How to specify the order of objects (and results)

[SteffenBrinckmann]

Hey,
let's say we take the example image under "Multiple processes" under https://www.researchobject.org/workflow-run-crate/profiles/process_run_crate/. In that image, let's say we want to subtract file result1.txt from input2.txt in createAction2.
How do we specify the order of operation, that we do A-B and not by accident B-A?
Same if the action has multiple outputs (first output becomes input for Action3 while second output becomes input for Action4)?

Json-ld by default has no order to the list. One has to manually enforce it.

[simleo]

In such cases it's probably better to use the Workflow Run Crate profile, using FormalParameter instances to distinguish the different types of input and output.

[SteffenBrinckmann]

This is also an issue. In the case above, A und B are of the same data-type and here the order is of importance.

[simleo]

What I had in mind is that the application could be wrapped in e.g. a CWL CommandLineTool that defines named parameters, and internally passes them to the wrapped tool in the required order. For instance:

cwlVersion: v1.2
class: CommandLineTool
baseCommand: [diff]

inputs:
  file1:
    type: File
    inputBinding:
      position: 1
  file2:
    type: File
    inputBinding:
      position: 2
outputs:
  diff_out:
    type: File
    outputBinding:
      glob: diff_out.txt
stdout: diff_out.txt
successCodes: [0, 1]

The RO-Crate metadata would refer to the wrapper's parameters, which have different names.

However, if one doesn't want to do the extra work and just stick to the Process Run Crate profile, there's the option of using position on the files. For instance:

{
    "@context": [
        "https://w3id.org/ro/crate/1.1/context",
        "https://w3id.org/ro/terms/workflow-run/context"
    ],
    "@graph": [
        {
            "@id": "ro-crate-metadata.json",
            "@type": "CreativeWork",
            "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
            "about": {"@id": "./"}
        },
        {
            "@id": "./",
            "@type": "Dataset",
            "conformsTo": {"@id": "https://w3id.org/ro/wfrun/process/0.5"},
            "hasPart": [
                {"@id": "A.txt"},
                {"@id": "B.txt"},
                {"@id": "C.txt"}
            ],
            "mentions": {"@id": "#diff_1"},
            "name": "diff of A and B",
            "description": "compute diff of A and B"
        },
        {   "@id": "https://w3id.org/ro/wfrun/process/0.5",
            "@type": "CreativeWork",
            "name": "Process Run Crate",
            "version": "0.5"
        },
        {
            "@id": "https://www.gnu.org/software/diffutils/",
            "@type": "SoftwareApplication",
            "url": "https://www.gnu.org/software/diffutils/",
            "name": "diff",
            "softwareVersion": "3.10"
        },
        {
            "@id": "#diff_1",
            "@type": "CreateAction",
            "name": "Diff of A and B",
            "description": "diff A.txt B.txt > C.txt",
            "endTime": "2025-05-20T11:50:00+02:00",
            "instrument": {"@id": "https://www.gnu.org/software/diffutils/"},
            "object": [
                {"@id": "A.txt"},
                {"@id": "B.txt"}
            ],
            "result": {"@id": "C.txt"}
        },
        {
            "@id": "A.txt",
            "@type": "File",
            "name": "file A",
            "position": 1
        },
        {
            "@id": "B.txt",
            "@type": "File",
            "name": "file B",
            "position": 2
        },
        {
            "@id": "C.txt",
            "@type": "File",
            "name": "file C"
        }
    ]
}

[SteffenBrinckmann]

In the latter case, the order is in the parameters, not in the function itself, which I find less intuitive.
From json-ld perspective, the container also works

{
  "@context": {
    "ex": "http://example.org/",
    "function": { "@id": "ex:function" },
    "args": {
      "@id": "ex:arguments",
      "@container": "@list"
    }
  },
  "@id": "_:call1",
  "function": "ex:add",
  "args": [2, 3]
}

But I did not find anybody who uses it.

[stain]

However, if one doesn't want to do the extra work and just stick to the Process Run Crate profile, there's the option of using position on the files.

