sequenceserver 3.1.1 → 3.1.3

data/public/js/report.js

@@ -3,10 +3,8 @@ import React, { Component } from 'react';
 import _ from 'underscore';
 
 import Sidebar from './sidebar';
+import Hits from './hits';
 import Circos from './circos';
-import { ReportQuery } from './query';
-import Hit from './hit';
-import HSP from './hsp';
 import AlignmentExporter from './alignment_exporter';
 import ReportPlugins from 'report_plugins';
 
@@ -21,11 +19,6 @@ class Report extends Component {
         super(props);
         // Properties below are internal state used to render results in small
         // slices (see updateState).
-        this.numUpdates = 0;
-        this.nextQuery = 0;
-        this.nextHit = 0;
-        this.nextHSP = 0;
-        this.maxHSPs = 3; // max HSPs to render in a cycle
         this.state = {
             user_warning: null,
             download_links: [],
@@ -34,8 +27,8 @@ class Report extends Component {
             program: '',
             program_version: '',
             submitted_at: '',
-            queries: [],
             results: [],
+            queries: [],
             querydb: [],
             params: [],
             stats: [],
@@ -43,7 +36,6 @@ class Report extends Component {
             allQueriesLoaded: false,
             cloud_sharing_enabled: false,
         };
-        this.prepareAlignmentOfSelectedHits = this.prepareAlignmentOfSelectedHits.bind(this);
         this.prepareAlignmentOfAllHits = this.prepareAlignmentOfAllHits.bind(this);
         this.setStateFromJSON = this.setStateFromJSON.bind(this);
         this.plugins = new ReportPlugins(this);
@@ -58,31 +50,66 @@ class Report extends Component {
     }
 
     pollPeriodically(path, callback, errCallback) {
-        var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];
+    var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];
         function poll() {
-            $.getJSON(path).complete(function (jqXHR) {
-                switch (jqXHR.status) {
-                case 202:
-                    var interval;
-                    if (intervals.length === 1) {
-                        interval = intervals[0];
+            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 {
-                        interval = intervals.shift();
+                        console.error("Network error:", error);
                     }
-                    setTimeout(poll, interval);
-                    break;
-                case 200:
-                    callback(jqXHR.responseJSON);
-                    break;
-                case 400:
-                case 422:
-                case 500:
-                    errCallback(jqXHR.responseJSON);
-                    break;
-                }
-            });
+                });
         }
 
+        function parseJSON(str) {
+            let parsedJson = str;
+            try {
+                parsedJson = JSON.parse(str);
+            } catch (e) {
+                console.error("Error parsing JSON:", e);
+            }
+
+            return parsedJson;
+        }
         poll();
     }
 
@@ -113,139 +140,6 @@ class Report extends Component {
         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(prevProps, prevState) {
-        // 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) {
-            this.affixSidebar();
-        }
-
-        // Queue next update if we have not rendered all results yet.
-        if (this.nextQuery < this.state.queries.length) {
-            // setTimeout is used to clear call stack and space out
-            // the updates giving the browser a chance to respond
-            // to user interactions.
-            setTimeout(() => this.updateState(), 25);
-        } else {
-            this.componentFinishedUpdating();
-        }
-
-        this.plugins.componentDidUpdate(prevProps, prevState);
-    }
-
-    /**
-   * Push next slice of results to React for rendering.
-   */
-    updateState() {
-        var results = [];
-        var numHSPsProcessed = 0;
-        while (this.nextQuery < this.state.queries.length) {
-            var query = this.state.queries[this.nextQuery];
-
-            // We may see a query multiple times during rendering because only
-            // 3 hsps 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(
-                    <ReportQuery
-                        key={'Query_' + query.id}
-                        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(...this.plugins.queryResults(query));
-            }
-
-            while (this.nextHit < query.hits.length) {
-                var hit = query.hits[this.nextHit];
-                // We may see a hit multiple times during rendering because only
-                // 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}
-                            onChange={this.prepareAlignmentOfSelectedHits}
-                            {...this.props}
-                        />
-                    );
-                }
-
-                while (this.nextHSP < hit.hsps.length) {
-                    // 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}
-                        />
-                    );
-                    numHSPsProcessed++;
-                    if (numHSPsProcessed == this.maxHSPs) break;
-                }
-                // Are we here because we have iterated over all hsps of a hit,
-                // or because of the break clause in the inner loop?
-                if (this.nextHSP == hit.hsps.length) {
-                    this.nextHit = this.nextHit + 1;
-                    this.nextHSP = 0;
-                }
-                if (numHSPsProcessed == this.maxHSPs) break;
-            }
-
-            // Are we here because we have iterated over all hits of a query,
-            // or because of the break clause in the inner loop?
-            if (this.nextHit == query.hits.length) {
-                this.nextQuery = this.nextQuery + 1;
-                this.nextHit = 0;
-            }
-            if (numHSPsProcessed == this.maxHSPs) break;
-        }
-
-        // Push the components to react for rendering.
-        this.numUpdates++;
-        this.lastTimeStamp = Date.now();
-        this.setState({
-            results: this.state.results.concat(results),
-            veryBig: this.numUpdates >= 250,
-        });
-    }
-
     /**
    * Called after all results have been rendered.
    */
@@ -282,6 +176,7 @@ class Report extends Component {
         );
     }
 
