Merge branch '2639-async-process-for-get-questionnaire-pages' of gith…

…ub.com:opensrp/android-fhir into 2639-async-process-for-get-questionnaire-pages

.devcontainer/devcontainer.json

@@ -18,13 +18,15 @@
     //   "platform": "33",
     //   "build_tools": "33.0.1"
     // }
-  }
+  },
 
   // Use 'forwardPorts' to make a list of ports inside the container available locally.
   // "forwardPorts": [],
 
   // Use 'postCreateCommand' to run commands after the container is created.
-  // "postCreateCommand": "java -version",
+  // See https://github.com/google/android-fhir/issues/2614, which is blocked by
+  // https://github.com/akhildevelops/devcontainer-features/issues/9.
+  "postCreateCommand": "sudo chown -R vscode:vscode /opt/android/"
 
   // Configure tool-specific properties.
   // "customizations": {},

buildSrc/src/main/kotlin/Dependencies.kt

@@ -19,14 +19,6 @@ import org.gradle.api.artifacts.DependencyConstraint
 import org.gradle.kotlin.dsl.exclude
 
 object Dependencies {
-  object Cql {
-    const val evaluator = "org.opencds.cqf.fhir:cqf-fhir-cr:${Versions.Cql.clinicalReasoning}"
-    const val evaluatorFhirJackson =
-      "org.opencds.cqf.fhir:cqf-fhir-jackson:${Versions.Cql.clinicalReasoning}"
-    const val evaluatorFhirUtilities =
-      "org.opencds.cqf.fhir:cqf-fhir-utility:${Versions.Cql.clinicalReasoning}"
-  }
-
   object HapiFhir {
     const val fhirBaseModule = "ca.uhn.hapi.fhir:hapi-fhir-base"
     const val fhirClientModule = "ca.uhn.hapi.fhir:hapi-fhir-client"
@@ -139,11 +131,6 @@ object Dependencies {
   const val xmlUnit = "org.xmlunit:xmlunit-core:${Versions.xmlUnit}"
 
   object Versions {
-
-    object Cql {
-      const val clinicalReasoning = "3.0.0-PRE9-SNAPSHOT"
-    }
-
     const val androidFhirCommon = "0.1.0-alpha05"
     const val androidFhirEngine = "0.1.0-beta05"
     const val androidFhirKnowledge = "0.1.0-alpha03"
@@ -195,16 +182,17 @@ object Dependencies {
   }
 
   fun Configuration.removeIncompatibleDependencies() {
-    exclude(module = "xpp3")
-    exclude(module = "xpp3_min")
-    exclude(module = "xmlpull")
+    exclude(module = "hapi-fhir-caching-caffeine")
     exclude(module = "javax.json")
     exclude(module = "jcl-over-slf4j")
-    exclude(group = "org.apache.httpcomponents")
-    exclude(group = "org.antlr", module = "antlr4")
-    exclude(group = "org.eclipse.persistence", module = "org.eclipse.persistence.moxy")
-    exclude(module = "hapi-fhir-caching-caffeine")
+    exclude(module = "xmlpull")
+    exclude(module = "xpp3")
+    exclude(module = "xpp3_min")
+    exclude(group = "ch.qos.logback", module = "logback-classic")
     exclude(group = "com.github.ben-manes.caffeine", module = "caffeine")
+    exclude(group = "org.eclipse.persistence", module = "org.eclipse.persistence.moxy")
+    exclude(group = "org.antlr", module = "antlr4")
+    exclude(group = "org.apache.httpcomponents")
   }
 
   fun hapiFhirConstraints(): Map<String, DependencyConstraint.() -> Unit> {

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -72,17 +72,24 @@ fun Project.configureLicensee() {
     }
 
     // Jakarta XML Binding API
-    allowDependency("jakarta.xml.bind", "jakarta.xml.bind-api", "2.3.3") {
+    allowDependency("jakarta.xml.bind", "jakarta.xml.bind-api", "4.0.1") {
       because("BSD 3-clause.")
     }
 
     // Jakarta Activation API 2.1 Specification
-    allowDependency("jakarta.activation", "jakarta.activation-api", "1.2.2") {
+    allowDependency("jakarta.activation", "jakarta.activation-api", "2.1.2") {
       because(
         "Licensed under Eclipse Distribution License 1.0. http://www.eclipse.org/org/documents/edl-v10.php",
       )
     }
 
+    // Jakarta Annotation API 2.1 Specification
+    allowDependency("jakarta.annotation", "jakarta.annotation-api", "2.1.1") {
+      because(
+        "Licensed under EPL 2.0",
+      )
+    }
+
     // Javax Annotation API
     allowDependency("javax.annotation", "javax.annotation-api", "1.3.2") {
       because("Dual-licensed under CDDL 1.1 and GPL v2 with classpath exception.")
@@ -108,7 +115,7 @@ fun Project.configureLicensee() {
       because("BSD 3-clause. http://www.antlr.org/license.html")
     }
     // ANTLR 4
-    allowDependency("org.antlr", "antlr4-runtime", "4.10.1") {
+    allowDependency("org.antlr", "antlr4-runtime", "4.13.1") {
       because("BSD 3-clause. http://www.antlr.org/license.html")
     }
 
@@ -195,6 +202,12 @@ fun Project.configureLicensee() {
     allowDependency("com.ibm.icu", "icu4j", "72.1") {
       because("BSD, part MIT and Apache 2.0. https://github.com/unicode-org/icu/blob/main/LICENSE")
     }
+
+    // Logback
+    allowDependency("ch.qos.logback", "logback-classic", "1.4.14") { because("LGPL") }
+
+    // Logback
+    allowDependency("ch.qos.logback", "logback-core", "1.4.14") { because("LGPL") }
   }
 }
 

datacapture/src/main/java/com/google/android/fhir/datacapture/QuestionnaireViewModel.kt

@@ -37,6 +37,7 @@ import com.google.android.fhir.datacapture.extensions.createQuestionnaireRespons
 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.forEachItemPair
 import com.google.android.fhir.datacapture.extensions.hasDifferentAnswerSet
 import com.google.android.fhir.datacapture.extensions.isDisplayItem
 import com.google.android.fhir.datacapture.extensions.isEnableWhenReferencedBy
@@ -626,16 +627,13 @@ internal class QuestionnaireViewModel(application: Application, state: SavedStat
   /** Travers all [calculatedExpression] within a [Questionnaire] and evaluate them. */
   private suspend fun initializeCalculatedExpressions() {
     expressionEvaluator.detectExpressionCyclicDependency(questionnaire.item)
-    val itemsToBeCalculated =
-      questionnaire.item.flattened().filter { qItem -> qItem.calculatedExpression != null }
-    itemsToBeCalculated.forEach { qItem ->
-      // TODO: Traverse the two trees in parallel and match based on the pairs, the current
-      // implementation does not work well with nested items and repeated groups
-      // https://github.com/google/android-fhir/issues/2618
-      val qrItem =
-        questionnaireResponse.allItems.find { qrItem -> qrItem.linkId == qItem.linkId }
-          ?: return@forEach
-      updateAnswerWithCalculatedExpression(qItem, qrItem)
+    questionnaire.forEachItemPair(questionnaireResponse) {
+      questionnaireItem,
+      questionnaireResponseItem,
+      ->
+      if (questionnaireItem.calculatedExpression != null) {
+        updateAnswerWithCalculatedExpression(questionnaireItem, questionnaireResponseItem)
+      }
     }
   }
 

datacapture/src/main/java/com/google/android/fhir/datacapture/extensions/MoreQuestionnaires.kt

@@ -23,6 +23,9 @@ 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.Questionnaire.QuestionnaireItemComponent
+import org.hl7.fhir.r4.model.QuestionnaireResponse
+import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemComponent
 import org.hl7.fhir.r4.model.Resource
 import org.hl7.fhir.r4.model.ResourceType
 
@@ -160,6 +163,68 @@ enum class EntryMode(val value: String) {
   ;
 
   companion object {
-    fun from(type: String?): EntryMode? = values().find { it.value == type }
+    fun from(type: String?): EntryMode? = entries.find { it.value == type }
+  }
+}
+
+/**
+ * Applies `forEach` on each questionnaire item and questionnaire response item pair in the
+ * questionnaire and the given `questionnaireResponse`.
+ *
+ * Questionnaire items and questionnaire response items are visited in pre-order.
+ *
+ * Items nested under repeated groups and repeated questions will be repeated for each repeated
+ * group instance or answer provided by the user.
+ *
+ * Note: use this function only with a questionnaire response that has been packed using
+ * [QuestionnaireResponse.packRepeatedGroups].
+ */
+internal suspend fun Questionnaire.forEachItemPair(
+  questionnaireResponse: QuestionnaireResponse,
+  forEach:
+    suspend (
+      questionnaireItem: QuestionnaireItemComponent,
+      questionnaireResponseItem: QuestionnaireResponseItemComponent,
+    ) -> Unit,
+) {
+  forEachItemPair(item, questionnaireResponse.item, forEach)
+}
+
+private suspend fun forEachItemPair(
+  questionnaireItems: List<QuestionnaireItemComponent>,
+  questionnaireResponseItems: List<QuestionnaireResponseItemComponent>,
+  forEach:
+    suspend (
+      questionnaireItem: QuestionnaireItemComponent,
+      questionnaireResponseItem: QuestionnaireResponseItemComponent,
+    ) -> Unit,
+) {
+  require(questionnaireItems.size == questionnaireResponseItems.size)
+  questionnaireItems.zip(questionnaireResponseItems).forEach {
+    (questionnaireItem, questionnaireResponseItem) ->
+    require(questionnaireItem.linkId == questionnaireResponseItem.linkId)
+
+    // Apply forEach on the current questionnaire item and questionnaire response item
+    forEach(questionnaireItem, questionnaireResponseItem)
+
+    // For non-repeated groups, simply match the child questionnaire items with child questionnaire
+    // response items.
+    if (
+      questionnaireItem.type == Questionnaire.QuestionnaireItemType.GROUP &&
+        !questionnaireItem.repeats &&
+        questionnaireItem.item.isNotEmpty()
+    ) {
+      forEachItemPair(questionnaireItem.item, questionnaireResponseItem.item, forEach)
+    }
+
+    // The following block handles two separate cases:
+    // 1. questionnaire items nested under repeated group are repeated for each instance of the
+    // repeated group, each represented as an answer components in the questionnaire response item.
+    // 2. questionnaire items nested directly under question are repeated for each answer.
+    if (questionnaireItem.repeats && questionnaireItem.item.isNotEmpty()) {
+      questionnaireResponseItem.answer.forEach {
+        forEachItemPair(questionnaireItem.item, it.item, forEach)
+      }
+    }
   }
 }