diff options
| -rwxr-xr-x | bin/genenetwork2 | 4 | ||||
| -rwxr-xr-x | bin/test-website | 12 | ||||
| -rw-r--r-- | etc/default_settings.py | 1 | ||||
| -rw-r--r-- | test/lib/mapping.rb | 1 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 107 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/qtlreaper_mapping.py | 93 | ||||
| -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/ctl_setup.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/error.html | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/index_page_orig.html | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 8 |
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>") |