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-rwxr-xr-xbin/genenetwork24
-rwxr-xr-xbin/test-website12
-rw-r--r--etc/default_settings.py1
-rw-r--r--test/lib/mapping.rb1
-rw-r--r--wqflask/utility/tools.py1
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py107
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py93
-rw-r--r--wqflask/wqflask/templates/base.html28
-rw-r--r--wqflask/wqflask/templates/ctl_results.html2
-rw-r--r--wqflask/wqflask/templates/ctl_setup.html2
-rw-r--r--wqflask/wqflask/templates/error.html4
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html8
-rw-r--r--wqflask/wqflask/views.py8
13 files changed, 145 insertions, 126 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index b2de4c95..52d3155c 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -26,6 +26,10 @@ GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT"))
echo GN2_BASE_DIR=$GN2_BASE_DIR
+GIT_HASH=$(git rev-parse HEAD)
+GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
+export GN_VERSION=$(cat $GN2_BASE_DIR/VERSION)-$GIT_BRANCH-${GIT_HASH:0:9}
+echo GN_VERSION=$GN_VERSION
# Handle settings parameter (can be .py or .json)
settings=$1
diff --git a/bin/test-website b/bin/test-website
index c9a72a5e..be223d94 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -52,12 +52,12 @@ opts = OptionParser.new do |o|
options[:link_checker] = true
end
- o.on('--navigation-test', 'Check for navigation') do
- options[:navigation_test] = true
+ o.on('--navigation', 'Check for navigation') do
+ options[:navigation] = true
end
- o.on('--mapping-test', 'Check for mapping') do
- options[:mapping_test] = true
+ o.on('--mapping', 'Check for mapping') do
+ options[:mapping] = true
end
o.on('--skip-broken', 'Skip tests that are known to be broken') do
@@ -98,7 +98,7 @@ $: << File.join(libpath,'test/lib')
require 'main_web_functionality'
-if options[:all] or options[:mapping_test]
+if options[:all] or options[:mapping]
require 'mapping'
end
@@ -106,6 +106,6 @@ if options[:all] or options[:link_checker]
require 'link_checker'
end
-if options[:all] or options[:navigation_test]
+if options[:all] or options[:navigation]
require 'navigation'
end
diff --git a/etc/default_settings.py b/etc/default_settings.py
index fb3670dd..6acea637 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -18,6 +18,7 @@
import os
import sys
+GN_VERSION = open("../VERSION","r").read()
SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s'
SQLALCHEMY_POOL_RECYCLE = 3600
diff --git a/test/lib/mapping.rb b/test/lib/mapping.rb
index d6a3cd7b..20e5bd40 100644
--- a/test/lib/mapping.rb
+++ b/test/lib/mapping.rb
@@ -36,6 +36,7 @@ describe MappingTest do
json,
({'Content-Type' => 'application/x-www-form-urlencoded'}))
form = page.forms_with("marker_regression")[0]
+ p form
form.fields.select { |fld| fld.name == 'dataset' }.first.value.must_equal 'HC_M2_0606_P'
form.fields.select { |fld| fld.name == 'value:BXD1' }.first.value.must_equal "15.034"
end
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 31f838b3..df032e48 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -197,6 +197,7 @@ def show_settings():
# Cached values
+GN_VERSION = get_setting('GN_VERSION')
HOME = get_setting('HOME')
WEBSERVER_MODE = get_setting('WEBSERVER_MODE')
GN_SERVER_URL = get_setting('GN_SERVER_URL')
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 37ee42a7..200f2207 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -35,7 +35,7 @@ from utility import helper_functions
from utility import Plot, Bunch
from utility import temp_data
from utility.benchmark import Bench
-from wqflask.marker_regression import gemma_mapping, rqtl_mapping
+from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping
from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR
from utility.external import shell
@@ -170,7 +170,7 @@ class MarkerRegression(object):
if start_vars['pair_scan'] == "true":
self.pair_scan = True
if self.permCheck and self.num_perm > 0:
- perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
+ self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
else:
results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
elif self.mapping_method == "reaper":
@@ -201,7 +201,16 @@ class MarkerRegression(object):
self.control_marker = start_vars['control_marker']
self.do_control = start_vars['do_control']
logger.info("Running qtlreaper")
- results = self.gen_reaper_results()
+ results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait,
