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LaunchContext for initialExpression (#2025)
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* Use launchContext for initialExpression

* Test ResourceMapper

* Fix test

* Fix launchContexts for demo app when editing patient

* spotlessApply

* WIP

* Revert "WIP"

This reverts commit d2d53a2.

* spotlessApply

* Fix test

* Refactor validateLaunchContextExtension

* Remove QuestionnaireLaunchContextSet enum class

* Rename vars and functions

* Add code comment for MoreResourceTypes.kt

* Unit testing

* Fix post-merge-conflict

* spotlessApply

* Address review

* spotlessApply

* Revert un-intended changes

* Fix failing checks

* Remove check of must contain 2 sub-extensions

* Update Kdoc

* Revert

* validate launch context when using populate public API
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@FikriMilano
FikriMilano authored Oct 13, 2023
1 parent 633b482 commit caf4c14
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Showing 10 changed files with 433 additions and 234 deletions.
4 changes: 2 additions & 2 deletions catalog/src/main/java/com/google/android/fhir/catalog/DemoQuestionnaireFragment.kt
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Expand Up @@ -168,11 +168,11 @@ class DemoQuestionnaireFragment : Fragment() {
R.id.container,
QuestionnaireFragment.builder()
.setQuestionnaire(questionnaireJsonString)
.setQuestionnaireLaunchContexts(
.setQuestionnaireLaunchContextMap(
FhirContext.forR4Cached()
.newJsonParser()
.encodeResourceToString(Patient().apply { id = "P1" })
.let { listOf(it) },
.let { mapOf("patient" to it) },
)
.build(),
QUESTIONNAIRE_FRAGMENT_TAG,
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13 changes: 7 additions & 6 deletions datacapture/src/main/java/com/google/android/fhir/datacapture/QuestionnaireFragment.kt
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Expand Up @@ -352,10 +352,10 @@ class QuestionnaireFragment : Fragment() {
* user, etc. is "in context" at the time the questionnaire response is being completed:
* https://build.fhir.org/ig/HL7/sdc/StructureDefinition-sdc-questionnaire-launchContext.html
*
* @param launchContexts list of serialized resources
* @param launchContextMap map of launchContext name and serialized resources
*/
fun setQuestionnaireLaunchContexts(launchContexts: List<String>) = apply {
args.add(EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_JSON_STRINGS to launchContexts)
fun setQuestionnaireLaunchContextMap(launchContextMap: Map<String, String>) = apply {
args.add(EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_MAP to launchContextMap)
}

/**
Expand Down Expand Up @@ -454,9 +454,10 @@ class QuestionnaireFragment : Fragment() {
*/
internal const val EXTRA_QUESTIONNAIRE_RESPONSE_JSON_STRING = "questionnaire-response"

/** A list of JSON encoded strings extra for each questionnaire context. */
internal const val EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_JSON_STRINGS =
"questionnaire-launch-contexts"
/**
* A map of launchContext name and JSON encoded strings extra for each questionnaire context.
*/
internal const val EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_MAP = "questionnaire-launch-contexts"

/**
* A [URI][android.net.Uri] extra for streaming a JSON encoded questionnaire response.
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12 changes: 7 additions & 5 deletions datacapture/src/main/java/com/google/android/fhir/datacapture/QuestionnaireViewModel.kt
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Expand Up @@ -33,6 +33,7 @@ import com.google.android.fhir.datacapture.extensions.allItems
import com.google.android.fhir.datacapture.extensions.cqfExpression
import com.google.android.fhir.datacapture.extensions.createQuestionnaireResponseItem
import com.google.android.fhir.datacapture.extensions.entryMode
import com.google.android.fhir.datacapture.extensions.filterByCodeInNameExtension
import com.google.android.fhir.datacapture.extensions.flattened
import com.google.android.fhir.datacapture.extensions.hasDifferentAnswerSet
import com.google.android.fhir.datacapture.extensions.isDisplayItem
Expand Down Expand Up @@ -166,15 +167,16 @@ internal class QuestionnaireViewModel(application: Application, state: SavedStat

init {
questionnaireLaunchContextMap =
if (state.contains(QuestionnaireFragment.EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_JSON_STRINGS)) {
if (state.contains(QuestionnaireFragment.EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_MAP)) {

val launchContextJsonStrings: List<String> =
state[QuestionnaireFragment.EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_JSON_STRINGS]!!
val launchContextMapString: Map<String, String> =
state[QuestionnaireFragment.EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_MAP]!!

