diff options
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 52 |
1 files changed, 25 insertions, 27 deletions
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 8cea271d..02a3365b 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -82,20 +82,19 @@ class ShowTrait: if not blatsequence: # XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. seqs = () - with database_connection() as conn, conn.cursor() as cursor: - cursor.execute( - "SELECT Probe.Sequence, Probe.Name " - "FROM Probe, ProbeSet, ProbeSetFreeze, " - "ProbeSetXRef WHERE " - "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " - "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND " - "ProbeSetFreeze.Name = %s AND " - "ProbeSet.Name = %s AND " - "Probe.ProbeSetId = ProbeSet.Id ORDER " - "BY Probe.SerialOrder", - (self.this_trait.dataset.name, self.this_trait.name,) - ) - seqs = cursor.fetchall() + db_cursor.execute( + "SELECT Probe.Sequence, Probe.Name " + "FROM Probe, ProbeSet, ProbeSetFreeze, " + "ProbeSetXRef WHERE " + "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " + "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND " + "ProbeSetFreeze.Name = %s AND " + "ProbeSet.Name = %s AND " + "Probe.ProbeSetId = ProbeSet.Id ORDER " + "BY Probe.SerialOrder", + (self.this_trait.dataset.name, self.this_trait.name,) + ) + seqs = db_cursor.fetchall() if not seqs: raise ValueError else: @@ -109,19 +108,18 @@ class ShowTrait: # XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. seqs = () - with database_connection() as conn, conn.cursor() as cursor: - cursor.execute( - "SELECT Probe.Sequence, Probe.Name " - "FROM Probe, ProbeSet, ProbeSetFreeze, " - "ProbeSetXRef WHERE " - "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " - "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND " - "ProbeSetFreeze.Name = %s AND ProbeSet.Name = %s " - "AND Probe.ProbeSetId = ProbeSet.Id " - "ORDER BY Probe.SerialOrder", - (self.this_trait.dataset.name, self.this_trait.name,) - ) - seqs = cursor.fetchall() + db_cursor.execute( + "SELECT Probe.Sequence, Probe.Name " + "FROM Probe, ProbeSet, ProbeSetFreeze, " + "ProbeSetXRef WHERE " + "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " + "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND " + "ProbeSetFreeze.Name = %s AND ProbeSet.Name = %s " + "AND Probe.ProbeSetId = ProbeSet.Id " + "ORDER BY Probe.SerialOrder", + (self.this_trait.dataset.name, self.this_trait.name,) + ) + seqs = db_cursor.fetchall() for seqt in seqs: if int(seqt[1][-1]) % 2 == 1: blatsequence += '%3EProbe_' + \ |