matflow.OutputFileParser#

class matflow.OutputFileParser(output_files, output=None, script=None, environment=None, inputs=None, outputs=None, options=None, script_pass_env_spec=False, abortable=False, save_files=True, clean_up=None, rules=None)#

Bases: OutputFileParser

Represents a script that is run to parse output files from an action and create outputs.

Parameters:

output_files (list[FileSpec]) – The output files that this parser will parse.
output (Parameter) – The singular output parsed by this parser. Not to be confused with outputs (plural).
script (str) – The name of the file containing the output file parser source.
environment (Environment) – The environment to use to run the parser.
inputs (list[str]) – The other inputs to the parser.
outputs (list[str]) – Optional multiple outputs from the upstream actions of the schema that are required to parametrise this parser.
options (dict) – Miscellaneous options.
script_pass_env_spec (bool) – Whether to pass the environment specifier to the script.
abortable (bool) – Whether this script can be aborted.
save_files (list[str]) – The files that should be saved to the persistent store for the workflow.
clean_files (list[str]) – The files that should be immediately removed.
rules (list[ActionRule]) – Rules for whether to enable this parser.
clean_up (List[str] | None) –

Methods

`compose_source`	Generate the file contents of this output file parser source.
`from_json_like`	Make an instance of this class from JSON (or YAML) data.
`get_action_rules`	Get the rules that allow testing if this output file parser must be run or not for a given element.
`to_dict`	Serialize this object as a dictionary.
`to_json_like`	Serialize this object as an object structure that can be trivially converted to JSON.
`write_source`	Write the actual output parser to a file so it can be enacted.

Attributes

`abortable`	Whether this script can be aborted.
`app`
`clean_up`	The files that should be immediately removed.
`environment`	The environment to use to run the parser.
`inputs`	The other inputs to the parser.
`options`	Miscellaneous options.
`output`	The singular output parsed by this parser.
`outputs`	Optional multiple outputs from the upstream actions of the schema that are required to parametrise this parser.
`rules`	Rules for whether to enable this parser.
`save_files`	The files that should be saved to the persistent store for the workflow.
`script`	The name of the file containing the output file parser source.
`script_pass_env_spec`	Whether to pass the environment specifier to the script.
`output_files`	The output files that this parser will parse.

abortable: bool | None = False#: Whether this script can be aborted.

app = App(name='MatFlow', version='0.3.0a131')#

clean_up: List[str] | None = None#: The files that should be immediately removed.

compose_source(snip_path)#

Generate the file contents of this output file parser source.

Return type:: str

environment: Environment = None#: The environment to use to run the parser.

classmethod from_json_like(json_like, shared_data=None)#

Make an instance of this class from JSON (or YAML) data.

Parameters:

json_like – The data to deserialise.
shared_data – Shared context data.

Return type:

The deserialised object.

get_action_rules()#: Get the rules that allow testing if this output file parser must be run or not for a given element.

inputs: List[str] = None#: The other inputs to the parser.

options: Dict = None#: Miscellaneous options.

output: app.Parameter | None = None#: The singular output parsed by this parser. Not to be confused with outputs (plural).

output_files: List[app.FileSpec]#: The output files that this parser will parse.

outputs: List[str] = None#: Optional multiple outputs from the upstream actions of the schema that are required to parametrise this parser. Not to be confused with output (plural).

rules: List[app.ActionRule] | None = None#: Rules for whether to enable this parser.

save_files: List[str] | bool = True#: The files that should be saved to the persistent store for the workflow.

script: str = None#: The name of the file containing the output file parser source.

script_pass_env_spec: bool | None = False#: Whether to pass the environment specifier to the script.

to_dict()#: Serialize this object as a dictionary.

to_json_like(dct=None, shared_data=None, exclude=None, path=None)#: Serialize this object as an object structure that can be trivially converted to JSON. Note that YAML can also be produced from the result of this method; it just requires a different final serialization step.

write_source(action, env_spec)#

Write the actual output parser to a file so it can be enacted.

Parameters:: env_spec (Dict[str, Any]) –