val launchContexts = launchContextJsonStrings.map { parser.parseResource(it) as Resource }
val launchContextMapResource =
launchContextMapString.mapValues { parser.parseResource(it.value) as Resource }
questionnaire.questionnaireLaunchContexts?.let { launchContextExtensions ->
validateLaunchContextExtensions(launchContextExtensions)
launchContexts.associateBy { it.resourceType.name.lowercase() }
filterByCodeInNameExtension(launchContextMapResource, launchContextExtensions)
}
} else {
null
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88 changes: 36 additions & 52 deletions ...apture/src/main/java/com/google/android/fhir/datacapture/extensions/MoreQuestionnaires.kt
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Expand Up @@ -16,12 +16,15 @@

package com.google.android.fhir.datacapture.extensions

import org.hl7.fhir.exceptions.FHIRException
import org.hl7.fhir.r4.model.CanonicalType
import org.hl7.fhir.r4.model.CodeType
import org.hl7.fhir.r4.model.Coding
import org.hl7.fhir.r4.model.Expression
import org.hl7.fhir.r4.model.Extension
import org.hl7.fhir.r4.model.Questionnaire
import org.hl7.fhir.r4.model.Resource
import org.hl7.fhir.r4.model.ResourceType

/**
* The StructureMap url in the
Expand Down Expand Up @@ -64,73 +67,54 @@ internal fun Questionnaire.findVariableExpression(variableName: String): Express
*/
internal fun validateLaunchContextExtensions(launchContextExtensions: List<Extension>) =
launchContextExtensions.forEach { launchExtension ->
validateLaunchContextExtension(
Extension().apply {
addExtension(launchExtension.extension.firstOrNull { it.url == "name" })
addExtension(launchExtension.extension.firstOrNull { it.url == "type" })
},
)
validateLaunchContextExtension(launchExtension)
}

/**
* Checks that the extension:name extension exists and its value contains a valid code from
* [QuestionnaireLaunchContextSet]
* Verifies the existence of extension:name and extension:type with valid name system and type
* values.
*/
private fun validateLaunchContextExtension(launchExtension: Extension) {
check(launchExtension.extension.size == 2) {
"The extension:name or extension:type extension is missing in $EXTENSION_SDC_QUESTIONNAIRE_LAUNCH_CONTEXT"
}
val nameCoding =
launchExtension.getExtensionByUrl("name")?.value as? Coding
?: error(
"The extension:name is missing or is not of type Coding in $EXTENSION_SDC_QUESTIONNAIRE_LAUNCH_CONTEXT",
)

val isValidExtension =
QuestionnaireLaunchContextSet.values().any {
launchExtension.equalsDeep(
Extension().apply {
addExtension(
Extension().apply {
url = "name"
setValue(
Coding().apply {
code = it.code
display = it.display
system = it.system
},
)
},
)
addExtension(
Extension().apply {
url = "type"
setValue(CodeType().setValue(it.resourceType))
},
)
},
val typeCodeType =
launchExtension.getExtensionByUrl("type")?.value as? CodeType
?: error(
"The extension:type is missing or is not of type CodeType in $EXTENSION_SDC_QUESTIONNAIRE_LAUNCH_CONTEXT",
)

val isValidResourceType =
try {
ResourceType.fromCode(typeCodeType.value) != null
} catch (exception: FHIRException) {
false
}
if (!isValidExtension) {

if (nameCoding.system != EXTENSION_LAUNCH_CONTEXT || !isValidResourceType) {
error(
"The extension:name extension and/or extension:type extension do not follow the format " +
"specified in $EXTENSION_SDC_QUESTIONNAIRE_LAUNCH_CONTEXT",
"The extension:name and/or extension:type do not follow the format specified in $EXTENSION_SDC_QUESTIONNAIRE_LAUNCH_CONTEXT",
)
}
}

