# * provides `output` publishing proxy to the inner function and
# * produce a result with attributes for
# * file: mapping of output flags to output filenames
-# * erroroutput: text results in case of error
+# * stdout: process STDOUT
+# * stderr: porcess STDERR
# * returncode: integer return code of wrapped command
#
# Note that the existence of the 'file' output map is expressed here, but
#
# TODO: Operation returns the output object when called with the shorter signature.
#
-@gmx.function_wrapper(output={'erroroutput': str, 'returncode': int})
+@gmx.function_wrapper(output={'stdout': str,
+ 'stderr': str,
+ 'returncode': int})
def cli(command: NDArray, shell: bool, output: OutputCollectionDescription, stdin: str = ''):
"""Execute a command line program in a subprocess.
>>> my_filename = "somefilename"
>>> result = cli(('exe', '--origin', 1.0, 2.0, 3.0, '-f', my_filename), shell=False)
>>> assert hasattr(result, 'file')
- >>> assert hasattr(result, 'erroroutput')
+ >>> assert hasattr(result, 'stdout')
+ >>> assert hasattr(result, 'stderr')
>>> assert hasattr(result, 'returncode')
Returns:
- A data structure with attributes for each of the results `file`, `erroroutput`, and `returncode`
+ A data structure with attributes for each of the results `file`, `stdout`, `stderr`, and `returncode`
Result object attributes:
* `file`: the mapping of CLI flags to filename strings resulting from the `output` kwarg
- * `erroroutput`: A string of error output (if any) if the process failed.
+ * `stdout`: A string mapping from process STDOUT.
+ * `stderr`: A string mapping from process STDERR; it will be the
+ error output (if any) if the process failed.
* `returncode`: return code of the subprocess.
"""
- # Note: we could make provisions for stdio filehandles in a future version. E.g.
- # * STDOUT is available if a consuming operation is bound to `output.stdout`.
- # * STDERR is available if a consuming operation is bound to `output.stderr`.
- # * Otherwise, STDOUT and/or STDERR is(are) closed when command is called.
-
# In the operation implementation, we expect the `shell` parameter to be intercepted by the
# wrapper and set to False.
if shell:
# TODO: (FR9) Can OS input/output filehandles be a responsibility of
# the code providing 'resources'?
- erroroutput = ''
+ stdout = ''
+ stderr = ''
logger.debug('executing subprocess')
try:
completed_process = subprocess.run(command,
input=stdin,
check=True,
stdout=subprocess.PIPE,
- stderr=subprocess.STDOUT,
+ stderr=subprocess.PIPE,
encoding='utf-8',
universal_newlines=True
)
returncode = completed_process.returncode
# TODO: Resource management code should manage a safe data object for `output`.
- for line in completed_process.stdout.split('\n'):
- logger.debug(line)
+ logger.debug('STDOUT:')
+ if completed_process.stderr is not None:
+ for line in completed_process.stdout.split('\n'):
+ logger.debug(line)
+ else:
+ logger.debug('STDOUT is empty')
+ logger.debug('STDERR:')
+ if completed_process.stderr is not None:
+ for line in completed_process.stderr.split('\n'):
+ logger.debug(line)
+ else:
+ logger.debug('STDERR is empty')
+
+ stdout = completed_process.stdout
+ stderr = completed_process.stderr
+
except subprocess.CalledProcessError as e:
- logger.info("commandline operation had non-zero return status when calling {}".format(e.cmd))
- erroroutput = e.output
+ logger.info("commandline operation had non-zero return status"
+ "when calling {}".format(e.cmd))
+ stdout = e.stdout
+ stderr = e.stderr
returncode = e.returncode
+
# Publish outputs.
- output.erroroutput = erroroutput
+ output.stdout = stdout
+ output.stderr = stderr
output.returncode = returncode
The output node of the resulting operation handle contains
* ``file``: the mapping of CLI flags to filename strings resulting from the ``output_files`` kwarg
- * ``erroroutput``: A string of error output (if any) if the process failed.
+ * ``stdout``: A string mapping from process STDOUT.
+ * ``stderr``: A string mapping from process STDERR; it will be the
+ error output (if any) if the process failed.
* ``returncode``: return code of the subprocess.
"""
#
# TODO: (FR4+) Characterize the `file` dictionary key type:
# explicitly sequences rather than maybe-string/maybe-sequence-of-strings
- @gmx.function_wrapper(output={'erroroutput': str, 'returncode': int, 'file': dict})
- def merged_ops(erroroutput: str = None, returncode: int = None, file: dict = None,
+ @gmx.function_wrapper(output={'stdout': str,
+ 'stderr': str,
+ 'returncode': int,
+ 'file': dict})
+ def merged_ops(stdout: str = None,
+ stderr: str = None,
+ returncode: int = None,
+ file: dict = None,
output: OutputCollectionDescription = None):
- assert erroroutput is not None
+ assert stdout is not None
+ assert stderr is not None
assert returncode is not None
assert file is not None
assert output is not None
output.returncode = returncode
- output.erroroutput = erroroutput
+ output.stdout = stdout
+ output.stderr = stderr
if returncode == 0:
output.file = file
else:
# TODO: ``label`` kwarg
# TODO: input fingerprinting
cli_result = cli(**cli_args)
- merged_result = merged_ops(erroroutput=cli_result.output.erroroutput,
+ merged_result = merged_ops(stdout=cli_result.output.stdout,
+ stderr=cli_result.output.stderr,
returncode=cli_result.output.returncode,
file=output_files,
**kwargs)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff