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-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js156
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html285
2 files changed, 441 insertions, 0 deletions
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
new file mode 100644
index 00000000..1fe4cf75
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
@@ -0,0 +1,156 @@
+// Generated by CoffeeScript 1.8.0
+$(function() {
+ var apply_default, check_search_term, dataset_info, group_info, make_default, open_window, populate_dataset, populate_group, populate_species, populate_type, process_json, redo_dropdown;
+ process_json = function(data) {
+ window.jdata = data;
+ populate_species();
+ return apply_default();
+ };
+ $.ajax('/static/new/javascript/dataset_menu_structure.json', {
+ dataType: 'json',
+ success: process_json
+ });
+ populate_species = function() {
+ var species_list;
+ species_list = this.jdata.species;
+ redo_dropdown($('#species'), species_list);
+ return populate_group();
+ };
+ window.populate_species = populate_species;
+ populate_group = function() {
+ var group_list, species;
+ console.log("in populate group");
+ species = $('#species').val();
+ group_list = this.jdata.groups[species];
+ redo_dropdown($('#group'), group_list);
+ return populate_type();
+ };
+ window.populate_group = populate_group;
+ populate_type = function() {
+ var group, species, type_list;
+ console.log("in populate type");
+ species = $('#species').val();
+ group = $('#group').val();
+ type_list = this.jdata.types[species][group];
+ redo_dropdown($('#type'), type_list);
+ return populate_dataset();
+ };
+ window.populate_type = populate_type;
+ populate_dataset = function() {
+ var dataset_list, group, species, type;
+ console.log("in populate dataset");
+ species = $('#species').val();
+ group = $('#group').val();
+ type = $('#type').val();
+ console.log("sgt:", species, group, type);
+ dataset_list = this.jdata.datasets[species][group][type];
+ console.log("pop_dataset:", dataset_list);
+ return redo_dropdown($('#dataset'), dataset_list);
+ };
+ window.populate_dataset = populate_dataset;
+ redo_dropdown = function(dropdown, items) {
+ var item, _i, _len, _results;
+ console.log("in redo:", dropdown, items);
+ dropdown.empty();
+ _results = [];
+ for (_i = 0, _len = items.length; _i < _len; _i++) {
+ item = items[_i];
+ if (item.length > 2){
+ _results.push(dropdown.append($("<option data-id=\""+item[0]+"\" />").val(item[1]).text(item[2])));
+ } else {
+ _results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
+ }
+ }
+ return _results;
+ };
+ $('#species').change((function(_this) {
+ return function() {
+ return populate_group();
+ };
+ })(this));
+ $('#group').change((function(_this) {
+ return function() {
+ return populate_type();
+ };
+ })(this));
+ $('#type').change((function(_this) {
+ return function() {
+ return populate_dataset();
+ };
+ })(this));
+ open_window = function(url, name) {
+ var options;
+ options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900";
+ return open(url, name, options).focus();
+ };
+ group_info = function() {
+ var group, species, url;
+ species = $('#species').val();
+ group = $('#group').val();
+ url = "/" + species + "Cross.html#" + group;
+ return open_window(url, "Group Info");
+ };
+ $('#group_info').click(group_info);
+ dataset_info = function() {
+ var dataset, url;
+ accession_id = $('#dataset option:selected').data("id");
+ url = "http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + accession_id;
+ return open_window(url, "Dataset Info");
+ };
+ $('#dataset_info').click(dataset_info);
+ make_default = function() {
+ var holder, item, jholder, _i, _len, _ref;
+ alert("The current settings are now your default.")
+ holder = {};
+ _ref = ['species', 'group', 'type', 'dataset'];
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ item = _ref[_i];
+ holder[item] = $("#" + item).val();
+ }
+ jholder = JSON.stringify(holder);
+ return $.cookie('search_defaults', jholder, {
+ expires: 365
+ });
+ };
+ apply_default = function() {
+ var defaults, item, populate_function, _i, _len, _ref, _results;
+ defaults = $.cookie('search_defaults');
+ if (defaults) {
+ defaults = $.parseJSON(defaults);
+ } else {
+ defaults = {
+ species: "mouse",
+ group: "BXD",
+ type: "Hippocampus mRNA",
+ dataset: "HC_M2_0606_P"
+ };
+ }
+ _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]];
+ _results = [];
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ item = _ref[_i];
+ $("#" + item[0]).val(defaults[item[0]]);
+ if (item[1]) {
+ populate_function = "populate_" + item[1];
+ console.log("Calling:", populate_function);
+ _results.push(window[populate_function]());
+ } else {
+ _results.push(void 0);
+ }
+ }
+ return _results;
+ };
+ check_search_term = function() {
+ var or_search_term, and_search_term;
+ or_search_term = $('#or_search').val();
+ and_search_term = $('#and_search').val();
+ console.log("or_search_term:", or_search_term);
+ console.log("and_search_term:", and_search_term);
+ if (or_search_term === "" && and_search_term === "") {
+ alert("Please enter one or more search terms or search equations.");
+ return false;
+ }
+ };
+ $("#make_default").click(make_default);
+ return $("#btsearch").click(check_search_term);
+});
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
new file mode 100755
index 00000000..9fba0e31
--- /dev/null
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -0,0 +1,285 @@
+{% extends "base.html" %}
+{% block title %}GeneNetwork{% endblock %}
+{% block content %}
+<!-- Start of body -->
+
+<!--
+ <header class="jumbotron subhead" id="overview">
+ <div class="container">
+ <h1>GeneNetwork</h1>
+ <p class="lead">Open source bioinformatics for systems genetics</p>
+ </div>
+ </header>
+-->
+
+ <div class="container-fluid">
+
+ {{ flash_me() }}
+
+ <div class="row" style="width: 1400px !important;">
+
+ <div class="col-xs-5">
+ <section id="search">
+ <div class="page-header">
+ <h1>Select and search</h1>
+ </div>
+ <form method="get" action="/search" name="SEARCHFORM">
+ <fieldset>
+ <div style="padding: 20px" class="form-horizontal">
+
+ <div class="form-group">
+ <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label>
+ <div class="col-xs-10 controls input-append" style="padding-right: 0px;">
+ <div class="col-xs-8">
+ <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select>
+ </div>
+ <div class="col-xs-4">
+ <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button>
+ </div>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label>
+ <div class="col-xs-10 controls input-append">
+ <div class="col-xs-8">
+ <select name="group" id="group" class="form-control span3" style="width: 280px !important;"></select>
+ <i class="icon-question-sign"></i>
+ </div>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label>
+ <div class="col-xs-10 controls">
+ <div class="col-xs-8">
+ <select name="type" id="type" class="form-control span3" style="width: 280px !important;"></select>
+ </div>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
+ <div class="col-xs-10 controls input-append">
+ <div class="col-xs-10">
+ <select name="dataset" id="dataset" class="form-control span5" style="width: 340px !important;"></select>
+ <i class="icon-question-sign"></i>
+ </div>
+ <div class="col-xs-2">
+ <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button>
+ </div>
+ </div>
+ </div>
+
+ <!-- USER HELP -->
+ <!--<p >Databases marked with <b>**</b>-->
+ <!-- suffix are not public yet.<br>-->
+ <!-- Access requires <a href="/account.html" target=-->
+ <!-- "_blank" class="fs14">user login</a>.</p>-->
+ <!-- GET ANY SEARCH -->
+
+ <div class="form-group">
+ <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
+ <div class="col-xs-10 controls">
+ <div class="col-xs-8">
+ <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
+ </div>
+ </div>
+ </div>
+
+ <!-- GET ANY HELP -->
+ <div class="form-group">
+ <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
+ <div class="col-xs-10 controls">
+ <div class="col-xs-12 controls">
+ Enter terms, genes, ID numbers in the <b>Search</b> field.<br>
+ Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br>
+ Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>.
