383
- checkboxLabel: {
3384
- marginRight: 0,
3385
- '&:hover': {
3386
- backgroundColor: '#eee'
3387
- }
3388
- },
3389
- // this accordionBase element's small padding is used to give a margin to
3390
- // accordionColor it a "margin" because the virtualized elements can't really
3391
- // use margin in a conventional way (it doesn't affect layout)
3392
- accordionBase: {
3393
- display: 'flex'
3394
- },
3395
- accordionCard: {
3396
- padding: 3,
3397
- cursor: 'pointer',
3398
- display: 'flex'
3399
- },
3400
- nestingLevelMarker: {
3401
- position: 'absolute',
3402
- borderLeft: '1.5px solid #555'
3403
- },
3404
- // accordionColor set's display:flex so that the child accordionText use
3405
- // vertically centered text
3406
- accordionColor: {
3407
- background: (_theme$palette$tertia = theme.palette.tertiary) === null || _theme$palette$tertia === void 0 ? void 0 : _theme$palette$tertia.main,
3408
- color: (_theme$palette$tertia2 = theme.palette.tertiary) === null || _theme$palette$tertia2 === void 0 ? void 0 : _theme$palette$tertia2.contrastText,
3409
- width: '100%',
3410
- display: 'flex',
3411
- paddingLeft: 5
3412
- },
3413
- // margin:auto 0 to center text vertically
3414
- accordionText: {
3415
- margin: 'auto 0'
3416
- }
3417
- };
3418
- }); // An individual node in the track selector. Note: manually sets cursor:
3419
- // pointer improves usability for what can be clicked
3420
-
3421
- var Node = function Node(props) {
3422
- var data = props.data,
3423
- isOpen = props.isOpen,
3424
- style = props.style,
3425
- setOpen = props.setOpen;
3426
- var isLeaf = data.isLeaf,
3427
- nestingLevel = data.nestingLevel,
3428
- checked = data.checked,
3429
- id = data.id,
3430
- name = data.name,
3431
- _onChange = data.onChange,
3432
- toggleCollapse = data.toggleCollapse,
3433
- conf = data.conf,
3434
- onMoreInfo = data.onMoreInfo,
3435
- drawerPosition = data.drawerPosition;
3436
- var classes = useStyles$7();
3437
- var width = 10;
3438
- var marginLeft = nestingLevel * width + (isLeaf ? width : 0);
3439
- var unsupported = name && (name.endsWith('(Unsupported)') || name.endsWith('(Unknown)'));
3440
- var description = conf && readConfObject(conf, ['description']) || '';
3441
- return /*#__PURE__*/React.createElement("div", {
3442
- style: style,
3443
- className: !isLeaf ? classes.accordionBase : undefined
3444
- }, new Array(nestingLevel).fill(0).map(function (_, idx) {
3445
- return /*#__PURE__*/React.createElement("div", {
3446
- key: "mark-".concat(idx),
3447
- style: {
3448
- left: idx * width + 4,
3449
- height: style.height
3450
- },
3451
- className: classes.nestingLevelMarker
3452
- });
3453
- }), /*#__PURE__*/React.createElement("div", {
3454
- className: !isLeaf ? classes.accordionCard : undefined,
3455
- onClick: function onClick() {
3456
- toggleCollapse(id);
3457
- setOpen(!isOpen);
3458
- },
3459
- style: {
3460
- marginLeft: marginLeft,
3461
- whiteSpace: 'nowrap',
3462
- width: '100%'
3463
- }
3464
- }, /*#__PURE__*/React.createElement("div", {
3465
- className: !isLeaf ? classes.accordionColor : undefined
3466
- }, !isLeaf ? /*#__PURE__*/React.createElement("div", {
3467
- className: classes.accordionText
3468
- }, /*#__PURE__*/React.createElement(Typography, null, isOpen ? /*#__PURE__*/React.createElement(ArrowDropDownIcon, null) : /*#__PURE__*/React.createElement(ArrowRightIcon, null), name)) : /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement(Tooltip, {
3469
- title: description,
3470
- placement: drawerPosition === 'left' ? 'right' : 'left'
3471
- }, /*#__PURE__*/React.createElement(FormControlLabel, {
3472
- className: classes.checkboxLabel,
3473
- control: /*#__PURE__*/React.createElement(Checkbox, {
3474
- className: classes.compactCheckbox,
3475
- checked: checked,
3476
- onChange: function onChange() {
3477
- return _onChange(id);
3478
- },
3479
- color: "primary",
3480
- disabled: unsupported,
3481
- inputProps: {
3482
- 'data-testid': "htsTrackEntry-".concat(id)
3483
- }
3484
- }),
3485
- label: name
3486
- })), /*#__PURE__*/React.createElement(IconButton, {
3487
- onClick: function onClick(e) {
3488
- return onMoreInfo({
3489
- target: e.currentTarget,
3490
- id: id,
3491
- conf: conf
3492
- });
3493
- },
3494
- color: "secondary",
3495
- "data-testid": "htsTrackEntryMenu-".concat(id)
3496
- }, /*#__PURE__*/React.createElement(MoreIcon, null))))));
3497
- };
3498
-
3499
- var getNodeData = function getNodeData(node, nestingLevel, extra) {
3500
- var isLeaf = !!node.conf;
3501
- return {
3502
- data: _objectSpread2(_objectSpread2({
3503
- defaultHeight: isLeaf ? 22 : 40,
3504
- isLeaf: isLeaf,
3505
- isOpenByDefault: true,
3506
- nestingLevel: nestingLevel
3507
- }, node), extra),
3508
- nestingLevel: nestingLevel,
3509
- node: node
3510
- };
3511
- }; // this is the main tree component for the hierarchical track selector in note:
3512
- // in jbrowse-web the toolbar is position="sticky" which means the autosizer
3513
- // includes the height of the toolbar, so we subtract the given offsets
3514
-
3515
-
3516
- var HierarchicalTree = /*#__PURE__*/observer(function (_ref) {
3517
- var _session$getTrackActi;
3518
-
3519
- var height = _ref.height,
3520
- tree = _ref.tree,
3521
- model = _ref.model;
3522
- var filterText = model.filterText,
3523
- view = model.view;
3524
- var treeRef = useRef(null);
3525
-
3526
- var _useState = useState(),
3527
- _useState2 = _slicedToArray(_useState, 2),
3528
- info = _useState2[0],
3529
- setMoreInfo = _useState2[1];
3530
-
3531
- var session = getSession(model);
3532
- var drawerPosition = session.drawerPosition;
3533
- var extra = useMemo(function () {
3534
- return {
3535
- onChange: function onChange(trackId) {
3536
- return view.toggleTrack(trackId);
3537
- },
3538
- toggleCollapse: function toggleCollapse(pathName) {
3539
- return model.toggleCategory(pathName);
3540
- },
3541
- onMoreInfo: setMoreInfo,
3542
- drawerPosition: drawerPosition
3543
- };
3544
- }, [view, model, drawerPosition]);
3545
- var treeWalker = useCallback( /*#__PURE__*/runtime_1.mark(function treeWalker() {
3546
- var i, parentMeta, _i, curr;
3547
-
3548
- return runtime_1.wrap(function treeWalker$(_context) {
3549
- while (1) {
3550
- switch (_context.prev = _context.next) {
3551
- case 0:
3552
- i = 0;
3553
-
3554
- case 1:
3555
- if (!(i < tree.children.length)) {
3556
- _context.next = 7;
3557
- break;
3558
- }
3559
-
3560
- _context.next = 4;
3561
- return getNodeData(tree.children[i], 0, extra);
3562
-
3563
- case 4:
3564
- i++;
3565
- _context.next = 1;
3566
- break;
3567
-
3568
- case 7:
3569
-
3570
- _context.next = 10;
3571
- return;
3572
-
3573
- case 10:
3574
- parentMeta = _context.sent;
3575
- _i = 0;
3576
-
3577
- case 12:
3578
- if (!(_i < parentMeta.node.children.length)) {
3579
- _context.next = 19;
3580
- break;
3581
- }
3582
-
3583
- curr = parentMeta.node.children[_i];
3584
- _context.next = 16;
3585
- return getNodeData(curr, parentMeta.nestingLevel + 1, extra);
3586
-
3587
- case 16:
3588
- _i++;
3589
- _context.next = 12;
3590
- break;
3591
-
3592
- case 19:
3593
- _context.next = 7;
3594
- break;
3595
-
3596
- case 21:
3597
- case "end":
3598
- return _context.stop();
3599
- }
