def test_run_succeeds(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.chimeraprep = 'true'
params.pdbdb = '/foo'
chall = ChallengeDataTask(temp_dir, params)
chall.create_dir()
open(os.path.join(chall.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
task.run()
self.assertEqual(task.get_error(), None)
# test files get created
errfile = os.path.join(task.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), False)
compfile = os.path.join(task.get_dir(), D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(compfile), True)
stderr = os.path.join(task.get_dir(), 'true.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(task.get_dir(), 'true.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def test_create_readme_version_empty_summary(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.version = '1.0'
task = ChallengeDataTask(temp_dir, params)
blast = BlastNFilterTask(temp_dir, params)
blast.create_dir()
sfile = blast.get_blastnfilter_summary_file()
open(sfile, 'a').close()
task._create_readme(temp_dir)
readme = os.path.join(temp_dir,
ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
f = open(readme, 'r')
found = False
for line in f:
if re.match('^Celpprunner version: 1.0.*$', line):
found = True
break
f.close()
self.assertEqual(found, True)
finally:
shutil.rmtree(temp_dir)
def test_create_readme(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.version = '1.0'
task = ChallengeDataTask(temp_dir, params)
blast = BlastNFilterTask(temp_dir, params)
blast.create_dir()
sfile = blast.get_blastnfilter_summary_file()
f = open(sfile, 'w')
f.write('hello there\n')
f.flush()
f.close()
task._create_readme(temp_dir)
readme = os.path.join(temp_dir,
ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
f = open(readme, 'r')
found = False
for line in f:
print line
if re.match('^hello there.*$', line):
found = True
break
f.close()
self.assertEqual(found, True)
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_run_fails_cause_chimeraprep_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.chimeraprep = 'false'
params.pdbdb = '/foo'
chall = ChallengeDataTask(temp_dir, params)
chall.create_dir()
open(os.path.join(chall.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
task.run()
self.assertEqual(
task.get_error(),
'Non zero exit code: 1 received. Standard out: ' +
' Standard error: ')
# test file gets created
errfile = os.path.join(task.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
stderr = os.path.join(task.get_dir(), 'false.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(task.get_dir(), 'false.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def run(self):
"""Runs ChimeraProteinLigPrepTask after verifying BlastNFilterTask
was good
Method requires can_run() to be called before hand with
successful outcome
Otherwise method invokes D3RTask.start then this method
creates a directory and invokes blastnfilter script. Upon
completion results are analyzed and success or error status
is set appropriately and D3RTask.end is invoked
"""
super(ChimeraProteinLigPrepTask, self).run()
if self._can_run is False:
logger.debug(self.get_dir_name() +
' cannot run cause _can_run flag '
'is False')
return
try:
logger.debug('chimeraprep set to ' + self.get_args().chimeraprep)
except AttributeError:
self.set_error('chimeraprep not set')
self.end()
return
try:
logger.debug('pdbdb set to ' + self.get_args().pdbdb)
except AttributeError:
self.set_error('pdbdb not set')
self.end()
return
rdkitpython = ''
try:
logger.debug('rdkitpython set to ' + self.get_args().rdkitpython)
rdkitpython = self.get_args().rdkitpython
except AttributeError:
logger.debug
chall = ChallengeDataTask(self._path, self._args)
#
# chimeraprep.py --candidatedir <path to stage.3.challengedata> \
# --outdir <path to stage.4.chimeraligprep>
challdir = os.path.join(chall.get_dir(),
chall.get_celpp_challenge_data_dir_name())
cmd_to_run = (self.get_args().chimeraprep + ' --candidatedir ' +
challdir + ' --rdkitpython \'' + rdkitpython + '\'' +
' --pdbdb ' + self.get_args().pdbdb + ' --outdir ' +
self.get_dir())
chimeraprep_name = os.path.basename(self.get_args().chimeraprep)
self.run_external_command(chimeraprep_name, cmd_to_run, True)
