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_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 __init__(self, path, args):
super(DataImportTask, self).__init__(path, args)
self.set_name(DataImportTask.TASK_NAME)
makeblast = MakeBlastDBTask('', args)
self.set_stage(makeblast.get_stage() + 1)
self.set_status(D3RTask.UNKNOWN_STATUS)
self._maxretries = 3
self._retrysleep = 1
def test_get_set_of_pbdid_from_pdb_seqres_txt_no_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_where_pdbsequrl_is_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.run()
self.assertEqual(
task.get_error(), 'cannot download files cause '
'pdbsequrl not set')
finally:
shutil.rmtree(temp_dir)
def test_run_where_makeblastdb_is_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.pdbsequrl = 'pdbsequrl'
task = MakeBlastDBTask(temp_dir, params)
task.run()
self.assertEqual(
task.get_error(), 'cannot make blast database '
'cause makeblastdb 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 can_run(self):
"""Determines if task can actually run
This method first verifies the `MakeBlastDBTask` and
`DataImportTask` task have
`D3RTask.COMPLETE_STATUS` for status. The method then
verifies a `BlastNFilterTask` does not already exist.
If above is not true then self.set_error() is set
with information about the issue
:return: True if can run otherwise False
"""
self._can_run = False
self._error = None
# check blast
make_blastdb = MakeBlastDBTask(self._path, self._args)
make_blastdb.update_status_from_filesystem()
if make_blastdb.get_status() != D3RTask.COMPLETE_STATUS:
logger.info('Cannot run ' + self.get_name() + ' task ' +
'because ' + make_blastdb.get_name() + ' task' +
'has a status of ' + make_blastdb.get_status())
self.set_error(make_blastdb.get_name() + ' task has ' +
make_blastdb.get_status() + ' status')
return False
# check data import
data_import = DataImportTask(self._path, self._args)
data_import.update_status_from_filesystem()
if data_import.get_status() != D3RTask.COMPLETE_STATUS:
logger.info('Cannot run ' + self.get_name() + ' task ' +
'because ' + data_import.get_name() + ' task' +
'has a status of ' + data_import.get_status())
self.set_error(data_import.get_name() + ' task has ' +
data_import.get_status() + ' status')
return False
# check blast is not complete and does not exist
self.update_status_from_filesystem()
if self.get_status() == D3RTask.COMPLETE_STATUS:
logger.debug("No work needed for " + self.get_name() + " task")
return False
if self.get_status() != D3RTask.NOTFOUND_STATUS:
logger.warning(self.get_name() + " task was already " +
"attempted, but there was a problem")
self.set_error(self.get_dir_name() + ' already exists and ' +
'status is ' + self.get_status())
return False
self._can_run = True
return True
def test_constructor(self):
params = D3RParameters()
task = MakeBlastDBTask('/foo', params)
self.assertEqual(task.get_name(), 'makeblastdb')
self.assertEqual(task.get_stage(), 1)
self.assertEqual(task.get_status(), D3RTask.UNKNOWN_STATUS)
self.assertEqual(task.get_path(), '/foo')
self.assertEqual(task.get_dir_name(), 'stage.1.makeblastdb')
test_task.try_update_status_from_filesystem(self, task)
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_get_set_of_pbdid_from_pdb_seqres_txt_with_400k_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
f = open(task.get_pdb_seqres_txt(), 'w')
perms = itertools.permutations(
string.ascii_lowercase + '123456789', 4)
counter = 0
try:
limit = 400000
while counter < limit:
f.write('>' + ''.join(map(str, perms.next())) +
'_A mol:protein length:165 T4 LYSOZYME\n')
f.write('MVLSEGEWQLVLH\n')
counter += 1
except StopIteration:
pass
f.flush()
f.close()
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), counter)
finally:
shutil.rmtree(temp_dir)
def test_run_where_can_run_is_false(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
open(os.path.join(task.get_dir(), 'error'), 'a').close()
task.run()
self.assertEqual(task._can_run, False)
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)
def test_get_set_of_pbdid_from_pdb_seqres_txt_empty_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
