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-rwxr-xr-xbin/genenetwork292
-rw-r--r--etc/VERSION2
-rw-r--r--etc/default_settings.py2
-rw-r--r--wqflask/__init__.py1
-rw-r--r--wqflask/run_gunicorn.py19
-rw-r--r--wqflask/runserver.py2
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py10
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py17
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json24
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js1
-rw-r--r--wqflask/wqflask/templates/loading.html18
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html22
-rw-r--r--wqflask/wqflask/templates/show_trait.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html31
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html174
-rw-r--r--wqflask/wqflask/views.py3
-rw-r--r--wqflask/wsgi.py4
17 files changed, 295 insertions, 129 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index ccd9b1d9..34fbc72e 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -1,8 +1,11 @@
#! /bin/bash
#
+# This is the startup script for GN2. It sets the environment variables to pick
+# up a Guix profile and allows for overriding parameters.
+#
# Typical usage
#
-# env GN2_PROFILE=~/opt/genenetwork2-phewas ./bin/genenetwork2
+# env GN2_PROFILE=~/opt/genenetwork2-phewas ./bin/genenetwork2 ~/my_settings.py
#
# Where GN2_PROFILE points to the GNU Guix profile used for deployment.
#
@@ -22,8 +25,26 @@
# a -c switch, e.g.
#
# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py
+#
+# For development you may want to run
+#
+# env GN2_PROFILE=~/opt/gn-latest-guix WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2
+#
+# For staging and production we use gunicorn. Run with something like
+# (note you have to provide the server port). Provide a settings file!
+#
+# env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-prod
+#
+# For development use
+#
+# env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev
+#
+# For extra flexibility you can also provide gunicorn parameters yourself with something like
+#
+# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -gunicorn "--bind 0.0.0.0:5003 --workers=1 wsgi"
-SCRIPT=$(readlink -f "$0")
+SCRIPT=$(realpath "$0")
+echo SCRIPT=$SCRIPT
GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT"))
GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR)
@@ -42,15 +63,27 @@ else
fi
echo GN_VERSION=$GN_VERSION
+if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then
+ echo "Can not use $1 switch without default settings file"
+ exit 1
+fi
# Handle settings parameter (can be .py or .json)
-settings=$1
+if [ ! -z $1 ]; then
+ settings=$(realpath "$1")
+ if [ ! -e $settings ]; then
+ settings=$GN2_BASE_DIR/etc/default_settings.py
+ else
+ shift
+ fi
+fi
+
ext="${settings##*.}"
-if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then
+if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
overrides=$settings
- settings=$GN2_BASE_DIR/etc/default_settings.py
else
- shift
+ echo $settings
fi
+
if [ ! -e $settings ]; then
echo "ERROR: can not locate settings file - pass it in the command line"
exit 1
@@ -72,6 +105,8 @@ if [ -z $GN2_PROFILE ] ; then
if [ -d $GN2_PROFILE ]; then
echo "Best guess is $GN2_PROFILE"
fi
+ echo "ERROR: always set GN2_PROFILE"
+ exit 1
fi
if [ -z $GN2_PROFILE ]; then
read -p "PRESS [ENTER] TO CONTINUE..."
@@ -91,6 +126,9 @@ else
export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis"
export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
+ if [ ! -d $PYTHONPATH ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi
+ if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi
+ if [ ! -d $GEM_PATH ] ; then echo "GEM_PATH not valid "$GEM_PATH ; exit 1 ; fi
fi
if [ -z $PYTHONPATH ] ; then
echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!"
@@ -116,14 +154,50 @@ set|grep guix
set|grep $GN2_PROFILE
set|grep TMPDIR
-# Now handle command parameter -c
+# Now handle command parameter -c which runs python
if [ "$1" = '-c' ] ; then
cd $GN2_BASE_DIR/wqflask
cmd=${2#wqflask/}
echo PYTHONPATH=$PYTHONPATH
echo RUNNING COMMAND $cmd
python $cmd
- exit 0
+ exit $?
+fi
+# Now handle command parameter -cli which runs in bash
+if [ "$1" = "-cli" ] ; then
+ echo "HERE"
+ cd $GN2_BASE_DIR/wqflask
+ cmd=$2
+ echo PYTHONPATH=$PYTHONPATH
+ echo RUNNING COMMAND $cmd
+ $cmd
+ exit $?
