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-rwxr-xr-xwqflask/wqflask/correlation_matrix/show_corr_matrix.py2
-rwxr-xr-xwqflask/wqflask/do_search.py13
-rwxr-xr-xwqflask/wqflask/static/packages/bootstrap/css/bootstrap.css30
-rwxr-xr-xwqflask/wqflask/static/packages/bootstrap/css/docs.css14
-rw-r--r--wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css4
-rwxr-xr-xwqflask/wqflask/templates/base.html4
-rwxr-xr-xwqflask/wqflask/templates/collections/view.html107
-rwxr-xr-xwqflask/wqflask/templates/index_page.html49
-rwxr-xr-xwqflask/wqflask/templates/new_security/login_user.html2
-rwxr-xr-xwqflask/wqflask/templates/search_result_page.html18
-rwxr-xr-xwqflask/wqflask/templates/whats_new.html13
11 files changed, 130 insertions, 126 deletions
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 8bd5919b..d734117e 100755
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -193,7 +193,7 @@ class CorrelationMatrix(object):
m = robjects.r.matrix(corr_results_to_list, nrow=len(cols))
eigen = base.eigen(m)
print("eigen:", eigen)
- #pca = stats.princomp(m, cor = "TRUE")
+ pca = stats.princomp(m, cor = "TRUE")
print("pca:", pca)
return pca
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index f9082495..fd7bd916 100755
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -96,7 +96,7 @@ class QuickMrnaAssaySearch(DoSearch):
class MrnaAssaySearch(DoSearch):
- """A search within an mRNA expression dataset"""
+ """A search within an expression dataset, including mRNA, protein, SNP, but not phenotype or metabolites"""
DoSearch.search_types['ProbeSet'] = "MrnaAssaySearch"
@@ -358,7 +358,7 @@ class RifSearch(MrnaAssaySearch):
def run(self):
where_clause = """( %s.symbol = GeneRIF_BASIC.symbol and
MATCH (GeneRIF_BASIC.comment)
- AGAINST ('+%s' IN BOOLEAN MODE)) """ % (self.dataset.type, self.search_term)
+ AGAINST ('+%s' IN BOOLEAN MODE)) """ % (self.dataset.type, self.search_term[0])
from_clause = ", GeneRIF_BASIC "
query = self.compile_final_query(from_clause, where_clause)
@@ -375,8 +375,8 @@ class WikiSearch(MrnaAssaySearch):
and GeneRIF.versionId=0 and GeneRIF.display>0
and (GeneRIF.comment REGEXP '%s' or GeneRIF.initial = '%s')
""" % (self.dataset.type,
- "[[:<:]]"+self.search_term[0]+"[[:>:]]",
- self.search_term[0])
+ "[[:<:]]"+str(self.search_term[0])+"[[:>:]]",
+ str(self.search_term[0]))
from_clause = ", GeneRIF "
query = self.compile_final_query(from_clause, where_clause)
@@ -390,7 +390,7 @@ class GoSearch(MrnaAssaySearch):
def run(self):
field = 'GOterm.acc'
- go_id = 'GO:' + ('0000000'+self.search_term)[-7:]
+ go_id = 'GO:' + ('0000000'+self.search_term[0])[-7:]
statements = ("""%s.symbol=GOgene_product.symbol and
GOassociation.gene_product_id=GOgene_product.id and
@@ -651,8 +651,9 @@ class PositionSearch(DoSearch):
self.dataset.type,
max(self.mb_min, self.mb_max))
- def real_run(self):
+ def run(self):
+ self.setup()
self.query = self.compile_final_query(where_clause = self.where_clause)
return self.execute(self.query)
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
index 0bf1f944..3dc73a7a 100755
--- a/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/bootstrap.css
@@ -1038,7 +1038,7 @@ h2,
.h2,
h3,
.h3 {
- margin-top: 20px;
+ margin-top: 10px;
margin-bottom: 10px;
}
h1 small,
@@ -1080,27 +1080,27 @@ h6 .small,
}
h1,
.h1 {
- font-size: 36px;
+ font-size: 30px;
}
h2,
.h2 {
- font-size: 30px;