3600
- }
3601
- }, treeWalker);
3602
- }), [tree, extra]);
3603
- var conf = info === null || info === void 0 ? void 0 : info.conf;
3604
- var menuItems = conf && ((_session$getTrackActi = session.getTrackActionMenuItems) === null || _session$getTrackActi === void 0 ? void 0 : _session$getTrackActi.call(session, conf)) || [];
3605
- useEffect(function () {
3606
- treeRef.current.recomputeTree({
3607
- refreshNodes: true,
3608
- useDefaultHeight: true
3609
- });
3610
- }, [tree, filterText]);
3611
- return /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement(VariableSizeTree, {
3612
- ref: treeRef,
3613
- treeWalker: treeWalker,
3614
- height: height
3615
- }, Node), /*#__PURE__*/React.createElement(JBrowseMenu, {
3616
- anchorEl: info === null || info === void 0 ? void 0 : info.target,
3617
- menuItems: menuItems,
3618
- onMenuItemClick: function onMenuItemClick(_event, callback) {
3619
- callback();
3620
- setMoreInfo(undefined);
3621
- },
3622
- open: Boolean(info),
3623
- onClose: function onClose() {
3624
- return setMoreInfo(undefined);
3625
- }
3626
- }));
3627
- }); // Don't use autosizer in jest and instead hardcode a height, otherwise fails
3628
- // jest tests
3629
-
3630
- var AutoSizedHierarchicalTree = function AutoSizedHierarchicalTree(_ref2) {
3631
- var tree = _ref2.tree,
3632
- model = _ref2.model,
3633
- offset = _ref2.offset;
3634
- return typeof jest === 'undefined' ? /*#__PURE__*/React.createElement(AutoSizer, {
3635
- disableWidth: true
3636
- }, function (_ref3) {
3637
- var height = _ref3.height;
3638
- return /*#__PURE__*/React.createElement(HierarchicalTree, {
3639
- height: height - offset,
3640
- model: model,
3641
- tree: tree
3642
- });
3643
- }) : /*#__PURE__*/React.createElement(HierarchicalTree, {
3644
- height: 9000,
3645
- model: model,
3646
- tree: tree
3647
- });
3648
- };
3649
-
3650
- var Wrapper = function Wrapper(_ref4) {
3651
- var overrideDimensions = _ref4.overrideDimensions,
3652
- children = _ref4.children;
3653
- return overrideDimensions ? /*#__PURE__*/React.createElement("div", {
3654
- style: _objectSpread2({}, overrideDimensions)
3655
- }, children) : /*#__PURE__*/React.createElement(React.Fragment, null, children);
3656
- };
3657
-
3658
- var HierarchicalTrackSelectorContainer = /*#__PURE__*/observer(function (_ref5) {
3659
- var model = _ref5.model,
3660
- toolbarHeight = _ref5.toolbarHeight,
3661
- overrideDimensions = _ref5.overrideDimensions;
3662
- var classes = useStyles$7();
3663
- var session = getSession(model);
3664
-
3665
- var _useState3 = useState(null),
3666
- _useState4 = _slicedToArray(_useState3, 2),
3667
- anchorEl = _useState4[0],
3668
- setAnchorEl = _useState4[1];
3669
-
3670
- function handleFabClose() {
3671
- setAnchorEl(null);
3672
- }
3673
-
3674
- return /*#__PURE__*/React.createElement(Wrapper, {
3675
- overrideDimensions: overrideDimensions
3676
- }, /*#__PURE__*/React.createElement(HierarchicalTrackSelector, {
3677
- model: model,
3678
- toolbarHeight: toolbarHeight,
3679
- overrideDimensions: overrideDimensions
3680
- }), session.addConnectionConf || session.addTrackConf ? /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement(Fab, {
3681
- color: "secondary",
3682
- className: classes.fab,
3683
- onClick: function onClick(event) {
3684
- setAnchorEl(event.currentTarget);
3685
- }
3686
- }, /*#__PURE__*/React.createElement(AddIcon, null)), /*#__PURE__*/React.createElement(Menu, {
3687
- anchorEl: anchorEl,
3688
- open: Boolean(anchorEl),
3689
- onClose: function onClose() {
3690
- return setAnchorEl(null);
3691
- }
3692
- }, session.addConnectionConf ? /*#__PURE__*/React.createElement(MenuItem, {
3693
- onClick: function onClick() {
3694
- handleFabClose();
3695
- var widget = session.addWidget('AddConnectionWidget', 'addConnectionWidget');
3696
- session.showWidget(widget);
3697
- }
3698
- }, "Add connection") : null, session.addTrackConf ? /*#__PURE__*/React.createElement(MenuItem, {
3699
- onClick: function onClick() {
3700
- handleFabClose();
3701
- var widget = session.addWidget('AddTrackWidget', 'addTrackWidget', {
3702
- view: model.view.id
3703
- });
3704
- session.showWidget(widget);
3705
- }
3706
- }, "Add track") : null)) : null);
3707
- });
3708
- var HierarchicalTrackSelectorHeader = /*#__PURE__*/observer(function (_ref6) {
3709
- var model = _ref6.model,
3710
- setHeaderHeight = _ref6.setHeaderHeight,
3711
- setAssemblyIdx = _ref6.setAssemblyIdx,
3712
- assemblyIdx = _ref6.assemblyIdx;
3713
- var classes = useStyles$7();
3714
- var session = getSession(model);
3715
-
3716
- var _useState5 = useState(),
3717
- _useState6 = _slicedToArray(_useState5, 2),
3718
- connectionAnchorEl = _useState6[0],
3719
- setConnectionAnchorEl = _useState6[1];
3720
-
3721
- var _useState7 = useState(),
3722
- _useState8 = _slicedToArray(_useState7, 2),
3723
- menuAnchorEl = _useState8[0],
3724
- setMenuAnchorEl = _useState8[1];
3725
-
3726
- var _useState9 = useState(),
3727
- _useState10 = _slicedToArray(_useState9, 2),
3728
- modalInfo = _useState10[0],
3729
- setModalInfo = _useState10[1];
3730
-
3731
- var _useState11 = useState(),
3732
- _useState12 = _slicedToArray(_useState11, 2),
3733
- deleteDialogDetails = _useState12[0],
3734
- setDeleteDialogDetails = _useState12[1];
3735
-
3736
- var _useState13 = useState(false),
3737
- _useState14 = _slicedToArray(_useState13, 2),
3738
- connectionManagerOpen = _useState14[0],
3739
- setConnectionManagerOpen = _useState14[1];
3740
-
3741
- var _useState15 = useState(false),
3742
- _useState16 = _slicedToArray(_useState15, 2),
3743
- connectionToggleOpen = _useState16[0],
3744
- setConnectionToggleOpen = _useState16[1];
3745
-
3746
- var assemblyNames = model.assemblyNames;
3747
- var assemblyName = assemblyNames[assemblyIdx];
3748
-
3749
- function breakConnection(connectionConf, deletingConnection) {
3750
- var name = readConfObject(connectionConf, 'name');
3751
- var result = session.prepareToBreakConnection(connectionConf);
3752
-
3753
- if (result) {
3754
- var _result = _slicedToArray(result, 2),
3755
- safelyBreakConnection = _result[0],
3756
- dereferenceTypeCount = _result[1];
3757
-
3758
- if (Object.keys(dereferenceTypeCount).length > 0) {
3759
- setModalInfo({
3760
- connectionConf: connectionConf,
3761
- safelyBreakConnection: safelyBreakConnection,
3762
- dereferenceTypeCount: dereferenceTypeCount,
3763
- name: name
3764
- });
3765
- } else {
3766
- safelyBreakConnection();
3767
- }
3768
- }
3769
-
3770
- if (deletingConnection) {
3771
- setDeleteDialogDetails({
3772
- name: name,
3773
- connectionConf: connectionConf
3774
- });
3775
- }
3776
- }
3777
-
3778
- var connectionMenuItems = [{
3779
- label: 'Turn on/off connections...',
3780
- onClick: function onClick() {
3781
- return setConnectionToggleOpen(true);
3782
- }
3783
- }];
3784
-
3785
- if (session.addConnectionConf) {
3786
- connectionMenuItems.unshift({
3787
- label: 'Add connection',
3788
- onClick: function onClick() {
3789
- session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
3790
- }
3791
- });
3792
- connectionMenuItems.push({
3793
- label: 'Delete connections...',
3794
- onClick: function onClick() {
3795
- return setConnectionManagerOpen(true);
