sequenceserver 2.0.0 → 2.1.0

data/public/js/report.js

@@ -1,82 +1,25 @@
 import './jquery_world'; // for custom $.tooltip function
-import React from 'react';
+import React, { Component } from 'react';
 import _ from 'underscore';
 
 import Sidebar from './sidebar';
 import Circos from './circos';
-import Query from './query';
+import { ReportQuery } from './query';
 import Hit from './hit';
 import HSP from './hsp';
+import AlignmentExporter from './alignment_exporter';
 
-import SequenceModal from './sequence_modal';
-import ErrorModal from './error_modal';
 
-/**
- * Base component of report page. This component is later rendered into page's
- * '#view' element.
- */
-var Page = React.createClass({
-    render: function () {
-        return (
-            <div>
-                {/* Provide bootstrap .container element inside the #view for
-                    the Report component to render itself in. */}
-                <div className="container">
-                    <Report showSequenceModal={ _ => this.showSequenceModal(_) }
-                        getCharacterWidth={ () => this.getCharacterWidth() }
-                        showErrorModal={ (...args) => this.showErrorModal(...args) } />
-                </div>
-
-                {/* Add a hidden span tag containing chars used in HSPs */}
-                <pre className="pre-reset hsp-lines" ref="hspChars" hidden>
-                    ABCDEFGHIJKLMNOPQRSTUVWXYZ +-
-                </pre>
-
-                {/* Required by Grapher for SVG and PNG download */}
-                <canvas id="png-exporter" hidden></canvas>
-
-                <SequenceModal ref="sequenceModal"
-                    showErrorModal={ (...args) => this.showErrorModal(...args) }/>
-
-                <ErrorModal ref="errorModal" />
-            </div>
-        );
-    },
-
-    componentDidMount: function () {
-        var job_id = location.pathname.split('/').pop();
-        sessionStorage.setItem('job_id', job_id);
-    },
-
-    showSequenceModal: function (url) {
-        this.refs.sequenceModal.show(url);
-    },
 
-    showErrorModal: function (errorData, beforeShow) {
-        this.refs.errorModal.show(errorData, beforeShow);
-    },
-
-    getCharacterWidth: function () {
-        if (!this.characterWidth) {
-            var $hspChars = $(React.findDOMNode(this.refs.hspChars));
-            this.characterWidth = $hspChars.width() / 29;
-        }
-        return this.characterWidth;
-    }
-});
 
 /**
  * Renders entire report.
  *
  * Composed of Query and Sidebar components.
  */
-var Report = React.createClass({
-
-    // Model //
-
-    getInitialState: function () {
-        this.fetchResults();
-
+class Report extends Component {
+    constructor(props) {
+        super(props);
         // Properties below are internal state used to render results in small
         // slices (see updateState).
         this.numUpdates = 0;
@@ -84,92 +27,89 @@ var Report = React.createClass({
         this.nextHit = 0;
         this.nextHSP = 0;
         this.maxHSPs = 3; // max HSPs to render in a cycle
-
-        return {
-            search_id:       '',
+        this.state = {
+            search_id: '',
             seqserv_version: '',
-            program:         '',
+            program: '',
             program_version: '',
-            submitted_at:    '',
-            queries:         [],
-            results:         [],
-            querydb:         [],
-            params:          [],
-            stats:           []
+            submitted_at: '',
+            queries: [],
+            results: [],
+            querydb: [],
+            params: [],
+            stats: [],
+            alignment_blob_url: '',
+            allQueriesLoaded: false,
+            cloud_sharing_enabled: false,
         };
-    },
-
+        this.prepareAlignmentOfSelectedHits = this.prepareAlignmentOfSelectedHits.bind(this);
+        this.prepareAlignmentOfAllHits = this.prepareAlignmentOfAllHits.bind(this);
+        this.setStateFromJSON = this.setStateFromJSON.bind(this);
+    }
     /**
-     * Fetch results.
-     */
-    fetchResults: function () {
+   * Fetch results.
+   */
+    fetchResults() {
         var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];
         var component = this;
 
