Merge branch 'master' of github.com:opensrp/android-fhir into master-…

…release

benchmark/build.gradle.kts

@@ -87,6 +87,7 @@ dependencies {
   androidTestImplementation(Dependencies.truth)
 
   androidTestImplementation(project(":engine"))
+  androidTestImplementation(project(":implementationguide"))
   androidTestImplementation(project(":workflow"))
   androidTestImplementation(project(":workflow-testing"))
 }

benchmark/src/androidTest/java/com/google/android/fhir/benchmark/G_CqlEvaluatorBenchmark.kt

@@ -16,18 +16,22 @@
 
 package com.google.android.fhir.benchmark
 
+import android.content.Context
 import androidx.benchmark.junit4.BenchmarkRule
 import androidx.benchmark.junit4.measureRepeated
 import androidx.test.core.app.ApplicationProvider
 import androidx.test.ext.junit.runners.AndroidJUnit4
 import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.context.FhirVersionEnum
 import com.google.android.fhir.FhirEngineProvider
-import com.google.android.fhir.workflow.FhirOperator
+import com.google.android.fhir.implementationguide.IgManager
+import com.google.android.fhir.workflow.FhirOperatorBuilder
 import com.google.common.truth.Truth.assertThat
+import java.io.File
 import java.io.InputStream
 import kotlinx.coroutines.runBlocking
 import org.hl7.fhir.r4.model.Bundle
+import org.hl7.fhir.r4.model.Library
 import org.hl7.fhir.r4.model.Parameters
 import org.junit.Rule
 import org.junit.Test
@@ -48,20 +52,30 @@ class G_CqlEvaluatorBenchmark {
       val fhirOperator = runWithTimingDisabled {
         val fhirContext = FhirContext.forCached(FhirVersionEnum.R4)
         val jsonParser = fhirContext.newJsonParser()
+        val context: Context = ApplicationProvider.getApplicationContext()
 
         val patientImmunizationHistory =
           jsonParser.parseResource(open("/immunity-check/ImmunizationHistory.json")) as Bundle
         val fhirEngine = FhirEngineProvider.getInstance(ApplicationProvider.getApplicationContext())
+        val igManager = IgManager.createInMemory(context)
+        val lib = jsonParser.parseResource(open("/immunity-check/ImmunityCheck.json")) as Library
 
         runBlocking {
           for (entry in patientImmunizationHistory.entry) {
             fhirEngine.create(entry.resource)
           }
+          igManager.install(
+            File(context.filesDir, lib.name).apply {
+              writeText(jsonParser.encodeResourceToString(lib))
+            }
+          )
         }
 
-        val lib = jsonParser.parseResource(open("/immunity-check/ImmunityCheck.json")) as Bundle
-
-        FhirOperator(fhirContext, fhirEngine).also { it.loadLibs(lib) }
+        FhirOperatorBuilder(context)
+          .withFhirContext(fhirContext)
+          .withFhirEngine(fhirEngine)
+          .withIgManager(igManager)
+          .build()
       }
 
       val results =

buildSrc/src/main/kotlin/Dependencies.kt

@@ -155,6 +155,7 @@ object Dependencies {
     const val compiler = "androidx.room:room-compiler:${Versions.Androidx.room}"
     const val ktx = "androidx.room:room-ktx:${Versions.Androidx.room}"
     const val runtime = "androidx.room:room-runtime:${Versions.Androidx.room}"
+    const val testing = "androidx.room:room-testing:${Versions.Androidx.room}"
   }
 
   object Mlkit {
@@ -280,7 +281,7 @@ object Dependencies {
     const val slf4j = "1.7.36"
     const val sqlcipher = "4.5.0"
     const val timber = "5.0.1"
-    const val truth = "1.0.1"
+    const val truth = "1.1.3"
     const val woodstox = "6.2.7"
     const val xerces = "2.12.2"
     const val xmlUnit = "2.9.0"
@@ -291,9 +292,9 @@ object Dependencies {
       const val benchmarkJUnit = "1.1.0"
       const val core = "1.4.0"
       const val archCore = "2.1.0"
-      const val extJunit = "1.1.3"
+      const val extJunit = "1.1.5"
       const val rules = "1.4.0"
-      const val runner = "1.4.0"
+      const val runner = "1.5.2"
       const val fragmentVersion = "1.3.6"
     }
 

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -173,4 +173,5 @@ private val nonStandardLicenseUrls =
     // BSD-3
     "http://opensource.org/licenses/BSD-3-Clause",
     "http://www.opensource.org/licenses/bsd-license.php",
+    "https://asm.ow2.io/license.html",
   )

buildSrc/src/main/kotlin/Releases.kt

@@ -50,7 +50,7 @@ object Releases {
 
   object Engine : LibraryArtifact {
     override val artifactId = "engine"
-    override val version = "0.1.0-beta02-preview14-SNAPSHOT"
+    override val version = "0.1.0-beta03"
     override val name = "Android FHIR Engine Library"
   }
 

datacapture/src/main/java/com/google/android/fhir/datacapture/extensions/MoreQuestionnairesResponses.kt → buildSrc/src/main/kotlin/RoomSchemaArgProvider.kt

