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cleanup support for custom genome list
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@jrobinso
jrobinso committed Feb 5, 2024
1 parent f508fd7 commit 801acb1
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Showing 3 changed files with 90 additions and 57 deletions.
50 changes: 24 additions & 26 deletions js/app.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,6 @@ import {createSaveImageWidget} from './saveImageWidget.js'
import GtexUtils from "./gtexUtils.js"
import version from "./version.js"
import {createCircularViewResizeModal} from "./circularViewResizeModal.js"
import {convertToHubURL} from "./ucscUtils.js"

document.addEventListener("DOMContentLoaded", async (event) => await main(document.getElementById('igv-app-container'), igvwebConfig))

Expand Down Expand Up @@ -84,7 +83,7 @@ async function main(container, config) {
console.error(str)
const googleWarning = "true" === localStorage.getItem(googleWarningFlag)
//AlertSingleton.present(str)
if(!googleWarning) {
if (!googleWarning) {
localStorage.setItem(googleWarningFlag, "true")
alert(str)
}
Expand All @@ -103,14 +102,11 @@ async function main(container, config) {
try {
const lastGenomeId = localStorage.getItem("genomeID")
if (lastGenomeId && lastGenomeId !== igvConfig.genome) {
if (config.genomes.find(elem => elem.id === lastGenomeId)) {
if (config.genomes.find(elem => elem.id === lastGenomeId) ||
((lastGenomeId.startsWith("GCA_") || lastGenomeId.startsWith("GCF_")) && lastGenomeId.length >= 13))
{
igvConfig.genome = lastGenomeId
igvConfig.tracks = []
} else if((lastGenomeId.startsWith("GCA_") || lastGenomeId.startsWith("GCF_")) && lastGenomeId.length >= 13) {
const hubURL = convertToHubURL(lastGenomeId)
igvConfig.genome = {
hubURL: hubURL
}
}
}
} catch (e) {
Expand All @@ -131,7 +127,7 @@ async function main(container, config) {

const urlSet = browser.getTrackURLs()

for (const { element, url } of urlList) {
for (const {element, url} of urlList) {
if (urlSet.has(url)) {
element.setAttribute('disabled', true)
} else {
Expand Down Expand Up @@ -242,7 +238,7 @@ async function initializationHelper(browser, container, options) {
const trackLoader = async configurations => {
try {
// Add "searchable" attribute to non-indexed annotation tracks
for(let c of configurations) {
for (let c of configurations) {


}
Expand Down Expand Up @@ -301,9 +297,9 @@ async function initializationHelper(browser, container, options) {
document.querySelector('#igv-session-list-divider').style.display = 'none'
}

createSaveImageWidget({ browser, saveModal: document.getElementById('igv-app-svg-save-modal'), imageType: 'svg' })
createSaveImageWidget({browser, saveModal: document.getElementById('igv-app-svg-save-modal'), imageType: 'svg'})

createSaveImageWidget({ browser, saveModal: document.getElementById('igv-app-png-save-modal'), imageType: 'png' })
createSaveImageWidget({browser, saveModal: document.getElementById('igv-app-png-save-modal'), imageType: 'png'})

createShareWidgets(shareWidgetConfigurator(browser, container, options))

Expand Down Expand Up @@ -381,7 +377,7 @@ function createSampleInfoMenu(igvMain,

localFileInput.value = ''

await trackLoadHandler([ { type: 'sampleinfo', url: paths[ 0 ] } ])
await trackLoadHandler([{type: 'sampleinfo', url: paths[0]}])
})

// Dropbox
Expand All @@ -395,13 +391,14 @@ function createSampleInfoMenu(igvMain,
{
success: dbFiles => {

const configList = dbFiles.map(( { link } ) => {
return { type: 'sampleinfo', url: link }
const configList = dbFiles.map(({link}) => {
return {type: 'sampleinfo', url: link}
})

trackLoadHandler(configList)
},
cancel: () => {},
cancel: () => {
},
linkType: "preview",
multiselect: false,
folderselect: false,
Expand All @@ -422,8 +419,8 @@ function createSampleInfoMenu(igvMain,
googleDriveButton.addEventListener('click', () => {

const filePickerHandler = async responses => {
const paths = responses.map(({ url }) => url)
await trackLoadHandler([ { type: 'sampleinfo', url: paths[ 0 ] } ])
const paths = responses.map(({url}) => url)
await trackLoadHandler([{type: 'sampleinfo', url: paths[0]}])
}

GooglePicker.createDropdownButtonPicker(false, filePickerHandler)
Expand All @@ -433,7 +430,7 @@ function createSampleInfoMenu(igvMain,

// URL
const html =
`<div id="${ urlModalId }" class="modal">
`<div id="${urlModalId}" class="modal">
<div class="modal-dialog modal-lg">
Expand Down Expand Up @@ -477,17 +474,18 @@ function createSampleInfoMenu(igvMain,
fileLoadManager: new FileLoadManager(),
dataOnly: false,
doURL: true
};
}

const fileLoadWidget = new FileLoadWidget(fileLoadWidgetConfig)

Utils.configureModal(fileLoadWidget, urlModal, async fileLoadWidget => {
const paths = fileLoadWidget.retrievePaths()
await trackLoadHandler([ { type: 'sampleinfo', url: paths[ 0 ] } ])
await trackLoadHandler([{type: 'sampleinfo', url: paths[0]}])
return true
})

