FHIRStore Crash When Using CloudKit/CoreData

[advatar]

Description

When collecting samples like this:

private var healthKit: HealthKit {
        HealthKit {
            CollectSamples(
                [
                    HKClinicalType(.allergyRecord),
                    HKClinicalType(.clinicalNoteRecord),
                    HKClinicalType(.conditionRecord),
                    HKClinicalType(.coverageRecord),
                    HKClinicalType(.immunizationRecord),
                    HKClinicalType(.labResultRecord),
                    HKClinicalType(.medicationRecord),
                    HKClinicalType(.procedureRecord),
                    HKClinicalType(.vitalSignRecord)
                ],
                predicate: HKQuery.predicateForSamples(
                    withStart: Date.distantPast,
                    end: nil,
                    options: .strictEndDate
                ),
                deliverySetting: .anchorQuery(saveAnchor: false)
                //deliverySetting: .manual(safeAnchor: false)
            )
        }
    }

I often get crashes ending with:

SwiftUI/FetchCommon.swift:51: Fatal error: Can only invoke this method on the main queue

The traceback is like:

Reproduction

See above

Expected behavior

Samples should be collected and added to the FHIRStore without crashing

Additional context

I am doing something similar to t:

Code of Conduct

• I agree to follow this project's Code of Conduct and Contributing Guidelines

[PSchmiedmayer]

@advatar Thank you for reporting the issue!

Can you share the project that you are working on so we can try to reproduce the issue; is it open-source? From the stacktrace, it looks like you are using or trying to modify LLMonFHIR?

[advatar]

I am modifying that project but the rest is a bit too messy at the moment. One thing I noticed is that dependencies are a bit outdated due to the SpeziML -> SpeziLLM change. I can try and maybe get the same problem with LLMonFHIR.

…

On 16 Jan 2024, at 17:55, Paul Schmiedmayer ***@***.***> wrote: @advatar <https://github.com/advatar> Thank you for reporting the issue! Can you share the project that you are working on so we can try to reproduce the issue; is it open-source? From the stacktrace, it looks like you are using or trying to modify LLMonFHIR? — Reply to this email directly, view it on GitHub <#16 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAG77WCS47IYH26HPFJBR3YO2WJVAVCNFSM6AAAAABB5CCFLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJUGEZTQOBRGU>. You are receiving this because you were mentioned.

[advatar]

I modified LLMonFHIR like this:

.background(.afterAuthorizationAndApplicationWillLaunch, saveAnchor: true)

I did not get a crash and it works for one launch but next time I get "No health records are available"

btw, same thing with:

.anchorQuery(saveAnchor: true)

[advatar]

Hmm, I am using CoreData/CloudKit and noticed that the crash only happens if I do:

.environment(\.managedObjectContext, PersistenceController.shared.persistentContainer.viewContext)

on the HomeView

[PSchmiedmayer]

@advatar Can you share a minimally reproducible example that we can use to work on fixing the bug together? A very simple iOS app that just contains the necessary code to reproduce the results and only the necessary Stanford dependencies would be great. Ideally you can share it as an GitHub project; that would be perfect!

[advatar]

I will try. I live in Sweden and Clinical Records are not available in HealthKit. I am getting data from a national service, 23andme, microbiome and blood testing sites. Non of this is FHIR.

A couple of features that would be nice

• generation of Clinical Records in FHIR from minimal data; date, quantity, value f.i (the rest of the decoration can be via the JSON)
• differentiate between different types of Observations like Vital Signs vs Laboratory and Survey
• Possibility to query for repeated laboratory test to get a series in chronological order

Anyways, this project is a few years old and used CoreData etc. Cleaning up all of that. At the moment it does not crash as often.

[advatar]

Just a quick question. I have now implemented generation of FHIRResources and can filter on vital-signs and laboratory. I works and I can view lab results. However, there is no persistence, I have to create the resources every time.

I am doing something like this:

let resourceProxies =  DemoManager.shared.loadLabResultsDemo()
                        for resourceProxy in resourceProxies {
                            if let observation = resourceProxy.get(if: ModelsR4.Observation.self) {
                                let fhirResource = FHIRResource(resource: observation, displayName: resourceProxy.displayName)
                                fhirStore.insert(resource: fhirResource)
                            }
                        }

Do I need something else than insert?

[advatar]

• differentiate between different types of Observations like Vital Signs vs Laboratory and Survey

I did this for now:

extension Array where Element == FHIRResource {
    /// Filters the FHIR resources using the provided search text.
    /// - Parameter category: Filters the FHIR resources using the provided category string.
    /// - Returns: The filtered FHIR resources.
    public func filterByObservationCategory(with category: String) -> [FHIRResource] {
        if category.isEmpty {
            return self
        }
        
        return filter { resource in
            switch resource.versionedResource {
            case .r4(let r):
                if let o = r as? ModelsR4.Observation, let categoryString = o.category?.first?.coding?.first?.code?.value?.string {
                    return categoryString == category
                }
            case .dstu2(let r):
                if let o = r as? ModelsDSTU2.Observation, let categoryString = o.category?.coding?.first?.code?.value?.string {
                    return categoryString == category
                }
            }
            return false
        }
    }
}

[advatar]

This example is easily reproducible StanfordBDHG/LLMonFHIR#45