def test_get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres_w_hits(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
f = open(task.get_crystalph_tsv(), 'w')
f.write('PDB_ID _exptl_crystal_grow.pH\n')
f.write('4X09\t6.5\n')
f.write('4rfr\t8\n')
f.write('4XET\t6.2\n')
f.write('4XF1\t6.2\n')
f.write('4XF3\t6.2\n')
f.flush()
f.close()
makeblast = MakeBlastDBTask(temp_dir, params)
makeblast.create_dir()
f = open(makeblast.get_pdb_seqres_txt(), 'w')
f.write('>4rfr_A mol:protein length:154 MYOGLOBIN\n')
f.write('MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVK'
'HLKTEAEMKASEDLKKHG\n')
f.write('>102l_A mol:protein length:165 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKA'
'IGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAL'
'INMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRV'
'ITTFRTGTWDAYKNL\n')
f.flush()
f.close()
pdbset = task.get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres()
self.assertEqual(len(pdbset), 1)
self.assertEqual('4RFR' in pdbset, True)
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pdbid_from_crystalph_tsv_valid_entries(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
f = open(task.get_crystalph_tsv(), 'w')
f.write('PDB_ID _exptl_crystal_grow.pH\n')
f.write('4rfr 7.5\n')
f.write('4X09\t6.5\n')
f.write('4XET\t6.2\n')
f.write('4XF1\t6.2\n')
f.write('4XF3\t6.2\n')
f.flush()
f.close()
pdbid_set = task.get_set_of_pdbid_from_crystalph_tsv()
self.assertEqual(os.path.isfile(task.get_crystalph_tsv()), True)
self.assertEqual(len(pdbid_set), 5)
self.assertEqual('4RFR' in pdbid_set, True)
self.assertEqual('4X09' in pdbid_set, True)
self.assertEqual('4XET' in pdbid_set, True)
self.assertEqual('4XF1' in pdbid_set, True)
self.assertEqual('4XF3' in pdbid_set, True)
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pdbid_from_crystalph_tsv_invalid_entries(self):
"""Header missing and 4rfr has 3 columns
"""
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
f = open(task.get_crystalph_tsv(), 'w')
f.write('4X09\t6.5\n')
f.write('4rfr 7.5 8\n')
f.write('4XET\t6.2\n')
f.write('4XF1\t6.2\n')
f.write('4XF3\t6.2\n')
f.flush()
f.close()
pdbid_set = task.get_set_of_pdbid_from_crystalph_tsv()
self.assertEqual(os.path.isfile(task.get_crystalph_tsv()), True)
self.assertEqual(len(pdbid_set), 3)
self.assertEqual('4RFR' in pdbid_set, False)
self.assertEqual('4X09' in pdbid_set, False)
self.assertEqual('4XET' in pdbid_set, True)
self.assertEqual('4XF1' in pdbid_set, True)
self.assertEqual('4XF3' in pdbid_set, True)
finally:
shutil.rmtree(temp_dir)
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 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 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_get_set_of_pdbid_from_crystalph_tsv_nonexistant_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
pdbid_set = task.get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres()
self.assertEqual(len(pdbid_set), 0)
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_get_set_of_pdbid_from_crystalph_tsv_empty_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
open(task.get_crystalph_tsv(), 'a').close()
pdbid_set = task.get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres()
self.assertEqual(os.path.isfile(task.get_crystalph_tsv()), True)
self.assertEqual(len(pdbid_set), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pdbid_from_crystalph_tsv_internal_exception(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
open(task.get_crystalph_tsv(), 'a').close()
os.chmod(task.get_crystalph_tsv(), 0o000)
pdbid_set = task.get_set_of_pdbid_from_crystalph_tsv()
self.assertEqual(len(pdbid_set), 0)