3796
- }
3797
- });
3798
- }
3799
-
3800
- var assemblyMenuItems = assemblyNames.length > 1 ? [{
3801
- label: 'Select assembly...',
3802
- subMenu: assemblyNames.map(function (name, idx) {
3803
- return {
3804
- label: name,
3805
- onClick: function onClick() {
3806
- setAssemblyIdx(idx);
3807
- }
3808
- };
3809
- })
3810
- }] : [];
3811
- var menuItems = [{
3812
- label: 'Add track...',
3813
- onClick: function onClick() {
3814
- session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
3815
- view: model.view.id
3816
- }));
3817
- }
3818
- }].concat(assemblyMenuItems);
3819
- return /*#__PURE__*/React.createElement("div", {
3820
- ref: function ref(_ref7) {
3821
- return setHeaderHeight((_ref7 === null || _ref7 === void 0 ? void 0 : _ref7.getBoundingClientRect().height) || 0);
3822
- },
3823
- "data-testid": "hierarchical_track_selector"
3824
- }, /*#__PURE__*/React.createElement("div", {
3825
- style: {
3826
- display: 'flex'
3827
- }
3828
- }, session.addTrackConf && /*#__PURE__*/React.createElement(IconButton, {
3829
- className: classes.menuIcon,
3830
- onClick: function onClick(event) {
3831
- setMenuAnchorEl(event.currentTarget);
3832
- }
3833
- }, /*#__PURE__*/React.createElement(MenuIcon, null)), session.makeConnection && /*#__PURE__*/React.createElement(IconButton, {
3834
- className: classes.menuIcon,
3835
- onClick: function onClick(event) {
3836
- setConnectionAnchorEl(event.currentTarget);
3837
- }
3838
- }, /*#__PURE__*/React.createElement(Cable, null)), /*#__PURE__*/React.createElement(TextField, {
3839
- className: classes.searchBox,
3840
- label: "Filter tracks",
3841
- value: model.filterText,
3842
- onChange: function onChange(event) {
3843
- return model.setFilterText(event.target.value);
3844
- },
3845
- fullWidth: true,
3846
- InputProps: {
3847
- endAdornment: /*#__PURE__*/React.createElement(InputAdornment, {
3848
- position: "end"
3849
- }, /*#__PURE__*/React.createElement(IconButton, {
3850
- color: "secondary",
3851
- onClick: model.clearFilterText
3852
- }, /*#__PURE__*/React.createElement(ClearIcon, null)))
3853
- }
3854
- })), /*#__PURE__*/React.createElement(JBrowseMenu, {
3855
- anchorEl: connectionAnchorEl,
3856
- open: Boolean(connectionAnchorEl),
3857
- onMenuItemClick: function onMenuItemClick(_, callback) {
3858
- callback();
3859
- setConnectionAnchorEl(undefined);
3860
- },
3861
- onClose: function onClose() {
3862
- return setConnectionAnchorEl(undefined);
3863
- },
3864
- menuItems: connectionMenuItems
3865
- }), /*#__PURE__*/React.createElement(JBrowseMenu, {
3866
- anchorEl: menuAnchorEl,
3867
- open: Boolean(menuAnchorEl),
3868
- onMenuItemClick: function onMenuItemClick(_, callback) {
3869
- callback();
3870
- setMenuAnchorEl(undefined);
3871
- },
3872
- onClose: function onClose() {
3873
- return setMenuAnchorEl(undefined);
3874
- },
3875
- menuItems: menuItems
3876
- }), /*#__PURE__*/React.createElement(Suspense, {
3877
- fallback: /*#__PURE__*/React.createElement("div", null)
3878
- }, modalInfo ? /*#__PURE__*/React.createElement(CloseConnectionDialog, {
3879
- modalInfo: modalInfo,
3880
- setModalInfo: setModalInfo,
3881
- session: session
3882
- }) : deleteDialogDetails ? /*#__PURE__*/React.createElement(DeleteConnectionDialog, {
3883
- handleClose: function handleClose() {
3884
- return setDeleteDialogDetails(undefined);
3885
- },
3886
- deleteDialogDetails: deleteDialogDetails,
3887
- session: session
3888
- }) : null, connectionManagerOpen ? /*#__PURE__*/React.createElement(ManageConnectionsDialog, {
3889
- handleClose: function handleClose() {
3890
- return setConnectionManagerOpen(false);
3891
- },
3892
- breakConnection: breakConnection,
3893
- session: session
3894
- }) : null, connectionToggleOpen ? /*#__PURE__*/React.createElement(ToggleConnectionsDialog, {
3895
- handleClose: function handleClose() {
3896
- return setConnectionToggleOpen(false);
3897
- },
3898
- session: session,
3899
- breakConnection: breakConnection,
3900
- assemblyName: assemblyName
3901
- }) : null));
3902
- });
3903
- var HierarchicalTrackSelector = /*#__PURE__*/observer(function (_ref8) {
3904
- var model = _ref8.model,
3905
- _ref8$toolbarHeight = _ref8.toolbarHeight,
3906
- toolbarHeight = _ref8$toolbarHeight === void 0 ? 0 : _ref8$toolbarHeight;
3907
-
3908
- var _useState17 = useState(0),
3909
- _useState18 = _slicedToArray(_useState17, 2),
3910
- assemblyIdx = _useState18[0],
3911
- setAssemblyIdx = _useState18[1];
3912
-
3913
- var _useState19 = useState(0),
3914
- _useState20 = _slicedToArray(_useState19, 2),
3915
- headerHeight = _useState20[0],
3916
- setHeaderHeight = _useState20[1];
3917
-
3918
- var assemblyNames = model.assemblyNames;
3919
- var assemblyName = assemblyNames[assemblyIdx];
3920
- return assemblyName ? /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement(HierarchicalTrackSelectorHeader, {
3921
- model: model,
3922
- setHeaderHeight: setHeaderHeight,
3923
- setAssemblyIdx: setAssemblyIdx,
3924
- assemblyIdx: assemblyIdx
3925
- }), /*#__PURE__*/React.createElement(AutoSizedHierarchicalTree, {
3926
- tree: model.hierarchy(assemblyName),
3927
- model: model,
3928
- offset: toolbarHeight + headerHeight
3929
- })) : null;
3930
- });
3931
-
3932
- var HierarchicalTrackSelector$1 = {
3933
- __proto__: null,
3934
- 'default': HierarchicalTrackSelectorContainer
3935
- };
3936
-
3937
- var useStyles$8 = /*#__PURE__*/makeStyles(function (theme) {
3938
- return {
3939
- spacing: {
3940
- marginBottom: theme.spacing(3)
3941
- }
3942
- };
3943
- });
3944
-
3945
- function StatusMessage(_ref) {
3946
- var _trackAdapter$subadap;
3947
-
3948
- var trackAdapter = _ref.trackAdapter,
3949
- trackType = _ref.trackType;
3950
- var classes = useStyles$8();
3951
- return trackAdapter.type === 'SNPCoverageAdapter' ? /*#__PURE__*/React.createElement(Typography, {
3952
- className: classes.spacing
3953
- }, "Selected ", /*#__PURE__*/React.createElement("code", null, trackType), ". Using adapter", ' ', /*#__PURE__*/React.createElement("code", null, trackAdapter.type), " with subadapter", ' ', /*#__PURE__*/React.createElement("code", null, (_trackAdapter$subadap = trackAdapter.subadapter) === null || _trackAdapter$subadap === void 0 ? void 0 : _trackAdapter$subadap.type), ". Please enter a track name and, if necessary, update the track type.") : /*#__PURE__*/React.createElement(Typography, {
3954
- className: classes.spacing
3955
- }, "Using adapter ", /*#__PURE__*/React.createElement("code", null, trackAdapter.type), " and guessing track type", ' ', /*#__PURE__*/React.createElement("code", null, trackType), ". Please enter a track name and, if necessary, update the track type.");
3956
- }
3957
- /**
3958
- * categorizeAdapters takes a list of adapters and sorts their menu item elements under an appropriate ListSubheader
3959
- * element. In this way, adapters that are from external plugins can have headers that differentiate them from the
3960
- * out-of-the-box plugins.
3961
- * @param adaptersList - a list of adapters found in the PluginManager
3962
- * @returns a series of JSX elements that are ListSubheaders followed by the adapters
3963
- * found under that subheader
3964
- */
3965
-
3966
-
3967
