def get_loris_session_id(self):
"""
Greps the LORIS session.ID corresponding to the BIDS visit. Note,
if no BIDS visit are set, will use the default visit label value set
in the config module
:return: the session's ID in LORIS
:rtype: int
"""
# check if there are any visit label in BIDS structure, if not,
# will use the default visit label set in the config module
visit_label = self.bids_ses_id if self.bids_ses_id else self.default_vl
session = Session(verbose=self.verbose,
cand_id=self.cand_id,
center_id=self.center_id,
visit_label=visit_label)
loris_vl_info = session.get_session_info_from_loris(self.db)
if not loris_vl_info:
message = "ERROR: visit label " + visit_label + "does not exist in " + \
"the session table for candidate " + self.cand_id + \
"\nPlease make sure the visit label is created in the " + \
"database or run bids_import.py with the -s option -s if " + \
"you wish that the insertion pipeline creates the visit " + \
"label in the session table."
print(message)
exit(lib.exitcode.SELECT_FAILURE)
return loris_vl_info['ID']
def grep_or_create_visit_label_db_info(bids_id, cand_id, visit_label, db,
createvisit, verbose, loris_bids_dir,
center_id):
"""
Greps (or creates if candidate does not exist and createcand is true) the
BIDS candidate in the LORIS candidate's table and return a list of
candidates with their related fields from the database.
:parma bids_id : BIDS ID of the candidate
:type bids_id : str
:param cand_id : CandID to use to create the session
:type cand_id : int
:param visit_label : Visit label to use to create the session
:type visit_label : str
:param db : database handler object
:type db : object
:param createvisit : if true, creates the candidate in LORIS
:type createvisit : bool
:param verbose : if true, prints out information while executing
:type verbose : bool
:param loris_bids_dir: LORIS BIDS import root directory to copy data
:type loris_bids_dir: str
:return: session information grepped from LORIS for cand_id and visit_label
:rtype: dict
"""
session = Session(verbose,
cand_id=cand_id,
visit_label=visit_label,
center_id=center_id)
loris_vl_info = session.get_session_info_from_loris(db)
if not loris_vl_info and createvisit:
loris_vl_info = session.create_session(db)
# create the visit directory for in the candidate folder of the LORIS
# BIDS import directory
lib.utilities.create_dir(
loris_bids_dir + "sub-" + bids_id + "/ses-" + visit_label, verbose)
return loris_vl_info