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_get_set_of_pdbid_from_crystalph_tsv_no_header_invalid_lines(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
f = open(task.get_crystalph_tsv(), 'w')
f.write('hello\nx\n')
f.flush()
f.close()
pdbid_set = task.get_set_of_pdbid_from_crystalph_tsv()
self.assertEqual(os.path.isfile(task.get_crystalph_tsv()), True)
self.assertEqual(len(pdbid_set), 0)
finally:
shutil.rmtree(temp_dir)
def test_download_participant_list_no_filetransfer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
task._download_participant_list_csv()
self.assertEqual(
task.get_email_log(), '\nWARNING: Unable to download '
'participant_list.csv which means '
'external users will NOT get evaluation '
'email : \'NoneType\' object has no attribute '
'\'connect\'\n')
finally:
shutil.rmtree(temp_dir)
def test_tar_challenge_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
dimport = DataImportTask(temp_dir, params)
dimport.create_dir()
open(dimport.get_sequence_tsv(), 'a').close()
open(dimport.get_nonpolymer_tsv(), 'a').close()
open(dimport.get_crystalph_tsv(), 'a').close()
task = ChallengeDataTask(temp_dir, params)
task.create_dir()
chall_dir = task._create_challenge_dir()
final_log = os.path.join(chall_dir, 'final.log')
open(final_log, 'a').close()
task._create_readme(chall_dir)
task._copy_over_tsv_files(chall_dir)
# make a fake candidate
file_list = self.make_fake_candidate_dir(chall_dir, '5hib',
'2eb2', 'CSX')
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)
final_log = os.path.join(foodir, 'final.log')
self.assertEqual(os.path.isfile(final_log), False)
for fname in file_list:
chk = os.path.join(cdir, fname)
self.assertEqual(os.path.isfile(chk), True, chk)
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_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_get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres_no_seq(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
f = open(task.get_crystalph_tsv(), 'w')
f.write('PDB_ID _exptl_crystal_grow.pH\n')
f.write('4X09\t6.5\n')
f.write('4rfr\t8\n')
f.write('4XET\t6.2\n')
f.write('4XF1\t6.2\n')
f.write('4XF3\t6.2\n')
f.flush()
f.close()
pdbset = task.get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres()
self.assertEqual(len(pdbset), 0)
finally:
shutil.rmtree(temp_dir)
def test_append_standard_to_files(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
task.append_standard_to_files()
self.assertTrue(os.path.isfile(task.get_nonpolymer_tsv()))
self.assertTrue(os.path.isfile(task.get_sequence_tsv()))
self.assertTrue(os.path.isfile(task.get_crystalph_tsv()))
# now do it again, but this time make the append fail
# cause the nonpolymer_tsv is a directory
os.unlink(task.get_nonpolymer_tsv())
os.makedirs(task.get_nonpolymer_tsv())
task.append_standard_to_files()
finally:
shutil.rmtree(temp_dir)
def test_get_uploadable_files(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
self.assertEqual(task.get_uploadable_files(), [])
task.create_dir()
# test empty dir
self.assertEqual(task.get_uploadable_files(), [])
# test with only compinchi
open(task.get_components_inchi_file(), 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 1)
flist.index(task.get_components_inchi_file())
# test with crystal file
open(task.get_crystalph_tsv(), 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 2)
flist.index(task.get_components_inchi_file())
flist.index(task.get_crystalph_tsv())
# test with nonpolymer file
open(task.get_nonpolymer_tsv(), 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 3)
flist.index(task.get_components_inchi_file())
flist.index(task.get_crystalph_tsv())