+ self.dataset,
+ self.samples,
+ self.json_data,
+ self.num_perm,
+ self.bootCheck,
+ self.num_bootstrap,
+ self.do_control,
+ self.control_marker,
+ self.manhattan_plot)
elif self.mapping_method == "plink":
results = self.run_plink()
elif self.mapping_method == "pylmm":
@@ -468,98 +477,6 @@ class MarkerRegression(object):
return sample_list
- def gen_reaper_results(self):
- genotype = self.dataset.group.read_genotype_file()
-
- if self.manhattan_plot != True:
- genotype = genotype.addinterval()
-
- samples, values, variances, sample_aliases = self.this_trait.export_informative()
-
- trimmed_samples = []
- trimmed_values = []
- for i in range(0, len(samples)):
- #if self.this_trait.data[samples[i]].name2 in self.dataset.group.samplelist:
- if self.this_trait.data[samples[i]].name in self.samples:
- trimmed_samples.append(samples[i])
- trimmed_values.append(values[i])
-
- if self.num_perm < 100:
- self.suggestive = 0
- self.significant = 0
- else:
- self.perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=self.num_perm)
- self.suggestive = self.perm_output[int(self.num_perm*0.37-1)]
- self.significant = self.perm_output[int(self.num_perm*0.95-1)]
- self.highly_significant = self.perm_output[int(self.num_perm*0.99-1)]
-
- self.json_data['suggestive'] = self.suggestive
- self.json_data['significant'] = self.significant
-
- if self.control_marker != "" and self.do_control == "true":
- reaper_results = genotype.regression(strains = trimmed_samples,
- trait = trimmed_values,
- control = str(self.control_marker))
- if self.bootCheck:
- control_geno = []
- control_geno2 = []
- _FIND = 0
- for _chr in genotype:
- for _locus in _chr:
- if _locus.name == self.control_marker:
- control_geno2 = _locus.genotype
- _FIND = 1
- break
- if _FIND:
- break
- if control_geno2:
- _prgy = list(genotype.prgy)
- for _strain in trimmed_samples:
- _idx = _prgy.index(_strain)
- control_geno.append(control_geno2[_idx])
-
- self.bootstrap_results = genotype.bootstrap(strains = trimmed_samples,
- trait = trimmed_values,
- control = control_geno,
- nboot = self.num_bootstrap)
- else:
- reaper_results = genotype.regression(strains = trimmed_samples,
- trait = trimmed_values)
-
- if self.bootCheck:
- self.bootstrap_results = genotype.bootstrap(strains = trimmed_samples,
- trait = trimmed_values,
- nboot = self.num_bootstrap)
-
- self.json_data['chr'] = []
- self.json_data['pos'] = []
- self.json_data['lod.hk'] = []
- self.json_data['markernames'] = []
- #if self.additive:
- # self.json_data['additive'] = []
-
- #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
- qtl_results = []
- for qtl in reaper_results:
- reaper_locus = qtl.locus
- #ZS: Convert chr to int
- converted_chr = reaper_locus.chr
- if reaper_locus.chr != "X" and reaper_locus.chr != "X/Y":
- converted_chr = int(reaper_locus.chr)
- self.json_data['chr'].append(converted_chr)
- self.json_data['pos'].append(reaper_locus.Mb)
- self.json_data['lod.hk'].append(qtl.lrs)
- self.json_data['markernames'].append(reaper_locus.name)
- #if self.additive:
- # self.json_data['additive'].append(qtl.additive)
- locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb}
- qtl = {"lrs_value": qtl.lrs, "chr":converted_chr, "Mb":reaper_locus.Mb,
- "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive, "dominance":qtl.dominance}
- qtl_results.append(qtl)
-
- return qtl_results
-
-
def parse_plink_output(self, output_filename):
plink_results={}
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
new file mode 100644
index 00000000..b072584c
--- /dev/null
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -0,0 +1,93 @@
+def gen_reaper_results(this_trait, dataset, samples_before, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
+ genotype = dataset.group.read_genotype_file()
+
+ if manhattan_plot != True:
+ genotype = genotype.addinterval()
+
+ samples, values, variances, sample_aliases = this_trait.export_informative()
+
+ trimmed_samples = []
+ trimmed_values = []
+ for i in range(0, len(samples)):
+ if this_trait.data[samples[i]].name in samples_before:
+ trimmed_samples.append(samples[i])
+ trimmed_values.append(values[i])
+
+ perm_output = []
+ bootstrap_results = []
+
+ if num_perm < 100:
+ suggestive = 0
+ significant = 0
+ else:
+ perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=num_perm)
+ suggestive = perm_output[int(num_perm*0.37-1)]
+ significant = perm_output[int(num_perm*0.95-1)]
