Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

1 files changed, 267 insertions, 0 deletions

diff --git a/gn2/wqflask/templates/gsearch_gene.html b/gn2/wqflask/templates/gsearch_gene.html
new file mode 100644
index 00000000..6bc92377
--- /dev/null
+++ b/gn2/wqflask/templates/gsearch_gene.html
@@ -0,0 +1,267 @@
+{% extends "base.html" %}
+{% block title %}Search Results{% endblock %}
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+    <link href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css" rel="stylesheet" type="text/css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+
+    <div class="container">
+
+        <h3>GN searched for the term(s) <b>"{{ terms }}"</b> in 754 datasets and 39,765,944 traits across 10 species<br/>
+            and found <b>{{ trait_count }}</b> results that match your query.<br/>
+            You can filter these results by adding key words in the fields below<br/>
+            and you can also sort results on most columns.</h3>
+        <p>To study a record, click on its Record ID below.<br />Check records below and click Add button to add to selection.</p>
+
+        <div>
+            <br />
+            <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
+            <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
+            <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
+            <button class="btn btn-success" id="add" disabled ><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
+            <input type="text" id="searchbox" class="form-control" style="width: 180px; display: inline;" placeholder="Search This Table For ...">
+            <input type="text" id="select_top" class="form-control" style="width: 120px; display: inline;" placeholder="Select Top ...">
+            <form id="export_form" method="POST" action="/export_traits_csv" style="display: inline;">
+              <input type="hidden" name="headers" id="headers" value="{% for field in header_fields %}{{ field }},{% endfor %}">
+              <input type="hidden" name="database_name" id="database_name" value="None">
+              <input type="hidden" name="export_data" id="export_data" value="">
+              <button class="btn btn-default" id="export_traits">Download</button>
+            </form>
+            <br />
+            <br />
+            <div id="table_container" style="width: 2000px;">
+              <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;">
+                <tbody>
+                  <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
+                </tbody>
+              </table>
+            </div>
+        </div>
+    </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/table_functions.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/create_datatable.js"></script>
+
+    <script type='text/javascript'>
+      var getParams = function(url) {
+        let parser = document.createElement('a');
+        parser.href = url;
+        let params = parser.search.substring(1);
+        if(params.length > 0) {
+          return ('?'+params);
+        }
+        return params;
+      };
+    </script>
+
+    <script type='text/javascript'>
+      var traitsJson = {{ trait_list|safe }};
+    </script>
+
+    <script type="text/javascript" charset="utf-8">
+        $(document).ready( function () {
+            var tableId = "trait_table";
+
+            columnDefs = [
+              {
+                'orderDataType': "dom-checkbox",
+                'width': "5px",
+                'data': null,
+                'targets': 0,
+                'render': function(data) {
+                  return '<input type="checkbox" name="searchResult" class="trait_checkbox checkbox" value="' + data.hmac + '">'
+                }
+              },
+              {
+                'title': "Index",
+                'type': "natural",
+                'width': "30px",
+                'targets': 1,
+                'data': "index",
+                'defaultContent': "N/A"
+              },
+              {
+                'title': "Record",
+                'type': "natural",
+                'orderDataType': "dom-inner-text",
+                'width': "60px",
+                'data': null,
+                'targets': 2,
+                'render': function(data) {
+                  return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.name + '</a>'
+                }
+              },
+              {
+                'title': "Species",
+                'type': "natural",
+                'width': "60px",
+                'targets': 3,
+                'data': "species",
+                'defaultContent': "N/A"
+              },
+              {
+                'title': "Group",
+                'type': "natural",
+                'width': "150px",
+                'targets': 4,
+                'data': "group",
+                'defaultContent': "N/A"
+              },
+              {
+                'title': "Tissue",
+                'type': "natural",
+                'width': "150px",
+                'targets': 5,
+                'data': "tissue",
+                'defaultContent': "N/A"
+              },
+              {
+                'title': "Dataset",
+                'type': "natural",
+                'targets': 6,
+                'width': "320px",
+                'data': "dataset_fullname",
+                'defaultContent': "N/A"
+              },
+              {
+                'title': "Symbol",
+                'type': "natural",
+                'width': "60px",
+                'targets': 7,
+                'data': "symbol",
+                'defaultContent': "N/A"
+              },