flist.index(task.get_nonpolymer_tsv())
# test with sequence file
open(task.get_sequence_tsv(), 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 4)
flist.index(task.get_components_inchi_file())
flist.index(task.get_crystalph_tsv())
flist.index(task.get_nonpolymer_tsv())
flist.index(task.get_sequence_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_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_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_run_succeeds_no_ftp(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)
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)
stderr = os.path.join(chall.get_dir(),
'genchallenge.py.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(chall.get_dir(),
'genchallenge.py.stdout')
self.assertEqual(os.path.isfile(stdout), True)
# verify challenge directory is created and
# filled with valid files
chall_dir = os.path.join(chall.get_dir(),
chall.get_celpp_challenge_data_dir_name())
self.assertEqual(os.path.isdir(chall_dir), True)
readme = os.path.join(chall_dir, ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
crystal = os.path.join(chall_dir, DataImportTask.CRYSTALPH_TSV)
self.assertEqual(os.path.isfile(crystal), True)
seq = os.path.join(chall_dir, DataImportTask.SEQUENCE_TSV)
self.assertEqual(os.path.isfile(seq), True)
nonpoly = os.path.join(chall_dir, DataImportTask.NONPOLYMER_TSV)
self.assertEqual(os.path.isfile(nonpoly), True)
fivehibdir = os.path.join(chall_dir, '5hib')
fivehibtxt = os.path.join(fivehibdir, '5hib.txt')
self.assertEqual(os.path.isfile(fivehibtxt), True)
fivehibfas = os.path.join(fivehibdir, '5hib.fasta')
self.assertEqual(os.path.isfile(fivehibfas), True)
fivehicdir = os.path.join(chall_dir, '5hic')
fivehictxt = os.path.join(fivehicdir, '5hic.txt')
self.assertEqual(os.path.isfile(fivehictxt), True)
fivehicfas = os.path.join(fivehicdir, '5hic.fasta')
self.assertEqual(os.path.isfile(fivehicfas), True)
# verify tarball is created
tfile = chall.get_celpp_challenge_data_tar_file()
self.assertEqual(os.path.isfile(tfile), True)
foodir = os.path.join(temp_dir, 'foo')
os.mkdir(foodir)
tar = tarfile.open(tfile, 'r:*')
tar.extractall(path=foodir)
tar.close()
name = chall.get_celpp_challenge_data_dir_name()
cdir = os.path.join(foodir, name)
readme = os.path.join(cdir, ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
final = os.path.join(foodir, name, 'final.log')
self.assertEqual(os.path.isfile(final), False)
e_con = os.path.join(foodir, name, 'error_container')
self.assertEqual(os.path.isdir(e_con), False)
finally:
shutil.rmtree(temp_dir)
def test_can_run(self):
tempDir = tempfile.mkdtemp()
try:
# try where makeblastdb is not complete
params = D3RParameters()
blastTask = BlastNFilterTask(tempDir, params)
self.assertEqual(blastTask.can_run(), False)
# try where makeblastdb failed
blastDb = MakeBlastDBTask(tempDir, params)
blastDb.create_dir()
errorFile = os.path.join(blastDb.get_path(),
blastDb.get_dir_name(),
D3RTask.ERROR_FILE)
open(errorFile, 'a').close()
self.assertEqual(blastTask.can_run(), False)
self.assertEqual(blastTask.get_error(),
'makeblastdb task has error status')
# try where data import is not complete
completeFile = os.path.join(blastDb.get_path(),
blastDb.get_dir_name(),
D3RTask.COMPLETE_FILE)
open(completeFile, 'a').close()
self.assertEqual(blastTask.can_run(), False)
self.assertEqual(blastTask.get_error(),
'dataimport task has ' + 'notfound status')
# try where data import failed
dataImport = DataImportTask(tempDir, params)
dataImport.create_dir()
errorFile = os.path.join(dataImport.get_path(),
dataImport.get_dir_name(),
D3RTask.ERROR_FILE)
open(errorFile, 'a').close()
