R/qtl pair scan now works again, though it takes a while (10-15 minutes).

Added pop-up warning user about run-time for pair scan

Fixed links to GN2 github on the index page

Fixed a couple issues with the search result page text

Changed the appearance of the trait sample data table to match other tables (darker headers, etc)

7 files changed, 86 insertions, 70 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 1e0a618e..26da95b9 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -37,7 +37,7 @@ from utility import temp_data
 from utility.benchmark import Bench
 from wqflask.marker_regression import gemma_mapping
 
-from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND
+from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND, TEMPDIR
 from utility.external import shell
 from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
 
@@ -213,7 +213,8 @@ class MarkerRegression(object):
                     if 'lod_score' in marker.keys():
                         self.qtl_results.append(marker)
 
-            self.trimmed_markers = trim_markers_for_table(results)            
+            
+            self.trimmed_markers = results    
                         
             for qtl in enumerate(self.qtl_results):
                 self.json_data['chr1'].append(str(qtl['chr1']))
@@ -228,7 +229,7 @@ class MarkerRegression(object):
                 maf = self.maf,
                 manhattan_plot = self.manhattan_plot,
                 mapping_scale = self.mapping_scale,
-                qtl_results = self.qtl_results,
+                qtl_results = self.qtl_results
             )
 
         else:
@@ -388,7 +389,7 @@ class MarkerRegression(object):
         r_sum         = ro.r["sum"]                     # Map the sum function
         plot          = ro.r["plot"]                    # Map the plot function
         postscript    = ro.r["postscript"]              # Map the postscript function
-        png           = ro.r["png"]              # Map the png function
+        png           = ro.r["png"]                     # Map the png function
         dev_off       = ro.r["dev.off"]                 # Map the device off function
 
         print(r_library("qtl"))                         # Load R/qtl
@@ -430,7 +431,7 @@ class MarkerRegression(object):
             #print("Pair scan results:", result_data_frame)
 
             self.pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
-            png(file=TMPDIR+self.pair_scan_filename)
+            png(file=TEMPDIR+self.pair_scan_filename)
             plot(result_data_frame)
             dev_off()
             
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 519d1304..3b1a1205 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -135,6 +135,8 @@
 
   outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results. We recommend <A HREF=\"http://en.wikipedia.org/wiki/Winsorising\">winsorising</A> the outliers or simply deleting them.";
 
+  runtime_warning_text = "This function could take as long as 10-20 minutes to run, so please do not close your browser window until it finishes."
+  
   showalert = function(message, alerttype) {
     return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
   };
@@ -187,8 +189,20 @@
       $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
-      return submit_special(url);
-      //return do_ajax_post(url, form_data);
+      if ($('input[name=pair_scan]:checked').val() == "true") {
+        console.log("PAIR SCAN:", $('input[name=pair_scan]:checked').val())
+        run_pair_scan = confirm(runtime_warning_text)
+        if (run_pair_scan == true) {
+          submit_special(url);
+        }
+        else {
+          return false
+        }
+      }
+      else {
+        return submit_special(url);
+        //return do_ajax_post(url, form_data);
+      }
     };
   })(this));
 
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 5cc15682..9e029911 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -207,12 +207,12 @@
                         <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
                         UTHSC</li>
 
-                        <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
+                        <li>GeneNetwork 1 at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
                         Cloud (EC2)</a></li>
 
-                        <li>GeneNetwork Source Code at <a href="http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
+                        <li>GeneNetwork 1 Source Code at <a href="http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
 
-                        <li>GeneNetwork Source Code at <a href="https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
+                        <li>GeneNetwork 2 Source Code at <a href="https://github.com/genenetwork/genenetwork2" target="_blank">GitHub</a></li>
                     </ul>
                     <h3>GN1 Mirror and development sites</h3>
 