+              {
+                'title': "Description",
+                'type': "natural",
+                'data': null,
+                'width': "120px",
+                'targets': 8,
+                'render': function(data) {
+                  try {
+                      return decodeURIComponent(escape(data.description))
+                  } catch(err) {
+                      return escape(data.description)
+                  }
+                }
+              },
+              {
+                'title': "Location",
+                'type': "natural-minus-na",
+                'width': "125px",
+                'targets': 9,
+                'data': "location_repr",
+                'defaultContent': "N/A"
+              },
+              {
+                'title': "Mean",
+                'type': "natural-minus-na",
+                'orderSequence': [ "desc", "asc"],
+                'width': "30px",
+                'targets': 10,
+                'data': null,
+                'defaultContent': "N/A",
+                'render': function(data) {
+                  if (data.mean > 100) {
+                    return Math.log2(data.mean).toFixed(3)
+                  } else {
+                    return data.mean
+                  }
+                }
+              },
+              {
+                'title': "<div style='text-align: right; padding-right: 10px;'>Peak</div> <div style='text-align: right;'>-logP <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a></div>",
+                'type': "natural-minus-na",
+                'width': "60px",
+                'targets': 11,
+                'data': "LRS_score_repr",
+                'defaultContent': "N/A",
+                'orderSequence': [ "desc", "asc"]
+              },
+              {
+                'title': "Peak Location",
+                'type': "natural-minus-na",
+                'width': "125px",
+                'targets': 12,
+                'data': "max_lrs_text",
+                'defaultContent': "N/A"
+              },
+              {
+                'title': "Additive<br>Effect<a href=\"{{ url_for('glossary_blueprint.glossary') }}#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                'type': "natural-minus-na",
+                'width': "50px",
+                'targets': 13,
+                'data': "additive",
+                'defaultContent': "N/A",
+                'orderSequence': [ "desc", "asc"]
+              }
+            ]
+
+            tableSettings = {
+              'createdRow': function ( row, data, index ) {
+                    $('td', row).eq(0).attr("style", "text-align: center; padding: 0px 10px 2px 10px;");
+                    $('td', row).eq(1).attr("align", "right");
+                    $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
+                    if ($('td', row).eq(4).text().length > 30) {
+                        $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 30));
+                        $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
+                    }
+                    $('td', row).eq(5).attr('title', $('td', row).eq(5).text());
+                    if ($('td', row).eq(5).text().length > 35) {
+                        $('td', row).eq(5).text($('td', row).eq(5).text().substring(0, 35));
+                        $('td', row).eq(5).text($('td', row).eq(5).text() + '...')
+                    }
+                    $('td', row).eq(6).attr('title', $('td', row).eq(6).text());
+                    if ($('td', row).eq(6).text().length > 60) {
+                        $('td', row).eq(6).text($('td', row).eq(6).text().substring(0, 60));
+                        $('td', row).eq(6).text($('td', row).eq(6).text() + '...')
+                    }
+                    $('td', row).eq(8).attr('title', $('td', row).eq(8).text());
+                    if ($('td', row).eq(8).text().length > 60) {
+                        $('td', row).eq(8).text($('td', row).eq(8).text().substring(0, 60));
+                        $('td', row).eq(8).text($('td', row).eq(8).text() + '...')
+                    }
+                    $('td', row).slice(10,14).attr("align", "right");
+                    $('td', row).eq(1).attr('data-export', $('td', row).eq(1).text());
+                    $('td', row).eq(2).attr('data-export', $('td', row).eq(2).text());
+                    $('td', row).eq(3).attr('data-export', $('td', row).eq(3).text());
+                    $('td', row).eq(4).attr('data-export', $('td', row).eq(4).text());
+                    $('td', row).eq(5).attr('data-export', $('td', row).eq(5).text());
+                    $('td', row).eq(6).attr('data-export', $('td', row).eq(6).text());
+                    $('td', row).eq(7).attr('data-export', $('td', row).eq(7).text());
+                    $('td', row).eq(8).attr('data-export', $('td', row).eq(8).text());
+                    $('td', row).eq(9).attr('data-export', $('td', row).eq(9).text());
+                    $('td', row).eq(10).attr('data-export', $('td', row).eq(10).text());
+                    $('td', row).eq(11).attr('data-export', $('td', row).eq(11).text());
+                    $('td', row).eq(12).attr('data-export', $('td', row).eq(12).text());
+                    $('td', row).eq(13).attr('data-export', $('td', row).eq(13).text());
+                },
+                {% if trait_count <= 20 %}
+                "scroller":  false
+                {% else %}
+                "scroller": true
+                {% endif %}
+            }
+
+            create_table(tableId, traitsJson, columnDefs, tableSettings);
+
+        });
+        
+    </script>
+{% endblock %}