def test_get_plugin_and_folder_with_folder(self):
""" Test the get_plugin_and_folder function with too many inputs
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
plugin2, folder2 = mq2.get_plugin_and_folder(inputdir=folder)
self.assertEqual(plugin, plugin2)
self.assertEqual(folder, folder2)
def test_get_plugin_and_folder_with_folder(self):
""" Test the get_plugin_and_folder function with too many inputs
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
plugin2, folder2 = mq2.get_plugin_and_folder(
inputdir=folder)
self.assertEqual(plugin, plugin2)
self.assertEqual(folder, folder2)
def test_plugin_get_files(self):
""" Test the get_files method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
self.assertEqual(len(plugin.get_files(folder)), 1)
self.assertTrue(plugin.get_files(folder)[0].endswith('/rqtl_out.csv'))
self.assertEqual(plugin.get_files(None), [])
def test_run_mq2_from_file(self):
""" Test the run_mq2 function from a file.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputfile=TEST_INPUT_FILE)
mq2.run_mq2(plugin,
folder=TEST_INPUT_FILE,
lod_threshold=3)
self.assertEqual(read_file('qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls.exp')))
self.assertEqual(read_file('map.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'map.exp')))
self.assertEqual(read_file('map_with_qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'map_with_qtls.exp')))
self.assertEqual(read_file('qtls_matrix.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls_matrix.exp')))
self.assertEqual(read_file('qtls_with_mk.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls_with_mk.exp')))
self.assertEqual(read_file('MapChart.map'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'MapChart.exp')))
def test_plugin_get_files(self):
""" Test the get_files method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertEqual(len(plugin.get_files(folder)), 1)
self.assertTrue(plugin.get_files(folder)[0].endswith('/rqtl_out.csv'))
self.assertEqual(plugin.get_files(None), [])
def test_plugin_get_session_identifiers(self):
""" Test the get_session_identifiers method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertEqual(len(plugin.get_session_identifiers(folder)), 1)
self.assertEqual(plugin.get_session_identifiers(folder), ['2'])
self.assertEqual(plugin.get_session_identifiers(None), [])
def test_plugin_get_session_identifiers_failed(self):
""" Test the get_session_identifiers method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
self.assertRaises(MQ2.MQ2Exception,
plugin.get_session_identifiers,
folder=os.path.join(TEST_FOLDER, 'fake.xls'),
inputfile=folder)
def test_plugin_valid_file(self):
""" Test the valid_file method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertFalse(plugin.valid_file(TEST_INPUT_PASSED))
self.assertTrue(plugin.valid_file(
os.path.join(folder, 'rqtl_output', 'rqtl_out.csv')))
def test_plugin_valid_file(self):
""" Test the valid_file method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
self.assertFalse(plugin.valid_file(TEST_INPUT_PASSED))
self.assertTrue(
plugin.valid_file(
os.path.join(folder, 'rqtl_output', 'rqtl_out.csv')))
def test_run_mq2_invalid_input(self):
""" Test the run_mq2 function with an invalid MapQTL zip input.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_FAILED)
self.assertRaises(
MQ2.MQ2NoMatrixException,
mq2.run_mq2,
plugin, folder, lod_threshold=3, session=2)
def session(session_id):
""" Shows the session page.
This page shows the different experiments ran on this session.
A session being a MapQTL output zip file and a JoinMap map file,
experiments are defined by the parameters used to find the QTLs
within this MapQTL output.
@param session_id the session identifier uniquely identifying the
MapQTL zip file and the JoinMap map file.
