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Merge branch 'main' into security-automation-additions-latest-main
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@Rkareko
Rkareko authored Aug 9, 2023
2 parents a399ae6 + 09446b7 commit df74831
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Showing 15 changed files with 372 additions and 173 deletions.
147 changes: 92 additions & 55 deletions ...ne/src/main/java/org/smartregister/fhircore/engine/configuration/ConfigurationRegistry.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,6 @@ import okhttp3.RequestBody.Companion.toRequestBody
import org.hl7.fhir.r4.model.Base
import org.hl7.fhir.r4.model.Binary
import org.hl7.fhir.r4.model.Bundle
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent
import org.hl7.fhir.r4.model.Composition
import org.hl7.fhir.r4.model.ListResource
import org.hl7.fhir.r4.model.Resource
Expand Down Expand Up @@ -83,7 +82,7 @@ constructor(
val configCacheMap = mutableMapOf<String, Configuration>()
val localizationHelper: LocalizationHelper by lazy { LocalizationHelper(this) }
private val supportedFileExtensions = listOf("json", "properties")
private var isNonProxy_ = BuildConfig.IS_NON_PROXY_APK
private var _isNonProxy = BuildConfig.IS_NON_PROXY_APK

/**
* Retrieve configuration for the provided [ConfigType]. The JSON retrieved from [configsJsonMap]
Expand Down Expand Up @@ -131,7 +130,7 @@ constructor(
locale = Locale.getDefault(),
template = it,
)
.decodeJson<T>()
.decodeJson()
}

/**
Expand Down Expand Up @@ -229,40 +228,44 @@ constructor(
val parsedAppId = appId.substringBefore(TYPE_REFERENCE_DELIMITER).trim()
if (loadFromAssets) {
try {
context.assets
.open(String.format(COMPOSITION_CONFIG_PATH, parsedAppId))
.bufferedReader()
.readText()
.decodeResourceFromString<Composition>()
.run {
val iconConfigs =
retrieveCompositionSections().filter {
it.focus.hasIdentifier() && isIconConfig(it.focus.identifier.value)
}
if (iconConfigs.isNotEmpty()) {
val ids = iconConfigs.joinToString(DEFAULT_STRING_SEPARATOR) { it.focus.extractId() }
fhirResourceDataSource
.getResource(
"${ResourceType.Binary.name}?$ID=$ids&_count=$DEFAULT_COUNT",
)
.entry
.forEach { addOrUpdate(it.resource) }
val localCompositionResource =
context.assets
.open(String.format(COMPOSITION_CONFIG_PATH, parsedAppId))
.bufferedReader()
.readText()
.decodeResourceFromString<Composition>()

addOrUpdate(localCompositionResource)