/**
* The set of supported launch contexts, as per: http://hl7.org/fhir/uv/sdc/ValueSet/launchContext
* Filters the provided launch contexts by matching the keys with the `code` values found in the
* "name" extensions.
*/
private enum class QuestionnaireLaunchContextSet(
val code: String,
val display: String,
val system: String,
val resourceType: String,
) {
PATIENT("patient", "Patient", EXTENSION_LAUNCH_CONTEXT, "Patient"),
ENCOUNTER("encounter", "Encounter", EXTENSION_LAUNCH_CONTEXT, "Encounter"),
LOCATION("location", "Location", EXTENSION_LAUNCH_CONTEXT, "Location"),
USER_AS_PATIENT("user", "User", EXTENSION_LAUNCH_CONTEXT, "Patient"),
USER_AS_PRACTITIONER("user", "User", EXTENSION_LAUNCH_CONTEXT, "Practitioner"),
USER_AS_PRACTITIONER_ROLE("user", "User", EXTENSION_LAUNCH_CONTEXT, "PractitionerRole"),
USER_AS_RELATED_PERSON("user", "User", EXTENSION_LAUNCH_CONTEXT, "RelatedPerson"),
STUDY("study", "ResearchStudy", EXTENSION_LAUNCH_CONTEXT, "ResearchStudy"),
internal fun filterByCodeInNameExtension(
launchContexts: Map<String, Resource>,
launchContextExtensions: List<Extension>,
): Map<String, Resource> {
val nameCodes =
launchContextExtensions
.mapNotNull { extension -> (extension.getExtensionByUrl("name").value as? Coding)?.code }
.toSet()

return launchContexts.filterKeys { nameCodes.contains(it) }
}

/**
Expand Down
47 changes: 17 additions & 30 deletions datacapture/src/main/java/com/google/android/fhir/datacapture/mapping/ResourceMapper.kt
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Expand Up @@ -18,13 +18,16 @@ package com.google.android.fhir.datacapture.mapping

import com.google.android.fhir.datacapture.DataCapture
import com.google.android.fhir.datacapture.extensions.createQuestionnaireResponseItem
import com.google.android.fhir.datacapture.extensions.filterByCodeInNameExtension
import com.google.android.fhir.datacapture.extensions.initialExpression
import com.google.android.fhir.datacapture.extensions.logicalId
import com.google.android.fhir.datacapture.extensions.questionnaireLaunchContexts
import com.google.android.fhir.datacapture.extensions.targetStructureMap
import com.google.android.fhir.datacapture.extensions.toCodeType
import com.google.android.fhir.datacapture.extensions.toCoding
import com.google.android.fhir.datacapture.extensions.toIdType
import com.google.android.fhir.datacapture.extensions.toUriType
import com.google.android.fhir.datacapture.extensions.validateLaunchContextExtensions
import com.google.android.fhir.datacapture.fhirpath.fhirPathEngine
import java.lang.reflect.Field
import java.lang.reflect.Method
Expand Down Expand Up @@ -214,41 +217,42 @@ object ResourceMapper {
* Performs
* [Expression-based population](http://build.fhir.org/ig/HL7/sdc/populate.html#expression-based-population)
* and returns a [QuestionnaireResponse] for the [questionnaire] that is populated from the
* [resources].
* [launchContexts].
*/
suspend fun populate(
questionnaire: Questionnaire,
vararg resources: Resource,
launchContexts: Map<String, Resource>,
): QuestionnaireResponse {
populateInitialValues(questionnaire.item, *resources)
validateLaunchContextExtensions(questionnaire.questionnaireLaunchContexts ?: listOf())
val filteredLaunchContexts =
filterByCodeInNameExtension(
launchContexts,
questionnaire.questionnaireLaunchContexts ?: listOf(),
)
populateInitialValues(questionnaire.item, filteredLaunchContexts)
return QuestionnaireResponse().apply {
item = questionnaire.item.map { it.createQuestionnaireResponseItem() }
}
}