+ </div>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
+ <div class="col-xs-10 controls">
+ <div class="col-xs-8">
+ <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
+ </div>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
+ <div class="col-xs-10 controls">
+ <div class="col-xs-2 controls" style="width: 100px !important;">
+ <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
+ </div>
+ </div>
+ </div>
+
+ <!-- SEARCH, MAKE DEFAULT -->
+
+ <div class="form-group">
+ </div>
+
+ <input type="hidden" name="FormID" value="searchResult" class="form-control">
+ <!--!<input type="hidden" name="RISet" value="BXD">-->
+ </div>
+ </fieldset>
+ </form>
+ </section>
+ <section id="advanced">
+ <div class="page-header">
+ <h2>Advanced commands</h2>
+ </div>
+
+ <p>You can also use advanced commands. Copy these simple examples into the Get Any or Combined search fields:</p>
+
+ <ul>
+ <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
+ chromosome 1 between 25 and 30 Mb.</li>
+
+ <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
+ highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a>
+ linkage between 23 and 46.</li>
+
+ <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF" target="_blank">
+ GeneRIF</a> links.</li>
+
+ <li><b>WIKI=nicotine</b> searches <a href="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank">
+ GeneWiki</a> for genes that you or other users have annotated
+ with the word <i>nicotine</i>.</li>
+
+ <li><b>GO:0045202</b> searches for synapse-associated genes listed in the
+ <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank">
+ Gene Ontology</a>.</li>
+
+ <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b>
+ finds synapse-associated genes with <a href="http://www.genenetwork.org/glossary.html#E" target="_blank">
+ cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores
+ between 9 and 999.</li>
+
+ <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
+ finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E" target="_blank">
+ trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
+ scores between 9 and 999.</li>
+ </ul>
+ </section>
+ </div>
+ <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;">
+ <!--
+ <section id="tour-info">
+ <div class="page-header">
+ <h1>Tour and more info</h1>
+ </div>
+
+ <h3>Thirty minute tour</h3>
+ <p>
+ Take the 30 minute
+ GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target="_blank" class="fs14">tour</a> that includes screen shots and
+ typical steps in the analysis.
+ </p>
+
+ <h3>Even more info</h3>
+ <p>
+ For information about
+ resources and methods, select the Info buttons next to the Group
+ and Database fields above.
+ </p>
+
+ <p>The <a href="/conditionsofUse.html" target="_blank">conditions</a>
+ and <a href="/statusandContact.html" target="_blank">contact
+ </a> pages have information on the status of data sets
+ and advice on their use and citation.</p>
+
+ </section>
+ -->
+
+ <section id="websites">
+ <div class="page-header">
+ <h1>Affiliates and mirrors</h1>
+ </div>
+ <h3>Websites affiliated with GeneNetwork</h3>
+ <ul>
+ <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
+ browser</a> at UTHSC</li>
+
+ <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
+ UTHSC</li>
+
+ <li>GeneNetwork 1 at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
+ Cloud (EC2)</a></li>
+
+ <li>GeneNetwork 1 Source Code at <a href="http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
+
+ <li>GeneNetwork 2 Source Code at <a href="https://github.com/genenetwork/genenetwork2" target="_blank">GitHub</a></li>
+ </ul>
+ <h3>GN1 Mirror and development sites</h3>
+
+ <ul>
+ <li><a href="http://www.genenetwork.org/" target="_blank">Main GN1 site at UTHSC</a> (main site)</li>
+ <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">Germany at the HZI</a></li>
+ <li><a href="http://genenetwork.memphis.edu/" target="_blank">Memphis at the U of M</a></li>
+ </ul>
+ </section>
+
+ <!--<section id="getting-started">
+ <div class="page-header">
+ <h1>Getting started</h1>
+ </div>
+
+ <ol style="font-size:12px;font-family:verdana;color:black">
+ <li>Select <b>Species</b> (or All)</li>
+
+ <li>Select <b>Group</b> (a specific sample)</li>
+
+ <li>Select <b>Type</b> of data:
+
+ <ul>
+ <li>Phenotype (traits)</li>
+
+ <li>Genotype (markers)</li>
+
+ <li>Expression (mRNAs)</li>
+ </ul>
+ </li>
+
+ <li>Select a <b>Dataset</b></li>
+
+ <li>Enter terms in the search field: words,
+ genes, ID numbers, probes, advanced search commands</li>
+
+ <li>Click the <b>Search</b> button</li>
+
+ <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
+ </ol>
+
+ <h3>User Guide</h3>
+ <h5>Read the
+ <a href="http://www.genenetwork.org/index4.html" target="_blank">
+ user guide</a>.</h5>
+
+ </section>-->
+ </div>
+ </div>
+ </div>
+
+{%endblock%}
+
+{% block js %}
+ <script src="/static/new/javascript/dataset_select_menu_orig.js"></script>
+
+ <script>
+ function pressed(e) {
+ // Has the enter key been pressed?
+ if ( (window.event ? event.keyCode : e.which) == 13) {
+ // If enter key has been pressed and the search fields are non-empty
+ // manually submit the <form>
+ if( event.target.value.trim() != "" ) {
+ document.forms[1].submit();
+ }
+ }
+ }
+ </script>
+
+{% endblock %}