open(task.get_pdb_seqres_txt(), 'a').close()
self.assertEqual(os.path.isfile(task.get_pdb_seqres_txt()), True)
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres_empty_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()
makeblast = MakeBlastDBTask(temp_dir, params)
makeblast.create_dir()
open(makeblast.get_pdb_seqres_txt(), 'a').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_get_sequence_count_file_has_zero_size(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
open(task.get_pdb_seqres_txt(), 'a').close()
self.assertEqual(task._get_sequence_count_message(),
'# sequence(s): 0')
finally:
shutil.rmtree(temp_dir)
def test_run_where_download_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.pdbsequrl = 'file://doesnotexist'
params.makeblastdb = 'makeblastdb'
task = MakeBlastDBTask(temp_dir, params)
task._retrysleep = 0
task._maxretries = 1
task.run()
self.assertEqual(
task.get_error(),
'Unable to download file: ' + 'file://doesnotexist')
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pbdid_from_pdb_seqres_txt_file_no_seqs(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
f = open(task.get_pdb_seqres_txt(), 'w')
f.write('hi\nhow\nare\nyou')
f.flush()
f.close()
self.assertEqual(os.path.isfile(task.get_pdb_seqres_txt()), True)
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_sequence_count_file_has_multiple_seqs(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
f = open(task.get_pdb_seqres_txt(), 'w')
f.write('>hi\n>seq\n>are\n')
f.flush()
f.close()
self.assertEqual(task._get_sequence_count_message(),
'# sequence(s): 3')
finally:
shutil.rmtree(temp_dir)
def test_run_where_gunzip_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = open(fakegz, 'w')
f.write('hello\n')
f.flush()
f.close()
params.pdbsequrl = 'file://' + fakegz
params.makeblastdb = 'makeblastdb'
task = MakeBlastDBTask(temp_dir, params)
task._retrysleep = 0
task._maxretries = 1
task.run()
self.assertEqual(
task.get_error(),
'Unable to uncompress file: ' + task.get_pdb_seqres_txt())
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pbdid_from_pdb_seqres_txt_with_seqs(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
f = open(task.get_pdb_seqres_txt(), 'w')
f.write('>101m_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.write('>102l_A mol:protein length:154 MYOGLOBIN\n')
f.write('MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHL'
'KTEAEMKASEDLKKAGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKI'
'PIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG\n')
f.write('>103l_A mol:protein length:167 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNSLDAAKSELD'
'KAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRA'
'ALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAK'
'RVITTFRTGTWDAYKNL\n')
f.write('>10jj3m_A mol:protein length:154 MYOGLOBIN\n')
f.write('MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRF\n')
f.write('>104l_A mol:protein length:166 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSAAE\n')
f.write('>104l_B mol:protein length:166 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSAKNL\n')
f.flush()
f.close()
self.assertEqual(os.path.isfile(task.get_pdb_seqres_txt()), True)
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), 4)
self.assertEqual('101M' in pdbset, True)
self.assertEqual('102L' in pdbset, True)
self.assertEqual('103L' in pdbset, True)
self.assertEqual('104L' in pdbset, True)
finally:
shutil.rmtree(temp_dir)
def get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres(self):
"""Gets set of PDBIDs that are in both tsv and sequence file
Examines `DataImportTask.CRYSTALPH_TSV` and
`MakeBlastDBTask.PDB_SEQRES_TXT` and returns a set of PDBIDs
that are in both files
:returns: set of PDBIDs uppercase that are in both files above
"""
make_blastdb = MakeBlastDBTask(self._path, self._args)
if not os.path.isfile(make_blastdb.get_pdb_seqres_txt()):
logger.warning('No ' + make_blastdb.get_pdb_seqres_txt() +
' file found')
return set()
c_pdbid_set = self.get_set_of_pdbid_from_crystalph_tsv()
if len(c_pdbid_set) == 0:
