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, generates_files=<factory>, clean_up=<factory>, rules=<factory>, requires_dir=True)

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.

• generates_files (list[FileSpec]) – Files produced by the parser script itself (as opposed to the files it parses, given by output_files). Declaring them here makes them available as output_files.<label> parameters and selectable by the task schema’s save_files policy.

• clean_up (list[FileSpec]) – Files that should be removed from the working directory once they have been saved as workflow artifacts.

• rules (list[ActionRule]) – Rules for whether to enable this parser.

• requires_dir (bool) –

Methods

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.

Attributes

abortable	Whether this script can be aborted.
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.
requires_dir	Whether the parser requires a working directory.
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.
generates_files	Files produced by the parser script itself.
clean_up	Files to remove from the working directory once saved as artifacts.
rules	Rules for whether to enable this parser.

abortable: bool = False

Whether this script can be aborted.

clean_up: list[FileSpec]

Files to remove from the working directory once saved as artifacts.

environment: Environment | None = 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 (dict[str, Any]) – The data to deserialise.

• shared_data (Mapping | None) – Shared context data.

Return type:

The deserialised object.

generates_files: list[FileSpec]

Files produced by the parser script itself.

get_action_rules()

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

Return type:

list[ActionRule]

inputs: list[str] | None = None

The other inputs to the parser.

options: dict[str, Any] | None = None

Miscellaneous options.

output: Parameter | None = None

The singular output parsed by this parser. Not to be confused with outputs (plural).

output_files: list[FileSpec]

The output files that this parser will parse.

outputs: list[str] | None = None

Optional multiple outputs from the upstream actions of the schema that are required to parametrise this parser. Not to be confused with output (singular).

requires_dir: bool = True

Whether the parser requires a working directory.

rules: list[ActionRule]

Rules for whether to enable this parser.

script: str | None = None

The name of the file containing the output file parser source.

script_pass_env_spec: bool = False

Whether to pass the environment specifier to the script.

to_dict()

Serialize this object as a dictionary.

Return type:

dict[str, Any]

to_json_like(dct=None, shared_data=None, exclude=(), 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.

Parameters:

• dct (dict[str, JSONable] | None) –

• shared_data (_JSONDeserState) –

• exclude (Container[str | None]) –

• path (list | None) –

Return type:

tuple[JSONDocument, _JSONDeserState]