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Commit 099c1a9f authored by Vermaat's avatar Vermaat
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Fix for getGeneLocation query on PostgreSQL

SQLite accepted the incorrect non-aggregate use of columns missing from
the GROUP BY, whereas PostgreSQL did not.
parent d5ac9aa2
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......@@ -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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