public/js/report.js
import './jquery_world'; // for custom $.tooltip function
import React, { Component } from 'react';
import Sidebar from './sidebar';
import AlignmentExporter from './alignment_exporter';
import ReportPlugins from 'report_plugins';
import RunSummary from './report/run_summary';
import GraphicalOverview from './report/graphical_overview';
import AlignmentResults from './report/alignment_results';
/**
* Renders entire report.
*
* Composed of Query and Sidebar components.
*/
class Report extends Component {
constructor(props) {
super(props);
// Properties below are internal state used to render results in small
// slices (see updateState).
this.state = {
user_warning: null,
download_links: [],
search_id: '',
seqserv_version: '',
program: '',
program_version: '',
submitted_at: '',
results: [],
queries: [],
querydb: [],
params: [],
stats: [],
alignment_blob_url: '',
allQueriesLoaded: false,
cloud_sharing_enabled: false,
};
this.prepareAlignmentOfAllHits = this.prepareAlignmentOfAllHits.bind(this);
this.setStateFromJSON = this.setStateFromJSON.bind(this);
this.plugins = new ReportPlugins(this);
}
/**
* Fetch results.
*/
fetchResults() {
const path = location.pathname + '.json' + location.search;
this.pollPeriodically(path, this.setStateFromJSON, this.props.showErrorModal);
}
pollPeriodically(path, callback, errCallback) {
var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];
function poll() {
fetch(path)
.then(response => {
// Handle HTTP status codes
if (!response.ok) throw response;
return response.text().then(data => {
if (data) {
data = parseJSON(data);
};
return { status: response.status, data }
});
})
.then(({ status, data }) => {
switch (status) {
case 202:
var interval;
if (intervals.length === 1) {
interval = intervals[0];
} else {
interval = intervals.shift();
}
setTimeout(poll, interval);
break;
case 200:
callback(data);
break;
}
})
.catch(error => {
if (error.text) {
error.text().then(errData => {
errData = parseJSON(errData);
switch (error.status) {
case 400:
case 422:
case 500:
errCallback(errData);
break;
default:
console.error("Unhandled error:", error.status);
}
});
} else {
console.error("Network error:", error);
}
});
}
function parseJSON(str) {
let parsedJson = str;
try {
parsedJson = JSON.parse(str);
} catch (e) {
console.error("Error parsing JSON:", e);
}
return parsedJson;
}
poll();
}
/**
* Calls setState after any required modification to responseJSON.
*/
setStateFromJSON(responseJSON) {
this.lastTimeStamp = Date.now();
// the callback prepares the download link for all alignments
if (responseJSON.user_warning == 'LARGE_RESULT') {
this.setState({user_warning: responseJSON.user_warning, download_links: responseJSON.download_links});
} else {
this.setState(responseJSON, this.prepareAlignmentOfAllHits);
}
}
/**
* Called as soon as the page has loaded and the user sees the loading spinner.
* We use this opportunity to setup services that make use of delegated events
* bound to the window, document, or body.
*/
componentDidMount() {
this.fetchResults();
// This sets up an event handler which enables users to select text from
// hit header without collapsing the hit.
this.preventCollapseOnSelection();
this.toggleTable();
}
/**
* Called after all results have been rendered.
*/
componentFinishedUpdating() {
if (this.state.allQueriesLoaded) return;
this.shouldShowIndex() && this.setupScrollSpy();
this.setState({ allQueriesLoaded: true });
}
/**
* Returns loading message
*/
loadingJSX() {
return (
<div className="grid grid-cols-6 gap-4">
<div className="col-start-1 col-end-7 text-center pt-3">
<h1 className="mb-8 text-4xl">
<i className="fa fa-cog fa-spin"></i> BLAST-ing
</h1>
<div className="mb-5 w-full">
<p className="m-auto w-full md:w-6/12 text-sm">This can take some time depending on the size of your query and
database(s). The page will update automatically when BLAST is done.</p>
</div>
<p className="mb-9 text-sm">
You can bookmark the page and come back to it later or share the
link with someone.
</p>
<p className="text-sm">
{ process.env.targetEnv === 'cloud' && <b>If the job takes more than 10 minutes to complete, we will send you an email upon completion.</b> }
</p>
</div>
</div>
);
}
/* eslint-disable */
/**
* Return results JSX.