# assess the result
self.end()
def test_get_celpp_challenge_data_dir_name_path_not_found(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
self.assertEqual(task.get_celpp_challenge_data_dir_name(),
'celpp_week0_0')
finally:
shutil.rmtree(temp_dir)
def __init__(self, path, args):
super(ProteinLigPrepTask, self).__init__(path, args)
self.set_name(ProteinLigPrepTask.TASK_NAME)
# Make stage number one higher then BlastNFilter Stage
chall = ChallengeDataTask(path, args)
self.set_stage(chall.get_stage() + 1)
self.set_status(D3RTask.UNKNOWN_STATUS)
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_upload_challenge_file_uploader_is_none(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
chall = ChallengeDataTask(temp_dir, params)
chall._upload_challenge_file('/foo')
self.assertEqual(chall.get_email_log(), 'No uploader available '
'to upload challenge '
'data\n')
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_can_run_is_false(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.version = '1'
# return immediately cause can_run is false
chall = ChallengeDataTask(temp_dir, params)
chall.run()
self.assertEqual(chall.get_error(),
'blastnfilter task has notfound status')
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 __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 test_create_readme_unable_to_write_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.version = "1.0.0"
task = ChallengeDataTask(temp_dir, params)
try:
task._create_readme(os.path.join(temp_dir, 'doesnotexist'))
self.fail('Expected IOError')
except IOError:
pass
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_genchallenge_is_not_found(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.genchallenge = '/bin/doesnotexist'
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)
chall.run()
self.assertEqual(chall.get_error(),
'Caught Exception trying to run ' +
'/bin/doesnotexist --candidatedir ' +
blastnfilter.get_dir() + ' --pdbdb ' +
'/foo --outdir ' +
chall.get_dir() +
'/' + chall.get_celpp_challenge_data_dir_name() +
' : [Errno 2] No such file or directory')
# test files get created
errfile = os.path.join(chall.get_dir(),
D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_genchallenge_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.genchallenge = 'false'
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)
chall.run()
self.assertEqual(chall.get_error(),
'Non zero exit code: 1 received. Standard out: ' +
' Standard error: ')
# test file gets created
errfile = os.path.join(chall.get_dir(),
D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
stderr = os.path.join(chall.get_dir(),
'false.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(chall.get_dir(),
'false.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def test_get_celpp_challenge_data_dir_name(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
cyear = os.path.join(temp_dir, '2016')
cweek = os.path.join(cyear, 'dataset.week.5')
os.mkdir(cyear)
os.mkdir(cweek)
task = ChallengeDataTask(cweek, params)
task.create_dir()
self.assertEqual(task.get_celpp_challenge_data_dir_name(),
'celpp_week5_2016')
finally:
shutil.rmtree(temp_dir)
def test_tar_challenge_dir_unable_to_write_tarfile(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
chall_dir = task.get_celpp_challenge_data_dir_name()
try:
task._tar_challenge_dir(chall_dir)
self.fail('Expected IOError')
except IOError:
pass
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_chimeraprep_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
chall = ChallengeDataTask(temp_dir, params)
chall.create_dir()
open(os.path.join(chall.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
task.run()
self.assertEqual(task.get_error(), 'chimeraprep not set')
# test files get created
self.assertEqual(os.path.isdir(task.get_dir()), True)
errfile = os.path.join(task.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_chimeraprep_is_not_found_rdkitpython_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.chimeraprep = '/bin/doesnotexist'
params.pdbdb = '/foo'
params.rdkitpython = '/data/miniconda2/bin'
chall = ChallengeDataTask(temp_dir, params)
chall.create_dir()