logger.warning('No PDBIds found in ' + self.get_crystalph_tsv())
return set()
seq_pdbid_set = make_blastdb.get_set_of_pbdid_from_pdb_seqres_txt()
if len(seq_pdbid_set) == 0:
logger.warning('No PDBIds found in ' +
make_blastdb.get_pdb_seqres_txt())
return set()
common_pdbid = set()
# iterate through tsv pdb ids and return any found in
# sequence pdb id set
for id in c_pdbid_set:
if id in seq_pdbid_set:
common_pdbid.add(id)
logger.debug('Found ' + str(len(common_pdbid)) + ' PDBIDs in ' +
self.get_crystalph_tsv() + ' and ' +
make_blastdb.get_pdb_seqres_txt())
return common_pdbid
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_pbdid_from_pdb_seqres_txt_wrong_len_pdbids(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
f = open(task.get_pdb_seqres_txt(), 'w')
f.write('>1m_A mol:protein length:154 MYOGLOBIN\n')
f.write('MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVK'
'HLKTEAEMKASEDLKKHG\n')
f.write('>abcdel_A mol:protein length:165 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKA'
'IGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAL'
'INMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRV'
'ITTFRTGTWDAYKNL\n')
f.flush()
f.close()
self.assertEqual(os.path.isfile(task.get_pdb_seqres_txt()), True)
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_where_makeblastdb_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = gzip.open(fakegz, 'wb')
f.write('hello\n')
f.flush()
f.close()
params.pdbsequrl = 'file://' + fakegz
params.makeblastdb = 'false'
task = MakeBlastDBTask(temp_dir, params)
task._retrysleep = 0
task._maxretries = 1
task.run()
self.assertEqual(
task.get_error(), 'Non zero exit code: 1 '
'received. Standard out:'
' Standard error: ')
finally:
shutil.rmtree(temp_dir)
def test_run_with_blast_success_useoldseq_and_postanalysis_fail(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)
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.OLDSEQUENCE_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')
res.index(dataimport.get_sequence_tsv() +
' file not found falling back to ' +
dataimport.get_oldsequence_tsv())
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 main():
blasttask = BlastNFilterTask('', p)
dataimport = DataImportTask('', p)
challenge = ChallengeDataTask('', p)
glide = GlideTask('', p)
makedb = MakeBlastDBTask('', p)
prot = ProteinLigPrepTask('', p)
vina = AutoDockVinaTask('', p)
chimeraprep = ChimeraProteinLigPrepTask('', p)
desc = """
Version {version}
Runs the 9 stages (makedb, import, blast, challengedata,
proteinligprep, {chimeraprep}, extsubmission, glide, vina, &
evaluation) of CELPP processing pipeline
(http://www.drugdesigndata.org)
CELPP processing pipeline relies on a set of directories
with specific structure. The pipeline runs a set of stages
Each stage has a numerical value and a name. The numerical
value denotes order and the stage name identifies separate
tasks to run in the stage.
The filesystem structure of the stage is:
stage.<stage number>.<task name>
The stage(s) run are defined via the required --stage flag.
To run multiple stages serially just pass a comma delimited
list to the --stage flag. Example: --stage import,blast
NOTE: When running multiple stages serially the program will
not run subsequent stages if a task in a stage fails.
Also note order matters, ie putting blast,import will
cause celpprunner.py to run blast stage first.
This program drops a pid lockfile
(celpprunner.<stage>.lockpid) in celppdir to prevent duplicate
invocation.
When run, this program will examine the stage and see
if work can be done. If stage is complete or previous
steps have not completed, the program will exit silently.
If previous steps have failed or current stage already
exists in an error or uncomplete state then program will
report the error via email using addresses set in --email
flag. Errors will also be reported via stderr/stdout.
The program will also exit with nonzero exit code.
This program utilizes simple token files to denote stage
completion. If within the stage directory there is a:
'{complete}' file - then stage is done and no other
checking is done.