+fi
+if [ "$1" = '-gunicorn' ] ; then
+ cd $GN2_BASE_DIR/wqflask
+ cmd=$2
+ echo PYTHONPATH=$PYTHONPATH
+ echo RUNNING gunicorn $cmd
+ gunicorn $cmd
+ exit $?
+fi
+if [ "$1" = '-gunicorn-dev' ] ; then
+ cd $GN2_BASE_DIR/wqflask
+ echo PYTHONPATH=$PYTHONPATH
+ if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
+ cmd="--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload wsgi"
+ echo RUNNING gunicorn $cmd
+ gunicorn $cmd
+ exit $?
+fi
+if [ "$1" = '-gunicorn-prod' ] ; then
+ cd $GN2_BASE_DIR/wqflask
+ echo PYTHONPATH=$PYTHONPATH
+ if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
+ cmd="--bind 0.0.0.0:$SERVER_PORT --workers=32 --max-requests 1000 --timeout 1200 wsgi"
+ echo RUNNING gunicorn $cmd
+ gunicorn $cmd
+ exit $?
fi
echo "Starting the redis server:"
@@ -132,7 +206,7 @@ dbfilename gn2.rdb
" | redis-server - &
# Overrides for packages that are not yet public (currently r-auwerx)
-export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
+# export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
# Start the flask server running GN2
cd $GN2_BASE_DIR/wqflask
diff --git a/etc/VERSION b/etc/VERSION
index b624c74a..ca9e199c 100644
--- a/etc/VERSION
+++ b/etc/VERSION
@@ -1 +1 @@
-2.10rc5
+2.11-rc1
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 59e22f1a..699d21f1 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -27,7 +27,7 @@ import sys
GN_VERSION = open("../etc/VERSION","r").read()
SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
SQL_ALCHEMY_POOL_RECYCLE = 3600
-GN_SERVER_URL = "http://localhost:8880/"
+GN_SERVER_URL = "http://localhost:8880/" # REST API server
# ---- Flask configuration (see website)
TRAP_BAD_REQUEST_ERRORS = True
diff --git a/wqflask/__init__.py b/wqflask/__init__.py
index 315b709e..e69de29b 100644
--- a/wqflask/__init__.py
+++ b/wqflask/__init__.py
@@ -1 +0,0 @@
-from wqflask import app
diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py
new file mode 100644
index 00000000..14a2d689
--- /dev/null
+++ b/wqflask/run_gunicorn.py
@@ -0,0 +1,19 @@
+# Run with gunicorn, see ./bin/genenetwork2 for an example
+#
+# Run standalone with
+#
+# ./bin/genenetwork2 ./etc/default_settings.py -c run_gunicorn.py
+
+# from flask import Flask
+# application = Flask(__name__)
+
+print "Starting up Gunicorn process"
+
+from wqflask import app
+
+@app.route("/gunicorn")
+def hello():
+ return "<h1 style='color:blue'>Hello There!</h1>"
+
+if __name__ == "__main__":
+ app.run(host='0.0.0.0')
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 50f134db..a0c76e51 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -1,5 +1,7 @@
# Starts the webserver with the ./bin/genenetwork2 command
#
+# This uses Werkzeug WSGI, see ./run_gunicorn.py for the alternative
+#
# Please note, running with host set externally below combined with
# debug mode is a security risk unless you have a firewall setup, e.g.
#
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index bcb14451..087b95b4 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -79,6 +79,16 @@ class MarkerRegression(object):
self.samples.append(sample)
self.vals.append(value)
+ #ZS: Check if genotypes exist in the DB in order to create links for markers
+ if "geno_db_exists" in start_vars:
+ self.geno_db_exists = start_vars['geno_db_exists']
+ else:
+ try:
+ geno_dataset = data_set.create_dataset(self.dataset.group.name + "Geno")
+ self.geno_db_exists = "True"
+ except:
+ self.geno_db_exists = "False"
+
self.mapping_method = start_vars['method']
if "results_path" in start_vars:
self.mapping_results_path = start_vars['results_path']
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 93bd9d42..211cf187 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -174,6 +174,8 @@ class MarkerRegression(object):
if 'genofile_string' in start_vars:
self.genofile_string = start_vars['genofile_string']
+ self.geno_db_exists = start_vars['geno_db_exists']
+
#Needing for form submission when doing single chr mapping or remapping after changing options
self.samples = start_vars['samples']
self.vals = start_vars['vals']
@@ -576,7 +578,7 @@ class MarkerRegression(object):
self.gifmap = gifmap.__str__()
self.filename= webqtlUtil.genRandStr("Itvl_")
- intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='jpeg')
+ intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='png')
intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap')
#Scales plot differently for high resolution
@@ -616,7 +618,7 @@ class MarkerRegression(object):
else:
showLocusForm = intImg
- if self.permChecked and self.nperm > 0 and not self.multipleInterval and 0 < self.nperm:
+ if (self.permChecked and self.nperm > 0) and not (self.multipleInterval and 0 < self.nperm):
self.perm_filename = self.drawPermutationHistogram()
#perm_text_file = self.permutationTextFile()
@@ -1200,8 +1202,10 @@ class MarkerRegression(object):
if self.controlLocus and self.doControl != "false":
string2 = 'Using %s as control' % self.controlLocus
else:
- if self.mapping_method == "gemma":
+ if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
string2 = 'Using GEMMA mapping method with no control for other QTLs.'
+ elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
+ string2 = 'Using R/qtl mapping method with no control for other QTLs.'
elif self.mapping_method == "plink":
string2 = 'Using PLINK mapping method with no control for other QTLs.'
else:
@@ -1963,6 +1967,8 @@ class MarkerRegression(object):
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
LRS_LOD_Max = max(self.significant, LRS_LOD_Max)
+ else:
+ LRS_LOD_Max = 1.15*LRS_LOD_Max
#genotype trait will give infinite LRS
LRS_LOD_Max = min(LRS_LOD_Max, webqtlConfig.MAXLRS)
@@ -2164,10 +2170,7 @@ class MarkerRegression(object):
# Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max
if self.manhattan_plot == True:
- if previous_chr_as_int % 2 == 1:
- point_color = pid.grey
- else:
- point_color = pid.black
+ point_color = pid.black
canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=point_color, font=symbolFont)
else:
LRSCoordXY.append((Xc, Yc))
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 8de85a86..b7ebb9ed 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -2974,6 +2974,20 @@
]
]
},
+ "BXD-Harvested": {
+ "Liver mRNA": [
+ [
+ "843",
+ "UTHSC-BXD-Harv_Liv-0118",
+ "UTHSC BXD Harvested Liver RNA-Seq (Jan18) Log2 **"
+ ],
+ [
+ "842",
+ "UTHSC-BXD-Liv-0917",
+ "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **"
+ ]
+ ]
+ },
"BXD300": {
"Genotypes": [
[
@@ -3864,6 +3878,10 @@
"BXD Bone"
],
[
+ "BXD-Harvested",
+ "BXD NIA Longevity Study"
+ ],
+ [
"BXD300",
"BXD300"
],
@@ -5007,6 +5025,12 @@
"Phenotypes"
]
],
+ "BXD-Harvested": [
+ [
+ "Liver mRNA",
+ "Liver mRNA"
+ ]
+ ],
"BXD300": [
[
"Phenotypes",
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 2f1d836a..4d98f5d8 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -245,6 +245,7 @@
//$("#static_progress_bar_container").modal();
url = "/loading";
$('input[name=method]').val("gemma_bimbam");
+ $('input[name=num_perm]').val(0);
$('input[name=genofile]').val($('#genofile_gemma').val());
$('input[name=maf]').val($('input[name=maf_gemma]').val());
form_data = $('#trait_data_form').serialize();
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index cede0e86..46136ddb 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -1,20 +1,20 @@
<title>Loading Mapping Results</title>
<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
-<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/non-responsive.css" />
-<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
-<link rel="stylesheet" type="text/css" href="/static/packages/colorbox/example4/colorbox.css" />
-<link rel="stylesheet" type="text/css" href="/static/new/css/main.css" />
<form method="post" action="/marker_regression" name="loading_form" id="loading_form" class="form-horizontal">
{% for key, value in start_vars.iteritems() %}
<input type="hidden" name="{{ key }}" value="{{ value }}">
{% endfor %}
<div class="container">
- <div class="row">
- <div style="margin-left: 46%; margin-right: 50%; min-height: 100vh; display: flex; align-items: center;">
- <h1>Loading&nbsp;Mapping&nbsp;Results...</h1>
+ <div>
+ <div style="min-height: 80vh; display: flex; align-items: center;">
+ <div class="center-block" style="margin-left: 38%; margin-right: 38%; position: absolute; height:50px; width:24%; top:40%;">
+ <h1>Loading&nbsp;Mapping&nbsp;Results...</h1>
+ </div>
</div>
- <div class="progress center-block" style="margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
- <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div>
+ <div style="min-height: 80vh; display: flex; align-items: center;">
+ <div class="progress center-block" style="margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
+ <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div>
+ </div>
</div>
</div>
</div>
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index d13c68cd..08a934a6 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -15,6 +15,7 @@
<input type="hidden" name="trait_id" value="{{ this_trait.name }}">
<input type="hidden" name="dataset" value="{{ dataset.name }}">
<input type="hidden" name="genofile" value="{{ genofile_string }}">
+ <input type="hidden" name="geno_db_exists" value="{{ geno_db_exists }}">
<input type="hidden" name="results_path" value="{{ mapping_results_path }}">
<input type="hidden" name="method" value="{{ mapping_method }}">
{% for sample in samples %}
@@ -154,7 +155,7 @@
<div class="tab-pane active" id="gn1_map">
<div class="qtlcharts">
{{ gifmap|safe }}
- <img src="/generated/{{ filename }}.jpeg" usemap="#WebQTLImageMap">
+ <img src="/generated/{{ filename }}.png" usemap="#WebQTLImageMap">
{% if additiveChecked|upper == "ON" %}
<br>
<span style="white-space: nowrap;">A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values.</span>
@@ -180,10 +181,10 @@
</form>
{% if selectedChr == -1 %}
- <div style="width:{% if 'additive' in trimmed_markers[0] %}45%{% else %}35%{% endif %};">
- <h2>Results</h2>
- <div id="table_container">
- <table id="qtl_results" class="table table-hover table-striped nowrap">
+ <div class="container" style="padding-left: 30px; width:{% if 'additive' in trimmed_markers[0] %}45%{% else %}35%{% endif %};">
+ <h2>Mapping Statistics</h2>
+ <div id="table_container" style="border-style: solid; border-width: 1px; border-color: black;">
+ <table id="trait_table" class="table table-hover table-striped nowrap">
<thead>
<tr>
<th></th>
@@ -194,7 +195,7 @@
{% if plotScale != "physic" %}
<th>cM</th>
{% else %}
- <th>Mb</th>
+ <th align="right">Mb</th>
{% endif %}
{% if 'additive' in trimmed_markers[0] %}
<th>Add Eff</th>
@@ -209,11 +210,11 @@
<tr>
<td align="center" style="padding-right: 0px;">
<input type="checkbox" name="selectCheck"
- class="checkbox edit_sample_checkbox"
- value="{{ marker.name }}" checked="checked">
+ class="checkbox trait_checkbox"
+ value="{{ marker.name }}">
</td>
<td align="right">{{ loop.index }}</td>
- <td>{{ marker.name }}</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>
@@ -294,6 +295,7 @@
</script>
{% endif %}
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
{% if mapping_method != "gemma" and mapping_method != "plink" %}
<script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script>
@@ -304,7 +306,7 @@
<script type="text/javascript" charset="utf-8">
$(document).ready( function () {
console.time("Creating table");
- $('#qtl_results').DataTable( {
+ $('#trait_table').DataTable( {
{% if mapping_method != "reaper" %}
"columns": [
{ "type": "natural", "width": "5%" },
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index a291baf3..dd4325e7 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -28,7 +28,9 @@
-->
<div class="container">
<h2>Trait Data and Analysis for <b>{{ this_trait.name }}</b></h2>
+ {% if this_trait.dataset.type != 'Publish' %}
<h3>{{ this_trait.description_fmt }}</h3>
+ {% endif %}
</div>
<form method="post" action="/corr_compute" target="_blank" name="trait_page" id="trait_data_form"
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 2a62733e..1e6d41c2 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -8,6 +8,22 @@
<td>Tissue</td>
<td>{{ this_trait.dataset.tissue }}</td>
</tr>
+ <tr>
+ <td>Phenotype</td>
+ <td><div style="width:40%;">{{ this_trait.description_fmt }}</div></td>
+ </tr>
+ <tr>
+ <td>Authors</td>
+ <td><div style="width:40%;">{{ this_trait.authors }}</div></td>
+ </tr>
+ <tr>
+ <td>Title</td>
+ <td><div style="width:40%;">{{ this_trait.title }}</div></td>
+ </tr>
+ <tr>
+ <td>Journal</td>
+ <td>{{ this_trait.journal }} (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed">{{ this_trait.year }}</a>)</td>
+ </tr>
{% endif %}
{% if this_trait.dataset.type == 'ProbeSet' %}
{% if this_trait.symbol != None %}
@@ -50,22 +66,29 @@
</td>
</tr>
{% endif %}
+ {% if this_trait.pubmed_id or this_trait.geneid or this_trait.omim or this_trait.symbol %}
+ {% if this_trait.dataset.type != 'Publish' %}
<tr>
<td>Resource Links</td>
<td>
- {% if this_trait.geneid != None %}
+ {% if this_trait.pubmed_id %}
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed">
+ PubMed
+ </a>
+ {% endif %}
+ {% if this_trait.geneid %}
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{ this_trait.geneid }}" title="Info from NCBI Entrez Gene">
NCBI
</a>
&nbsp;&nbsp;
{% endif %}
- {% if this_trait.omim != None %}
+ {% if this_trait.omim %}
<a href="http://www.ncbi.nlm.nih.gov/omim/{{ this_trait.omim }}" title="Summary from On Mendelion Inheritance in Man">