-        function poll () {
-            $.getJSON(location.pathname + '.json')
-                .complete(function (jqXHR) {
-                    switch (jqXHR.status) {
-                    case 202:
-                        var interval;
-                        if (intervals.length === 1) {
-                            interval = intervals[0];
-                        }
-                        else {
-                            interval = intervals.shift();
-                        }
-                        setTimeout(poll, interval);
-                        break;
-                    case 200:
-                        component.setStateFromJSON(jqXHR.responseJSON);
-                        break;
-                    case 404:
-                    case 400:
-                    case 500:
-                        component.props.showErrorModal(jqXHR.responseJSON);
-                        break;
+        function poll() {
+            $.getJSON(location.pathname + '.json').complete(function (jqXHR) {
+                switch (jqXHR.status) {
+                case 202:
+                    var interval;
+                    if (intervals.length === 1) {
+                        interval = intervals[0];
+                    } else {
+                        interval = intervals.shift();
                     }
-                });
+                    setTimeout(poll, interval);
+                    break;
+                case 200:
+                    component.setStateFromJSON(jqXHR.responseJSON);
+                    break;
+                case 404:
+                case 400:
+                case 500:
+                    component.props.showErrorModal(jqXHR.responseJSON);
+                    break;
+                }
+            });
         }
 
         poll();
-    },
+    }
 
     /**
-     * Calls setState after any required modification to responseJSON.
-     */
-    setStateFromJSON: function(responseJSON) {
+   * Calls setState after any required modification to responseJSON.
+   */
+    setStateFromJSON(responseJSON) {
         this.lastTimeStamp = Date.now();
-        this.setState(responseJSON);
-    },
-
-    // Life-cycle methods //
-    render: function () {
-        return this.isResultAvailable() ?
-            this.resultsJSX() : this.loadingJSX();
-    },
-
+        // the callback prepares the download link for all alignments
+        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: function () {
+   * 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 for the first time after as BLAST results have been retrieved from
-     * the server and added to this.state by fetchResults. Only summary overview
-     * and circos would have been rendered at this point. At this stage we kick
-     * start iteratively adding 1 HSP to the page every 25 milli-seconds.
-     */
-    componentDidUpdate: function () {
-        // Log to console how long the last update take?
-        console.log((Date.now() - this.lastTimeStamp)/1000);
+   * Called for the first time after as BLAST results have been retrieved from
+   * the server and added to this.state by fetchResults. Only summary overview
+   * and circos would have been rendered at this point. At this stage we kick
+   * start iteratively adding 1 HSP to the page every 25 milli-seconds.
+   */
+    componentDidUpdate() {
+    // Log to console how long the last update take?
+        console.log((Date.now() - this.lastTimeStamp) / 1000);
 
         // Lock sidebar in its position on the first update.
         if (this.nextQuery == 0 && this.nextHit == 0 && this.nextHSP == 0) {
@@ -182,16 +122,15 @@ var Report = React.createClass({
             // the updates giving the browser a chance to respond
             // to user interactions.
             setTimeout(() => this.updateState(), 25);
-        }
-        else {
+        } else {
             this.componentFinishedUpdating();
         }
-    },
+    }
 
     /**
-     * Push next slice of results to React for rendering.
-     */
-    updateState: function() {
+   * Push next slice of results to React for rendering.
+   */
+    updateState() {
         var results = [];
         var numHSPsProcessed = 0;
         while (this.nextQuery < this.state.queries.length) {
@@ -200,12 +139,18 @@ var Report = React.createClass({
             // 3 hsps or are rendered in each cycle, but we want to create the
             // corresponding Query component only the first time we see it.
             if (this.nextHit == 0 && this.nextHSP == 0) {
-                results.push(<Query key={'Query_'+query.number} query={query}
-                    program={this.state.program} querydb={this.state.querydb}
-                    showQueryCrumbs={this.state.queries.length > 1}
-                    non_parse_seqids={this.state.non_parse_seqids}
-                    imported_xml={this.state.imported_xml}
-                    veryBig={this.state.veryBig} />);
+                results.push(
+                    <ReportQuery
+                        key={'Query_' + query.number}
+                        query={query}
+                        program={this.state.program}
+                        querydb={this.state.querydb}
+                        showQueryCrumbs={this.state.queries.length > 1}
+                        non_parse_seqids={this.state.non_parse_seqids}
+                        imported_xml={this.state.imported_xml}
+                        veryBig={this.state.veryBig}
+                    />
+                );
             }
 
