c2587413555c7cabd82b21c578d5a6f99599e7d7 jrobinso Tue Sep 16 09:45:03 2025 -0700 Bug -- missing await diff --git src/hg/js/igvFileHelper.js src/hg/js/igvFileHelper.js index 1184fe71ab9..3b230f51099 100644 --- src/hg/js/igvFileHelper.js +++ src/hg/js/igvFileHelper.js @@ -1,771 +1,771 @@ // Helper functions for using igv.js with local files in the UCSC genome browser // // The UCSC browser does not use modules, so wrap code in a self-executing function to limit // scope of variables to this file. (function () { const indexExtensions = new Set(['bai', 'csi', 'tbi', 'idx', 'crai']); const requireIndex = new Set(['bam', 'cram']); // File scope variables const IGV_STORAGE_KEY = "igvSession"; let filePicker = null; let igvBrowser = null; let isDragging = false; let sessionAutoSaveTimer = null; // Create a BroadcastChannel for communication between the UCSC browser page and the file picker page. const channel = new BroadcastChannel('igv_file_channel'); // Message types for communication between browser page and file picker page const MSG = { SELECTED_FILES: 'selectedFiles', RESTORE_FILES: 'restoreFiles', REMOVED_TRACK: 'removedTrack', LOAD_URL: 'loadURL', FILE_PICKER_READY: 'filePickerReady', PING: 'ping', PONG: 'pong' }; /** * A mock File object that wraps a real File object. The purpose of this class is to provide a stable * identifier (id) for the file that can be used to restore the File object on page refresh. The object * looks like a File object to igv.js but has an extra "id" attribute. */ class MockFile { constructor(id, file, name) { this.id = id; this.file = file; this.name = name || (file ? file.name : undefined); this.type = 'MockFile'; } slice(start, end) { this.checkFile(); return this.file.slice(start, end); } async text() { this.checkFile(); return this.file.text(); } async arrayBuffer() { this.checkFile(); return this.file.arrayBuffer(); } checkFile() { if (!this.file) { throw new Error(`Connection to file ${this.name} is not available. Please re-select the file.`); } } } /** * Initialize igv.js, creating an igvBrowser if a session is found in local storage. The existence of a * global "igvBrowser" variable indicates igv.js has already been initialized. * * @returns {Promise<void>} */ async function initIgvUcsc() { if (window.igvBrowser) { //console.log("igvBrowser already exists"); return; } // Retrieve the igv session for this genome, if any, from local storage. // TODO -- in the future this might come from the UCSC session (cart) const db = getDb(); let sessionString = getSessionStorage()[db]; if (sessionString) { const igvSession = JSON.parse(igv.uncompressSession(`blob:${sessionString}`)); // Reconnect any file-based tracks to the actual File objects. if (igvSession.tracks) { const failed = await restoreTrackConfigurations(igvSession.tracks); if (failed.length > 0) { const sendRestoreRequest = () => channel.postMessage({type: "restoreFiles", files: failed}); if (filePicker && !filePicker.closed) { sendRestoreRequest(); return; - } else if (pingFilePicker()) { + } else if (await pingFilePicker()) { // A file picker is open, but (apparently) doesn't have references to the requested files. // Send a request to restore the files, which will bring the file picker to the front and // prompt the user to select the files. sendRestoreRequest(); } else { // Open a file picker and prompt user to select files to restore the connections. filePicker = openFilePicker(); filePicker.onload = () => { channel.postMessage({type: "restoreFiles", files: failed}); }; } } } await createIGVBrowser(igvSession); } } /** * Given a list of files, return a list of track configurations. Each configuration contains a url (MockFile) and * optionally an indexURL (MockFile). * * NOTE: igv uses the "url" and "indexURL" fiels for local files as well as URLs. * * @param files * @returns {*[]} */ function getTrackConfigurations(files) { // Index look up table, key is the data file name, value is {id, file} const indexLUT = new Map(); // Separate data files from index files const dataFiles = []; for (let {id, file} of files) { const name = file.name; const {dataPath, extension} = getExtension(name); if (indexExtensions.has(extension)) { // key is the data file name const key = dataPath; indexLUT.set(key, {id, file}); } else { dataFiles.push({id, file}); } } // Now create configurations, matching index files to corresponding data files when possible const configurations = []; for (let {id, file} of dataFiles) { const filename = file.name; const {extension} = getExtension(filename); if (indexLUT.has(filename)) { const indexURL = indexLUT.get(filename); configurations.push({ id: id, url: new MockFile(id, file), indexURL: new MockFile(indexURL.id, indexURL.file) }); } else if (requireIndex.has(extension)) { throw new Error(`Unable to load track file ${filename} - you must select both ${filename} and its corresponding index file`); } else { configurations.push({url: new MockFile(id, file)}); } } return configurations; } /** * Given a file name return the data path (file name without extension) and the extension. If no extension * is present the extension is the empty string. * * @param name * @returns {{dataPath, extension: string}|{dataPath: string, extension: string}} */ function getExtension(name) { const idx = name.lastIndexOf('.'); if (idx > 0) { let dataPath = name.substring(0, idx); const extension = name.substring(idx + 1); // Special case for Picard file convention if ('bai' === extension && !dataPath.endsWith('.bam')) { dataPath = dataPath + '.bam'; } else if ('crai' === extension && !dataPath.endsWith('.cram')) { dataPath = dataPath + '.cram'; } return {dataPath, extension}; } else { return { dataPath: name, extension: '' }; } } /** * Called upon a page reload to restore file references in the track configurations. Returns a list of file * descriptors {id, name} for files that could not be restored. * * @param trackConfigurations * @returns {Promise<*[]>} */ async function restoreTrackConfigurations(trackConfigurations) { const failed = []; for (let config of trackConfigurations) { if (config.url && 'MockFile' === config.url.type) { const {id, name} = config.url; const file = await restoreFile(id); if (!file) { failed.push({id, name}); } config.url = new MockFile(id, file, name); } if (config.indexURL && 'MockFile' === config.indexURL.type) { const {id, name} = config.indexURL; const file = await restoreFile(id); if (!file) { failed.push({id, name}); } config.indexURL = new MockFile(id, file, name); } } return failed; } /** * Attempt to restore a File object given its id by sending a "getFile" message on the BroadcastChannel and waiting for * a "file" message in response. If no response is received within 1/2 a second undefined is returned. * * NOTE: the 1/2 second timeout is arbitrary, and could be reduced to improve responsiveness. * * @param id * @returns {Promise<unknown>} */ async function restoreFile(id) { return new Promise((resolve) => { const previousOnMessage = channel.onmessage; const timeoutId = setTimeout(() => { cleanup(); console.error(`Timeout waiting for file with id: ${id}`); resolve(undefined); }, 500); function cleanup() { channel.onmessage = previousOnMessage; clearTimeout(timeoutId); } channel.onmessage = function (event) { try { const msg = event.data; if (msg.type === 'file') { cleanup(); resolve(msg.data); } } catch (error) { cleanup(); console.error(error); resolve(undefined); } }; channel.postMessage({type: 'getFile', id}); }); } /** * Update the igv.js browser to reflect a change in the UCSC browser start position. This is called * when the user drags a UCSC track image to a new position. It is intended for small changes, and * works by shifting the igv.js predrawn track image. This will not work for large position * changes, or for changes in resolution. * * @param newPortalStart */ function updateIgvStartPosition(newPortalStart) { // TODO -- this is hacky, add new function to igv.js if (igvBrowser && !isDragging) { const rf = igvBrowser.referenceFrameList[0]; const d = newPortalStart - 1 - rf.start; rf.shift(d); const allTracks = igvBrowser.findTracks(t => true); for (let track of allTracks) { const viewports = track.trackView.viewports; for (let vp of viewports) { vp.shift(); } } } } /** * Return the session storage object, which is a dictionary of {genomeID: sessionString} * @returns {any|{}} */ function getSessionStorage() { // Retrieve igv session string from local storage. // TODO -- in the future this might come from the UCSC session (cart) const localStorageString = localStorage.getItem(IGV_STORAGE_KEY); return localStorageString ? JSON.parse(localStorageString) : {}; } /** * Update the igv session in local storage. This is called periodically and on adding tracks. Ideally this * would be called on IGV state change, but we don't have a means to capture all state changes. */ function updateSessionStorage() { if (igvBrowser) { //setCartVar("igvState", igvSession, null, false); const sessionDict = getSessionStorage(); const db = getDb(); sessionDict[db] = igvBrowser.compressedSession(); localStorage.setItem(IGV_STORAGE_KEY, JSON.stringify(sessionDict)); } else { localStorage.removeItem(IGV_STORAGE_KEY); } } /** * Start a timer to periodically save the igv session to local storage. When / if we are able to * reliably capture IGV state changes we can eliminate this and just save on state change. * * @param intervalMs */ function startSessionAutoSave(intervalMs = 1000) { if (sessionAutoSaveTimer !