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is_copy = _hash_file(file_path) in previous_files_hash
nifti_import.nifti2db(file_path, file_type, is_copy, step_id, db_conn, 'session_id_by_patient' in config,
'visit_id_in_patient_id' in config)
elif file_type:
is_copy = _hash_file(file_path) in previous_files_hash
others_import.others2db(
file_path, file_type, is_copy, step_id, db_conn)
if sys.version_info.major == 3 and sys.version_info.minor < 5:
matches = []
for root, dirnames, filenames in os.walk(folder):
for filename in fnmatch.filter(filenames, '*'):
matches.append(os.path.join(root, filename))
for file_path in matches:
process_file(file_path)
else:
for file_path in glob.iglob(os.path.join(folder, ""**/*""), recursive=True):
process_file(file_path)
logging.info(""Closing database connection..."")
db_conn.close()
return step_id"
4669,"def create_provenance(dataset, software_versions=None, db_url=None):
""""""Create (or get if already exists) a provenance entity, store it in the database and get back a provenance ID.
Arguments:
:param dataset: Name of the data set.
:param software_versions: (optional) Version of the software components used to get the data. It is a dictionary
that accepts the following fields:
- matlab_version
- spm_version
- spm_revision
- fn_called
- fn_version
- others
:param db_url: (optional) Database URL. If not defined, it looks for an Airflow configuration file.
:return: Provenance ID.
""""""
logging.info(""Connecting to database..."")
db_conn = connection.Connection(db_url)
try:
matlab_version = software_versions['matlab_version']
except (KeyError, TypeError):
matlab_version = None
try:
spm_version = software_versions['spm_version']
except (KeyError, TypeError):
spm_version = None
try:
spm_revision = software_versions['spm_revision']
except (KeyError, TypeError):
spm_revision = None
try:
fn_called = software_versions['fn_called']
except (KeyError, TypeError):
fn_called = None
try:
fn_version = software_versions['fn_version']
except (KeyError, TypeError):
fn_version = None
try:
others = software_versions['others']
except (KeyError, TypeError):
others = None
provenance = db_conn.db_session.query(db_conn.Provenance).filter_by(
dataset=dataset, matlab_version=matlab_version, spm_version=spm_version, spm_revision=spm_revision,
fn_called=fn_called, fn_version=fn_version, others=others
).first()
if not provenance:
provenance = db_conn.Provenance(
dataset=dataset, matlab_version=matlab_version, spm_version=spm_version, spm_revision=spm_revision,
fn_called=fn_called, fn_version=fn_version, others=others
)
db_conn.db_session.merge(provenance)
db_conn.db_session.commit()
provenance = db_conn.db_session.query(db_conn.Provenance).filter_by(
dataset=dataset, matlab_version=matlab_version, spm_version=spm_version, spm_revision=spm_revision,
fn_called=fn_called, fn_version=fn_version, others=others
).first()
provenance_id = provenance.id
logging.info(""Closing database connection..."")
db_conn.close()
return provenance_id"
4670,"def check_sockets(self):
'''
Check for new messages on sockets and respond accordingly.
.. versionchanged:: 0.11.3
Update routes table by setting ``df_routes`` property of
:attr:`parent.canvas_slave`.