Datadictionnary sync through API

pdelcroix · February 18, 2025, 8:01am

Dear community

I am trying to upload a source in a form of a FHIR CodeSystem but I either receive no feedback from the API or nothing happen on OCL (I tied to follow as much as possible the docs).

is there hidden constraints ? is there a mapping available between codesystem concept properties and OCL concept fields that are not covered in FHIR Codesystem concept base fields ? if I fall back on using the “json line” format (btw, quite annoying to generate, why not supporting json list) is there python library that define models for OCL Concept and help with sync ?

bit of context; we are trying to build a visual authoring tool and the datadictionary should have the form of a FHIR CodeSystem but ideally we want to rely on OCL to manage the data dictionary (do mapping, translation etc)

any feedback will be appreciated

Patrick

Edit: in the past I generated those model to interact with OCL because ocldev was lacking it: who-smart-ig-tools/ocl_map/models.py at main · SwissTPH/who-smart-ig-tools · GitHub

pdelcroix · February 18, 2025, 3:36pm

I manage to upload my CodeSystem by creating a converter from my old code base on some, AI and testing

github.com

SwissTPH/tricc/blob/develop/tricc_oo/converters/codesystem_to_ocl.py

from typing import Dict, List, Any
import json
from fhir.resources.codesystem import CodeSystem
from tricc_oo.models.ocl import (
    OCLConcept,
    OCLSource,
    OCLDetailedName,
    OCLDetailedDescription,
    OclConstants,
    get_data_type
)

def extract_properties_metadata(fhir_cs: CodeSystem) -> Dict[str, Dict]:
    """
    Extracts property definitions from FHIR CodeSystem and converts them to OCL attribute types
    """
    property_types = {}
    if hasattr(fhir_cs, 'property') and fhir_cs.property:
        for prop in fhir_cs.property:
            # Map FHIR property types to OCL datatypes

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but I still did not manage to convert it back to CodeSystem from OCL
https://app.openconceptlab.org/#/users/pdelcroix/sources/ALM

Any idea on what I am doing wrong ?

pdelcroix · February 19, 2025, 3:45pm

the upload issue is that I was not setting up the owner_type; what is annoying that there is no error message I had to check the delta from a concept export

I have to find a way to make it mandatory in pydantic model while not having it for embedded concept in sources

I manage to get the CodeSystem, the issue was:

Lack of canonical URL on the source
custom source attributes (url, version, )

jamlung · February 25, 2025, 1:29pm

Hi @pdelcroix ! Sorry for the late reply - I only just saw this post. Love to see this work, and would be very interested in keeping up!

Looks like you were able to get the upload working, which is great. We do need to improve our feedback for uploads to help users to troubleshoot.

If you still need to get the CodeSystem back from OCL, then we can troublehott that now. Did you save a version of your Source in OCL? OCL won’t return a CodeSystem unless a version has been saved (not counting the HEAD version, that is). I only see HEAD version for that example source though.

pdelcroix · February 26, 2025, 1:24pm

thank you it works now

regarding the payload do you have a CodeSystem OCL profile ?

I tried start it using AI but concept-class looks wrong and I might have missed properties like inactive …

Any resource I missed ?