'error' file - then stage failed.
'start' file - then stage is running.
Notification of stage start and end will be sent to
addresses set via --email flag.
Unless --customweekdir is set, this program will
examine the 'celppdir' (last argument passed on
commandline) to find the latest directory with this path:
<year>/dataset.week.#
The program will find the latest <year> and within
that year the dataset.week.# with highest #. The output
directories created will be put within this directory.
Setting --customweekdir will cause program to use 'celppdir'
path.
Setting the --createweekdir flag will instruct this
program to create a new directory for the current
celpp week/year before running any stage processing.
NOTE: CELPP weeks start on Friday and end on Thursday
and week # follows ISO8601 rules so week numbers
at the end and start of the year are a bit
wonky.
Breakdown of behavior of program is defined by
value passed with --stage flag:
If --stage '{createchallenge}'
This is NOT a stage, but has the same effect as
calling --stage makedb,import,blast,challengedata
The four stages that need to run to generate the challenge
data package.
If --stage 'makedb'
In this stage the file {pdb_seqres} is downloaded from
an ftp site set by --pdbsequrl.
This file is then gunzipped and NCBI makeblastdb
(set by --makeblastdb) is run on it to create a blast
database. The files are stored in {makeblastdb_dirname}
If --stage 'import'
In this stage 4 files are downloaded from urls specified
by --compinchi and --pdbfileurl flags on the commandline
into {dataimport_dirname} directory.
The tsv files are (--pdbfileurl flag sets url to
download these files from):
{nonpolymer_tsv}
{sequence_tsv}
{crystal_tsv}
The Components ich file is (--compinchi flag sets base url to
download this file from):
{compinchi_ich}
This stage will just wait and retry if any of the tsv files
have NOT been updated since the start of the current
celpp week as determined by a HEAD request. To bypass
this delay add --skipimportwait flag. --importsleep denotes
the time to wait before re-examining the update time of the
tsv files and --importretry sets number of times to retry
before giving up.
If --stage 'blast'
Verifies {dataimport_dirname} exists and has '{complete}'
file. Also verifies {makeblastdb_dirname} exists and has
'{complete}' file. If both conditions are met then the
'blast' stage is run which invokes script set by
--blastnfilter flag and output stored in
{blast_dirname}.
Requires --pdbdb to be set to a directory with valid PDB
database files.
Note: --blastnfilter script is killed after time set with
--blastnfiltertimeout flag.
If --stage 'challengedata'
Verifies {blast_dirname} exists and has '{complete}'
file. If complete, this stage runs which invokes program
set in --genchallenge flag to create a challenge dataset
file. The --pdbdb flag must also be set when calling this
stage. If --ftpconfig is set with {challengepath} field then
this stage will also upload the challenge dataset tarfile
to the ftp server with path set by {challengepath}. The
code will also upload a {latest_txt} file containing name
of the tarfile to the same destination overwriting any
{latest_txt} file that already exists.
Example file for --ftpconfig:
{host} some.ftp.com
{user} bob
{passn} mypass
{path} /celpp
{challengepath} /challenge
{submissionpath} /submissions
If --stage '{chimeraprep}'
Verifies {challenge_dirname} exists and has '{complete}'
file. If complete, this stage runs which invokes program
set in --chimeraprep flag to prepare pdb and inchi files
storing output in {chimeraprep_dirname}. --pdbdb flag
must also be set when calling this stage.
If --stage 'proteinligprep'
Verifies {challenge_dirname} exists and has '{complete}'
file. If complete, this stage runs which invokes program
set in --proteinligprep flag to prepare pdb and inchi files
storing output in {proteinligprep_dirname}. --pdbdb flag
must also be set when calling this stage.
If --stage 'extsubmission'
Connects to server specified by --ftpconfig and downloads
external docking submissions from {submissionpath} on remote
server.
