From 55ca04e1023d6e7f1a5ecad6e618dd7da3dce06f Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Sat, 4 Oct 2014 00:14:33 +0200
Subject: [PATCH] Fix crash in position converter batch job
Fixes Trac#174
---
mutalyzer/Scheduler.py | 9 ++++++++-
tests/test_scheduler.py | 18 ++++++++++++++++--
2 files changed, 24 insertions(+), 3 deletions(-)
diff --git a/mutalyzer/Scheduler.py b/mutalyzer/Scheduler.py
index f8d0dee8..e6f102d3 100644
--- a/mutalyzer/Scheduler.py
+++ b/mutalyzer/Scheduler.py
@@ -19,6 +19,7 @@ import os # os.path.exists
import smtplib # smtplib.STMP
from email.mime.text import MIMEText # MIMEText
from sqlalchemy import func
+from sqlalchemy.orm.exc import NoResultFound
import mutalyzer
from mutalyzer.config import settings
@@ -557,7 +558,13 @@ Mutalyzer batch scheduler""" % url)
if not skip :
try :
#process
- assembly = Assembly.get(int(batch_job.argument))
+ try:
+ assembly = Assembly.by_name_or_alias(batch_job.argument)
+ except NoResultFound:
+ O.addMessage(__file__, 3, 'ENOASSEMBLY',
+ 'Not a valid assembly: ' + str(batch_job.argument))
+ raise
+
converter = Converter(assembly, O)
#Also accept chr accNo
diff --git a/tests/test_scheduler.py b/tests/test_scheduler.py
index a722f331..fc5e4abe 100644
--- a/tests/test_scheduler.py
+++ b/tests/test_scheduler.py
@@ -17,7 +17,7 @@ from mutalyzer import File
from mutalyzer import output
from mutalyzer import Scheduler
-from fixtures import database, cache
+from fixtures import database, cache, hg19, hg19_transcript_mappings
from utils import MutalyzerTest
from utils import fix
@@ -36,7 +36,7 @@ class TestScheduler(MutalyzerTest):
batch_file = StringIO.StringIO('\n'.join(variants) + '\n')
job, columns = file_instance.parseBatchFile(batch_file)
result_id = scheduler.addJob('test@test.test', job, columns,
- job_type)
+ job_type, argument=argument)
batch_job = BatchJob.query.filter_by(result_id=result_id).one()
@@ -229,3 +229,17 @@ class TestScheduler(MutalyzerTest):
with patch.object(Entrez, 'efetch', mock_efetch):
self._batch_job(variants, expected, 'name-checker')
+
+ @fix(hg19, hg19_transcript_mappings)
+ def test_position_converter(self):
+ """
+ Simple position converter batch job.
+ """
+ variants = ['chr11:g.111959695G>T']
+ expected = [['chr11:g.111959695G>T',
+ '',
+ 'NC_000011.9:g.111959695G>T',
+ 'NM_003002.2:c.274G>T',
+ 'NM_012459.2:c.-2203C>A',
+ 'NR_028383.1:n.-2173C>A']]
+ self._batch_job(variants, expected, 'position-converter', 'hg19')
--
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