- function categorizeAdapters(adaptersList) {
3968
- var currentCategory = ''; // eslint-disable-next-line @typescript-eslint/no-explicit-any
3969
-
3970
- var items = [];
3971
- adaptersList.forEach(function (adapter) {
3972
- var _adapter$adapterMetad;
3973
-
3974
- if ((_adapter$adapterMetad = adapter.adapterMetadata) !== null && _adapter$adapterMetad !== void 0 && _adapter$adapterMetad.category) {
3975
- var _adapter$adapterMetad2, _adapter$adapterMetad7, _adapter$adapterMetad8;
3976
-
3977
- if (currentCategory !== ((_adapter$adapterMetad2 = adapter.adapterMetadata) === null || _adapter$adapterMetad2 === void 0 ? void 0 : _adapter$adapterMetad2.category)) {
3978
- var _adapter$adapterMetad3, _adapter$adapterMetad4, _adapter$adapterMetad5, _adapter$adapterMetad6;
3979
-
3980
- currentCategory = (_adapter$adapterMetad3 = adapter.adapterMetadata) === null || _adapter$adapterMetad3 === void 0 ? void 0 : _adapter$adapterMetad3.category;
3981
- items.push( /*#__PURE__*/React.createElement(ListSubheader, {
3982
- key: (_adapter$adapterMetad4 = adapter.adapterMetadata) === null || _adapter$adapterMetad4 === void 0 ? void 0 : _adapter$adapterMetad4.category,
3983
- value: (_adapter$adapterMetad5 = adapter.adapterMetadata) === null || _adapter$adapterMetad5 === void 0 ? void 0 : _adapter$adapterMetad5.category
3984
- }, (_adapter$adapterMetad6 = adapter.adapterMetadata) === null || _adapter$adapterMetad6 === void 0 ? void 0 : _adapter$adapterMetad6.category));
3985
- }
3986
-
3987
- items.push( /*#__PURE__*/React.createElement(MenuItem, {
3988
- key: adapter.name,
3989
- value: adapter.name
3990
- }, (_adapter$adapterMetad7 = adapter.adapterMetadata) !== null && _adapter$adapterMetad7 !== void 0 && _adapter$adapterMetad7.displayName ? (_adapter$adapterMetad8 = adapter.adapterMetadata) === null || _adapter$adapterMetad8 === void 0 ? void 0 : _adapter$adapterMetad8.displayName : adapter.name));
3991
- }
3992
- });
3993
- return items;
3994
- }
3995
-
3996
- function getAdapterTypes(pluginManager) {
3997
- return pluginManager.getElementTypesInGroup('adapter');
3998
- }
3999
-
4000
- function getTrackTypes(pluginManager) {
4001
- return pluginManager.getElementTypesInGroup('track');
4002
- }
4003
-
4004
- var TrackAdapterSelector = /*#__PURE__*/observer(function (_ref2) {
4005
- var model = _ref2.model;
4006
- var classes = useStyles$8();
4007
- var session = getSession(model);
4008
- var trackAdapter = model.trackAdapter; // prettier-ignore
4009
-
4010
- var adapters = getAdapterTypes(getEnv(session).pluginManager);
4011
- return /*#__PURE__*/React.createElement(TextField, {
4012
- className: classes.spacing,
4013
- value: (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) !== 'UNKNOWN' ? trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type : '',
4014
- label: "adapterType",
4015
- helperText: "Select an adapter type",
4016
- select: true,
4017
- fullWidth: true,
4018
- onChange: function onChange(event) {
4019
- model.setAdapterHint(event.target.value);
4020
- },
4021
- SelectProps: {
4022
- // @ts-ignore
4023
- SelectDisplayProps: {
4024
- 'data-testid': 'adapterTypeSelect'
4025
- }
4026
- }
4027
- }, adapters // Excludes any adapter with the 'adapterMetadata.hiddenFromGUI' property, and anything with the 'adapterMetadata.category' property
4028
- .filter(function (elt) {
4029
- var _elt$adapterMetadata, _elt$adapterMetadata2;
4030
-
4031
- return !((_elt$adapterMetadata = elt.adapterMetadata) !== null && _elt$adapterMetadata !== void 0 && _elt$adapterMetadata.hiddenFromGUI) && !((_elt$adapterMetadata2 = elt.adapterMetadata) !== null && _elt$adapterMetadata2 !== void 0 && _elt$adapterMetadata2.category);
4032
- }).map(function (elt) {
4033
- var _elt$adapterMetadata3, _elt$adapterMetadata4;
4034
-
4035
- return /*#__PURE__*/React.createElement(MenuItem, {
4036
- key: elt.name,
4037
- value: elt.name
4038
- }, (_elt$adapterMetadata3 = elt.adapterMetadata) !== null && _elt$adapterMetadata3 !== void 0 && _elt$adapterMetadata3.displayName ? (_elt$adapterMetadata4 = elt.adapterMetadata) === null || _elt$adapterMetadata4 === void 0 ? void 0 : _elt$adapterMetadata4.displayName : elt.name);
4039
- }), categorizeAdapters(adapters.filter(function (elt) {
4040
- var _elt$adapterMetadata5;
4041
-
4042
- return !((_elt$adapterMetadata5 = elt.adapterMetadata) !== null && _elt$adapterMetadata5 !== void 0 && _elt$adapterMetadata5.hiddenFromGUI);
4043
- })));
4044
- });
4045
-
4046
- function UnknownAdapterPrompt(_ref3) {
4047
- var model = _ref3.model;
4048
- var classes = useStyles$8();
4049
- return /*#__PURE__*/React.createElement(React.Fragment, null, /*#__PURE__*/React.createElement(Typography, {
4050
- className: classes.spacing
4051
- }, "JBrowse was not able to guess the adapter type for this data, but it may be in the list below. If not, you can", ' ', /*#__PURE__*/React.createElement(Link, {
4052
- href: "https://github.com/GMOD/jbrowse-components/releases",
4053
- target: "_blank",
4054
- rel: "noopener noreferrer"
4055
- }, "check for new releases"), ' ', "of JBrowse to see if they support this data type or", ' ', /*#__PURE__*/React.createElement(Link, {
4056
- href: "https://github.com/GMOD/jbrowse-components/issues/new",
4057
- target: "_blank",
4058
- rel: "noopener noreferrer"
4059
- }, "file an issue"), ' ', "and add a feature request for this data type."), /*#__PURE__*/React.createElement(TrackAdapterSelector, {
4060
- model: model
4061
- }));
4062
- }
4063
-
4064
- var TrackTypeSelector = /*#__PURE__*/observer(function (_ref4) {
4065
- var model = _ref4.model;
4066
- var classes = useStyles$8();
4067
- var session = getSession(model);
4068
- var trackType = model.trackType;
4069
- var trackTypes = getTrackTypes(getEnv(session).pluginManager);
4070
- return /*#__PURE__*/React.createElement(TextField, {
4071
- className: classes.spacing,
4072
- value: trackType,
4073
- label: "trackType",
4074
- helperText: "Select a track type",
4075
- select: true,
4076
- fullWidth: true,
4077
- onChange: function onChange(event) {
4078
- model.setTrackType(event.target.value);
4079
- },
4080
- SelectProps: {
4081
- // @ts-ignore
4082
- SelectDisplayProps: {
4083
- 'data-testid': 'trackTypeSelect'
4084
- }
4085
- }
4086
- }, trackTypes.map(function (_ref5) {
4087
- var name = _ref5.name;
4088
- return /*#__PURE__*/React.createElement(MenuItem, {
4089
- key: name,
4090
- value: name
4091
- }, name);
4092
- }));
4093
- });
4094
- var TrackAssemblySelector = /*#__PURE__*/observer(function (_ref6) {
4095
- var model = _ref6.model;
4096
- var session = getSession(model);
4097
- var assembly = model.assembly;
4098
- return /*#__PURE__*/React.createElement(TextField, {
4099
- value: assembly,
4100
- label: "assemblyName",
4101
- helperText: "Assembly to which the track will be added",
4102
- select: true,
4103
- fullWidth: true,
4104
- onChange: function onChange(event) {
4105
- return model.setAssembly(event.target.value);
4106
- },
4107
- SelectProps: {
4108
- // @ts-ignore
4109
- SelectDisplayProps: {
4110
- 'data-testid': 'assemblyNameSelect'
4111
- }
4112
- }
4113
- }, session.assemblies.map(function (conf) {
4114
- return readConfObject(conf, 'name');
4115
