Fixed a couple issues with the template that caused the

regular search results and show trait page to not display

5 files changed, 165 insertions, 57 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index d7328441..9b0a3dcc 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -735,8 +735,10 @@ class MrnaAssayDataSet(DataSet):
             trait_location_value = 1000000
 
             if this_trait.chr and this_trait.mb:
+                print("this_trait.chr is:", this_trait.chr)
+                print("this_trait.mb is:", this_trait.mb)
                 try:
-                    trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
+                    trait_location_value = float(this_trait.chr)*1000 + float(this_trait.mb)
                 except:
                     if this_trait.chr.upper() == 'X':
                         trait_location_value = 20*1000 + this_trait.mb
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index ad74f6cc..63aa481e 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -42,7 +42,7 @@ from utility import formatting
     #def __init__(self, key, result_fields):
     #    self.key = key
     #    self.result_fields = result_fields
-
+    
 
 class SearchResultPage(object):
     #maxReturn = 3000
@@ -73,6 +73,7 @@ class SearchResultPage(object):
             self.quick = True
             self.search_terms = kw['q']
             print("self.search_terms is: ", self.search_terms)
+            self.trait_type = kw['trait_type']
             self.quick_search()
         else:
             self.results = []
@@ -91,7 +92,7 @@ class SearchResultPage(object):
 
         """
         self.trait_list = []
-
+        
         species = webqtlDatabaseFunction.retrieve_species(self.dataset.group.name)
         
         # result_set represents the results for each search term; a search of 
@@ -100,7 +101,7 @@ class SearchResultPage(object):
         for result in self.results:
             if not result:
                 continue
-
+            
             #### Excel file needs to be generated ####
 
             print("foo locals are:", locals())
@@ -123,42 +124,46 @@ class SearchResultPage(object):
                     FROM QuickSearch
                     WHERE MATCH (terms)
                           AGAINST ('{}' IN BOOLEAN MODE) """.format(search_terms)
-        #print("query is: ", query)
         
         with Bench("Doing QuickSearch Query: "):
             dbresults = g.db.execute(query, no_parameters=True).fetchall()
         #print("results: ", pf(results))
-
+        
         self.results = collections.defaultdict(list)
-
+        
         type_dict = {'PublishXRef': 'phenotype',
                    'ProbeSetXRef': 'mrna_assay',
                    'GenoXRef': 'genotype'}
-
+        
         self.species_groups = {}
+        
         for dbresult in dbresults:
             this_result = {}
             this_result['table_name'] = dbresult.table_name
-            this_result['key'] = dbresult.the_key
-            this_result['result_fields'] = json.loads(dbresult.result_fields)
-            this_species = this_result['result_fields']['species']
-            this_group = this_result['result_fields']['group_name']
-            if this_species not in self.species_groups:
-                self.species_groups[this_species] = {}
-            if type_dict[dbresult.table_name] not in self.species_groups[this_species]:
-                self.species_groups[this_species][type_dict[dbresult.table_name]] = []
-            if this_group not in self.species_groups[this_species][type_dict[dbresult.table_name]]:
-                self.species_groups[this_species][type_dict[dbresult.table_name]].append(this_group)
-            #if type_dict[dbresult.table_name] not in self.species_groups:
-            #    self.species_groups[type_dict[dbresult.table_name]] = {}
-            #if this_species not in self.species_groups[type_dict[dbresult.table_name]]:
-            #    self.species_groups[type_dict[dbresult.table_name]][this_species] = []
-            #if this_group not in self.species_groups[type_dict[dbresult.table_name]][this_species]:
-            #    self.species_groups[type_dict[dbresult.table_name]][this_species].append(this_group)
-            self.results[type_dict[dbresult.table_name]].append(this_result)
-
-        #print("results: ", pf(self.results['phenotype']))
-
+            if self.trait_type == type_dict[dbresult.table_name] or self.trait_type == 'all':
+                this_result['key'] = dbresult.the_key
+                this_result['result_fields'] = json.loads(dbresult.result_fields)
+                this_species = this_result['result_fields']['species']
+                this_group = this_result['result_fields']['group_name']
+                if this_species not in self.species_groups:
+                    self.species_groups[this_species] = {}
+                if type_dict[dbresult.table_name] not in self.species_groups[this_species]:
+                    self.species_groups[this_species][type_dict[dbresult.table_name]] = []
+                if this_group not in self.species_groups[this_species][type_dict[dbresult.table_name]]:
+                    self.species_groups[this_species][type_dict[dbresult.table_name]].append(this_group)
+                #if type_dict[dbresult.table_name] not in self.species_groups:
+                #    self.species_groups[type_dict[dbresult.table_name]] = {}
+                #if this_species not in self.species_groups[type_dict[dbresult.table_name]]:
+                #    self.species_groups[type_dict[dbresult.table_name]][this_species] = []
+                #if this_group not in self.species_groups[type_dict[dbresult.table_name]][this_species]:
+                #    self.species_groups[type_dict[dbresult.table_name]][this_species].append(this_group)
+                self.results[type_dict[dbresult.table_name]].append(this_result)
+            
+        import redis
+        Redis = redis.Redis()
+        
+        
+        
     #def get_group_species_tree(self):
     #    self.species_groups = collections.default_dict(list)
     #    for key in self.results:
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index b4376ce3..a9f2cb24 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -32,7 +32,14 @@
                     </div>
                     <form method="get" action="/search"  name="SEARCHFORM">
                         <fieldset>
-                            <label for="quick">Search:</label>
+                            <div class="input-prepend">
+                                <select id="trait_type" name="trait_type" class="span2">
+                                    <option value="all">All</option>
+                                    <option value="mrna_assay">Molecular Assays</option>
+                                    <option value="phenotype">Phenotypes</option>
+                                    <option value="genotype">Genotypes</option>
+                                </select>
+                            </div>
                             <div class="input-append">
                                 <input class="input-xlarge"
                                     id="quick" name="q"
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index 01588924..b0e38708 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -26,7 +26,11 @@
             {% endif %}
         </ul>
 
