sequenceserver 3.0.1 → 3.1.1

data/public/js/grapher.js

@@ -2,6 +2,7 @@ import _ from 'underscore';
 import React, { createRef } from 'react';
 
 import './svgExporter'; // create handlers for SVG and PNG download buttons
+import CollapsePreferences from './collapse_preferences';
 
 // Each instance of Grapher is added to this object once the component has been
 // mounted. This is so that grapher can be iterated over and redrawn on window
@@ -16,22 +17,30 @@ export default function Grapher(Graph) {
     return class extends React.Component {
         constructor(props) {
             super(props);
-            this.state = { collapsed: Graph.canCollapse() && this.props.collapsed };
+            this.name = Graph.name();
+            this.collapsePreferences = new CollapsePreferences(this);
+            let isCollapsed = this.collapsePreferences.preferenceStoredAsCollapsed();
+            this.state = { collapsed: Graph.canCollapse() && (this.props.collapsed || isCollapsed) };
             this.svgContainerRef = createRef();
         }
 
-        collapseId() {
-            return Graph.collapseId(this.props);
+        graphId() {
+            return Graph.graphId(this.props);
         }
 
         render() {
-            var cssClasses = Graph.className() + ' grapher';
-            return (
-                <div ref="grapher" className={cssClasses}>
-                    {this.header()}
-                    {this.svgContainerJSX()}
-                </div>
-            );
+            // Do not render when Graph.name() is null
+            if (Graph.name() === null) {
+                return null;
+            } else {
+                var cssClasses = Graph.className() + ' grapher';
+                return (
+                    <div ref="grapher" className={cssClasses}>
+                        {this.header()}
+                        {this.svgContainerJSX()}
+                    </div>
+                );
+            }
         }
 
         header() {
@@ -39,10 +48,9 @@ export default function Grapher(Graph) {
                 return <div className="grapher-header">
                     <h4
                         className="caption"
-                        data-toggle="collapse"
-                        data-target={'#' + this.collapseId()}
+                        onClick={() => this.collapsePreferences.toggleCollapse()}
                     >
-                        {this.state.collapsed ? this.plusIcon() : this.minusIcon()}
+                        {this.collapsePreferences.renderCollapseIcon()}
               &nbsp;{Graph.name()}
                     </h4>
                     {!this.state.collapsed && this.graphLinksJSX()}
@@ -54,14 +62,6 @@ export default function Grapher(Graph) {
             }
         }
 
-        minusIcon() {
-            return <i className="fa fa-minus-square-o"></i>;
-        }
-
-        plusIcon() {
-            return <i className="fa fa-plus-square-o"></i>;
-        }
-
         graphLinksJSX() {
             return (
                 <div className="hit-links graph-links">
@@ -82,14 +82,14 @@ export default function Grapher(Graph) {
             return (
                 <div
                     ref={this.svgContainerRef}
-                    id={this.collapseId()}
+                    id={this.graphId()}
                     className={cssClasses}
                 ></div>
             );
         }
 
         componentDidMount() {
-            Graphers[this.collapseId()] = this;
+            Graphers[this.graphId()] = this;
 
             // Draw visualisation for the first time. Visualisations are
             // redrawn when browser window is resized.
@@ -129,17 +129,3 @@ $(window).resize(
         });
     }, 125)
 );
-
-// Swap-icon and toggle .graph-links on collapse.
-$('body').on('hidden.bs.collapse', '.collapse', function () {
-    var component = Graphers[$(this).attr('id')];
-    if (component) {
-        component.setState({ collapsed: true });
-    }
-});
-$('body').on('shown.bs.collapse', '.collapse', function () {
-    var component = Graphers[$(this).attr('id')];
-    if (component) {
-        component.setState({ collapsed: false });
-    }
-});

data/public/js/hits_overview.js

@@ -1,6 +1,6 @@
 import d3 from 'd3';
 import _ from 'underscore';
-import Grapher from './grapher';
+import Grapher from 'grapher';
 import * as Helpers from './visualisation_helpers';
 import Utils from './utils';
 