+ font-size: 24px;
}
h3,
.h3 {
- font-size: 24px;
+ font-size: 18px;
}
h4,
.h4 {
- font-size: 18px;
+ font-size: 14px;
}
h5,
.h5 {
- font-size: 14px;
+ font-size: 12px;
}
h6,
.h6 {
- font-size: 12px;
+ font-size: 10px;
}
p {
margin: 0 0 10px;
@@ -2884,7 +2884,7 @@ fieldset[disabled] .btn-default.active {
}
.btn-primary {
color: #fff;
- background-color: #428bca;
+ background-color: #369;
border-color: #357ebd;
}
.btn-primary:hover,
@@ -3872,7 +3872,7 @@ select[multiple].input-group-sm > .input-group-btn > .btn {
}
.navbar {
position: relative;
- min-height: 50px;
+ min-height: 30px;
border: 1px solid transparent;
}
/*
@@ -3987,10 +3987,10 @@ select[multiple].input-group-sm > .input-group-btn > .btn {
}
.navbar-brand {
float: left;
- height: 50px;
- padding: 15px 15px;
- font-size: 18px;
- line-height: 20px;
+ height: 30px;
+ padding: 6px 15px;
+ font-size: 15px;
+ line-height: 18px;
}
.navbar-brand:hover,
.navbar-brand:focus {
@@ -4738,8 +4738,8 @@ a.thumbnail.active {
color: #333;
}
.alert {
- padding: 15px;
- margin-bottom: 20px;
+ padding: 10px;
+ margin-bottom: 5px;
border: 1px solid transparent;
border-radius: 4px;
}
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/docs.css b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
index ea4d6994..b95c44ed 100755
--- a/wqflask/wqflask/static/packages/bootstrap/css/docs.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/docs.css
@@ -27,7 +27,7 @@ h3 code {
-------------------------------------------------- */
body > .navbar {
- font-size: 14px;
+ font-size: 12px;
font-weight: bold;
}
@@ -98,16 +98,16 @@ hr.soften {
}
.jumbotron h1 {
- font-size: 80px;
+ font-size: 60px;
font-weight: bold;
letter-spacing: -1px;
line-height: 1;
}
.jumbotron p {
- font-size: 20px;
+ font-size: 15px;
font-weight: 300;
- line-height: 30px;
- margin-bottom: 30px;
+ line-height: 20px;
+ margin-bottom: 10px;
}
/* Link styles (used on .masthead-links as well) */
@@ -230,10 +230,10 @@ hr.soften {
border-bottom: 1px solid #ddd;
}
.subhead h1 {
- font-size: 40px;
+ font-size: 30px;
}
.subhead p {
- margin-bottom: 20px;
+ margin-bottom: 10px;
}
.subhead .navbar {
display: none;
diff --git a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css
index c3a11092..076b6dae 100644
--- a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css
+++ b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css
@@ -13,7 +13,7 @@ body {
/* Finesse the page header spacing */
.page-header {
- margin-bottom: 30px;
+ margin-bottom: 10px;
}
.page-header .lead {
margin-bottom: 10px;
@@ -68,7 +68,7 @@ body {
float: left;
}
.navbar-nav > li > a {
- padding: 15px;
+ padding: 5px;
}
/* Redeclare since we override the float above */
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 240481cc..3d4e6d28 100755
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -42,7 +42,6 @@
{% macro flash_me() -%}
{% with messages = get_flashed_messages(with_categories=true) %}
{% if messages %}
- <br />
<div class="container">
{% for category, message in messages %}
<div class="alert {{ category }}">{{ message }}</div>
@@ -72,7 +71,7 @@
<div>
<ul class="nav navbar-nav">
<li class="">
- <a href="/">Home</a>
+ <a href="/">Search</a>
</li>
<li class="">
<a href="/help">Help</a>
@@ -143,7 +142,6 @@
<a href="http://en.wikipedia.org/wiki/Linux">linux</a>,
<a href="http://www.python.org/">python</a> and good intentions.
