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_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 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()
