From 099c1a9f30f7cb308d8dbce3c0675f21f3d9e60b Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Fri, 30 Jan 2015 13:07:09 +0100
Subject: [PATCH] Fix for getGeneLocation query on PostgreSQL
SQLite accepted the incorrect non-aggregate use of columns missing from
the GROUP BY, whereas PostgreSQL did not.
---
mutalyzer/services/rpc.py | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
diff --git a/mutalyzer/services/rpc.py b/mutalyzer/services/rpc.py
index fe79c8d1..e70b238d 100644
--- a/mutalyzer/services/rpc.py
+++ b/mutalyzer/services/rpc.py
@@ -1351,11 +1351,12 @@ class MutalyzerService(ServiceBase):
session.query(func.min(TranscriptMapping.start),
func.max(TranscriptMapping.stop),
TranscriptMapping.orientation,
- Chromosome) \
+ Chromosome.name,
+ Chromosome.accession) \
.filter(TranscriptMapping.chromosome.has(assembly=assembly),
TranscriptMapping.gene == gene) \
.join(TranscriptMapping.chromosome) \
- .group_by(TranscriptMapping.chromosome,
+ .group_by(Chromosome.id,
TranscriptMapping.orientation) \
.first()
@@ -1364,15 +1365,16 @@ class MutalyzerService(ServiceBase):
raise Fault("EARG",
"No location was found for gene %s." % gene)
- start, stop, orientation, chromosome = mapping
+ start, stop, orientation, chromosome_name, chromosome_accession \
+ = mapping
result = GeneLocation()
result.gene = gene
result.start = start
result.stop = stop
result.orientation = orientation
- result.chromosome_name = chromosome.name
- result.chromosome_accession = chromosome.accession
+ result.chromosome_name = chromosome_name
+ result.chromosome_accession = chromosome_accession
result.assembly_name = assembly.name
result.assembly_alias = assembly.alias
--
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