Handling '.' in class and property names

[adeel-ansari]

Some ontologies use '.' in the property and class names. Example here: http://hl7.org/fhir/patient-example.ttl.html

If we use a tool such as TopBraidComposer to generate the SHACL shapes, the shapes also have '.' in the names.

I think this causes problems with some of the forge commands because I think in forge the '.' means we're trying to access another property. I don't think it expects that it's part of the name.

Is there a way to handle '.' is shapes and property names?

[MFSY]

Hi @adeel-ansari, Thank you for reporting this. Can you give more details about the error you are facing ? Which forge commands cause issues ?

[adeel-ansari]

Hi @MFSY ,

I last tried this back in Oct 2020 so I will try to re-create the issue. Unfortunately, when running the notebook (upgraded from forge 0.3.3 to 0.5.2) now I'm receiving another error ( RecursionError: maximum recursion depth exceeded while calling a Python object).

If I recall, there were issues with commands described in the tutorials (tutorial 01):

• jane = Resource(type="Person", name="Jane Doe")
• jane.email
• association.agent.email

If I tried with our SHACL shapes something like patient.name.HumanName.family it wouldn't work.

From the link above, the PatientName portion looks like this:

fhir:Patient.name [ fhir:index 0; fhir:HumanName.use [ fhir:value "official" ]; fhir:HumanName.family [ fhir:value "Chalmers" ]; fhir:HumanName.given [ fhir:value "Peter"; fhir:index 0 ], [ fhir:value "James"; fhir:index 1 ] ]

If needed, I can share the context, shapes, sample data.

[adeel-ansari]

@MFSY , I downgraded to 0.3.3 and it got rid of the recursion error. Here's an example of where I'm having trouble accessing some of the patient attributes.

forge.template("patient", output="json", only_required=True)

data = {
    "type": "patient",
    "fhir:Patient.active": [
        {
            "@type": "fhir:boolean",
            "fhir:value":"False"
        }
    ]
}

resource_patient = forge.from_json(data)
print(type(resource_patient))
forge.validate(resource_patient)

The output is:

{
    "type": "Patient"
}
<class 'kgforge.core.resource.Resource'>
<action> _validate_one
<succeeded> True

print(resource_patient)

{
    type: patient
    "fhir:Patient.active":
    [
        {
            @type: fhir:boolean
            "fhir:value": False
        }
    ]
}

From here I'm not sure how to access the attribute fhir:Patient.active. if I try:

resource_patient['fhir:Patient.active']

TypeError: 'Resource' object is not subscriptable

Maybe I need to access the attribute differently or modify the context?

[MFSY]

Hi @adeel-ansari ,

Thanks for the detailed description. resource_patient is a Resource so it is not possible to access its member as with a python dict.

I recommend to use one of the two following options to access such type of property:

resource_patient .__getitem__('fhir:Patient.active'): this is using an internal accessor.

or

resource_patient_json = forge.as_json(resource_patient)
 resource_patient_json['fhir:Patient.active']
 # Once your are done, then get back a resource from the json
resource_patient = forge.from_json(resource_patient_json)

About the forge version, we recommend to use the latest as many fixes are being made. As for the recursion error, please open another ticket for us to have look.

[adeel-ansari]

Thanks @MFSY, I tried the second approach successfully. I'll let you know if this approach causes any problems for any further forge functionality.

I think the first approach (getitem) may need me to upgrade. I'll try it once the recursion error is resolved. Opening a ticket for that soon.

Thanks for the help.