Resolve conflicts

5 files changed, 28 insertions, 35 deletions

diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 5511af06..e99ef7b5 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -92,24 +92,22 @@ class MrnaAssayTissueData(object):
     def get_symbol_values_pairs(self):
         id_list = [self.data[symbol].data_id for symbol in self.data]
 
-        print("id_list:", id_list)
-
         symbol_values_dict = {}
 
-        query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value
-                   FROM TissueProbeSetXRef, TissueProbeSetData
-                   WHERE TissueProbeSetData.Id IN {} and
-                         TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
+        if len(id_list) > 0:
+            query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value
+                       FROM TissueProbeSetXRef, TissueProbeSetData
+                       WHERE TissueProbeSetData.Id IN {} and
+                             TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
 
-        print("TISSUE QUERY:", query)
-        logger.sql(query)
+            logger.sql('tissue query',query)
 
-        results = g.db.execute(query).fetchall()
-        for result in results:
-            if result.Symbol.lower() not in symbol_values_dict:
-                symbol_values_dict[result.Symbol.lower()] = [result.value]
-            else:
-                symbol_values_dict[result.Symbol.lower()].append(result.value)
+            results = g.db.execute(query).fetchall()
+            for result in results:
+                if result.Symbol.lower() not in symbol_values_dict:
+                    symbol_values_dict[result.Symbol.lower()] = [result.value]
+                else:
+                    symbol_values_dict[result.Symbol.lower()].append(result.value)
 
         #for symbol in self.data:
         #    data_id = self.data[symbol].data_id
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index afde3dbe..9566c192 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -82,13 +82,7 @@ class GeneralTrait(object):
                     dataset=self.dataset.name,
                     description=self.description_display,
                     mean=self.mean)
-
-
-    def get_info(self):
-        """For lots of traits just use get_trait_info in dataset instead...that will be way
-        more efficient"""
-        self.dataset.get_trait_info([self],
-            webqtlDatabaseFunction.retrieve_species(self.dataset.group.name))
+                    
 
     def get_name(self):
         stringy = ""
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 958a1e43..4ea8407c 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -297,13 +297,13 @@ def view_collection():
     params = request.args
     print("PARAMS in view collection:", params)
 
-    if "uc_id" in params:
-        uc_id = params['uc_id']
-        uc = model.UserCollection.query.get(uc_id)
-        traits = json.loads(uc.members)
-        print("traits are:", traits)
-    else:
-        traits = AnonCollection().get_traits()
+    #if "uc_id" in params:
+    uc_id = params['uc_id']
+    uc = model.UserCollection.query.get(uc_id)
+    traits = json.loads(uc.members)
+    print("traits are:", traits)
+    #else:
+    #    traits = AnonCollection().get_traits()
 
     print("in view_collection traits are:", traits)
 
@@ -316,7 +316,6 @@ def view_collection():
 
         trait_ob = trait.GeneralTrait(name=name, dataset_name=dataset_name)
         trait_ob.retrieve_info(get_qtl_info=True)
-        trait_ob.get_info()
         trait_obs.append(trait_ob)
 
         json_version.append(trait_ob.jsonable())
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 71f03d05..401059fd 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -167,9 +167,13 @@ class CorrelationResults(object):
                 self.trait_symbol_dict = self.dataset.retrieve_genes("Symbol")
 
                 tissue_corr_data = self.do_tissue_correlation_for_all_traits()
-                for trait in tissue_corr_data.keys()[:self.return_number]:
-                    self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
-
+                if tissue_corr_data != None:
+                    for trait in tissue_corr_data.keys()[:self.return_number]:
+                        self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
+                else:
+                    for trait, values in self.target_dataset.trait_data.iteritems():
+                        self.get_sample_r_and_p_values(trait, values)
+                        
             elif self.corr_type == "lit":
                 self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId")
                 lit_corr_data = self.do_lit_correlation_for_all_traits()
@@ -244,7 +248,7 @@ class CorrelationResults(object):
                         trait_object.tissue_corr = 0
                         trait_object.tissue_pvalue = 0
                         trait_object.lit_corr = 0
-                        if self.corr_type == "tissue":
+                        if self.corr_type == "tissue" and tissue_corr_data != None:
                             trait_object.tissue_corr = tissue_corr_data[trait][1]
                             trait_object.tissue_pvalue = tissue_corr_data[trait][2]
                         elif self.corr_type == "lit":
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 123aec33..a924c7c9 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -102,8 +102,6 @@ views.py).
             this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
             self.trait_list.append(this_trait)
 
-        self.dataset.get_trait_info(self.trait_list, species)
-
     #def get_group_species_tree(self):
     #    self.species_groups = collections.default_dict(list)
     #    for key in self.results: