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-rw-r--r--wqflask/wqflask/db_info.py127
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py10
-rw-r--r--wqflask/wqflask/static/new/css/marker_regression.css4
-rw-r--r--wqflask/wqflask/static/new/javascript/search_results.js22
-rw-r--r--wqflask/wqflask/templates/base.html4
-rw-r--r--wqflask/wqflask/templates/gsearch_gene.html16
-rw-r--r--wqflask/wqflask/templates/gsearch_pheno.html17
-rw-r--r--wqflask/wqflask/templates/info_page.html92
-rw-r--r--wqflask/wqflask/templates/mapping_results.html139
-rw-r--r--wqflask/wqflask/templates/search_result_page.html15
-rw-r--r--wqflask/wqflask/templates/tutorials.html1
-rw-r--r--wqflask/wqflask/user_login.py4
-rw-r--r--wqflask/wqflask/views.py13
13 files changed, 336 insertions, 128 deletions
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
new file mode 100644
index 00000000..f04e38bf
--- /dev/null
+++ b/wqflask/wqflask/db_info.py
@@ -0,0 +1,127 @@
+import httplib, urllib2
+import re
+
+from flask import Flask, g
+
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
+class InfoPage(object):
+ def __init__(self, start_vars):
+ self.info = None
+ self.gn_accession_id = None
+ if 'gn_accession_id' in start_vars:
+ self.gn_accession_id = start_vars['gn_accession_id']
+ self.info_page_name = start_vars['info_page_name']
+
+ self.get_info()
+ self.get_datasets_list()
+
+ def get_info(self, create=False):
+ query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " +
+ "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " +
+ "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " +
+ "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " +
+ "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " +
+ "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " +
+ "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " +
+ "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " +
+ "FROM InfoFiles " +
+ "LEFT JOIN Species USING (SpeciesId) " +
+ "LEFT JOIN Tissue USING (TissueId) " +
+ "LEFT JOIN InbredSet USING (InbredSetId) " +
+ "LEFT JOIN GeneChip USING (GeneChipId) " +
+ "LEFT JOIN AvgMethod USING (AvgMethodId) " +
+ "LEFT JOIN Datasets USING (DatasetId) " +
+ "LEFT JOIN Investigators USING (InvestigatorId) " +
+ "LEFT JOIN Organizations USING (OrganizationId) " +
+ "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
+
+ if self.gn_accession_id:
+ final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id)
+ results = g.db.execute(final_query).fetchone()
+ if self.info_page_name and not results:
+ final_query = query_base + "InfoPageName={}".format(self.info_page_name)
+ elif self.info_page_name:
+ final_query = query_base + "InfoPageName={}".format(self.info_page_name)
+ results = g.db.execute(final_query).fetchone()
+ else:
+ raise 'No correct parameter found'
+
+ if results:
+ self.info = process_query_results(results)
+
+ if (not results or len(results) < 1) and self.info_page_name and create:
+ insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name)
+ return self.get_info()
+
+ if not self.gn_accession_id and self.info:
+ self.gn_accession_id = self.info['accession_id']
+ if not self.info_page_name and self.info:
+ self.info_page_name = self.info['info_page_name']
+
+ def get_datasets_list(self):
+ self.filelist = []
+ try:
+ response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id)
+ data = response.read()
+
+ matches = re.findall(r"<tr>.+?</tr>", data, re.DOTALL)
+ for i, match in enumerate(matches):
+ if i == 0:
+ continue
+ cells = re.findall(r"<td.+?>.+?</td>", match, re.DOTALL)
+ full_filename = re.search(r"<a href=\"(.+?)\"", cells[1], re.DOTALL).group(1).strip()
+ filename = full_filename.split("/")[-1]
+ filesize = re.search(r">(.+?)<", cells[2]).group(1).strip()
+ filedate = "N/A" #ZS: Since we can't get it for now
+
+ self.filelist.append([filename, filedate, filesize])
+ except Exception, e:
+ pass
+
+def process_query_results(results):
+ info_ob = {
+ 'info_page_name': results[0],
+ 'accession_id': results[1],
+ 'menu_name': results[2],
+ 'taxonomy_id': results[3],
+ 'tissue_name': results[4],
+ 'group_name': results[5],
+ 'gene_chip_name': results[6],
+ 'geo_platform': results[7],
+ 'avg_method_name': results[8],
+ 'dataset_name': results[9],
+ 'geo_series': results[10],
+ 'publication_title': results[11],