"""
print 'mq2 %s -- %s -- %s' % (datetime.datetime.now(), request.remote_addr,
request.url)
if session_id == CONFIG.get('mq2', 'sample_session'):
global UPLOAD_FOLDER
UPLOAD_FOLDER = os.path.join(os.path.abspath(__file__),
APP.static_folder)
upload_folder = os.path.join(UPLOAD_FOLDER, session_id)
try:
plugin, folder = get_plugin_and_folder(
inputzip=os.path.join(upload_folder, 'input.zip'))
except IOError:
flash('Could not extract the zip archive.', 'errors')
return redirect(url_for('index'))
if plugin.session_name:
form = InputFormSession(sessions=sorted(
plugin.get_session_identifiers(folder)),
sessions_label=plugin.session_name)
else:
form = InputForm()
if not (session_id in os.listdir(UPLOAD_FOLDER)
or session_id in os.listdir(APP.static_folder)):
flash('This session does not exists')
return redirect(url_for('index'))
if form.validate_on_submit():
lod_threshold = form.lod_threshold.data
session = None
if plugin.session_name:
session = form.session.data
output = None
try:
output = mq2_run(session_id,
plugin,
folder,
lod_threshold=lod_threshold,
session=session)
except MQ2Exception, err:
form.errors['MQ2'] = err
if output:
flash("Experiment already run in experiment: <a href='%s'>"
"%s</a>" %
(url_for('results', session_id=session_id,
exp_id=output), output))
def test_run_mq2_invalid_session(self):
""" Test the run_mq2 function with MapQTL zip input and the
wrong session identifier.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertRaises(
MQ2.MQ2NoSuchSessionException,
mq2.run_mq2,
plugin, folder, lod_threshold=3, session=1)
def test_run_mq2_invalid_lod(self):
""" Test the run_mq2 function with MapQTL zip input and an
invalid LOD threshold.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertRaises(
MQ2.MQ2Exception,
mq2.run_mq2,
plugin, folder=folder, lod_threshold='a', session=2)
def test_run_mq2_no_folder(self):
""" Test the run_mq2 function with MapQTL zip input and without
folder.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertRaises(
MQ2.MQ2Exception,
mq2.run_mq2,
plugin, folder=None, lod_threshold=3, session=2)
def test_run_mq2_kw(self):
""" Test the run_mq2 function with MapQTL zip input of a Kruskal-Wallis
analysis.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_KW)
self.assertRaises(
MQ2.MQ2Exception,
mq2.run_mq2,
plugin, folder, lod_threshold=3, session=2)
def test_plugin_get_session_identifiers_failed(self):
""" Test the get_session_identifiers method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertRaises(
MQ2.MQ2Exception,
plugin.get_session_identifiers,
folder=os.path.join(TEST_FOLDER, 'fake.xls'),
inputfile=folder)
def test_run_mq2_no_folder(self):
""" Test the run_mq2 function with MapQTL zip input and without
folder.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertRaises(
MQ2.MQ2Exception,
mq2.run_mq2,
plugin, folder=None, lod_threshold=3, session=2)
def test_plugin_valid_file(self):
""" Test the valid_file method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
self.assertFalse(plugin.valid_file(TEST_INPUT_PASSED))
self.assertTrue(
plugin.valid_file(os.path.join(folder,
os.listdir(folder)[0])))
self.assertFalse(plugin.valid_file(TEST_FAKE_INPUT_FILE))
def test_run_mq2_invalid_lod(self):
""" Test the run_mq2 function with MapQTL zip input and an
invalid LOD threshold.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertRaises(
MQ2.MQ2Exception,
mq2.run_mq2,
plugin, folder=folder, lod_threshold='a', session=2)
def test_plugin_get_files(self):
""" Test the get_files method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertEqual(len(plugin.get_files(folder)), 2)
self.assertTrue(
plugin.get_files(folder)[0].endswith(
'/Session 2 (IM)_A_trait01.mqo'))
self.assertEqual(plugin.get_files(None), [])
def test_get_plugin_and_folder(self):
""" Test the get_plugin_and_folder function with MapQTL zip
input.
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
self.assertTrue(
os.path.basename(folder).startswith(
date.today().strftime('%Y%m%d')))
self.assertEqual(plugin.name, 'CSV plugin')
self.assertEqual(plugin.session_name, None)
def test_get_plugin_and_folder(self):
""" Test the get_plugin_and_folder function with MapQTL zip
input.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertTrue(os.path.basename(
folder).startswith(date.today().strftime('%Y%m%d')))
self.assertEqual(plugin.name, 'CSV plugin')
self.assertEqual(plugin.session_name, None)
def test_plugin_valid_file(self):
""" Test the valid_file method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertFalse(plugin.valid_file(TEST_INPUT_PASSED))
self.assertTrue(plugin.valid_file(
os.path.join(folder,os.listdir(folder)[0])))
self.assertFalse(plugin.valid_file(
TEST_FAKE_INPUT_FILE))
def session(session_id):
""" Shows the session page.
This page shows the different experiments ran on this session.
A session being a MapQTL output zip file and a JoinMap map file,
experiments are defined by the parameters used to find the QTLs
within this MapQTL output.
@param session_id the session identifier uniquely identifying the
MapQTL zip file and the JoinMap map file.
