@jbrowse/plugin-data-management 1.7.11 → 2.0.0
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.
- package/dist/AddConnectionWidget/components/AddConnectionWidget.js +115 -162
- package/dist/AddConnectionWidget/components/AddConnectionWidget.js.map +1 -0
- package/dist/AddConnectionWidget/components/ConfigureConnection.js +33 -32
- package/dist/AddConnectionWidget/components/ConfigureConnection.js.map +1 -0
- package/dist/AddConnectionWidget/components/ConnectionTypeSelect.js +48 -64
- package/dist/AddConnectionWidget/components/ConnectionTypeSelect.js.map +1 -0
- package/dist/AddConnectionWidget/index.js +10 -20
- package/dist/AddConnectionWidget/index.js.map +1 -0
- package/dist/AddConnectionWidget/model.js +7 -15
- package/dist/AddConnectionWidget/model.js.map +1 -0
- package/dist/AddTrackWidget/components/AddTrackWidget.js +206 -230
- package/dist/AddTrackWidget/components/AddTrackWidget.js.map +1 -0
- package/dist/AddTrackWidget/components/ConfirmTrack.js +268 -385
- package/dist/AddTrackWidget/components/ConfirmTrack.js.map +1 -0
- package/dist/AddTrackWidget/components/TrackSourceSelect.js +28 -55
- package/dist/AddTrackWidget/components/TrackSourceSelect.js.map +1 -0
- package/dist/AddTrackWidget/index.js +10 -20
- package/dist/AddTrackWidget/index.js.map +1 -0
- package/dist/AddTrackWidget/model.js +150 -174
- package/dist/AddTrackWidget/model.js.map +1 -0
- package/dist/AssemblyManager/AssemblyAddForm.js +162 -282
- package/dist/AssemblyManager/AssemblyAddForm.js.map +1 -0
- package/dist/AssemblyManager/AssemblyEditor.js +12 -23
- package/dist/AssemblyManager/AssemblyEditor.js.map +1 -0
- package/dist/AssemblyManager/AssemblyManager.js +102 -132
- package/dist/AssemblyManager/AssemblyManager.js.map +1 -0
- package/dist/AssemblyManager/AssemblyTable.d.ts +1 -1
- package/dist/AssemblyManager/AssemblyTable.js +60 -84
- package/dist/AssemblyManager/AssemblyTable.js.map +1 -0
- package/dist/AssemblyManager/index.js +8 -14
- package/dist/AssemblyManager/index.js.map +1 -0
- package/dist/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js +49 -50
- package/dist/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js.map +1 -0
- package/dist/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js +28 -44
- package/dist/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js.map +1 -0
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts +1 -0
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +416 -639
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map +1 -0
- package/dist/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js +45 -74
- package/dist/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js.map +1 -0
- package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js +57 -91
- package/dist/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js.map +1 -0
- package/dist/HierarchicalTrackSelectorWidget/index.js +10 -20
- package/dist/HierarchicalTrackSelectorWidget/index.js.map +1 -0
- package/dist/HierarchicalTrackSelectorWidget/model.d.ts +3 -1
- package/dist/HierarchicalTrackSelectorWidget/model.js +247 -285
- package/dist/HierarchicalTrackSelectorWidget/model.js.map +1 -0
- package/dist/PluginStoreWidget/components/CustomPluginForm.js +140 -202
- package/dist/PluginStoreWidget/components/CustomPluginForm.js.map +1 -0
- package/dist/PluginStoreWidget/components/InstalledPlugin.js +112 -127
- package/dist/PluginStoreWidget/components/InstalledPlugin.js.map +1 -0
- package/dist/PluginStoreWidget/components/InstalledPluginsList.js +22 -45
- package/dist/PluginStoreWidget/components/InstalledPluginsList.js.map +1 -0
- package/dist/PluginStoreWidget/components/PluginCard.js +95 -110
- package/dist/PluginStoreWidget/components/PluginCard.js.map +1 -0
- package/dist/PluginStoreWidget/components/PluginStoreWidget.js +188 -227
- package/dist/PluginStoreWidget/components/PluginStoreWidget.js.map +1 -0
- package/dist/PluginStoreWidget/index.d.ts +0 -1
- package/dist/PluginStoreWidget/index.js +10 -28
- package/dist/PluginStoreWidget/index.js.map +1 -0
- package/dist/PluginStoreWidget/model.js +21 -26
- package/dist/PluginStoreWidget/model.js.map +1 -0
- package/dist/SetDefaultSession/SetDefaultSession.js +34 -58
- package/dist/SetDefaultSession/SetDefaultSession.js.map +1 -0
- package/dist/SetDefaultSession/index.js +8 -14
- package/dist/SetDefaultSession/index.js.map +1 -0
- package/dist/index.js +109 -147
- package/dist/index.js.map +1 -0
- package/dist/ucsc-trackhub/configSchema.js +18 -28
- package/dist/ucsc-trackhub/configSchema.js.map +1 -0
- package/dist/ucsc-trackhub/index.js +10 -22
- package/dist/ucsc-trackhub/index.js.map +1 -0
- package/dist/ucsc-trackhub/model.js +150 -128
- package/dist/ucsc-trackhub/model.js.map +1 -0
- package/dist/ucsc-trackhub/ucscAssemblies.js +3 -9
- package/dist/ucsc-trackhub/ucscAssemblies.js.map +1 -0
- package/dist/ucsc-trackhub/ucscTrackHub.js +458 -491
- package/dist/ucsc-trackhub/ucscTrackHub.js.map +1 -0
- package/esm/AddConnectionWidget/components/AddConnectionWidget.d.ts +9 -0
- package/esm/AddConnectionWidget/components/AddConnectionWidget.js +86 -0
- package/esm/AddConnectionWidget/components/AddConnectionWidget.js.map +1 -0
- package/esm/AddConnectionWidget/components/ConfigureConnection.d.ts +2 -0
- package/esm/AddConnectionWidget/components/ConfigureConnection.js +11 -0
- package/esm/AddConnectionWidget/components/ConfigureConnection.js.map +1 -0
- package/esm/AddConnectionWidget/components/ConnectionTypeSelect.d.ts +8 -0
- package/esm/AddConnectionWidget/components/ConnectionTypeSelect.js +24 -0
- package/esm/AddConnectionWidget/components/ConnectionTypeSelect.js.map +1 -0
- package/esm/AddConnectionWidget/index.d.ts +2 -0
- package/esm/AddConnectionWidget/index.js +4 -0
- package/esm/AddConnectionWidget/index.js.map +1 -0
- package/esm/AddConnectionWidget/model.d.ts +5 -0
- package/esm/AddConnectionWidget/model.js +7 -0
- package/esm/AddConnectionWidget/model.js.map +1 -0
- package/esm/AddTrackWidget/components/AddTrackWidget.d.ts +7 -0
- package/esm/AddTrackWidget/components/AddTrackWidget.js +139 -0
- package/esm/AddTrackWidget/components/AddTrackWidget.js.map +1 -0
- package/esm/AddTrackWidget/components/ConfirmTrack.d.ts +7 -0
- package/esm/AddTrackWidget/components/ConfirmTrack.js +247 -0
- package/esm/AddTrackWidget/components/ConfirmTrack.js.map +1 -0
- package/esm/AddTrackWidget/components/TrackSourceSelect.d.ts +7 -0
- package/esm/AddTrackWidget/components/TrackSourceSelect.js +27 -0
