diff options
| -rwxr-xr-x | bin/genenetwork2 | 4 | ||||
| -rwxr-xr-x | bin/test-website | 12 | ||||
| -rw-r--r-- | etc/default_settings.py | 5 | ||||
| -rw-r--r-- | test/lib/mapping.rb | 1 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 16 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/qtlreaper_mapping.py | 186 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/base.html | 28 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/ctl_results.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/error.html | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/index_page_orig.html | 64 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 12 |
12 files changed, 196 insertions, 143 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 d8e57f38..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 @@ -50,6 +51,10 @@ LOG_BENCH = True # Log bench marks USE_REDIS = True # REDIS caching (note that redis will be phased out) USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls +# Paths to JS libraries + +TWITTER_POST_FETCHER_JS_PATH = os.environ['HOME']+"/genenetwork/Twitter-Post-Fetcher" + # ---- Path overrides for Genenetwork # TMPDIR is normally picked up from the environment HOME=os.environ['HOME'] 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 5105ba42..df032e48 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -121,7 +121,7 @@ def assert_writable_dir(dir): fh.close() os.remove(fn) except IOError: - raise Exception('Unable to write to directory ' + dir ) + raise Exception('Unable to write test.txt to directory ' + dir ) return dir def mk_dir(dir): @@ -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') @@ -231,3 +232,5 @@ if os.environ.get('WQFLASK_OVERRIDES'): else: OVERRIDES[k] = cmd logger.debug(OVERRIDES) + +assert_dir(get_setting("TWITTER_POST_FETCHER_JS_PATH")) diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index fbd9a816..fef0d8a0 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -201,14 +201,14 @@ class MarkerRegression(object): self.control_marker = start_vars['control_marker'] self.do_control = start_vars['do_control'] logger.info("Running qtlreaper") - 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, + 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": diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 568991f7..b072584c 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -1,93 +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
+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 c3826a90..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 %} - Join the <a href="http://listserv.uthsc.edu/mailman/listinfo/genenetwork-dev">mailing list</a> </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/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 73d3e718..1694eae5 100755 --- a/wqflask/wqflask/templates/index_page_orig.html +++ b/wqflask/wqflask/templates/index_page_orig.html @@ -1,5 +1,10 @@ {% extends "base.html" %} {% block title %}GeneNetwork{% endblock %} +{% block css %} +<style TYPE="text/css"> + p.interact { display: none; } +</style> +{% endblock %} {% block content %} <!-- Start of body --> @@ -166,8 +171,17 @@ </ul> </section> </div> + <div style="padding-left:120px" class="col-xs-4" style="width: 600px !important;"> - <!-- + <section id="news-section"> + <div class="page-header"> + <h1>News</h1> + </div> + <div id="tweets"></div> + <div align="right"> + <a href="https://twitter.com/GeneNetwork2">more news items...</a> + </div> + <!-- <section id="tour-info"> <div class="page-header"> <h1>Tour and more info</h1> @@ -194,34 +208,37 @@ </section> --> + </section> <section id="websites"> <div class="page-header"> - <h1>Affiliates and mirrors</h1> + <h2>Links</h2> </div> - <h3>Websites affiliated with GeneNetwork</h3> + <h3>GeneNetwork v2:</h3> + <ul> + <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 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> + <h3>Affiliates</h3> + <ul> <li><a href="http://ucscbrowser.genenetwork.org/">Genome browser</a> at UTHSC</li> <li><a href="http://galaxy.genenetwork.org/">Galaxy</a> at UTHSC</li> - <li>GeneNetwork 1 at <a href="http://ec2.genenetwork.org/">Amazon - Cloud (EC2)</a></li> + </ul> - <li>GeneNetwork 1 Source Code at <a href="http://sourceforge.net/projects/genenetwork/">SourceForge</a></li> - <li>GeneNetwork 2 Source Code at <a href="https://github.com/genenetwork/genenetwork2">GitHub</a></li> - </ul> - <h3>GN1 Mirror and development sites</h3> - <ul> - <li><a href="http://www.genenetwork.org/">Main GN1 site at UTHSC</a> (main site)</li> - <li><a href="http://genenetwork.helmholtz-hzi.de/">Germany at the HZI</a></li> - <li><a href="http://gn2.genenetwork.org/">Memphis at the U of M</a></li> - </ul> - </section> + </section> <!--<section id="getting-started"> <div class="page-header"> @@ -282,4 +299,21 @@ } </script> + <script type="text/javascript" src="/twitter/js/twitterFetcher_min.js"></script> + + <script type="text/javascript"> + var configProfile = { + "profile": {"screenName": 'GeneNetwork2'}, + "domId": 'tweets', + "maxTweets": 5, + "enableLinks": true, + "showUser": false, + "showTime": true, + "showImages": false, + "lang": 'en' + }; + twitterFetcher.fetch(configProfile); + </script> + + {% endblock %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 33fab84d..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>") @@ -143,6 +143,10 @@ def tmp_page(img_path): return render_template("show_image.html", img_base64 = bytesarray ) +@app.route("/twitter/<path:filename>") +def bd_files(filename): + bd_path = app.config['TWITTER_POST_FETCHER_JS_PATH'] + return send_from_directory(bd_path, filename) #@app.route("/data_sharing") #def data_sharing_page(): |