From 7f91c87c21e32ccd36ea73607c4038016684a5e5 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 21 Jun 2016 10:50:00 +0000
Subject: Menu: re-introduce old menu

---
 .../new/javascript/dataset_select_menu_orig.js     | 156 +++++++++++
 wqflask/wqflask/templates/index_page_orig.html     | 285 +++++++++++++++++++++
 2 files changed, 441 insertions(+)
 create mode 100644 wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
 create mode 100755 wqflask/wqflask/templates/index_page_orig.html

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 %}
-- 
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