public/js/form.js
import React, { Component, createRef } from 'react';
import { SearchButton } from './search_button';
import { SearchQueryWidget } from './query';
import DatabasesTree from './databases_tree';
import { Databases } from './databases';
import _ from 'underscore';
import { Options } from 'options';
import QueryStats from 'query_stats';
/**
* Search form.
*
* Top level component that initialises and holds all other components, and
* facilitates communication between them.
*/
export class Form extends Component {
constructor(props) {
super(props);
this.state = {
databases: [],
preSelectedDbs: [],
currentlySelectedDbs: [],
preDefinedOpts: {},
tree: {},
residuesInQuerySequence: 0,
blastMethod: ''
};
this.useTreeWidget = this.useTreeWidget.bind(this);
this.determineBlastMethods = this.determineBlastMethods.bind(this);
this.handleSequenceTypeChanged = this.handleSequenceTypeChanged.bind(this);
this.handleSequenceChanged = this.handleSequenceChanged.bind(this);
this.handleDatabaseTypeChanged = this.handleDatabaseTypeChanged.bind(this);
this.handleDatabaseSelectionChanged = this.handleDatabaseSelectionChanged.bind(this);
this.handleAlgoChanged = this.handleAlgoChanged.bind(this);
this.handleFormSubmission = this.handleFormSubmission.bind(this);
this.formRef = createRef();
this.setButtonState = this.setButtonState.bind(this);
}
componentDidMount() {
/**
* Fetch data to initialise the search interface from the server. These
* include list of databases to search against, advanced options to
* apply when an algorithm is selected, and a query sequence that
* the user may want to search in the databases.
*/
var search = location.search.split(/\?|&/).filter(Boolean);
var job_id = sessionStorage.getItem('job_id');
if (job_id) {
search.unshift(`job_id=${job_id}`);
}
$.getJSON(`searchdata.json?${search.join('&')}`, function (data) {
/* Update form state (i.e., list of databases and predefined
* advanced options.
*/
this.setState({
tree: data['tree'],
databases: data['database'],
preSelectedDbs: data['preSelectedDbs'],
preDefinedOpts: data['options'],
blastTaskMap: data['blastTaskMap']
});
/* Pre-populate the form with server sent query sequences
* (if any).
*/
if (data['query']) {
this.refs.query.value(data['query']);
}
setTimeout(function () {
$('.jstree_div').click();
}, 1000);
}.bind(this));
/* Enable submitting form on Cmd+Enter */
$(document).on('keydown', (e) => {
var $button = $('#method');
if (!$button.is(':disabled') &&
e.ctrlKey && e.key === 'Enter') {
$button.trigger('click');
}
});
// show overlay to create visual feedback on button click
$('#method').on('click', () => {
$('#overlay').css('display', 'block');
});
}
useTreeWidget() {
return !_.isEmpty(this.state.tree);
}
handleFormSubmission(evt) {
evt.preventDefault();
const form = this.formRef.current;
const formData = new FormData(form);
formData.append('method', this.refs.button.state.methods[0]);
fetch(window.location.href, {
method: 'POST',
body: formData
}).then(res => {
//remove overlay when form is submitted
$('#overlay').css('display', 'none');
// redirect
if (res.redirected && res.url) {
// setTimeout is needed here as a workaround because safari doesnt allow async calling of window.open
// so setTimeout makes the method get called on the main thread.
setTimeout(() => {
window.open(res.url, $('#toggleNewTab').is(':checked') ? '_blank' : '_self');
}, 0);
}
});
}
determineBlastMethods() {
var database_type = this.databaseType;
var sequence_type = this.sequenceType;
if (this.refs.query.isEmpty()) {
return [];
}
//database type is always known
switch (database_type) {
case 'protein':
switch (sequence_type) {
case undefined:
return ['blastp', 'blastx'];
case 'protein':
return ['blastp'];
case 'nucleotide':
return ['blastx'];
}
break;
case 'nucleotide':
switch (sequence_type) {
case undefined:
return ['tblastn', 'blastn', 'tblastx'];
case 'protein':
return ['tblastn'];
case 'nucleotide':
return ['blastn', 'tblastx'];
}
break;
}
return [];
}
handleSequenceChanged(residuesInQuerySequence) {
if(residuesInQuerySequence !== this.state.residuesInQuerySequence)
this.setState({ residuesInQuerySequence: residuesInQuerySequence});
}
handleSequenceTypeChanged(type) {
this.sequenceType = type;
this.setButtonState();
}
handleDatabaseTypeChanged(type) {
this.databaseType = type;
this.setButtonState();
}
setButtonState() {
this.refs.button.setState({
hasQuery: !this.refs.query.isEmpty(),
hasDatabases: !!this.databaseType,
methods: this.determineBlastMethods()
});
}
handleDatabaseSelectionChanged(selectedDbs) {
if (!_.isEqual(selectedDbs, this.state.currentlySelectedDbs))
this.setState({ currentlySelectedDbs: selectedDbs });
}
handleAlgoChanged(algo) {
if (algo in this.state.preDefinedOpts) {
this.setState({ blastMethod: algo });
}
else {
this.setState({ blastMethod: ''});
}
}
residuesInSelectedDbs() {
return this.state.currentlySelectedDbs.reduce((sum, db) => sum + parseInt(db.ncharacters, 10), 0);
}
render() {
return (
<div>
<div id="overlay" style={{ position: 'absolute', top: 0, left: 0, width: '100vw', height: '100vw', background: 'rgba(0, 0, 0, 0.2)', display: 'none', zIndex: 99 }} />
<div className="fixed top-0 left-0 w-full max-h-8 px-8" data-notifications id="notifications">
<FastqNotification />
<NucleotideNotification />
<ProteinNotification />
<MixedNotification />
</div>
<form id="blast" ref={this.formRef} onSubmit={this.handleFormSubmission}>
<div className="px-4">
<SearchQueryWidget ref="query" onSequenceTypeChanged={this.handleSequenceTypeChanged} onSequenceChanged={this.handleSequenceChanged}/>
{this.useTreeWidget() ?
<DatabasesTree ref="databases"
databases={this.state.databases} tree={this.state.tree}
preSelectedDbs={this.state.preSelectedDbs}
onDatabaseTypeChanged={this.handleDatabaseTypeChanged}
onDatabaseSelectionChanged={this.handleDatabaseSelectionChanged} />
:
<Databases ref="databases" databases={this.state.databases}
preSelectedDbs={this.state.preSelectedDbs}
onDatabaseTypeChanged={this.handleDatabaseTypeChanged}
onDatabaseSelectionChanged={this.handleDatabaseSelectionChanged} />
}
<Options blastMethod={this.state.blastMethod} predefinedOptions={this.state.preDefinedOpts[this.state.blastMethod] || {}} blastTasks={(this.state.blastTaskMap || {})[this.state.blastMethod]} />
</div>
<div className="py-6"></div> {/* add a spacer so that the sticky action bar does not hide any contents */}
<div className="pb-4 pt-2 px-4 sticky bottom-0 md:flex flex-row md:space-x-4 items-center justify-end bg-gradient-to-t to-gray-100/90 from-white/90">
<QueryStats
residuesInQuerySequence={this.state.residuesInQuerySequence} numberOfDatabasesSelected={this.state.currentlySelectedDbs.length} residuesInSelectedDbs={this.residuesInSelectedDbs()}
currentBlastMethod={this.state.blastMethod}
/>
<label className="block my-4 md:my-2">
<input type="checkbox" id="toggleNewTab" /> Open results in new tab
</label>
<SearchButton ref="button" onAlgoChanged={this.handleAlgoChanged} />
</div>
</form>
</div>
);
}
}
class ProteinNotification extends Component {
render() {
return (
<div
data-role="notification"
id="protein-sequence-notification"
style={{ display: 'none' }}>
<div
className="bg-blue-100 border rounded border-blue-800 px-4 py-2 my-2">
Detected: amino-acid sequence(s).
</div>
</div>
);
}
}
class NucleotideNotification extends Component {
render() {
return (<div
data-role="notification"
id="nucleotide-sequence-notification"
style={{ display: 'none' }}>
<div
className="bg-blue-100 border rounded border-blue-800 px-4 py-2 my-2">
Detected: nucleotide sequence(s).
</div>
</div>
);
}
}
class FastqNotification extends Component {
render() {
return (<div
data-role="notification"
id="fastq-sequence-notification"
style={{ display: 'none' }}>
<div
className="bg-blue-100 border rounded border-blue-800 px-4 py-2 my-2">
Detected FASTQ and automatically converted to FASTA.
</div>
</div>
);
}
}
class MixedNotification extends Component {
render() {
return (
<div
data-role="notification"
id="mixed-sequence-notification"
style={{ display: 'none' }}>
<div
className="alert-danger col-md-10 col-md-offset-1">
Error: mixed nucleotide and amino-acid sequences detected.
</div>
</div>
);
}
}