Submissions should be named:
celpp_weekXX_YYYY_dockedresults_ZZZZ.tar.gz as documented here:
https://github.com/drugdata/d3r/wiki/Proposed-challenge-docked\
-results-file-structure
For each submission a directory named stage.X.ZZZZ.extsubmission
will be created and uncompressed contents of package will be
stored in that directory. If data does not conform properly
'error' file will be placed in directory denoting failure
If --stage 'glide'
Verifies {proteinligprep_dirname} exists and has a '{complete}'
file within it. If complete, this stage runs which invokes
program set in --glide flag to perform docking via glide
storing output in {glide_dirname}
If --stage 'vina'
Verifies {proteinligprep_dirname} exists and has a '{complete}'
file within it. If complete, this stage runs which invokes
program set in --vina flag to perform docking via AutoDock Vina
storing output in {vina_dirname}
If --stage 'evaluation'
Finds all stage.{dockstage}.<algo> directories with '{complete}'
files in them which do not end in name '{webdata}' and runs
script set via --evaluation parameter storing the result of
the script into stage.{evalstage}.<algo>.evaluation. --pdbdb flag
must also be set when calling this stage.
""".format(makeblastdb_dirname=makedb.get_dir_name(),
dataimport_dirname=dataimport.get_dir_name(),
blast_dirname=blasttask.get_dir_name(),
challenge_dirname=challenge.get_dir_name(),
createchallenge=CREATE_CHALLENGE,
proteinligprep_dirname=prot.get_dir_name(),
glide_dirname=glide.get_dir_name(),
vina_dirname=vina.get_dir_name(),
dockstage=str(glide.get_stage()),
evalstage=str(glide.get_stage() + 1),
complete=blasttask.COMPLETE_FILE,
chimeraprep_dirname=chimeraprep.get_dir_name(),
chimeraprep=CHIMERA_PREP,
compinchi_ich=DataImportTask.COMPINCHI_ICH,
pdb_seqres=MakeBlastDBTask.PDB_SEQRES_TXT_GZ,
nonpolymer_tsv=DataImportTask.NONPOLYMER_TSV,
sequence_tsv=DataImportTask.SEQUENCE_TSV,
crystal_tsv=DataImportTask.CRYSTALPH_TSV,
webdata=EvaluationTaskFactory.WEB_DATA_SUFFIX,
latest_txt=ChallengeDataTask.LATEST_TXT,
host=FtpFileTransfer.HOST,
user=FtpFileTransfer.USER,
passn=FtpFileTransfer.PASS,
path=FtpFileTransfer.PATH,
challengepath=FtpFileTransfer.CHALLENGEPATH,
submissionpath=FtpFileTransfer.SUBMISSIONPATH,
version=d3r.__version__)
theargs = _parse_arguments(desc, sys.argv[1:])
theargs.program = sys.argv[0]
theargs.version = d3r.__version__
util.setup_logging(theargs)
try:
run_stages(theargs)
except Exception:
logger.exception("Error caught exception")
sys.exit(2)
def run(self):
"""Runs blastnfilter task after verifying dataimport was good
Method requires can_run() to be called before hand with
successful outcome
Otherwise method invokes D3RTask.start then this method
creates a directory and invokes blastnfilter script and
postanalysis script. Upon completion results are
analyzed and success or error status is set
appropriately and D3RTask.end is invoked
"""
super(BlastNFilterTask, self).run()
if self._can_run is False:
logger.debug(self.get_dir_name() +
' cannot run cause _can_run flag '
'is False')
return
data_import = DataImportTask(self._path, self._args)
make_blastdb = MakeBlastDBTask(self._path, self._args)
try:
loglevel = self.get_args().loglevel
except AttributeError:
logger.debug('No log level set in arguments using WARNING')
loglevel = 'WARNING'
