From 5a3f413da480123e3ad943b5f556e0a557f185cc Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 9 May 2013 22:54:34 +0000
Subject: Just added some print statements so I can show matrix/vector shapes
 to Tony

---
 wqflask/base/data_set.py                           |  2 +-
 .../wqflask/marker_regression/marker_regression.py |  5 +++--
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py              | 24 +++++++++++++++-------
 3 files changed, 21 insertions(+), 10 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1520b180..d7328441 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -385,7 +385,7 @@ class PhenotypeDataSet(DataSet):
                 continue   # for now
                 if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users):
                     description = this_trait.pre_publication_description
-            this_trait.description_display = description
+            this_trait.description_display = unicode(description, "utf8")
 
             if not this_trait.year.isdigit():
                 this_trait.pubmed_text = "N/A"
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 6ae1318e..334ce631 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -78,8 +78,9 @@ class MarkerRegression(object):
             
             genotype_matrix = np.array(trimmed_genotype_data).T
             
-            print("pheno_vector is: ", pf(pheno_vector))
-            print("genotype_matrix is: ", pf(genotype_matrix))
+            print("pheno_vector: ", pf(pheno_vector))
+            print("genotype_matrix: ", pf(genotype_matrix))
+            print("genotype_matrix.shape: ", pf(genotype_matrix.shape))
             
             t_stats, p_values = lmm.run(
                 pheno_vector,
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index fc021a0b..62fb0fbd 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -58,6 +58,10 @@ def run_human(pheno_vector,
 
     identifier = str(uuid.uuid4())
     
+    print("pheno_vector: ", pf(pheno_vector))
+    print("kinship_matrix: ", pf(kinship_matrix))
+    print("kinship_matrix.shape: ", pf(kinship_matrix.shape))
+
     lmm_vars = pickle.dumps(dict(
         pheno_vector = pheno_vector,
         covariate_matrix = covariate_matrix,
@@ -70,12 +74,12 @@ def run_human(pheno_vector,
         pheno_vector = pheno_vector[keep]
         #print("pheno_vector shape is now: ", pf(pheno_vector.shape))
         covariate_matrix = covariate_matrix[keep,:]
-        print("kinship_matrix shape is: ", pf(kinship_matrix.shape))
+        #print("kinship_matrix shape is: ", pf(kinship_matrix.shape))
         #print("len(keep) is: ", pf(keep.shape))
         kinship_matrix = kinship_matrix[keep,:][:,keep]
 
     n = kinship_matrix.shape[0]
-    print("n is:", n)
+    #print("n is:", n)
     lmm_ob = LMM(pheno_vector,
                 kinship_matrix,
                 covariate_matrix)
@@ -86,7 +90,7 @@ def run_human(pheno_vector,
     p_values = []
     t_stats = []
 
-    print("input_file: ", plink_input_file)
+    #print("input_file: ", plink_input_file)
 
     with Bench("Opening and loading pickle file"):
         with gzip.open(plink_input_file, "rb") as input_file:
@@ -103,6 +107,8 @@ def run_human(pheno_vector,
 
         with Bench("Create list of inputs"):
             inputs = list(plink_input)
+            
+        print("len(genotypes): ", len(inputs))
 
         with Bench("Divide into chunks"):
             results = chunks.divide_into_chunks(inputs, 64)
@@ -116,7 +122,7 @@ def run_human(pheno_vector,
         
         timestamp = datetime.datetime.utcnow().isoformat()
 
-        print("Starting adding loop")
+        #print("Starting adding loop")
         for part, result in enumerate(results):
             #data = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
             holder = pickle.dumps(dict(
@@ -126,10 +132,10 @@ def run_human(pheno_vector,
                 result = result
             ), pickle.HIGHEST_PROTOCOL)
             
-            print("Adding:", part)
+            #print("Adding:", part)
             Redis.rpush(key, zlib.compress(holder))
-        print("End adding loop")
-        print("***** Added to {} queue *****".format(key))
+        #print("End adding loop")
+        #print("***** Added to {} queue *****".format(key))
         for snp, this_id in plink_input:
             #with Bench("part before association"):
             if count > 2000:
@@ -157,6 +163,10 @@ def run_human(pheno_vector,
     return p_values, t_stats
 
 
+#class HumanAssociation(object):
+#    def __init__(self):
+#        
+
 def human_association(snp,
                       n,
                       keep,
-- 
cgit v1.2.3


From 04b61737236b837e91355b66cbaab3549bc39140 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 16 May 2013 23:31:54 +0000
Subject: Made the first level of quick search tabs species, followed by trait
 type (was the opposite before Rob commented on it earlier today)

