[Feature Request] [RO-Crate] Normalize File and Dataset URIs

[HLWeil]

If one entity is defined in multiple places in the ARC but starts with ./ in some and directly with the folder name in others. They get not correctly flattened into the same object, and therefore erroneously appear as separate objects in the RO-Crate metadata json.

Now, if we normalize this, should we use with or without the preceeding ./ as a convention?

@floWetzels @kMutagene @Brilator

[floWetzels]

I would prefer to always use the ./ prefix, but this is also not a hill I will die on.

[Brilator]

If we're setting convention, I would go for the preceeding ./.

For me the bigger confusion is that dataset files are referenced in Output [Data] columns as e.g. ./assays/myAssay/dataset/myDataFile of annotation tables in ./assays/myAssay/isa.assays.xlsx:myAnnotationTable relative to ARC root rather than relative to that annotation table / isa.assay path.

I'm not suggesting to change this... It makes sense. And I think, the "full" ARC-rooted path incl. ./ makes most sense.

[floWetzels]

I think the actual entries in the tables or in the ARC scaffold representation are a different topic. Ideally, our tools would detect equivalent paths and unify them in the RO-Crate representation, using some convention. This gives the end user maximum freedom while retaining robustness in exchange formats.