Sample questionnaire modified by duplicating items. linkid of each item is unique

Following discussions between @yigit @florina-muntenescu @jingtang10, we decided to make fhir engine a singleton per process + db name to avoid racing conditions when updating the db

• Modify FhirEngine's API so that it's impossible to create another instance if there is already one (i.e. caching). At the moment in the referende app this is ensured by the initialization code in FhirApplication.kt using by lazy. But we want to be in the engine itself
• Mark the inMemory() API as internal since we're only using it in tests and definitly don't want users to actually create in-memory db
• Simplify the initialization code and remove the db name option (it's not used anywhere anyway)

@jingtang10 could you add CI tools like travis for checking build is successful and that tests successfully run

Originally posted by @githengi in #1 (comment)

lets create a central dependency file instead of hardcoding them
(similar to https://cs.android.com/androidx/platform/frameworks/support/+/androidx-master-dev:buildSrc/src/main/kotlin/androidx/build/dependencies/Dependencies.kt?q=Dependencies.kt)

I clearly have a file w/o copyright and spotlessCheck does not give any error

We want to remove all java code in the codebase and move fully to kotlin.

We need to establish the min API level for the SDK.

1. testing on at least emulators to see if the sdk works on lower API levels
2. document this in the README file

add the spotless plugin for code-style & copyright checks.
https://github.com/diffplug/spotless/tree/master/plugin-gradle

we can also remove idea files once it is merged.

• Use a loading spinner instead of the Snackbar
• Remove/fix About button functionality.
• Use Sync button in the toolbar correctly to sync with external hapi server

The timezone format currently supported by FHIR Search, FHIRPath etc. currently is a subset of ISO8601:

yyyy-mm-ddThh:mm:ss[Z|(+|-)hh:mm]

In Android SimpleDateFormat shows 'X' pattern for ISO 8601 only be supported in API Level 24+ (Nougat+) only.

This is required for Sync implementation to work correctly. Otherwise in API 21 it throws exception java.lang.IllegalArgumentException: Unknown pattern character 'X' while using
SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSSXXX", Locale.US)

Related to Issue #110

When syncing from the hapi test server, we use the id field from the patient object, it is of the form "baseurl/patient/id/history/historyid". What this means is that when there's a new version of patient we will treat it as a new (duplicated) patient in the db.

The fix is to use the actual patient id (which is a number on hapi test server) rather than the URL. In the hapi structures lib it's patient.getIdElement().getIdPart() (java).

We have an API to store a single resource. We need another API to store resources in batch.

we've not made the call yet but it would greatly simplify the code + ide experience.

the room PR already uses room but it is tiny so easy to move to java if we decide against kotlin.

lets keep the auto-value cleanup as a separate PR so that we can just revert.

Numeric input which is a whole number. Note that some validation will be needed to make sure that it is indeed a whole number that is being typed in

not important now but we should probably do these preparations async using the viewmodel scope.
can be a followup

Originally posted by @yigit in #97 (comment)

See issue #49.

While running master on API level 19, there's this error:

05-15 12:09:05.044 3357-3357/com.google.fhirengine.example E/AndroidRuntime: FATAL EXCEPTION: main
Process: com.google.fhirengine.example, PID: 3357
java.lang.VerifyError: org/apache/log4j/config/PropertySetter
at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:805)
at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:768)
at org.apache.log4j.PropertyConfigurator.configureRootCategory(PropertyConfigurator.java:648)
at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:514)
at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:580)
at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:526)
at org.apache.log4j.LogManager.(LogManager.java:127)
at org.slf4j.impl.Log4jLoggerFactory.(Log4jLoggerFactory.java:66)
at org.slf4j.impl.StaticLoggerBinder.(StaticLoggerBinder.java:72)
at org.slf4j.impl.StaticLoggerBinder.(StaticLoggerBinder.java:45)
at org.slf4j.LoggerFactory.bind(LoggerFactory.java:150)
at org.slf4j.LoggerFactory.performInitialization(LoggerFactory.java:124)
at org.slf4j.LoggerFactory.getILoggerFactory(LoggerFactory.java:412)
at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:357)
at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:383)
at ca.uhn.fhir.context.FhirContext.(FhirContext.java:80)
at com.google.fhirengine.resource.ResourceModule.getFhirContext(ResourceModule.java:29)
at com.google.fhirengine.resource.ResourceModule_GetFhirContextFactory.proxyGetFhirContext(ResourceModule_GetFhirContextFactory.java:27)
at com.google.fhirengine.DaggerFhirEngineComponent.getIParser(DaggerFhirEngineComponent.java:34)
at com.google.fhirengine.DaggerFhirEngineComponent.getDatabaseImpl(DaggerFhirEngineComponent.java:38)
at com.google.fhirengine.DaggerFhirEngineComponent.getFhirEngineImpl(DaggerFhirEngineComponent.java:62)
at com.google.fhirengine.DaggerFhirEngineComponent.getFhirEngine(DaggerFhirEngineComponent.java:75)
at com.google.fhirengine.example.MainActivity.onCreate(MainActivity.java:95)
at android.app.Activity.performCreate(Activity.java:5231)
at android.app.Instrumentation.callActivityOnCreate(Instrumentation.java:1087)
at android.app.ActivityThread.performLaunchActivity(ActivityThread.java:2159)
at android.app.ActivityThread.handleLaunchActivity(ActivityThread.java:2245)
at android.app.ActivityThread.access$800(ActivityThread.java:135)
at android.app.ActivityThread$H.handleMessage(ActivityThread.java:1196)
at android.os.Handler.dispatchMessage(Handler.java:102)
at android.os.Looper.loop(Looper.java:136)
at android.app.ActivityThread.main(ActivityThread.java:5017)
at java.lang.reflect.Method.invokeNative(Native Method)
at java.lang.reflect.Method.invoke(Method.java:515)
at com.android.internal.os.ZygoteInit$MethodAndArgsCaller.run(ZygoteInit.java:779)
at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:595)
at dalvik.system.NativeStart.main(Native Method)

which is an issue due to missing java libraries on Android which are used by HAPI FHIR.

Potentially investigate: https://stackoverflow.com/questions/30185857/apache-log4j-in-android-gives-exception-java-lang-verifyerror-org-apache-log4j

The timezone format currently supported by FHIR Search, FHIRPath etc. currently is a subset of ISO8601:

yyyy-mm-ddThh:mm:ss[Z|(+|-)hh:mm]

In Android SimpleDateFormat shows 'X' pattern for ISO 8601 only be supported in API Level 24+ (Nougat+) only.

This is required for Sync implementation to work correctly. Otherwise in API 21 it throws exception java.lang.IllegalArgumentException: Unknown pattern character 'X' while using
SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSSXXX", Locale.US)

Related to Issue #110

Each Resource in FHIR can have a lastUpdated timestamp to track when it last changed. We should add a column in ResourceEntity to support it. Ref Resource.

with our min sdk version 21, we probably don't need to use AppCompatActivity in the reference app

Unable to instantiate fragment com.google.android.fhir.datacapture.QuestionnaireFragment: could not find Fragment constructor

We need to implement mapping of Search Parameters to the underlying data type of the property. Currently, we are assuming the accessors are named getXXElement for date and getXX for all other SearchParamDefinition types. For example Patient.birthDate has getBirthDateElement(). However, this is not universally true in HAPI FHIR. E.g. Observation.effective does not have a getEffectiveElement method.

we need some tool to generate the API files so that if API changes, we can track what has changed.

We use metalava in AndroidX but it is probably useless by itself. I can check what is used in dropbox/store and just copy that one probably.

#33 (comment)

what title says, lets replace the custom cursor implementation w/ room.

Currently testing how the datacapture lib behaves when items in the sample questionnaire are duplicated. When the questionnaire view goes over one screen the submit but does not appear.

Refer to video in issue #132

robolectric runs tests on main thread which becomes a problem w/ room.

The official recommendation for Room is to actually test on a device since different SQLite versions on devices have different issues and we probably need to support really old devices.

Until then, we'll need to allow main thread queries in room. If we decide to keep it, we should at least make it a test only option.

Clarify the steps to take for loading patient list while starting from scratch or deleting local database.

In recent github action runs for PRs, tests for API 29 consistently failed due to out of memory issue. e.g:

com.google.fhirengine.db.impl.DatabaseImplTest > select_invalidResourceType_shouldThrowIllegalArgumentException[test(AVD) - 10] FAILED
java.lang.OutOfMemoryError: OutOfMemoryError thrown while trying to throw an exception; no stack trace available

See trace: https://github.com/google/android-fhir/runs/824594488

Note this doesn't happen for API 24 or 27, nor does this happen locally.

we have some entities (StringIndex, ReferenceIndex) that seem to have the same structure that is driven from a generic structure in FHIR engine.
it might make sense to merge them into one so that wen can add any type of index easily.

I'm not fully sure why it is this way right now so just keeping this issue as a note. we may or may not want to do this.

When you try to launch MainActivity on master branch.

