Merge pull request #256 from genenetwork/development

Variety of changes

3 files changed, 11 insertions, 7 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4959457a..dbdbb51c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -169,7 +169,7 @@ def mescape(*items):
 class Markers(object):
     """Todo: Build in cacheing so it saves us reading the same file more than once"""
     def __init__(self, name):
-        json_data_fh = open(locate(name + '.json','genotype/json'))
+        json_data_fh = open(locate(name + ".json",'genotype/json'))
         try:
             markers = json.load(json_data_fh)
         except:
@@ -334,7 +334,10 @@ class DatasetGroup(object):
         else:
             marker_class = Markers            
 
-        self.markers = marker_class(self.name)
+        if self.genofile:
+            self.markers = marker_class(self.genofile[:-5])
+        else:
+            self.markers = marker_class(self.name)
 
     def get_f1_parent_strains(self):
         try:
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index e22a51e4..acc055d8 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -206,6 +206,8 @@ class GeneralTrait(object):
                 formatted = self.description
                 if self.probe_target_description:
                     formatted += "; " + self.probe_target_description
+            else:
+                formatted = "Not available"
         elif self.dataset.type == 'Publish':
             if self.confidential:
                 formatted = self.pre_publication_description
@@ -290,7 +292,6 @@ def retrieve_sample_data(trait, dataset, samplelist=None):
             name, value, variance, num_cases, name2 = item
             if not samplelist or (samplelist and name in samplelist):
                 trait.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
-                
     return trait
         
 def convert_location_to_value(chromosome, mb):
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 845a7224..24de8dcb 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -44,9 +44,9 @@ class webqtlCaseData(object):
 
     def __repr__(self):
         str = "<webqtlCaseData> "
-        if self.value:
+        if self.value != None:
             str += "value=%2.3f" % self.value
-        if self.variance:
+        if self.variance != None:
             str += " variance=%2.3f" % self.variance
         if self.num_cases:
             str += " ndata=%d" % self.num_cases
@@ -66,14 +66,14 @@ class webqtlCaseData(object):
 
     @property
     def display_value(self):
-        if self.value:
+        if self.value != None:
             return "%2.3f" % self.value
         else:
             return "x"
 
     @property
     def display_variance(self):
-        if self.variance:
+        if self.variance != None:
             return "%2.3f" % self.variance
         else:
             return "x"