def run(self):
lock = lock_file.LockFile(self.lock_file)
try:
self._import_reads_and_update_db()
except:
lock.stop()
raise Exception("Error immport reads or updating database")
lock.stop()
def test_init_and_stop(self):
'''test init and stop'''
tmp_file = 'test.lock_file'
utils.make_empty_file(tmp_file)
with self.assertRaises(lock_file.Error):
lock_file.LockFile(tmp_file)
os.unlink(tmp_file)
lock = lock_file.LockFile(tmp_file)
self.assertTrue(os.path.exists(tmp_file))
os.unlink(tmp_file)
with self.assertRaises(lock_file.Error):
lock.stop()
lock = lock_file.LockFile(tmp_file)
self.assertTrue(os.path.exists(tmp_file))
lock.stop()
self.assertFalse(os.path.exists(tmp_file))
def test_init_and_stop(self):
"""test init and stop"""
tmp_file = "test.lock_file"
utils.make_empty_file(tmp_file)
with self.assertRaises(Exception):
lock_file.LockFile(tmp_file)
os.unlink(tmp_file)
lock = lock_file.LockFile(tmp_file)
self.assertTrue(os.path.exists(tmp_file))
os.unlink(tmp_file)
with self.assertRaises(Exception):
lock.stop()
lock = lock_file.LockFile(tmp_file)
self.assertTrue(os.path.exists(tmp_file))
lock.stop()
self.assertFalse(os.path.exists(tmp_file))
def run(options):
lock = lock_file.LockFile(
os.path.join(options.pipeline_root, "generic_pipeline.lock"))
database = db.Db(options.db_config_file)
database.make_generic_pipeline_jobs_tsv(
options.outfile,
options.pipeline_root,
options.pipeline_name,
pipeline_version=options.pipeline_version,
dataset_name=options.dataset_name,
)
database.commit_and_close()
lock.stop()
def run(options):
lock = lock_file.LockFile(os.path.join(options.pipeline_root, 'qc.lock'))
database = db.Db(options.db_config_file)
database.make_qc_jobs_tsv(
options.outfile,
options.pipeline_root,
options.reference_id,
options.reference_root,
pipeline_version=options.pipeline_version,
dataset_name=options.dataset_name,
)
database.commit_and_close()
lock.stop()
def run(options):
lock = lock_file.LockFile(
os.path.join(options.pipeline_root, "remove_contam.lock"))
database = db.Db(options.db_config_file)
database.make_remove_contam_jobs_tsv(
options.outfile,
options.pipeline_root,
options.reference_id,
options.reference_root,
dataset_name=options.dataset_name,
)
database.commit_and_close()
lock.stop()
def run(options):
lock = lock_file.LockFile(
os.path.join(options.pipeline_root, 'remove_contam.lock'))
database = db.Db(options.db_config_file)
database.make_remove_contam_jobs_tsv(
options.outfile,
options.pipeline_root,
0,
'/fake/path/to/refs/',
dataset_name=options.dataset_name,
faking_it=True,
)
database.commit_and_close()
lock.stop()
def run(options):
lock = lock_file.LockFile(os.path.join(options.pipeline_root, 'mykrobe_predict.lock'))
database = db.Db(options.db_config_file)
database.make_variant_call_or_mykrobe_jobs_tsv(
'mykrobe_predict',
options.outfile,
options.pipeline_root,
options.reference_id,
options.reference_root,
pipeline_version=options.pipeline_version,
dataset_name=options.dataset_name,
)
database.commit_and_close()
lock.stop()
def run(options):
using_db = None not in (
options.db_config_file,
options.pipeline_references_root,
options.name,
)
if using_db and options.outdir:
print(
"Error! If adding to database, must use --db_config_file,--pipeline_references_root,--name.",
file=sys.stderr,
)
print("Otherwise, use --outdir.", file=sys.stderr)
sys.exit(1)
if using_db:
lock = lock_file.LockFile(
os.path.join(options.pipeline_references_root,
"add_reference.lock"))
database = db.Db(options.db_config_file)
ref_id = database.add_reference(options.name)
database.commit_and_close()
lock.stop()
else:
ref_id = None
ref_dir = reference_dir.ReferenceDir(
pipeline_references_root_dir=options.pipeline_references_root,
reference_id=ref_id,
directory=options.outdir,
)
genome_is_big = options.contam_tsv is not None
using_cortex = options.contam_tsv is None
ref_dir.make_index_files(
options.fasta_file,
genome_is_big,
using_cortex,
cortex_mem_height=options.cortex_mem_height,
)
if options.contam_tsv is not None:
ref_dir.add_remove_contam_metadata_tsv(options.contam_tsv)