             while (this.nextHit < query.hits.length) {
@@ -214,14 +159,22 @@ var Report = React.createClass({
                 // 10 hsps are rendered in each cycle, but we want to create the
                 // corresponding Hit component only the first time we see it.
                 if (this.nextHSP == 0) {
-                    results.push(<Hit key={'Query_'+query.number+'_Hit_'+hit.number} query={query}
-                        hit={hit} algorithm={this.state.program} querydb={this.state.querydb}
-                        selectHit={this.selectHit} imported_xml={this.state.imported_xml}
-                        non_parse_seqids={this.state.non_parse_seqids}
-                        showQueryCrumbs={this.state.queries.length > 1}
-                        showHitCrumbs={query.hits.length > 1}
-                        veryBig={this.state.veryBig}
-                        {... this.props} />
+                    results.push(
+                        <Hit
+                            key={'Query_' + query.number + '_Hit_' + hit.number}
+                            query={query}
+                            hit={hit}
+                            algorithm={this.state.program}
+                            querydb={this.state.querydb}
+                            selectHit={this.selectHit}
+                            imported_xml={this.state.imported_xml}
+                            non_parse_seqids={this.state.non_parse_seqids}
+                            showQueryCrumbs={this.state.queries.length > 1}
+                            showHitCrumbs={query.hits.length > 1}
+                            veryBig={this.state.veryBig}
+                            onChange={this.prepareAlignmentOfSelectedHits}
+                            {...this.props}
+                        />
                     );
                 }
 
@@ -229,9 +182,22 @@ var Report = React.createClass({
                     // Get nextHSP and increment the counter.
                     var hsp = hit.hsps[this.nextHSP++];
                     results.push(
-                        <HSP key={'Query_'+query.number+'_Hit_'+hit.number+'_HSP_'+hsp.number}
-                            query={query} hit={hit} hsp={hsp} algorithm={this.state.program}
-                            showHSPNumbers={hit.hsps.length > 1} {... this.props} />
+                        <HSP
+                            key={
+                                'Query_' +
+                query.number +
+                '_Hit_' +
+                hit.number +
+                '_HSP_' +
+                hsp.number
+                            }
+                            query={query}
+                            hit={hit}
+                            hsp={hsp}
+                            algorithm={this.state.program}
+                            showHSPNumbers={hit.hsps.length > 1}
+                            {...this.props}
+                        />
                     );
                     numHSPsProcessed++;
                     if (numHSPsProcessed == this.maxHSPs) break;
@@ -259,147 +225,163 @@ var Report = React.createClass({
         this.lastTimeStamp = Date.now();
         this.setState({
             results: this.state.results.concat(results),
-            veryBig: this.numUpdates >= 250
+            veryBig: this.numUpdates >= 250,
         });
-    },
+    }
 
     /**
-     * Called after all results have been rendered.
-     */
-    componentFinishedUpdating: function () {
+   * 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: function () {
+   * Returns loading message
+   */
+    loadingJSX() {
         return (
-            <div
-                className="row">
-                <div
-                    className="col-md-6 col-md-offset-3 text-center">
+            <div className="row">
+                <div className="col-md-6 col-md-offset-3 text-center">
                     <h1>
                         <i className="fa fa-cog fa-spin"></i>&nbsp; BLAST-ing
                     </h1>
                     <p>
-                        <br/>
-                        This can take some time depending on the size of your query and
-                        database(s). The page will update automatically when BLAST is
-                        done.
-                        <br/>
-                        <br/>
-                        You can bookmark the page and come back to it later or share
-                        the link with someone.
+                        <br />
+            This can take some time depending on the size of your query and
+            database(s). The page will update automatically when BLAST is done.
+                        <br />
+                        <br />
+            You can bookmark the page and come back to it later or share the
+            link with someone.
                     </p>
                 </div>
             </div>
         );
-    },
+    }
 
     /**
-     * Return results JSX.
-     */
-    resultsJSX: function () {
+   * Return results JSX.
+   */
+    resultsJSX() {
         return (
-            <div className="row">
+            <div className="row" id="results">
                 <div className="col-md-3 hidden-sm hidden-xs">
-                    <Sidebar data={this.state}
+                    <Sidebar
+                        data={this.state}
                         atLeastOneHit={this.atLeastOneHit()}
-                        shouldShowIndex={this.shouldShowIndex()} />
+                        shouldShowIndex={this.shouldShowIndex()}
+                        allQueriesLoaded={this.state.allQueriesLoaded}
+                        cloudSharingEnabled={this.state.cloud_sharing_enabled}
+                    />
                 </div>
                 <div className="col-md-9">
-                    { this.overviewJSX() }
-                    { this.circosJSX() }
-                    { this.state.results }
+                    {this.overviewJSX()}
+                    {this.circosJSX()}
+                    {this.state.results}
                 </div>
             </div>
         );
-    },
+    }
 
