Representing environment variables about workflow-run-crate HOT 5 CLOSED

I guess this could be modeled as a list of https://schema.org/PropertyValue where the PropertyValue.name is the environment variable name (like ALGORITHM_OVERRIDE) and the PropertyValue.value is the actual string value used (revised in this made-up example).

from workflow-run-crate.

PropertyValue using name and value seems a good choice for the retrospective part. For the prospective part, where there is no value and the focus is on the name / type, it seems less straightforward. Additionally, we need a way to link them to the tool / workflow (prospective) or action (retrospective). There are analogies with workflow / tool parameters.

from workflow-run-crate.

Both ComputationalTool and ComputationalWorkflow have input, which is a list of FormalParameter.

I think we should also represent environment variables as FormalParameters, but extending both ComputationalWorkflow and ComputationalTool in order to have an additional property environment, where to list the possible environment variables as FormalParameter. Then, depending on whether it is either the prospective or the retrospective provenance being represented, those instances of FormalParameter will or wont have listed the values at through workExample property.

from workflow-run-crate.

If env vars are represented as FormalParameter on the prospective side, then they should probably be represented by PropertyValue on the retrospective side. These should be listed in the relevant CreateAction, but with which property? Reuse environment?

from workflow-run-crate.

Here' s how it would look like (BTW, ComputationalTool is not in the RO-Crate context, we're using SoftwareApplication for tools):

{
    "@id": "foo.cwl",
    "@type": "SoftwareApplication",
    ...
    "environment": [
        {"@id": "foo.cwl#api_token"}
    ]
},
{
    "@id": "foo.cwl#api_token",
    "@type": "FormalParameter",
    "additionalType": "Text",
    "name": "API_TOKEN",
},
{
    "@id": "#cb04c897-eb92-4c53-8a38-bcc1a16fd650",
    "@type": "CreateAction",
    "instrument": {"@id": "foo.cwl"},
    ...
    "environment": [
        {"@id": "#api_token-pv"}
    ]
},
{
    "@id": "#api_token-pv",
    "@type": "PropertyValue",
    "exampleOfWork": {"@id": "foo.cwl#api_token"},
    "name": "API_TOKEN",
    "value": "nGh9_v8nhv8h49388a44w89hK_aof0q"
}

from workflow-run-crate.