Add workflow input / output files

[paulzierep]

There was a request to add input output information to a workflow, file type would be useful.
But a quick check showed that the information that can be requested form workflowhub is not very useful imo.
For some reason file type is not included.

import json

for wf in data:
    wfhub_wf = get_request_json(
        f"https://{prefix}workflowhub.eu{wf['links']['self']}",
        header,
    )

    internals = wfhub_wf["data"]["attributes"]["internals"]

    io = {
        "inputs": internals.get("inputs", []),
        "outputs": internals.get("outputs", []),
    }

    print(json.dumps(io, indent=2))
    break

Output

{
  "inputs": [
    {
      "id": "#main/Bacterial genome contigs",
      "name": "#main/Bacterial genome contigs",
      "description": "The input for this workflow is a single FASTA file containing contigs of one bacterial genome.",
      "type": [
        {
          "type": "File"
        }
      ],
      "default_value": null
    },
    {
      "id": "#main/Reference Allele Scheme",
      "name": "#main/Reference Allele Scheme",
      "description": "Reference Allele Scheme (from pubMLST,  BIGSdb, Enterobase, or cgMLST.org) that will be used by CoreProfiler to compare the contigs to and identify corresponding alleles.",
      "type": [
        {
          "type": "string"
        }
      ],
      "default_value": null
    }
  ],
  "outputs": [
    {
      "id": "#main/CoreProfiler allele calling report",
      "name": "#main/CoreProfiler allele calling report",
      "description": null,
      "type": [
        {
          "type": "File"
        }
      ],
      "source_ids": [
        "#main/CoreProfiler/output_file"
      ]
    },
    {
      "id": "#main/Extracted cgMLST results by ToolDistillator",
      "name": "#main/Extracted cgMLST results by ToolDistillator",
      "description": null,
      "type": [
        {
          "type": "File"
        }
      ],
      "source_ids": [
        "#main/ToolDistillator extraction/output_json"
      ]
    },
    {
      "id": "#main/Information about temporary alleles found by CoreProfiler",
      "name": "#main/Information about temporary alleles found by CoreProfiler",
      "description": null,
      "type": [
        {
          "type": "File"
        }
      ],
      "source_ids": [
        "#main/CoreProfiler/profiles_w_tmp_alleles"
      ]
    },
    {
      "id": "#main/Newly detected alleles by CoreProfiler",
      "name": "#main/Newly detected alleles by CoreProfiler",
      "description": null,
      "type": [
        {
          "type": "File"
        }
      ],
      "source_ids": [
        "#main/CoreProfiler/outfa"
      ]
    },
    {
      "id": "#main/Summarized cgMLST ToolDistillator results",
      "name": "#main/Summarized cgMLST ToolDistillator results",
      "description": null,
      "type": [
        {
          "type": "File"
        }
      ],
      "source_ids": [
        "#main/ToolDistillator summarize/summary_json"
      ]
    }
  ]
}

[bebatut]

It is probably because the format is not set up in the workflow (.ga itself). It gets auto-generated
at runtime based on connections:

[paulzierep]

It is probably because the format is not set up in the workflow (.ga itself). It gets auto-generated at runtime based on connections:

Good point, but the output could have it ...

[bebatut]

Probably only the workflow_outputs elements in the steps are used to fill in the WorkflowHub, and not the outputs elements in the step:

        "4": {
            "annotation": "Summarizes several ToolDistillator JSON files into a unique JSON file",
            ...
            "outputs": [
                {
                    "name": "summary_json",
                    "type": "json"
                }
            ],
           ...
            "workflow_outputs": [
                {
                    "label": "Summarized cgMLST ToolDistillator results",
                    "output_name": "summary_json",
                    "uuid": "208bd650-48c2-4a18-9807-e818272b8bb0"
                }
            ]
        }
    },

[paulzierep]

First step to get tool outputs: #583