private suspend fun populateInitialValues(
questionnaireItems: List<Questionnaire.QuestionnaireItemComponent>,
vararg resources: Resource,
launchContexts: Map<String, Resource>,
) {
questionnaireItems.forEach { populateInitialValue(it, *resources) }
questionnaireItems.forEach { populateInitialValue(it, launchContexts) }
}

private suspend fun populateInitialValue(
questionnaireItem: Questionnaire.QuestionnaireItemComponent,
vararg resources: Resource,
launchContexts: Map<String, Resource>,
) {
check(questionnaireItem.initial.isEmpty() || questionnaireItem.initialExpression == null) {
"QuestionnaireItem item is not allowed to have both initial.value and initial expression. See rule at http://build.fhir.org/ig/HL7/sdc/expressions.html#initialExpression."
}

questionnaireItem.initialExpression
?.let {
fhirPathEngine
.evaluate(
selectPopulationContext(resources.asList(), it),
it.expression.removePrefix("%"),
)
.singleOrNull()
fhirPathEngine.evaluate(launchContexts, null, null, null, it.expression).firstOrNull()
}
?.let {
// Set initial value for the questionnaire item. Questionnaire items should not have both
Expand All @@ -258,24 +262,7 @@ object ResourceMapper {
mutableListOf(Questionnaire.QuestionnaireItemInitialComponent().setValue(value))
}

populateInitialValues(questionnaireItem.item, *resources)
}

/**
* Returns the population context for the questionnaire/group.
*
* The resource of the same type as the expected type of the initial expression will be selected
* first. Otherwise, the first resource in the list will be selected.
*
* TODO: rewrite this using the launch context and population context.
*/
private fun selectPopulationContext(
resources: List<Resource>,
initialExpression: Expression,
): Resource? {
val resourceType = initialExpression.expression.substringBefore(".").removePrefix("%")
return resources.singleOrNull { it.resourceType.name.lowercase() == resourceType.lowercase() }
?: resources.firstOrNull()
populateInitialValues(questionnaireItem.item, launchContexts)
}

/**
Expand Down
6 changes: 3 additions & 3 deletions datacapture/src/test/java/com/google/android/fhir/datacapture/QuestionnaireViewModelTest.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ import ca.uhn.fhir.context.FhirContext
import ca.uhn.fhir.parser.IParser
import com.google.android.fhir.datacapture.QuestionnaireFragment.Companion.EXTRA_ENABLE_REVIEW_PAGE
import com.google.android.fhir.datacapture.QuestionnaireFragment.Companion.EXTRA_QUESTIONNAIRE_JSON_STRING
import com.google.android.fhir.datacapture.QuestionnaireFragment.Companion.EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_JSON_STRINGS
import com.google.android.fhir.datacapture.QuestionnaireFragment.Companion.EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_MAP
import com.google.android.fhir.datacapture.QuestionnaireFragment.Companion.EXTRA_QUESTIONNAIRE_RESPONSE_JSON_STRING
import com.google.android.fhir.datacapture.QuestionnaireFragment.Companion.EXTRA_READ_ONLY
import com.google.android.fhir.datacapture.QuestionnaireFragment.Companion.EXTRA_SHOW_CANCEL_BUTTON
Expand Down Expand Up @@ -4410,8 +4410,8 @@ class QuestionnaireViewModelTest {
}
state.set(EXTRA_QUESTIONNAIRE_JSON_STRING, printer.encodeResourceToString(questionnaire))
state.set(
EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_JSON_STRINGS,
listOf(printer.encodeResourceToString(patient)),
EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_MAP,
mapOf("patient" to printer.encodeResourceToString(patient)),
)

val viewModel = QuestionnaireViewModel(context, state)
Expand Down
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