- package/esm/AddTrackWidget/components/TrackSourceSelect.js.map +1 -0
- package/esm/AddTrackWidget/index.d.ts +2 -0
- package/esm/AddTrackWidget/index.js +4 -0
- package/esm/AddTrackWidget/index.js.map +1 -0
- package/esm/AddTrackWidget/model.d.ts +51 -0
- package/esm/AddTrackWidget/model.js +154 -0
- package/esm/AddTrackWidget/model.js.map +1 -0
- package/esm/AssemblyManager/AssemblyAddForm.d.ts +6 -0
- package/esm/AssemblyManager/AssemblyAddForm.js +132 -0
- package/esm/AssemblyManager/AssemblyAddForm.js.map +1 -0
- package/esm/AssemblyManager/AssemblyEditor.d.ts +5 -0
- package/esm/AssemblyManager/AssemblyEditor.js +8 -0
- package/esm/AssemblyManager/AssemblyEditor.js.map +1 -0
- package/esm/AssemblyManager/AssemblyManager.d.ts +6 -0
- package/esm/AssemblyManager/AssemblyManager.js +69 -0
- package/esm/AssemblyManager/AssemblyManager.js.map +1 -0
- package/esm/AssemblyManager/AssemblyTable.d.ts +13 -0
- package/esm/AssemblyManager/AssemblyTable.js +62 -0
- package/esm/AssemblyManager/AssemblyTable.js.map +1 -0
- package/esm/AssemblyManager/index.d.ts +1 -0
- package/esm/AssemblyManager/index.js +2 -0
- package/esm/AssemblyManager/index.js.map +1 -0
- package/esm/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.d.ts +13 -0
- package/esm/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js +26 -0
- package/esm/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.js.map +1 -0
- package/esm/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.d.ts +13 -0
- package/esm/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js +24 -0
- package/esm/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.js.map +1 -0
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts +11 -0
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js +326 -0
- package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js.map +1 -0
- package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.d.ts +10 -0
- package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js +45 -0
- package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js.map +1 -0
- package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.d.ts +11 -0
- package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js +57 -0
- package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js.map +1 -0
- package/esm/HierarchicalTrackSelectorWidget/index.d.ts +2 -0
- package/esm/HierarchicalTrackSelectorWidget/index.js +4 -0
- package/esm/HierarchicalTrackSelectorWidget/index.js.map +1 -0
- package/esm/HierarchicalTrackSelectorWidget/model.d.ts +61 -0
- package/esm/HierarchicalTrackSelectorWidget/model.js +200 -0
- package/esm/HierarchicalTrackSelectorWidget/model.js.map +1 -0
- package/esm/PluginStoreWidget/components/CustomPluginForm.d.ts +9 -0
- package/esm/PluginStoreWidget/components/CustomPluginForm.js +109 -0
- package/esm/PluginStoreWidget/components/CustomPluginForm.js.map +1 -0
- package/esm/PluginStoreWidget/components/InstalledPlugin.d.ts +11 -0
- package/esm/PluginStoreWidget/components/InstalledPlugin.js +77 -0
- package/esm/PluginStoreWidget/components/InstalledPlugin.js.map +1 -0
- package/esm/PluginStoreWidget/components/InstalledPluginsList.d.ts +9 -0
- package/esm/PluginStoreWidget/components/InstalledPluginsList.js +16 -0
- package/esm/PluginStoreWidget/components/InstalledPluginsList.js.map +1 -0
- package/esm/PluginStoreWidget/components/PluginCard.d.ts +10 -0
- package/esm/PluginStoreWidget/components/PluginCard.js +61 -0
- package/esm/PluginStoreWidget/components/PluginCard.js.map +1 -0
- package/esm/PluginStoreWidget/components/PluginStoreWidget.d.ts +7 -0
- package/esm/PluginStoreWidget/components/PluginStoreWidget.js +106 -0
- package/esm/PluginStoreWidget/components/PluginStoreWidget.js.map +1 -0
- package/esm/PluginStoreWidget/index.d.ts +2 -0
- package/esm/PluginStoreWidget/index.js +4 -0
- package/esm/PluginStoreWidget/index.js.map +1 -0
- package/esm/PluginStoreWidget/model.d.ts +13 -0
- package/esm/PluginStoreWidget/model.js +20 -0
- package/esm/PluginStoreWidget/model.js.map +1 -0
- package/esm/SetDefaultSession/SetDefaultSession.d.ts +6 -0
- package/esm/SetDefaultSession/SetDefaultSession.js +34 -0
- package/esm/SetDefaultSession/SetDefaultSession.js.map +1 -0
- package/esm/SetDefaultSession/index.d.ts +1 -0
- package/esm/SetDefaultSession/index.js +2 -0
- package/esm/SetDefaultSession/index.js.map +1 -0
- package/esm/index.d.ts +27 -0
- package/esm/index.js +70 -0
- package/esm/index.js.map +1 -0
- package/esm/ucsc-trackhub/configSchema.d.ts +2 -0
- package/esm/ucsc-trackhub/configSchema.js +18 -0
- package/esm/ucsc-trackhub/configSchema.js.map +1 -0
- package/esm/ucsc-trackhub/index.d.ts +2 -0
- package/esm/ucsc-trackhub/index.js +3 -0
- package/esm/ucsc-trackhub/index.js.map +1 -0
- package/esm/ucsc-trackhub/model.d.ts +15 -0
- package/esm/ucsc-trackhub/model.js +82 -0
- package/esm/ucsc-trackhub/model.js.map +1 -0
- package/esm/ucsc-trackhub/ucscAssemblies.d.ts +2 -0
- package/esm/ucsc-trackhub/ucscAssemblies.js +201 -0
- package/esm/ucsc-trackhub/ucscAssemblies.js.map +1 -0
- package/esm/ucsc-trackhub/ucscTrackHub.d.ts +6 -0
- package/esm/ucsc-trackhub/ucscTrackHub.js +348 -0
- package/esm/ucsc-trackhub/ucscTrackHub.js.map +1 -0
- package/package.json +19 -11
- package/src/AddConnectionWidget/components/AddConnectionWidget.js +14 -10
- package/src/AddConnectionWidget/components/ConnectionTypeSelect.tsx +2 -4
- package/src/AddConnectionWidget/components/__snapshots__/AddConnectionWidget.test.js.snap +63 -67
- package/src/AddTrackWidget/components/AddTrackWidget.test.js +4 -4
- package/src/AddTrackWidget/components/AddTrackWidget.tsx +5 -5
- package/src/AddTrackWidget/components/ConfirmTrack.tsx +22 -22
- package/src/AddTrackWidget/components/TrackSourceSelect.tsx +9 -5
- package/src/AddTrackWidget/components/__snapshots__/AddTrackWidget.test.js.snap +76 -95
- package/src/AssemblyManager/AssemblyAddForm.tsx +5 -11
- package/src/AssemblyManager/AssemblyManager.tsx +8 -8
- package/src/AssemblyManager/AssemblyTable.tsx +10 -10
- package/src/HierarchicalTrackSelectorWidget/components/CloseConnectionDialog.tsx +1 -1
- package/src/HierarchicalTrackSelectorWidget/components/DeleteConnectionDialog.tsx +1 -1
- package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.js +1 -1
- package/src/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.tsx +15 -13
- package/src/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.tsx +6 -6
