def merge_cat(args):
if not os.path.exists(args.target):
args.target = os.path.join(args.archive, cat._subdir, os.path.basename(args.target))
if not os.path.exists(args.target):
tgt = cat.new()
else:
tgt = json.load(open(args.target, 'rU'))
if not tgt['namespace'] == cat._ns:
raise ValueError("'%s' is not a catalog" % args.target)
log.info("appending to '%s', resources=%d", args.target, len(tgt['resources']))
for source in args.source:
src = json.load(open(source, 'rU'))
if not src['namespace'] == cat._ns:
log.error("'%s' is not a catalog; skipping" % source)
continue
log.info("reading from '%s', resources=%d", source, len(src['resources']))
cat.merge(src, tgt, args.no_confirm)
json.dump(tgt, open(args.target, 'wt'), indent=2, separators=(',', ': '))
log.info("wrote merged catalog '%s', resources=%d", args.target, len(tgt['resources']))
def store_files(args):
log.info("version: %s", nbank.__version__)
log.info("run time: %s", datetime.datetime.now())
cfg = nbank.get_config(args.archive)
if cfg is None:
raise ValueError("%s not a neurobank archive. Use '-A' or set NBANK_PATH in environment." %
args.archive)
if args.read_stdin:
args.file.extend(l.strip() for l in sys.stdin)
if len(args.file) == 0:
raise ValueError("no files specified")
if os.path.exists(args.catalog):
raise ValueError("catalog '%s' already exists. Write to a new file, then merge" % args.catalog)
files = []
for fname in args.file:
if not os.path.isfile(fname) and not os.path.isdir(fname):
log.warn("warning: '%s' is not a file or directory - skipping", fname)
continue
path, base, ext = util.fileparts(fname)
try:
id = args.func_id(fname)
except IOError as e:
if os.path.exists(fname):
log.warn(
"warning: '%s' is a directory, can't be used a a source file - skipping",
fname
)
else:
log.warn("warning: '%s' does not exist - skipping", fname)
continue
if cfg['policy'][args.target]['keep_filename']:
id += '_' + base
if args.suffix:
id += '_' + args.suffix
if cfg['policy'][args.target]['keep_extension']:
id += ext
try:
mode = int(cfg['policy'][args.target]['mode'], base=8)
except (KeyError, ValueError) as e:
log.warn("E: %s", e)
mode = 0o440
tgt = nbank.store_file(fname, args.archive, id, mode)
if args.target == 'data' and tgt is None:
# id collisions are errors for data files. This should never happen
# with uuids
raise ValueError("id assigned to '%s' already exists in archive: %s" % (fname, id))
files.append({'id': id, 'name': base + ext})
if tgt is not None:
# file was moved to database
log.info("%s -> %s", fname, id)
if args.link:
try:
os.symlink(os.path.abspath(tgt), os.path.join(path, id))
except OSError as e:
log.warn("error creating link: %s", e)
else:
log.info("'%s' already in archive as '%s'", fname, id)
json.dump(cat.new(files), open(args.catalog, 'wt'), indent=2, separators=(',', ': '))
log.info("wrote resource catalog to '%s'", args.catalog)
