From aea9dfba4a599f969dd10536789ba34e28362443 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 31 Jan 2011 16:16:15 +0000
Subject: [PATCH] Added unittests for /getGS and /Variant_info.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@178 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
src/tests/test_wsgi.py | 45 ++++++++++++++++++++++++++++++++++++++++--
src/wsgi.py | 10 +++++-----
2 files changed, 48 insertions(+), 7 deletions(-)
diff --git a/src/tests/test_wsgi.py b/src/tests/test_wsgi.py
index 26e25424..ac667c05 100755
--- a/src/tests/test_wsgi.py
+++ b/src/tests/test_wsgi.py
@@ -9,7 +9,7 @@ Uses WebTest, see:
I just installed webtest by 'easy_install webtest'.
-@todo: Tests for /upload, /getGS, and /Variant_info.
+@todo: Tests for /upload.
"""
#import logging; logging.basicConfig()
@@ -444,12 +444,53 @@ facilisi."""
def test_soap_documentation(self):
"""
Test the SOAP documentation generated from the WSDL.
- """
+ """
r = self.app.get('/documentation')
self.assertEqual(r.content_type, 'text/html')
r.mustcontain('Web Service: Mutalyzer')
+ def test_getgs(self):
+ """
+ Test the /getGS interface used by LOVD2.
+ """
+ r = self.app.get('/getGS?variantRecord=NM_003002.2&forward=1&mutationName=NG_012337.1:g.7055C%3ET')
+ r.mustcontain('0 Errors',
+ '0 Warnings',
+ 'Raw variant 1: substitution at 7055',
+ '<a href="#bottom" class="hornav">go to bottom</a>',
+ '<input value="NG_012337.1(SDHD_v001):g.7055C>T" type="text" name="mutationName" style="width:100%">')
+
+ def test_variantinfo_g2c(self):
+ """
+ Test the /Variant_info interface used by LOVD2 (g to c).
+ """
+ r = self.app.get('/Variant_info?LOVD_ver=2.0-29&build=hg19&acc=NM_203473.1&var=g.48374289_48374389del')
+ self.assertEqual(r.content_type, 'text/plain')
+ expected = '\n'.join(['1020', '0', '1072', '48', '48374289', '48374389', 'del'])
+ self.assertEqual(r.body, expected)
+
+ def test_variantinfo_c2g(self):
+ """
+ Test the /Variant_info interface used by LOVD2 (c to g).
+ """
+ r = self.app.get('/Variant_info?LOVD_ver=2.0-29&build=hg19&acc=NM_203473.1&var=c.1020_1072%2B48del')
+ self.assertEqual(r.content_type, 'text/plain')
+ expected = '\n'.join(['1020', '0', '1072', '48', '48374289', '48374389', 'del'])
+ self.assertEqual(r.body, expected)
+
+ def test_variantinfo_c2g_downstream(self):
+ """
+ Test the /Variant_info interface used by LOVD2 (c variant downstream
+ notation to g).
+ """
+ r = self.app.get('/Variant_info?LOVD_ver=2.0-29&build=hg19&acc=NM_203473.1&var=c.1709%2Bd187del')
+ self.assertEqual(r.content_type, 'text/plain')
+ expected = '\n'.join(['1709', '187', '1709', '187', '48379389', '48379389', 'del'])
+ self.assertEqual(r.body, expected)
+
if __name__ == '__main__':
# Usage:
# ./test_wsgi.py -v
+ # Or, selecting a specific test:
+ # ./test_wsgi.py -v TestWSGI.test_getgs_del
unittest.main()
diff --git a/src/wsgi.py b/src/wsgi.py
index 6ac42294..4f8fcca9 100644
--- a/src/wsgi.py
+++ b/src/wsgi.py
@@ -311,8 +311,6 @@ class GetGS:
the first transcript. LOVD supplies the NM of the transcript needed but
this was ignored. This helper allows LOVD to get the requested
transcript variant from a genomic reference.
-
- @todo: Test this.
"""
def GET(self):
"""
@@ -328,8 +326,12 @@ class GetGS:
i = web.input(mutationName=None, variantRecord=None, forward=None)
+ # Todo: The following is probably a problem elsewhere too.
+ # We stringify the variant, because a unicode string crashes
+ # Bio.Seq.reverse_complement in Mapper.py:607.
+
# We are only interested in the legend
- Mutalyzer.process(i.mutationName, C, O)
+ Mutalyzer.process(str(i.mutationName), C, O)
legends = O.getOutput("legends")
@@ -531,8 +533,6 @@ class PositionConverter:
class VariantInfo:
"""
The I{g.} to I{c.} and vice versa interface for LOVD.
-
- @todo: Tests.
"""
def GET(self):
"""
--
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