def test_transfer_fedids_files(self):
soakdb_rows = SoakdbFiles.objects.all()
soakdb_rows.delete()
run_luigi_worker(FindSoakDBFiles(filepath=str(self.working_dir + '*')))
print('TESTING FEDIDS: test_transfer_fedids_files')
transfer = run_luigi_worker(
TransferAllFedIDsAndDatafiles(
date=self.date, soak_db_filepath=str(self.working_dir + '*')))
self.assertTrue(transfer)
def test_transfers(self):
print('TESTING TRANSFERS: test_transfers')
find_file = run_luigi_worker(
FindSoakDBFiles(filepath=str(self.working_dir + '*')))
self.assertTrue(find_file)
test_new_file = run_luigi_worker(
TransferNewDataFile(data_file=self.db_full_path,
soak_db_filepath=str(self.working_dir + '*')))
self.assertTrue(test_new_file)
# get the status value from soakdb entry for current file
status = list(SoakdbFiles.objects.values_list('status', flat=True))
# check == 2 (not changed - ie. has been successfully added)
self.assertEqual(int(status[0]), 2)
def test_findsoakdb(self):
print('TESTING FINDSOAKDB: test_findsoakdb')
os.chdir(self.working_dir)
print(os.path.join(self.working_dir) + '*')
find_file = run_luigi_worker(
FindSoakDBFiles(filepath=str(self.working_dir + '*')))
self.assertTrue(find_file)
def test_run_ranker(self):
subwell_directory = 'SubwellImages'
plate_directories = [
x[0] for x in os.walk(os.path.join(os.getcwd(), subwell_directory))
if os.path.join(os.getcwd(), 'SubwellImages') not in x
]
imagers = []
plate_types = []
plates = []
for plate in plate_directories:
components = plate.split('/')
plate_components = components[-1].split('_')
print(plate_components)
imagers.append(
str(plate_components[-1].split('-')[0]) + '-' +
plate_components[-1].split('-')[1])
plate_types.append(plate_components[-1].split('-')[2])
plates.append(components[-1])
print(imagers)
print(plate_types)
print(plates)
ranker = run_luigi_worker(
RunRanker(plate=plates[0],
plate_type=plate_types[0],
imager=imagers[0]))
self.assertTrue(ranker)
self.assertTrue(
os.path.isfile(
'ranker_jobs/RANK_90j8_2018-04-11_RI1000-0081-2drop.sh'))
def test_find_pandda_logs(self):
find_logs = run_luigi_worker(
FindPanddaLogs(
search_path=
'/dls/science/groups/i04-1/software/luigi_pipeline/pipelineDEV/tests/docking_files/panddas_alice',
soak_db_filepath=str(self.working_dir + '*')))
self.assertTrue(find_logs)
def test_grid_prep(self):
grid_prep = run_luigi_worker(
luigi_classes.prepare_dock.GridPrepADT(
ligand_file_name=self.ligand_pdbqt,
receptor_file_name=self.protein_pdbqt,
docking_dir='',
root_dir=self.working_dir))
self.assertTrue(grid_prep)
def test_add_pandda_runs(self):
remove_files = []
log_files = pf.find_log_files(
'/dls/science/groups/i04-1/software/luigi_pipeline/pipelineDEV/tests/docking_files/'
)
log_files = log_files.split()
for log_file in log_files:
pver, input_dir, output_dir, sites_file, events_file, err = pf.get_files_from_log(
log_file)
if not err and sites_file and events_file and '0.1.' not in pver:
remove_path = str('/'.join(log_file.split('/')[:-1]))
remove_files.append(remove_path)
add_run = run_luigi_worker(
AddPanddaRun(log_file=log_file,
pver=pver,
input_dir=input_dir,
output_dir=output_dir,
sites_file=sites_file,
events_file=events_file))
self.assertTrue(add_run)
add_sites = run_luigi_worker(
AddPanddaSites(log_file=log_file,
pver=pver,
input_dir=input_dir,
output_dir=output_dir,
