sequenceserver 1.1.0.beta5 → 1.1.0.beta6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: be938473a96a624d49f6f1d6cca850ada57f3995
-  data.tar.gz: 5bdc65f1b01dcc252bf5a005d667146c9a17336f
+  metadata.gz: da64719d5d51834a93bd4071cf01f7dd9f45dfce
+  data.tar.gz: 071fa0cfc1d276a53d613b43fab36e85180a3e8e
 SHA512:
-  metadata.gz: f64187ebc30bfc0f065a546e86e85f9731bfd86f625b48147a93035349a12807de7f19ce80be5a6a59c04894b0a344d25fa83d98fbb86d7c01809c90faf23dbe
-  data.tar.gz: 82b4a22069f4116551ea7d98ed62624d5ba9cdb190305db9f36426cbef8a7caea95849366273158a328a43d902d15c0bd4797568d76021bc603ef947fa484d7b
+  metadata.gz: 6f5486cf92ad273fd348fcd3d2dbcf4656b6bccd70f4040e2013e787b4ee68cd9c2d0c26473eb21a4ba2c0eb0d240d6f2f955110cd3f1442ddb37df94a8f5fc9
+  data.tar.gz: bdaf284e009ee77987e2c89652fcdbe3501d783c5cdb0a568dac29535072dde48db28c716b6371ee6eb2dd31cdac364954033a58d886ce2b9eb9d30f941943cf

data/lib/sequenceserver/blast/job.rb

@@ -36,7 +36,7 @@ module SequenceServer
       def raise!
         return true if exitstatus == 0
 
-        stderr = File.readlines(this.stderr)
+        stderr = File.readlines(self.stderr)
         if exitstatus == 1 # error in query sequence or options; see [1]
           error = stderr.grep(ERROR_LINE)
           error = stderr if error.empty?

data/lib/sequenceserver/database.rb

@@ -215,7 +215,7 @@ module SequenceServer
         default = 0
         print 'Enter taxid (optional): '
         user_response = STDIN.gets.strip
-        user_response && Integer(user_response) || default
+        user_response.empty? && default || Integer(user_response)
       rescue
         puts 'taxid should be a number'
         retry

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '1.1.0.beta5'
+  VERSION = '1.1.0.beta6'
 end

data/public/js/alignmentsoverview.js

@@ -10,7 +10,7 @@ class Graph {
   }
 
   static className() {
-    return 'alignment-overview collapse in';
+    return 'alignment-overview';
   }
 
   static collapseId(props) {
@@ -22,9 +22,10 @@ class Graph {
   }
 
   constructor($svgContainer, props) {
-    $queryDiv = $svgContainer.parents('.resultn')
-    hits = this.extractData(props.query.hits, props.query.number)
-    this.graphIt($queryDiv, $svgContainer, 0, 20, null, hits);
+      this.svg_container = $svgContainer;
+      $queryDiv = $svgContainer.parents('.resultn');
+      hits = this.extractData(props.query.hits, props.query.number);
+      this.graphIt($queryDiv, $svgContainer, 0, 20, null, hits);
   }
 
   extractData(query_hits, number) {
@@ -50,13 +51,10 @@ class Graph {
   }
 
   setupTooltip() {
-    $('[data-toggle="tooltip"]').tooltip({
-        'placement': 'top',
-        'container': 'body',
-        'html': 'true',
-        'delay': 0,
-        'white-space': 'nowrap'
-    });
+      this.svg_container.find('[data-toggle="tooltip"]').tooltip({
+          'placement': 'top', 'container': 'body', 'html': 'true',
+          'delay': 0, 'white-space': 'nowrap'
+      });
   }
 
   setupClick($graphDiv) {
@@ -67,18 +65,6 @@ class Graph {
     });
   }
 
-  setupResponsiveness($queryDiv, $graphDiv, index, opts, hits) {
-    var currentWidth = $(window).width();
-    var debounced_draw = _.debounce(_.bind(function () {
-        if (currentWidth !== $(window).width()) {
-            var shownHits = $queryDiv.find('.ghit > g').length;
-            this.graphIt($queryDiv, $graphDiv, shownHits, index, opts, hits);
-            currentWidth = $(window).width();
-        }
-    },this), 125);
-    $(window).resize(debounced_draw);
-  }
-
   graphControls($queryDiv, $graphDiv, isInit, opts, hits) {
     var MIN_HITS_TO_SHOW = 20;
 