+ 'dataset_status_name': results[12],
+ 'dataset_summary': results[13],
+ 'about_cases': results[14],
+ 'about_tissue': results[15],
+ 'about_data_processing': results[16],
+ 'acknowledgement': results[17],
+ 'experiment_design': results[18],
+ 'contributors': results[19],
+ 'citation': results[20],
+ 'notes': results[21],
+ 'investigator_firstname': results[22],
+ 'investigator_lastname': results[23],
+ 'investigator_address': results[24],
+ 'investigator_city': results[25],
+ 'investigator_state': results[26],
+ 'investigator_zipcode': results[27],
+ 'investigator_country': results[28],
+ 'investigator_phone': results[29],
+ 'investigator_email': results[30],
+ 'investigator_url': results[31],
+ 'organization_name': results[32],
+ 'investigator_id': results[33],
+ 'dataset_id': results[34],
+ 'dataset_status_is': results[35],
+ 'about_platform': results[36],
+ 'info_file_title': results[37],
+ 'specifics': results[38]
+ }
+
+ return info_ob
+ \ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 9bde343c..8a44b3fd 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -401,9 +401,7 @@ class RunMapping(object):
rs = marker['name'],
pos = this_ps
)
- #if 'p_value' in marker:
- # logger.debug("P EXISTS:", marker['p_value'])
- #else:
+
if 'lrs_value' in marker and marker['lrs_value'] > 0:
browser_marker['p_wald'] = 10**-(marker['lrs_value']/4.61)
elif 'lod_score' in marker and marker['lod_score'] > 0:
@@ -417,6 +415,12 @@ class RunMapping(object):
if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
highest_chr = marker['chr']
if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
+ if 'Mb' in marker.keys():
+ marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['Mb'])
+ elif 'cM' in marker.keys():
+ marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['cM'])
+ else:
+ marker['display_pos'] = "N/A"
self.qtl_results.append(marker)
with Bench("Exporting Results"):
diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css
index f1a26a83..e0a5ceea 100644
--- a/wqflask/wqflask/static/new/css/marker_regression.css
+++ b/wqflask/wqflask/static/new/css/marker_regression.css
@@ -62,6 +62,10 @@ table.dataTable tbody td {
padding: 4px 20px 2px 10px;
}
+table.dataTable tbody tr.selected {
+ background-color: #ffee99;
+}
+
table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td {
border-top: 1px solid #ccc;
border-right: 1px solid #ccc;
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 4e87d67a..685d6291 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -259,14 +259,16 @@ $(function() {
let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"]
let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"]
+ let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A
+
function sort_NAs(a, b, sort_function){
- if (a === "N/A" && b === "N/A") {
+ if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) {
return 0;
}
- if (a === "N/A"){
+ if (na_equivalent_vals.includes(a)){
return 1
}
- if (b === "N/A") {
+ if (na_equivalent_vals.includes(b)) {
return -1;
}
return sort_function(a, b)
@@ -281,4 +283,18 @@ $(function() {
}
});
+ $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col )
+ {
+ return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
+ return $('input', td).prop('checked') ? '1' : '0';
+ } );
+ };
+
+ $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col )
+ {
+ return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
+ return $(td).text();
+ } );
+ }
+
}); \ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 50562200..e6802cc4 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -4,7 +4,9 @@
<head>
<meta charset="utf-8">
- <title>{% block title %}{% endblock %}</title>
+
+ <title>{% block title %}{% endblock %} GeneNetwork 2</title>
+
<meta name="description" content="">
<meta name="author" content="">
<link rel="icon" type="image/png" sizes="64x64" href="/static/new/images/CITGLogo.png">
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 478d6f5f..d2c78d65 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -59,20 +59,6 @@
</script>
<script type="text/javascript" charset="utf-8">
- $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $('input', td).prop('checked') ? '1' : '0';
- } );
- };
-
- $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $(td).text();
- } );
- }
-
$(document).ready( function () {