- }).map(function (name) {
4116
- return /*#__PURE__*/React.createElement(MenuItem, {
4117
- key: name,
4118
- value: name
4119
- }, name);
4120
- }));
4121
- });
4122
-
4123
- function ConfirmTrack(_ref7) {
4124
- var model = _ref7.model;
4125
- var classes = useStyles$8();
4126
- var trackName = model.trackName,
4127
- trackAdapter = model.trackAdapter,
4128
- trackType = model.trackType,
4129
- warningMessage = model.warningMessage,
4130
- adapterHint = model.adapterHint;
4131
-
4132
- if (model.unsupported) {
4133
- return /*#__PURE__*/React.createElement(Typography, {
4134
- className: classes.spacing
4135
- }, "This version of JBrowse cannot display data of this type. It is possible, however, that there is a newer version that can display them. You can", ' ', /*#__PURE__*/React.createElement(Link, {
4136
- href: "https://github.com/GMOD/jbrowse-components/releases",
4137
- target: "_blank",
4138
- rel: "noopener noreferrer"
4139
- }, "check for new releases"), ' ', "of JBrowse or", ' ', /*#__PURE__*/React.createElement(Link, {
4140
- href: "https://github.com/GMOD/jbrowse-components/issues/new",
4141
- target: "_blank",
4142
- rel: "noopener noreferrer"
4143
- }, "file an issue"), ' ', "and add a feature request for this data type.");
4144
- }
4145
-
4146
- if ((trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) === UNKNOWN) {
4147
- return /*#__PURE__*/React.createElement(UnknownAdapterPrompt, {
4148
- model: model
4149
- });
4150
- }
4151
-
4152
- if (adapterHint === '' && trackAdapter) {
4153
- model.setAdapterHint(trackAdapter.type);
4154
- }
4155
-
4156
- if (!(trackAdapter !== null && trackAdapter !== void 0 && trackAdapter.type)) {
4157
- return /*#__PURE__*/React.createElement(Typography, null, "Could not recognize this data type.");
4158
- }
4159
-
4160
- return /*#__PURE__*/React.createElement("div", null, trackAdapter ? /*#__PURE__*/React.createElement(StatusMessage, {
4161
- trackAdapter: trackAdapter,
4162
- trackType: trackType
4163
- }) : null, warningMessage ? /*#__PURE__*/React.createElement(Typography, {
4164
- style: {
4165
- color: 'orange'
4166
- }
4167
- }, warningMessage) : null, /*#__PURE__*/React.createElement(TextField, {
4168
- className: classes.spacing,
4169
- label: "trackName",
4170
- helperText: "A name for this track",
4171
- fullWidth: true,
4172
- value: trackName,
4173
- onChange: function onChange(event) {
4174
- return model.setTrackName(event.target.value);
4175
- },
4176
- inputProps: {
4177
- 'data-testid': 'trackNameInput'
4178
- }
4179
- }), /*#__PURE__*/React.createElement(TrackAdapterSelector, {
4180
- model: model
4181
- }), /*#__PURE__*/React.createElement(TrackTypeSelector, {
4182
- model: model
4183
- }), /*#__PURE__*/React.createElement(TrackAssemblySelector, {
4184
- model: model
4185
- }));
4186
- }
4187
-
4188
- var ConfirmTrack$1 = /*#__PURE__*/observer(ConfirmTrack);
4189
-
4190
- var useStyles$9 = /*#__PURE__*/makeStyles(function (theme) {
4191
- return {
4192
- paper: {
4193
- display: 'flex',
4194
- flexDirection: 'column',
4195
- padding: theme.spacing(1)
4196
- },
4197
- spacer: {
4198
- height: theme.spacing(8)
4199
- }
4200
- };
4201
- });
4202
-
4203
- function TrackSourceSelect(_ref) {
4204
- var model = _ref.model;
4205
- var classes = useStyles$9();
4206
- var rootModel = getRoot(model);
4207
- return /*#__PURE__*/React.createElement(Paper, {
4208
- className: classes.paper
4209
- }, /*#__PURE__*/React.createElement(FileSelector$1, {
4210
- name: "Main file",
4211
- description: "",
4212
- location: model.trackData,
4213
- setLocation: model.setTrackData,
4214
- setName: model.setTrackName,
4215
- rootModel: rootModel
4216
- }), /*#__PURE__*/React.createElement("div", {
4217
- className: classes.spacer
4218
- }), /*#__PURE__*/React.createElement(FileSelector$1, {
4219
- name: "Index file",
4220
- description: "(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.",
4221
- location: model.indexTrackData,
4222
- setLocation: model.setIndexTrackData,
4223
- setName: model.setTrackName,
4224
- rootModel: rootModel
4225
- }));
4226
- }
4227
-
4228
- var TrackSourceSelect$1 = /*#__PURE__*/observer(TrackSourceSelect);
4229
-
4230
- var useStyles$a = /*#__PURE__*/makeStyles(function (theme) {
4231
- return {
4232
- root: {
4233
- marginTop: theme.spacing(1)
4234
- },
4235
- stepper: {
4236
- backgroundColor: theme.palette.background["default"]
4237
- },
4238
- button: {
4239
- marginTop: theme.spacing(1),
4240
- marginRight: theme.spacing(1)
4241
- },
4242
- actionsContainer: {
4243
- marginBottom: theme.spacing(2)
4244
- },
4245
- stepContent: {
4246
- margin: theme.spacing(1)
4247
- },
4248
- alertContainer: {
4249
- padding: "".concat(theme.spacing(2), "px 0px ").concat(theme.spacing(2), "px 0px")
4250
- }
4251
- };
4252
- });
4253
- var steps = ['Enter track data', 'Confirm track type'];
4254
-
4255
- function AddTrackWidget(_ref) {
4256
- var model = _ref.model;
4257
-
4258
- var _useState = useState(0),
4259
- _useState2 = _slicedToArray(_useState, 2),
4260
- activeStep = _useState2[0],
4261
- setActiveStep = _useState2[1];
4262
-
4263
- var classes = useStyles$a();
4264
- var session = getSession(model);
4265
- var assembly = model.assembly,
4266
- trackAdapter = model.trackAdapter,
4267
- trackData = model.trackData,
4268
- trackName = model.trackName,
4269
- trackType = model.trackType;
4270
-
4271
- var _useState3 = useState(),
4272
- _useState4 = _slicedToArray(_useState3, 2),
4273
- trackErrorMessage = _useState4[0],
4274
- setTrackErrorMessage = _useState4[1];
4275
-
4276
- function getStepContent(step) {
4277
- switch (step) {
4278
- case 0:
4279
- return /*#__PURE__*/React.createElement(TrackSourceSelect$1, {
4280
- model: model
4281
- });
4282
-
4283
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4284
- return /*#__PURE__*/React.createElement(ConfirmTrack$1, {
4285
- model: model
4286
- });
4287
-
4288
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4289
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4290
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4291
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4292
-
4293
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4294
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4295
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4296
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4297
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4298
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4299
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4300
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4301
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4302
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4303
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4304
- if (!(activeStep !== steps.length - 1)) {
4305
- _context.next = 3;
4306
- break;
4307
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4308
-
4309
- setActiveStep(activeStep + 1);
4310
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4311
-
4312
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4313
- trackId = "".concat(trackName.toLowerCase().replace(/ /g, '_'), "-").concat(Date.now()).concat(session.adminMode ? '' : '-sessionTrack');
