Searches work for the full access human datasets with mRNA assay

searches, and the trait page can be loaded

Need to get marker regression page working with human data now

5 files changed, 28 insertions, 10 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 10f047f8..71efc9b2 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -185,9 +185,8 @@ class DataSet(object):
         
         self.group = DatasetGroup(self)   # sets self.group and self.group_id and gets genotype
         self.species = species.TheSpecies(self)
-    
-       
-        
+
+
     def get_desc(self):
         """Gets overridden later, at least for Temp...used by trait's get_given_name"""
         return None
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 9278c80d..1a0efcee 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -65,6 +65,9 @@ class MarkerRegression(object):
         pheno_vector = np.array([float(val) for val in self.vals if val!="x"])
         genotype_matrix = np.array(trimmed_genotype_data).T
 
+        print("pheno_vector is: ", pf(pheno_vector))
+        print("genotype_matrix is: ", pf(genotype_matrix))
+
         t_stats, p_values = lmm.run(
             pheno_vector,
             genotype_matrix,
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index fde30944..080568f0 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -57,15 +57,18 @@ class SearchResultPage():
         #    self.dataset_groups = map(lambda x: x[1], results)
         #    self.dataset_group_ids = map(lambda x: x[2], results)
         #else:
-        if kw['q']:
+        
+        self.results = []
+        
+        if 'q' in kw:
             self.quick_search = True
             self.search_terms = kw['q']
+            self.quick_search()
         else:
             self.quick_search = False
             self.search_terms = kw['search_terms']
             self.dataset = create_dataset(kw['dataset'])
-
-        self.search()
+            self.search()
         self.gen_search_result()
 
 
@@ -95,13 +98,24 @@ class SearchResultPage():
             self.trait_list.append(this_trait)
 
         self.dataset.get_trait_info(self.trait_list, species)
+        
+    def quick_search(self):
+
+        return True
+
+        #search_gene
+        #search_geno
+        #searhch_pheno
+        #search_mrn
+        #searhc_publish
 
 
     def search(self):
         self.search_terms = parser.parse(self.search_terms)
         print("After parsing:", self.search_terms)
 
-        self.results = []
+        
+        
         for a_search in self.search_terms:
             print("[kodak] item is:", pf(a_search))
             search_term = a_search['search_term']
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 12d512b2..5c064359 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1552,8 +1552,10 @@ class ShowTrait(object):
             all_samples_ordered = (self.dataset.group.parlist +
                                    self.dataset.group.f1list +
                                    self.dataset.group.samplelist)
-        else:
+        elif self.dataset.group.f1list:
             all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
+        else:
+            all_samples_ordered = self.dataset.group.samplelist
 
         this_trait_samples = set(this_trait.data.keys())
 
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 8a05173f..46a307b7 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -34,10 +34,10 @@
                     </div>
                     <form method="get" action="/search"  name="SEARCHFORM">
                         <fieldset>
-                            <label for="tfor">Search:</label>
+                            <label for="quick">Search:</label>
                             <div class="input-append">
                                 <input class="input-xlarge"
-                                    id="tfor" name="q"
+                                    id="quick" name="q"
                                     type="text" maxlength="500">
                                     
                                 <input id="btsearch" type="submit"