</p>
- <p>Special thanks to CYP1A2 and AHR.</p>
<br />
<p>GeneNetwork is supported by:</p>
<UL>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 237a0d4e..3d777866 100755
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -1,5 +1,10 @@
{% extends "base.html" %}
{% block title %}View Collection{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+{% endblock %}
{% block content %}
<!-- Start of body -->
{% if uc %}
@@ -10,13 +15,7 @@
'This collection has {}.'.format(numify(trait_obs|count, "record", "records"))) }}
{% endif %}
<div class="container">
- <div class="page-header">
- <h1>Your Collection</h1>
- {% if uc %}
- <h2>{{ uc.name }}</h2>
- {% endif %}
-
- <div class="form-group">
+ <div>
{% if uc %}
<form action="/collections/delete" method="post">
{% if uc %}
@@ -51,40 +50,18 @@
<input type="submit" class="btn btn-primary" value="Heatmap" />
</div>
</form>
- </div>
-
- <!--
- <form action="/corr_matrix" method="post">
- {% if uc %}
- <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
- {% endif %}
- <input type="hidden" name="trait_list" id="trait_list" value= "
- {% for this_trait in trait_obs %}
- {{ this_trait.name }}:{{ this_trait.dataset.name }},
- {% endfor %}" >
- <input type="submit"
- class="btn btn-small"
- value="Correlation Matrix" />
- </form>
- <form action="/heatmap" method="post">
- {% if uc %}
- <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
- {% endif %}
- <input type="hidden" name="trait_list" id="trait_list" value= "
- {% for this_trait in trait_obs %}
- {{ this_trait.name }}:{{ this_trait.dataset.name }},
- {% endfor %}" >
- <input type="submit"
- class="btn btn-small"
- value="Heatmap" />
- </form>
- -->
</div>
-
-
- <div class="bs-docs-example">
- <table class="table table-hover" id='trait_table'>
+ <div>
+ <br />
+ <br />
+ <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>
+ <br />
+ <br />
+ <table class="table table-hover table-striped" id='trait_table'>
<thead>
<tr>
<th></th>
@@ -126,15 +103,7 @@
</tbody>
</table>
-
<br />
-
- <button class="btn" id="select_all"><i class="icon-ok"></i> Select All</button>
- <button class="btn" id="deselect_all"><i class="icon-remove"></i> Deselect All</button>
- <button class="btn" id="invert"><i class="icon-resize-vertical"></i> Invert</button>
- <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Add Record to Other Collection</button>
- <button class="btn" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Remove Record</button>
- <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
</div>
</div>
@@ -144,4 +113,48 @@
{% block js %}
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+ <script language="javascript" type="text/javascript">
+ $(document).ready( function () {
+ console.time("Creating table");
+ $('#trait_table').dataTable( {
+ "aoColumns": [
+ { "bSortable": false },
+ { "sType": "natural" },
+ { "sType": "natural",
+ "sWidth": "35%" },
+ { "sType": "natural",
+ "sWidth": "15%" },
+ { "sType": "cust-txt" },
+ { "sType": "natural",
+ "sWidth": "10%" },
+ { "sType": "natural",
+ "sWidth": "15%" },
+ { "sType": "cust-txt" }
+ ],
+ "columns": [
+ { "width": "50%" },
+ null,
+ null,
+ null,
+ null,
+ null
+ ],
+ "sDom": "ftir",
+ "iDisplayLength": -1,
+ "autoWidth": true,
+ "bLengthChange": true,
+ "bDeferRender": true,
+ "bSortClasses": false
+ } );
+ console.timeEnd("Creating table");
+ });
+
+ </script>
+
+
{% endblock %}
+
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 1caca702..adc004a5 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -16,7 +16,7 @@
{{ flash_me() }}
- <div class="row" style="width: 1200px !important;">
+ <div class="row" style="width: 1400px !important;">
<div class="col-xs-5 col-xs-5">
<section id="search">
@@ -72,15 +72,20 @@
</div>
<!-- GET ANY HELP -->
+ <div class="form-group">
+ <label for="tfor" class="col-xs-1 control-label" style="width: 65px !important;"></label>
+ <div class="col-xs-10 controls">
+ <p>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></p>
+ </div>
+ </div>
- <p>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></p>
- <!-- SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
+ <!-- SEARCH, MAKE DEFAULT -->
<div class="form-group">
@@ -90,9 +95,6 @@
<div class="col-xs-4 controls" style="width: 150px !important;">