$('#trait_table tr').click(function(event) {
@@ -252,7 +238,7 @@
'sDom': "pitirp",
'autoWidth': true,
'iDisplayLength': 500,
- 'deferRender': true,
+ 'deferRender': false,
'paging': true,
'orderClasses': true,
'processing': true,
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index eb998d15..c44231f3 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -59,20 +59,6 @@
</script>
<script type="text/javascript" charset="utf-8">
- $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $('input', td).prop('checked') ? '1' : '0';
- } );
- };
-
- $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $(td).text();
- } );
- }
-
$(document).ready( function () {
$('#trait_table tr').click(function(event) {
@@ -172,6 +158,7 @@
'title': "Record",
'type': "natural",
'data': null,
+ 'orderDataType': "dom-inner-text",
'render': function(data, type, row, meta) {
return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
}
@@ -252,7 +239,7 @@
'order': [[1, "asc" ]],
'sDom': "pitirp",
'autoWidth': false,
- 'deferRender': true,
+ 'deferRender': false,
'iDisplayLength': 500,
'paging': true,
'orderClasses': true,
diff --git a/wqflask/wqflask/templates/info_page.html b/wqflask/wqflask/templates/info_page.html
new file mode 100644
index 00000000..d8b7d74c
--- /dev/null
+++ b/wqflask/wqflask/templates/info_page.html
@@ -0,0 +1,92 @@
+{% extends "base.html" %}
+{% block title %}Policies{% endblock %}
+{% block content %}
+
+<h1 id="parent-fieldname-title">Data Set Group: {{ info.dataset_name }}
+<!--<a href="/infoshare/manager/member-studies-edit.html?DatasetId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>-->
+<span style="color:red;">{{ info.info_page_name }}</span>
+</h1>
+<table border="0" width="100%">
+<tr>
+<td valign="top" width="50%">
+<table name="info_table" cellSpacing=0 cellPadding=5 width=100% border=0>
+ <tr><td><b>Data Set:</b> {{ info.info_file_title }} <!--<a href="/infoshare/manager/member-infofile-edit.html?GN_AccesionId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>--></td></tr>
+ <tr><td><b>GN Accession:</b> GN{{ gn_accession_id }}</td></tr>
+ <tr><td><b>GEO Series:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_series }}" target="_blank">{{ info.geo_series }}</a></td></tr>
+ <tr><td><b>Title:</b> {{ info.publication_title }}</td></tr>
+ <tr><td><b>Organism:</b> <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id={{ info.taxonomy_id }}" target="_blank">{{ info.menu_name }}</a></td></tr>
+ <tr><td><b>Group:</b> {{ info.group_name }}</td></tr>
+ <tr><td><b>Tissue:</b> {{ info.tissue_name }}</td></tr>
+ <tr><td><b>Dataset Status:</b> {{ info.dataset_status_name }}</td></tr>
+ <tr><td><b>Platforms:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_platform }}" target="_blank">{{ info.gene_chip_name }}</a></td></tr>
+ <tr><td><b>Normalization:</b> {{ info.avg_method_name }}</td></tr>
+</table>
+</td>
+<td valign="top" width="50%">
+<table border="0" width="100%">
+ <tr>
+ <td><b>Contact Information</b></td>
+ </tr>
+ <tr>
+ <td>
+ {{ info.investigator_first_name }} {{ info.inveestigator_last_name }}<br>
+ {{ info.organization_name }} <br>
+ {{ info.investigator_address }}<br>
+ {{ info.investigator_city }}, {{ info.investigator_state }} {{ info.investigator_zipcode }} {{ info.investigator_country }}<br>
+ Tel. {{ info.investigator_phone }}<br>
+ {{ info.investigator_email }}<br>
+ <a href="{{ info.investigator_url }}" target="_blank">Website</a>
+ </td>
+ </tr>
+
+<tr>
+ <td><b>Download datasets and supplementary data files</b></td>
+</tr>
+<tr>
+ <td>
+ <ul style="line-height: 160%">
+ {% for file in filelist %}
+ <li><a href="http://datafiles.genenetwork.org/download/GN{{ gn_accession_id }}/{{ file[0] }}">{{ file[0] }} ({{ file[2] }})</a></li>
+ {% endfor %}
+ </ul>
+ </td>
+</tr>
+
+<tr><td>
+</td></tr>
+
+</table>
+</td>
+</tr>
+</table>
+<HR>
+<p>
+<table name="info_table" width="100%" border="0" cellpadding="5" cellspacing="0">
+<tr><td><span style="font-size:115%%;font-weight:bold;">Specifics of this Data Set:</span></td></tr>
+ <tr><td> {{ info.specifics|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%%;font-weight:bold;">Summary:</span></td></tr>
+ <tr><td> {{ info.dataset_summary|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">About the cases used to generate this set of data:</span></td></tr>