     /**
-     * Renders report overview.
-     */
-    overviewJSX: function () {
+   * Renders report overview.
+   */
+    overviewJSX() {
         return (
             <div className="overview">
                 <p>
-                    <strong>SequenceServer {this.state.seqserv_version}</strong> using <strong>{this.state.program_version}</strong>
-                    {this.state.submitted_at && `, query submitted on ${this.state.submitted_at}`}
+                    <strong>SequenceServer {this.state.seqserv_version}</strong> using{' '}
+                    <strong>{this.state.program_version}</strong>
+                    {this.state.submitted_at &&
+            `, query submitted on ${this.state.submitted_at}`}
                 </p>
                 <p>
-                    <strong> Databases: </strong>{
-                        this.state.querydb.map((db) => { return db.title; }).join(', ')
-                    } ({this.state.stats.nsequences} sequences,&nbsp;
+                    <strong> Databases: </strong>
+                    {this.state.querydb
+                        .map((db) => {
+                            return db.title;
+                        })
+                        .join(', ')}{' '}
+          ({this.state.stats.nsequences} sequences,&nbsp;
                     {this.state.stats.ncharacters} characters)
                 </p>
                 <p>
-                    <strong>Parameters: </strong> {
-                        _.map(this.state.params, function (val, key) {
-                            return key + ' ' + val;
-                        }).join(', ')
-                    }
+                    <strong>Parameters: </strong>{' '}
+                    {_.map(this.state.params, function (val, key) {
+                        return key + ' ' + val;
+                    }).join(', ')}
                 </p>
                 <p>
-                    Please cite: <a href="https://doi.org/10.1093/molbev/msz185">https://doi.org/10.1093/molbev/msz185</a>
+          Please cite:{' '}
+                    <a href="https://doi.org/10.1093/molbev/msz185">
+            https://doi.org/10.1093/molbev/msz185
+                    </a>
                 </p>
             </div>
         );
-    },
+    }
 
     /**
-     * Return JSX for circos if we have at least one hit.
-     */
-    circosJSX: function () {
-        return this.atLeastTwoHits()
-            ? <Circos queries={this.state.queries}
-                program={this.state.program} collapsed="true"/>
-            : <span></span>;
-    },
+   * Return JSX for circos if we have at least one hit.
+   */
+    circosJSX() {
+        return this.atLeastTwoHits() ? (
+            <Circos
+                queries={this.state.queries}
+                program={this.state.program}
+                collapsed="true"
+            />
+        ) : (
+            <span></span>
+        );
+    }
 
     // Controller //
 
     /**
-     * Returns true if results have been fetched.
-     *
-     * A holding message is shown till results are fetched.
-     */
-    isResultAvailable: function () {
+   * Returns true if results have been fetched.
+   *
+   * A holding message is shown till results are fetched.
+   */
+    isResultAvailable() {
         return this.state.queries.length >= 1;
-    },
+    }
 
     /**
-     * Returns true if we have at least one hit.
-     */
-    atLeastOneHit: function () {
-        return this.state.queries.some(query => query.hits.length > 0);
-    },
+   * Returns true if we have at least one hit.
+   */
+    atLeastOneHit() {
+        return this.state.queries.some((query) => query.hits.length > 0);
+    }
 
     /**
-     * Does the report have at least two hits? This is used to determine
-     * whether Circos should be enabled or not.
-     */
-    atLeastTwoHits: function () {
+   * Does the report have at least two hits? This is used to determine
+   * whether Circos should be enabled or not.
+   */
+    atLeastTwoHits() {
         var hit_num = 0;
-        return this.state.queries.some(query => {
+        return this.state.queries.some((query) => {
             hit_num += query.hits.length;
             return hit_num > 1;
         });
-    },
+    }
 
     /**
-     * Returns true if index should be shown in the sidebar. Index is shown
-     * only for 2 and 8 queries.
-     */
-    shouldShowIndex: function () {
+   * 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: function () {
+   * 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) {
@@ -415,52 +397,53 @@ var Report = React.createClass({
                 $this.off('mouseup mousemove', handler);
             });
         });
-    },
+    }
 
     /* Handling the fa icon when Hit Table is collapsed */
-    toggleTable: function () {
-        $('body').on('mousedown', '.resultn > .section-content > .table-hit-overview > .caption', function (event) {
-            var $this = $(this);
-            $this.on('mouseup mousemove', function handler(event) {
-                $this.find('i').toggleClass('fa-minus-square-o fa-plus-square-o');
-                $this.off('mouseup mousemove', handler);
-            });
-        });
-    },
-
-
+    toggleTable() {
+        $('body').on(
+            'mousedown',
+            '.resultn > .section-content > .table-hit-overview > .caption',
+            function (event) {
+                var $this = $(this);
+                $this.on('mouseup mousemove', function handler(event) {
+                    $this.find('i').toggleClass('fa-minus-square-o fa-plus-square-o');
+                    $this.off('mouseup mousemove', handler);
+                });
+            }
+        );
+    }
 
