def state_str(self, _id, state):
return '%s [%s, %d files, %s]' % (
_id,
state['mod_time'].strftime(reaper.DATE_FORMAT),
state['file_cnt'],
reaper.hrsize(state['size']),
)
def reap(self, _id, item, tempdir):
try:
pfile = scipfile.PFile(item['path'], timezone=self.timezone)
except (IOError, scipfile.PFileError):
success = None
log.warning('skipping %s (disappeared or unparsable)' % _id)
else:
if pfile.patient_id.strip('/').lower() in self.blacklist:
success = None
log.info('discarding %s' % _id)
elif not re.match(self.whitelist, pfile.patient_id):
success = None
log.info('ignoring %s (non-matching patient ID)' % _id)
else:
name_prefix = pfile.series_uid + '_' + str(pfile.acq_no)
reap_path = tempdir + '/' + name_prefix + '_' + scipfile.PFile.filetype
os.mkdir(reap_path)
auxfiles = [(ap, _id + '_' + ap.rsplit('_', 1)[-1]) for ap in glob.glob(item['path'] + '_' + pfile.series_uid + '_*')]
log.debug('staging %s%s' % (_id, ', ' + ', '.join([af[1] for af in auxfiles]) if auxfiles else ''))
os.symlink(item['path'], os.path.join(reap_path, _id))
for af in auxfiles:
os.symlink(af[0], os.path.join(reap_path, af[1]))
pfile_size = reaper.hrsize(item['state']['size'])
metadata = {
'filetype': scipfile.PFile.filetype,
'timezone': self.timezone,
'header': {
'group': pfile.nims_group_id,
'project': pfile.nims_project,
'session': pfile.nims_session_id,
'session_no': pfile.series_no,
'session_desc': pfile.series_desc,
'acquisition': pfile.nims_acquisition_id,
'acquisition_no': pfile.acq_no,
'timestamp': pfile.nims_timestamp,
},
}
reap_start = datetime.datetime.utcnow()
auxfile_str = ' + %d aux files' % len(auxfiles) if auxfiles else ''
log.info('reaping.zip %s [%s%s]' % (_id, pfile_size, auxfile_str))
try:
reaper.create_archive(reap_path+'.zip', reap_path, os.path.basename(reap_path), metadata)
shutil.rmtree(reap_path)
except (IOError):
success = False
log.warning('reap error %s%s' % (_id, ' or aux files' if auxfiles else ''))
else:
success = True
reap_time = (datetime.datetime.utcnow() - reap_start).total_seconds()
log.info('reaped.zip %s [%s%s] in %.1fs' % (_id, pfile_size, auxfile_str, reap_time))
self.reap_peripheral_data(tempdir, pfile, name_prefix, _id)
return success
def state_str(self, _id, state):
return '%s, [%s, %s]' % (_id, state['mod_time'].strftime(reaper.DATE_FORMAT), reaper.hrsize(state['size']))