+ highly_significant = perm_output[int(num_perm*0.99-1)]
+
+ json_data['suggestive'] = suggestive
+ json_data['significant'] = significant
+
+ if control_marker != "" and do_control == "true":
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values,
+ control = str(control_marker))
+ if bootCheck:
+ control_geno = []
+ control_geno2 = []
+ _FIND = 0
+ for _chr in genotype:
+ for _locus in _chr:
+ if _locus.name == control_marker:
+ control_geno2 = _locus.genotype
+ _FIND = 1
+ break
+ if _FIND:
+ break
+ if control_geno2:
+ _prgy = list(genotype.prgy)
+ for _strain in trimmed_samples:
+ _idx = _prgy.index(_strain)
+ control_geno.append(control_geno2[_idx])
+
+ bootstrap_results = genotype.bootstrap(strains = trimmed_samples,
+ trait = trimmed_values,
+ control = control_geno,
+ nboot = num_bootstrap)
+ else:
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values)
+
+ if bootCheck:
+ bootstrap_results = genotype.bootstrap(strains = trimmed_samples,
+ trait = trimmed_values,
+ nboot = num_bootstrap)
+
+ json_data['chr'] = []
+ json_data['pos'] = []
+ json_data['lod.hk'] = []
+ json_data['markernames'] = []
+ #if self.additive:
+ # self.json_data['additive'] = []
+
+ #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
+ qtl_results = []
+ for qtl in reaper_results:
+ reaper_locus = qtl.locus
+ #ZS: Convert chr to int
+ converted_chr = reaper_locus.chr
+ if reaper_locus.chr != "X" and reaper_locus.chr != "X/Y":
+ converted_chr = int(reaper_locus.chr)
+ json_data['chr'].append(converted_chr)
+ json_data['pos'].append(reaper_locus.Mb)
+ json_data['lod.hk'].append(qtl.lrs)
+ json_data['markernames'].append(reaper_locus.name)
+ #if self.additive:
+ # self.json_data['additive'].append(qtl.additive)
+ locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb}
+ qtl = {"lrs_value": qtl.lrs, "chr":converted_chr, "Mb":reaper_locus.Mb,
+ "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive, "dominance":qtl.dominance}
+ qtl_results.append(qtl)
+
+
+ return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 946e6add..210c5708 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -95,29 +95,27 @@
</form>
</div>
- {% block content %}{% endblock %}
+ {% block content %}
+ {% endblock %}
- <!-- Footer
- ================================================== -->
<footer class="footer">
<div class="container">
-
- <p>
-
-GeneNetwork is a framework for web based genetics
- launched in 1994 as
+ <p>GeneNetwork is a framework for web based genetics
+ launched in 1994 as
<a href="http://www.ncbi.nlm.nih.gov/pubmed?term=8043953">
The Portable Dictionary of the Mouse Genome</a> (previously <a href="https://www.ncbi.nlm.nih.gov/pubmed/15043217">WebQTL</a>).
</p>
- <p>Operated by
+ <p>
+ Operated by
<a href="mailto:rwilliams@uthsc.edu">Rob Williams</a>,
<a href="mailto:lyan6@uthsc.edu">Lei Yan</a>,
- <a href="mailto:zachary.a.sloan@gmail.com">Zachary Sloan</a>, and
- <a href="mailto:acenteno@uthsc.edu">Arthur Centeno</a>.
+ <a href="mailto:zachary.a.sloan@gmail.com">Zachary Sloan</a>,
+ <a href="mailto:acenteno@uthsc.edu">Arthur Centeno</a> and
+ <a href="http://thebird.nl/">Pjotr Prins</a>.
</p>
<p>Published in
<a href="http://joss.theoj.org/papers/10.21105/joss.00025"><img src="https://camo.githubusercontent.com/846b750f582ae8f1d0b4f7e8fee78bed705c88ba/687474703a2f2f6a6f73732e7468656f6a2e6f72672f7061706572732f31302e32313130352f6a6f73732e30303032352f7374617475732e737667" alt="JOSS" data-canonical-src="http://joss.theoj.org/papers/10.21105/joss.00025/status.svg" style="max-width:100%;"></a>
- </p>
+ </p>
<br />
<p>GeneNetwork is supported by:</p>
<UL>
@@ -143,8 +141,12 @@ GeneNetwork is a framework for web based genetics
</li>
</UL>
<!--</p>-->
+ <p>
+ Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <a href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</a> and find us on <a href="https://webchat.freenode.net/">IRC</a> (#genenetwork channel).
+ {% if version: %}
+ <p><small>GeneNetwork v{{ version }}</small></p>
+ {% endif %}
- Development and source code on <a href="https://github.com/genenetwork/">github</a> with <a href="https://github.com/genenetwork/genenetwork2/issues">issue tracker</a> and <a href="https://github.com/genenetwork/genenetwork2/blob/master/README.md">documentation</a>. Join the <a href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</a> and find us on <a href="https://webchat.freenode.net/">IRC</a> (#genenetwork channel).
