From 43eb99c11d8ef371bba926a3a63bf599b56820ae Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Fri, 31 May 2013 16:01:31 +0000
Subject: Fixed the location column for the quick search page

Began writing some jquery to automatically open the first tab
within each species tab on the quick search page (not done yet)
---
 wqflask/base/trait.py                       |   2 +-
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py       |   2 +
 wqflask/wqflask/templates/quick_search.html | 110 ++--------------------------
 wqflask/wqflask/views.py                    |   2 +-
 4 files changed, 12 insertions(+), 104 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7c1c035c..dde8b8d8 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -302,7 +302,7 @@ class GeneralTrait:
 
             #XZ: assign SQL query result to trait attributes.
             for i, field in enumerate(self.dataset.display_fields):
-                setattr(self, field, traitInfo[i])
+                setattr(self, field, str(traitInfo[i]))
 
             if self.dataset.type == 'Publish':
                 self.confidential = 0
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 62fb0fbd..5bfc3a01 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -243,6 +243,8 @@ def run(pheno_vector,
     with Bench("LMM_ob fitting"):
         lmm_ob.fit()
 
+    print("genotype_matrix: ", genotype_matrix.shape)
+
     with Bench("Doing GWAS"):
         t_stats, p_values = GWAS(pheno_vector,
                                 genotype_matrix,
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index 5877a840..01588924 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -105,7 +105,7 @@
                                         {% 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>
@@ -114,7 +114,7 @@
                                             <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>Chr {{ result.result_fields['chr'] }}: {{ result.result_fields['mb'] }}</td>
                                             <td>{{ result.result_fields['mean'] }}</td>
                                             <td>{{ result.result_fields['lrs'] }}</td>
                                         </tr>
@@ -168,105 +168,6 @@
 
 {% 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>
@@ -274,9 +175,14 @@
     <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");
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 1af324b2..4480e8da 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -80,7 +80,7 @@ def search_page():
         print("key is:", pf(key))
         with Bench("Loading cache"):
             result = Redis.get(key)
-
+            
         if result:
             print("Cache hit!!!")
             with Bench("Loading results"):
-- 
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