From 9173f1e03f51cb141b0efa35b5e81c632b9a2689 Mon Sep 17 00:00:00 2001
From: Lei Yan
Date: Tue, 8 Oct 2013 17:50:08 -0500
Subject: Literature correlation works when it is selected as the sorted
 correlation type (that is, when it is run again all traits in a database)

Added a function to data_set.py that gets all the gene_ids in the
data set. Not sure if having a separate function for getting
the gene_ids and another for getting the gene symbols makes sense.
---
 wqflask/base/data_set.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5d21c901..16f9da5d 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1078,7 +1078,20 @@ class MrnaAssayDataSet(DataSet):
 
     def retrieve_gene_symbols(self):
         query = """
-                    select ProbeSet.Name, ProbeSet.Symbol
+                    select ProbeSet.Name, ProbeSet.Symbol, ProbeSet.GeneId
+                    from ProbeSet,ProbeSetXRef
+                    where ProbeSetXRef.ProbeSetFreezeId = %s and
+                    ProbeSetXRef.ProbeSetId=ProbeSet.Id;
+                """ % (self.id)
+        results = g.db.execute(query).fetchall()
+        symbol_dict = {}
+        for item in results:
+            symbol_dict[item[0]] = item[1]
+        return symbol_dict
+    
+    def retrieve_gene_ids(self):
+        query = """
+                    select ProbeSet.Name, ProbeSet.GeneId
                     from ProbeSet,ProbeSetXRef
                     where ProbeSetXRef.ProbeSetFreezeId = %s and
                     ProbeSetXRef.ProbeSetId=ProbeSet.Id;
-- 
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