Allow entities to be passed in as `properties` values when initialising an entity

[elichad]

Example demonstrating the issue:

from rocrate.model import ContextEntity, Person
from rocrate.rocrate import ROCrate

crate = ROCrate()

alice = crate.add(
    Person(
        crate,
        "https://orcid.org/0000-0000-0000-0000",
        properties={"name": "Alice Doe", "affiliation": "University of Flatland"},
    )
)
bob = crate.add(
    Person(
        crate,
        "https://orcid.org/0000-0000-0000-0001",
        properties={"name": "Bob Doe", "affiliation": "University of Flatland"},
    )
)

data = crate.add_file(
    "data.csv",
    properties={
        "name": "Data file",
        "encodingFormat": "text/csv",
        "author": [alice, bob],
    },
)

crate.write("out_crate")

Running this yields an error:

Traceback (most recent call last):
  File "/home/eli/roc/testing/crate.py", line 30, in <module>
    crate.write("crate_out")
  File "/home/eli/roc/testing/.venv-zenodo/lib/python3.12/site-packages/rocrate/rocrate.py", line 453, in write
    writable_entity.write(base_path)
  File "/home/eli/roc/testing/.venv-zenodo/lib/python3.12/site-packages/rocrate/model/metadata.py", line 80, in write
    json.dump(as_jsonld, outfile, indent=4, sort_keys=True)
. . .
TypeError: Object of type Person is not JSON serializable

This is because including the author entities in properties isn't supported. Instead I would have to use

data = crate.add_file(
    "data.csv",
    properties={
        "name": "Data file",
        "encodingFormat": "text/csv",
    },
)
data["author"] = [alice, bob]

In my opinion this is a less intuitive way of doing things, and it's not straightforward for the user to understand why the second method works and the first one doesn't.

Solution

Behind the scenes we are using a custom setter to set individual properties, but Entity.__init__() skips activating that function when handling the properties argument, the referenced entities don't get connected properly. We can update that __init__ function so that it triggers __setitem__. This way, both methods of setting the author would be equivalent.