- package/src/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.tsx +7 -7
- package/src/HierarchicalTrackSelectorWidget/components/__snapshots__/HierarchicalTrackSelector.test.js.snap +122 -115
- package/src/PluginStoreWidget/components/CustomPluginForm.tsx +11 -14
- package/src/PluginStoreWidget/components/InstalledPlugin.tsx +9 -8
- package/src/PluginStoreWidget/components/InstalledPluginsList.tsx +1 -1
- package/src/PluginStoreWidget/components/PluginCard.tsx +10 -11
- package/src/PluginStoreWidget/components/PluginStoreWidget.tsx +9 -9
- package/src/PluginStoreWidget/components/__snapshots__/PluginStoreWidget.test.js.snap +267 -217
- package/src/PluginStoreWidget/index.js +0 -1
- package/src/SetDefaultSession/SetDefaultSession.tsx +1 -1
- package/dist/AddConnectionWidget/components/AddConnectionWidget.test.js +0 -279
- package/dist/AddTrackWidget/components/AddTrackWidget.test.js +0 -218
- package/dist/AddTrackWidget/index.test.js +0 -292
- package/dist/AssemblyManager/AssemblyManager.test.js +0 -113
- package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.test.js +0 -191
- package/dist/HierarchicalTrackSelectorWidget/model.test.js +0 -28
- package/dist/PluginStoreWidget/components/PluginStoreWidget.test.js +0 -201
- package/dist/PluginStoreWidget/model.test.js +0 -17
- package/dist/SetDefaultSession/SetDefaultSession.test.js +0 -75
- package/dist/index.test.js +0 -56
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import React, { useEffect, useState } from 'react';
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import { readConfObject } from '@jbrowse/core/configuration';
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import { supportedIndexingAdapters, getSession, isElectron, } from '@jbrowse/core/util';
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import { Card, CardContent, Checkbox, FormControl, FormControlLabel, IconButton, InputLabel, InputAdornment, ListSubheader, Link, List, ListItem, MenuItem, Paper, TextField, Typography, } from '@mui/material';
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import { makeStyles } from 'tss-react/mui';
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// icons
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import DeleteIcon from '@mui/icons-material/Delete';
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import AddIcon from '@mui/icons-material//Add';
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import { observer } from 'mobx-react';
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import { getEnv } from 'mobx-state-tree';
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import { UNKNOWN } from '@jbrowse/core/util/tracks';
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const useStyles = makeStyles()(theme => ({
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spacing: {
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marginBottom: theme.spacing(3),
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},
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paper: {
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display: 'flex',
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flexDirection: 'column',
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padding: theme.spacing(1),
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},
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spacer: {
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height: theme.spacing(8),
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},
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card: {
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marginTop: theme.spacing(1),
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},
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}));
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function StatusMessage({ trackAdapter, trackType, }) {
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var _a;
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const { classes } = useStyles();
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return trackAdapter.type === 'SNPCoverageAdapter' ? (React.createElement(Typography, { className: classes.spacing },
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"Selected ",
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React.createElement("code", null, trackType),
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". Using adapter",
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' ',
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React.createElement("code", null, trackAdapter.type),
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" with subadapter",
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' ',
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React.createElement("code", null, (_a = trackAdapter.subadapter) === null || _a === void 0 ? void 0 : _a.type),
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". Please enter a track name and, if necessary, update the track type.")) : (React.createElement(Typography, { className: classes.spacing },
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"Using adapter ",
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React.createElement("code", null, trackAdapter.type),
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" and guessing track type",
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' ',
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React.createElement("code", null, trackType),
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". Please enter a track name and, if necessary, update the track type."));
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}
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/**
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* element. In this way, adapters that are from external plugins can have headers that differentiate them from the
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* out-of-the-box plugins.
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* @param adaptersList - a list of adapters found in the PluginManager
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* found under that subheader
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*/
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function categorizeAdapters(adaptersList) {
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// eslint-disable-next-line @typescript-eslint/no-explicit-any