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index ab4a36bb..1ccb2b27 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -44,7 +44,7 @@
                    </tr>
                 </thead>
                 <tbody>
-                    {% for marker in filtered_markers %}
+                    {% for marker in trimmed_markers %}
                         <tr>
                             <td>{{loop.index}}</td>
                             <td>{{marker.name}}</td>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 4b4f3584..02c97862 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -21,44 +21,30 @@
            to find all records
                 {% for word in search_terms %}
                     {% if word.key|lower == "rif" %}
-                    with <u>GeneRIF</u> containing <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+                    with <u>GeneRIF</u> containing <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
                     {% elif word.key|lower == "go" %}
-                    with <u>Gene Ontology ID</u> <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+                    with <u>Gene Ontology ID</u> <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
                     {% elif word.key|lower == "wiki" %}
-                    with <u>GeneWiki</u> containing <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+                    with <u>GeneWiki</u> containing <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
                     {% elif word.key|lower == "mean" %}
-                    with <u>MEAN</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if not loop.last %} and {% endif %}
+                    with <u>MEAN</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
                     {% elif word.key|lower == "lrs" or word.key|lower == "translrs" or word.key|lower == "cislrs" %}
                     {% if word.search_term|length == 1 %}
-                    with {% if word.key|lower == "translrs" %}trans{% elif word.key|lower == "cislrs" %}cis{% endif %}LRS {% if word.separator == ">" %} greater than {% elif word.separator == "<" %} less than {% elif word.separator == ">=" %} greater than or equal to {% elif word.separator == "<=" %} less than or equal to {% endif %} <strong>{{ word.search_term[0] }}</strong>{% if not loop.last %} and {% endif %}
+                    with {% if word.key|lower == "translrs" %}trans{% elif word.key|lower == "cislrs" %}cis{% endif %}LRS {% if word.separator == ">" %} greater than {% elif word.separator == "<" %} less than {% elif word.separator == ">=" %} greater than or equal to {% elif word.separator == "<=" %} less than or equal to {% endif %} <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
                     {% elif word.search_term|length == 2 %}
-                    with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if not loop.last %} and {% endif %}
+                    with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
                     {% elif word.search_term|length == 3 %}
-                    with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong>{% if not loop.last %} and {% endif %}
+                    with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
                     {% elif word.search_term|length == 5 %}
-                    with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong> between <strong>{{ word.search_term[3] }}</strong> and <strong>{{ word.search_term[4] }}</strong> Mb{% if not loop.last %} and {% endif %}
+                    with <u>LRS</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong> on chromosome <strong>{{ word.search_term[2] }}</strong> between <strong>{{ word.search_term[3] }}</strong> and <strong>{{ word.search_term[4] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %}
                     {% endif %}
                     {% elif word.key|lower == "position" %}
-                    with <u>target genes</u> on chromosome <strong>{% if word.search_term[0].split('chr')|length > 1 %}{{ word.search_term[0].split('chr')[1] }}{% elif word.search_term[0].split('CHR')|length > 1 %}{{ word.search_term[0].split('CHR')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if not loop.last %} and {% endif %}
+                    with <u>target genes</u> on chromosome <strong>{% if word.search_term[0].split('chr')|length > 1 %}{{ word.search_term[0].split('chr')[1] }}{% elif word.search_term[0].split('CHR')|length > 1 %}{{ word.search_term[0].split('CHR')[1] }}{% else %}{{ word.search_term[0] }}{% endif %}</strong> between <strong>{{ word.search_term[1] }}</strong> and <strong>{{ word.search_term[2] }}</strong> Mb{% if loop.last %}.{% else %} and {% endif %}
                     {% else %}
-                    with {{ word.key|lower }} matching {{ word.search_term[0] }}
+                    that match the term {{ word.search_term[0] }}.
                     {% endif %}
-                    <!--<strong>{{word.search_term[0]}}</strong> {% if not loop.last %} or {% endif %}-->
-                {% endfor %}.
-
-        </p>
-
-        <!--
-        <ul>
-            {% if search_terms %}
-            <li>
-                {% for word in search_terms %}
-                    <strong>{{word.search_term[0]}}</strong> {% if not loop.last %} or {% endif %}
                 {% endfor %}
-            </li>
-            {% endif %}
-        </ul>
-        -->
+        </p>
 
         <p>To study a record, click on its ID below. Check records below and click Add button to add to selection.</p>
 
