def test_experiment(self):
"""Checks that the form works for an experiment. """
# Upload input
stream = open(TEST_INPUT)
post = self.app.post('/', data=dict(
mapqtl_input=stream),
follow_redirects=True)
stream.close()
self.assertTrue(post.status_code, 200)
self.assertTrue('<p> Session identifier: <span style="color:red">'
in post.data)
motif = re.compile('\n(.*)</span>\n\s+</p>\n')
output = motif.search(post.data)
session_id = output.group(1).strip()
# Give threshold and session
post2 = self.app.post('/session/%s/' % session_id,
data=dict(lod_threshold=3, session=2),
follow_redirects=True)
self.assertTrue(post2.status_code, 200)
motif = re.compile('<li><a href="/session/.*>(.*)</a>')
output = motif.search(post2.data)
exp_id = output.group(1).strip()
self.assertTrue('<p> Session identifier: <span style="color:red">'
in post2.data)
# Check results
post3 = self.app.get('/session/%s/%s/' % (session_id, exp_id),
follow_redirects=True)
self.assertTrue(post3.status_code, 200)
self.assertTrue('qtls_matrix.csv</a> -- Matrix giving for each'
in post3.data)
self.assertTrue('map.csv</a> -- The genetic map extracted'
in post3.data)
self.assertTrue('map_with_qtls.csv</a> -- Representation'
in post3.data)
post4 = self.app.post('/session/%s/' % session_id,
data=dict(lod_threshold=3, session=2),
follow_redirects=True)
self.assertTrue(post4.status_code, 200)
self.assertTrue('<li>Experiment already run in experiment: ' in
post4.data)
post5 = self.app.get('/session/%s/%s/marker/E36M48-330' % (session_id,
exp_id),
follow_redirects=True)
self.assertTrue(post5.status_code, 200)
self.assertTrue('MQ² results for marker E36M48-330' in post5.data)
self.assertTrue('2 QTLs found' in post5.data)
self.assertTrue('A_trait07' in post5.data)
self.assertTrue('A_trait11' in post5.data)
upload_folder = CONFIG.get('mq2', 'upload_folder')
shutil.rmtree(os.path.join(upload_folder, session_id))
def test_experiment(self):
"""Checks that the form works for an experiment. """
# Upload input
stream = open(TEST_INPUT)
post = self.app.post('/',
data=dict(mapqtl_input=stream),
follow_redirects=True)
stream.close()
self.assertTrue(post.status_code, 200)
self.assertTrue(
'<p> Session identifier: <span style="color:red">' in post.data)
motif = re.compile('\n(.*)</span>\n\s+</p>\n')
output = motif.search(post.data)
session_id = output.group(1).strip()
# Give threshold and session
post2 = self.app.post('/session/%s/' % session_id,
data=dict(lod_threshold=3, session=2),
follow_redirects=True)
self.assertTrue(post2.status_code, 200)
motif = re.compile('<li><a href="/session/.*>(.*)</a>')
output = motif.search(post2.data)
exp_id = output.group(1).strip()
self.assertTrue(
'<p> Session identifier: <span style="color:red">' in post2.data)
# Check results
post3 = self.app.get('/session/%s/%s/' % (session_id, exp_id),
follow_redirects=True)
self.assertTrue(post3.status_code, 200)
self.assertTrue(
'qtls_matrix.csv</a> -- Matrix giving for each' in post3.data)
self.assertTrue(
'map.csv</a> -- The genetic map extracted' in post3.data)
self.assertTrue(
'map_with_qtls.csv</a> -- Representation' in post3.data)
post4 = self.app.post('/session/%s/' % session_id,
data=dict(lod_threshold=3, session=2),
follow_redirects=True)
self.assertTrue(post4.status_code, 200)
self.assertTrue(
'<li>Experiment already run in experiment: ' in post4.data)
post5 = self.app.get('/session/%s/%s/marker/E36M48-330' %
(session_id, exp_id),
follow_redirects=True)
self.assertTrue(post5.status_code, 200)
self.assertTrue('MQ² results for marker E36M48-330' in post5.data)
self.assertTrue('2 QTLs found' in post5.data)
self.assertTrue('A_trait07' in post5.data)
self.assertTrue('A_trait11' in post5.data)
upload_folder = CONFIG.get('mq2', 'upload_folder')
shutil.rmtree(os.path.join(upload_folder, session_id))
def test_sample_session(self):
"""Checks that the form works for an existing session. """
session_id = CONFIG.get('mq2', 'sample_session')
post = self.app.post('/', data=dict(
session_id=session_id),
follow_redirects=True)
self.assertTrue(post.status_code, 200)
if session_id == 'A MQ² session identifier provided as example in the front page':
self.assertTrue('<li>This session does not exists</li>'
in post.data)
else:
self.assertTrue('<p> Session identifier: <span style="color:red">'
in post.data)
def test_sample_session(self):
"""Checks that the form works for an existing session. """
session_id = CONFIG.get('mq2', 'sample_session')
post = self.app.post('/',
data=dict(session_id=session_id),
follow_redirects=True)
self.assertTrue(post.status_code, 200)
if session_id == 'A MQ² session identifier provided as example in the front page':
self.assertTrue(
'<li>This session does not exists</li>' in post.data)
else:
self.assertTrue('<p> Session identifier: <span style="color:red">'
in post.data)
def test_sample_data(self):
"""Checks that the form works to upload the demo dataset. """
stream = open(TEST_INPUT)
post = self.app.post('/', data=dict(
mapqtl_input=stream),
follow_redirects=True)
stream.close()
self.assertTrue(post.status_code, 200)
self.assertTrue('<p> Session identifier: <span style="color:red">'
in post.data)
motif = re.compile('\n(.*)</span>\n\s+</p>\n')
output = motif.search(post.data)
session_id = output.group(1).strip()
post = self.app.post('/session/%s/' % session_id)
self.assertTrue(post.status_code, 200)
self.assertTrue('<p> Session identifier: <span style="color:red">'
in post.data)
self.assertTrue('%s</span></p>\n' % session_id)
upload_folder = CONFIG.get('mq2', 'upload_folder')
shutil.rmtree(os.path.join(upload_folder, session_id))
def test_sample_data(self):
"""Checks that the form works to upload the demo dataset. """
stream = open(TEST_INPUT)
post = self.app.post('/',
data=dict(mapqtl_input=stream),
follow_redirects=True)
stream.close()
self.assertTrue(post.status_code, 200)
self.assertTrue(
'<p> Session identifier: <span style="color:red">' in post.data)
motif = re.compile('\n(.*)</span>\n\s+</p>\n')
output = motif.search(post.data)
session_id = output.group(1).strip()
post = self.app.post('/session/%s/' % session_id)
self.assertTrue(post.status_code, 200)
self.assertTrue(
'<p> Session identifier: <span style="color:red">' in post.data)
self.assertTrue('%s</span></p>\n' % session_id)
upload_folder = CONFIG.get('mq2', 'upload_folder')
shutil.rmtree(os.path.join(upload_folder, session_id))