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const items = [];
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adaptersList.forEach(adapter => {
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var _a, _b, _c, _d, _e, _f, _g, _h;
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if ((_a = adapter.adapterMetadata) === null || _a === void 0 ? void 0 : _a.category) {
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if (currentCategory !== ((_b = adapter.adapterMetadata) === null || _b === void 0 ? void 0 : _b.category)) {
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currentCategory = (_c = adapter.adapterMetadata) === null || _c === void 0 ? void 0 : _c.category;
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items.push(React.createElement(ListSubheader, { key: (_d = adapter.adapterMetadata) === null || _d === void 0 ? void 0 : _d.category, value: (_e = adapter.adapterMetadata) === null || _e === void 0 ? void 0 : _e.category }, (_f = adapter.adapterMetadata) === null || _f === void 0 ? void 0 : _f.category));
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}
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items.push(React.createElement(MenuItem, { key: adapter.name, value: adapter.name }, ((_g = adapter.adapterMetadata) === null || _g === void 0 ? void 0 : _g.displayName)
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? (_h = adapter.adapterMetadata) === null || _h === void 0 ? void 0 : _h.displayName
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: adapter.name));
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}
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});
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return items;
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}
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function getAdapterTypes(pluginManager) {
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return pluginManager.getElementTypesInGroup('adapter');
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}
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function getTrackTypes(pluginManager) {
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return pluginManager.getElementTypesInGroup('track');
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}
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const TextIndexingConfig = observer(({ model }) => {
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const { classes } = useStyles();
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const [value1, setValue1] = useState('');
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const [value2, setValue2] = useState('');
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const [attributes, setAttributes] = useState(['Name', 'ID']);
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const [exclude, setExclude] = useState(['CDS', 'exon']);
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const sections = [
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{
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label: 'Indexing attributes',
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values: attributes,
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},
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{
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label: 'Feature types to exclude',
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values: exclude,
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},
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];
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useEffect(() => {
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model.setTextIndexingConf({ attributes, exclude });
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}, [model, attributes, exclude]);
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return (React.createElement(Paper, { className: classes.paper },
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React.createElement(InputLabel, null, "Indexing configuration"),
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sections.map((section, index) => (React.createElement(Card, { raised: true, key: section.label, className: classes.card },
|
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102
|
+
React.createElement(CardContent, null,
|
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103
|
+
React.createElement(InputLabel, null, section.label),
|
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104
|
+
React.createElement(List, { disablePadding: true },
|
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105
|
+
section.values.map((val, idx) => (React.createElement(ListItem, { key: idx, disableGutters: true },
|
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106
|
+
React.createElement(TextField, { value: val, InputProps: {
|
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107
|
+
endAdornment: (React.createElement(InputAdornment, { position: "end" },
|
|
108
|
+
React.createElement(IconButton, { color: "secondary", onClick: () => {
|
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109
|
+
const newAttr = section.values.filter((a, i) => {
|
|
110
|
+
return i !== idx;
|
|
111
|
+
});
|
|
112
|
+
index === 0
|
|
113
|
+
? setAttributes(newAttr)
|
|
114
|
+
: setExclude(newAttr);
|
|
115
|
+
} },
|
|
116
|
+
React.createElement(DeleteIcon, null)))),
|
|
117
|
+
} })))),
|
|
118
|
+
React.createElement(ListItem, { disableGutters: true },
|
|
119
|
+
React.createElement(TextField, { value: index === 0 ? value1 : value2, placeholder: "add new", onChange: event => {
|
|
120
|
+
index === 0
|
|
121
|
+
? setValue1(event.target.value)
|
|
122
|
+
: setValue2(event.target.value);
|
|
123
|
+
}, InputProps: {
|
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124
|
+
endAdornment: (React.createElement(InputAdornment, { position: "end" },
|
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125
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+
React.createElement(IconButton, { onClick: () => {
|
|
126
|
+
if (index === 0) {
|
|
127
|
+
const newAttr = attributes;
|
|
128
|
+
newAttr.push(value1);
|
|
129
|
+
setAttributes(newAttr);
|
|
130
|
+
setValue1('');
|
|
131
|
+
}
|
|
132
|
+
else {
|
|
133
|
+
const newFeat = exclude;
|
|
134
|
+
newFeat.push(value2);
|
|
135
|
+
setExclude(newFeat);
|
|
136
|
+
setValue2('');
|
|
137
|
+
}
|
|
138
|
+