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 228ef362..ff5f0c87 100755
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -77,20 +77,20 @@
     {% for sample_type in sample_groups %}
         <div class="sample_group" style="width:{{ trait_table_width }}%;">
             <h3>{{ sample_type.header }}</h3>
-
+            <div id="table_container" style="background-color: #eeeeee; border: 1px solid black;">
             <table class="table-hover table-striped" id="samples_{{ sample_type.sample_group_type }}" style="float: left;">
                 <thead>
                     <tr>
-                        <th></th>
-                        <th>Index</th>
-                        <th>Sample</th>
-                        <th>Value</th>
+                        <th style="background-color: #eeeeee;"></th>
+                        <th style="background-color: #eeeeee;">Index</th>
+                        <th style="background-color: #eeeeee;">Sample</th>
+                        <th style="background-color: #eeeeee;">Value</th>
                         {% if sample_type.se_exists() %}
-                        <th>&nbsp;</th>
-                        <th>SE</th>
+                        <th style="background-color: #eeeeee;">&nbsp;</th>
+                        <th style="background-color: #eeeeee;">SE</th>
                         {% endif %}
                         {% for attribute in sample_type.attributes|sort() %}
-                        <th>
+                        <th style="background-color: #eeeeee;">
                             {{ sample_type.attributes[attribute].name }}
                         </th>
                         {% endfor %}
@@ -144,6 +144,7 @@
                     {% endfor %}
                 </tbody>
             </table>
+            </div>
         </div>
         {% endfor %}
     <!--</div>-->
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b7fcfa1d..df1f77bc 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -457,33 +457,47 @@ def marker_regression_page():
 
         result = template_vars.__dict__
 
-        #for item in template_vars.__dict__.keys():
-        #    print("  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
-        
-        gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
-
-        #qtl_length = len(result['js_data']['qtl_results'])
-        #print("qtl_length:", qtl_length)
-        pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
-        #print("pickled result length:", len(pickled_result))
-        Redis.set(key, pickled_result)
-        Redis.expire(key, 1*60)
-
-    with Bench("Rendering template"):
-        if result['pair_scan'] == True:
-            img_path = result['pair_scan_filename']
-            print("img_path:", img_path)
-            initial_start_vars = request.form
-            print("initial_start_vars:", initial_start_vars)
-            imgfile = open(TEMPDIR + '/' + img_path, 'rb')
-            imgdata = imgfile.read()
-            imgB64 = imgdata.encode("base64")
-            bytesarray = array.array('B', imgB64)
-            result['pair_scan_array'] = bytesarray
-            rendered_template = render_template("pair_scan_results.html", **result)
+        if result['pair_scan']:
+            with Bench("Rendering template"):
+                img_path = result['pair_scan_filename']
+                print("img_path:", img_path)
+                initial_start_vars = request.form
+                print("initial_start_vars:", initial_start_vars)
+                imgfile = open(TEMPDIR + img_path, 'rb')
+                imgdata = imgfile.read()
+                imgB64 = imgdata.encode("base64")
+                bytesarray = array.array('B', imgB64)
+                result['pair_scan_array'] = bytesarray
+                rendered_template = render_template("pair_scan_results.html", **result)        
         else:
-            #rendered_template = render_template("marker_regression.html", **result)
-            rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
+            #for item in template_vars.__dict__.keys():
+            #    print("  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
+            
+            gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
+
+            pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+            print("pickled result length:", len(pickled_result))
+            Redis.set(key, pickled_result)
+            Redis.expire(key, 1*60)
+            
+            with Bench("Rendering template"):
+                rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
+
+    # with Bench("Rendering template"):
+        # if result['pair_scan'] == True:
+            # img_path = result['pair_scan_filename']
+            # print("img_path:", img_path)
+            # initial_start_vars = request.form
+            # print("initial_start_vars:", initial_start_vars)
+            # imgfile = open(TEMPDIR + '/' + img_path, 'rb')
+            # imgdata = imgfile.read()
+            # imgB64 = imgdata.encode("base64")
+            # bytesarray = array.array('B', imgB64)
+            # result['pair_scan_array'] = bytesarray
+            # rendered_template = render_template("pair_scan_results.html", **result)
+        # else:
+            # rendered_template = render_template("marker_regression.html", **result)
+            # rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
 
     return rendered_template