== null) return; // already running sessionAutoSaveTimer = setInterval(updateSessionStorage, intervalMs); } function stopSessionAutoSave() { if (sessionAutoSaveTimer !== null) { clearInterval(sessionAutoSaveTimer); sessionAutoSaveTimer = null; } } // Detect a page refresh (visibility change to hidden) and save the session to local storage. This is meant to // simulate UCSC browser session handling. // XX TODO - not enough time for sending an HTTP request to update cart - need a better system! // document.onvisibilitychange = () => { // if (document.visibilityState === "hidden") { // if (igvBrowser) { // //setCartVar("igvState", igvSession, null, false); // //const igvSession = igvBrowser.compressedSession(); // //localStorage.setItem("igvSession", igvSession); // } // } // }; // The "Add IGV track" button handler. The button opens the file picker window, unless // it is already open in which case it brings that window to the front. Tracks are added // from the filePicker page by selecting track files. - window.addEventListener("DOMContentLoaded", () => { + window.addEventListener("DOMContentLoaded", async () => { document.getElementById('hgtIgv').addEventListener('click', async function (e) { e.preventDefault(); // our if (filePicker && !filePicker.closed) { filePicker.focus(); return; } else { // A filePicker might be open from a previous instance of this page. We can detect this by sending // a message on the channel and waiting briefly for a response, but we cannot get a reference to the window // so we ask the user to bring it to the front. - const responded = await pingFilePicker(channel); + const responded = await pingFilePicker(); if (responded) { alert("File picker is already open. Please switch to that window."); } else { // No filePicker found, open a new one. filePicker = openFilePicker(); } } }); }); /** * Send a "ping" message to the file picker window and wait up to 100 msec for a "pong" response. Used to * determine if a file picker window is already open. * @param channel * @returns {Promise<unknown>} */ async function pingFilePicker() { const waitForResponse = new Promise((resolve) => { const originalOnMessage = channel.onmessage; channel.onmessage = (event) => { if (event.data && event.data.type === "pong") { channel.onmessage = originalOnMessage; resolve(true); } }; setTimeout(() => { channel.onmessage = originalOnMessage; resolve(false); }, 100); }); channel.postMessage({type: "ping"}); const responded = await waitForResponse; return responded; } function openFilePicker() { return window.open('../admin/filePicker.html', 'filePicker' + Date.now(), 'width=600,height=1000'); } /** * Update the track names in the left hand column of the IGV row in the image table. */ function updateTrackNames() { document.getElementById('igv_namediv').innerHTML = ""; // Clear any existing content // Add track names to the left hand column. if(!igvBrowser) return; const allTracks = igvBrowser.findTracks(t => t.type); let top = 0; for (let track of allTracks) { if ('sequence' !== track.type) { const labelContainer = document.createElement('div'); labelContainer.style.position = 'absolute'; // Use relative positioning labelContainer.style.top = `${top}px`; // Position the element at the current value of "top" labelContainer.style.left = '0'; labelContainer.style.right = '0'; // span full width of the enclosing td via igv_namediv labelContainer.style.width = '100%'; // optional, for clarity const gearDiv = document.createElement('div'); gearDiv.style.position = 'absolute'; gearDiv.style.left = '5px'; gearDiv.style.width = '15px'; gearDiv.style.height = '15px'; gearDiv.style.maxWidth = '15px'; gearDiv.style.maxHeight = '15px'; gearDiv.style.overflow = 'hidden'; gearDiv.style.cursor = 'pointer'; const cog = igv.createIcon('cog', 'grey'); // Ensure the underlying SVG is 15x15 const svg = cog.tagName && cog.tagName.toLowerCase() === 'svg' ? cog : cog.querySelector('svg'); if (svg) { svg.setAttribute('width', '15'); svg.setAttribute('height', '15'); svg.style.width = '15px'; svg.style.height = '15px'; } gearDiv.appendChild(cog); gearDiv.setAttribute('data-track-id', track.id); // Set the track ID attribute labelContainer.appendChild(gearDiv); gearDiv.addEventListener("click", (e) => { e.stopPropagation(); e.preventDefault(); const trackId = e.currentTarget.getAttribute('data-track-id'); const matchingTracks = igvBrowser.findTracks(t => t.id === trackId); if (matchingTracks.length > 0) { const trackView = matchingTracks[0].trackView; trackView.trackGearPopup.presentMenuList( trackView, igvBrowser.menuUtils.trackMenuItemList(trackView), igvBrowser.config); } }); // Move the track gear popup location, and hide its true parent. This is a bit hacky, but // moving the gear popover to a new parent has undesired side effects. const popover = track.trackView.trackGearPopup.popover; if (popover) { popover.parentElement.style.width = '0px'; // don't use display=none, that breaks the popup popover.parentElement.style.height = '0px'; popover.style.left = "-100px"; } const trackLabelDiv = document.createElement('div'); trackLabelDiv.textContent = track.name; // Set the track name as the label trackLabelDiv.style.right = '5px'; // Set a fixed width for the label div trackLabelDiv.style.textAlign = 'right'; // Right-justify the text labelContainer.appendChild(trackLabelDiv); document.getElementById('igv_namediv').appendChild(labelContainer); } top += track.trackView.viewports[0].viewportElement.clientHeight; // Adjust top for the next element } } /** * Insert a new row into the image table for the IGV browser. The igv browser object is a super-track of * sorts, containing all igv.js tracks in the session. In the future we might want to allocate a row * for each igv.js track, but this will require some refactoring of igv.js. * * @returns {HTMLTableRowElement} */ function insertIGVRow() { const imgTbl = document.getElementById('imgTbl'); const tbody = imgTbl.querySelector('tbody'); const igvRow = document.createElement('tr'); igvRow.id = "tr_igv"; igvRow.innerHTML = ` <td style="background: grey"> <div style="width:13px"></div> </td> <td style="position: relative"> <div id="igv_namediv" style="position:absolute; top:0; bottom:0; left:0; right:0;"></div> </td> <td> <div id="igv_div" style="width: auto"></div> </td> `; tbody.appendChild(igvRow); return igvRow; } /** * Create an IGV browser instance and insert it into the image table in a new row. The IGV browser essentially becomes * a track in the UCSC browser context. This function is called when the user adds the first IGV track, or * the igv session is restored on page reload. * * @param config -- The IGV browser configuration object. Must include a reference genome, but might also include * an initial locus or tracks. * @returns {Promise<Browser>} */ async function createIGVBrowser(config) { // Override locus in the IGV session with the UCSC locus // TODO -- should we use genomePos here? const ucscImageWidth = document.getElementById("td_data_ruler").clientWidth; const resolution = (hgTracks.winEnd - hgTracks.winStart) / ucscImageWidth; config.locus = {chr: hgTracks.chromName, start: hgTracks.winStart, bpPerPixel: resolution}; console.log("Creating IGV browser with config: ", config); if (document.getElementById("tr_igv")) { console.warn("IGV track row already exists ???"); // TODO -- how can this happen? return; } const igvRow = insertIGVRow(); // Ammend the igv config to remove most of the IGV widgets. We only want the track display area. Object.assign(config, { showNavigation: false, showIdeogram: false, showRuler: false, //showSequence: false, // Uncomment this to hide igv sequence track showAxis: false, showTrackDragHandles: false, showAxisColumn: false, gearColumnPosition: 'left', showGearColumn: false, //showTrackLabels: false, // Uncomment this to hide the "floating div" igv track labels formEmbedMode: true, // works around hotkey issues affecting igv input elements disableZoom: true, // disable zooming in igv, use UCSC zoom controls minimumBases: 0 // No lower limit on bases per pixel, this is controlled by UCSC zoom }); const div = document.getElementById("igv_div"); igvBrowser = await igv.createBrowser(div, config); updateTrackNames(); // Add event handler to remove IGV row from table if all IGV tracks are removed. igvBrowser.on('trackremoved', function (track) { channel.postMessage({type: "removedTrack", config: track.config}); const allTracks = igvBrowser.findTracks(t => "sequence" !== t.type); // ignore sequence track if (allTracks.length === 0) { igvRow.remove(); igvBrowser = null; updateSessionStorage(); stopSessionAutoSave(); // stop auto save timer delete window.igvBrowser; } updateTrackNames(); }); // Add event handler to track igv.js track panning. On the UCSC side this should be treated // as if the user had dragged a track image igvBrowser.on('trackdrag', e => { isDragging = true; const newStart = igvBrowser.referenceFrameList[0].start; igv.ucscTrackpan(newStart); } ); // Notify UCSC browser that igv.js track panning has ended. igvBrowser.on('trackdragend', () => { isDragging = false; igv.ucscTrackpanEnd(); } ); window.igvBrowser = igvBrowser; // Start the session auto-save timer. This will periodically save