@jbrowse/plugin-wiggle/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js

JBrowse 2 wiggle adapters, tracks, etc.

import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
import { useState } from 'react';
import { getSession, isElectron, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
import { storeBlobLocation } from '@jbrowse/core/util/tracks';
import { Button, Paper, TextField } from '@mui/material';
import { observer } from 'mobx-react';
import { makeStyles } from 'tss-react/mui';
const useStyles = makeStyles()(theme => ({
    paper: {
        margin: theme.spacing(),
        padding: theme.spacing(),
    },
    submit: {
        marginTop: 25,
        marginBottom: 100,
        display: 'block',
    },
}));
function makeFileLocation(file) {
    return isElectron
        ? {
            localPath: window.require('electron').webUtils.getPathForFile(file),
            locationType: 'LocalPathLocation',
        }
        : storeBlobLocation({ blob: file });
}
function doSubmit({ trackName, val, model, }) {
    var _a;
    const session = getSession(model);
    try {
        const trackId = [
            `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
            session.adminMode ? '' : '-sessionTrack',
        ].join('');
        let bigWigs;
        try {
            bigWigs = JSON.parse(val);
        }
        catch (e) {
            bigWigs = val
                .split(/\n|\r\n|\r/)
                .map(f => f.trim())
                .filter(f => !!f);
        }
        const obj = typeof bigWigs[0] === 'string' ? { bigWigs } : { subadapters: bigWigs };
        if (isSessionWithAddTracks(session)) {
            session.addTrackConf({
                trackId,
                type: 'MultiQuantitativeTrack',
                name: trackName,
                assemblyNames: [model.assembly],
                adapter: {
                    type: 'MultiWiggleAdapter',
                    ...obj,
                },
            });
            (_a = model.view) === null || _a === void 0 ? void 0 : _a.showTrack(trackId);
        }
        model.clearData();
        if (isSessionModelWithWidgets(session)) {
            session.hideWidget(model);
        }
    }
    catch (e) {
        console.error(e);
        session.notifyError(`${e}`, e);
    }
}
const MultiWiggleAddTrackWorkflow = observer(function ({ model, }) {
    const { classes } = useStyles();
    const [val, setVal] = useState('');
    const [trackName, setTrackName] = useState(`MultiWiggle${+Date.now()}`);
    return (_jsxs(Paper, { className: classes.paper, children: [_jsxs("ul", { children: [_jsx("li", { children: "Enter list of URLs for bigwig files in the textbox" }), _jsx("li", { children: "Or, use the button below the text box to select files from your computer" })] }), _jsx(TextField, { multiline: true, fullWidth: true, rows: 10, value: val, placeholder: "Paste list of URLs here, or use file selector below", variant: "outlined", onChange: event => {
                    setVal(event.target.value);
                } }), _jsxs(Button, { variant: "outlined", component: "label", children: ["Choose Files from your computer", _jsx("input", { type: "file", hidden: true, multiple: true, onChange: ({ target }) => {
                            setVal(JSON.stringify([...(target.files || [])].map(file => ({
                                type: 'BigWigAdapter',
                                bigWigLocation: makeFileLocation(file),
                                source: file.name,
                            })), null, 2));
                        } })] }), _jsx(TextField, { value: trackName, helperText: "Track name", onChange: event => {
                    setTrackName(event.target.value);
                } }), _jsx(Button, { variant: "contained", className: classes.submit, onClick: () => {
                    doSubmit({ trackName, val, model });
                }, children: "Submit" }), _jsx("p", { children: "Additional notes: " }), _jsxs("ul", { children: [_jsxs("li", { children: ["The list of bigwig files in the text box can be a list of URLs, or a list of elements like", ' ', _jsx("code", { children: `[{"type":"BigWigAdapter","bigWigLocation":{"uri":"http://host/file.bw"}, "color":"green","source":"name for subtrack"}]` }), ' ', "to apply e.g. the color attribute to the view"] }), _jsx("li", { children: "Adding local files will update the textbox with JSON contents that are ready to submit with the \"Submit\" button" })] })] }));
});
export default MultiWiggleAddTrackWorkflow;