[BUG] `JsonController.LDGraph.fromROCrateJsonString(jsonString);` does not normalize ro-crate json ids

[Freymaurer]

This behavior was noticed for this ro-crate-json file:

arc-ro-crate-metadata (1).json

For the following code:

const ldgraph = JsonController.LDGraph.fromROCrateJsonString(jsonString);

const files = ldGraph.value.Nodes.filter((n) =>
      ROCrate.LDFile.validate(
          n,
          ldGraph.value?.TryGetContext() as any
      )
  );
console.log(files)

I get the following objects:

[
{
    "properties": {},
    "id": "assays/Imaging/dataset/control/Image2.lsm",
    "schemaType@178": [
        "File"
    ],
    "additionalType@179": [],
    "init@175-1": 1,
    "name": "assays/Imaging/dataset/control/Image2.lsm",
    "sha256": "ecac512e5a224cc6b98e79250ff15b9e6fffef72088289165cde5230033da17f",
    "contentSize": "751515343b"
},
{
    "properties": {},
    "id": "./runs/model_training/training_data_resampled/image4.tif",
    "schemaType@178": [
        "File"
    ],
    "additionalType@179": [],
    "init@175-1": 1,
    "name": "./runs/model_training/training_data_resampled/image4.tif",
    "sha256": "7ee83854892e7a77780b4f11aea8fb48e179230520fc2475ccd1574429ba537f",
    "contentSize": "45636233b"
}
]

Please pay attention to:

• "./runs/model_training/training_data_resampled/image4.tif"
• "assays/Imaging/dataset/control/Image2.lsm"

One with ./ and one without. I used this id field for comparisons with paths, and the paths are always without ./:

const arc = JsonController.ARC.fromROCrateJsonString(jsonString)
const paths = arc.value.FileSystem.Tree.ToFilePaths(true);

Which returns the following (all without ./):

"runs/model_training/training_data_resampled/image4.tif",
"assays/ModelTraining/dataset/test_images_masks/image22.tif"

Expected

Should be unified, instead run/-paths are not normalized.

[HLWeil]

Hey @Freymaurer,

as far as I see it, this is not a problem of the reader function. The json file you shared already contains those two objects:

Line 191;

    {
      "@id": "assays/Imaging/dataset/control/Image2.lsm",
      "@type": "File",
      "name": "assays/Imaging/dataset/control/Image2.lsm"
    },

Line 13950:

    {
      "@id": "./assays/Imaging/dataset/control/Image2.lsm",
      "@type": "File",
      "name": "./assays/Imaging/dataset/control/Image2.lsm"
    },

The one without the ./ is referenced from the assay perspective, while the other one is referenced from the run perspective. I guess the json-ld file is the output from arc-export? I'll see what's behind this in ARCtrl.