}, disabled: index === 0 ? value1 === '' : value2 === '', color: "secondary", "data-testid": `stringArrayAdd-Feat` },
|
|
139
|
+
React.createElement(AddIcon, null)))),
|
|
140
|
+
} })))))))));
|
|
141
|
+
});
|
|
142
|
+
const TrackAdapterSelector = observer(({ model }) => {
|
|
143
|
+
const { classes } = useStyles();
|
|
144
|
+
const session = getSession(model);
|
|
145
|
+
const { trackAdapter } = model;
|
|
146
|
+
// prettier-ignore
|
|
147
|
+
const adapters = getAdapterTypes(getEnv(session).pluginManager);
|
|
148
|
+
return (React.createElement(TextField, { className: classes.spacing, value: (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) !== 'UNKNOWN' ? trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type : '', label: "adapterType", helperText: "Select an adapter type", select: true, fullWidth: true, onChange: event => {
|
|
149
|
+
model.setAdapterHint(event.target.value);
|
|
150
|
+
}, SelectProps: {
|
|
151
|
+
// @ts-ignore
|
|
152
|
+
SelectDisplayProps: { 'data-testid': 'adapterTypeSelect' },
|
|
153
|
+
} },
|
|
154
|
+
adapters
|
|
155
|
+
// Excludes any adapter with the 'adapterMetadata.hiddenFromGUI' property, and anything with the 'adapterMetadata.category' property
|
|
156
|
+
.filter(elt => {
|
|
157
|
+
var _a, _b;
|
|
158
|
+
return !((_a = elt.adapterMetadata) === null || _a === void 0 ? void 0 : _a.hiddenFromGUI) &&
|
|
159
|
+
!((_b = elt.adapterMetadata) === null || _b === void 0 ? void 0 : _b.category);
|
|
160
|
+
})
|
|
161
|
+
.map(elt => {
|
|
162
|
+
var _a, _b;
|
|
163
|
+
return (React.createElement(MenuItem, { key: elt.name, value: elt.name }, ((_a = elt.adapterMetadata) === null || _a === void 0 ? void 0 : _a.displayName)
|
|
164
|
+
? (_b = elt.adapterMetadata) === null || _b === void 0 ? void 0 : _b.displayName
|
|
165
|
+
: elt.name));
|
|
166
|
+
}),
|
|
167
|
+
categorizeAdapters(adapters.filter(elt => { var _a; return !((_a = elt.adapterMetadata) === null || _a === void 0 ? void 0 : _a.hiddenFromGUI); }))));
|
|
168
|
+
});
|
|
169
|
+
function UnknownAdapterPrompt({ model }) {
|
|
170
|
+
const { classes } = useStyles();
|
|
171
|
+
return (React.createElement(React.Fragment, null,
|
|
172
|
+
React.createElement(Typography, { className: classes.spacing },
|
|
173
|
+
"JBrowse was not able to guess the adapter type for this data, but it may be in the list below. If not, you can",
|
|
174
|
+
' ',
|
|
175
|
+
React.createElement(Link, { href: "https://github.com/GMOD/jbrowse-components/releases", target: "_blank", rel: "noopener noreferrer" }, "check for new releases"),
|
|
176
|
+
' ',
|
|
177
|
+
"of JBrowse to see if they support this data type or",
|
|
178
|
+
' ',
|
|
179
|
+
React.createElement(Link, { href: "https://github.com/GMOD/jbrowse-components/issues/new", target: "_blank", rel: "noopener noreferrer" }, "file an issue"),
|
|
180
|
+
' ',
|
|
181
|
+
"and add a feature request for this data type."),
|
|
182
|
+
React.createElement(TrackAdapterSelector, { model: model })));
|
|
183
|
+
}
|
|
184
|
+
const TrackTypeSelector = observer(({ model }) => {
|
|
185
|
+
const { classes } = useStyles();
|
|
186
|
+
const session = getSession(model);
|
|
187
|
+
const { trackType } = model;
|
|
188
|
+
const trackTypes = getTrackTypes(getEnv(session).pluginManager);
|
|
189
|
+
return (React.createElement(TextField, { className: classes.spacing, value: trackType, label: "trackType", helperText: "Select a track type", select: true, fullWidth: true, onChange: event => {
|
|
190
|
+
model.setTrackType(event.target.value);
|
|
191
|
+
}, SelectProps: {
|
|
192
|
+
// @ts-ignore
|
|
193
|
+
SelectDisplayProps: { 'data-testid': 'trackTypeSelect' },
|
|
194
|
+
} }, trackTypes.map(({ name }) => (React.createElement(MenuItem, { key: name, value: name }, name)))));
|
|
195
|
+
});
|
|
196
|
+
const TrackAssemblySelector = observer(({ model }) => {
|
|
197
|
+
const session = getSession(model);
|
|
198
|
+
const { assembly } = model;
|
|
199
|
+
return (React.createElement(TextField, { value: assembly, label: "assemblyName", helperText: "Assembly to which the track will be added", select: true, fullWidth: true, onChange: event => model.setAssembly(event.target.value), SelectProps: {
|
|
200
|
+
// @ts-ignore
|
|
201
|
+
SelectDisplayProps: { 'data-testid': 'assemblyNameSelect' },
|
|
202
|
+
} }, session.assemblies
|
|
203
|
+
.map(conf => readConfObject(conf, 'name'))
|
|
204
|
+
.map(name => (React.createElement(MenuItem, { key: name, value: name }, name)))));
|
|
205
|
+
});
|
|
206
|
+
function ConfirmTrack({ model }) {
|
|
207
|
+
const { classes } = useStyles();
|
|
208
|
+
const [check, setCheck] = useState(true);
|
|
209
|
+
const { trackName, trackAdapter, trackType, warningMessage, adapterHint } = model;
|
|
210
|
+
if (model.unsupported) {
|
|
211
|
+
return (React.createElement(Typography, { className: classes.spacing },
|
|
212
|
+
"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",
|
|
213
|
+
' ',
|
|
214
|
+
React.createElement(Link, { href: "https://github.com/GMOD/jbrowse-components/releases", target: "_blank", rel: "noopener noreferrer" }, "check for new releases"),
|
|
215
|
+
' ',
|
|
216
|
+
"of JBrowse or",
|
|
217
|
+
' ',
|
|
218
|
+
React.createElement(Link, { href: "https://github.com/GMOD/jbrowse-components/issues/new", target: "_blank", rel: "noopener noreferrer" }, "file an issue"),
|
|
219
|
+
' ',
|
|
220
|
+
"and add a feature request for this data type."));
|
|
221
|
+
}
|
|
222
|
+
if ((trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) === UNKNOWN) {
|
|
223
|
+
return React.createElement(UnknownAdapterPrompt, { model: model });
|
|
224
|
+
}
|
|
225
|
+
if (adapterHint === '' && trackAdapter) {
|
|
226
|
+
model.setAdapterHint(trackAdapter.type);
|
|
227
|
+
}
|
|
228
|
+
if (!(trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type)) {
|
|
229
|
+
return React.createElement(Typography, null, "Could not recognize this data type.");
|
|
230
|
+
}
|
|
231
|
+
const supportedForIndexing = supportedIndexingAdapters(trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type);
|
|
232
|
+
return (React.createElement("div", null,
|
|
233
|
+
trackAdapter ? (React.createElement(StatusMessage, { trackAdapter: trackAdapter, trackType: trackType })) : null,
|
|
234
|
+
warningMessage ? (React.createElement(Typography, { style: { color: 'orange' } }, warningMessage)) : null,
|
|
235
|
+