@@ -393,8 +379,6 @@ class Graph {
     // been drawn for first time.
     if (index === 0) {
         this.graphControls($queryDiv, $graphDiv, true, opts, inhits);
-        // Redraw the SVG on a browser resize...
-        // this.setupResponsiveness($queryDiv, $graphDiv, index, opts, inhits);
     }
     // Refresh tooltip each time graph is redrawn.
     this.setupTooltip();

data/public/js/grapher.js

@@ -64,9 +64,11 @@ export default function Grapher(Graph) {
         }
 
         svgContainerJSX () {
+            var cssClasses = Graph.className() + ' svg-container collapse';
+            if (!this.state.collapsed) cssClasses += ' in';
             return (
                 <div ref="svgContainer" id={this.collapseId()}
-                    className={"svg-container " + Graph.className()}>
+                    className={cssClasses}>
                 </div>
             );
         }

data/public/js/lengthdistribution.js

@@ -13,7 +13,7 @@ class Graph {
   }
 
   static className() {
-    return 'length-distribution collapse in';
+    return 'length-distribution';
   }
 
   static collapseId(props) {
@@ -31,11 +31,6 @@ class Graph {
 
     this._margin = {top: 30, right: 25, bottom: 55, left: 12.5};
     this.initiate($svg_container.width(), $svg_container.height());
-    var test = $('#Collapse_length_'+props.query.number);
-    test.removeClass('in');
-    test.parent().find('.caption').find('i').
-        removeClass('fa-minus-square-o').addClass('fa-plus-square-o');
-    test.parent().find('.graph-links').hide();
   }
 
   initiate(width, height) {
@@ -80,13 +75,10 @@ class Graph {
   }
 
   setupTooltip() {
-    $('[data-toggle="tooltip"]').tooltip({
-      'placement': 'top',
-      'container': 'body',
-      'html': 'true',
-      'delay': 0,
-      'white-space': 'nowrap'
-    });
+      this.svg_container.find('[data-toggle="tooltip"]').tooltip({
+          'placement': 'top', 'container': 'body', 'html': 'true',
+          'delay': 0, 'white-space': 'nowrap'
+      });
   }
 
   setupResponsiveness() {

data/public/js/report.js

@@ -10,7 +10,7 @@ import GraphicalOverview from './alignmentsoverview';
 //import Kablammo from './kablammo';
 import './sequence';
 import AlignmentExporter from './alignment_exporter';
-//import LengthDistribution from './lengthdistribution';
+import LengthDistribution from './lengthdistribution';
 import Circos from './circos';
 
 
@@ -677,14 +677,9 @@ var Query = React.createClass({
                 </div>
                 {this.numhits() &&
                     (
-                        <div
-                            className="section-content">
-
-                            <GraphicalOverview key={"GO_"+this.props.query.number} query={this.props.query} program={this.props.data.program}/>
-
-                            {/*
-                            <LengthDistribution key={"LD_"+this.props.query.id} query={this.props.query} algorithm={this.props.data.program}/>
-                            */}
+                        <div className="section-content">
+                            <GraphicalOverview key={"GO_"+this.props.query.number} query={this.props.query} program={this.props.data.program} collapsed={this.props.data.veryBig}/>
+                            <LengthDistribution key={"LD_"+this.props.query.id} query={this.props.query} algorithm={this.props.data.program} collapsed="true"/>
                             <HitsTable key={"HT_"+this.props.query.number} query={this.props.query}/>
                             <div
                                 id="hits">
@@ -796,16 +791,12 @@ var SideBar = React.createClass({
     render: function () {
         return (
             <div className="sidebar">
-                { this.showIndex() && this.index() }
+                { this.props.shouldShowIndex && this.index() }
                 { this.downloads() }
             </div>
         )
     },
 