-        <div id="species_level" class="tabbable"> <!-- Only required for left/right tabs -->
+
+        <div class="tabbable"> <!-- Only required for left/right tabs -->
+            {% if trait_type == 'all' %}
+                {% include 'all_results.html' %}
+            {% else %}
             <ul class="nav nav-tabs">
                 {% for species in species_groups %}
                 <li> <a href="#tab{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
@@ -34,11 +38,12 @@
             </ul>
             <div class="tab-content">
                 {% for species in species_groups %}
-                <div class="tab-pane" id="tab{{ loop.index }}">
-                    <div id="trait_type_level" class="tabbable tabs-left">
+                <div class="tab-pane active" id="tab{{ loop.index }}">
+                    <div>
+                        {#
                         <ul class="nav nav-tabs">
                             {% if species_groups[species]['phenotype'] %}
-                            <li> <a href="#tab{{ loop.index }}_1" data-toggle="tab">Phenotype</a></li>
+                            <li class="active"> <a href="#tab{{ loop.index }}_1" data-toggle="tab">Phenotype</a></li>
                             {% endif %}
                             {% if species_groups[species]['mrna_assay'] %}
                             <li> <a href="#tab{{ loop.index }}_2" data-toggle="tab">mRNA Assay</a></li>
@@ -47,9 +52,9 @@
                             <li> <a href="#tab{{ loop.index }}_3" data-toggle="tab">Genotype</a></li>
                             {% endif %}
                         </ul>
-                        <div class="tab-content">
-                            {% if species_groups[species]['phenotype'] %}
-                            <div class="tab-pane active" id="tab{{ loop.index }}_1">
+                        #}
+                        <div>
+                            {% if trait_type == 'phenotype' and species_groups[species]['phenotype'] %}
                                 <table id="pheno_results" class="table table-hover table-striped table-bordered">
                                     <thead>
                                         <tr>
@@ -82,10 +87,8 @@
                                         {% endfor %}
                                     </tbody>
                                 </table>
-                            </div>
                             {% endif %}
-                            {% if species_groups[species]['mrna_assay'] %}
-                            <div class="tab-pane" id="tab{{ loop.index }}_2">
+                            {% if trait_type == 'mrna_assay' and species_groups[species]['mrna_assay'] %}
                                 <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
                                     <thead>
                                         <tr>
@@ -105,7 +108,7 @@
                                         {% if result.result_fields['species'] == species %}
                                         <tr>
                                             <td>
-                                                <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}">
+                                                <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
                                                    {{ result.result_fields['name'] }}
                                                 </a>
                                             </td>
@@ -114,18 +117,16 @@
                                             <td>{{ result.result_fields['dataset_name'] }}</td>
                                             <td>{{ result.result_fields['symbol'] }}</td>
                                             <td>{{ result.result_fields['description'] }}</td>
-                                            <td>Chr {{ result.result_fields['chr'] }}: {{ result.result_fields['mb'] }}</td>
+                                            <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
                                             <td>{{ result.result_fields['mean'] }}</td>
                                             <td>{{ result.result_fields['lrs'] }}</td>
                                         </tr>
                                         {% endif %}
                                         {% endfor %}
                                     </tbody>
-                                </table>       
-                            </div>
+                                </table>
                             {% endif %}
-                            {% if species_groups[species]['genotype'] %}
-                            <div class="tab-pane" id="tab{{ loop.index }}_3">
+                            {% if trait_type == 'genotype' and species_groups[species]['genotype'] %}
                                 <table id="geno_results" class="table table-hover table-striped table-bordered">
                                     <thead>
                                         <tr>
@@ -153,14 +154,14 @@
                                         {% endif %}
                                         {% endfor %}
                                     </tbody>
-                                </table>   
-                            </div>
+                                </table>
                             {% endif %}
                         </div>
                     </div>
                 </div>
                 {% endfor %}
             </div>
+            {% endif %}
         </div>
     </div>
 
