Merge branch 'testing' of https://github.com/genenetwork/genenetwork2

4 files changed, 59 insertions, 0 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 9f2f06f3..9e01be3e 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -7,6 +7,7 @@ from pprint import pformat as pf
 
 import string
 import math
+import random
 import sys
 import datetime
 import os
@@ -30,6 +31,7 @@ from flask import Flask, g
 from base.trait import GeneralTrait
 from base import data_set
 from base import species
+from base import webqtlConfig
 from utility import webqtlUtil
 from utility import helper_functions
 from utility import Plot, Bunch
@@ -78,6 +80,12 @@ class MarkerRegression(object):
                     self.vals.append(value)
 
         self.mapping_method = start_vars['method']
+        if "results_path" in start_vars:
+            self.mapping_results_path = start_vars['results_path']
+        else:
+            mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+            self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
+
         if start_vars['manhattan_plot'] == "True":
             self.manhattan_plot = True
         else:
@@ -269,6 +277,8 @@ class MarkerRegression(object):
                     if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
                         self.qtl_results.append(marker)
 
+            export_mapping_results(self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
+
             self.trimmed_markers = trim_markers_for_table(results)
 
             if self.mapping_method != "gemma":
@@ -598,6 +608,32 @@ def create_snp_iterator_file(group):
     with gzip.open(snp_file_base, "wb") as fh:
         pickle.dump(data, fh, pickle.HIGHEST_PROTOCOL)
 
+def export_mapping_results(markers, results_path, mapping_scale, score_type):
+    with open(results_path, "w+") as output_file:
+        output_file.write("Name\tChr\t")
+        if mapping_scale == "physic":
+            output_file.write("Mb\t" + score_type)
+        else:
+            output_file.write("Cm\t" + score_type)
+        if "additive" in markers[0].keys():
+            output_file.write("\tAdditive")
+        if "dominance" in markers[0].keys():
+            output_file.write("\tDominance")
+        output_file.write("\n")
+        for i, marker in enumerate(markers):
+            logger.debug("THE MARKER:", marker)
+            output_file.write(marker['name'] + "\t" + str(marker['chr']) + "\t" + str(marker['Mb']) + "\t")
+            if "lod_score" in marker.keys():
+                output_file.write(str(marker['lod_score']))
+            else:
+                output_file.write(str(marker['lrs_value']))
+            if "additive" in marker.keys():
+                output_file.write("\t" + str(marker['additive']))
+            if "dominance" in marker.keys():
+                output_file.write("\t" + str(marker['dominance']))
+            if i < (len(markers) - 1):
+                output_file.write("\n")
+
 def trim_markers_for_table(markers):
     num_markers = len(markers)
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index a26d1426..ff1fb492 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -178,6 +178,7 @@ class MarkerRegression(object):
         self.samples = start_vars['samples']
         self.vals = start_vars['vals']
         self.mapping_method = start_vars['mapping_method']
+        self.mapping_results_path = start_vars['mapping_results_path']
         if self.mapping_method == "rqtl_geno":
             self.mapmethod_rqtl_geno = start_vars['method']
             self.mapmodel_rqtl_geno = start_vars['model']
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 5c457275..d13c68cd 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="results_path" value="{{ mapping_results_path }}">
         <input type="hidden" name="method" value="{{ mapping_method }}">
         {% for sample in samples %}
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
@@ -46,6 +47,9 @@
               {% if genofile_string is defined %}
               <b>Genotypes:</b> {{ genofile_string.split(":")[1] }}
               {% endif %}
+              <br>
+              <br>
+              <a href="javascript:export_mapping_results();" target="_blank" >Download Full Results</a>
           </div>
           <div id="gn1_map_options" class="col-xs-5" style="outline: 3px double #AAAAAA; padding: 10px; margin: 10px;">
             <div class="col-xs-8" style="padding: 0px;">
@@ -407,6 +411,11 @@
         }
         {% endif %}
 
+        export_mapping_results = function() {
+            $('#marker_regression_form').attr('action', '/export_mapping_results');
+            return $('#marker_regression_form').submit();
+        }
+
     </script>
 
 {% endblock %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 174bf1e4..40806450 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -557,6 +557,7 @@ def marker_regression_page():
         'trait_id',
         'dataset',
         'method',
+        'mapping_results_path',
         'trimmed_markers',
         'selected_chr',
         'chromosomes',
@@ -672,6 +673,18 @@ def marker_regression_page():
 
     return rendered_template
 
+@app.route("/export_mapping_results", methods = ('POST',))
+def export_mapping_results():
+    logger.info("request.form:", request.form)
+    logger.error(request.url)
+    file_path = request.form.get("results_path")
+    results_csv = open(file_path, "r").read()
+    response = Response(results_csv,
+                        mimetype='text/csv',
+                        headers={"Content-Disposition":"attachment;filename=mapping_results.csv"})
+
+    return response
+
 
 @app.route("/export", methods = ('POST',))
 def export():