-    showIndex: function () {
-        return this.props.data.queries.length <= 8;
-    },
-
     index: function () {
         return (
             <div className="index">
@@ -986,35 +977,22 @@ var Report = React.createClass({
 
     // Internal helpers. //
 
-    /**
-     * Fetch results.
-     */
-    fetch_results: function () {
-        var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];
+    // Life-cycle methods. //
 
-        $.getJSON(location.pathname + '.json')
-        .complete(_.bind(function (jqXHR) {
-            switch (jqXHR.status) {
-            case 202:
-                var interval;
-                if (intervals.length === 1) {
-                    interval = intervals[0];
-                }
-                else {
-                    interval = intervals.shift;
-                }
-                setTimeout(this.fetch_results, interval);
-                break;
-            case 200:
-                this.setState(jqXHR.responseJSON);
-                break;
-            case 404:
-            case 400:
-            case 500:
-                showErrorModal(jqXHR.responseJSON);
-                break;
-            }
-        }, this));
+    getInitialState: function () {
+        return {
+            search_id:       '',
+            program:         '',
+            program_version: '',
+            queries:         [],
+            querydb:         [],
+            params:          [],
+            stats:           []
+        };
+    },
+
+    render: function () {
+        return (this.isResultAvailable() ? this.resultsJSX() : this.loadingJSX());
     },
 
     /**
@@ -1027,17 +1005,9 @@ var Report = React.createClass({
     },
 
     /**
-     * Returns true if sidebar should be shown.
-     *
-     * Sidebar is not shown if there is only one query and there are no hits
-     * corresponding to the query.
+     * Returns loading message
      */
-    shouldShowSidebar: function () {
-        return !(this.state.queries.length == 1 &&
-                 this.state.queries[0].hits.length == 0);
-    },
-
-    loading: function () {
+    loadingJSX: function () {
         return (
             <div
                 className="row">
@@ -1063,6 +1033,59 @@ var Report = React.createClass({
         );
     },
 
+    /**
+     * Return results JSX.
+     */
+    resultsJSX: function () {
+        return (
+            <div className="row">
+                { this.shouldShowSidebar() &&
+                    (
+                        <div
+                            className="col-md-3 hidden-sm hidden-xs">
+                            <SideBar data={this.state} shouldShowIndex={this.shouldShowIndex()}/>
+                        </div>
+                    )
+                }
+                <div className={this.shouldShowSidebar() ?
+                    'col-md-9' : 'col-md-12'}>
+                    { this.overview() }
+                    <Circos queries={this.state.queries}
+                        program={this.state.program} collapsed="true"/>
+                    {
+                        _.map(this.state.queries, _.bind(function (query) {
+                            return (
+                                <Query key={"Query_"+query.id} query={query} data={this.state}
+                                    selectHit={this.selectHit}/>
+                                );
+                        }, this))
+                    }
+                </div>
+            </div>
+        );
+    },
+
+    /**
+     * Returns true if sidebar should be shown.
+     *
+     * Sidebar is not shown if there is only one query and there are no hits
+     * corresponding to the query.
+     */
+    shouldShowSidebar: function () {
+        return !(this.state.queries.length == 1 &&
+                 this.state.queries[0].hits.length == 0);
+    },
+
+    /**
+     * Returns true if index should be shown in the sidebar.
+     *
+     * Index is not shown in the sidebar if there are more than eight queries
+     * in total.
+     */
+    shouldShowIndex: function () {
+        return this.state.queries.length <= 8;
+    },
+
     /**
      * Renders report overview.
      */
@@ -1095,36 +1118,79 @@ var Report = React.createClass({
         );
     },
 
