Better support for external links

[apdavison]

(i.e., to online instances outside the local Collection)

• Link objects are now properly serialized in JSON-LD
• Links can now be annotated with a list of types that they may be pointing to - this allows collections that contain Links to validate
• The Link class is now directly available in the top-level openminds module.

Example:

from openminds import Link
from openminds.v4.controlled_terms import Species
from openminds.v4.core import DatasetVersion

mouse = Link(
    "https://openminds.om-i.org/instances/species/musMusculus",
    allowed_types=[Species]
)

my_dsv = DatasetVersion(
    ...,
    study_targets=[mouse]
)

(this is perhaps a bad example, since all instances in the openMINDS instances library are anyway directly available (e.g. mouse = Species.mus_musculus, but it serves to illustrate the idea)

[apdavison]

I'm unsure whether allowed_types or expected_types is the most appropriate name.

[Raphael-Gazzotti]

It would be better to avoid hardcoding the version and namespace of the instances.

I would also move:
"definitely_mouse = Link(
"https://openminds.om-i.org/instances/species/musMusculus",
allowed_types=[Species],
)"

just on top of "my_dsv2 = DatasetVersion(study_targets=[definitely_mouse])"

[apdavison]

"better to avoid hardcoding" - do you mean the test should iterate over all versions, and introspect the namespace from the version?

"would also move" - I think this is a matter of taste. I think that by grouping the Link creation on consecutive lines it makes the test easier to understand.

[Raphael-Gazzotti]

Yes to the first option, because it will require to be adjusted for each new version (v5.0 and above).
The second point seems fair.

[apdavison]

It doesn't need to be adjusted for new versions, the test would work with any openminds version, I chose v4 for no particular reason.