def wrapper(mic_file):
"""
Generates the MIC Wrapper:a directory structure and commands required to run your model component using the
information gathered from previous steps
- You must pass the MIC_FILE (mic.yaml) as an argument using the (-f) option or run the
command from the same directory as mic.yaml
mic pkg wrapper -f <mic_file>
Example:
mic pkg wrapper -f mic/mic.yaml
"""
# Searches for mic file if user does not provide one
mic_file = check_mic_path(mic_file)
log_command(logging, "wrapper", mic_file=mic_file)
try:
info_start_wrapper()
mic_config_file = Path(mic_file)
user_execution_directory = mic_config_file.parent.parent
repro_zip_trace_dir = find_dir(REPRO_ZIP_TRACE_DIR,
user_execution_directory)
repro_zip_trace_dir = Path(repro_zip_trace_dir)
repro_zip_config_file = repro_zip_trace_dir / REPRO_ZIP_CONFIG_FILE
mic_directory_path = mic_config_file.parent
mic_inputs = get_inputs(mic_config_file)
mic_parameters = get_parameters(mic_config_file)
mic_outputs = get_outputs_mic(mic_config_file)
mic_configs = get_configs(mic_config_file)
mic_code = get_code(mic_config_file)
spec = get_spec(mic_config_file)
reprozip_spec = get_spec(repro_zip_config_file)
logging.info("Generating wrapper code")
code = f"""{generate_pre_runner(spec, user_execution_directory)}
{generate_runner(reprozip_spec, user_execution_directory, mic_inputs, mic_outputs, mic_parameters)}"""
render_bash_color(mic_directory_path)
render_run_sh(mic_directory_path, mic_inputs, mic_parameters,
mic_outputs, code)
render_io_sh(mic_directory_path, mic_inputs, mic_parameters,
mic_configs)
render_output(mic_directory_path, mic_outputs, False)
copy_code_to_src(mic_code, user_execution_directory,
mic_directory_path / SRC_DIR)
copy_config_to_src(mic_configs, user_execution_directory,
mic_directory_path / SRC_DIR)
info_end_wrapper(mic_directory_path / SRC_DIR / RUN_FILE)
logging.info("wrapper done")
except Exception as e:
logging.exception(f"Wrapper failed: {e}")
click.secho("Failed", fg="red")
click.secho(e)
def check_config(mic_config_arg):
files = get_configs(Path(mic_config_arg))
assert files == {
'basins_bsn': {
'format': 'bsn',
'path': 'TxtInOut/basins.bsn'
},
'file_cio': {
'format': 'cio',
'path': 'TxtInOut/file.cio'
}
}
def inputs(mic_file, custom_inputs):
"""
Describe the inputs of your model using the information obtained by the `trace` command. To identify which inputs have
been automatically detected, execute `mic pkg inputs -f mic/mic.yaml` and then inspect the mic.yaml file
- You must pass the MIC_FILE (mic.yaml) as an argument using the (-f) option or run the
command from the same directory as mic.yaml
- Identify undetected files in or directories in mic.yaml and add them as arguments to the `inputs` command
mic pkg inputs -f <mic_file> [undetected files]...
Usage example:
mic pkg inputs -f mic/mic.yaml input.txt inputs_directory
"""
# Searches for mic file if user does not provide one
mic_file = check_mic_path(mic_file)
log_command(logging,
"inputs",
mic_file=mic_file,
custom_inputs=custom_inputs)
try:
info_start_inputs()
mic_config_file = Path(mic_file)
mic_directory_path = mic_config_file.parent
user_execution_directory = mic_config_file.parent.parent
repro_zip_trace_dir = find_dir(REPRO_ZIP_TRACE_DIR,
user_execution_directory)
repro_zip_trace_dir = Path(repro_zip_trace_dir)
repro_zip_config_file = repro_zip_trace_dir / REPRO_ZIP_CONFIG_FILE
spec = get_spec(repro_zip_config_file)
custom_inputs = [
str(user_execution_directory /
Path(i).relative_to(user_execution_directory))
for i in list(custom_inputs)
]
inputs_reprozip = get_inputs_outputs_reprozip(
spec, user_execution_directory)
logging.debug("Inputs found from reprozip: {}".format(inputs_reprozip))
# obtain config: if a file is a config cannot be a input
config_files = get_configs(mic_config_file)
config_files_list = [
str(user_execution_directory / item[PATH_KEY])
for key, item in config_files.items()
] if config_files else []
code_files = find_code_files(spec, inputs_reprozip, config_files_list,
user_execution_directory)
logging.debug("code files found from reprozip: {}".format(code_files))
new_inputs = []
inputs_reprozip += list(custom_inputs)
data_dir = mic_directory_path.absolute() / DATA_DIR
if data_dir.exists():
shutil.rmtree(data_dir)
data_dir.mkdir()
_outputs = get_outputs_reprozip(spec, user_execution_directory)
for _input in inputs_reprozip:
item = user_execution_directory / _input
name = Path(_input).name
if str(item) in config_files_list or str(
item) in code_files or str(item) in _outputs:
logging.info(f"Ignoring the config as an input: {item}")
else:
# Deleting the outputs of the inputs.
if item.is_dir():
if sorted([str(i)
for i in item.iterdir()]) == sorted(_outputs):
logging.info(f"Skipping: {item}")
else:
logging.info(
f"""Compressing the input directory ({name})""")
zip_file = compress_directory(
item, user_execution_directory)
dst_dir = data_dir
dst_file = dst_dir / Path(zip_file).name
if dst_file.exists():
os.remove(dst_file)
shutil.move(str(zip_file), str(dst_dir))
new_inputs.append(zip_file)
click.secho(f"""Input {name} added """, fg="blue")
logging.info("Input added: {}".format(name))
else:
new_inputs.append(item)
dst_file = mic_directory_path / DATA_DIR / str(item.name)
shutil.copy(item, dst_file)
click.secho(f"""Input {name} added """, fg="blue")
logging.info("Input added: {}".format(name))
info_end_inputs(new_inputs)
write_spec(mic_config_file, INPUTS_KEY,
relative(new_inputs, user_execution_directory))
write_spec(mic_config_file, CODE_KEY,
relative(code_files, user_execution_directory))
logging.info("inputs done")
except Exception as e:
logging.exception(f"Inputs failed: {e}")
click.secho("Failed", fg="red")
click.secho(e)
def test_get_configs():
assert get_configs(mic_1) == {'config_json': {'format': 'json', 'path': 'config.json'}}
assert get_configs(mic_empty) == {}
def check_config(mic_config_arg):
files = get_configs(Path(mic_config_arg))
assert files == {'config_json': {'path': 'config.json', 'format': 'json'}}