# verify sequence.tsv file exists on filesystem.
# if not fall back to oldsequence.tsv file
sequencetsv = data_import.get_sequence_tsv()
if not os.path.isfile(sequencetsv):
logger.warning(sequencetsv + ' file not found. falling '
'back to old file')
self.append_to_email_log('\n ' + sequencetsv + ' file not found ' +
'falling back to ' +
data_import.get_oldsequence_tsv() + '\n')
sequencetsv = data_import.get_oldsequence_tsv()
cmd_to_run = (self.get_args().blastnfilter + ' --nonpolymertsv ' +
data_import.get_nonpolymer_tsv() + ' --sequencetsv ' +
sequencetsv + ' --pdbblastdb ' + make_blastdb.get_dir() +
' --compinchi ' +
data_import.get_components_inchi_file() +
' --crystalpH ' + data_import.get_crystalph_tsv() +
' --pdbdb ' + self.get_args().pdbdb + ' --log ' +
loglevel + ' --outdir ' + self.get_dir())
blastnfilter_name = os.path.basename(self.get_args().blastnfilter)
self.run_external_command(
blastnfilter_name,
cmd_to_run,
False,
)
self.set_status(D3RTask.COMPLETE_STATUS)
cmd_to_run = (self.get_args().postanalysis + ' --compinchi ' +
data_import.get_components_inchi_file() + ' ' +
self.get_dir())
postanalysis_name = os.path.basename(self.get_args().postanalysis)
self.run_external_command(postanalysis_name, cmd_to_run, False)
try:
# examine output to get candidate hit count DR-12
hit_stats = self._parse_blastnfilter_output_for_hit_stats()
if hit_stats is not None:
self.append_to_email_log(hit_stats)
except Exception:
logger.exception("Error caught exception")
# assess the result
self.end()
def get_task_list_for_stage(theargs, stage_name):
"""Factory method that generates a list of tasks for given stage
Using stage_name get the list of tasks that need to
be run.
:param theargs: parameters set via commandline along with
``theargs.latest_weekly`` which should be set to
to base directory where stages will be run
:param stage_name: Name of stage to run
"""
if stage_name is None:
raise NotImplementedError('stage_name is None')
task_list = []
logger.debug('Getting task list for ' + stage_name)
if stage_name == CREATE_CHALLENGE:
task_list.append(MakeBlastDBTask(theargs.latest_weekly, theargs))
task_list.append(DataImportTask(theargs.latest_weekly, theargs))
task_list.append(BlastNFilterTask(theargs.latest_weekly, theargs))
task_list.append(ChallengeDataTask(theargs.latest_weekly, theargs))
if stage_name == 'makedb':
task_list.append(MakeBlastDBTask(theargs.latest_weekly, theargs))
if stage_name == 'import':
task_list.append(DataImportTask(theargs.latest_weekly, theargs))
if stage_name == 'blast':
task_list.append(BlastNFilterTask(theargs.latest_weekly, theargs))
if stage_name == 'challengedata':
task_list.append(ChallengeDataTask(theargs.latest_weekly, theargs))
if stage_name == 'proteinligprep':
task_list.append(ProteinLigPrepTask(theargs.latest_weekly, theargs))
if stage_name == 'glide':
task_list.append(GlideTask(theargs.latest_weekly, theargs))
if stage_name == 'vina':
task_list.append(AutoDockVinaTask(theargs.latest_weekly, theargs))
if stage_name == CHIMERA_PREP:
task_list.append(
ChimeraProteinLigPrepTask(theargs.latest_weekly, theargs))
if stage_name == 'extsubmission':
extfac = ExternalDataSubmissionFactory(theargs.latest_weekly, theargs)
task_list.extend(extfac.get_external_data_submissions())
if stage_name == 'evaluation':
# use util function call to get all evaluation tasks
# append them to the task_list
eval_task_factory = EvaluationTaskFactory(theargs.latest_weekly,
theargs)
task_list.extend(eval_task_factory.get_evaluation_tasks())
if len(task_list) is 0:
raise NotImplementedError('uh oh no tasks for ' + stage_name +
' stage')
return task_list