     /**
-     * Affixes the sidebar.
-     */
-    affixSidebar: function () {
+   * Affixes the sidebar.
+   */
+    affixSidebar() {
         var $sidebar = $('.sidebar');
         var sidebarOffset = $sidebar.offset();
         if (sidebarOffset) {
             $sidebar.affix({
                 offset: {
-                    top: sidebarOffset.top
-                }
+                    top: sidebarOffset.top,
+                },
             });
         }
-    },
+    }
 
     /**
-     * For the query in viewport, highlights corresponding entry in the index.
-     */
-    setupScrollSpy: function () {
-        $('body').scrollspy({target: '.sidebar'});
-    },
+   * For the query in viewport, highlights corresponding entry in the index.
+   */
+    setupScrollSpy() {
+        $('body').scrollspy({ target: '.sidebar' });
+    }
 
     /**
-     * Event-handler when hit is selected
-     * Adds glow to hit component.
-     * Updates number of Fasta that can be downloaded
-     */
-    selectHit: function (id) {
-
+   * Event-handler when hit is selected
+   * Adds glow to hit component.
+   * Updates number of Fasta that can be downloaded
+   */
+    selectHit(id) {
         var checkbox = $('#' + id);
-        var num_checked  = $('.hit-links :checkbox:checked').length;
+        var num_checked = $('.hit-links :checkbox:checked').length;
 
         if (!checkbox || !checkbox.val()) {
             return;
@@ -475,17 +458,15 @@ var Report = React.createClass({
             $hit.next('.hsp').addClass('glow');
             $('.download-fasta-of-selected').enable();
             $('.download-alignment-of-selected').enable();
-        }
-        else {
+        } else {
             $hit.removeClass('glow');
             $hit.next('.hsp').removeClass('glow');
         }
 
         var $a = $('.download-fasta-of-selected');
         var $b = $('.download-alignment-of-selected');
-        
-        if (num_checked >= 1)
-        {
+
+        if (num_checked >= 1) {
             $a.find('.text-bold').html(num_checked);
             $b.find('.text-bold').html(num_checked);
         }
@@ -494,7 +475,72 @@ var Report = React.createClass({
             $a.addClass('disabled').find('.text-bold').html('');
             $b.addClass('disabled').find('.text-bold').html('');
         }
-    },
-});
+    }
+    populate_hsp_array(hit, query_id){
+        return hit.hsps.map(hsp => Object.assign(hsp, {hit_id: hit.id, query_id}));
+    }
+
+    prepareAlignmentOfSelectedHits() {
+        var sequence_ids = $('.hit-links :checkbox:checked').map(function () {
+            return this.value;
+        }).get();
+
+        if(!sequence_ids.length){
+            // remove attributes from link if sequence_ids array is empty
+            $('.download-alignment-of-selected').attr('href', '#').removeAttr('download');
+            return;
+
+        }
+        if(this.state.alignment_blob_url){
+            // always revoke existing url if any because this method will always create a new url
+            window.URL.revokeObjectURL(this.state.alignment_blob_url);
+        }
+        var hsps_arr = [];
+        var aln_exporter = new AlignmentExporter();
+        const self = this;
+        _.each(this.state.queries, _.bind(function (query) {
+            _.each(query.hits, function (hit) {
+                if (_.indexOf(sequence_ids, hit.id) != -1) {
+                    hsps_arr = hsps_arr.concat(self.populate_hsp_array(hit, query.id));
+                }
+            });
+        }, this));
+        const filename = 'alignment-' + sequence_ids.length + '_hits.txt';
+        const blob_url = aln_exporter.prepare_alignments_for_export(hsps_arr, filename);
+        // set required download attributes for link
+        $('.download-alignment-of-selected').attr('href', blob_url).attr('download', filename);
+        // track new url for future removal
+        this.setState({alignment_blob_url: blob_url});
+    }
+
+    prepareAlignmentOfAllHits() {
+        // Get number of hits and array of all hsps.
+        var num_hits = 0;
+        var hsps_arr = [];
+        if(!this.state.queries.length){
+            return;
+        }
+        this.state.queries.forEach(
+            (query) => query.hits.forEach(
+                (hit) => {
+                    num_hits++;
+                    hsps_arr = hsps_arr.concat(this.populate_hsp_array(hit, query.id));
+                }
+            )
+        );
+
+        var aln_exporter = new AlignmentExporter();
+        var file_name = `alignment-${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() {
+        return this.isResultAvailable() ? this.resultsJSX() : this.loadingJSX();
+    }
+}
 
-React.render(<Page/>, document.getElementById('view'));
+export default Report;