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

LZRS · 2024-03-19T14:49:59Z

Allow normal questionnaire submission
Collect validation errors on CQL evaluations
Collect validation errors on StructureMap extractions
Collect validation errors on PlanDef extractions
Refine validation error dialog with clear details

Submission seems somewhat slowed down because of validation

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).

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

View reviewed changes

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 DO NOT MERGE 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

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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pld commented Apr 18, 2024

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ellykits Jun 21, 2024

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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