Validate extracted fhir resources while in debug #2874

LZRS · 2023-11-21T07:37:21Z

IMPORTANT: Where possible all PRs must be linked to a Github issue

Depends on #2825
Fixes #2853

Engineer Checklist

I have written Unit tests for any new feature(s) and edge cases for bug fixes
I have added any strings visible on UI components to the strings.xml file
I have updated the CHANGELOG.md file for any notable changes to the codebase
I have run ./gradlew spotlessApply and ./gradlew spotlessCheck to check my code follows the project's style guide
I have built and run the FHIRCore app to verify my change fixes the issue and/or does not break the app
I have checked that this PR does NOT introduce breaking changes that require an update to Content and/or Configs? If it does add a sample here or a link to exactly what changes need to be made to the content.

Code Reviewer Checklist

I have verified Unit tests have been written for any new feature(s) and edge cases
I have verified any strings visible on UI components are in the strings.xml file
I have verifed the CHANGELOG.md file has any notable changes to the codebase
I have verified the solution has been implemented in a configurable and generic way for reuseable components
I have built and run the FHIRCore app to verify the change fixes the issue and/or does not break the app

codecov · 2023-11-21T08:30:22Z

Codecov Report

Attention: Patch coverage is 33.96226% with 35 lines in your changes missing coverage. Please review.

Project coverage is 27.1%. Comparing base (490c294) to head (045f2bc).
Report is 2 commits behind head on main.

Files	Patch %	Lines
...e/quest/ui/questionnaire/QuestionnaireViewModel.kt	0.0%	30 Missing ⚠️
...re/engine/util/extension/FhirValidatorExtension.kt	78.2%	3 Missing and 2 partials ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##              main   #2874    +/-   ##
========================================
  Coverage     27.0%   27.1%            
- Complexity     720     733    +13     
========================================
  Files          269     275     +6     
  Lines        13517   13756   +239     
  Branches      2433    2491    +58     
========================================
+ Hits          3662    3733    +71     
- Misses        9373    9528   +155     
- Partials       482     495    +13

Flag	Coverage Δ
engine	`64.6% <78.2%> (+<0.1%)`	⬆️
geowidget	`11.4% <ø> (ø)`
quest	`5.2% <0.0%> (+0.4%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
...re/engine/util/extension/FhirValidatorExtension.kt	`78.2% <78.2%> (ø)`
...e/quest/ui/questionnaire/QuestionnaireViewModel.kt	`2.7% <0.0%> (-0.1%)`	⬇️

android/engine/src/main/java/org/smartregister/fhircore/engine/di/FhirValidatorModule.kt

ellykits

Minor code change request. Otherwise looks good 👍

android/engine/src/main/java/org/smartregister/fhircore/engine/di/FhirValidatorModule.kt

