def _ls(irods_path):
cmd = CommandWrapper(["ils", irods_path])
cmd()
def remove_header_line(lines):
return lines[1:]
def remove_redundant_whitespace(lines):
return [l.strip() for l in lines]
def deal_with_collections(lines):
fixed_lines = []
for l in lines:
if l.startswith("C"):
_, path = l.split()
l = os.path.basename(path)
fixed_lines.append(l)
return fixed_lines
text = cmd.stdout.strip()
lines = text.split("\n")
return deal_with_collections(
remove_redundant_whitespace(
remove_header_line(lines)
)
)
def _get_text(irods_path):
"""Get raw text from iRODS."""
# Command to get contents of file to stdout.
cmd = CommandWrapper([
"iget",
irods_path,
"-"
])
return cmd()
def _get_checksum(irods_path):
# Get the hash.
cmd = CommandWrapper(["ichksum", "-K", irods_path])
cmd()
line = cmd.stdout.strip()
info = line.split()
compound_chksum = info[1]
alg, checksum = compound_chksum.split(":")
return checksum
def _put_text(irods_path, text):
"""Put raw text into iRODS."""
with tempfile.NamedTemporaryFile() as fh:
fpath = fh.name
fh.write(text)
fh.flush()
cmd = CommandWrapper([
"iput",
"-f",
fpath,
irods_path
])
cmd()
assert not os.path.isfile(fpath)
def _get_size_and_timestamp_with_cache(self, irods_path):
if self._use_cache:
if irods_path in self._size_and_timestamp_cache:
return self._size_and_timestamp_cache[irods_path]
cmd = CommandWrapper(["ils", "-l", irods_path])
cmd()
text = cmd.stdout.strip()
first_line = text.split("\n")[0].strip()
info = first_line.split()
size_in_bytes_str = info[3]
size_in_bytes = int(size_in_bytes_str)
time_str = info[4]
dt = datetime.datetime.strptime(time_str, "%Y-%m-%d.%H:%M")
utc_timestamp = int(time.mktime(dt.timetuple()))
return size_in_bytes, utc_timestamp
def _build_size_and_timestamp_cache(self):
cmd = CommandWrapper(["ils", "-l", self._data_abspath])
cmd()
text = cmd.stdout.strip()
for line in text.split("\n")[1:]:
line = line.strip()
info = line.split()
size_in_bytes_str = info[3]
size_in_bytes = int(size_in_bytes_str)
time_str = info[4]
dt = datetime.datetime.strptime(time_str, "%Y-%m-%d.%H:%M")
utc_timestamp = int(time.mktime(dt.timetuple()))
fname = info[6]
fpath = os.path.join(self._data_abspath, fname)
self._size_and_timestamp_cache[fpath] = (
size_in_bytes,
utc_timestamp
)
def _get_metadata_with_cache(self, irods_path, key):
if self._use_cache:
if irods_path in self._metadata_cache:
if key in self._metadata_cache[irods_path]:
return self._metadata_cache[irods_path][key]
cmd = CommandWrapper(["imeta", "ls", "-d", irods_path, key])
cmd()
text = cmd.stdout
value_line = text.split('\n')[2]
value = value_line.split(":")[1]
value = value.strip()
if self._use_cache:
self._metadata_cache.setdefault(
irods_path, {}).update({key: value})
return value
def _rm(irods_path):
cmd = CommandWrapper(["irm", "-rf", irods_path])
cmd()
def _cp(fpath, irods_path):
cmd = CommandWrapper(["iput", "-f", fpath, irods_path])
cmd()
def _mkdir(irods_path):
cmd = CommandWrapper(["imkdir", irods_path])
cmd()
def _path_exists(irods_path):
cmd = CommandWrapper(["ils", irods_path])
cmd(exit_on_failure=False)
return cmd.success()
def _get_file(irods_path, local_abspath):
cmd = CommandWrapper(["iget", irods_path, local_abspath])
cmd()
def _put_metadata(irods_path, key, value):
cmd = CommandWrapper(["imeta", "set", "-d", irods_path, key, value])
cmd()