Merge branch 'testing' of github.com:genenetwork/genenetwork2 into gn-testing

3 files changed, 29 insertions, 8 deletions

diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 4ac2213c..6d99af65 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -14,10 +14,13 @@ from utility.logger import getLogger
 logger = getLogger(__name__ )
 
 class TheSpecies(object):
-    def __init__(self, dataset):
-        self.dataset = dataset
-        #print("self.dataset is:", pf(self.dataset.__dict__))
-        self.chromosomes = Chromosomes(self.dataset)
+    def __init__(self, dataset=None, species_name=None):
+        if species_name != None:
+            self.name = species_name
+            self.chromosomes = Chromosomes(species=self.name)
+        else:
+            self.dataset = dataset
+            self.chromosomes = Chromosomes(dataset=self.dataset)
 
 class IndChromosome(object):
     def __init__(self, name, length):
@@ -30,11 +33,21 @@ class IndChromosome(object):
         return self.length / 1000000
 
 class Chromosomes(object):
-    def __init__(self, dataset):
-        self.dataset = dataset
+    def __init__(self, dataset=None, species=None):
         self.chromosomes = collections.OrderedDict()
+        if species != None:
+            query = """
+                Select
+                        Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species
+                where
+                        Chr_Length.SpeciesId = Species.SpeciesId AND
+                        Species.Name = '%s'
+                Order by OrderId
+                """ % species.capitalize()
+        else:
+            self.dataset = dataset
 
-        query = """
+            query = """
                 Select
                         Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet
                 where
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 3daf9ea9..e57d4176 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -189,7 +189,8 @@ def get_sample_data():
         trait_dict['symbol'] = trait_ob.symbol
         trait_dict['location'] = trait_ob.location_repr
     elif trait_ob.dataset.type == "Publish":
-        trait_dict['pubmed_link'] = trait_ob.pubmed_link
+        if trait_ob.pubmed_id:
+            trait_dict['pubmed_link'] = trait_ob.pubmed_link
         trait_dict['pubmed_text'] = trait_ob.pubmed_text
 
     return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 24de8dcb..76f06cc6 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -77,3 +77,10 @@ class webqtlCaseData(object):
             return "%2.3f" % self.variance
         else:
             return "x"
+
+    @property
+    def display_num_cases(self):
+        if self.num_cases != None:
+            return "%d" % self.num_cases
+        else:
+            return "x"