</div>
</footer>
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index a5cb1c08..00ccecb6 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -4,7 +4,7 @@
{% block content %} <!-- Start of body -->
<div class="container">
<h1>CTL Results</h1>
- {{(request.form['trait_list'].split(',')|length -1)}} phenotypes as input<br>
+ {{(request.form['trait_list'].split(',')|length)}} phenotypes as input<br>
<h3>Network Figure</h3>
<a href="/tmp/{{ results['imgurl1'] }}">
<img alt="Embedded Image" src="data:image/png;base64,
diff --git a/wqflask/wqflask/templates/ctl_setup.html b/wqflask/wqflask/templates/ctl_setup.html
index 51553322..a05379a8 100644
--- a/wqflask/wqflask/templates/ctl_setup.html
+++ b/wqflask/wqflask/templates/ctl_setup.html
@@ -12,7 +12,7 @@
</div>
{% else %}
<h1>CTL analysis parameters</h1>
- {{(request.form['trait_list'].split(',')|length -1)}} traits as input
+ {{(request.form['trait_list'].split(',')|length)}} traits as input
<form action="/ctl_results" method="post" class="form-horizontal">
<input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
diff --git a/wqflask/wqflask/templates/error.html b/wqflask/wqflask/templates/error.html
index 7ab2bf2f..c707a4fc 100644
--- a/wqflask/wqflask/templates/error.html
+++ b/wqflask/wqflask/templates/error.html
@@ -35,7 +35,7 @@
</p>
<pre>
- {{ stack[0] }}
+ GeneNetwork v{{ version }} {{ stack[0] }}
{{ message }} (error)
{{ stack[-3] }}
{{ stack[-2] }}
@@ -50,7 +50,7 @@
<a href="#Stack" class="btn btn-default" data-toggle="collapse">Toggle full stack trace</a>
<div id="Stack" class="collapse">
<pre>
- {% for line in stack %} {{ line }}
+ GeneNetwork v{{ version }} {% for line in stack %} {{ line }}
{% endfor %}
</pre>
</div>
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 7b085573..1694eae5 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -216,13 +216,13 @@
</div>
<h3>GeneNetwork v2:</h3>
<ul>
- <li><a href="http://gn2.genenetwork.org/">Main</a> at UTHSC</li>
- <li><a href="http://test-gn2.genenetwork.org/">Staging</a> at UTHSC</li>
+ <li><a href="http://gn2.genenetwork.org/">Main website</a> at UTHSC</li>
+ <li><a href="http://test-gn2.genenetwork.org/">Testing website</a> at UTHSC</li>
</ul>
<h3>GeneNetwork v1:</h3>
<ul>
- <li><a href="http://www.genenetwork.org/">Main</a> at UTHSC</li>
- <li><a href="http://genenetwork.helmholtz-hzi.de/">Germany</a> at the HZI</li>
+ <li><a href="http://www.genenetwork.org/">Main website</a> at UTHSC</li>
+ <li><a href="http://genenetwork.helmholtz-hzi.de/">Website</a> at the HZI (Germany)</li>
<li><a href="http://ec2.genenetwork.org/">Amazon
Cloud (EC2)</a></li>
</ul>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index a5b2870d..fb52165a 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -51,7 +51,7 @@ from wqflask.wgcna import wgcna_analysis
from wqflask.ctl import ctl_analysis
from utility import temp_data
-from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL
+from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION
from base import webqtlFormData
from base.webqtlConfig import GENERATED_IMAGE_DIR
@@ -108,7 +108,7 @@ def handle_bad_request(e):
list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ]
animation = random.choice(list)
- resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation))
+ resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation,version=GN_VERSION))
# logger.error("Set cookie %s with %s" % (err_msg, animation))
resp.set_cookie(err_msg[:32],animation)
@@ -124,10 +124,10 @@ def index_page():
g.cookie_session.import_traits_to_user()
if USE_GN_SERVER:
# The menu is generated using GN_SERVER
- return render_template("index_page.html", gn_server_url = GN_SERVER_URL)
+ return render_template("index_page.html", gn_server_url = GN_SERVER_URL, version=GN_VERSION)
else:
# Old style static menu (OBSOLETE)
- return render_template("index_page_orig.html")
+ return render_template("index_page_orig.html", version=GN_VERSION)
@app.route("/tmp/<img_path>")
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 19:41:24 +0000