+    /* eslint-disable */
     /**
    * Return results JSX.
    */
@@ -300,12 +195,20 @@ class Report extends Component {
                 <div className="col-md-9">
                     {this.overviewJSX()}
                     {this.circosJSX()}
-                    {this.plugins.generateStats()}
+                    {this.plugins.generateStats(this.state.queries)}
                     {this.state.results}
+                    <Hits
+                        state={this.state}
+                        componentFinishedUpdating={(_) => this.componentFinishedUpdating(_)}
+                        populate_hsp_array={this.populate_hsp_array.bind(this)}
+                        plugins={this.plugins}
+                        {...this.props}
+                    />
                 </div>
             </div>
         );
     }
+    /* eslint-enable */
 
 
     warningJSX() {
@@ -477,20 +380,7 @@ class Report extends Component {
         );
     }
 
-    /**
-   * Affixes the sidebar.
-   */
-    affixSidebar() {
-        var $sidebar = $('.sidebar');
-        var sidebarOffset = $sidebar.offset();
-        if (sidebarOffset) {
-            $sidebar.affix({
-                offset: {
-                    top: sidebarOffset.top,
-                },
-            });
-        }
-    }
+
 
     /**
    * For the query in viewport, highlights corresponding entry in the index.
@@ -499,84 +389,10 @@ class Report extends Component {
         $('body').scrollspy({ target: '.sidebar' });
     }
 
-    /**
-   * 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;
-
-        if (!checkbox || !checkbox.val()) {
-            return;
-        }
-
-        var $hit = $(checkbox.data('target'));
-
-        // Highlight selected hit and enable 'Download FASTA/Alignment of
-        // selected' links.
-        if (checkbox.is(':checked')) {
-            $hit.addClass('glow');
-            $hit.next('.hsp').addClass('glow');
-            $('.download-fasta-of-selected').enable();
-            $('.download-alignment-of-selected').enable();
-        } else {
-            $hit.removeClass('glow');
-            $hit.next('.hsp').removeClass('glow');
-            $('.download-fasta-of-selected').attr('href', '#').removeAttr('download');
-        }
-
-        var $a = $('.download-fasta-of-selected');
-        var $b = $('.download-alignment-of-selected');
-
-        if (num_checked >= 1) {
-            $a.find('.text-bold').html(num_checked);
-            $b.find('.text-bold').html(num_checked);
-        }
-
-        if (num_checked == 0) {
-            $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;

data/public/js/report_root.js

@@ -17,6 +17,8 @@ class Page extends Component {
         this.showErrorModal = this.showErrorModal.bind(this);
         this.getCharacterWidth = this.getCharacterWidth.bind(this);
         this.hspChars = createRef();
+        this.sequenceModal = createRef();
+        this.errorModal = createRef();
     }
     componentDidMount() {
         var job_id = location.pathname.split('/').pop();
@@ -24,11 +26,11 @@ class Page extends Component {
     }
 
     showSequenceModal(url) {
-        this.refs.sequenceModal.show(url);
+        this.sequenceModal.current.show(url);
     }
 
     showErrorModal(errorData, beforeShow) {
-        this.refs.errorModal.show(errorData, beforeShow);
+        this.errorModal.current.show(errorData, beforeShow);
     }
 
     getCharacterWidth() {
@@ -60,11 +62,11 @@ class Page extends Component {
                 <canvas id="png-exporter" hidden></canvas>
 
                 <SequenceModal
-                    ref="sequenceModal"
+                    ref={this.sequenceModal}
                     showErrorModal={(...args) => this.showErrorModal(...args)}
                 />
 
-                <ErrorModal ref="errorModal" />
+                <ErrorModal ref={this.errorModal} />
             </div>
         );
     }
@@ -72,4 +74,4 @@ class Page extends Component {
 
 
 const root = createRoot(document.getElementById('view'));
-root.render(<Page />);
+root.render(<Page />);

data/public/js/search.js

@@ -1,32 +1,49 @@
-import "./jquery_world";
-import React, { Component } from "react";
-import { createRoot } from "react-dom/client";
-import { DnD } from "./dnd";
-import { Form } from "./form";
-import { SearchHeaderPlugin } from "search_header_plugin";
+import './jquery_world';
+import React, { Component } from 'react';
+import { createRoot } from 'react-dom/client';
+import { DnD } from './dnd';
+import { Form } from './form';
+import { SearchHeaderPlugin } from 'search_header_plugin';
 
 /**
  * Clear sessionStorage on reload.
  */
-if (performance.navigation.type == performance.navigation.TYPE_RELOAD) {
+const navigationEntry = performance.getEntriesByType('navigation')[0];
+if (navigationEntry && navigationEntry.type === 'reload') {
   sessionStorage.clear();
   history.replaceState(null, "", location.href.split("?")[0]);
 }
 
 class Page extends Component {
+  constructor(props) {
+    super(props);
+    this.dnd = React.createRef();
+    this.form = React.createRef();
+  }
+
   componentDidMount() {
-    this.refs.dnd.setState({ query: this.refs.form.refs.query });
+    this.dnd.current.setState({ query: this.form.current.query.current })
   }
+
   render() {
     return (
       <div>
         <SearchHeaderPlugin />
-        <DnD ref="dnd" />
-        <Form ref="form" />
+        <DnD ref={this.dnd} />
+        <Form ref={this.form} />
       </div>
     );
   }
 }
 
-const root = createRoot(document.getElementById("view"));
+const root = createRoot(document.getElementById('view'));
 root.render(<Page />);
+
+document.addEventListener('DOMContentLoaded', () => {
+    const closeButton = document.querySelector('.js--close-help');
+    if (closeButton) {
+        closeButton.addEventListener('click', function() {
+            document.querySelector('[data-help-modal]').classList.add('hidden');
+        });
+    }
+});