I am hesitant to this, while using position is an obvious one to reach for, and we should start on 1 as argv traditionally has the command in 0, however this means that each file can only be in one position. But there could be two different processes that use the same file in different positions. This is part of reason for why we invented the FormalParameter glue record, but it does not have provision for position, it was indeed inspired by Galaxy/CWL/Taverna where there is always a name for these parameters. But each workflow wrapper may give different names to these and map them differently to command line arguments. (e.g. "-i file.txt" vs "--input file.txt" vs "file.txt")

How about using https://schema.org/ListItem which also have position - that would be an indirection that gives an order for that particular usage. You would need to change your process to use a https://schema.org/ItemList as input, which is a bit inconvenient and a bit against the current Process profile.. perhaps there is a way we can keep this list on the side but connected to the action, so that the individual files can still be there in object ?

For instance, as we have already introduced environment to point to shell environment, we can also create our own arguments in that namespace for the arguments as an ItemList:

{
    "@context": [
        "https://w3id.org/ro/crate/1.1/context",
        "https://w3id.org/ro/terms/workflow-run/context"
    ],
    "@graph": [
        {
            "@id": "ro-crate-metadata.json",
            "@type": "CreativeWork",
            "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
            "about": {"@id": "./"}
        },
        {
            "@id": "./",
            "@type": "Dataset",
            "conformsTo": {"@id": "https://w3id.org/ro/wfrun/process/0.5"},
            "hasPart": [
                {"@id": "A.txt"},
                {"@id": "B.txt"},
                {"@id": "C.txt"}
            ],
            "mentions": {"@id": "#diff_1"},
            "name": "diff of A and B",
            "description": "compute diff of A and B"
        },
        {   "@id": "https://w3id.org/ro/wfrun/process/0.5",
            "@type": "CreativeWork",
            "name": "Process Run Crate",
            "version": "0.5"
        },
        {
            "@id": "https://www.gnu.org/software/diffutils/",
            "@type": "SoftwareApplication",
            "url": "https://www.gnu.org/software/diffutils/",
            "name": "diff",
            "softwareVersion": "3.10"
        },
        {
            "@id": "#diff_1",
            "@type": "CreateAction",
            "name": "Diff of A and B",
            "description": "diff A.txt B.txt > C.txt",
            "endTime": "2025-05-20T11:50:00+02:00",
            "instrument": {"@id": "https://www.gnu.org/software/diffutils/"},
            "object": [
                {"@id": "A.txt"},
                {"@id": "B.txt"}
            ],
            "arguments": {"@id": "#diff_1_args"},
            "result": {"@id": "C.txt"}
        },
        {
            "@id": "A.txt",
            "@type": "File",
            "name": "file A"
        },
 
        {
            "@id": "B.txt",
            "@type": "File",
            "name": "file B"
        },
        {
            "@id": "C.txt",
            "@type": "File",
            "name": "file C"
        },
        {
            "@id": "#diff_1_arg_1",
            "@type": "ListItem",
            "position": 1,
            "item": { 
                "@id": "A.txt"
            }
        },
        {
            "@id": "#diff_1_arg_2",
            "@type": "ListItem",
            "position": 2,
            "item": { 
                "@id": "B.txt"
            }
        },
        {
            "@id": "#diff_1_args",
            "@type": "ItemList",
            "itemListElement": [
                {"@id": "#diff_1_arg_1"},
                {"@id": "#diff_1_arg_2"}
            ]
        }        
    ]
}

Not sure how we should represent then all the string arguments, as position allow a Text, this could also be "--input" or we could have this better in the name of the ListItem - but it could be there are non-file inputs as well like this, --format xml where we probably want "xml" as a value connected to --format beyond just the order.

[stain]

@container

I think we should try avoid using deeper JSON-LD trickery, as it goes a bit against RO-Crate style. See also discussion about (not) using @value ResearchObject/ro-crate#464 and representing other objects #94.

I think what you're aiming for here in this issue is to add argument position more like an annotation, the tool did not, at a conceptual level, primarily consume a list of filenames, but some files. The arguments is just how we told the tool about this. So that is why I propose to have some ListItem on the side. Yet it has to become connected to the action otherwise you could again find two different list items with two different positions, for the same file.