def format_command(dset, command, **kwds):
"""Plug in placeholders in `command`.
Parameters
----------
dset : Dataset
command : str or list
`kwds` is passed to the `format` call. `inputs` and `outputs` are converted
to GlobbedPaths if necessary.
Returns
-------
formatted command (str)
"""
command = normalize_command(command)
sfmt = SequenceFormatter()
for k, v in dset.config.items("datalad.run.substitutions"):
sub_key = k.replace("datalad.run.substitutions.", "")
if sub_key not in kwds:
kwds[sub_key] = v
for name in ["inputs", "outputs"]:
io_val = kwds.pop(name, None)
if not isinstance(io_val, GlobbedPaths):
io_val = GlobbedPaths(io_val, pwd=kwds.get("pwd"))
kwds[name] = list(map(quote_cmdlinearg, io_val.expand(dot=False)))
return sfmt.format(command, **kwds)
def format_command(dset, command, **kwds):
"""Plug in placeholders in `command`.
Parameters
----------
dset : Dataset
command : str or list
`kwds` is passed to the `format` call. `inputs` and `outputs` are converted
to GlobbedPaths if necessary.
Returns
-------
formatted command (str)
"""
command = normalize_command(command)
sfmt = SequenceFormatter()
for k, v in dset.config.items("datalad.run.substitutions"):
sub_key = k.replace("datalad.run.substitutions.", "")
if sub_key not in kwds:
kwds[sub_key] = v
for name in ["inputs", "outputs"]:
io_val = kwds.pop(name, None)
if not isinstance(io_val, GlobbedPaths):
io_val = GlobbedPaths(io_val, pwd=kwds.get("pwd"))
kwds[name] = list(map(shlex_quote, io_val.expand(dot=False)))
return sfmt.format(command, **kwds)
def format_command(command, **kwds):
"""Plug in placeholders in `command`.
Parameters
----------
dset : Dataset
command : str or list
`kwds` is passed to the `format` call.
Returns
-------
formatted command (str)
"""
command = normalize_command(command)
sfmt = SequenceFormatter()
return sfmt.format(command, **kwds)
def format_command(command, **kwds):
"""Plug in placeholders in `command`.
Parameters
----------
command : str or list
`kwds` is passed to the `format` call. `inputs` and `outputs` are converted
to GlobbedPaths if necessary.
Returns
-------
formatted command (str)
"""
command = normalize_command(command)
sfmt = SequenceFormatter()
for name in ["inputs", "outputs"]:
io_val = kwds.pop(name, None)
if not isinstance(io_val, GlobbedPaths):
io_val = GlobbedPaths(io_val, pwd=kwds.get("pwd"))
kwds[name] = io_val.expand(dot=False)
return sfmt.format(command, **kwds)
def run_command(cmd, dataset=None, inputs=None, outputs=None, expand=None,
message=None, rerun_info=None, rerun_outputs=None, sidecar=None):
rel_pwd = rerun_info.get('pwd') if rerun_info else None
if rel_pwd and dataset:
# recording is relative to the dataset
pwd = normpath(opj(dataset.path, rel_pwd))
rel_pwd = relpath(pwd, dataset.path)
else:
pwd, rel_pwd = get_command_pwds(dataset)
ds = require_dataset(
dataset, check_installed=True,
purpose='tracking outcomes of a command')
# not needed ATM
#refds_path = ds.path
# delayed imports
from datalad.cmd import Runner
lgr.debug('tracking command output underneath %s', ds)
if not rerun_info and ds.repo.dirty: # Rerun already takes care of this.
yield get_status_dict(
'run',
ds=ds,
status='impossible',
message=('unsaved modifications present, '
'cannot detect changes by command'))
return
cmd = normalize_command(cmd)
inputs = GlobbedPaths(inputs, pwd=pwd,
expand=expand in ["inputs", "both"])
if inputs:
for res in ds.get(inputs.expand(full=True), on_failure="ignore"):
yield res
outputs = GlobbedPaths(outputs, pwd=pwd,
expand=expand in ["outputs", "both"],
warn=not rerun_info)
if outputs:
for res in _unlock_or_remove(ds, outputs.expand(full=True)):
yield res
if rerun_outputs is not None:
# These are files we need to unlock/remove for a rerun that aren't
# included in the explicit outputs. Unlike inputs/outputs, these are
# full paths, so we can pass them directly to unlock.
for res in _unlock_or_remove(ds, rerun_outputs):
yield res
sfmt = SequenceFormatter()
cmd_expanded = sfmt.format(cmd,
pwd=pwd,
dspath=ds.path,
inputs=inputs.expand(dot=False),
outputs=outputs.expand(dot=False))
# we have a clean dataset, let's run things
exc = None
cmd_exitcode = None
runner = Runner(cwd=pwd)
try:
lgr.info("== Command start (output follows) =====")
runner.run(
cmd_expanded,
# immediate output
log_online=True,
# not yet sure what we should do with the command output
# IMHO `run` itself should be very silent and let the command talk
log_stdout=False,
log_stderr=False,
expect_stderr=True,
expect_fail=True,
# TODO stdin
)
except CommandError as e:
# strip our own info from the exception. The original command output
# went to stdout/err -- we just have to exitcode in the same way
exc = e
cmd_exitcode = e.code
if rerun_info and rerun_info.get("exit", 0) != cmd_exitcode:
# we failed in a different way during a rerun. This can easily
# happen if we try to alter a locked file
#
# TODO add the ability to `git reset --hard` the dataset tree on failure
# we know that we started clean, so we could easily go back, needs gh-1424
# to be able to do it recursively
raise exc
lgr.info("== Command exit (modification check follows) =====")
# amend commit message with `run` info:
# - pwd if inside the dataset
# - the command itself
# - exit code of the command
run_info = {
'cmd': cmd,
'exit': cmd_exitcode if cmd_exitcode is not None else 0,
'chain': rerun_info["chain"] if rerun_info else [],
'inputs': inputs.paths,
'outputs': outputs.paths,
}
if rel_pwd is not None:
# only when inside the dataset to not leak information
run_info['pwd'] = rel_pwd
if ds.id:
run_info["dsid"] = ds.id
record = json.dumps(run_info, indent=1, sort_keys=True, ensure_ascii=False)
use_sidecar = sidecar or (
sidecar is None and
ds.config.get('datalad.run.record-sidecar', default=False))
if use_sidecar:
# record ID is hash of record itself
from hashlib import md5
record_id = md5(record.encode('utf-8')).hexdigest()
record_dir = ds.config.get('datalad.run.record-directory', default=op.join('.datalad', 'runinfo'))
record_path = op.join(ds.path, record_dir, record_id)
if not op.lexists(record_path):
# go for compression, even for minimal records not much difference, despite offset cost
# wrap in list -- there is just one record
dump2stream([run_info], record_path, compressed=True)
# compose commit message
msg = u"""\
[DATALAD RUNCMD] {}
=== Do not change lines below ===
{}
^^^ Do not change lines above ^^^
"""
msg = msg.format(
message if message is not None else _format_cmd_shorty(cmd),
'"{}"'.format(record_id) if use_sidecar else record)
msg = assure_bytes(msg)
if not rerun_info and cmd_exitcode:
msg_path = opj(relpath(ds.repo.repo.git_dir), "COMMIT_EDITMSG")
with open(msg_path, "wb") as ofh:
ofh.write(msg)
lgr.info("The command had a non-zero exit code. "
"If this is expected, you can save the changes with "
"'datalad save -r -F%s .'",
msg_path)
raise exc
else:
for r in ds.add('.', recursive=True, message=msg):
yield r