+ <tr><td> {{ info.about_cases|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">About the tissue used to generate this set of data:</span></td></tr>
+ <tr><td> {{ info.about_tissue|safe }}<br><br></td></tr>
+ <tr><td><span style="font-size:115%; font-weight:bold;">About the array platform:</span></td></tr>
+ <tr><td> {{ info.about_platform|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">About data values and data processing:</span></td></tr>
+ <tr><td> {{ info.about_data_processing|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Notes:</span></td></tr>
+ <tr><td> {{ info.notes|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Experiment Type:</span></td></tr>
+ <tr><td> {{ info.experiment_design|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Contributor:</span></td></tr>
+ <tr><td> {{ info.contributors|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Citation:</span></td></tr>
+ <tr><td> {{ info.citation|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Data source acknowledgment:</span></td></tr>
+ <tr><td> {{ info.acknowledgement|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Study Id:</span></td></tr>
+ <tr><td> {{ info.dataset_id }}<br><br></td></tr>
+</table>
+</p>
+
+{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 8edda548..41d760c0 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -228,71 +228,61 @@
<button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
<br />
<br />
- <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}500{% else %}470{% endif %}px;">
- <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer">
- <thead>
- <tr>
- <th></th>
- <th>Row</th>
- <th>Marker</th>
- <th>{{ LRS_LOD }}</th>
- <th>Chr</th>
- {% if plotScale != "physic" %}
- <th>cM</th>
- {% else %}
- <th align="right">Mb</th>
- {% endif %}
- {% if 'additive' in trimmed_markers[0] %}
- <th>Add Eff</th>
- {% endif %}
- {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %}
- <th>Dom Eff</th>
- {% endif %}
- </tr>
- </thead>
- <tbody>
- {% for marker in trimmed_markers %}
- <tr>
- <td align="center" style="padding: 1px 0px 1px 0px;">
- <input type="checkbox" name="selectCheck"
- class="checkbox trait_checkbox"
- value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}">
- </td>
- <td align="right">{{ loop.index }}</td>
- <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td>
- {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}
- {% if 'lod_score' in marker %}
- <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
- {% else %}
- <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td>
- {% endif %}
- {% else %}
- {% if 'lod_score' in marker %}
- <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td>
- {% else %}
- <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
- {% endif %}
- {% endif %}
- <td align="right">{{marker.chr}}</td>
- {% if plotScale != "physic" %}
- {% if 'cM' in marker %}
- <td align="right">{{ '%0.3f' | format(marker.cM|float) }}</td>
- {% else %}
- <td align="right">{{ '%0.3f' | format(marker.Mb|float) }}</td>
- {% endif %}
- {% else %}
- <td align="right">{{ '%0.6f' | format(marker.Mb|float) }}</td>
- {% endif %}
- {% if 'additive' in marker %}
- <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td>
- {% endif %}
- {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}
- <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td>
- {% endif %}
- </tr>
- {% endfor %}
- </tbody>
- </table>
+ <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;">
+ <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Row</th>
+ <th>Marker</th>
+ {% if LRS_LOD == "-log(p)" %}
+ <th>–log(p)</th>
+ {% else %}
+ <th>{{ LRS_LOD }}</th>
+ {% endif %}
+ <th>Position ({% if plotScale == "physic" %}Mb{% else %}cM{% endif %})</th>
+ {% if 'additive' in trimmed_markers[0] %}
+ <th>Add Eff</th>
+ {% endif %}
+ {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %}
+ <th>Dom Eff</th>
+ {% endif %}
+ </tr>
+ </thead>
+ <tbody>
+ {% for marker in trimmed_markers %}
+ <tr>
+ <td align="center" style="padding: 1px 0px 1px 0px;">
+ <input type="checkbox" name="selectCheck"
+ class="checkbox trait_checkbox"
+ value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}">
+ </td>
+ <td align="right">{{ loop.index }}</td>
+ <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td>
+ {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}