LZRS · 2024-01-25T14:28:48Z

Getting this error

FATAL EXCEPTION: main
                                                                                                    Process: org.smartregister.opensrp.ecbis, PID: 6802
                                                                                                    java.lang.IllegalStateException: com.github.benmanes.caffeine.cache.SSMSW
                                                                                                    	at com.github.benmanes.caffeine.cache.LocalCacheFactory.newBoundedLocalCache(LocalCacheFactory.java:95)
                                                                                                    	at com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalManualCache.<init>(BoundedLocalCache.java:3417)
                                                                                                    	at com.github.benmanes.caffeine.cache.BoundedLocalCache$BoundedLocalLoadingCache.<init>(BoundedLocalCache.java:3752)
                                                                                                    	at com.github.benmanes.caffeine.cache.Caffeine.build(Caffeine.java:1105)
                                                                                                    	at org.hl7.fhir.common.hapi.validation.validator.VersionSpecificWorkerContextWrapper.<init>(VersionSpecificWorkerContextWrapper.java:80)
                                                                                                    	at org.hl7.fhir.common.hapi.validation.validator.VersionSpecificWorkerContextWrapper.newVersionSpecificWorkerContextWrapper(VersionSpecificWorkerContextWrapper.java:770)
                                                                                                    	at org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator.provideWorkerContext(FhirInstanceValidator.java:246)
                                                                                                    	at org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator.validate(FhirInstanceValidator.java:225)
                                                                                                    	at org.hl7.fhir.common.hapi.validation.validator.BaseValidatorBridge.doValidate(BaseValidatorBridge.java:22)
                                                                                                    	at org.hl7.fhir.common.hapi.validation.validator.BaseValidatorBridge.validateResource(BaseValidatorBridge.java:45)
                                                                                                    	at org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator.validateResource(FhirInstanceValidator.java:26)
                                                                                                    	at ca.uhn.fhir.validation.FhirValidator.validateResource(FhirValidator.java:343)
                                                                                                    	at ca.uhn.fhir.validation.FhirValidator.doValidate(FhirValidator.java:264)
                                                                                                    	at ca.uhn.fhir.validation.FhirValidator.validateWithResult(FhirValidator.java:252)
                                                                                                    	at ca.uhn.fhir.validation.FhirValidator.validateWithResult(FhirValidator.java:211)
                                                                                                    	at org.smartregister.fhircore.engine.util.extension.FhirValidatorExtensionKt$checkResourceValid$2.invokeSuspend(FhirValidatorExtension.kt:34)
                                                                                                    	at org.smartregister.fhircore.engine.util.extension.FhirValidatorExtensionKt$checkResourceValid$2.invoke(Unknown Source:14)
                                                                                                    	at org.smartregister.fhircore.engine.util.extension.FhirValidatorExtensionKt$checkResourceValid$2.invoke(Unknown Source:12)
                                                                                                    	at kotlinx.coroutines.intrinsics.UndispatchedKt.startUndispatchedOrReturn(Undispatched.kt:78)
                                                                                                    	at kotlinx.coroutines.BuildersKt__Builders_commonKt.withContext(Builders.common.kt:167)
                                                                                                    	at kotlinx.coroutines.BuildersKt.withContext(Unknown Source:1)
                                                                                                    	at org.smartregister.fhircore.engine.util.extension.FhirValidatorExtensionKt.checkResourceValid(FhirValidatorExtension.kt:33)
                                                                                                    	at org.smartregister.fhircore.engine.util.extension.FhirValidatorExtensionKt.checkResourceValid$default(FhirValidatorExtension.kt:27)
                                                                                                    	at org.smartregister.fhircore.quest.ui.questionnaire.QuestionnaireViewModel$handleQuestionnaireSubmission$1.invokeSuspend(QuestionnaireViewModel.kt:219)
                                                                                                    	at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33)
                                                                                                    	at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:108)
                                                                                                    	at android.os.Handler.handleCallback(Handler.java:942)
                                                                                                    	at android.os.Handler.dispatchMessage(Handler.java:99)
                                                                                                    	at android.os.Looper.loopOnce(Looper.java:201)
                                                                                                    	at android.os.Looper.loop(Looper.java:288)
                                                                                                    	at android.app.ActivityThread.main(ActivityThread.java:7872)
                                                                                                    	at java.lang.reflect.Method.invoke(Native Method)
                                                                                                    	at com.android.internal.os.RuntimeInit$MethodAndArgsCaller.run(RuntimeInit.java:548)
                                                                                                    	at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:936)
                                                                                                    	Suppressed: kotlinx.coroutines.internal.DiagnosticCoroutineContextException: [StandaloneCoroutine{Cancelling}@c8aef04, Dispatchers.Main.immediate]
                                                                                                    Caused by: java.lang.reflect.InvocationTargetException
                                                                                                    	at java.lang.reflect.Constructor.newInstance0(Native Method)
                                                                                                    	at java.lang.reflect.Constructor.newInstance(Constructor.java:343)
                                                                                                    	at com.github.benmanes.caffeine.cache.LocalCacheFactory.newBoundedLocalCache(LocalCacheFactory.java:92)
                                                                                                    	... 33 more
2024-01-25 17:16:51.374  6802-6802  AndroidRuntime          org.smartregister.opensrp.ecbis      E  Caused by: java.lang.Error: java.lang.NoSuchFieldException: No field threadLocalRandomProbe in class Ljava/lang/Thread; (declaration of 'java.lang.Thread' appears in /apex/com.android.art/javalib/core-oj.jar-transformed)
                                                                                                    	at com.github.benmanes.caffeine.cache.UnsafeAccess.objectFieldOffset(UnsafeAccess.java:57)
                                                                                                    	at com.github.benmanes.caffeine.cache.StripedBuffer.<clinit>(StripedBuffer.java:88)
                                                                                                    	at com.github.benmanes.caffeine.cache.BoundedLocalCache.<init>(BoundedLocalCache.java:243)
                                                                                                    	at com.github.benmanes.caffeine.cache.SS.<init>(SS.java:31)
                                                                                                    	at com.github.benmanes.caffeine.cache.SSMS.<init>(SSMS.java:64)
                                                                                                    	at com.github.benmanes.caffeine.cache.SSMSW.<init>(SSMSW.java:41)
                                                                                                    	... 36 more
                                                                                                    Caused by: java.lang.NoSuchFieldException: No field threadLocalRandomProbe in class Ljava/lang/Thread; (declaration of 'java.lang.Thread' appears in /apex/com.android.art/javalib/core-oj.jar-transformed)
                                                                                                    	at java.lang.Class.getDeclaredField(Native Method)
                                                                                                    	at com.github.benmanes.caffeine.cache.UnsafeAccess.objectFieldOffset(UnsafeAccess.java:55)
                                                                                                    	... 41 more

pld · 2024-04-18T13:27:24Z

hi @LZRS is the only remaining issue that the error dialogs are not great? I think we should get this merged and have that be in a cleanup issue cc @ellykits @ndegwamartin

LZRS · 2024-04-18T13:56:24Z

hi @LZRS is the only remaining issue that the error dialogs are not great? I think we should get this merged and have that be in a cleanup issue cc @ellykits @ndegwamartin

Yeah it is the only remaining issue. I can finish up on the tests and have it as ready for review

…ed-resources

pld · 2024-06-17T19:46:43Z

@LZRS I think this'll be good to go with a bit more coverage!

@ellykits you have a requested changes open, can you please take another look?

Thank you!

…ed-resources

...est/src/main/java/org/smartregister/fhircore/quest/ui/questionnaire/QuestionnaireActivity.kt

android/engine/src/main/java/org/smartregister/fhircore/engine/di/FhirValidatorModule.kt

...ine/src/main/java/org/smartregister/fhircore/engine/util/extension/FhirValidatorExtension.kt

ellykits · 2024-06-21T13:48:07Z

...ine/src/main/java/org/smartregister/fhircore/engine/util/extension/FhirValidatorExtension.kt

+  vararg resource: Resource,
+  isDebug: Boolean = BuildConfig.BUILD_TYPE.contains("debug", ignoreCase = true),
+): List<ValidationResult> {
+  if (!isDebug) return emptyList()


Does this mean validation will only be triggered for debug apks?

Yeah, it would only be triggered for debug because the performance implications it might have for non-debug apps

...ine/src/main/java/org/smartregister/fhircore/engine/util/extension/FhirValidatorExtension.kt

...est/src/main/java/org/smartregister/fhircore/quest/ui/questionnaire/QuestionnaireActivity.kt

ndegwamartin · 2024-07-22T12:19:30Z

Recommending we strip out the UI stuff in this version, see my comment here.

…ed-resources

ellykits · 2024-08-07T09:59:32Z

@LZRS Create a follow-up GitHub issue based on @ndegwamartin's comment below.

Recommending we strip out the UI stuff in this version, see #2853 (comment).

* Validate extracted fhir resources while in debug * Format validation error messages * Show validation result in dialog after submission * Use macos-13 for ci job runner * Fix failing QuestionnaireViewModelTest tests * add missing paren * Refactor to just send FhirValidator error messages to logcat --------- Co-authored-by: Peter Lubell-Doughtie <[email protected]> Co-authored-by: Sebastian <[email protected]> Co-authored-by: Benjamin Mwalimu <[email protected]> Co-authored-by: Elly Kitoto <[email protected]>

LZRS self-assigned this Nov 21, 2023

LZRS force-pushed the main-validate-extracted-resources branch from 3d36461 to f8b6965 Compare November 27, 2023 22:13

ellykits requested changes Nov 30, 2023

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android/engine/src/main/java/org/smartregister/fhircore/engine/di/FhirValidatorModule.kt Outdated Show resolved Hide resolved

android/engine/src/main/java/org/smartregister/fhircore/engine/di/FhirValidatorModule.kt Outdated Show resolved Hide resolved

LZRS force-pushed the main-validate-extracted-resources branch from f8b6965 to 33fd86e Compare December 1, 2023 03:18