OMIM
</a>
&nbsp;&nbsp;
{% endif %}
- {% if this_trait.symbol != None %}
+ {% if this_trait.symbol %}
<a href="http://www.genotation.org/Getd2g.pl?gene_list={{ this_trait.symbol }}" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
Genotation
</a>
@@ -77,6 +100,8 @@
{% endif %}
</td>
</tr>
+ {% endif %}
+ {% endif %}
</table>
<div style="margin-bottom:15px;" class="btn-toolbar">
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 77f78415..dcec2b9e 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -6,16 +6,16 @@
<ul class="nav nav-pills">
{% if dataset.group.mapping_id == "1" %}
<li class="active">
- <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
+ <a href="#gemma" data-toggle="tab">GEMMA</a>
</li>
<li>
- <a href="#pylmm" data-toggle="tab">pyLMM</a>
+ <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
</li>
<li>
<a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
</li>
<li>
- <a href="#gemma" data-toggle="tab">GEMMA</a>
+ <a href="#pylmm" data-toggle="tab">pyLMM</a>
</li>
{% endif %}
{% for mapping_method in dataset.group.mapping_names %}
@@ -37,7 +37,60 @@
<div class="tab-content">
{# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #}
{% if dataset.group.mapping_id == "1" %}
- <div class="tab-pane active" id="interval_mapping">
+ <div class="tab-pane active" id="gemma">
+ <div style="padding-top: 10px;" class="form-horizontal">
+ {% if genofiles and genofiles|length>0 %}
+ <div class="mapping_method_fields form-group">
+ <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+ <div style="margin-left: 20px;" class="col-xs-8 controls">
+ <select id="genofile_gemma" class="form-control">
+ {% for item in genofiles %}
+ <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
+ {% endif %}
+ <div class="mapping_method_fields form-group">
+ <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
+ <div style="margin-left: 20px;" class="col-xs-3 controls">
+ <input name="maf_gemma" value="0.01" type="text" class="form-control">
+ </div>
+ </div>
+ <div class="mapping_method_fields form-group">
+ <label class="col-xs-4 control-label">Use LOCO</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <label class="radio-inline">
+ <input type="radio" name="use_loco" value="True">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="use_loco" value="False" checked="">
+ No
+ </label>
+ </div>
+ </div>
+ </div>
+ <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
+ <div class="mapping_method_fields form-group">
+ <button type="button" id="select_covariates" class="btn btn-default">
+ Select Covariates
+ </button>
+ <button type="button" id="remove_covariates" class="btn btn-default">
+ Remove Covariates
+ </button>
+ </div>
+ </div>
+
+ <div class="form-group">
+ <div class="col-xs-4 controls">
+ <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
+ Compute
+ </button>
+ </div>
+ </div>
+ </div>
+ <div class="tab-pane" id="interval_mapping">
<div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
@@ -131,62 +184,6 @@
<!--<div id="alert_placeholder"></div>-->
</div>
</div>
- <div class="tab-pane" id="pylmm">
- <div style="margin-top: 20px" class="form-horizontal">
- {% if genofiles and genofiles|length>0 %}
- <div class="mapping_method_fields form-group">
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
- <select id="genofile_pylmm" class="form-control">
- {% for item in genofiles %}
- <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
- {% endfor %}
- </select>
- </div>
- </div>
- {% endif %}
-<!--
- <div class="mapping_method_fields form-group">
- <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
- {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
- <input name="control_pylmm" value="{{ nearest_marker }}" type="text" />
- {% else %}
- <input name="control_pylmm" value="" type="text" />
- {% endif %}
- <label class="radio-inline">
- <input type="radio" name="do_control_pylmm" value="true">
- Yes
- </label>
- <label class="radio-inline">
- <input type="radio" name="do_control_pylmm" value="false" checked="">
- No
- </label>
- </div>
- </div>
- <div class="mapping_method_fields form-group">
- <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