the igv session to local storage. // When / if we can reliably capture IGV state changes we can eliminate this and just save on state change. startSessionAutoSave(); return igvBrowser; } // Respond to messages from the filePicker window. channel.onmessage = async function (event) { const msg = event.data; if (!msg || !msg.type) return; switch (msg.type) { case MSG.SELECTED_FILES: console.log("Received selected files: ", event.data.files); const configs = getTrackConfigurations(event.data.files); loadIGVTracks(configs); break; case MSG.LOAD_URL: loadIGVTracks([event.data.config]); break; // NOTE: The file picker ready message does not appear to be used. case MSG.FILE_PICKER_READY: const filesToRestore = JSON.parse(sessionStorage.getItem('filesToRestore')); if (filesToRestore) { channel.postMessage({type: MSG.RESTORE_FILES, files: filesToRestore}); sessionStorage.removeItem('filesToRestore'); } break; } }; /** * Load one or more tracks into the igvBrowser. If the igvBrowser does not exist it is created. * * @param configs * @returns {Promise<void>} */ async function loadIGVTracks(configs) { if (configs.length > 0) { // Create igvBrowser if needed -- i.e. this is the first track being added. State needs to be obtained // from the UCSC browser for genome and locus. if (typeof (window.igvBrowser) === 'undefined' || window.igvBrowser === null) { const defaultConfig = { reference: await getMinimalReference(getDb()), // locus: genomePos.get() }; igvBrowser = await createIGVBrowser(defaultConfig); } // First search for existing tracks referencing the same files. This is to handle the situation // of a user closing the file picker window, thus loosing file references, then reopening the file picker // to restore them. const newConfigs = []; for (let config of configs) { const matchingTracks = igvBrowser.findTracks(t => config.id === t.id); if (matchingTracks.length > 0) { // Just select the first matching track, there should only be one. Restore its file reference(s). matchingTracks[0].config.url.file = config.url.file; if (config.indexURL) { matchingTracks[0].config.indexURL.file = config.indexURL.file; } } else { // This is a new track newConfigs.push(config); } } await igvBrowser.loadTrackList(newConfigs); updateTrackNames(); updateSessionStorage(); } } /* get first line of text from URL */ async function getLine(url, {timeoutMs = 10000} = {}) { const ctrl = new AbortController(); const t = setTimeout(() => ctrl.abort(), timeoutMs); const res = await fetch(url, { headers: {Accept: "text/plain"}, signal: ctrl.signal, }).catch(err => { // surface timeouts/aborts as regular errors throw new Error(`Request failed: ${err.message}`); }); clearTimeout(t); if (!res.ok) throw new Error(`HTTP ${res.status} ${res.statusText}`); const text = await res.text(); // Return a single line (trim and take first line) return text.trim().split(/\r?\n/, 1)[0]; } /** * Return a minimal reference object for the given genomeID. We don't need or want default IGV tracks, only the * reference sequence. * * Eventually expand or reimplement this function to support all UCSC browser genomes. * * @param genomeID * @returns {{id: string, twoBitURL: string}} */ async function getMinimalReference(genomeID) { const currentURL = window.location.href; const upOneDirURL = currentURL.substring(0, currentURL.lastIndexOf('/')); const apiUrl = upOneDirURL + `/hubApi?cmd=/list/files;genome=${genomeID};format=text;skipContext=1;fileType=2bit`; try { const twoBitURL = await getLine(apiUrl); return { "id": genomeID, "twoBitURL": twoBitURL, }; } catch (e) { console.error(e); alert("Internal Error: Cannot get 2bit file from " + apiUrl); return null; } } /** * Parse a IGV / UCSC style locus string, e.g. "chr1:1000-2000" or "chr1:1000" or "chr1", and return * a locus object {chr, start, end}. The start is 0-based, end is 1-based. * * @param locusString * @returns {{chr: *, start: (number|number), end: (number|*)}} */ function parseLocusString(locusString) { const locusRegex = /^([^:]+)(?::(\d+)(?:-(\d+))?)?$/; const match = locusString.match(locusRegex); if (!match) { throw new Error(`Invalid locus string: ${locusString}`); } const chr = match[1]; let start = match[2] ? parseInt(match[2].replace(",", ""), 10) - 1 : 0; // Convert to 0-based let end = match[3] ? parseInt(match[3].replace(",", ""), 10) : start + 100; // Default to 100bp if no end provided if (isNaN(start) || isNaN(end) || start < 0 || end <= start) { throw new Error(`Invalid start or end in locus string: ${locusString}`); } return {chr, start, end}; } // Attach helper functions to the igv object igv.initIgvUcsc = initIgvUcsc; igv.updateIgvStartPosition = updateIgvStartPosition; } ) ();