4314
- assemblyInstance = session.assemblyManager.get(assembly);
4315
-
4316
- if (trackAdapter && trackAdapter.type !== 'UNKNOWN') {
4317
- // @ts-ignore
4318
- session.addTrackConf({
4319
- trackId: trackId,
4320
- type: trackType,
4321
- name: trackName,
4322
- assemblyNames: [assembly],
4323
- adapter: _objectSpread2(_objectSpread2({}, trackAdapter), {}, {
4324
- sequenceAdapter: getConf(assemblyInstance, ['sequence', 'adapter'])
4325
- })
4326
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4327
-
4328
- if (model.view) {
4329
- model.view.showTrack(trackId);
4330
- } else {
4331
- session.notify('Open a new view, or use the track selector in an existing view, to view this track', 'info');
4332
- }
4333
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4334
- model.clearData(); // @ts-ignore
4335
-
4336
- session.hideWidget(model);
4337
- } else {
4338
- setTrackErrorMessage('Failed to add track.\nThe configuration of this file is not currently supported.');
4339
- }
4340
-
4341
- case 6:
4342
- case "end":
4343
- return _context.stop();
4344
- }
4345
- }
4346
- }, _callee);
4347
- }));
4348
- return _handleNext.apply(this, arguments);
4349
- }
4350
-
4351
- function handleBack() {
4352
- setTrackErrorMessage(undefined);
4353
- setActiveStep(activeStep - 1);
4354
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4355
-
4356
- function isNextDisabled() {
4357
- switch (activeStep) {
4358
- case 0:
4359
- return !trackData;
4360
-
4361
- case 1:
4362
- return !(trackName && trackType && trackAdapter !== null && trackAdapter !== void 0 && trackAdapter.type && assembly);
4363
-
4364
- default:
4365
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4366
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4367
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4368
-
4369
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4370
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4371
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4372
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4373
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4374
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4375
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4376
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4377
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4378
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4379
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4380
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4381
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4382
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4383
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4384
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4385
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4386
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4387
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4388
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4389
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4390
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4391
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4392
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4393
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4394
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4395
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4396
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4397
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4398
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4399
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4400
-
4401
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4402
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4403
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4404
- };
4405
-
4406
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4407
- var connectionType = props.connectionType,
4408
- model = props.model,
4409
- setModelReady = props.setModelReady;
4410
- var ConfigEditorComponent = connectionType.configEditorComponent || ConfigurationEditor;
4411
- return /*#__PURE__*/React.createElement(Suspense, {
4412
- fallback: /*#__PURE__*/React.createElement("div", null, "Loading...")
4413
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4414
- model: {
4415
- target: model
4416
- },
4417
- setModelReady: setModelReady
4418
- }));
4419
- });
4420
-
4421
- function ConnectionTypeSelect(props) {
4422
- var connectionTypeChoices = props.connectionTypeChoices,
4423
- connectionType = props.connectionType,
4424
- setConnectionType = props.setConnectionType;
4425
- useEffect(function () {
4426
- if (!connectionType.name) {
4427
- setConnectionType(connectionTypeChoices[0]);
4428
- }
4429
- });
4430
-
4431
- function handleChange(event) {
4432
- setConnectionType(connectionTypeChoices.find(function (connectionTypeChoice) {
4433
- return connectionTypeChoice.name === event.target.value;
4434
- }));
4435
- }
4436
-
4437
- if (!connectionType.name) {
4438
- return null;
4439
- }
4440
-
4441
- return /*#__PURE__*/React.createElement("form", {
4442
- autoComplete: "off"
4443
- }, /*#__PURE__*/React.createElement(TextField$1, {
4444
- value: connectionType.name,
4445
- label: "connectionType",
4446
- helperText: connectionType.description ? /*#__PURE__*/React.createElement(React.Fragment, null, connectionType.description, connectionType.url ? /*#__PURE__*/React.createElement(IconButton$1, {
4447
- href: connectionType.url,
4448
- rel: "noopener noreferrer",
4449
- target: "_blank",
4450
- color: "secondary"
4451
- }, /*#__PURE__*/React.createElement(OpenInNewIcon, null)) : null) : null,
4452
- select: true,
4453
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4454
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4455
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4456
- }, connectionTypeChoices.map(function (connectionTypeChoice) {
4457
- return /*#__PURE__*/React.createElement(MenuItem$1, {
4458
- key: connectionTypeChoice.name,
4459
- value: connectionTypeChoice.name
4460
- }, connectionTypeChoice.displayName || connectionTypeChoice.name);
4461
- })));
4462
- }
4463
-
4464
- var useStyles$b = /*#__PURE__*/makeStyles$1(function (theme) {
4465
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4466
- root: {
4467
- marginTop: theme.spacing(1)
4468
- },
4469
- stepper: {
4470
- backgroundColor: theme.palette.background["default"]
4471
- },
4472
- button: {
4473
- marginTop: theme.spacing(1),
4474
- marginRight: theme.spacing(1)
4475
- },
4476
- actionsContainer: {
4477
- marginBottom: theme.spacing(2)
4478
- }
4479
- };
4480
- });
4481
- var steps$1 = ['Select a Connection Type', 'Configure Connection'];
4482
-
4483
- function AddConnectionWidget(_ref) {
4484
- var model = _ref.model;
4485
-
4486
- var _useState = useState({}),
4487
- _useState2 = _slicedToArray(_useState, 2),
4488
- connectionType = _useState2[0],
4489
- setConnectionType = _useState2[1];
4490
-
4491
- var _useState3 = useState({}),
4492
- _useState4 = _slicedToArray(_useState3, 2),
4493
- configModel = _useState4[0],
4494
- setConfigModel = _useState4[1];
4495
-
4496
- var _useState5 = useState(true),
4497
- _useState6 = _slicedToArray(_useState5, 2),
4498
- configModelReady = _useState6[0],
4499
- setConfigModelReady = _useState6[1];
4500
-
4501
- var _useState7 = useState(0),
4502
- _useState8 = _slicedToArray(_useState7, 2),
4503
- activeStep = _useState8[0],
4504
- setActiveStep = _useState8[1];
4505
-
4506
- var classes = useStyles$b();
4507
- var session = getSession(model);
4508
-
4509
- var _getEnv = getEnv(session),
4510
- pluginManager = _getEnv.pluginManager;
4511
-
4512
- function handleSetConnectionType(newConnectionType) {
4513
- setConnectionType(newConnectionType);
4514
- setConfigModel(newConnectionType.configSchema.create({
4515
- connectionId: "".concat(newConnectionType.name, "-").concat(Date.now())
4516
- }, getEnv(model)));
4517
- }
4518
-
4519
- function stepContent() {
4520
- switch (activeStep) {
4521
- case 0:
4522
- return /*#__PURE__*/React.createElement(ConnectionTypeSelect, {
4523
- connectionTypeChoices: pluginManager.getElementTypesInGroup('connection'),
4524
- connectionType: connectionType,
4525
- setConnectionType: handleSetConnectionType
4526
- });
4527
-
4528
- case 1:
4529
- return /*#__PURE__*/React.createElement(ConfigureConnection, {
4530
- connectionType: connectionType,
4531
- model: configModel,
4532
- setModelReady: setConfigModelReady
4533
- });
4534
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4535
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4536
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4537
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4538
- }
4539
-
4540
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4541
- if (activeStep === steps$1.length - 1) {
4542
- handleFinish();
4543
- } else {
4544
- setActiveStep(activeStep + 1);
4545
- }
4546
- }
4547
-
4548
- function handleBack() {
4549
- setActiveStep(activeStep - 1);
4550
- }
4551
-
4552
- function handleFinish() {
4553
- var connectionConf = session.addConnectionConf(configModel);
4554
- session.makeConnection(connectionConf);
4555
- session.hideWidget(model);
4556
- }
4557
-
4558
- function checkNextEnabled() {
4559
- if (activeStep === 0 && connectionType.name || activeStep === 1 && configModel && configModelReady) {
4560
- return true;
4561
- }
4562
-
4563
- return false;
4564
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4565
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4566
- return /*#__PURE__*/React.createElement("div", {
4567
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4568
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4569
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4570
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4571
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4573
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4576
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4577
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4578
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4579
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4580
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4581
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4582
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4583
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4584
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4585
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4586
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4587
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4588
- }, activeStep === steps$1.length - 1 ? 'Connect' : 'Next'))));
4589
- })));
4590
- }
4591
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4592
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4593
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4594
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4595
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4596
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4597
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4598
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4599
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4600
- };
4601
-
4602
- function CloseConnectionDialog$1(_ref) {
4603
- var _ref$modalInfo = _ref.modalInfo,
4604
- modalInfo = _ref$modalInfo === void 0 ? {} : _ref$modalInfo,
4605
- setModalInfo = _ref.setModalInfo;
4606
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4607
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4608
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4609
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4610
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4611
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4612
- var _ref3 = _slicedToArray(_ref2, 2),
4613
- key = _ref3[0],
4614
- value = _ref3[1];
4615
-
4616
- return /*#__PURE__*/React.createElement(ListItem, {
4617
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4618
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4619
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4620
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4621
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4622
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4623
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4624
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4625
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4626
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4627
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4628
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4629
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4630
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4631
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4632
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4633
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4634
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4635
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4636
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4637
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4638
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4639
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4640
- __proto__: null,
4641
- 'default': CloseConnectionDialog$2
4642
- };
4643
-
4644
- function DeleteConnectionDialog$1(_ref) {
4645
- var deleteDialogDetails = _ref.deleteDialogDetails,
4646
- session = _ref.session,
4647
- handleClose = _ref.handleClose;
4648
- var connectionConf = deleteDialogDetails.connectionConf,
4649
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4650
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4651
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4652
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4653
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4654
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4655
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4656
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4657
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4658
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4659
- color: "primary",
4660
- onClick: function onClick() {
4661
- if (connectionConf) {
4662
- var _session$deleteConnec;
