def test_upload_files_where_file_upload_raises_exception(self):
mockftp = MockFtp()
mockftp.put = Mock(side_effect=IOError('hi'))
mockftp.close = Mock(return_value=None)
foo = FtpFileTransfer(None)
foo.set_connection(mockftp)
foo.set_remote_dir('/remote')
foo.set_host('hosty')
temp_dir = tempfile.mkdtemp()
try:
foo.connect()
valid_file = os.path.join(temp_dir, 'valid')
f = open(valid_file, 'a')
f.write('hi')
f.flush()
f.close()
self.assertEqual(foo.upload_files([valid_file]), False)
self.assertEqual(foo.get_error_msg(), 'Error during upload')
self.assertEqual(foo.get_upload_summary(),
'Error during upload\n'
'0 (0 bytes) files uploaded in 0 '
'seconds to host hosty:/remote')
foo.disconnect()
mockftp.put.assert_called_with(valid_file,
os.path.normpath('/remote' +
valid_file))
finally:
shutil.rmtree(temp_dir)
def test_upload_challenge_file_uploader_successful(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
yeardir = os.path.join(temp_dir, '2017')
os.mkdir(yeardir)
weekdir = os.path.join(yeardir, 'dataset.week.1')
os.mkdir(weekdir)
chall = ChallengeDataTask(weekdir, params)
chall.create_dir()
mockftp = D3RParameters()
mockftp.put = Mock(side_effect=[3, 5])
ftp = FtpFileTransfer(None)
ftp.set_remote_challenge_dir('/challenge')
ftp.set_connection(mockftp)
ftp.connect()
chall.set_file_transfer(ftp)
tarball = os.path.join(chall.get_dir(), 'celppweek1_2017.tar.gz')
f = open(tarball, 'w')
f.write('hi')
f.flush()
f.close()
latest_file = os.path.join(chall.get_dir(),
ChallengeDataTask.LATEST_TXT)
chall._upload_challenge_file(tarball)
f = open(latest_file, 'r')
line = f.readline()
self.assertEqual(line, 'celppweek1_2017.tar.gz')
f.close()
ftp.disconnect()
finally:
shutil.rmtree(temp_dir)
def test_upload_files_multiple_valid_files(self):
mockftp = MockFtp()
mockftp.put = Mock(return_value=3)
mockftp.close = Mock(return_value=None)
foo = FtpFileTransfer(None)
foo.set_connection(mockftp)
foo.set_remote_dir('/remote')
foo.set_host('hosty')
temp_dir = tempfile.mkdtemp()
try:
foo.connect()
valid_file = os.path.join(temp_dir, 'valid')
f = open(valid_file, 'a')
f.write('hi')
f.flush()
f.close()
afile = os.path.join(temp_dir, 'hi')
open(afile, 'a').close()
self.assertEqual(foo.upload_files([valid_file, afile]), True)
self.assertEqual(foo.get_error_msg(), None)
self.assertTrue('2 (6 bytes) files uploaded in ' in
foo.get_upload_summary())
self.assertTrue(' seconds to host hosty:/remote' in
foo.get_upload_summary())
foo.disconnect()
self.assertEqual(mockftp.put.call_count, 2)
mockftp.close.assert_not_called()
finally:
shutil.rmtree(temp_dir)
def test_upload_challenge_file_uploader_upload_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
yeardir = os.path.join(temp_dir, '2016')
os.mkdir(yeardir)
weekdir = os.path.join(yeardir, 'dataset.week.50')
os.mkdir(weekdir)
chall = ChallengeDataTask(weekdir, params)
chall.create_dir()
mockftp = D3RParameters()
mockftp.put = Mock(side_effect=IOError('hi'))
ftp = FtpFileTransfer(None)
ftp.set_remote_challenge_dir('/challenge')
ftp.set_connection(mockftp)
ftp.connect()
chall.set_file_transfer(ftp)
tarball = os.path.join(chall.get_dir(), 'celppweek50_2016.tar.gz')
f = open(tarball, 'w')
f.write('hi')
f.flush()
f.close()
try:
chall._upload_challenge_file(tarball)
self.fail('Expected exception')
except Exception as e:
self.assertEqual(str(e),
'Unable to upload ' + tarball +
' to /challenge/celppweek50_2016.tar.gz : ' +
'hi')
ftp.disconnect()
finally:
shutil.rmtree(temp_dir)
def test_run_success_with_ftp_upload(self):
temp_dir = tempfile.mkdtemp()
try:
script = self.create_gen_challenge_script(temp_dir)
params = D3RParameters()
params.genchallenge = script
params.pdbdb = '/foo'
params.version = '1'
blastnfilter = BlastNFilterTask(temp_dir, params)
blastnfilter.create_dir()
open(os.path.join(blastnfilter.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
chall = ChallengeDataTask(temp_dir, params)
mockftp = D3RParameters()
mockftp.put = Mock(side_effect=[3, 5])
ftp = FtpFileTransfer(None)
ftp.set_remote_challenge_dir('/challenge')
ftp.set_connection(mockftp)
chall.set_file_transfer(ftp)
dimport = DataImportTask(temp_dir, params)
dimport.create_dir()
ctsv = dimport.get_crystalph_tsv()
f = open(ctsv, 'w')
f.write('crystal')
f.flush()
f.close()
nonpoly = dimport.get_nonpolymer_tsv()