localCompositionResource.run {
val iconConfigs =
retrieveCompositionSections().filter {
it.focus.hasIdentifier() && isIconConfig(it.focus.identifier.value)
}
populateConfigurationsMap(
composition = this,
loadFromAssets = true,
appId = parsedAppId,
configsLoadedCallback = configsLoadedCallback,
context = context,
)
if (iconConfigs.isNotEmpty()) {
val ids = iconConfigs.joinToString(DEFAULT_STRING_SEPARATOR) { it.focus.extractId() }
fhirResourceDataSource
.getResource(
"${ResourceType.Binary.name}?$ID=$ids&_count=$DEFAULT_COUNT",
)
.entry
.forEach { addOrUpdate(it.resource) }
}
populateConfigurationsMap(
composition = this,
loadFromAssets = true,
appId = parsedAppId,
configsLoadedCallback = configsLoadedCallback,
context = context,
)
}
} catch (fileNotFoundException: FileNotFoundException) {
Timber.e("Missing app configs for app ID: $parsedAppId", fileNotFoundException)
withContext(dispatcherProvider.main()) { configsLoadedCallback(false) }
}
} else {
fhirEngine.searchCompositionByIdentifier(appId)?.run {
populateConfigurationsMap(context, this, false, appId, configsLoadedCallback)
fhirEngine.searchCompositionByIdentifier(parsedAppId)?.run {
populateConfigurationsMap(context, this, false, parsedAppId, configsLoadedCallback)
}
}
}
Expand Down Expand Up @@ -300,8 +303,14 @@ constructor(
val configIdentifier = it.focus.identifier.value
val referenceResourceType = it.focus.reference.substringBefore(TYPE_REFERENCE_DELIMITER)
if (isAppConfig(referenceResourceType) && !isIconConfig(configIdentifier)) {
val configBinary = fhirEngine.get<Binary>(it.focus.extractId())
configsJsonMap[configIdentifier] = configBinary.content.decodeToString()
val extractedId = it.focus.extractId()
try {
val configBinary = fhirEngine.get<Binary>(extractedId)
configsJsonMap[configIdentifier] = configBinary.content.decodeToString()
} catch (resourceNotFoundException: ResourceNotFoundException) {
Timber.e("Missing Binary file with ID :$extractedId")
withContext(dispatcherProvider.main()) { configsLoadedCallback(false) }
}
}
}
}
Expand Down Expand Up @@ -356,13 +365,16 @@ constructor(
*/
@Throws(UnknownHostException::class, HttpException::class)
suspend fun fetchNonWorkflowConfigResources() {
sharedPreferencesHelper.read(SharedPreferenceKey.APP_ID.name, null)?.let { appId: String ->
fhirEngine.searchCompositionByIdentifier(appId)?.let { composition ->
sharedPreferencesHelper.read(SharedPreferenceKey.APP_ID.name, null)?.let { appId ->
val parsedAppId = appId.substringBefore(TYPE_REFERENCE_DELIMITER).trim()
fhirEngine.searchCompositionByIdentifier(parsedAppId)?.let { composition ->
composition
.retrieveCompositionSections()
.groupBy { it.focus.reference?.split(TYPE_REFERENCE_DELIMITER)?.firstOrNull() ?: "" }
.filter {
it.key in
.groupBy { section ->
section.focus.reference?.split(TYPE_REFERENCE_DELIMITER)?.firstOrNull() ?: ""
}
.filter { entry ->
entry.key in
listOf(
ResourceType.Questionnaire.name,
ResourceType.StructureMap.name,
Expand Down Expand Up @@ -435,22 +447,25 @@ constructor(
resourceIdList: List<String>,
): Bundle {
val resultBundle =
fhirResourceDataSource.post(
"",
generateRequestBundle(resourceType, resourceIdList)
.encodeResourceToString()
.toRequestBody(NetworkModule.JSON_MEDIA_TYPE),
)
if (isNonProxy()) {
fhirResourceDataSourceGetBundle(resourceType, resourceIdList)
} else
fhirResourceDataSource.post(
requestBody =
generateRequestBundle(resourceType, resourceIdList)
.encodeResourceToString()
.toRequestBody(NetworkModule.JSON_MEDIA_TYPE),
)
resultBundle.entry?.forEach { bundleEntryComponent ->
when (bundleEntryComponent.resource) {
is Bundle -> {
val bundle = bundleEntryComponent.resource as Bundle
bundle.entry.forEach { entryComponent ->
when (entryComponent.resource) {
is Bundle -> {
val bundle = entryComponent.resource as Bundle
addOrUpdate(bundle)
bundle.entry.forEach { innerEntryComponent ->
val thisBundle = entryComponent.resource as Bundle
addOrUpdate(thisBundle)
thisBundle.entry.forEach { innerEntryComponent ->
saveListEntryResource(innerEntryComponent)
}
}
Expand Down Expand Up @@ -489,9 +504,9 @@ constructor(
bundle.entry.forEach { entryComponent ->
when (entryComponent.resource) {
is Bundle -> {
val bundle = entryComponent.resource as Bundle
addOrUpdate(bundle)
bundle.entry.forEach { innerEntryComponent ->
val thisBundle = entryComponent.resource as Bundle
addOrUpdate(thisBundle)
thisBundle.entry.forEach { innerEntryComponent ->
saveListEntryResource(innerEntryComponent)
}
}
Expand All @@ -509,7 +524,7 @@ constructor(
}
}

private suspend fun saveListEntryResource(entryComponent: BundleEntryComponent) {
private suspend fun saveListEntryResource(entryComponent: Bundle.BundleEntryComponent) {
addOrUpdate(entryComponent.resource)
Timber.d(
"Fetched and processed List reference ${entryComponent.resource.resourceType}/${entryComponent.resource.id}",
Expand All @@ -521,7 +536,6 @@ constructor(
* resource, or create it if not found.
*/
suspend fun <R : Resource> addOrUpdate(resource: R) {
if (resource == null) return
withContext(dispatcherProvider.io()) {
resource.updateLastUpdated()
try {
Expand Down Expand Up @@ -551,19 +565,19 @@ constructor(
}
}