LZRS force-pushed the main-validate-extracted-resources branch 5 times, most recently from 8a36cfd to b74de76 Compare January 23, 2024 13:39

LZRS marked this pull request as ready for review January 23, 2024 15:20

LZRS requested review from ellykits, dubdabasoduba and ndegwamartin January 23, 2024 15:40

LZRS enabled auto-merge (squash) January 23, 2024 15:41

LZRS disabled auto-merge January 23, 2024 15:41

ellykits requested changes Jan 25, 2024

View reviewed changes

android/engine/src/main/java/org/smartregister/fhircore/engine/di/FhirValidatorModule.kt Outdated Show resolved Hide resolved

LZRS force-pushed the main-validate-extracted-resources branch from b74de76 to 1cf49f6 Compare January 25, 2024 14:11

LZRS marked this pull request as draft January 25, 2024 14:17

LZRS added the DNM label Jan 25, 2024

LZRS changed the base branch from main to upgrade-sdk-libraries February 5, 2024 13:40

LZRS mentioned this pull request Feb 6, 2024

Support for validating resources before saving to local db #2853

Closed

Base automatically changed from upgrade-sdk-libraries to main February 7, 2024 15:51

LZRS force-pushed the main-validate-extracted-resources branch from fb327b9 to 27d7949 Compare March 11, 2024 00:24

ndegwamartin modified the milestone: Sprint 6 (Mar 11th - Mar 22nd) Mar 11, 2024

LZRS force-pushed the main-validate-extracted-resources branch 2 times, most recently from 882883f to f3fff5e Compare March 18, 2024 14:08

Validate extracted fhir resources while in debug

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0e8d407

Merge remote-tracking branch 'origin/main' into main-validate-extract…

d644028

…ed-resources

LZRS force-pushed the main-validate-extracted-resources branch from f315d06 to 3ca54c0 Compare April 29, 2024 23:36

LZRS added 2 commits April 30, 2024 11:03

Use macos-13 for ci job runner

415e647

Merge remote-tracking branch 'origin/main' into main-validate-extract…

e093834

…ed-resources

LZRS force-pushed the main-validate-extracted-resources branch from 3ca54c0 to e093834 Compare April 30, 2024 08:05

LZRS and others added 4 commits May 7, 2024 12:31

Fix failing QuestionnaireViewModelTest tests

a74d563

Merge remote-tracking branch 'origin/main' into main-validate-extract…

d44e8a3

…ed-resources

Merge branch 'main' into main-validate-extracted-resources

6326fb1

Merge branch 'main' into main-validate-extracted-resources

e1c9cf1

add missing paren

452efa7

pld force-pushed the main-validate-extracted-resources branch from 69aeb05 to 452efa7 Compare June 17, 2024 20:32

Merge remote-tracking branch 'origin/main' into main-validate-extract…

e4c0821

…ed-resources

SebaMutuku reviewed Jun 21, 2024

View reviewed changes

...est/src/main/java/org/smartregister/fhircore/quest/ui/questionnaire/QuestionnaireActivity.kt Outdated Show resolved Hide resolved

Merge branch 'main' into main-validate-extracted-resources

76af29f

ellykits requested changes Jun 21, 2024

View reviewed changes

Merge branch 'main' into main-validate-extracted-resources

303f03b

LZRS added 2 commits July 27, 2024 03:58

Merge remote-tracking branch 'origin/main' into main-validate-extract…

73d4d6e

…ed-resources

Refactor to just send FhirValidator error messages to logcat

5e59ef5

LZRS force-pushed the main-validate-extracted-resources branch from dc4c215 to 5e59ef5 Compare July 27, 2024 02:06

ellykits approved these changes Aug 7, 2024

View reviewed changes

Merge branch 'main' into main-validate-extracted-resources

045f2bc

LZRS marked this pull request as ready for review August 7, 2024 09:52

ellykits merged commit 8b5d9f6 into main Aug 7, 2024
4 of 5 checks passed

ellykits deleted the main-validate-extracted-resources branch August 7, 2024 09:59

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Validate extracted fhir resources while in debug #2874

Validate extracted fhir resources while in debug #2874

LZRS commented Nov 21, 2023 •

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LZRS Jun 21, 2024

ndegwamartin commented Jul 22, 2024

ellykits commented Aug 7, 2024

Validate extracted fhir resources while in debug #2874

Validate extracted fhir resources while in debug #2874

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