challdir = os.path.join(chall.get_dir(),
chall.get_celpp_challenge_data_dir_name())
open(os.path.join(chall.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
task.run()
self.assertEqual(
task.get_error(), 'Caught Exception trying to run ' +
'/bin/doesnotexist --candidatedir ' + challdir +
' --rdkitpython \'/data/miniconda2/bin\' ' + '--pdbdb ' +
'/foo --outdir ' + task.get_dir() +
' : [Errno 2] No such file or directory')
# test files get created
errfile = os.path.join(task.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds_one_evaluation_and_no_emailer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.postevaluation = 'echo'
etask = EvaluationTask(
temp_dir, 'foo_dock.' + EvaluationTaskFactory.SCORING_SUFFIX,
None, params)
etask.create_dir()
task = PostEvaluationTask(temp_dir, params)
ctask = ChallengeDataTask(temp_dir, params)
task.run()
self.assertEqual(task.get_error(), None)
self.assertEqual(task.get_status(), D3RTask.COMPLETE_STATUS)
cfile = os.path.join(task.get_dir(), D3RTask.COMPLETE_FILE)
self.assertTrue(os.path.isfile(cfile))
stdout_file = os.path.join(task.get_dir(),
'echo' + D3RTask.STDOUT_SUFFIX)
self.assertTrue(os.path.isfile(stdout_file))
f = open(stdout_file, 'r')
data = f.read()
f.close()
ctaskdir = os.path.join(ctask.get_dir(),
ctask.get_celpp_challenge_data_dir_name())
self.assertTrue(' --evaluationdir ' + etask.get_dir() in data)
self.assertTrue(' --challengedir ' + ctaskdir in data)
self.assertTrue('--stageprefix stage.7. --evaluationsuffix ' +
'.extsubmission.evaluation$|.evaluation$' in data)
stderr_file = os.path.join(task.get_dir(),
'echo' + D3RTask.STDERR_SUFFIX)
self.assertTrue(os.path.isfile(stderr_file))
finally:
shutil.rmtree(temp_dir)
def test_create_readme_version_unset_and_no_summary_txt(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
task._create_readme(temp_dir)
readme = os.path.join(temp_dir,
ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
f = open(readme, 'r')
found = False
for line in f:
if re.match('^Celpprunner version: Unknown.*$', line):
found = True
break
f.close()
self.assertEqual(found, True)
finally:
shutil.rmtree(temp_dir)
def test_copy_over_tsv_files(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
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()
task = ChallengeDataTask(temp_dir, params)
task.create_dir()
challenge_dir = task._create_challenge_dir()
self.assertEqual(os.path.isdir(challenge_dir), True)
task._copy_over_tsv_files(challenge_dir)
cop_ctsv = os.path.join(challenge_dir,
DataImportTask.CRYSTALPH_TSV)
self.assertEqual(os.path.isfile(cop_ctsv), True)
f = open(cop_ctsv)
self.assertEqual(f.readline(), 'crystal')
f.close()
cop_nonpoly = os.path.join(challenge_dir,
DataImportTask.NONPOLYMER_TSV)
self.assertEqual(os.path.isfile(cop_nonpoly), True)
f = open(cop_nonpoly)
self.assertEqual(f.readline(), 'nonpoly')
f.close()
cop_seq = os.path.join(challenge_dir,
DataImportTask.SEQUENCE_TSV)
self.assertEqual(os.path.isfile(cop_seq), True)
f = open(cop_seq)
self.assertEqual(f.readline(), 'seq')
f.close()
finally:
shutil.rmtree(temp_dir)
def test_can_run(self):
temp_dir = tempfile.mkdtemp()
try:
# no blast task found so it cannot run
params = D3RParameters()
proteinligprep = ProteinLigPrepTask(temp_dir, params)
self.assertEqual(proteinligprep.can_run(), False)
self.assertEqual(proteinligprep.get_error(),
'challengedata task has notfound status')
# challenge filter running
chall = ChallengeDataTask(temp_dir, params)
chall.create_dir()
open(os.path.join(chall.get_dir(), D3RTask.START_FILE),
'a').close()
proteinligprep = ProteinLigPrepTask(temp_dir, params)
self.assertEqual(proteinligprep.can_run(), False)
self.assertEqual(proteinligprep.get_error(),
'challengedata task has start status')
# blastnfilter failed
error_file = os.path.join(chall.get_dir(), D3RTask.ERROR_FILE)
open(error_file, 'a').close()
proteinligprep = ProteinLigPrepTask(temp_dir, params)
self.assertEqual(proteinligprep.can_run(), False)
self.assertEqual(proteinligprep.get_error(),
'challengedata task has error status')
# blastnfilter success
os.remove(error_file)
open(os.path.join(chall.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
proteinligprep = ProteinLigPrepTask(temp_dir, params)
self.assertEqual(proteinligprep.can_run(), True)
self.assertEqual(proteinligprep.get_error(), None)
# proteinligprep task exists already
proteinligprep = ProteinLigPrepTask(temp_dir, params)
proteinligprep.create_dir()
self.assertEqual(proteinligprep.can_run(), False)
self.assertEqual(
proteinligprep.get_error(),
proteinligprep.get_dir_name() +
' already exists and status is unknown')
# proteinlibprep already complete
proteinligprep = ProteinLigPrepTask(temp_dir, params)
open(os.path.join(proteinligprep.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
self.assertEqual(proteinligprep.can_run(), False)
self.assertEqual(proteinligprep.get_error(), None)
finally:
shutil.rmtree(temp_dir)
def test_copy_over_tsv_files_no_dataimport(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
task.create_dir()
challenge_dir = task._create_challenge_dir()
self.assertEqual(os.path.isdir(challenge_dir), True)
task._copy_over_tsv_files(challenge_dir)
finally:
shutil.rmtree(temp_dir)
def test_upload_challenge_file_challenge_file_is_none(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
chall = ChallengeDataTask(temp_dir, params)
chall._upload_challenge_file(None)
chall.set_file_transfer(params)
self.assertEqual(chall.get_email_log(), 'challenge_file is None in'
' _upload_challenge_file'
'\n')
finally:
shutil.rmtree(temp_dir)
def test_upload_challenge_file_no_remote_challenge_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
chall = ChallengeDataTask(temp_dir, params)
ftp = FtpFileTransfer(None)
chall.set_file_transfer(ftp)
chall._upload_challenge_file('/foo')
self.assertEqual(chall.get_email_log(), 'No remote challenge'
' directory set for '
'ftp upload\n')
finally:
shutil.rmtree(temp_dir)
def can_run(self):
"""Determines if task can actually run
This method first verifies the `BlastNFilterTask` task
has `D3RTask.COMPLETE_STATUS` for
status. The method then verifies a `ProteinLigPrepTask` does
not already exist. If above is not true then self.set_error()
is set with information about the issue
:return: True if can run otherwise False
"""
self._can_run = False
self._error = None
# check blast
chall = ChallengeDataTask(self._path, self._args)
chall.update_status_from_filesystem()
if chall.get_status() != D3RTask.COMPLETE_STATUS:
logger.info('Cannot run ' + self.get_name() + 'task ' +
'because ' + chall.get_name() + 'task' +
'has a status of ' + chall.get_status())
self.set_error(chall.get_name() + ' task has ' +
chall.get_status() + ' status')
return False
# check this task is not complete and does not exist
self.update_status_from_filesystem()
if self.get_status() == D3RTask.COMPLETE_STATUS:
logger.debug("No work needed for " + self.get_name() + " task")
return False
if self.get_status() != D3RTask.NOTFOUND_STATUS:
logger.warning(self.get_name() + " task was already " +
"attempted, but there was a problem")
self.set_error(self.get_dir_name() + ' already exists and ' +
'status is ' + self.get_status())
return False
self._can_run = True
return True
def test_tar_challenge_dir_nothing_but_readme(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
task.create_dir()
chall_dir = task._create_challenge_dir()
task._create_readme(chall_dir)
self.assertEqual(os.path.isdir(chall_dir), True)
name = task.get_celpp_challenge_data_dir_name()
tfile = task._tar_challenge_dir(name)
self.assertEqual(os.path.isfile(tfile), True)
foodir = os.path.join(temp_dir, 'foo')
tar = tarfile.open(tfile, 'r:*')
tar.extractall(path=foodir)
tar.close()
cdir = os.path.join(foodir, name)
readme = os.path.join(cdir, ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
finally:
shutil.rmtree(temp_dir)
def test_create_challenge_dir_unable_to_make_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
cyear = os.path.join(temp_dir, '2016')
cweek = os.path.join(cyear, 'dataset.week.5')
os.mkdir(cyear)
os.mkdir(cweek)
task = ChallengeDataTask(cweek, params)
task.create_dir()
cdir = os.path.join(task.get_dir(),
task.get_celpp_challenge_data_dir_name())
open(cdir, 'a').close()
try:
task._create_challenge_dir()
self.fail('Expected OSError')
except OSError:
pass
finally:
shutil.rmtree(temp_dir)