"""
print 'mq2 %s -- %s -- %s' % (datetime.datetime.now(),
request.remote_addr, request.url)
if session_id == CONFIG.get('mq2', 'sample_session'):
global UPLOAD_FOLDER
UPLOAD_FOLDER = os.path.join(os.path.abspath(__file__),
APP.static_folder)
upload_folder = os.path.join(UPLOAD_FOLDER, session_id)
try:
plugin, folder = get_plugin_and_folder(
inputzip=os.path.join(upload_folder, 'input.zip'))
except IOError:
flash('Could not extract the zip archive.', 'errors')
return redirect(url_for('index'))
if plugin.session_name:
form = InputFormSession(
sessions=sorted(plugin.get_session_identifiers(folder)),
sessions_label=plugin.session_name)
else:
form = InputForm()
if not (session_id in os.listdir(UPLOAD_FOLDER) or
session_id in os.listdir(APP.static_folder)):
flash('This session does not exists')
return redirect(url_for('index'))
if form.validate_on_submit():
lod_threshold = form.lod_threshold.data
session = None
if plugin.session_name:
session = form.session.data
output = None
try:
output = mq2_run(session_id, plugin, folder,
lod_threshold=lod_threshold, session=session)
except MQ2Exception, err:
form.errors['MQ2'] = err
if output:
flash("Experiment already run in experiment: <a href='%s'>"
"%s</a>" % (url_for('results', session_id=session_id,
exp_id=output), output))
def test_plugin_get_session_identifiers(self):
""" Test the get_session_identifiers method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
self.assertEqual(len(plugin.get_session_identifiers(folder)), 1)
self.assertEqual(plugin.get_session_identifiers(folder), ['Sheet1'])
self.assertEqual(plugin.get_session_identifiers(None), [])
self.assertEqual(
plugin.get_session_identifiers(
folder=os.path.join(TEST_FOLDER, 'fake.xls')), [])
self.assertEqual(plugin.get_session_identifiers(inputfile=folder), [])
def test_plugin_get_session_identifiers(self):
""" Test the get_session_identifiers method of the plugin.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
self.assertEqual(len(plugin.get_session_identifiers(folder)), 1)
self.assertEqual(plugin.get_session_identifiers(folder), ['Sheet1'])
self.assertEqual(plugin.get_session_identifiers(None), [])
self.assertEqual(plugin.get_session_identifiers(
folder=os.path.join(TEST_FOLDER, 'fake.xls')), [])
self.assertEqual(plugin.get_session_identifiers(
inputfile=folder), [])
def test_run_mq2(self):
""" Test the run_mq2 function from a zip archive.
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
mq2.run_mq2(plugin, folder, lod_threshold=3, session='Sheet1')
self.assertEqual(
read_file('qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'xls', 'qtls.exp')))
self.assertEqual(
read_file('map.csv'),
read_file(os.path.join(TEST_FOLDER, 'xls', 'map.exp')))
self.assertEqual(
read_file('map_with_qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'xls', 'map_with_qtls.exp')))
self.assertEqual(
read_file('qtls_with_mk.csv'),
read_file(os.path.join(TEST_FOLDER, 'xls', 'qtls_with_mk.exp')))
def test_run_mq2(self):
""" Test the run_mq2 function from a zip archive.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
mq2.run_mq2(plugin, folder, lod_threshold=3, session='Sheet1')
self.assertEqual(read_file('qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'xls', 'qtls.exp')))
self.assertEqual(read_file('map.csv'),
read_file(os.path.join(
TEST_FOLDER, 'xls', 'map.exp')))
self.assertEqual(read_file('map_with_qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'xls', 'map_with_qtls.exp')))
self.assertEqual(read_file('qtls_with_mk.csv'),
read_file(os.path.join(
TEST_FOLDER, 'xls', 'qtls_with_mk.exp')))
def test_run_mq2_from_file(self):
""" Test the run_mq2 function from a file.
"""
plugin, folder = mq2.get_plugin_and_folder(inputfile=TEST_INPUT_FILE)
mq2.run_mq2(plugin, folder=TEST_INPUT_FILE, lod_threshold=3)
self.assertEqual(
read_file('qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls.exp')))
self.assertEqual(
read_file('map.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'map.exp')))
self.assertEqual(
read_file('map_with_qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'map_with_qtls.exp')))
self.assertEqual(
read_file('qtls_matrix.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls_matrix.exp')))
self.assertEqual(
read_file('qtls_with_mk.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls_with_mk.exp')))
self.assertEqual(
read_file('MapChart.map'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'MapChart.exp')))
def test_run_mq2(self):
""" Test the run_mq2 function with MapQTL zip input.
"""
plugin, folder = mq2.get_plugin_and_folder(inputzip=TEST_INPUT_PASSED)
mq2.run_mq2(plugin, folder, lod_threshold=3, session=2)
self.assertEqual(
read_file('qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls.exp')))
self.assertEqual(
read_file('map.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'map.exp')))
self.assertEqual(
read_file('map_with_qtls.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'map_with_qtls.exp')))
self.assertEqual(
read_file('qtls_matrix.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls_matrix.exp')))
self.assertEqual(
read_file('qtls_with_mk.csv'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'qtls_with_mk.exp')))
self.assertEqual(
read_file('MapChart.map'),
read_file(os.path.join(TEST_FOLDER, 'csv', 'MapChart.exp')))
def test_run_mq2(self):
""" Test the run_mq2 function with MapQTL zip input.
"""
plugin, folder = mq2.get_plugin_and_folder(
inputzip=TEST_INPUT_PASSED)
mq2.run_mq2(plugin, folder, lod_threshold=3, session=2)
self.assertEqual(read_file('qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls.exp')))
self.assertEqual(read_file('map.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'map.exp')))
self.assertEqual(read_file('map_with_qtls.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'map_with_qtls.exp')))
self.assertEqual(read_file('qtls_matrix.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls_matrix.exp')))
self.assertEqual(read_file('qtls_with_mk.csv'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'qtls_with_mk.exp')))
self.assertEqual(read_file('MapChart.map'),
read_file(os.path.join(
TEST_FOLDER, 'csv', 'MapChart.exp')))
