def get_available_finished_run_ids(conf):
"""Get the list of the available runs.
Arguments:
conf: configuration dictionary
"""
result = set()
for hiseq_data_path in hiseq_run.get_hiseq_data_paths(conf):
files = os.listdir(hiseq_data_path)
for f in files:
if os.path.isdir(hiseq_data_path + '/' + f) and \
hiseq_run.check_run_id(f, conf) and \
hiseq_run.check_end_run(f, conf):
result.add(f)
return result
def get_available_new_run_ids(conf):
"""Get the list of the available runs.
Arguments:
conf: configuration dictionary
"""
result = set()
hiseq_run_ids_do_not_process = hiseq_run.load_deny_run_ids(conf)
for hiseq_data_path in hiseq_run.get_hiseq_data_paths(conf):
files = os.listdir(hiseq_data_path)
for f in files:
# Do not process denied runs
if f in hiseq_run_ids_do_not_process:
continue
if not (os.path.isdir(hiseq_data_path + '/' + f) and hiseq_run.check_run_id(f, conf)):
# No valid entry
continue
# NextSeq sequencer create this file after clusterisation step
if not os.path.exists(hiseq_data_path + '/' + f + '/RunInfo.xml'):
continue
if common.get_rta_major_version(f, conf) == 1 and \
not os.path.exists(hiseq_data_path + '/' + common.FIRST_BASE_REPORT_FILE):
continue
if not hiseq_run.check_end_run(f, conf):
# TODO
# os.path.exists(hiseq_data_path + '/' + f + '/First_Base_Report.htm'):
result.add(f)
return result
def is_sync_step_enable(conf):
"""Check if all parameters useful for synchronization step are defined
Arguments:
conf: configuration dictionary
"""
# Synchronization step: True
if common.is_conf_value_equals_true(SYNC_STEP_KEY, conf):
# Check bcl path must be defined
if common.is_conf_key_exists(BCL_DATA_PATH_KEY, conf):
bcl_path = conf[BCL_DATA_PATH_KEY]
# Check bcl not same hiseq output path
for path in hiseq_run.get_hiseq_data_paths(conf):
if path == bcl_path:
error('Configuration error.',
'Basecalling path and hiseq output data path must be different: ' + bcl_path, conf)
return False
return True
return False