<input id="make_default" type="submit" class="btn btn-default form-control" value="Make Default">
</div>
- <div class="col-xs-5 controls" style="width: 200px !important;">
- <input type="submit" class="btn btn-default form-control" value="Advanced Search">
- </div>
</div>
<input type="hidden" name="FormID" value="searchResult" class="form-control">
@@ -113,12 +115,16 @@
<p>To try them out copy these examples into the search field:</p>
<ul>
- <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
+ <!--<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>
+ linkage between 23 and 46.</li>-->
+
+ <li><b>MEAN=(15 16)</b> finds highly expressed genes (15 to 16 log2 units).</li>
+
+ <li><b>LRS=(23 46)</b> finds genes 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="http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank">
GeneRIF</a> links.</li>
@@ -127,7 +133,7 @@
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
+ <!--<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>
@@ -139,9 +145,10 @@
<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>
+ scores between 9 and 999.</li>-->
</ul>
</section>
+ <!--
<section id="tour-info">
<div class="page-header">
<h1>Tour and more info</h1>
@@ -167,6 +174,7 @@
and advice on their use and citation.</p>
</section>
+ -->
<section id="websites">
<div class="page-header">
@@ -214,17 +222,6 @@
<li><a href="http://genenetwork.epfl.ch/" target="_blank">
Switzerland</a> at the EPFL</li>
</ul>
- <h3>History and archive</h3>
-
- <p>The
- <a href="http://artemis.uthsc.edu" target="_blank">
- time machine</a>
- has earlier versions that correspond to specific publication dates.
- </p>
-
- <h3>The next generation</h3>
- <p>Try the <a href="http://alexandria.uthsc.edu/" target="_blank">
- development</a> site to explore experimental data and features.</p>
</section>
<!--<section id="getting-started">
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 61df445c..ecf8278c 100755
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -13,7 +13,7 @@
<h4>Don't have an account?</h4>
- <a href="/n/register" class="btn btn-info modalize">Create a new account</a>
+ <a href="/n/register" class="btn btn-primary modalize">Create a new account</a>
<hr />
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 5e63a237..055ab979 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -14,9 +14,15 @@
<input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
- <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a></p>
+ <p>We searched <a href="/dbdoc/{{dataset.fullname}}">{{ dataset.fullname }}</a>
+ to find all records that match
+ {% for word in search_terms %}
+ <strong>{{word.search_term[0]}}</strong> {% if not loop.last %} or {% endif %}
+ {% endfor %}.
+
+ </p>
- <p>To find all records that match:</p>
+ <!--
<ul>
{% if search_terms %}
<li>
@@ -26,9 +32,9 @@
</li>
{% endif %}
</ul>
+ -->
- <p>To study a record, click on its ID below.<br />
- Check records below and click Add button to add to selection.</p>
+ <p>To study a record, click on its ID below. Check records below and click Add button to add to selection.</p>
<div>
<br />
@@ -174,7 +180,7 @@
null,
null
],
- "sDom": "ftir",
+ "sDom": "tir",
"iDisplayLength": -1,
"autoWidth": true,
"bLengthChange": true,
@@ -205,7 +211,7 @@
null,
null
],
- "sDom": "ftir",
+ "sDom": "tir",
"iDisplayLength": -1,
"autoWidth": true,
"bLengthChange": true,
diff --git a/wqflask/wqflask/templates/whats_new.html b/wqflask/wqflask/templates/whats_new.html
index dca9e7b3..753c0d7d 100755
--- a/wqflask/wqflask/templates/whats_new.html
+++ b/wqflask/wqflask/templates/whats_new.html
@@ -3,25 +3,14 @@
{% block content %}
<!-- Start of body -->
- <TR>
- <TD bgColor=#eeeeee class="solidBorder">
- <Table width= "100%" cellSpacing=0 cellPadding=5><TR>
<!-- Body Start from Here -->
- <TD valign="top" height="200" width="100%" bgcolor="#eeeeee">
-
- <P class="title">Latest Updates and News from Genenetwork <A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P>
-
-
+ <P class="title">Latest Updates and News from Genenetwork </P>
{% for news_item in news_items %}
<h4>{{ news_item.title }} ({{ news_item.date }})</h4>
{{ news_item.details | safe }}
<br /><br />
{% endfor %}
- <p />
-
- </TD>
- </TR>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 16:04:43 +0000