@@ -17,7 +17,7 @@ class Graph {
         return 'alignment-overview';
     }
 
-    static collapseId(props) {
+    static graphId(props) {
         return 'alignment_'+props.query.number;
     }
 

data/public/js/kablammo.js

@@ -1,6 +1,6 @@
 import d3 from 'd3';
 import _ from 'underscore';
-import Grapher from './grapher';
+import Grapher from 'grapher';
 import * as Helpers from './visualisation_helpers';
 
 /**
@@ -30,7 +30,7 @@ class Graph {
         return 'kablammo';
     }
 
-    static collapseId(props) {
+    static graphId(props) {
         return 'kablammo_'+props.query.number+'_'+props.hit.number;
     }
 

data/public/js/length_distribution.js

@@ -1,6 +1,6 @@
 import d3 from 'd3';
 import _ from 'underscore';
-import Grapher from './grapher';
+import Grapher from 'grapher';
 import * as Helpers from './visualisation_helpers';
 
 /**
@@ -20,7 +20,7 @@ class Graph {
         return 'length-distribution';
     }
 
-    static collapseId(props) {
+    static graphId(props) {
         return 'length_'+props.query.number;
     }
 
@@ -254,7 +254,7 @@ class Graph {
             .attr('dy', '0')
             .attr('transform','rotate(-90)');
 
-        var yContainer = this.svg.append('g')
+        this.svg.append('g')
             .attr('class','axis axis--y')
             .attr('transform','translate('+this._margin.left+',0)')
             .call(y_axis);

data/public/js/null_plugins/grapher/histogram.js

@@ -0,0 +1,25 @@
+import Grapher from 'grapher';
+
+class Graph {
+    static canCollapse() {
+        return false;
+    }
+
+    static name() {
+        return null;
+    }
+
+    static className() {
+        return null;
+    }
+
+    static dataName(_props) {
+        return null;
+    }
+
+    static graphId() {
+        return null;
+    }
+}
+
+export default Grapher(Graph);

data/public/js/null_plugins/options.js

@@ -0,0 +1,3 @@
+import { Options } from '../options';
+
+export { Options };

data/public/js/null_plugins/query_stats.js

@@ -0,0 +1,11 @@
+import React from 'react';
+
+class QueryStats extends React.Component{
+    render () {}
+
+    componentDidUpdate() {
+      console.log("Query stats:", this.props)
+    }
+}
+
+export default QueryStats;

data/public/js/null_plugins/report_plugins.js

@@ -1,3 +1,4 @@
+import Histogram from 'histogram';
 
 class ReportPlugins {
     constructor(parent) {
@@ -13,6 +14,10 @@ class ReportPlugins {
     queryResults(_query) {
         return [];
     }
+
+    generateStats() {
+        return (<Histogram />);
+    }
 }
 
-export default ReportPlugins;
+export default ReportPlugins;