@@ -168,6 +169,105 @@
 
 {% endblock %}
 
+                {#
+                    <table id="pheno_results" class="table table-hover table-striped table-bordered">
+                        <thead>
+                            <tr>
+                            <th>Id</th>
+                            <th>Species</th>
+                            <th>Group</th>
+                            <th>Description</th>
+                            <th>LRS</th>
+                            <th>Year</th>
+                            <th>Authors</th>
+                            </tr>
+                        </thead>
+                        <tbody>
+                            {% for result in results.phenotype %}
+                            <tr>
+                                <td>{{ result.result_fields['phenotype_id'] }}</td>
+                                <td>{{ result.result_fields['species'] }}</td>
+                                <td>{{ result.result_fields['group_name'] }}</td>
+                                <td>{{ result.result_fields['description'] }}</td>
+                                <td>{{ result.result_fields['lrs'] }}</td>
+                                <td>
+                                    <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
+                                        {{ result.result_fields['year'] }}
+                                    </a>
+                                </td>
+                                <td>{{ result.result_fields['authors'] }}</td>
+                            </tr>
+                            {% endfor %}
+                        </tbody>
+                    </table>
+                </div>
+                <div class="tab-pane" id="tab2">
+                    <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
+                        <thead>
+                            <tr>
+                            <th>Record ID</th>
+                            <th>Species</th>
+                            <th>Group</th>
+                            <th>Data Set</th>
+                            <th>Symbol</th>
+                            <th>Description</th>
+                            <th>Location</th>
+                            <th>Mean Expr</th>
+                            <th>Max LRS</th>
+                            </tr>
+                        </thead>
+                        <tbody>
+                            {% for result in results.mrna_assay %}
+                            <tr>
+                                <td>
+                                    <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
+                                       {{ result.result_fields['name'] }}
+                                    </a>
+                                </td>
+                                <td>{{ result.result_fields['species'] }}</td>
+                                <td>{{ result.result_fields['group_name'] }}</td>
+                                <td>{{ result.result_fields['dataset_name'] }}</td>
+                                <td>{{ result.result_fields['symbol'] }}</td>
+                                <td>{{ result.result_fields['description'] }}</td>
+                                <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
+                                <td>{{ result.result_fields['mean'] }}</td>
+                                <td>{{ result.result_fields['lrs'] }}</td>
+                            </tr>
+                            {% endfor %}
+                        </tbody>
+                    </table>                    
+                </div>
+                <div class="tab-pane" id="tab3">
+                    <table id="geno_results" class="table table-hover table-striped table-bordered">
+                        <thead>
+                            <tr>
+                            <th>Marker</th>
+                            <th>Species</th>
+                            <th>Group</th>
+                            <th>Data Set</th>
+                            <th>Location</th>
+                            </tr>
+                        </thead>
+                        <tbody>
+                            {% for result in results.genotype %}
+                            <tr>
+                                <td>
+                                    <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
+                                        {{ result.result_fields['marker_name'] }}
+                                    </a>
+                                </td>
+                                <td>{{ result.result_fields['species'] }}</td>
+                                <td>{{ result.result_fields['group_name'] }}</td>
+                                <td>{{ result.result_fields['dataset_name'] }}</td>
+                                <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
+                            </tr>
+                            {% endfor %}
+                        </tbody>
+                    </table>                     
+                </div>
+                #}
+
+
 {% block js %}  
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
@@ -175,16 +275,9 @@
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
 
+    
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
-            
-            $("div[id^='tab'").bind('click', function(){
-                tab_id = $(this).attr('id');
-                $("a[href^='"+tab_id+"']").first().trigger('click');
-            });
-            
-            $('#species_level ul li:first').addClass('active');
-            $('#trait_type_level ul li:first').addClass('active');
             console.time("Creating table");
             $('#pheno_results, #mrna_assay_results, #geno_results').dataTable( {
                 //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
@@ -210,3 +303,4 @@
         });
     </script>
 {% endblock %}
+
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index c3abfc9f..b57c3c21 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -19,11 +19,11 @@
             BLAT Specifity
         </a>
     </dt>
-    <dd>{{ "%.1f" % (this_trait.probe_set_specificity) }}</dd>
+    <dd>{{ "%s" % (this_trait.probe_set_specificity) }}</dd>
     {% endif %}
     {% if this_trait.probe_set_blat_score %}
     <dt>BLAT Score</dt>
-    <dd>{{ "%i" % (this_trait.probe_set_blat_score) }}</dd>
+    <dd>{{ "%s" % (this_trait.probe_set_blat_score) }}</dd>
     {% endif %}
 </dl>