React.createElement(TextField, { className: classes.spacing, label: "trackName", helperText: "A name for this track", fullWidth: true, value: trackName, onChange: event => model.setTrackName(event.target.value), inputProps: { 'data-testid': 'trackNameInput' } }),
|
|
236
|
+
React.createElement(TrackAdapterSelector, { model: model }),
|
|
237
|
+
React.createElement(TrackTypeSelector, { model: model }),
|
|
238
|
+
React.createElement(TrackAssemblySelector, { model: model }),
|
|
239
|
+
isElectron && supportedForIndexing && (React.createElement(FormControl, null,
|
|
240
|
+
React.createElement(FormControlLabel, { label: 'Index track for text searching?', control: React.createElement(Checkbox, { checked: check, onChange: e => {
|
|
241
|
+
setCheck(e.target.checked);
|
|
242
|
+
model.setTextIndexTrack(e.target.checked);
|
|
243
|
+
} }) }))),
|
|
244
|
+
isElectron && check && supportedForIndexing ? (React.createElement(TextIndexingConfig, { model: model })) : null));
|
|
245
|
+
}
|
|
246
|
+
export default observer(ConfirmTrack);
|
|
247
|
+
//# sourceMappingURL=ConfirmTrack.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"ConfirmTrack.js","sourceRoot":"","sources":["../../../src/AddTrackWidget/components/ConfirmTrack.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAClD,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EACL,yBAAyB,EACzB,UAAU,EACV,UAAU,GACX,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,IAAI,EACJ,WAAW,EACX,QAAQ,EACR,WAAW,EACX,gBAAgB,EAChB,UAAU,EACV,UAAU,EACV,cAAc,EACd,aAAa,EACb,IAAI,EACJ,IAAI,EACJ,QAAQ,EACR,QAAQ,EACR,KAAK,EACL,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,QAAQ;AACR,OAAO,UAAU,MAAM,4BAA4B,CAAA;AACnD,OAAO,OAAO,MAAM,0BAA0B,CAAA;AAG9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAA;AACxC,OAAO,EAAE,OAAO,EAAE,MAAM,2BAA2B,CAAA;AAMnD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,YAAY,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC/B;IACD,KAAK,EAAE;QACL,OAAO,EAAE,MAAM;QACf,aAAa,EAAE,QAAQ;QACvB,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC1B;IACD,MAAM,EAAE;QACN,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,IAAI,EAAE;QACJ,SAAS,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC5B;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,aAAa,CAAC,EACrB,YAAY,EACZ,SAAS,GAIV;;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,YAAY,CAAC,IAAI,KAAK,oBAAoB,CAAC,CAAC,CAAC,CAClD,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,OAAO;;QAC3B,kCAAO,SAAS,CAAQ;;QAAgB,GAAG;QACpD,kCAAO,YAAY,CAAC,IAAI,CAAQ;;QAAiB,GAAG;QACpD,kCAAO,MAAA,YAAY,CAAC,UAAU,0CAAE,IAAI,CAAQ;gFAEjC,CACd,CAAC,CAAC,CAAC,CACF,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,OAAO;;QACtB,kCAAO,YAAY,CAAC,IAAI,CAAQ;;QAAyB,GAAG;QAC1E,kCAAO,SAAS,CAAQ;gFAEb,CACd,CAAA;AACH,CAAC;AAED;;;;;;;GAOG;AACH,SAAS,kBAAkB,CACzB,YAAkE;IAElE,IAAI,eAAe,GAAG,EAAE,CAAA;IACxB,8DAA8D;IAC9D,MAAM,KAAK,GAAQ,EAAE,CAAA;IACrB,YAAY,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE;;QAC7B,IAAI,MAAA,OAAO,CAAC,eAAe,0CAAE,QAAQ,EAAE;YACrC,IAAI,eAAe,MAAK,MAAA,OAAO,CAAC,eAAe,0CAAE,QAAQ,CAAA,EAAE;gBACzD,eAAe,GAAG,MAAA,OAAO,CAAC,eAAe,0CAAE,QAAQ,CAAA;gBACnD,KAAK,CAAC,IAAI,CACR,oBAAC,aAAa,IACZ,GAAG,EAAE,MAAA,OAAO,CAAC,eAAe,0CAAE,QAAQ,EACtC,KAAK,EAAE,MAAA,OAAO,CAAC,eAAe,0CAAE,QAAQ,IAEvC,MAAA,OAAO,CAAC,eAAe,0CAAE,QAAQ,CACpB,CACjB,CAAA;aACF;YACD,KAAK,CAAC,IAAI,CACR,oBAAC,QAAQ,IAAC,GAAG,EAAE,OAAO,CAAC,IAAI,EAAE,KAAK,EAAE,OAAO,CAAC,IAAI,IAC7C,CAAA,MAAA,OAAO,CAAC,eAAe,0CAAE,WAAW;gBACnC,CAAC,CAAC,MAAA,OAAO,CAAC,eAAe,0CAAE,WAAW;gBACtC,CAAC,CAAC,OAAO,CAAC,IAAI,CACP,CACZ,CAAA;SACF;IACH,CAAC,CAAC,CAAA;IACF,OAAO,KAAK,CAAA;AACd,CAAC;AAED,SAAS,eAAe,CAAC,aAA4B;IACnD,OAAO,aAAa,CAAC,sBAAsB,CAAC,SAAS,CAGlD,CAAA;AACL,CAAC;AAED,SAAS,aAAa,CAAC,aAA4B;IACjD,OAAO,aAAa,CAAC,sBAAsB,CAAC,OAAO,CAAuB,CAAA;AAC5E,CAAC;AAED,MAAM,kBAAkB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA4B,EAAE,EAAE;IAC1E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACxC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACxC,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC,CAAA;IAC5D,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IACvD,MAAM,QAAQ,GAAG;QACf;YACE,KAAK,EAAE,qBAAqB;YAC5B,MAAM,EAAE,UAAU;SACnB;QACD;YACE,KAAK,EAAE,0BAA0B;YACjC,MAAM,EAAE,OAAO;SAChB;KACF,CAAA;IACD,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,mBAAmB,CAAC,EAAE,UAAU,EAAE,OAAO,EAAE,CAAC,CAAA;IACpD,CAAC,EAAE,CAAC,KAAK,EAAE,UAAU,EAAE,OAAO,CAAC,CAAC,CAAA;IAEhC,OAAO,CACL,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,oBAAC,UAAU,iCAAoC;QAC9C,QAAQ,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,KAAK,EAAE,EAAE,CAAC,CAChC,oBAAC,IAAI,IAAC,MAAM,QAAC,GAAG,EAAE,OAAO,CAAC,KAAK,EAAE,SAAS,EAAE,OAAO,CAAC,IAAI;YACtD,oBAAC,WAAW;gBACV,oBAAC,UAAU,QAAE,OAAO,CAAC,KAAK,CAAc;gBACxC,oBAAC,IAAI,IAAC,cAAc;oBACjB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,GAAW,EAAE,GAAW,EAAE,EAAE,CAAC,CAChD,oBAAC,QAAQ,IAAC,GAAG,EAAE,GAAG,EAAE,cAAc;wBAChC,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,UAAU,EAAE;gCACV,YAAY,EAAE,CACZ,oBAAC,cAAc,IAAC,QAAQ,EAAC,KAAK;oCAC5B,oBAAC,UAAU,IACT,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;4CACZ,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;gDAC7C,OAAO,CAAC,KAAK,GAAG,CAAA;4CAClB,CAAC,CAAC,CAAA;4CACF,KAAK,KAAK,CAAC;gDACT,CAAC,CAAC,aAAa,CAAC,OAAO,CAAC;gDACxB,CAAC,CAAC,UAAU,CAAC,OAAO,CAAC,CAAA;wCACzB,CAAC;wCAED,oBAAC,UAAU,OAAG,CACH,CACE,CAClB;6BACF,GACD,CACO,CACZ,CAAC;oBACF,oBAAC,QAAQ,IAAC,cAAc;wBACtB,oBAAC,SAAS,IACR,KAAK,EAAE,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EACpC,WAAW,EAAC,SAAS,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;gCAChB,KAAK,KAAK,CAAC;oCACT,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC;oCAC/B,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;4BACnC,CAAC,EACD,UAAU,EAAE;gCACV,YAAY,EAAE,CACZ,oBAAC,cAAc,IAAC,QAAQ,EAAC,KAAK;oCAC5B,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE;4CACZ,IAAI,KAAK,KAAK,CAAC,EAAE;gDACf,MAAM,OAAO,GAAa,UAAU,CAAA;gDACpC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;gDACpB,aAAa,CAAC,OAAO,CAAC,CAAA;gDACtB,SAAS,CAAC,EAAE,CAAC,CAAA;6CACd;iDAAM;gDACL,MAAM,OAAO,GAAa,OAAO,CAAA;gDACjC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;gDACpB,UAAU,CAAC,OAAO,CAAC,CAAA;gDACnB,SAAS,CAAC,EAAE,CAAC,CAAA;6CACd;wCACH,CAAC,EACD,QAAQ,EAAE,KAAK,KAAK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@@ -0,0 +1,27 @@
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1
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import React from 'react';
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2
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import { FileSelector } from '@jbrowse/core/ui';