data/public/js/null_plugins/search_header_plugin.js

@@ -0,0 +1,4 @@
+export const SearchHeaderPlugin = () => {
+    return '';
+};
+

data/public/js/options.js

@@ -3,80 +3,185 @@ import React, { Component } from 'react';
 export class Options extends Component {
     constructor(props) {
         super(props);
-        this.state = { preOpts: {}, value: '', method: '' };
-        this.updateBox = this.updateBox.bind(this);
-        this.optionsJSX = this.optionsJSX.bind(this);
-        this.showAdvancedOptions = this.showAdvancedOptions.bind(this);
+
+        this.state = {
+            textValue: '',
+            objectValue: this.defaultObjectValue(),
+            paramsMode: 'advanced'
+        };
+
+        this.onTextValueChanged = this.onTextValueChanged.bind(this);
+        this.optionsPresetsJSX = this.optionsPresetsJSX.bind(this);
+        this.advancedParamsJSX = this.advancedParamsJSX.bind(this);
+        this.showAdvancedOptionsHelp = this.showAdvancedOptionsHelp.bind(this);
+    }
+
+
+    defaultObjectValue() {
+        return {
+            max_target_seqs: '',
+            evalue: '',
+            task: ''
+        };
+    };
+
+    componentDidUpdate(prevProps) {
+        if (prevProps.predefinedOptions !== this.props.predefinedOptions) {
+            let defaultOptions = this.props.predefinedOptions.default || {attributes: []};
+            let advancedOptions = this.props.predefinedOptions['last search'] || defaultOptions || {attributes: []};
+            let initialTextValue = advancedOptions.attributes.join(' ').trim();
+            let parsedOptions = this.parsedOptions(initialTextValue);
+            this.setState({ textValue: initialTextValue, objectValue: parsedOptions});
+        }
+    }
+
+    onTextValueChanged(textValue) {
+        let parsedOptions = this.parsedOptions(textValue.toString());
+
+        this.setState({
+            textValue: textValue.toString(),
+            objectValue: parsedOptions
+        });
     }
 
-    updateBox(value) {
-        this.setState({ value: value });
+    parsedOptions(textValue) {
+        const words = textValue.split(" ");
+        let parsedOptions = this.defaultObjectValue();
+        // Iterate through the words in steps of 2, treating each pair as an option and its potential value
+        for (let i = 0; i < words.length; i += 2) {
+            // Ensure there is a pair available
+            if (words[i]) {
+                if (words[i].startsWith("-")) {
+                    const optionName = words[i].substring(1).trim();
+
+                    if (words[i + 1]) {
+                        // Use the second word as the value for this option
+                        parsedOptions[optionName] = words[i + 1];
+                    } else {
+                        // No value found for this option, set it to null or a default value
+                        parsedOptions[optionName] = null;
+                    }
+                }
+            }
+        }
+
+        return parsedOptions;
     }
 
+    optionsPresetsJSX() {
+        return (
+            <div id="options-presets" className="w-full">
+                { Object.keys(this.props.predefinedOptions).length > 1 && <>
+                    <h3 className="w-full font-medium border-b border-seqorange mb-2">Settings</h3>
+
+                    <p className="text-sm">Choose a predefined setting or customize BLAST parameters.</p>
+                    {this.presetListJSX()}
+                </>}
+            </div>
+        );
+    }
 
