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:param message: Response message
:param content_type: Pika BasicProperties content_type value
:param headers: Message header properties
:param mandatory: The mandatory flag
:param immediate: The immediate flag
:returns: Boolean corresponding to the success of publishing
:rtype: bool
""""""
logger.debug(""Publishing message"")
try:
self._connect()
return self._do_publish(mandatory=mandatory,
immediate=immediate,
content_type=content_type,
headers=headers,
message=message)
except pika.exceptions.AMQPConnectionError:
logger.error(""AMQPConnectionError occurred. Message not published."")
raise PublishMessageError
except NackError:
# raised when a message published in publisher-acknowledgments mode
# is returned via `Basic.Return` followed by `Basic.Ack`.
logger.error(""NackError occurred. Message not published."")
raise PublishMessageError
except UnroutableError:
# raised when a message published in publisher-acknowledgments
# mode is returned via `Basic.Return` followed by `Basic.Ack`.
logger.error(""UnroutableError occurred. Message not published."")
raise PublishMessageError
except Exception:
logger.exception(""Unknown exception occurred. Message not published."")
raise PublishMessageError"
4668,"def visit(folder, provenance_id, step_name, previous_step_id=None, config=None, db_url=None, is_organised=True):
""""""Record all files from a folder into the database.
Note:
If a file has been copied from a previous processing step without any transformation, it will be detected and
marked in the DB. The type of file will be detected and stored in the DB (NIFTI, DICOM, ...). If a files
(e.g. a DICOM file) contains some meta-data, those will be stored in the DB.
Arguments:
:param folder: folder path.
:param provenance_id: provenance label.
:param step_name: Name of the processing step that produced the folder to visit.
:param previous_step_id: (optional) previous processing step ID. If not defined, we assume this is the first
processing step.
:param config: List of flags:
- boost: (optional) When enabled, we consider that all the files from a same folder share the same meta-data.
When enabled, the processing is (about 2 times) faster. This option is enabled by default.
- session_id_by_patient: Rarely, a data set might use study IDs which are unique by patient (not for the whole
study).
E.g.: LREN data. In such a case, you have to enable this flag. This will use PatientID + StudyID as a session
ID.
- visit_id_in_patient_id: Rarely, a data set might mix patient IDs and visit IDs. E.g. : LREN data. In such a
case, you have to enable this flag. This will try to split PatientID into VisitID and PatientID.
- visit_id_from_path: Enable this flag to get the visit ID from the folder hierarchy instead of DICOM meta-data
(e.g. can be useful for PPMI).
- repetition_from_path: Enable this flag to get the repetition ID from the folder hierarchy instead of DICOM
meta-data (e.g. can be useful for PPMI).
:param db_url: (optional) Database URL. If not defined, it looks for an Airflow configuration file.
:param is_organised: (optional) Disable this flag when scanning a folder that has not been organised yet
(should only affect nifti files).
:return: return processing step ID.
""""""
config = config if config else []
logging.info(""Visiting %s"", folder)
logging.info(""-> is_organised=%s"", str(is_organised))
logging.info(""-> config=%s"", str(config))
logging.info(""Connecting to database..."")
db_conn = connection.Connection(db_url)
step_id = _create_step(db_conn, step_name, provenance_id, previous_step_id)
previous_files_hash = _get_files_hash_from_step(db_conn, previous_step_id)
checked = dict()
def process_file(file_path):
logging.debug(""Processing '%s'"" % file_path)
file_type = _find_type(file_path)
if ""DICOM"" == file_type:
is_copy = _hash_file(file_path) in previous_files_hash
leaf_folder = os.path.split(file_path)[0]
if leaf_folder not in checked or 'boost' not in config:
ret = dicom_import.dicom2db(file_path, file_type, is_copy, step_id, db_conn,
'session_id_by_patient' in config, 'visit_id_in_patient_id' in config,
'visit_id_in_patient_id' in config, 'repetition_from_path' in config)
try:
checked[leaf_folder] = ret['repetition_id']
except KeyError:
# TODO: Remove it when dicom2db will be more stable
logging.warning(""Cannot find repetition ID !"")
else:
dicom_import.extract_dicom(
file_path, file_type, is_copy, checked[leaf_folder], step_id)
elif ""NIFTI"" == file_type and is_organised: