add started_at_time, ended_at_time slot to workflow execution activity

[wdduncan]

@cmungall I just noticed that the workflow execution activity class does not have started at time, ended at time slots:

workflow execution activity:
    is_a: activity
    in_subset: 
      - workflow subset
    description: >-
      Represents an instance of an execution of a particular workflow
    slots:
      - execution resource
      - git url
      - has input
      - has output
      - type  # custom slot that specifies object type
    slot_usage:
      was associated with:
        required: false
        description: >-
          the agent/entity associated with the generation of the file
        range: workflow execution activity
        inlined: false # allow for strings of IDs

However, the data coming from Aim 2 does have the these slots. E.g.:

{
    "id": "nmdc:f2fc8f5aade3092ea97769f0a892d2a9",
    "name": "MAGs activiity 1781_86101",
    "was_informed_by": "gold:Gp0115663",
    "started_at_time": "2021-01-10",
    "ended_at_time": "2021-01-10",
    "type": "nmdc:MAGsAnalysisActivity",
    "execution_resource": "NERSC - Cori",
    "git_url": "https://img.jgi.doe.gov",
    ...
}

I think we should add these slots to the schema.

Thoughts?

[wdduncan]

related to issue microbiomedata/nmdc-runtime#5

[cmungall]

it's inherited from activity

[wdduncan]

@cmungall Yes. You are right :)

However, the started at time and ended at time slots are not required. If I remove the started at time and ended at time properties, it validates against the jsonschema. E.g., this is valid:

{"activity_set":
[
  {
    "id": "nmdc:647b163bdcb9528b8dcc8ab9b506c957",
    "name": "MetagenomeAnnotation activity for gold:Gp0324040",
    "was_informed_by": "gold:Gp0324040",
    "type": "nmdc:MetagenomeAnnotation",
    "execution_resource": "NERSC - Cori",
    "git_url": "https://github.com/microbiomedata/mg_annotation/releases/tag/0.1",
    "has_input": [
      "nmdc:7e0bb15dc62ea4a5ae94f51af347129f"
    ],
    "has_output": [
      "nmdc:dca7ca0cc779868ceac63aa3af6a3070",
      "nmdc:c177fd732e25dda4d2afa10159e8d0b4",
      "nmdc:b09c3cd4ad025e106e51f3234bf3850f",
      "nmdc:1fd680ec996ea2043fd34468e5c3464a",
      "nmdc:7796820582563a8b3867de9554b1a8ac"
    ]
  },
  {
    "id": "nmdc:0e9fb1e720caf88f61ab8bc4d866af7e",
    "name": "MetagenomeAnnotation activity for gold:Gp0324044",
    "was_informed_by": "gold:Gp0324044",
    "type": "nmdc:MetagenomeAnnotation",
    "execution_resource": "NERSC - Cori",
    "git_url": "https://github.com/microbiomedata/mg_annotation/releases/tag/0.1",
    "has_input": [
      "nmdc:6a455b07be6e9c6b3f0631858a8ade17"
    ],
    "has_output": [
      "nmdc:6d6bc7279ced7706d60024621e3bd32f",
      "nmdc:50f2fe8d10b7f498c092ad58d84566e9",
      "nmdc:1aa4f17a80bf5f1783b044261bd0122e",
      "nmdc:a17065ca9209cb2774e2364c6d4a4e09",
      "nmdc:2ac6dc3b3e885520db0e4604c641cde3"
    ]
  }
]
}