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 append_standard_to_files(self):
"""Appends standard 1FCZ to tsv files as mapped below
NONPOLYMER_TSV_STANDARD is appended to `get_nonpolymer_tsv()`
CRYSTALPH_TSV_STANDARD is appended to `get_crystalph_tsv()`
SEQUENCE_TSV_STANDARD is appended to `get_sequence_tsv()`
SEQUENCE_TSV_STANDARD is appended to `get_oldsequence_tsv()`
"""
logger.debug('Appending 1FCZ standard to tsv files')
try:
util.append_string_to_file(self.get_nonpolymer_tsv(),
DataImportTask.NONPOLYMER_TSV_STANDARD)
util.append_string_to_file(self.get_sequence_tsv(),
DataImportTask.SEQUENCE_TSV_STANDARD)
util.append_string_to_file(self.get_oldsequence_tsv(),
DataImportTask.SEQUENCE_TSV_STANDARD)
util.append_string_to_file(self.get_crystalph_tsv(),
DataImportTask.CRYSTALPH_TSV_STANDARD)
self.append_to_email_log('\nAppending 1FCZ standard to tsv'
' files\n')
nonpoly_count = util.get_file_line_count(self.get_nonpolymer_tsv())
seq_count = util.get_file_line_count(self.get_sequence_tsv())
crystal_count = util.get_file_line_count(self.get_crystalph_tsv())
inchi_count = util.get_file_line_count(
self.get_components_inchi_file())
self.append_to_email_log('Line counts:\n')
self.append_to_email_log(
str(inchi_count) + ' ' + DataImportTask.COMPINCHI_ICH + '\n')
self.append_to_email_log(
str(nonpoly_count) + ' ' + DataImportTask.NONPOLYMER_TSV +
'\n')
self.append_to_email_log(
str(seq_count) + ' ' + DataImportTask.SEQUENCE_TSV + '\n')
self.append_to_email_log(
str(seq_count) + ' ' + DataImportTask.OLDSEQUENCE_TSV + '\n')
self.append_to_email_log(
str(crystal_count) + ' ' + DataImportTask.CRYSTALPH_TSV + '\n')
except IOError:
logger.exception('Error appending standard to file')
def test_get_file_line_count(self):
temp_dir = tempfile.mkdtemp()
try:
try:
# Try with double None
util.get_file_line_count(None)
self.fail('Expected TypeError')
except TypeError:
pass
try:
# try on non existant file
util.get_file_line_count(os.path.join(temp_dir, 'non'))
except IOError:
pass
# try on empty file
open(os.path.join(temp_dir, 'empty'), 'a').close()
self.assertEqual(
util.get_file_line_count(os.path.join(temp_dir, 'empty')), 0)
# try on file with data
util.append_string_to_file(os.path.join(temp_dir, 'three'),
'h\no\nw\n')
self.assertEqual(
util.get_file_line_count(os.path.join(temp_dir, 'three')), 3)
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)
