def test_download_participant_list_file_not_found(self):
temp_dir = tempfile.mkdtemp()
try:
foo = FtpFileTransfer(None)
mockftp = D3RParameters()
mockftp.get = Mock()
foo.set_remote_dir('/foo')
foo.set_connection(mockftp)
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.set_file_transfer(foo)
task.create_dir()
task._download_participant_list_csv()
self.assertEqual(
task.get_email_log(),
'\nWARNING: participant_list.csv not downloaded '
'which means external users will NOT get '
'evaluation email\n')
mockftp.get\
.assert_called_with('/foo/' +
DataImportTask.PARTICIPANT_LIST_CSV,
local=task.get_participant_list_csv())
finally:
shutil.rmtree(temp_dir)
def _get_participant_database(self):
"""Creates `ParticipantDatabase`
:returns: ParticipantDatabase
"""
dimport = DataImportTask(self.get_path(), self.get_args())
csvfile = dimport.get_participant_list_csv()
pfac = ParticipantDatabaseFromCSVFactory(csvfile)
return pfac.get_participant_database()
def test_download_participant_list_success(self):
temp_dir = tempfile.mkdtemp()
try:
foo = FtpFileTransfer(None)
mockftp = D3RParameters()
mockftp.get = Mock()
foo.set_remote_dir('/foo')
foo.set_connection(mockftp)
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.set_file_transfer(foo)
task.create_dir()
open(task.get_participant_list_csv(), 'a').close()
task._download_participant_list_csv()
self.assertEqual(task.get_email_log(), None)
mockftp.get\
.assert_called_with('/foo/' +
DataImportTask.PARTICIPANT_LIST_CSV,
local=task.get_participant_list_csv())
finally:
shutil.rmtree(temp_dir)
def test_run_all_success(self):
temp_dir = tempfile.mkdtemp()
try:
fakeftp = FtpFileTransfer(None)
mftp = D3RParameters()
fakeftp.set_connection(mftp)
fakeftp.set_remote_dir('/foo2')
mftp.get = Mock()
params = D3RParameters()
params.pdbfileurl = 'file://' + temp_dir
params.compinchi = 'file://' + temp_dir
make_blast = MakeBlastDBTask(temp_dir, params)
make_blast.create_dir()
open(os.path.join(make_blast.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
task = DataImportTask(temp_dir, params)
task.set_file_transfer(fakeftp)
task._retrysleep = 0
open(os.path.join(temp_dir, task.NONPOLYMER_TSV), 'a').close()
open(os.path.join(temp_dir, task.SEQUENCE_TSV), 'a').close()
open(os.path.join(temp_dir, task.OLDSEQUENCE_TSV), 'a').close()
open(os.path.join(temp_dir, task.CRYSTALPH_TSV), 'a').close()
open(os.path.join(temp_dir, task.COMPINCHI_ICH), 'a').close()
task.run()
self.assertEquals(task.get_error(), None)
# check line count is 1 now which indicates
# standard was added
self.assertEqual(
util.get_file_line_count(task.get_nonpolymer_tsv()), 1)
self.assertEqual(util.get_file_line_count(task.get_sequence_tsv()),
1)
self.assertEqual(
util.get_file_line_count(task.get_oldsequence_tsv()), 1)
self.assertEqual(
util.get_file_line_count(task.get_crystalph_tsv()), 1)
mftp.get.assert_called_with('/foo2/' +
DataImportTask.PARTICIPANT_LIST_CSV,
local=task.get_participant_list_csv())
finally:
shutil.rmtree(temp_dir)
def test_get_participant_database_with_valid_csvfile(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
dimport = DataImportTask(temp_dir, params)
dimport.create_dir()
csvfile = dimport.get_participant_list_csv()
f = open(csvfile, 'w')
f.write('name,d3rusername,guid,email\n')
f.write('joe,jj,123,[email protected]\n')
f.flush()
f.close()
etf = EvaluationTaskFactory(temp_dir, params)
pdb = etf._get_participant_database()
p = pdb.get_participant_by_guid('123')
self.assertEqual(p.get_email(), '*****@*****.**')
finally:
shutil.rmtree(temp_dir)
def test_get_external_submitter_email_participant_not_found(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
dimport = DataImportTask(temp_dir, params)
dimport.create_dir()
csvfile = dimport.get_participant_list_csv()
f = open(csvfile, 'w')
f.write('name,d3rusername,guid,email\n')
f.write('joe,jj,123,[email protected]\n')
f.flush()
f.close()
fac = ParticipantDatabaseFromCSVFactory(csvfile)
params = D3RParameters()
dtask = D3RTask('/foo', params)
dtask.set_name('444' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
task = EvaluationTask(temp_dir, dtask.get_name(), dtask, params)
emailer = EvaluationEmailer(fac.get_participant_database(), None)
self.assertEqual(emailer._get_external_submitter_email(task), None)
self.assertEqual(emailer.get_message_log(),
'\nNo participant found with guid: 444\n')
finally:
shutil.rmtree(temp_dir)
def test_get_participant_list_csv(self):
params = D3RParameters()
task = DataImportTask('/foo', params)
self.assertEqual(
task.get_participant_list_csv(), '/foo/' + task.get_dir_name() +
'/' + DataImportTask.PARTICIPANT_LIST_CSV)