+    componentDidMount: function () {
+        this.fetchResults();
+    },
+
     /**
-     * Renders results per query.
+     * Fetch results.
      */
-    results: function () {
-        return (
-            <div className="row">
-                { this.shouldShowSidebar() &&
-                    (
-                        <div
-                            className="col-md-3 hidden-sm hidden-xs">
-                            <SideBar data={this.state}/>
-                        </div>
-                    )
+    fetchResults: function () {
+        var intervals = [200, 400, 800, 1200, 2000, 3000, 5000];
+
+        $.getJSON(location.pathname + '.json')
+        .complete(_.bind(function (jqXHR) {
+            switch (jqXHR.status) {
+            case 202:
+                var interval;
+                if (intervals.length === 1) {
+                    interval = intervals[0];
                 }
-                <div className={this.shouldShowSidebar() ?
-                    'col-md-9' : 'col-md-12'}>
-                    { this.overview() }
-                    <Circos queries={this.state.queries}
-                        program={this.state.program} collapsed="true"/>
-                    {
-                        _.map(this.state.queries, _.bind(function (query) {
-                            return (
-                                <Query key={"Query_"+query.id} query={query} data={this.state}
-                                    selectHit={this.selectHit}/>
-                                );
-                        }, this))
-                    }
-                </div>
-            </div>
-        );
+                else {
+                    interval = intervals.shift;
+                }
+                setTimeout(this.fetchResults, interval);
+                break;
+            case 200:
+                this.updatePage(jqXHR.responseJSON);
+                break;
+            case 404:
+            case 400:
+            case 500:
+                showErrorModal(jqXHR.responseJSON);
+                break;
+            }
+        }, this));
+    },
+
+    updatePage: function(responseJSON) {
+        var queries = responseJSON.queries;
+
+        // Render results for first 50 queries and set flag if total queries is
+        // more than 250.
+        var numHits = 0;
+        responseJSON.veryBig = queries.length > 250;
+        //responseJSON.veryBig = !_.every(queries, (query) => {
+            //numHits += query.hits.length;
+            //return (numHits <= 500);
+        //});
+        responseJSON.queries = queries.splice(0, 50);
+        this.setState(responseJSON);
+
+        // Render results for remaining queries.
+        var update = function () {
+            if (queries.length > 0) {
+                this.setState({
+                    queries: this.state.queries.concat(queries.splice(0, 50))
+                });
+                setTimeout(update.bind(this), 500);
+            }
+            else {
+                this.componentFinishedUpdating();
+            }
+        };
+        setTimeout(update.bind(this), 500);
+    },
+
+    /**
+     * Locks Sidebar in its position, prevents folding of hits during
+     * text-selection, etc.
+     */
+    componentFinishedUpdating: function () {
+        this.affixSidebar();
+        this.shouldShowIndex() && this.setupScrollSpy();
+        this.setupHitSelection();
+        this.setupDownloadLinks();
     },
 
     /**
@@ -1191,57 +1257,19 @@ var Report = React.createClass({
             });
         });
     },
-
-    // Life-cycle methods. //
-
-    getInitialState: function () {
-        return {
-            search_id:       '',
-            program:         '',
-            program_version: '',
-            queries:         [],
-            querydb:         [],
-            params:          [],
-            stats:           []
-        };
-    },
-
-    render: function () {
-        return (this.isResultAvailable() && this.results() || this.loading());
-    },
-
-    componentDidMount: function () {
-        this.fetch_results();
-    },
-
-    /**
-     * Locks Sidebar in its position.
-     * Prevents folding of hits during text-selection
-     */
-    componentDidUpdate: function () {
-        this.affixSidebar();
-        this.setupScrollSpy();
-        this.setupHitSelection();
-        this.setupDownloadLinks();
-    }
 });
 
 var Page = React.createClass({
     render: function () {
         return (
             <div>
-                <div
-                    className="container">
+                <div className="container">
                     <Report ref="report"/>
                 </div>
 
-                <div
-                  id='circos-demo' className='modal'>
-                </div>
+                <div id='circos-demo' className='modal'></div>
 
-                <canvas
-                    id="png-exporter" hidden>
-                </canvas>
+                <canvas id="png-exporter" hidden></canvas>
             </div>
         );
     }