def test_download_file_where_file_exists(self):
temp_dir = tempfile.mkdtemp()
try:
tfile = os.path.join(temp_dir, 'hi')
open(tfile, 'a').close()
dloader = SignorDownloader('http://hi', tfile)
dloader._download_file('http://hi', tfile)
finally:
shutil.rmtree(temp_dir)
def test_get_download_url(self):
dloader = SignorDownloader('hi', None)
self.assertEqual(
'hi/' + SignorDownloader.PATHWAYDATA_DOWNLOAD_SCRIPT + 'haha',
dloader._get_download_url('haha'))
self.assertEqual(
'hi/' + SignorDownloader.PATHWAYDATA_DOWNLOAD_SCRIPT +
'haha&relations=only',
dloader._get_download_url('haha', relationsonly=True))
def test_download_pathways_list_error(self):
dloader = SignorDownloader('http://hi', None)
with requests_mock.mock() as m:
m.get('http://hi/' + SignorDownloader.PATHWAYDATA_SCRIPT,
status_code=500,
text='hehe')
try:
dloader._download_pathways_list()
self.fail('Expected NDExLoadSignorError')
except NDExLoadSignorError as ne:
self.assertEqual('Got status code of 500 from signor', str(ne))
def test_download_entity_file_error(self):
dloader = SignorDownloader('http://hi', None)
with requests_mock.mock() as m:
m.post('http://hi/' + SignorDownloader.DOWNLOAD_COMPLEXES,
status_code=500,
text='hehe')
try:
dloader._download_entity_file('entitytype', 'foo')
self.fail('Expected NDExLoadSignorError')
except NDExLoadSignorError as ne:
self.assertEqual('Got status code of 500 from signor', str(ne))
def test_get_proteinfamily_map(self):
temp_dir = tempfile.mkdtemp()
try:
dloader = SignorDownloader(None, temp_dir)
pfile = dloader.get_proteinfamily_file()
self.write_fake_signor_pf_file(pfile)
res = dloader.get_proteinfamily_map()
self.assertEqual(['P27361', 'P28482'], res['ERK1/2'])
self.assertEqual(['P27361', 'P28482'], res['SIGNOR-PF1'])
self.assertEqual(['Q9HBW0', 'Q9UBY5', 'Q92633'], res['LPAR'])
self.assertEqual(['Q9HBW0', 'Q9UBY5', 'Q92633'], res['SIGNOR-PF2'])
finally:
shutil.rmtree(temp_dir)
def test_get_complexes_map(self):
temp_dir = tempfile.mkdtemp()
try:
dloader = SignorDownloader(None, temp_dir)
pfile = dloader.get_complexes_file()
self.write_fake_signor_complexes_file(pfile)
res = dloader.get_complexes_map()
self.assertEqual(['P23511', 'P25208', 'Q13952'], res['NFY'])
self.assertEqual(['P23511', 'P25208', 'Q13952'], res['SIGNOR-C1'])
self.assertEqual(['P68104', 'Q8TB45'], res['mTORC2'])
self.assertEqual(['P68104', 'Q8TB45'], res['SIGNOR-C2'])
finally:
shutil.rmtree(temp_dir)
def test_download_entity_file_success(self):
dloader = SignorDownloader('http://hi', None)
temp_dir = tempfile.mkdtemp()
try:
with requests_mock.mock() as m:
m.post('http://hi/' + SignorDownloader.DOWNLOAD_COMPLEXES,
status_code=200,
text='hehe')
tfile = os.path.join(temp_dir, 'hi')
dloader._download_entity_file('entitytype', tfile)
self.assertEqual(True, os.path.isfile(tfile))
with open(tfile, 'r') as f:
self.assertEqual('hehe', f.read())
finally:
shutil.rmtree(temp_dir)
def test_download_pathways_list_success(self):
temp_dir = tempfile.mkdtemp()
dloader = SignorDownloader('http://hi', temp_dir)
try:
with requests_mock.mock() as m:
m.get('http://hi/' + SignorDownloader.PATHWAYDATA_SCRIPT,
status_code=200,
text='hehe')
tfile = dloader.get_pathway_list_file()
dloader._download_pathways_list()
self.assertEqual(True, os.path.isfile(tfile))
with open(tfile, 'r') as f:
self.assertEqual('hehe', f.read())
finally:
shutil.rmtree(temp_dir)
def test_get_pathways_map(self):
temp_dir = tempfile.mkdtemp()
try:
dloader = SignorDownloader(None, temp_dir)
with open(dloader.get_pathway_list_file(), 'w') as f:
f.write('SIGNOR-AC\tAdipogenesis\n')
f.write('SIGNOR-AD\tAlzheimer Disease\n')
f.write('SIGNOR-AML\tAcute Myeloid Leukemia\n')
f.write('SIGNOR-AML-IDH/TET\tAML-IDH/TET\n')
res = dloader.get_pathways_map()
self.assertEqual('Adipogenesis', res['SIGNOR-AC'])
self.assertEqual('Alzheimer Disease', res['SIGNOR-AD'])
self.assertEqual('Acute Myeloid Leukemia', res['SIGNOR-AML'])
self.assertEqual('AML-IDH/TET', res['SIGNOR-AML-IDHTET'])
finally:
shutil.rmtree(temp_dir)
def test_get_complexes_file(self):
dloader = SignorDownloader(None, 'f')
self.assertEqual(os.path.join('f', SignorDownloader.COMPLEXES_FILE),
dloader.get_complexes_file())
def test_get_pathway_list_file(self):
dloader = SignorDownloader(None, 'f')
self.assertEqual(os.path.join('f', SignorDownloader.PATHWAY_LIST_FILE),
dloader.get_pathway_list_file())
def test_get_fulldownload_url(self):
dloader = SignorDownloader('hi', None)
self.assertEqual('hi/' + SignorDownloader.GETDATA_SCRIPT + 'yo',
dloader._get_fulldownload_url('yo'))