*/
resultsJSX() {
return (
<div className="grid grid-cols-1 md:grid-cols-4 gap-4 print:grid-cols-1" id="results">
<div className="hidden md:col-span-1 md:block print:hidden">
<Sidebar
data={this.state}
atLeastOneHit={this.atLeastOneHit()}
shouldShowIndex={this.shouldShowIndex()}
allQueriesLoaded={this.state.allQueriesLoaded}
cloudSharingEnabled={this.state.cloud_sharing_enabled}
/>
</div>
<div className="col-span-1 md:col-span-3 print:col-span-1">
<RunSummary
seqserv_version={this.state.seqserv_version}
program_version={this.state.program_version}
submitted_at={this.state.submitted_at}
querydb={this.state.querydb}
stats={this.state.stats}
params={this.state.params}
/>
<GraphicalOverview
queries={this.state.queries}
prorgam={this.state.program}
plugins={this.plugins}
/>
<AlignmentResults
state={this.state}
populate_hsp_array={this.populate_hsp_array.bind(this)}
componentFinishedUpdating={(_) => this.componentFinishedUpdating(_)}
plugins={this.plugins}
{...this.props}
/>
</div>
</div>
);
}
/* eslint-enable */
warningJSX() {
return(
<div className="mx-auto max-w-7xl px-4 sm:px-6 lg:px-8">
<div className="grid grid-cols-6 gap-4">
<div className="col-start-1 col-end-7 text-center">
<h1 className="mb-4 text-4xl">
<i className="fa fa-exclamation-triangle"></i> Warning
</h1>
<p className="mb-2">
The BLAST result might be too large to load in the browser. If you have a powerful machine you can try loading the results anyway. Otherwise, you can download the results and view them locally.
</p>
<p className="mb-2">
{this.state.download_links.map((link, index) => {
return (
<a href={link.url} className="btn btn-secondary" key={'download_link_' + index} >
{link.name}
</a>
);
})}
</p>
<p>
<a href={location.pathname + '?bypass_file_size_warning=true'} className="py-2 px-3 border border-transparent rounded-md shadow-sm text-white bg-seqblue hover:bg-seqorange focus:outline-none focus:ring-2 focus:ring-offset-2 focus:ring-seqorange">
View results in browser anyway
</a>
</p>
</div>
</div>
</div>
);
}
// Controller //
/**
* Returns true if results have been fetched.
*
* A holding message is shown till results are fetched.
*/
isResultAvailable() {
return this.state.queries.length >= 1;
}
/**
* Indicates the response contains a warning message for the user
* in which case we should not render the results and render the
* warning instead.
**/
isUserWarningPresent() {
return this.state.user_warning;
}
/**
* Returns true if we have at least one hit.
*/
atLeastOneHit() {
return this.state.queries.some((query) => query.hits.length > 0);
}
/**
* Returns true if index should be shown in the sidebar. Index is shown
* only for 2 and 8 queries.
*/
shouldShowIndex() {
var num_queries = this.state.queries.length;
return num_queries >= 2 && num_queries <= 12;
}
/**
* Prevents folding of hits during text-selection.
*/
preventCollapseOnSelection() {
$('body').on('mousedown', '.hit > .section-header > h4', function (event) {
var $this = $(this);
$this.on('mouseup mousemove', function handler(event) {
if (event.type === 'mouseup') {
// user wants to toggle
var hitID = $this.parents('.hit').attr('id');
$(`div[data-parent-hit=${hitID}]`).toggle();
$this.find('i').toggleClass('fa-square-minus fa-square-plus');
$($this.data('parent-id')).toggleClass('print:hidden');
} else {
// user wants to select
$this.attr('data-toggle', '');
}
$this.off('mouseup mousemove', handler);
});
});
}
/* Handling the fa icon when Hit Table is collapsed */
/* TODO:JOKO check if this method still being used? */
toggleTable() {
$('body').on(
'mousedown',
'.resultn .caption[data-toggle="collapse"]',
function (event) {
var $this = $(this);
$this.on('mouseup mousemove', function handler(event) {
$this.find('i').toggleClass('fa-square-minus fa-square-plus');
$this.off('mouseup mousemove', handler);
});
}
);
}
/**
* For the query in viewport, highlights corresponding entry in the index.
*/
setupScrollSpy() {
var sectionIds = $('a.side-nav');
$(document).scroll(function(){
sectionIds.each(function(){
var container = $(this).attr('href');
var containerOffset = $(container).offset().top;
var containerHeight = $(container).outerHeight();
var containerBottom = containerOffset + containerHeight;
var scrollPosition = $(document).scrollTop();
if(scrollPosition < containerBottom - 20 && scrollPosition >= containerOffset - 20){
$(this).addClass('active');
} else {
$(this).removeClass('active');
}
});
});
}
populate_hsp_array(hit, query_id){
return hit.hsps.map(hsp => Object.assign(hsp, {hit_id: hit.id, query_id}));
}
prepareAlignmentOfAllHits() {
// Get number of hits and array of all hsps.
var num_hits = 0;
var hsps_arr = [];
if(!this.state.queries.length){
return;
}
this.state.queries.forEach(
(query) => query.hits.forEach(
(hit) => {
num_hits++;
hsps_arr = hsps_arr.concat(this.populate_hsp_array(hit, query.id));
}
)
);
var aln_exporter = new AlignmentExporter();
var file_name = `alignment-${num_hits}_hits.txt`;
const blob_url = aln_exporter.prepare_alignments_for_export(hsps_arr, file_name);
$('.download-alignment-of-all')
.attr('href', blob_url)
.attr('download', file_name);
return false;
}
render() {
if (this.isUserWarningPresent()) {
return this.warningJSX();
} else if (this.isResultAvailable()) {
return this.resultsJSX();
} else {
return this.loadingJSX();
}
}
}
export default Report;