}

function configureGoogleSignInButton() {

if (true === googleEnabled) {
Expand All @@ -505,7 +503,7 @@ function configureGoogleSignInButton() {

if (currentUserProfile) {
const name = currentUserProfile.email || currentUserProfile.name || ''
signInOutButton.innerText = `Sign Out ${ name }`
signInOutButton.innerText = `Sign Out ${name}`
} else {
signInOutButton.innerText = 'Sign In'
}
Expand Down Expand Up @@ -656,13 +654,13 @@ async function initializeDropbox() {
}
}

function guid () {
return ("0000" + (Math.random() * Math.pow(36, 4) << 0).toString(36)).slice(-4);
function guid() {
return ("0000" + (Math.random() * Math.pow(36, 4) << 0).toString(36)).slice(-4)
}

function isFile(object) {
if(!object) {
return false;
if (!object) {
return false
}
return typeof object !== 'function' &&
(object instanceof File ||
Expand Down
80 changes: 66 additions & 14 deletions js/genomeWidgets.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,9 @@
import {AlertSingleton, createURLModal,EventBus,FileLoadManager,FileLoadWidget,Utils} from '../node_modules/igv-widgets/dist/igv-widgets.js'
import Globals from "./globals.js";

const MAX_CUSTOM_GENOMES = 5
let fileLoadWidget;
let knownGenomeIds = new Set();

function createGenomeWidgets({$igvMain, urlModalId, genomeFileLoad}) {

Expand Down Expand Up @@ -59,13 +61,27 @@ function createGenomeWidgets({$igvMain, urlModalId, genomeFileLoad}) {
});
}

/**
* Initialize the genome selection widget with pre-defined and user-defined genomes. Because of the way these
* items are added in 'genomeDropdownLayout' they are added in reverse order.
*
* @param browser
* @param genomes
* @param $dropdown_menu
* @returns {Promise<void>}
*/
async function initializeGenomeWidgets(browser, genomes, $dropdown_menu) {
try {

const genomeMap = await getAppLaunchGenomes(genomes);
// Start with predefined genomes. This can return undefined.
let genomeMap = await getAppLaunchGenomes(genomes);

if (genomeMap) {
genomeDropdownLayout({ browser, genomeMap, $dropdown_menu });
// Add user loaded genomes
genomeMap = addCustomGenomes(genomeMap || new Map())

if(genomeMap.size > 0) {
genomeDropdownLayout({browser, genomeMap, $dropdown_menu});
knownGenomeIds = new Set(genomeMap.keys())
}

} catch (e) {
Expand All @@ -78,7 +94,6 @@ async function getAppLaunchGenomes(genomes) {
if (undefined === genomes) {
return undefined;
}

if (Array.isArray(genomes)) {
return buildMap(genomes);
} else {
Expand All @@ -98,6 +113,20 @@ async function getAppLaunchGenomes(genomes) {
}
}

function addCustomGenomes(genomeMap) {
const customGenomeString = localStorage.getItem("customGenomes")
if(customGenomeString) {
const customGenomeJson = JSON.parse(customGenomeString)
if(customGenomeJson.length > 0) {
genomeMap.set('-', '-')
for (let json of customGenomeJson.reverse()) {
genomeMap.set(json.id, json)
}
}
}
return genomeMap
}

function buildMap(arrayOrJson) {

const map = new Map()
Expand All @@ -118,27 +147,35 @@ function buildMap(arrayOrJson) {
function genomeDropdownLayout({browser, genomeMap, $dropdown_menu}) {

// discard all buttons preceeding the divider div
// TODO -- does this use of find assume there is 1 dropdown-divider? Searching by ID would be more robust.
let $divider = $dropdown_menu.find('.dropdown-divider');
$divider.nextAll().remove();

for (let [ key, value ] of genomeMap) {

const $button = createButton(value.name);
$button.insertAfter($divider);
if('-' === key) {
// Add separator
// TODO -- style this, <hr> is a hack
$('<div class="dropdown-divider"></div>').insertAfter($divider)

$button.data('id', key);
} else {
const $button = createButton(value.name);
$button.insertAfter($divider);

const str = `click.genome-dropdown.${ key }`;
$button.data('id', key);

$button.on(str, async () => {
const str = `click.genome-dropdown.${key}`;

const id = $button.data('id');
$button.on(str, async () => {

if (id !== browser.genome.id) {
await loadGenome(value);
}
const id = $button.data('id');

});
if (id !== browser.genome.id) {
await loadGenome(value);
}

});
}

} // for (...)

Expand All @@ -159,7 +196,22 @@ async function loadGenome(genomeConfiguration) {
g = await Globals.browser.loadGenome(genomeConfiguration);
if(g.id) {
try {

// Last loaded genome ID, reloaded automatically on next page load
localStorage.setItem("genomeID", g.id)

// If this is a previously unknown genome add it to the custom list.
if(!knownGenomeIds.has(g.id)) {
knownGenomeIds.add(g.id)
const customGenomeString = localStorage.getItem("customGenomes")
let customGenomeJson = customGenomeString ? JSON.parse(customGenomeString) : []
customGenomeJson.unshift(g)
if(customGenomeJson.length > MAX_CUSTOM_GENOMES) {
customGenomeJson = customGenomeJson.slice(0,MAX_CUSTOM_GENOMES)
}
localStorage.setItem("customGenomes", JSON.stringify(customGenomeJson))
}

} catch (e) {
console.error(e)
}
Expand Down
17 changes: 0 additions & 17 deletions js/ucscUtils.js
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