if has_pending_jobs(fw, other_exam['fw_id']):
pending_jobs = True
break
if pending_jobs:
print('Gears have not finished on this scanid. Skipping . . .')
continue
#Download data according to template
#path information for data to be downloaded
pid = exam['scanid'].split('_')[0]
visit = 'visit' + exam['scanid'].split('_')[1]
session = 'session' + exam['scanid'].split('_')[2]
downloaded_scanids.append([pid, visit, session, exam['study']])
scanidpath = pjoin(rawdata_root, pid, visit, session)
#gen list of acquisitions associated with this exam
fw_acqs = fw.get_session_acquisitions(exam['fw_id'])
study_template = studies_template[exam['study']]
for acquisition in study_template:
for fw_acq in fw_acqs:
#download acquisition files from study template
if fw_acq['label'] == acquisition or fw_acq[
'label'] == acquisition + '_func':
for download_pair in study_template[acquisition]:
for file in fw_acq['files']:
#modify file types
if '.7' in file['name'] and (file['name'][0] == 'E' or
file['name'][0] == 'P'):
fw.modify_acquisition_file(fw_acq['_id'],
file['name'],
body={'type': 'pfile'})
#download files
# add behavioral to rawdata
call('cp -r %s %s' %
(pjoin(root, folder),
root.replace(lucas_scanid_path, rawdatapath)),
shell=True)
#add behavioral to flywheel
found_run_on_fw = False
run = False
if '/fmri/' in root:
folder_list = pjoin(root, folder).split('/')
for i in range(len(folder_list)):
if folder_list[i] == 'fmri':
run = folder_list[i + 1]
break
for exam in flywheel_exams:
fw_acqs = fw.get_session_acquisitions(
exam['fw_id'])
for fw_acq in fw_acqs:
if fw_acq['label'] == run:
found_run_on_fw = True
for behav_path in files_under_behavioral:
print('uploading %s' % behav_path)
fw.upload_file_to_acquisition(
fw_acq['_id'], behav_path)
if not found_run_on_fw:
if run:
print(
'run %s not found, creating acquisition behavioral under flywheel exam id %s'
% (run, flywheel_exams[0]['fw_id']))
else:
print(
'creating acquisition behavioral under flywheel exam id %s'