def setUpModule():
config = IniParser().read_ini("download.ini")
# Download intact file from source
section_intact = config["INTACT"]
file_url = section_intact['location'] + section_intact['files']
status = FTPDownload.download(file_url, TEST_DATA_DIR, INTACT)
logger.warn("Download status for intact " + str(status))
section_bioplex = config["BIOPLEX"]
file_url = section_bioplex['location'] + section_bioplex['files']
status = HTTPDownload.download(file_url, TEST_DATA_DIR, BIOPLEX)
logger.warn("Download status for bioplex " + str(status))
def check_intact_data(self, child_doc, parent_doc):
config = IniParser().read_ini("download.ini")
self.assertEqual(getattr(child_doc, "interaction_source"), 'intact', 'interaction_source is intact')
# Get interactors already stored in our pipeline
interactors = getattr(child_doc, 'interactors')
pydgin_interactors = [interactor['interactor'] for interactor in interactors]
# add parent id as well
parent_id = parent_doc.doc_id()
pydgin_interactors.append(parent_id)
self.assertEqual(parent_id, child_doc.parent(), 'Parent id ok')
# Download intact file from source and search for the parent entrez id interactors
section_intact = config["INTACT"]
file_url = section_intact['location'] + section_intact['files']
status = FTPDownload.download(file_url, '/tmp', 'intact.zip')
# status = True
if status:
parent_intact = set()
zf = zipfile.ZipFile('/tmp/intact.zip', 'r')
my_regex = re.escape(parent_id)
if 'intact.txt' in zf.namelist():
target_path = zf.extract(member='intact.txt', path='/tmp')
with open(target_path, encoding='utf-8') as csvfile:
reader = csv.reader(csvfile, delimiter='\t', quoting=csv.QUOTE_NONE)
for row in reader:
line = '\t'.join(row)
match = re.search(my_regex, line)
if match:
parent_intact.add(line)
intact_interactors = set()
for line in parent_intact:
result_list = re.findall(r"(ENSG[0-9]*)", line)
if result_list:
intact_interactors |= set(result_list) # union operator
self.assertEqual(len(pydgin_interactors), len(intact_interactors), "Interactors size equal")
def test_ftp(self):
''' Test downloading over FTP. '''
self.assertTrue(FTPDownload.download('ftp://ftp.ebi.ac.uk/pub/databases/embl/README',
'/tmp', 'ftp.test'),
'FTP download test')
def test_ftp_mtime(self):
''' Test mtime from a file on a FTP server. '''
self.assertTrue(FTPDownload.mtime('ftp://ftp.ebi.ac.uk/pub/databases/embl/README') > 0,
'FTP file/dir exists')
def test_ftp_exists(self):
''' Test FTP exists. '''
self.assertTrue(FTPDownload.exists('ftp://ftp.ebi.ac.uk/'), 'FTP file/dir exists')
self.assertFalse(FTPDownload.exists('ftp://ftp.ebi.ac.uk/xxxx'), 'FTP file/dir exists')
