Merge github.com:genenetwork/genenetwork2 into acenteno

1 files changed, 24 insertions, 21 deletions

diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 6fec5dcd..8f8e2b0a 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import collections
 
 from flask import g
@@ -7,14 +5,15 @@ from flask import g
 from utility import db_tools
 from utility import Bunch
 
-from MySQLdb import escape_string as escape
+from utility.db_tools import escape
+from gn3.db_utils import database_connector
 
-from pprint import pformat as pf
 
 from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
+
 
-class MrnaAssayTissueData(object):
+class MrnaAssayTissueData:
 
     def __init__(self, gene_symbols=None):
         self.gene_symbols = gene_symbols
@@ -23,7 +22,7 @@ class MrnaAssayTissueData(object):
 
         self.data = collections.defaultdict(Bunch)
 
-        query =  '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
+        query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
                         from (
                         select Symbol, max(Mean) as maxmean
                         from TissueProbeSetXRef
@@ -34,29 +33,31 @@ class MrnaAssayTissueData(object):
         # Due to the limit size of TissueProbeSetFreezeId table in DB,
         # performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
         if len(gene_symbols) == 0:
-            query +=  '''Symbol!='' and Symbol Is Not Null group by Symbol)
+            query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
                 as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
                 and t.Mean = x.maxmean;
                     '''
         else:
             in_clause = db_tools.create_in_clause(gene_symbols)
 
-            #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
+            # ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
             query += ''' Symbol in {} group by Symbol)
                 as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
                 and t.Mean = x.maxmean;
                     '''.format(in_clause)
 
-        results = g.db.execute(query).fetchall()
 
-        lower_symbols = []
+        # lower_symbols = []
+        lower_symbols = {}
         for gene_symbol in gene_symbols:
+            # lower_symbols[gene_symbol.lower()] = True
             if gene_symbol != None:
-                lower_symbols.append(gene_symbol.lower())
-
+                lower_symbols[gene_symbol.lower()] = True
+        results = list(g.db.execute(query).fetchall())
         for result in results:
             symbol = result[0]
-            if symbol.lower() in lower_symbols:
+            if symbol  is not None and lower_symbols.get(symbol.lower()):
+
                 symbol = symbol.lower()
 
                 self.data[symbol].gene_id = result.GeneId
@@ -67,16 +68,16 @@ class MrnaAssayTissueData(object):
                 self.data[symbol].probe_target_description = result.Probe_Target_Description
 
     ###########################################################################
-    #Input: cursor, symbolList (list), dataIdDict(Dict)
-    #output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
+    # Input: cursor, symbolList (list), dataIdDict(Dict)
+    # output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
     #        key is symbol, value is one list of expression values of one probeSet;
-    #function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
-    #Attention! All keys are lower case!
+    # function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
+    # Attention! All keys are lower case!
     ###########################################################################
 
     def get_symbol_values_pairs(self):
         id_list = [self.data[symbol].data_id for symbol in self.data]
-        
+
         symbol_values_dict = {}
 
         if len(id_list) > 0:
@@ -85,11 +86,13 @@ class MrnaAssayTissueData(object):
                        WHERE TissueProbeSetData.Id IN {} and
                              TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
 
+
             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)
+                    symbol_values_dict[result.Symbol.lower()].append(
+                        result.value)
 
-        return symbol_values_dict
\ No newline at end of file
+        return symbol_values_dict