Add extractObservationBased functionallity

[ryuuzake]

Closes #976

Sorry for no update for a long time. I made the code to recursively extract all the results into Observation. I think the code needs many refactor to match the project structure. I would change it based on your review @fongsean

[fongsean]

Thanks @ryuuzake. I'll have a look soon.

[ryuuzake]

@fongsean please don't merge this PR yet. I still need to fix some bugs

[lamurian]

There's an issue that we're currently checking on. Per FHIR SDC specification, the questionnaire item is extracted only if it contains sdc-questionnaire-observationExtract extension set as true. Currently, we extract any item included in the Questionnaire resource, which does not completely comply with FHIR SDC.

Reiterating through the conceptual algorithm in SDC specification:

• Start at the root of the Questionnaire and progress down through the items.
• For a particular item, if the item itself or any of its codings have observationExtract set to 'true', then that item is to be extracted (if possible) and the presumption is that descendant items will also be extracted.
• The presumption of "will extract" will change to false only if an item explicitly sets observationExtract = false at the 'item' level. It is still possible that descendant items might turn extraction back on again. I.e. the full depth must be traversed to catch all extraction candidates.
• If an item is presumed to be extracted, it will extract if there are item.codes for that item that aren't explicitly marked with observationExtract=false.
• The observation-extract-category extension only comes into play if a determination has been made that extraction will occur. The observation-extract-category on an item will override that declared on the base questionnaire or ancestor items. If there is a desire to add multiple categories, all must be declared on an item.

---

For testing purpose, I included a questionnaire.json file. This resource contains a PHQ-2 instrument, which consists of two questions about depression. After implementing this conceptual algorithm, @ryuuzake and I will follow this testing procedure:

1. Render questionnaire.json in Smart Forms Playground
2. Fill in all questions
3. Click extract

Case 1:

• Objective: Extract all items.
• Procedure: Ensure that both items contain sdc-questionnaire-observationExtract set as true.
• Expected output: 2 Observation resources, each for item 1 and item 2.

Case 2:

• Objective: Extract only the first question.
• Procedure: Set sdc-questionnaire-observationExtract as false for the second question.
• Expected output: 1 Observation resource for item 1.

Case 3:

• Objective: Extract only the second question.
• Procedure: Delete sdc-questionnaire-observationExtract extension from the first item.
• Expected output: 1 Observation resource for item 2.

Questionnaire resource: questionnaire.json

Flat text of the questionnaire resource

Use this if the attachment above is not accessible. ```json { "resourceType": "Questionnaire", "id": "phq-2-questionnaire", "meta": { "versionId": "1", "lastUpdated": "2024-09-06T15:33:00Z" }, "title": "PHQ-2 Depression Screening", "status": "active", "date": "2024-08-29T12:00:00Z", "publisher": "Konsulin", "description": "Patient Health Questionnaire-2 (PHQ-2) for depression screening.", "subjectType": [ "Patient" ], "item": [ { "linkId": "phq2-1", "text": "Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?", "type": "choice", "code": [ { "system": "http://snomed.info/sct", "code": "28669007", "display": "Anhedonia" } ], "answerOption": [ { "valueCoding": { "code": "0", "display": "Not at all" } }, { "valueCoding": { "code": "1", "display": "Several days" } }, { "valueCoding": { "code": "2", "display": "More than half the days" } }, { "valueCoding": { "code": "3", "display": "Nearly every day" } } ], "extension": [ { "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract", "valueBoolean": true } ] }, { "linkId": "phq2-2", "text": "Over the last 2 weeks, how often have you been bothered by feeling down, depressed, or hopeless?", "type": "choice", "code": [ { "system": "http://snomed.info/sct", "code": "307077003", "display": "Feeling hopeless" } ], "answerOption": [ { "valueCoding": { "code": "0", "display": "Not at all" } }, { "valueCoding": { "code": "1", "display": "Several days" } }, { "valueCoding": { "code": "2", "display": "More than half the days" } }, { "valueCoding": { "code": "3", "display": "Nearly every day" } } ], "extension": [ { "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract", "valueBoolean": true } ] } ] } ```

[ryuuzake]

Hi @fongsean thanks for the wait. I already fix the bugs and confirm with @lamurian

[fongsean]

Hi both, thanks for validating with the SDC spec and putting in work to address the issues.

Code looks amazing - happy that @ryuuzake is using the generic recursive function for traversal. There are many use cases in the codebase which I previously written that can adopt it.

I've added two comments. I'll resolve my part and push it to your branch again. Other parts looks great. Once we resolve these two things, I will publish v0.40.0 and merge it into main.

Thanks!

[ryuuzake]

Hi @fongsean, I already integrate your changes to my PR