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_download_files_with_wait_all_successful(self):
temp_dir = tempfile.mkdtemp()
try:
prev_friday = util.get_previous_friday_from_date(
datetime.now(tzlocal()))
sat = prev_friday + timedelta(days=1)
dse = sat - datetime(1970, 01, 01, tzinfo=tzutc())
secs_since_epoch = self.get_total_seconds(dse)
nonpoly = os.path.join(temp_dir, DataImportTask.NONPOLYMER_TSV)
f = open(nonpoly, 'w')
f.write('nonpoly\n')
f.flush()
f.close()
os.utime(nonpoly, (secs_since_epoch, secs_since_epoch))
seq = os.path.join(temp_dir, DataImportTask.SEQUENCE_TSV)
f = open(seq, 'w')
f.write('seq\n')
f.flush()
f.close()
os.utime(seq, (secs_since_epoch, secs_since_epoch))
oldseq = os.path.join(temp_dir, DataImportTask.OLDSEQUENCE_TSV)
f = open(oldseq, 'w')
f.write('oldseq\n')
f.flush()
f.close()
os.utime(oldseq, (secs_since_epoch, secs_since_epoch))
crystal = os.path.join(temp_dir, DataImportTask.CRYSTALPH_TSV)
f = open(crystal, 'w')
f.write('crystal\n')
f.flush()
f.close()
os.utime(crystal, (secs_since_epoch, secs_since_epoch))
comp = os.path.join(temp_dir, DataImportTask.COMPINCHI_ICH)
f = open(comp, 'w')
f.write('comp\n')
f.flush()
f.close()
params = D3RParameters()
params.skipimportwait = False
params.importretry = 2
params.importsleep = 0
params.compinchi = 'file://' + temp_dir
task = DataImportTask(temp_dir, params)
task.create_dir()
val = task._download_files('file://' + temp_dir)
self.assertEqual(task.get_error(), None)
self.assertTrue(val)
finally:
shutil.rmtree(temp_dir)
def test_can_run_does_not_exist_or_error(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
# no make blast db
self.assertEquals(task.can_run(), False)
self.assertEquals(task.get_error(),
'makeblastdb task has notfound status')
self.assertEquals(task._can_run, False)
make_blast = MakeBlastDBTask(temp_dir, params)
make_blast.create_dir()
# make blast db failed
err_file = os.path.join(make_blast.get_dir(), D3RTask.ERROR_FILE)
open(err_file, 'a').close()
self.assertEquals(task.can_run(), False)
self.assertEquals(task.get_error(),
'makeblastdb task has error status')
self.assertEquals(task._can_run, False)
os.remove(err_file)
# make blast db success
open(os.path.join(make_blast.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
self.assertEquals(task.can_run(), True)
self.assertEquals(task.get_error(), None)
self.assertEquals(task._can_run, True)
task.create_dir()
open(os.path.join(task.get_dir(), D3RTask.ERROR_FILE), 'a').close()
self.assertEquals(task.can_run(), False)
self.assertEquals(task._can_run, False)
self.assertEquals(
task.get_error(),
task.get_dir_name() + ' already exists and ' + 'status is ' +
D3RTask.ERROR_STATUS)
finally:
shutil.rmtree(temp_dir)
def test_run_can_run_flag_false(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.pdbfileurl = 'file://' + temp_dir
params.compinchi = 'file://' + temp_dir
task = DataImportTask(temp_dir, params)
task._can_run = False
task.run()
self.assertEquals(task.get_error(), None)
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_can_run_with_complete_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
open(os.path.join(task.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
self.assertEquals(task.can_run(), False)
self.assertEquals(task.get_error(), None)
self.assertEquals(task._can_run, False)
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_download_files_fail(self):
temp_dir = tempfile.mkdtemp()
try:
nonpoly = os.path.join(temp_dir, DataImportTask.NONPOLYMER_TSV)
f = open(nonpoly, 'w')
f.write('nonpoly\n')
f.flush()
f.close()
seq = os.path.join(temp_dir, DataImportTask.SEQUENCE_TSV)
f = open(seq, 'w')
f.write('seq\n')
f.flush()
f.close()
oldseq = os.path.join(temp_dir, DataImportTask.OLDSEQUENCE_TSV)
f = open(oldseq, 'w')
f.write('oldseq\n')
f.flush()
f.close()
crystal = os.path.join(temp_dir, DataImportTask.CRYSTALPH_TSV)
f = open(crystal, 'w')
f.write('crystal\n')
f.flush()
f.close()
params = D3RParameters()
params.skipimportwait = True
params.compinchi = 'file://' + temp_dir
task = DataImportTask(temp_dir, params)
task.create_dir()
val = task._download_files('file://' + temp_dir)
self.assertEqual(
task.get_error(), 'Unable to download file from '
'file://' + temp_dir + ' to ' +
task.get_components_inchi_file())
self.assertFalse(val)
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)