4663
-
4664
- (_session$deleteConnec = session.deleteConnection) === null || _session$deleteConnec === void 0 ? void 0 : _session$deleteConnec.call(session, connectionConf);
4665
- }
4666
-
4667
- handleClose();
4668
- }
4669
- }, "OK")));
4670
- }
4671
-
4672
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4673
-
4674
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4675
- __proto__: null,
4676
- 'default': DeleteConnectionDialog$2
4677
- };
4678
-
4679
- var useStyles$c = /*#__PURE__*/makeStyles(function (theme) {
4680
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4681
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4682
- position: 'absolute',
4683
- right: theme.spacing(1),
4684
- top: theme.spacing(1),
4685
- color: theme.palette.grey[500]
4686
- },
4687
- connectionContainer: {
4688
- margin: theme.spacing(4),
4689
- width: 500
4690
- }
4691
- };
4692
- });
4693
-
4694
- function ManageConnectionsDlg(_ref) {
4695
- var session = _ref.session,
4696
- handleClose = _ref.handleClose,
4697
- breakConnection = _ref.breakConnection;
4698
- var classes = useStyles$c();
4699
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4700
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4701
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4702
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4704
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4705
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4707
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4708
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4709
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4710
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4711
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4712
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4713
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4714
- var name = readConfObject(conf, 'name');
4715
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4716
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4717
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4718
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4719
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4720
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4721
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4722
- color: "error"
4723
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4724
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4725
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4726
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4727
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4728
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4729
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4730
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4731
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4732
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4733
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4734
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4735
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4736
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4737
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4738
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4739
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4740
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4741
- 'default': ManageConnectionsDialog$1
4742
- };
4743
-
4744
- var useStyles$d = /*#__PURE__*/makeStyles(function (theme) {
4745
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4746
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4747
- position: 'absolute',
4748
- right: theme.spacing(1),
4749
- top: theme.spacing(1),
4750
- color: theme.palette.grey[500]
4751
- },
4752
- connectionContainer: {
4753
- width: 500,
4754
- margin: theme.spacing(4)
4755
- }
4756
- };
4757
- });
4758
-
4759
- function ToggleConnectionDialog(_ref) {
4760
- var session = _ref.session,
4761
- handleClose = _ref.handleClose,
4762
- assemblyName = _ref.assemblyName,
4763
- breakConnection = _ref.breakConnection;
4764
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4765
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4766
- connectionInstances = session.connectionInstances;
4767
- var assemblySpecificConnections = connections.filter(function (c) {
4768
- var configAssemblyNames = readConfObject(c, 'assemblyNames');
4769
-
4770
- if (configAssemblyNames.length === 0) {
4771
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4772
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4773
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4774
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4775
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4776
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4777
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4778
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4779
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4780
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4781
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4782
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4783
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4784
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4785
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4786
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4788
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4789
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4790
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4791
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4792
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4793
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4794
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4795
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4796
- onChange: function onChange() {
4797
- if (connectionInstances !== null && connectionInstances !== void 0 && connectionInstances.find(function (conn) {
4798
- return conn.name === readConfObject(conf, 'name');
4799
- })) {
4800
- breakConnection(conf);
4801
- } else {
4802
- var _session$makeConnecti;
4803
-
4804
- (_session$makeConnecti = session.makeConnection) === null || _session$makeConnecti === void 0 ? void 0 : _session$makeConnecti.call(session, conf);
4805
- }
4806
- },
4807
- color: "primary"
4808
- }),
4809
- label: name
4810
- }));
4811
- }), !assemblySpecificConnections.length ? /*#__PURE__*/React.createElement(Typography, null, "No connections found for ", assemblyName) : null)), /*#__PURE__*/React.createElement(DialogActions, null, /*#__PURE__*/React.createElement(Button, {
4812
- onClick: function onClick() {
4813
- return handleClose();
4814
- },
4815
- variant: "contained",
4816
- color: "primary"
4817
- }, "Close")));
4818
- }
4819
-
4820
- var ToggleConnectionsDialog$1 = /*#__PURE__*/observer(ToggleConnectionDialog);
4821
-
4822
- var ToggleConnectionsDialog$2 = {
4823
- __proto__: null,
4824
- 'default': ToggleConnectionsDialog$1
4825
- };
4826
-
4827
- export default _default;
4828
- export { AssemblyManager, SetDefaultSession };
4829
- //# sourceMappingURL=plugin-data-management.esm.js.map