Merge /home/zas1024/gene

9 files changed, 24 insertions, 50 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 9fa7beb3..f25e7974 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -322,7 +322,7 @@ class DatasetGroup(object):
             self.incparentsf1 = 0
             self.genotype = genotype_1
 
-        self.samplelist = list(genotype.prgy)
+        self.samplelist = list(self.genotype.prgy)
 
 
 #class DataSets(object):
@@ -440,10 +440,12 @@ class DataSet(object):
         
     def get_trait_data(self, sample_list=None):
         if sample_list:
-            self.samplelist = sample_list + self.group.parlist + self.group.f1list
+            self.samplelist = sample_list
         else:
-            self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
-        
+            self.samplelist = self.group.samplelist
+            
+        if (self.group.parlist + self.group.f1list) in self.samplelist:
+            self.samplelist += self.group.parlist + self.group.f1list
         
         query = """
             SELECT Strain.Name, Strain.Id FROM Strain, Species
@@ -503,8 +505,8 @@ class DataSet(object):
                         and {}Freeze.Name = '{}'
                         and {}.Id = {}XRef.{}Id
                         order by {}.Id
-                        """.format(*mescape(self.type, self.type, self.type, self.type,
-                                   self.name, dataset_type, self.type, self.type, dataset_type))
+                        """.format(*mescape(self.type, self.type, self.type, self.name, 
+                                    dataset_type, self.type, dataset_type, dataset_type))
             else:
                 query += """
                         WHERE {}XRef.{}FreezeId = {}Freeze.Id
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index a5c80674..8f23165c 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -178,10 +178,10 @@ class CorrelationResults(object):
                     trait_object.lit_corr = lit_corr_data[trait][1]
                 self.correlation_results.append(trait_object)
             
-            if self.corr_type != "lit":
+            if self.corr_type != "lit" and self.dataset.type == "ProbeSet":
                 self.do_lit_correlation_for_trait_list()
             
-            if self.corr_type != "tissue":
+            if self.corr_type != "tissue" and self.dataset.type == "ProbeSet":
                 self.do_tissue_correlation_for_trait_list()
             
             #print("self.correlation_results: ", pf(self.correlation_results))
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 8efba6a7..a14eeb44 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -29,9 +29,9 @@
 {% macro header(main, second) %}
     <header class="jumbotron subhead" id="overview">
         <div class="container">
-            <h1>Login</h1>
+            <h1>{{ main }}</h1>
             <p class="lead">
-               Gain access to GeneNetwork.
+               {{ second }}
             </p>               
         </div>
     </header>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 4d09cf20..7e149506 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -6,12 +6,8 @@
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
 {% endblock %}
 {% block content %}
-
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>Correlation</h1>
-        </div>
-    </header>
+    
+    {{ header("Correlation", 'Trait: {} Dataset: {}'.format(this_trait.name, dataset.name)) }}
 
     <table id="corr_results" class="table table-hover table-striped table-bordered">
         <thead>
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 98682e57..d177a7bd 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -3,8 +3,6 @@
 {% block content %}
 <!-- Start of body -->
 
-
-
     <header class="jumbotron subhead" id="overview">
         <div class="container">
             <h1>GeneNetwork</h1>
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 9260acab..64d2e9b7 100644
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -9,14 +9,8 @@
 {% endblock %}
 {% block content %} <!-- Start of body -->
 
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>Marker Regression</h1>
-            <p class="lead">
-                {{ this_trait.name }}: {{ this_trait.description_fmt }}
-            </p>
-        </div>
-    </header>
+    {{ header("Marker Regression",
+        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
 
     <div class="container">
         <div>
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index b0e38708..2f268c5a 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -2,14 +2,9 @@
 {% block title %}QuickSearch Results{% endblock %}
 {% block content %}
 <!-- Start of body -->
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>QuickSearch Results</h1>
-            <p class="lead">
-                GeneNetwork found {{ numify(results|count, "record", "records") }}.
-            </p>
-        </div>
-    </header>
+
+    {{ header("QuickSearch Results",
+        'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
 
     <div class="container">
         <div class="page-header">
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 11f68bba..1fe7cce9 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -2,14 +2,8 @@
 {% block title %}Search Results{% endblock %}
 {% block content %}
 <!-- Start of body -->
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>Search Results</h1>
-            <p class="lead">
-                GeneNetwork found {{ numify(results|count, "record", "records") }}.
-            </p>
-        </div>
-    </header>
+    {{ header("Search Results",
+        'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
 
     <div class="container">
         <div class="page-header">
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 799245c3..e3c84de7 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -7,14 +7,9 @@
 {% endblock %}
 {% block content %} <!-- Start of body -->
 
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>{{ this_trait.symbol}}</h1>
-            <p class="lead">
-                {{ this_trait.name }}: {{ this_trait.description_fmt }}
-            </p>
-        </div>
-    </header>
+    {{ header("{}".format(this_trait.symbol),
+        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+
 
     <form method="post" action="/corr_compute" name="trait_page" id="trait_data_form"
     class="form-horizontal">