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3
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import { Paper } from '@mui/material';
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4
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import { makeStyles } from 'tss-react/mui';
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5
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import { getRoot } from 'mobx-state-tree';
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6
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import { observer } from 'mobx-react';
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7
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const useStyles = makeStyles()(theme => ({
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paper: {
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display: 'flex',
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flexDirection: 'column',
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padding: theme.spacing(1),
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},
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spacer: {
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height: theme.spacing(8),
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},
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}));
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17
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function TrackSourceSelect({ model }) {
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18
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const { classes } = useStyles();
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19
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// eslint-disable-next-line @typescript-eslint/no-explicit-any
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const rootModel = getRoot(model);
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return (React.createElement(Paper, { className: classes.paper },
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React.createElement(FileSelector, { name: "Main file", description: "", location: model.trackData, setLocation: model.setTrackData, setName: model.setTrackName, rootModel: rootModel }),
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React.createElement("div", { className: classes.spacer }),
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+
React.createElement(FileSelector, { name: "Index file", description: "(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.", location: model.indexTrackData, setLocation: model.setIndexTrackData, setName: model.setTrackName, rootModel: rootModel })));
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}
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26
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+
export default observer(TrackSourceSelect);
|
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|
+
//# sourceMappingURL=TrackSourceSelect.js.map
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1
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{"version":3,"file":"TrackSourceSelect.js","sourceRoot":"","sources":["../../../src/AddTrackWidget/components/TrackSourceSelect.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,KAAK,EAAE,MAAM,eAAe,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,MAAM;QACf,aAAa,EAAE,QAAQ;QACvB,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC1B;IACD,MAAM,EAAE;QACN,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAA4B;IAC5D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,8DAA8D;IAC9D,MAAM,SAAS,GAAG,OAAO,CAAM,KAAK,CAAC,CAAA;IAErC,OAAO,CACL,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,oBAAC,YAAY,IACX,IAAI,EAAC,WAAW,EAChB,WAAW,EAAC,EAAE,EACd,QAAQ,EAAE,KAAK,CAAC,SAAS,EACzB,WAAW,EAAE,KAAK,CAAC,YAAY,EAC/B,OAAO,EAAE,KAAK,CAAC,YAAY,EAC3B,SAAS,EAAE,SAAS,GACpB;QACF,6BAAK,SAAS,EAAE,OAAO,CAAC,MAAM,GAAI;QAClC,oBAAC,YAAY,IACX,IAAI,EAAC,YAAY,EACjB,WAAW,EAAC,qHAAqH,EACjI,QAAQ,EAAE,KAAK,CAAC,cAAc,EAC9B,WAAW,EAAE,KAAK,CAAC,iBAAiB,EACpC,OAAO,EAAE,KAAK,CAAC,YAAY,EAC3B,SAAS,EAAE,SAAS,GACpB,CACI,CACT,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,iBAAiB,CAAC,CAAA"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AddTrackWidget/index.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,OAAO,EAAE,OAAO,IAAI,iBAAiB,EAAE,MAAM,SAAS,CAAA;AACtD,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAAC,gBAAgB,EAAE,EAAE,CAAC,CAAA"}
|
|
@@ -0,0 +1,51 @@
|
|
|
1
|
+
import { Instance } from 'mobx-state-tree';
|
|
2
|
+
import PluginManager from '@jbrowse/core/PluginManager';
|
|
3
|
+
import { FileLocation } from '@jbrowse/core/util/types';
|
|
4
|
+
interface IndexingAttr {
|
|
5
|
+
attributes: string[];
|
|
6
|
+
exclude: string[];
|
|
7
|
+
}
|
|
8
|
+
export default function f(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
|
|
9
|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
10
|
+
type: import("mobx-state-tree").ISimpleType<"AddTrackWidget">;
|
|
11
|
+
view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
|
|
12
|
+
}, {
|
|
13
|
+
trackSource: string;
|
|
14
|
+
trackData: FileLocation | undefined;
|
|
15
|
+
indexTrackData: FileLocation | undefined;
|
|
16
|
+
altAssemblyName: string;
|
|
17
|
+
altTrackName: string;
|
|
18
|
+
altTrackType: string;
|
|
19
|
+
adapterHint: string;
|
|
20
|
+
textIndexTrack: boolean;
|
|
21
|
+
textIndexingConf: IndexingAttr | undefined;
|
|
22
|
+
} & {
|
|
23
|
+
setAdapterHint(obj: string): void;
|
|
24
|
+
setTrackSource(str: string): void;
|
|
25
|
+
setTextIndexingConf(conf: IndexingAttr): void;
|
|
26
|
+
setTextIndexTrack(flag: boolean): void;
|
|
27
|
+
setTrackData(obj: FileLocation): void;
|
|
28
|
+
setIndexTrackData(obj: FileLocation): void;
|
|
29
|
+
setAssembly(str: string): void;
|
|
30
|
+
setTrackName(str: string): void;
|
|
31
|
+
setTrackType(str: string): void;
|
|
32
|
+
clearData(): void;
|
|
33
|
+
} & {
|
|
34
|
+
readonly trackAdapter: import("@jbrowse/core/util/tracks").AdapterConfig | undefined;
|
|
35
|
+
readonly trackName: string;
|
|
36
|
+
readonly isFtp: boolean;
|
|
37
|
+
readonly isRelativeTrackUrl: boolean;
|
|
38
|
+
readonly isRelativeIndexUrl: boolean;
|
|
39
|
+
readonly isRelativeUrl: boolean;
|
|
40
|
+
readonly trackHttp: any;
|
|
41
|
+
readonly indexHttp: any;
|
|
42
|
+
readonly wrongProtocol: any;
|
|
43
|
+
readonly unsupported: boolean;
|
|
44
|
+
readonly assembly: any;
|
|
45
|
+
