From 7ff0dcda04dc853620bb5162180f18db596f1574 Mon Sep 17 00:00:00 2001
From: Lei Yan
Date: Thu, 21 Aug 2014 18:56:29 +0000
Subject: Committer: Lei Yan <lei@penguin.uthsc.edu> On branch master

---
 wqflask/base/data_set.py                         | 4 ++--
 wqflask/base/trait.py                            | 8 +-------
 wqflask/wqflask/correlation/show_corr_results.py | 6 +-----
 wqflask/wqflask/templates/correlation_page.html  | 8 ++++----
 4 files changed, 8 insertions(+), 18 deletions(-)

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index c2a05c90..3fb7203d 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -579,10 +579,10 @@ class DataSet(object):
                         """.format(*mescape(self.type, self.type, self.type, self.type,
                                    self.name, dataset_type, self.type, self.type, dataset_type))
                         
-            print("trait data query: ", query)
+            #print("trait data query: ", query)
             
             results = g.db.execute(query).fetchall()
-            print("query results:", results)
+            #print("query results:", results)
             trait_sample_data.append(results)
 
         trait_count = len(trait_sample_data[0])
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 2bbd1f2a..71691899 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -315,7 +315,7 @@ class GeneralTrait(object):
                             ProbeSet.Name = '%s'
                     """ % (escape(display_fields_string),
                            escape(self.dataset.name),
-                           escape(self.name))
+                           escape(str(self.name)))
             trait_info = g.db.execute(query).fetchone()
         #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
         # to avoid the problem of same marker name from different species.
@@ -340,10 +340,6 @@ class GeneralTrait(object):
                                      """ % (string.join(self.dataset.display_fields,','),
                                             self.dataset.type, self.name)
             trait_info = g.db.execute(query).fetchone()
-
-
-        #self.cursor.execute(query)
-        #trait_info = self.cursor.fetchone()
         if trait_info:
             self.haveinfo = True
 
@@ -440,8 +436,6 @@ class GeneralTrait(object):
                                     PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
                                     PublishFreeze.Id =%s
                             """, (self.name, self.dataset.id)).fetchone()
-                    #self.cursor.execute(query)
-                    #trait_qtl = self.cursor.fetchone()
                     if trait_qtl:
                         self.locus, self.lrs = trait_qtl
                     else:
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 06cf1915..f35fe075 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -164,7 +164,7 @@ class CorrelationResults(object):
 
             for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
                 print("trait name:", trait)
-                trait_object = GeneralTrait(dataset=self.dataset, name=trait, get_qtl_info=True)
+                trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True)
                 
                 (trait_object.sample_r,
                 trait_object.sample_p,
@@ -474,10 +474,6 @@ class CorrelationResults(object):
                 this_trait_vals.append(sample_value)
                 target_vals.append(target_sample_value)
 
-        # print("trait:", trait)
-        print("this_trait_vals: %s" % this_trait_vals)
-        print("target_vals: %s" % target_vals)
-
         this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
             this_trait_vals, target_vals)
 
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 88f6d65a..fc5aca42 100755
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -24,7 +24,7 @@
             <table id="corr_results" class="table table-hover table-striped table-bordered">
                 <thead>
                     <tr>
-                    {% if dataset.type == 'ProbeSet' %}
+                    {% if target_dataset.type == 'ProbeSet' %}
                         <th>Trait</th>
                         <th>Symbol</th>
                         <th>Description</th>
@@ -47,7 +47,7 @@
                         <th>Tissue rho</th>
                         <th>Tissue p(rho)</th>
                         {% endif %}
-                    {% elif dataset.type == "Publish" %}
+                    {% elif target_dataset.type == "Publish" %}
                         <th>Record ID</th>
                         <th>Phenotype</th>
                         <th>Authors</th>
@@ -67,7 +67,7 @@
                 <tbody>
                 {% for trait in correlation_results %}
                     <tr>
-                    {% if dataset.type == 'ProbeSet' %}
+                    {% if target_dataset.type == 'ProbeSet' %}
                         <td><a href="/show_trait?trait_id={{trait.name}}&amp;dataset={{trait.dataset.name}}">{{ trait.name }}</a></td>
                         <td>{{ trait.symbol }}</td>
                         <td>{{ trait.description }} <br><br> <b>Aliases</b>: {{ trait.alias }}</td>
@@ -81,7 +81,7 @@
                         <td>{{'%0.3f'|format(trait.lit_corr)}}</td>
                         <td>{{'%0.3f'|format(trait.tissue_corr)}}</td>
                         <td>{{'%0.3e'|format(trait.tissue_pvalue)}}</td>
-                    {% elif dataset.type == "Publish" %}
+                    {% elif target_dataset.type == "Publish" %}
                         <td><a href="/show_trait?trait_id={{trait.name}}&amp;dataset={{trait.dataset.name}}">{{ trait.name }}</a></td>
                         <td>{{ trait.post_publication_description }}</td>
                         <td>{{ trait.authors }}</td>
-- 
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