---
 wqflask/wqflask/search_results.py           | 19 ++++---
 wqflask/wqflask/templates/quick_search.html | 86 +++++++++++------------------
 2 files changed, 45 insertions(+), 60 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 5f3c036f..9b2751e0 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -74,7 +74,6 @@ class SearchResultPage(object):
             self.search_terms = kw['q']
             print("self.search_terms is: ", self.search_terms)
             self.quick_search()
-            self.get_group_species_tree()
         else:
             self.results = []
             #self.quick_search = False
@@ -144,12 +143,18 @@ class SearchResultPage(object):
             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 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] = collections.defaultdict(list)
-            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)
+            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']))
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index 9d5b0c74..5877a840 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -25,33 +25,31 @@
             </li>
             {% endif %}
         </ul>
-        
-        <p>To study a record, click on its ID below.<br />
-        Check records below and click Add button to add to selection.</p>
 
-        <div class="tabbable"> <!-- Only required for left/right tabs -->
+        <div id="species_level" class="tabbable"> <!-- Only required for left/right tabs -->
             <ul class="nav nav-tabs">
-                {% if results.phenotype %}
-                <li class="active"> <a href="#tab1" data-toggle="tab">Phenotype</a></li>
-                {% endif %}
-                {% if results.mrna_assay %}
-                <li>                <a href="#tab2" data-toggle="tab">mRNA Assay</a></li>
-                {% endif %}
-                {% if results.genotype %}
-                <li>                <a href="#tab3" data-toggle="tab">Genotype</a></li>
-                {% endif %}
+                {% for species in species_groups %}
+                <li> <a href="#tab{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
+                {% endfor %}
             </ul>
             <div class="tab-content">
-                <div class="tab-pane active" id="tab1">
-                    <div class="tabbable tabs-left">
+                {% for species in species_groups %}
+                <div class="tab-pane" id="tab{{ loop.index }}">
+                    <div id="trait_type_level" class="tabbable tabs-left">
                         <ul class="nav nav-tabs">
-                            {% for species in species_groups.phenotype %}
-                            <li> <a href="#tab1_{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
-                            {% endfor %}
+                            {% if species_groups[species]['phenotype'] %}
+                            <li> <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>
+                            {% endif %}
+                            {% if species_groups[species]['genotype'] %}
+                            <li> <a href="#tab{{ loop.index }}_3" data-toggle="tab">Genotype</a></li>
+                            {% endif %}
                         </ul>
                         <div class="tab-content">
-                            {% for species in species_groups.phenotype %}
-                            <div class="tab-pane active" id="tab{{ loop.index }}">
+                            {% if species_groups[species]['phenotype'] %}
+                            <div class="tab-pane active" id="tab{{ loop.index }}_1">
                                 <table id="pheno_results" class="table table-hover table-striped table-bordered">
                                     <thead>
                                         <tr>
@@ -85,20 +83,9 @@
                                     </tbody>
                                 </table>
                             </div>
-                            {% endfor %}
-                        </div>
-                    </div>
-                </div>
-                <div class="tab-pane active" id="tab2">
-                    <div class="tabbable tabs-left">
-                        <ul class="nav nav-tabs">
-                            {% for species in species_groups.mrna_assay %}
-                            <li> <a href="#tab2_{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
-                            {% endfor %}
-                        </ul>
-                        <div class="tab-content">
-                            {% for species in species_groups.mrna_assay %}
-                            <div class="tab-pane active" id="tab{{ loop.index }}">
+                            {% endif %}
+                            {% if species_groups[species]['mrna_assay'] %}
+                            <div class="tab-pane" id="tab{{ loop.index }}_2">
                                 <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
                                     <thead>
                                         <tr>
@@ -136,20 +123,9 @@
                                     </tbody>
                                 </table>       
                             </div>
-                            {% endfor %}
-                        </div>
-                    </div>
-                </div>
-                <div class="tab-pane active" id="tab3">
-                    <div class="tabbable tabs-left">
-                        <ul class="nav nav-tabs">
-                            {% for species in species_groups.genotype %}
-                            <li> <a href="#tab3_{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
-                            {% endfor %}
-                        </ul>
-                        <div class="tab-content">
-                            {% for species in species_groups.genotype %}
-                            <div class="tab-pane active" id="tab{{ loop.index }}">
+                            {% endif %}
+                            {% if species_groups[species]['genotype'] %}
+                            <div class="tab-pane" id="tab{{ loop.index }}_3">
                                 <table id="geno_results" class="table table-hover table-striped table-bordered">
                                     <thead>
                                         <tr>
@@ -179,14 +155,19 @@
                                     </tbody>
                                 </table>   
                             </div>
-                            {% endfor %}
+                            {% endif %}
                         </div>
                     </div>
                 </div>
+                {% endfor %}
             </div>
         </div>
     </div>
-    
+
+<!-- End of body -->
+
+{% endblock %}
+
                 {#
                     <table id="pheno_results" class="table table-hover table-striped table-bordered">
                         <thead>
@@ -285,9 +266,6 @@
                 </div>
                 #}
 
