refactor code for iterating mrna tissue data

1 files changed, 34 insertions, 5 deletions

diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index f1929518..0220d73b 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -6,6 +6,7 @@ from utility import db_tools
 from utility import Bunch
 
 from utility.db_tools import escape
+from gn3.db_utils import database_connector
 
 
 from utility.logger import getLogger
@@ -44,16 +45,42 @@ class MrnaAssayTissueData(object):
                 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
+
+        import time
+        # initial_time = time.time()
+        # conn,cursor = database_connector()
+        # cursor.execute(query)
+        # for result in cursor.fetchall():
+        #     symbol = result[0]
+        #     self.data[symbol].gene_id = result[1]
+        #     self.data[symbol].data_id = result[2]
+        #     self.data[symbol].chr = result[3]
+        #     self.data[symbol].mb = result[4]
+        #     self.data[symbol].description = result[5]
+        #     self.data[symbol].probe_target_description = result[6]
+
+
+        # print("my loop takes>>>>",time.time()-initial_time)
+        # conn.close()
+        # r
+
+        # takes 5 seconds
+        initial_time = time.time()
+        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
+            # exists = lower_symbols.get(symbol.lower())
+            # 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
@@ -62,6 +89,7 @@ class MrnaAssayTissueData(object):
                 self.data[symbol].mb = result.Mb
                 self.data[symbol].description = result.description
                 self.data[symbol].probe_target_description = result.Probe_Target_Description
+        print("time taken in the loop is",time.time()-initial_time)
 
     ###########################################################################
     #Input: cursor, symbolList (list), dataIdDict(Dict)
@@ -82,6 +110,7 @@ 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: