def test_run_all_compinchi_fail(self):
temp_dir = tempfile.mkdtemp()
try:
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._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()
task.run()
self.assertEquals(
task.get_error(), 'Unable to download file ' + 'from ' +
params.compinchi + ' to ' + task.get_components_inchi_file())
finally:
shutil.rmtree(temp_dir)
def test_run_pdbfileurl_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task._retrysleep = 0
task.run()
self.assertEquals(
task.get_error(),
'cannot download files' + ' cause pdbfileurl not set')
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_run_all_nonpolymer_fail(self):
temp_dir = tempfile.mkdtemp()
try:
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._retrysleep = 0
task.run()
self.assertEquals(
task.get_error(), 'Unable to download file ' + 'from ' +
params.pdbfileurl + ' to ' + task.get_nonpolymer_tsv())
finally:
shutil.rmtree(temp_dir)
def test_run_all_success_except_participant_download_fails(self):
temp_dir = tempfile.mkdtemp()
try:
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._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)
self.assertTrue(task.get_email_log().startswith(
'\nWARNING: Unable to download'))
finally:
shutil.rmtree(temp_dir)