sites_file=sites_file,
events_file=events_file,
soakdb_filename=os.path.join(
self.working_dir,
'soakDBDataFile.sqlite')))
self.assertTrue(add_sites)
if os.path.isfile(str(log_file + '.sites.done')):
os.remove(str(log_file + '.sites.done'))
def test_get_plate_types(self):
# test the GetPlateTypes task runs
test = run_luigi_worker(GetPlateTypes())
# test that task was successful
self.assertTrue(test)
# get csv files creates by task
two_drops = glob.glob('barcodes_2drop/*.csv')
three_drops = glob.glob('barcodes_3drop/*.csv')
# check that files were created
self.assertTrue(two_drops)
self.assertTrue(three_drops)
def test_run_autodock(self):
run_autodock = run_luigi_worker(luigi_classes.run_dock.RunAutoDock(ligand_pdbqt=self.ligand_pdbqt,
receptor_pdbqt=self.protein_pdbqt,
docking_dir='',
root_dir=self.working_dir))
self.assertTrue(run_autodock)
self.assertTrue(os.path.isfile(os.path.join(self.working_dir, 'autodock.job.id')))
out, job_id = kill_job(self.working_dir, 'autodock.job.id')
# make sure communicated with queue successfully
self.assertTrue(str(job_id) in out.decode('ascii'))
def test_check_files(self):
print('TESTING CHECK_FILES: test_check_files')
check_files = run_luigi_worker(
CheckFiles(soak_db_filepath=str(self.working_dir + '*')))
self.assertTrue(check_files)
# get the status value from soakdb entry for current file
print('\n')
print('status:')
status = list(SoakdbFiles.objects.values_list('status', flat=True))
print(status)
print('\n')
def test_lig_prep(self):
# run test data on luigi worker
lig_prep = run_luigi_worker(luigi_classes.prepare_dock.PrepLigand(
root_dir=self.working_dir, ligand_sdf=self.ligand_sdf, docking_dir=''))
# check that the task was run successfully
self.assertTrue(lig_prep)
# define the file that should have been produced, and the example file
expected_file = os.path.join(self.root_dir, 'comp_chem', self.ligand_sdf.replace('.pdb', '_prepared.pdbqt'))
produced_file = os.path.join(self.working_dir, str(self.ligand_sdf).replace('.pdb', '_prepared.pdbqt'))
# run file checks
self.file_checks(expected_file=expected_file, produced_file=produced_file)
def test_protein_prep(self):
# run test data on luigi worker
protein_prep = run_luigi_worker(luigi_classes.prepare_dock.PrepProtein(
root_dir=self.working_dir, protein_pdb=self.protein_pdb, docking_dir=''))
# check that the job ran successfully
self.assertTrue(protein_prep)
# define the file that should have been produced, and the example file
expected_file = os.path.join(self.root_dir, 'comp_chem', self.protein_pdb.replace('.pdb', '_prepared.pdbqt'))
produced_file = os.path.join(self.working_dir, str(self.protein_pdb).replace('.pdb', '_prepared.pdbqt'))
# run file checks
self.file_checks(expected_file=expected_file, produced_file=produced_file)
def test_vina(self):
# run vina task via luigi
vina_submit = run_luigi_worker(luigi_classes.run_dock.RunVinaDock(root_dir=self.working_dir,
docking_dir='',
ligand_pdbqt=self.ligand_pdbqt,
receptor_pdbqt=self.protein_pdbqt))
# check job ran successfully, and that a job id was generated from cluster
self.assertTrue(vina_submit)
self.assertTrue(os.path.isfile(os.path.join(self.working_dir, 'vina.job.id')))
out, job_id = kill_job(self.working_dir, 'vina.job.id')
# make sure communicated with queue successfully
self.assertTrue(str(job_id) in out.decode('ascii'))