def test_run_stages_invalid_stage(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
theargs.stage = 'foo'
os.mkdir(os.path.join(temp_dir, '2015'))
os.mkdir(os.path.join(temp_dir, '2015', 'dataset.week.1'))
try:
celpprunner.run_stages(theargs)
except NotImplementedError as e:
self.assertEquals(e.message, 'uh oh no tasks for foo stage')
finally:
shutil.rmtree(temp_dir)
def test_run_stages_makedb_blast_chall_proteinligprep_glide_no_error(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.pdbdb = '/pdbdb'
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'makedb,blast,challengedata,proteinligprep,glide'
d_import_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.IMPORT_DIR_NAME)
os.makedirs(d_import_dir)
open(os.path.join(d_import_dir,
D3RTask.COMPLETE_FILE), 'a').close()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = gzip.open(fakegz, 'wb')
f.write('hello\n')
f.flush()
f.close()
theargs.pdbsequrl = 'file://'+fakegz
theargs.makeblastdb = 'echo'
theargs.blastnfilter = 'echo'
theargs.postanalysis = 'true'
theargs.proteinligprep = 'echo'
theargs.glide = 'echo'
theargs.genchallenge = 'echo'
self.assertEqual(celpprunner.run_stages(theargs), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_blast(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'blast'
theargs.pdbdb = '/pdbdb'
makedb_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.MAKEDB_DIR_NAME)
os.makedirs(makedb_dir)
open(os.path.join(makedb_dir, 'complete'), 'a').close()
d_import_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.IMPORT_DIR_NAME)
os.makedirs(d_import_dir)
open(os.path.join(d_import_dir, 'complete'), 'a').close()
theargs.blastnfilter = 'echo'
theargs.postanalysis = 'true'
self.assertEqual(celpprunner.run_stages(theargs), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_no_weekly_datasetfound(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
self.assertEqual(celpprunner.run_stages(theargs), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_customweekdir_set(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
theargs.customweekdir = True
theargs.createweekdir = True
theargs.stage = ''
try:
self.assertEquals(celpprunner.run_stages(theargs), 0)
self.fail('Expected NotImplementedError')
except NotImplementedError:
pass
finally:
shutil.rmtree(temp_dir)
def test_run_stages_blast_stage_data_import_missing(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
theargs.stage = 'blast'
os.mkdir(os.path.join(temp_dir, '2015'))
os.mkdir(os.path.join(temp_dir, '2015', 'dataset.week.1'))
makedb_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.MAKEDB_DIR_NAME)
os.makedirs(makedb_dir)
open(os.path.join(makedb_dir, 'complete'), 'a').close()
self.assertEquals(celpprunner.run_stages(theargs), 1)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_blast_has_error(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'blast'
os.mkdir(os.path.join(temp_dir, TestCelppRunner.MAKEDB_DIR_NAME))
open(os.path.join(temp_dir, TestCelppRunner.MAKEDB_DIR_NAME,
'error'),
'a').close()
os.mkdir(os.path.join(temp_dir, '2015'))
os.mkdir(os.path.join(temp_dir, '2015', 'dataset.week.1'))
self.assertEqual(celpprunner.run_stages(theargs), 1)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_makedb_through_glide(self):
"""This should test the following stages will run
makedb,import,blast,challengedata,proteinligprep,glide,vina
"""
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.pdbdb = '/pdbdb'
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'makedb,import,blast,challengedata,proteinligprep,' \
'chimeraprep,glide,vina'
d_import_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.IMPORT_DIR_NAME)
os.makedirs(d_import_dir)
open(os.path.join(d_import_dir,
D3RTask.COMPLETE_FILE), 'a').close()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = gzip.open(fakegz, 'wb')
f.write('hello\n')
f.flush()
f.close()
theargs.pdbsequrl = 'file://' + fakegz
theargs.pdbfileurl = 'file://' + fakegz
theargs.compinchi = 'file://' + fakegz
theargs.version = '1.0.0'
theargs.makeblastdb = 'echo'
theargs.blastnfilter = 'echo'
theargs.postanalysis = 'true'
theargs.proteinligprep = 'echo'
theargs.glide = 'echo'
theargs.vina = 'echo'
theargs.genchallenge = 'echo'
theargs.chimeraprep = 'echo'
self.assertEqual(celpprunner.run_stages(theargs), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_challenge_and_proteinligprep_no_error(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.pdbdb = '/pdbdb'
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'challengedata,proteinligprep'
blastdb_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.BLAST_DIR_NAME)
os.makedirs(blastdb_dir)
open(os.path.join(blastdb_dir, 'complete'), 'a').close()
theargs.proteinligprep = 'echo'
theargs.genchallenge = 'echo'
self.assertEqual(celpprunner.run_stages(theargs), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_blast_and_proteinligprep_blast_has_error(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'blast,proteinligprep'
os.mkdir(os.path.join(temp_dir, TestCelppRunner.MAKEDB_DIR_NAME))
open(os.path.join(temp_dir, TestCelppRunner.MAKEDB_DIR_NAME,
'complete'),
'a').close()
d_import_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.IMPORT_DIR_NAME)
os.makedirs(d_import_dir)
open(os.path.join(d_import_dir, D3RTask.ERROR_FILE), 'a').close()
theargs.blastnfilter = 'echo'
theargs.proteinligprep = 'echo'
self.assertEqual(celpprunner.run_stages(theargs), 1)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_createweekdir_set(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = os.path.join(temp_dir)
theargs.createweekdir = True
theargs.stage = ''
d = date.today()
celp_week = util.get_celpp_week_of_year_from_date(d)
try:
self.assertEquals(celpprunner.run_stages(theargs), 0)
self.fail('Expected NotImplementedError')
except NotImplementedError:
pass
expected_dir = os.path.join(temp_dir, str(celp_week[1]),
'dataset.week.' + str(celp_week[0]))
self.assertEquals(os.path.isdir(expected_dir), True)
finally:
shutil.rmtree(temp_dir)