f = open(nonpoly, 'w')
f.write('nonpoly')
f.flush()
f.close()
seq = dimport.get_sequence_tsv()
f = open(seq, 'w')
f.write('seq')
f.flush()
f.close()
chall.run()
self.assertEqual(chall.get_error(), None)
# verify test files get created
errfile = os.path.join(chall.get_dir(),
D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), False)
compfile = os.path.join(chall.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(compfile), True)
ftp.disconnect()
finally:
shutil.rmtree(temp_dir)
def test_download_file_success(self):
mockftp = MockFtp()
mockftp.get = Mock()
mockftp.close = Mock(return_value=None)
foo = FtpFileTransfer(None)
foo.set_connection(mockftp)
foo.connect()
self.assertTrue(foo.download_file('/a/b', '/c/d'))
self.assertEqual(foo.get_error_msg(), None)
foo.disconnect()
mockftp.get.assert_called_with('/a/b', local='/c/d')
def test_delete_file_fail(self):
mockftp = MockFtp()
mockftp.delete = Mock(side_effect=IOError('error'))
mockftp.close = Mock(return_value=None)
foo = FtpFileTransfer(None)
foo.set_connection(mockftp)
foo.connect()
self.assertFalse(foo.delete_file('/a/b'))
self.assertEqual(foo.get_error_msg(), 'Unable to delete /a/b : error')
foo.disconnect()
mockftp.delete.assert_called_with('/a/b')
def test_delete_file_success(self):
mockftp = MockFtp()
mockftp.delete = Mock(return_value='hello')
mockftp.close = Mock(return_value=None)
foo = FtpFileTransfer(None)
foo.set_connection(mockftp)
foo.connect()
self.assertTrue(foo.delete_file('/a/b'))
self.assertEqual(foo.get_error_msg(), None)
foo.disconnect()
mockftp.delete.assert_called_with('/a/b')
def test_download_file_fail(self):
mockftp = MockFtp()
mockftp.get = Mock(side_effect=IOError('error'))
mockftp.close = Mock(return_value=None)
foo = FtpFileTransfer(None)
foo.set_connection(mockftp)
foo.connect()
self.assertFalse(foo.download_file('/a/b', '/c/d'))
self.assertEqual(foo.get_error_msg(), 'Unable to download /a/b to '
'/c/d : error')
foo.disconnect()
mockftp.get.assert_called_with('/a/b', local='/c/d')
def test_list_files_fail(self):
mockftp = MockFtp()
mockftp.list = Mock(side_effect=IOError('error'))
mockftp.close = Mock(return_value=None)
foo = FtpFileTransfer(None)
foo.set_connection(mockftp)
foo.connect()
filelist = foo.list_files('/foo2')
self.assertTrue(filelist is None)
foo.disconnect()
self.assertEqual(foo.get_error_msg(), 'Unable to get file list '
'for /foo2 : error')
mockftp.list.assert_called_with('/foo2', extra=True)
def test_list_files_success(self):
mockftp = MockFtp()
mockftp.list = Mock(return_value=[{'directory': 'd', 'name': '.'},
{'directory': 'd', 'name': '..'},
{'directory': 'd', 'name': 'foo'},
{'directory': '-', 'name': 'file'}])
mockftp.close = Mock(return_value=None)
foo = FtpFileTransfer(None)
foo.set_connection(mockftp)
foo.connect()
filelist = foo.list_files('/foo')
self.assertTrue(len(filelist) == 1)
self.assertEqual(filelist[0], 'file')
foo.disconnect()
mockftp.list.assert_called_with('/foo', extra=True)
def test_upload_file_direct_put_throws_exception(self):
temp_dir = tempfile.mkdtemp()
try:
mockftp = MockFtp()
mockftp.put = Mock(side_effect=IOError('hi'))
foo = FtpFileTransfer(None)
foo.set_connection(mockftp)
foo.connect()
afile = os.path.join(temp_dir, 'afile')
open(afile, 'a').close()
self.assertEqual(foo.upload_file_direct(afile, '/foo', 'name'),
False)
self.assertEqual(foo.get_error_msg(), 'Unable to upload ' + afile +
' to /foo/name : hi')
foo.disconnect()
finally:
shutil.rmtree(temp_dir)
def test_upload_file_direct_success(self):
temp_dir = tempfile.mkdtemp()
try:
mockftp = MockFtp()
mockftp.put = Mock(return_value=3)
foo = FtpFileTransfer(None)
foo.set_connection(mockftp)
foo.connect()
afile = os.path.join(temp_dir, 'afile')
open(afile, 'a').close()
self.assertEqual(foo.upload_file_direct(afile, '/foo', 'name'),
True)
self.assertEqual(foo.get_error_msg(), None)
self.assertEqual(foo.get_upload_summary(), '1 (3 bytes) files '
'uploaded in 0 seconds'
' to host Unset:')
foo.disconnect()
finally:
shutil.rmtree(temp_dir)
def test_disconnect(self):
# test disconnect where _ftp is None
foo = FtpFileTransfer(None)
foo.disconnect()
# test disconnect where _ftp is set and
# so is _alt_ftp_con
foo = FtpFileTransfer(None)
foo.set_connection('hi')
foo.connect()
foo.disconnect()