readonly trackType: string;
|
|
46
|
+
} & {
|
|
47
|
+
readonly warningMessage: "" | "Warning: JBrowse cannot access files using the ftp protocol" | "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." | "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";
|
|
48
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
49
|
+
export declare type AddTrackStateModel = ReturnType<typeof f>;
|
|
50
|
+
export declare type AddTrackModel = Instance<AddTrackStateModel>;
|
|
51
|
+
export {};
|
|
@@ -0,0 +1,154 @@
|
|
|
1
|
+
import { types } from 'mobx-state-tree';
|
|
2
|
+
import { ElementId } from '@jbrowse/core/util/types/mst';
|
|
3
|
+
import { guessAdapter, guessTrackType, UNSUPPORTED, getFileName, } from '@jbrowse/core/util/tracks';
|
|
4
|
+
function isAbsoluteUrl(url = '') {
|
|
5
|
+
try {
|
|
6
|
+
new URL(url);
|
|
7
|
+
return true;
|
|
8
|
+
}
|
|
9
|
+
catch (error) {
|
|
10
|
+
return url.startsWith('/');
|
|
11
|
+
}
|
|
12
|
+
}
|
|
13
|
+
export default function f(pluginManager) {
|
|
14
|
+
return types
|
|
15
|
+
.model('AddTrackModel', {
|
|
16
|
+
id: ElementId,
|
|
17
|
+
type: types.literal('AddTrackWidget'),
|
|
18
|
+
view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
|
|
19
|
+
})
|
|
20
|
+
.volatile(() => ({
|
|
21
|
+
trackSource: 'fromFile',
|
|
22
|
+
trackData: undefined,
|
|
23
|
+
indexTrackData: undefined,
|
|
24
|
+
// alts
|
|
25
|
+
altAssemblyName: '',
|
|
26
|
+
altTrackName: '',
|
|
27
|
+
altTrackType: '',
|
|
28
|
+
adapterHint: '',
|
|
29
|
+
textIndexTrack: true,
|
|
30
|
+
textIndexingConf: undefined,
|
|
31
|
+
}))
|
|
32
|
+
.actions(self => ({
|
|
33
|
+
setAdapterHint(obj) {
|
|
34
|
+
self.adapterHint = obj;
|
|
35
|
+
},
|
|
36
|
+
setTrackSource(str) {
|
|
37
|
+
self.trackSource = str;
|
|
38
|
+
},
|
|
39
|
+
setTextIndexingConf(conf) {
|
|
40
|
+
self.textIndexingConf = conf;
|
|
41
|
+
},
|
|
42
|
+
setTextIndexTrack(flag) {
|
|
43
|
+
self.textIndexTrack = flag;
|
|
44
|
+
},
|
|
45
|
+
setTrackData(obj) {
|
|
46
|
+
self.trackData = obj;
|
|
47
|
+
},
|
|
48
|
+
setIndexTrackData(obj) {
|
|
49
|
+
self.indexTrackData = obj;
|
|
50
|
+
},
|
|
51
|
+
setAssembly(str) {
|
|
52
|
+
self.altAssemblyName = str;
|
|
53
|
+
},
|
|
54
|
+
setTrackName(str) {
|
|
55
|
+
self.altTrackName = str;
|
|
56
|
+
},
|
|
57
|
+
setTrackType(str) {
|
|
58
|
+
self.altTrackType = str;
|
|
59
|
+
},
|
|
60
|
+
clearData() {
|
|
61
|
+
self.trackSource = '';
|
|
62
|
+
self.altTrackName = '';
|
|
63
|
+
self.altTrackType = '';
|
|
64
|
+
self.altAssemblyName = '';
|
|
65
|
+
self.adapterHint = '';
|
|
66
|
+
self.indexTrackData = undefined;
|
|
67
|
+
self.trackData = undefined;
|
|
68
|
+
self.textIndexingConf = undefined;
|
|
69
|
+
self.textIndexTrack = true;
|
|
70
|
+
},
|
|
71
|
+
}))
|
|
72
|
+
.views(self => ({
|
|
73
|
+
get trackAdapter() {
|
|
74
|
+
const { trackData, indexTrackData, adapterHint } = self;
|
|
75
|
+
return trackData
|
|
76
|
+
? guessAdapter(trackData, indexTrackData, adapterHint, self)
|
|
77
|
+
: undefined;
|
|
78
|
+
},
|
|
79
|
+
get trackName() {
|
|
80
|
+
return (self.altTrackName ||
|
|
81
|
+
(self.trackData ? getFileName(self.trackData) : ''));
|
|
82
|
+
},
|
|
83
|
+
get isFtp() {
|
|
84
|
+
var _a, _b;
|
|
85
|
+
const { trackData: track, indexTrackData: index } = self;
|
|
86
|
+
return !!(
|
|
87
|
+
// @ts-ignore
|
|
88
|
+
(((_a = index === null || index === void 0 ? void 0 : index.uri) === null || _a === void 0 ? void 0 : _a.startsWith('ftp://')) || ((_b = track === null || track === void 0 ? void 0 : track.uri) === null || _b === void 0 ? void 0 : _b.startsWith('ftp://'))));
|
|
89
|
+
},
|
|
90
|
+
get isRelativeTrackUrl() {
|
|
91
|
+
var _a;
|
|
92
|
+
// @ts-ignore
|
|
93
|
+
const uri = (_a = self.trackData) === null || _a === void 0 ? void 0 : _a.uri;
|
|
94
|
+
return uri ? !isAbsoluteUrl(uri) : false;
|
|
95
|
+
},
|
|
96
|
+
get isRelativeIndexUrl() {
|
|
97
|
+
var _a;
|
|
98
|
+
// @ts-ignore
|
|
99
|
+
const uri = (_a = self.indexTrackData) === null || _a === void 0 ? void 0 : _a.uri;
|
|
100
|
+
return uri ? !isAbsoluteUrl(uri) : false;
|
|
101
|
+
},
|
|
102
|
+
get isRelativeUrl() {
|
|
103
|
+
return this.isRelativeIndexUrl || this.isRelativeTrackUrl;
|
|
104
|
+
},
|
|
105
|
+
get trackHttp() {
|
|
106
|
+
var _a, _b;
|
|
107
|
+
// @ts-ignore
|
|
108
|
+
return (_b = (_a = self.trackData) === null || _a === void 0 ? void 0 : _a.uri) === null || _b === void 0 ? void 0 : _b.startsWith('http://');
|
|
109
|
+
},
|
|
110
|
+
get indexHttp() {
|
|
111
|
+
var _a, _b;
|
|
112
|
+
// @ts-ignore
|
|
113
|
+
return (_b = (_a = self.indexTrackData) === null || _a === void 0 ? void 0 : _a.uri) === null || _b === void 0 ? void 0 : _b.startsWith('http://');
|
|
114
|
+
},
|
|
115
|
+
get wrongProtocol() {
|
|
116
|
+
return (window.location.protocol === 'https:' &&
|
|
117
|
+
(this.trackHttp || this.indexHttp));
|
|
118
|
+
},
|
|
119
|
+
get unsupported() {
|
|
120
|
+
var _a;
|
|
121
|
+
return ((_a = this.trackAdapter) === null || _a === void 0 ? void 0 : _a.type) === UNSUPPORTED;
|
|
122
|
+
},
|
|
123
|
+
get assembly() {
|
|
124
|
+
var _a;
|
|
125
|
+
return self.altAssemblyName || ((_a = self.view.assemblyNames) === null || _a === void 0 ? void 0 : _a[0]);
|
|
126
|
+
},
|
|
127
|
+
get trackType() {
|
|
128
|
+
return (self.altTrackType ||
|
|
129
|
+
(this.trackAdapter
|
|
130
|
+
? guessTrackType(this.trackAdapter.type, self)
|
|
131
|
+
: ''));
|
|
132
|
+
},
|
|
133
|
+
}))
|
|
134
|
+
.views(self => ({
|
|
135
|
+
get warningMessage() {
|
|
136
|
+
if (self.isFtp) {
|
|
137
|
+
return `Warning: JBrowse cannot access files using the ftp protocol`;
|
|
138
|
+
}
|
|
139
|
+
else if (self.isRelativeUrl) {
|
|
140
|
+
return `Warning: one or more of your files do not provide the protocol e.g.
|
|
141
|
+
https://, please provide an absolute URL unless you are sure a
|
|
142
|
+
relative URL is intended.`;
|
|
143
|
+
}
|
|
144
|
+
else if (self.wrongProtocol) {
|
|
145
|
+
return `Warning: You entered a http:// resources but we cannot access HTTP
|
|
146
|
+
resources from JBrowse when it is running on https. Please use an
|
|
147
|
+
https URL for your track, or access the JBrowse app from the http
|
|
148
|
+
protocol`;
|
|
149
|
+
}
|
|
150
|
+
return '';
|
|
151
|
+
},
|
|
152
|
+
}));
|
|
153
|
+
}
|
|
154
|
+
//# sourceMappingURL=model.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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