date, fieldstr = mtr.info_from_tarfile(localizer)
except:
logging.error('Error pulling info from {}'.format(localizer))
logging.error('skipping {}'.format(sub))
continue
arda_dirname = mtr.make_dirname(date, visitstr, fieldstr + 'T')
print arda_dirname
ardadir = mtr.os.path.join(arda, subid, arda_dirname)
exists, _ = mtr.glob_file(ardadir)
if exists:
logging.warn('{} exists, skipping'.format(ardadir))
continue
os.makedirs(ardadir)
for scan in scans:
newfile = mtr.fname_presuffix(scan, prefix = subid,
newpath = ardadir)
mtr.copy_file_withdate(scan, newfile)
logging.info('copy: {}'.format(newfile))
scannotes = glob(os.path.join(sub, '*scan*notes*.txt' ))
try:
mtr.copy_file_withdate(scannotes[0], ardadir)
logging.info('{} copy scannotes'.format(ardadir))
except:
logging.info('{} missing scan notes'.format(sub))
## get files
## make outdir
## rename and move files
# has multiple visits in raw, fix
logging.error('%s multiple visits, %s skipping'%(raw, dates))
continue
#dates and fields are all good
else:
dirname = mtr.make_dirname(date, visit_number, field)
ardadir = mtr.os.path.join(arda, subid, dirname)
exists, _ = mtr.glob_file(ardadir)
if not exists:
os.makedirs(ardadir)
# tar zip individual scans to destdir
for renamed in newnames:
cmd = mtr.renamed_archive_copy(renamed, ardadir)
os.system(cmd)
logging.info('copied raw and converted to %s'%(ardadir))
mtr.copy_file_withdate(raw, ardadir)
mtr.clean_tmpdir(tmpdir)
#deal with scan notes
# scan notes
notes_exist, sync_notes = mtr.get_scannotes_fromsync(raw, visit_number)
if notes_exist:
_, notes_name = os.path.split(sync_notes)
arda_notes = os.path.join(ardadir, notes_name)
arda_notes_exist, _ = mtr.glob_file(arda_notes)
if arda_notes_exist:
same = mtr.compare_filedates(sync_notes, arda_notes)
if not same:
mtr.copy_file_withdate(sync_notes,ardadir)
logging.info('updated %s'%(arda_notes))