-<!-- End of body -->
-
-{% endblock %}
 
 {% block js %}  
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
@@ -299,6 +277,8 @@
     
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
+            $('#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>>",
-- 
cgit v1.2.3


From 668d6be6286c646cb1ce8cc4d415aa65640bc84c Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Fri, 17 May 2013 23:05:36 +0000
Subject: Did a little work with quick search page

---
 wqflask/wqflask/search_results.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 9b2751e0..ad74f6cc 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
@@ -91,7 +91,7 @@ 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 +100,7 @@ class SearchResultPage(object):
         for result in self.results:
             if not result:
                 continue
-            
+
             #### Excel file needs to be generated ####
 
             print("foo locals are:", locals())
@@ -128,13 +128,13 @@ class SearchResultPage(object):
         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 = {}
@@ -156,9 +156,9 @@ class SearchResultPage(object):
             #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']))
-        
+
     #def get_group_species_tree(self):
     #    self.species_groups = collections.default_dict(list)
     #    for key in self.results:
-- 
cgit v1.2.3


From aeb0e9b723c296709381807af136ccc33b84365e Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Tue, 21 May 2013 22:22:00 +0000
Subject: Added caching to the search page (for both regular and quick
 searckes)

---
 wqflask/wqflask/do_search.py              |  8 ++++----
 wqflask/wqflask/templates/index_page.html |  3 ---
 wqflask/wqflask/views.py                  | 34 +++++++++++++++++++++----------
 3 files changed, 27 insertions(+), 18 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 1b1b56fb..7b3e0869 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -36,7 +36,7 @@ class DoSearch(object):
     def execute(self, query):
         """Executes query and returns results"""
         query = self.normalize_spaces(query)
-        print("in do_search query is:", pf(query))
+        #print("in do_search query is:", pf(query))
         results = g.db.execute(query, no_parameters=True).fetchall()
         #results = self.cursor.fetchall()
         return results
@@ -90,7 +90,7 @@ class QuickMrnaAssaySearch(DoSearch):
                     AGAINST ('%s' IN BOOLEAN MODE))
                             """ % (escape(self.search_term[0]))
 
-        print("final query is:", pf(query))
+        #print("final query is:", pf(query))
 
         return self.execute(query)
 
@@ -134,7 +134,7 @@ class MrnaAssaySearch(DoSearch):
                                     where_clause,
                                     escape(self.dataset.id)))        
 
-        print("query is:", pf(query))
+        #print("query is:", pf(query))
 
         return query
 
@@ -155,7 +155,7 @@ class MrnaAssaySearch(DoSearch):
                             """ % (escape(self.search_term[0]),
                             escape(str(self.dataset.id)))
 
-        print("final query is:", pf(query))
+        #print("final query is:", pf(query))
 
         return self.execute(query)
 
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 0cc1c353..b4376ce3 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -9,7 +9,6 @@
         <div class="container">
             <h1>GeneNetwork</h1>
             <p class="lead">Open source bioinformatics for systems genetics</p>
-            <p>- Lei Yan</p>
         </div>
     </header>
 
@@ -43,11 +42,9 @@
                                     class="btn btn-primary" value="Search">
                             </div>
                         </fieldset>
-                       
                     </form>
                 </section>
                 <section id="search">
-                    
                     <div class="page-header">
                         <h1>Select and search</h1>
                     </div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 8531561a..1af324b2 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -76,17 +76,28 @@ def search_page():
         else:
             return render_template("data_sharing.html", **template_vars.__dict__)
     else:
-        print("calling search_results.SearchResultPage")
-        the_search = search_results.SearchResultPage(request.args)
-        print("template_vars is:", pf(the_search.__dict__))
-        #print("trait_list is:", pf(the_search.__dict__['trait_list'][0].__dict__))
-        #for trait in the_search.trait_list:
-        #    print(" -", trait.description_display)
-
-        if the_search.quick:
-            return render_template("quick_search.html", **the_search.__dict__)
+        key = "search_results:v2:" + json.dumps(request.args, sort_keys=True)
+        print("key is:", pf(key))
+        with Bench("Loading cache"):
+            result = Redis.get(key)
+
+        if result:
+            print("Cache hit!!!")
+            with Bench("Loading results"):
+                result = pickle.loads(result)
         else:
-            return render_template("search_result_page.html", **the_search.__dict__)
+            print("calling search_results.SearchResultPage")
+            the_search = search_results.SearchResultPage(request.args)
+            result = the_search.__dict__
+            
+            print("result: ", pf(result))
+            Redis.set(key, pickle.dumps(result))
+            Redis.expire(key, 60*60)
+
+        if result['quick']:
+            return render_template("quick_search.html", **result)
+        else:
+            return render_template("search_result_page.html", **result)
 
 
 @app.route("/whats_new")
@@ -171,9 +182,10 @@ def marker_regression_page():
     for key, value in initial_start_vars.iteritems():
         if key in wanted or key.startswith(('value:')):
             start_vars[key] = value
-    
+
     version = "v14"
     key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
+    print("key is:", pf(key))
     with Bench("Loading cache"):
         result = Redis.get(key)
     
-- 
cgit v1.2.3


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"):
-- 
cgit v1.2.3


From 7938d8c6cbdfe866ebf9ec62dec0fe5c43cf2d6f Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Wed, 12 Jun 2013 22:45:57 +0000
Subject: Fixed a couple issues with the template that caused the regular
 search results and show trait page to not display

---
 wqflask/base/data_set.py                          |   4 +-
 wqflask/wqflask/search_results.py                 |  59 +++++----
 wqflask/wqflask/templates/index_page.html         |   9 +-
 wqflask/wqflask/templates/quick_search.html       | 146 ++++++++++++++++++----
 wqflask/wqflask/templates/show_trait_details.html |   4 +-
 5 files changed, 165 insertions(+), 57 deletions(-)

(limited to 'wqflask')

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>
 
-- 
cgit v1.2.3


From aac1dd2f9c5b216b24c6e35676ba5d50f9d5d3c2 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 13 Jun 2013 20:15:30 +0000
Subject: Put the template html for the quick search page when all trait types
 are displayed in a separate file that is included in quick_search.html

---
 wqflask/wqflask/templates/all_results.html | 134 +++++++++++++++++++++++++++++
 1 file changed, 134 insertions(+)
 create mode 100644 wqflask/wqflask/templates/all_results.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/templates/all_results.html b/wqflask/wqflask/templates/all_results.html
new file mode 100644
index 00000000..a42e42d8
--- /dev/null
+++ b/wqflask/wqflask/templates/all_results.html
@@ -0,0 +1,134 @@
+            <ul class="nav nav-tabs">
+                {% for species in species_groups %}
+                <li> <a href="#tab{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
+                {% endfor %}
+            </ul>
+            <div class="tab-content">
+                {% for species in species_groups %}
+                <div class="tab-pane active" id="tab{{ loop.index }}">
+                    <div class="tabbable tabs-left">
+                        <ul class="nav nav-tabs">
+                            {% if species_groups[species]['phenotype'] %}
+                            <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>
+                            {% endif %}
+                            {% if species_groups[species]['genotype'] %}
+                            <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">
+                                <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 %}
+                                        {% if result.result_fields['species'] == species %}
+                                        <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>
+                                        {% endif %}
+                                        {% endfor %}
+                                    </tbody>
+                                </table>
+                            </div>
+                            {% endif %}
+                            {% if species_groups[species]['mrna_assay'] %}
+                            <div class="tab-pane" id="tab{{ loop.index }}_2">
+                                <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 %}
+                                        {% 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'] }}"
+                                                   {{ 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>
+                                        {% endif %}
+                                        {% endfor %}
+                                    </tbody>
+                                </table>       
+                            </div>
+                            {% endif %}
+                            {% if species_groups[species]['genotype'] %}
+                            <div class="tab-pane" id="tab{{ loop.index }}_3">
+                                <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 %}
+                                        {% if result.result_fields['species'] == species %}
+                                        <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>
+                                        {% endif %}
+                                        {% endfor %}
+                                    </tbody>
+                                </table>   
+                            </div>
+                            {% endif %}
+                        </div>
+                    </div>
+                </div>
+                {% endfor %}
+            </div>
\ No newline at end of file
-- 
cgit v1.2.3