self.assertEqual(blastTask.can_run(), False)
self.assertEqual(blastTask.get_error(),
'dataimport task has error status')
# try where blast can run
os.remove(errorFile)
completeFile = os.path.join(dataImport.get_dir(),
D3RTask.COMPLETE_FILE)
open(completeFile, 'a').close()
self.assertEqual(blastTask.can_run(), True)
self.assertEqual(blastTask.get_error(), None)
# try where blast exists
blastTask.create_dir()
self.assertEqual(blastTask.can_run(), False)
self.assertEqual(
blastTask.get_error(),
blastTask.get_dir_name() + ' already exists and' +
' status is unknown')
# try where blast is complete
completeFile = os.path.join(blastTask.get_path(),
blastTask.get_dir_name(),
D3RTask.COMPLETE_FILE)
open(completeFile, 'a').close()
self.assertEqual(blastTask.can_run(), False)
self.assertEqual(blastTask.get_error(), None)
finally:
shutil.rmtree(tempDir)
def test_run_with_blast_success_usenewsequencetsv(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.blastnfilter = '/bin/echo'
params.postanalysis = os.path.join(temp_dir, 'foo.py')
params.pdbdb = '/pdbdb'
blasttask = BlastNFilterTask(temp_dir, params)
blasttask._can_run = True
txt_file = os.path.join(blasttask.get_dir(), 'summary.txt')
txt_contents = ('INPUT SUMMARY\\n' + ' sequences: 177\\n' +
' complexes: 149\\n')
# create fake blastnfilter script that makes csv files
f = open(params.postanalysis, 'w')
f.write('#! /usr/bin/env python\n\n')
f.write('f = open(\'' + txt_file + '\', \'w\')\n')
f.write('f.write(\'' + txt_contents + '\\n\')\n')
f.write('f.flush()\nf.close()\n')
f.flush()
f.close()
os.chmod(params.postanalysis, stat.S_IRWXU)
dtask = DataImportTask(temp_dir, params)
dtask.create_dir()
open(dtask.get_sequence_tsv(), 'a').close()
blasttask.run()
self.assertEqual(blasttask.get_status(), D3RTask.COMPLETE_STATUS)
self.assertEqual(blasttask.get_error(), None)
complete_file = os.path.join(blasttask.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(complete_file), True)
std_err_file = os.path.join(blasttask.get_dir(), 'echo.stderr')
self.assertEqual(os.path.isfile(std_err_file), True)
std_out_file = os.path.join(blasttask.get_dir(), 'echo.stdout')
dataimport = DataImportTask(temp_dir, params)
makeblast = MakeBlastDBTask(temp_dir, params)
f = open(std_out_file, 'r')
echo_out = f.read().replace('\n', '')
echo_out.index('--nonpolymertsv ' +
os.path.join(temp_dir, dataimport.get_dir_name(),
DataImportTask.NONPOLYMER_TSV))
echo_out.index(' --sequencetsv ' +
os.path.join(temp_dir, dataimport.get_dir_name(),
DataImportTask.SEQUENCE_TSV))
echo_out.index(' --pdbblastdb ' +
os.path.join(temp_dir, makeblast.get_dir_name()))
echo_out.index(' --compinchi ' +
os.path.join(temp_dir, dataimport.get_dir_name(),
DataImportTask.COMPINCHI_ICH))
echo_out.index(' --outdir ' +
os.path.join(temp_dir, blasttask.get_dir_name()))
echo_out.index(' --crystalpH ' +
os.path.join(temp_dir, dataimport.get_dir_name(),
DataImportTask.CRYSTALPH_TSV))
echo_out.index(' --pdbdb /pdbdb ')
f.close()
self.assertEqual(os.path.isfile(std_out_file), True)
self.assertEquals(blasttask.get_status(), D3RTask.COMPLETE_STATUS)
self.assertEquals(
os.path.exists(
os.path.join(blasttask.get_dir(), 'foo.py.stderr')), True)
self.assertEquals(
os.path.exists(
os.path.join(blasttask.get_dir(), 'foo.py.stdout')), True)
res = blasttask.get_email_log().rstrip('\n')
res.index('/bin/echo')
res.index('# txt files found: 0')
res.index('Output from summary.txt')
res.index(' sequences: 177')
res.index(' complexes: 149')
self.assertEqual(
res.find(dataimport.get_sequence_tsv() +
' file not found falling back to ' +
dataimport.get_oldsequence_tsv()), -1)
finally:
shutil.rmtree(temp_dir)