# test disconnect where _ftp is set and
# _alt_ftp_con is None
foo = FtpFileTransfer(None)
mockftp = MockFtp()
mockftp.close = Mock(side_effect=Exception())
foo.set_connection(mockftp)
foo.connect()
foo._alt_ftp_con = None
foo.disconnect()
mockftp.close.assert_any_call()
class ExternalDataSubmissionFactory(object):
"""Factory to create ExternalDataSubmissionObjects
"""
DOCKEDRESULTS = '_dockedresults_'
def __init__(self, path, args):
"""Constructor
"""
try:
logger.debug('ftpconfig set to ' + args.ftpconfig)
self._file_transfer = FtpFileTransfer(args.ftpconfig)
except Exception:
logger.exception('Caught exception')
self._file_transfer = None
self._path = path
self._args = args
ctask = ChallengeDataTask(path, args)
self._chall_dir_name = ctask.get_celpp_challenge_data_dir_name()
def get_args(self):
return self._args
def get_path(self):
return self._path
def _get_challenge_package_results_file_name(self, dir_name):
return (self._chall_dir_name +
ExternalDataSubmissionFactory.DOCKEDRESULTS +
dir_name + ChallengeDataTask.TAR_GZ_SUFFIX)
def set_file_transfer(self, filetransfer):
"""Sets file transfer
"""
self._file_transfer = filetransfer
def get_file_transfer(self):
"""Gets file transfer
"""
return self._file_transfer
def _get_submission_dirs(self, remote_dir):
"""Gets list of directories under `remote_dir`
:param remote_dir: path on remote server to examine
:returns: list of directory names without path prefix
:raises AttributeError: if `get_file_transfer()` is None
"""
dlist = self._file_transfer.list_dirs(remote_dir)
if dlist is None:
logger.debug('No directories returned')
return []
logger.debug('Found ' + str(len(dlist)) + ' directories on ' +
remote_dir)
return dlist
def _get_challenge_data_package_file(self, remote_dir, dir_name):
"""Gets challenge data package file under `remote_dir` / `dir_name`
if it exists
:returns: Path to remote challenge file upon success or None if
not found
:raises AttributeError if `get_file_transfer()` is None
"""
ft = self.get_file_transfer()
flist = ft.list_files(os.path.normpath(os.path.join(remote_dir,
dir_name)))
if flist is None:
logger.info('No files found in ' + dir_name)
return None
logger.debug('Found ' + str(len(flist)) + ' files in ' + dir_name)
chall_fname = self._get_challenge_package_results_file_name(dir_name)
logger.debug('Looking for ' + chall_fname + ' file in directory')
for entry in flist:
if entry == chall_fname:
logger.info('Found matching entry ' + entry)
return os.path.normpath(os.path.join(remote_dir,
dir_name,
chall_fname))
else:
logger.debug('Encountered non challenge file: ' + entry)
return None
def _remove_latest_txt(self):
"""Removes the latest.txt file from ftp server if found
"""
try:
ft = self.get_file_transfer()
latest_txt = os.path.join(ft.get_remote_challenge_dir(),
ChallengeDataTask.LATEST_TXT)
logger.info('Attempting to remove ' + latest_txt)
val = ft.delete_file(latest_txt)
logger.info('Return value from delete call ' + str(val))
except Exception:
logger.exception('Caught exception trying to remove latest.txt')
def get_external_data_submissions(self):
"""Generate ExternalDataSubmission objects
Method should examine the submission directory on the
remote server via FtpFileTransfer(args.ftpconfig)
for each directory under submission directory
look for a celpp_weekXX_YYYY_dockedresults_ZZZZ.tar.gz file
where ZZZZ matches name of directory under submission directory
Regardless if its found or not create new ExternalDataSubmission
object and pass ZZZZ for name and path to .tar.gz file as
remotefile if the tar.gz file was found otherwise pass None
along with args. Append this object to list and
return it
"""
task_list = []
try:
self._file_transfer.connect()
self._remove_latest_txt()
subdir = self._file_transfer.get_remote_submission_dir()
dlist = self._get_submission_dirs(subdir)
for d in dlist:
chall_file = self._get_challenge_data_package_file(subdir, d)
if chall_file is not None:
et = ExternalDataSubmissionTask(self.get_path(), d,
chall_file,
self.get_args())
logger.info('Added ExternalData Submission Task: ' +
et.get_dir_name())
task_list.append(et)
except Exception:
logger.exception('Caught exception')
finally:
try:
self._file_transfer.disconnect()
except Exception:
logger.exception('Caught exception disconnecting')
return task_list