@VisibleForTesting fun isNonProxy(): Boolean = isNonProxy_
@VisibleForTesting fun isNonProxy(): Boolean = _isNonProxy

@VisibleForTesting
fun setNonProxy(nonProxy: Boolean) {
isNonProxy_ = nonProxy
_isNonProxy = nonProxy
}

private fun generateRequestBundle(resourceType: String, idList: List<String>): Bundle {
val bundleEntryComponents = mutableListOf<BundleEntryComponent>()
val bundleEntryComponents = mutableListOf<Bundle.BundleEntryComponent>()

idList.forEach {
bundleEntryComponents.add(
BundleEntryComponent().apply {
Bundle.BundleEntryComponent().apply {
request =
Bundle.BundleEntryRequestComponent().apply {
url = "$resourceType/$it"
Expand All @@ -579,6 +593,29 @@ constructor(
}
}

private suspend fun fhirResourceDataSourceGetBundle(
resourceType: String,
resourceIds: List<String>,
): Bundle {
val bundleEntryComponents = mutableListOf<Bundle.BundleEntryComponent>()

resourceIds.forEach {
val responseBundle =
fhirResourceDataSource.getResource("$resourceType?${Composition.SP_RES_ID}=$it")
responseBundle?.let {
bundleEntryComponents.add(
Bundle.BundleEntryComponent().apply {
resource = responseBundle.entry?.first()?.resource
},
)
}
}
return Bundle().apply {
type = Bundle.BundleType.COLLECTION
entry = bundleEntryComponents
}
}

companion object {
const val BASE_CONFIG_PATH = "configs/%s"
const val COMPOSITION_CONFIG_PATH = "configs/%s/composition_config.json"
Expand Down
2 changes: 1 addition & 1 deletion ...ava/org/smartregister/fhircore/engine/data/remote/fhir/resource/FhirResourceDataSource.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ class FhirResourceDataSource @Inject constructor(private val resourceService: Fh
return resourceService.getResource(path)
}

suspend fun post(path: String, requestBody: RequestBody): Bundle {
suspend fun post(path: String = "", requestBody: RequestBody): Bundle {
return resourceService.post(path, requestBody)
}

Expand Down
5 changes: 3 additions & 2 deletions android/engine/src/main/java/org/smartregister/fhircore/engine/task/FhirCarePlanGenerator.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ constructor(
val defaultRepository: DefaultRepository,
val fhirTaskUtil: FhirTaskUtil,
) {
val structureMapUtilities by lazy {
private val structureMapUtilities by lazy {
StructureMapUtilities(transformSupportServices.simpleWorkerContext, transformSupportServices)
}

Expand All @@ -84,7 +84,8 @@ constructor(
subject: Resource,
data: Bundle = Bundle(),
): CarePlan? {
return generateOrUpdateCarePlan(fhirEngine.get(planDefinitionId), subject, data)
val planDefinition = defaultRepository.loadResource<PlanDefinition>(planDefinitionId)
return planDefinition?.let { generateOrUpdateCarePlan(it, subject, data) }
}

suspend fun generateOrUpdateCarePlan(
Expand Down
2 changes: 1 addition & 1 deletion android/engine/src/main/res/values/strings.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@
<string name="replace_photo">Replace photo</string>
<string name="take_photo">Take photo</string>
<string name="edit">Edit</string>
<string name="application_not_supported">Application %1$s not found</string>
<string name="application_not_supported">Error loading application %1$s configs</string>
<string name="eCBIS_app_name" translatable="false">eCBIS</string>
<string name="invalid_login_credentials">username or password is invalid</string>
<string name="invalid_form_id">Invalid form ID attached</string>
Expand Down
20 changes: 19 additions & 1 deletion android/engine/src/test/java/org/smartregister/fhircore/engine/app/fakes/Faker.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,14 @@ package org.smartregister.fhircore.engine.app.fakes

import androidx.test.platform.app.InstrumentationRegistry
import io.mockk.coEvery
import io.mockk.just
import io.mockk.mockk
import io.mockk.runs
import io.mockk.spyk
import java.util.Calendar
import java.util.Date
import kotlinx.coroutines.runBlocking
import kotlinx.coroutines.test.UnconfinedTestDispatcher
import kotlinx.serialization.json.Json
import org.hl7.fhir.r4.model.Bundle
import org.hl7.fhir.r4.model.CarePlan
Expand All @@ -49,9 +52,22 @@ object Faker {
useAlternativeNames = true
}

private val testDispatcher = UnconfinedTestDispatcher()

val testDispatcherProvider =
object : DispatcherProvider {
override fun default() = testDispatcher

override fun io() = testDispatcher

override fun main() = testDispatcher

override fun unconfined() = testDispatcher
}

fun buildTestConfigurationRegistry(
sharedPreferencesHelper: SharedPreferencesHelper = mockk(),
dispatcherProvider: DispatcherProvider = mockk(),
dispatcherProvider: DispatcherProvider = testDispatcherProvider,
): ConfigurationRegistry {
val fhirResourceService = mockk<FhirResourceService>()
val fhirResourceDataSource = spyk(FhirResourceDataSource(fhirResourceService))
Expand Down Expand Up @@ -83,6 +99,8 @@ object Faker {
),
)

coEvery { configurationRegistry.addOrUpdate(any()) } just runs

runBlocking {
configurationRegistry.loadConfigurations(
appId = APP_DEBUG,
Expand Down
14 changes: 6 additions & 8 deletions ...rc/test/java/org/smartregister/fhircore/engine/configuration/ConfigurationRegistryTest.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,6 @@ import io.mockk.just
import io.mockk.mockk
import io.mockk.runs
import io.mockk.spyk
import javax.inject.Inject
import kotlinx.coroutines.test.runTest
import okhttp3.RequestBody
import org.hl7.fhir.r4.model.Binary
Expand Down Expand Up @@ -75,19 +74,17 @@ class ConfigurationRegistryTest : RobolectricTest() {
@kotlinx.coroutines.ExperimentalCoroutinesApi
@get:Rule(order = 1)
val coroutineRule = CoroutineTestRule()

@Inject lateinit var configRegistry: ConfigurationRegistry
var fhirEngine: FhirEngine = mockk()
lateinit var context: Context
private lateinit var fhirResourceDataSource: FhirResourceDataSource
private val fhirEngine: FhirEngine = mockk()
private val context: Context = ApplicationProvider.getApplicationContext()
private val fhirResourceService = mockk<FhirResourceService>()
private lateinit var fhirResourceDataSource: FhirResourceDataSource
private lateinit var configRegistry: ConfigurationRegistry

@Before
@kotlinx.coroutines.ExperimentalCoroutinesApi
fun setUp() {
hiltRule.inject()
fhirResourceDataSource = spyk(FhirResourceDataSource(fhirResourceService))
context = ApplicationProvider.getApplicationContext()
val sharedPreferencesHelper =
SharedPreferencesHelper(context, GsonBuilder().setLenient().create())
configRegistry =
Expand All @@ -99,6 +96,7 @@ class ConfigurationRegistryTest : RobolectricTest() {
AppConfigService(context),
Faker.json,
)
configRegistry.setNonProxy(false)
Assert.assertNotNull(configRegistry)
}

Expand Down Expand Up @@ -329,7 +327,7 @@ class ConfigurationRegistryTest : RobolectricTest() {
coEvery {
fhirResourceDataSource.getResource("$resourceKey?_id=$resourceId&_count=200")
} returns bundle
coEvery { fhirResourceDataSource.post(any(), any()) } returns bundle
coEvery { fhirResourceDataSource.getResource(any()) } returns bundle
runTest {
configRegistry.fhirEngine.create(composition)
configRegistry.setNonProxy(true)
Expand Down
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