-    optionsJSX() {
-        return <span className="input-group-btn dropdown">
-            <button className="btn bnt-sm btn-default dropdown-toggle"
-                data-toggle="dropdown">
-                <i className="fa fa-caret-down"></i>
-            </button>
-            <ul id='advanced-params-dropdown'
-                className="dropdown-menu dropdown-menu-right">
+    presetListJSX() {
+        return (
+            <ul className="text-sm my-1">
                 {
-                    Object.entries(this.state.preOpts).map(
-                        ([key, value], index) => {
-                            value = value.join(' ');
-                            if (value.trim() === this.state.value.trim())
-                                var className = 'yellow-background';
-                            return <li key={index} className={className}
-                                onClick={() => this.updateBox(value)}>
-                                <strong>{key}:</strong>&nbsp;{value}
-                            </li>;
+                    Object.entries(this.props.predefinedOptions).map(
+                        ([key, config], index) => {
+                            let textValue = config.attributes.join(' ').trim();
+                            let description = config.description || textValue;
+
+                            return (
+                                <label key={index} className={`block w-full px-2 py-1 hover:bg-gray-200 cursor-pointer`}>
+                                    <input
+                                        type="radio"
+                                        name="predefinedOption"
+                                        value={textValue}
+                                        checked={textValue === this.state.textValue}
+                                        onChange={() => this.onTextValueChanged(textValue)}
+                                    />
+                                    <strong className="ml-2">{key}:</strong>&nbsp;{description}
+                                </label>
+                            );
                         }
                     )
                 }
             </ul>
-        </span>;
+        )
+    }
+
+    advancedParamsJSX() {
+        if (this.state.paramsMode !== 'advanced') {
+            return null;
+        }
+
+        let classNames = 'flex-grow block px-4 py-1 text-gray-900 border border-gray-300 rounded-lg bg-gray-50 text-base';
+
+        if (this.state.textValue) {
+            classNames += ' bg-yellow-100';
+        }
+
+        return(
+            <div className="w-full">
+                <div className="flex items-end">
+                    <label className="flex items-center" htmlFor="advanced">
+                        Advanced parameters
+                    </label>
+
+                    {this.props.blastMethod &&
+                        <button
+                            className="text-seqblue ml-2"
+                            type="button"
+                            onClick={this.showAdvancedOptionsHelp}
+                            data-toggle="modal" data-target="#help">
+                            See available options
+                            <i className="fa fa-question-circle ml-1 w-3 h-4 fill-current"></i>
+                        </button>
+                    }
+
+                    {!this.props.blastMethod &&
+                        <span className="text-gray-600 ml-2 text-sm hidden sm:block">
+                            Select databases and fill in the query to see options.
+                        </span>
+                    }
+                </div>
+
+                <div className='flex-grow flex w-full'>
+                    <input type="text" className={classNames}
+                        onChange={e => this.onTextValueChanged(e.target.value)}
+                        id="advanced"
+                        name="advanced"
+                        value={this.state.textValue}
+                        placeholder="eg: -evalue 1.0e-5 -num_alignments 100"
+                        title="View, and enter advanced parameters."
+                    />
+                </div>
+                <div className="text-sm text-gray-600 mt-2">
+                    Options as they would appear in a command line when calling BLAST eg: <i>-evalue 1.0e-5 -num_alignments 100</i>
+                </div>
+            </div>
+        )
     }
-    showAdvancedOptions(e) {
+
+    showAdvancedOptionsHelp(e) {
         const ids = ['blastn', 'tblastn', 'blastp', 'blastx', 'tblastx'];
-        const method = this.state.method.toLowerCase();
+        const method = this.props.blastMethod.toLowerCase();
         // hide options for other algorithms and only show for selected algorithm
         for (const id of ids) {
-            $(`#${id}`)[id === method ? 'show' : 'hide']();
+            if (id === method) {
+                document.getElementById(id).classList.remove('hidden')
+            } else {
+                document.getElementById(id).classList.add('hidden');
+            }
         }
+        document.querySelector('[data-help-modal]').classList.remove('hidden')
     }
+
     render() {
-        var classNames = 'form-control';
-        if (this.state.value.trim()) {
-            classNames += ' yellow-background';
-        }
         return (
-            <div className="col-md-7">
-                <div className="form-group">
-                    <div className="col-md-12">
-                        <div className="input-group">
-                            <label className="control-label" htmlFor="advanced">
-                                Advanced parameters:
-                                {/* only show link to advanced parameters if blast method is known */}
-                                {this.state.method && <sup style={{ marginLeft: '2px' }}>
-                                    <a href=''
-                                        onClick={this.showAdvancedOptions}
-                                        data-toggle="modal" data-target="#help">
-                                        <i className="fa fa-question-circle"></i>
-                                    </a>
-                                </sup>}
-                            </label>
-                            <input type="text" className={classNames}
-                                onChange={e => this.updateBox(e.target.value)}
-                                id="advanced" name="advanced" value={this.state.value}
-                                placeholder="eg: -evalue 1.0e-5 -num_alignments 100"
-                                title="View, and enter advanced parameters."
-                            />
-                            {Object.keys(this.state.preOpts).length > 1 && this.optionsJSX()}
-                        </div>
-                    </div>
-                </div>
+            <div className="flex-grow flex flex-col items-start sm:items-center space-y-4">
+                {this.optionsPresetsJSX()}
+
+                {this.advancedParamsJSX()}
             </div>
         );
     }