- <div class="col-xs-12 controls">
- <label class="radio-inline">
- <input type="radio" name="manhattan_plot_pylmm" value="True">
- Yes
- </label>
- <label class="radio-inline">
- <input type="radio" name="manhattan_plot_pylmm" value="False" checked="">
- No
- </label>
- </div>
- </div>
--->
- <div class="form-group">
- <div style="padding-left:15px;" class="controls">
- <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
- </div>
- </div>
- </div>
- </div>
<div class="tab-pane" id="rqtl_geno">
<div style="margin-top: 20px" class="form-horizontal">
@@ -294,13 +291,13 @@
</div>
</div>
</div>
- <div class="tab-pane" id="gemma">
- <div style="padding-top: 10px;" class="form-horizontal">
+ <div class="tab-pane" id="pylmm">
+ <div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
<label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left: 20px;" class="col-xs-8 controls">
- <select id="genofile_gemma" class="form-control">
+ <select id="genofile_pylmm" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
{% endfor %}
@@ -308,42 +305,45 @@
</div>
</div>
{% endif %}
+<!--
<div class="mapping_method_fields form-group">
- <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
- <div style="margin-left: 20px;" class="col-xs-3 controls">
- <input name="maf_gemma" value="0.01" type="text" class="form-control">
+ <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+ <div style="margin-left: 20px;" class="col-xs-4 controls">
+ {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
+ <input name="control_pylmm" value="{{ nearest_marker }}" type="text" />
+ {% else %}
+ <input name="control_pylmm" value="" type="text" />
+ {% endif %}
+ <label class="radio-inline">
+ <input type="radio" name="do_control_pylmm" value="true">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="do_control_pylmm" value="false" checked="">
+ No
+ </label>
</div>
</div>
<div class="mapping_method_fields form-group">
- <label class="col-xs-4 control-label">Use LOCO</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
+ <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
+ <div class="col-xs-12 controls">
<label class="radio-inline">
- <input type="radio" name="use_loco" value="True">
+ <input type="radio" name="manhattan_plot_pylmm" value="True">
Yes
</label>
<label class="radio-inline">
- <input type="radio" name="use_loco" value="False" checked="">
+ <input type="radio" name="manhattan_plot_pylmm" value="False" checked="">
No
</label>
</div>
</div>
- </div>
- <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
- <div class="mapping_method_fields form-group">
- <button type="button" id="select_covariates" class="btn btn-default">
- Select Covariates
- </button>
- <button type="button" id="remove_covariates" class="btn btn-default">
- Remove Covariates
- </button>
- </div>
- </div>
-
- <div class="form-group">
- <div class="col-xs-4 controls">
- <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
- Compute
- </button>
+-->
+ <div class="form-group">
+ <div style="padding-left:15px;" class="controls">
+ <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression">
+ <i class="icon-ok-circle icon-white"></i> Compute
+ </button>
+ </div>
</div>
</div>
</div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 68e779a1..4e81c29c 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -557,6 +557,7 @@ def marker_regression_page():
wanted = (
'trait_id',
'dataset',
+ 'geno_db_exists',
'method',
'mapping_results_path',
'trimmed_markers',
@@ -765,7 +766,7 @@ def corr_scatter_plot_page():
def submit_bnw():
logger.error(request.url)
template_vars = get_bnw_input(request.form)
- return render_template("empty_collection.html", **{'tool':'Correlation Matrix'})
+ return render_template("empty_collection.html", **{'tool':'Correlation Matrix'})
# Todo: Can we simplify this? -Sam
def sharing_info_page():
diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py
new file mode 100644
index 00000000..be9c7b37
--- /dev/null
+++ b/wqflask/wsgi.py
@@ -0,0 +1,4 @@
+from run_gunicorn import app as application # expect application as a name
+
+if __name__ == "__main__":
+ application.run()
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 21:41:57 +0000