+ {% if 'lod_score' in marker %}
+ <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
+ {% else %}
+ <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td>
+ {% endif %}
+ {% else %}
+ {% if 'lod_score' in marker %}
+ <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td>
+ {% else %}
+ <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
+ {% endif %}
+ {% endif %}
+ <td align="right">{{ marker.display_pos }}</td>
+ {% if 'additive' in marker %}
+ <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td>
+ {% endif %}
+ {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}
+ <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td>
+ {% endif %}
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
</div>
</div>
{% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %}
@@ -362,8 +352,7 @@
"columns": [
{ "type": "natural", "width": "5%" },
{ "type": "natural", "width": "8%" },
- { "type": "natural", "width": "25%" },
- { "type": "natural" },
+ { "type": "natural", "width": "20%" },
{ "type": "natural" },
{ "type": "natural" }{% if 'additive' in qtlresults[0] %},
{ "type": "natural" }{% endif %}{% if 'dominance' in qtlresults[0] and dataset.group.genetic_type != "riset" %},
@@ -395,16 +384,16 @@
$('td', row).eq(9).attr("align", "right");
},
"columns": [
- { "bSortable": false},
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
+ { "orderDataType": "dom-checkbox" },
+ { "type": "natural"},
+ { "type": "natural" , "orderDataType": "dom-inner-text" },
+ { "type": "natural" , "orderDataType": "dom-inner-text" },
+ { "type": "natural" , "orderDataType": "dom-inner-text" },
{ "type": "natural" },
{ "type": "natural" },
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" , "orderDataType": "dom-inner-text" },
{ "type": "natural" }
],
"columnDefs": [ {
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 53373b41..282e752d 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -174,21 +174,6 @@
</script>
<script type="text/javascript" charset="utf-8">
-
- $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $('input', td).prop('checked') ? '1' : '0';
- } );
- };
-
- $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $(td).text();
- } );
- }
-
$(document).ready( function () {
$('#trait_table tr').click(function(event) {
diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html
index 3e6ef01c..f9d12ba5 100644
--- a/wqflask/wqflask/templates/tutorials.html
+++ b/wqflask/wqflask/templates/tutorials.html
@@ -15,3 +15,4 @@ and initial mapping results for Rat GWAS P50 as implemented in GeneNetwork.org</
</TR></TABLE>
{% endblock %}
+
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 9331f369..077a799b 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -453,7 +453,9 @@ def register_user(params):
user_details['confirmed'] = 1
user_details['registration_info'] = basic_info()
- save_user(user_details, user_details['user_id'])
+
+ if len(errors) == 0:
+ save_user(user_details, user_details['user_id'])
return errors
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index fc9949a8..3d623736 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -37,6 +37,7 @@ from wqflask import gsearch
from wqflask import update_search_results
from wqflask import docs
from wqflask import news
+from wqflask import db_info
from wqflask.submit_bnw import get_bnw_input
from base.data_set import create_dataset, DataSet # Used by YAML in marker_regression
from wqflask.show_trait import show_trait
@@ -908,12 +909,24 @@ def snp_browser_page():
return render_template("snp_browser.html", **template_vars.__dict__)
+@app.route("/db_info", methods=('GET',))
+def db_info_page():
+ template_vars = db_info.InfoPage(request.args)
+
+ return render_template("info_page.html", **template_vars.__dict__)
+
@app.route("/tutorial/WebQTLTour", methods=('GET',))
def tutorial_page():
#ZS: Currently just links to GN1
logger.info(request.url)
return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/")
+@app.route("/tutorial/security", methods=('GET',))
+def security_tutorial_page():
+ #ZS: Currently just links to GN1
+ logger.info(request.url)
+ return render_template("admin/security_help.html")
+
@app.route("/submit_bnw", methods=('POST',))
def submit_bnw():
logger.info(request.url)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 18:08:23 +0000