2020-07-28 12:30:33.190 8863-8863/com.google.fhirengine.example E/AndroidRuntime: FATAL EXCEPTION: main
Process: com.google.fhirengine.example, PID: 8863
java.lang.NoSuchMethodError: No static method create(Lcom/google/fhirengine/db/Database;)Lcom/google/fhirengine/cql/FhirEngineDataProvider; in class Lcom/google/fhirengine/cql/FhirEngineDataProvider$Factory; or its super classes (declaration of 'com.google.fhirengine.cql.FhirEngineDataProvider$Factory' appears in /data/app/com.google.fhirengine.example-uoheiqp6VCcDKfyR9_GnEg==/base.apk!classes6.dex)
at com.google.fhirengine.FhirServices$Builder.build(FhirServices.kt:63)
at com.google.fhirengine.FhirEngineBuilder.build(FhirEngineBuilder.kt:50)
at com.google.fhirengine.example.FhirApplication.constructFhirEngine(FhirApplication.kt:46)
at com.google.fhirengine.example.FhirApplication.access$constructFhirEngine(FhirApplication.kt:33)
at com.google.fhirengine.example.FhirApplication$fhirEngine$2.invoke(FhirApplication.kt:36)
at com.google.fhirengine.example.FhirApplication$fhirEngine$2.invoke(FhirApplication.kt:33)
at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74)
at com.google.fhirengine.example.FhirApplication.getFhirEngine(Unknown Source:2)
at com.google.fhirengine.example.FhirApplication.access$getFhirEngine$p(FhirApplication.kt:33)
at com.google.fhirengine.example.FhirApplication$Companion.fhirEngine(FhirApplication.kt:52)
at com.google.fhirengine.example.FhirApplication.fhirEngine(Unknown Source:2)
at com.google.fhirengine.example.MainActivity.onCreate(MainActivity.java:62)
at android.app.Activity.performCreate(Activity.java:7802)
at android.app.Activity.performCreate(Activity.java:7791)
at android.app.Instrumentation.callActivityOnCreate(Instrumentation.java:1299)
at android.app.ActivityThread.performLaunchActivity(ActivityThread.java:3245)
at android.app.ActivityThread.handleLaunchActivity(ActivityThread.java:3409)
at android.app.servertransaction.LaunchActivityItem.execute(LaunchActivityItem.java:83)
at android.app.servertransaction.TransactionExecutor.executeCallbacks(TransactionExecutor.java:135)
at android.app.servertransaction.TransactionExecutor.execute(TransactionExecutor.java:95)
at android.app.ActivityThread$H.handleMessage(ActivityThread.java:2016)
at android.os.Handler.dispatchMessage(Handler.java:107)
at android.os.Looper.loop(Looper.java:214)
at android.app.ActivityThread.main(ActivityThread.java:7356)
at java.lang.reflect.Method.invoke(Native Method)
at com.android.internal.os.RuntimeInit$MethodAndArgsCaller.run(RuntimeInit.java:492)
at com.android.internal.os.ZygoteInit.main(ZygoteInit.java:930)

Add lockscreen requirements in the SDK
https://developer.android.com/reference/android/app/KeyguardManager#isDeviceSecure()

Please note that this API is available from API level 23, and the SDK's min API level is 21. We can probably fall back to https://developer.android.com/reference/android/app/KeyguardManager#isKeyguardSecure() for API<23.

https://developer.android.com/training/articles/security-config

This tasks is not top priority and would probably be the best if those who are not super familiar with Kotlin can contribute. Simply state what you're working on and send a PR and link it to this issue. Thanks all!

One use case is:
To populate local db with sample Fhir objects for the Sample App to work in case hardcoded sync doesn't get back any objects from the external Hapi server.

We index search parameters in FhirIndexerImpl.kt by type. We extract the object instances by splitting the path in the SearchParamDefinition and walking the Resource members depth-first. With splitting the path by dot notation, e.g. Observation.code.value we are missing out on Search params which do not conform to this pattern. E.g. SP_PHONE in Patient is Patient.telecom.where(system='phone').

We should try out the HAPI FHIR splitting logic:

@Override
	public String[] split(String thePaths) {
		if (getContext().getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
			if (!thePaths.contains("|")) {
				return new String[]{thePaths};
			}
			return SPLIT_R4.split(thePaths);
		} else {
			if (!thePaths.contains("|") && !thePaths.contains(" or ")) {
				return new String[]{thePaths};
			}
			return SPLIT.split(thePaths);
		}
	}

https://developer.android.com/training/articles/security-key-attestation#certificate_schema_verifiedbootstate

Only proceed with the operation if the VerifiedBootStatus is

• Verified

Will not proceed if the VerifiedBootStatus is

• SelfSigned
• Unverified, or
• Failed

Since resourceID + resourceType are 1:1 with SQLite ID, it can be used as foreign key instead. This will save space in index tables.

ktlintApplyToIdea updates the .idea config to have the same code style as we use in presubmit checks. In this issue we should do 2 things:

1. get the ktlintApplyToIdea command to work locally
2. add the step to the README file

Use androidx.lifecycle.observe instead of java observe.

to avoid race condition between different processes

• Show search results for Observations referred by a given Patient
• When no objects available from sync, import json bundle as local Fhir resources [Removed]
• Use the sync button in the toolbar to actually sync results from external Fhir Resources
• Remove dependence on CqlLoader for firing the sync.
• Remove SamplePatients.kt if it's no longer needed.