@@ -14,10 +14,16 @@
  * limitations under the License.
  */
 
-package com.google.android.fhir.datacapture.extensions
+import java.io.File
+import org.gradle.api.tasks.InputDirectory
+import org.gradle.api.tasks.PathSensitive
+import org.gradle.api.tasks.PathSensitivity
+import org.gradle.process.CommandLineArgumentProvider
 
-import org.hl7.fhir.r4.model.QuestionnaireResponse
+// https://developer.android.com/training/data-storage/room/migrating-db-versions#test
+class RoomSchemaArgProvider(
+  @get:InputDirectory @get:PathSensitive(PathSensitivity.RELATIVE) val schemaDir: File
+) : CommandLineArgumentProvider {
 
-/** Pre-order list of all questionnaire response items in the questionnaire. */
-val QuestionnaireResponse.allItems: List<QuestionnaireResponse.QuestionnaireResponseItemComponent>
-  get() = item.flatMap { it.descendant }
+  override fun asArguments() = listOf("-Aroom.schemaLocation=${schemaDir.path}")
+}

datacapture/sampledata/text_questionnaire_decimal.json

@@ -0,0 +1,11 @@
+{
+  "resourceType": "Questionnaire",
+  "status": "active",
+  "item": [
+    {
+      "linkId": "1",
+      "type": "decimal",
+      "text": "Enter a decimal"
+    }
+  ]
+}

datacapture/src/androidTest/java/com/google/android/fhir/datacapture/QuestionnaireUiEspressoTest.kt

@@ -41,8 +41,10 @@ import com.google.android.fhir.datacapture.validation.QuestionnaireResponseValid
 import com.google.android.fhir.datacapture.validation.Valid
 import com.google.android.fhir.datacapture.views.factories.localDate
 import com.google.android.fhir.datacapture.views.factories.localDateTime
+import com.google.android.material.textfield.TextInputEditText
 import com.google.android.material.textfield.TextInputLayout
 import com.google.common.truth.Truth.assertThat
+import java.math.BigDecimal
 import java.time.LocalDate
 import java.time.LocalDateTime
 import java.util.Calendar
@@ -112,6 +114,49 @@ class QuestionnaireUiEspressoTest {
     }
   }
 
+  @Test
+  fun integerTextEdit_typingZeroBeforeAnyIntegerShouldKeepZeroDisplayed() {
+    // Do not skip cursor when typing on the numeric field if the initial value is set to 0
+    // as from an integer comparison, leading zeros do not change how the answer is saved.
+    // e.g whether 000001 or 1 is input, the answer saved will be 1.
+    buildFragmentFromQuestionnaire("/text_questionnaire_integer.json")
+
+    onView(withId(R.id.text_input_edit_text)).perform(typeText("0"))
+    assertThat(getQuestionnaireResponse().item.first().answer.first().valueIntegerType.value)
+      .isEqualTo(0)
+
+    onView(withId(R.id.text_input_edit_text)).perform(typeText("01"))
+    assertThat(getQuestionnaireResponse().item.first().answer.first().valueIntegerType.value)
+      .isEqualTo(1)
+
+    onView(withId(R.id.text_input_edit_text)).check { view, _ ->
+      assertThat((view as TextInputEditText).text.toString()).isEqualTo("001")
+    }
+
+    assertThat(getQuestionnaireResponse().item.first().answer.first().valueIntegerType.value)
+      .isEqualTo(1)
+  }
+
+  @Test
+  fun decimalTextEdit_typingZeroBeforeAnyIntegerShouldKeepZeroDisplayed() {
+    buildFragmentFromQuestionnaire("/text_questionnaire_decimal.json")
+
+    onView(withId(R.id.text_input_edit_text)).perform(typeText("0."))
+    assertThat(getQuestionnaireResponse().item.first().answer.first().valueDecimalType.value)
+      .isEqualTo(BigDecimal.valueOf(0.0))
+
+    onView(withId(R.id.text_input_edit_text)).perform(typeText("01"))
+    assertThat(getQuestionnaireResponse().item.first().answer.first().valueDecimalType.value)
+      .isEqualTo(BigDecimal.valueOf(0.01))
+
+    onView(withId(R.id.text_input_edit_text)).check { view, _ ->
+      assertThat((view as TextInputEditText).text.toString()).isEqualTo("0.01")
+    }
+
+    assertThat(getQuestionnaireResponse().item.first().answer.first().valueDecimalType.value)
+      .isEqualTo(BigDecimal.valueOf(0.01))
+  }
+
   @Test
   fun dateTimePicker_shouldShowErrorForWrongDate() {
     buildFragmentFromQuestionnaire("/component_date_time_picker.json")

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

@@ -303,6 +303,10 @@ class QuestionnaireFragment : Fragment() {
       args.add(EXTRA_QUESTIONNAIRE_RESPONSE_JSON_URI to questionnaireResponseUri)
     }
 
+    fun setQuestionnaireResourceContext(questionnaireResourceContext: String) = apply {
+      args.add(EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_JSON_STRING to questionnaireResourceContext)
+    }
+
     /**
      * An [Boolean] extra to control if the questionnaire is read-only. If review page and read-only
      * are both enabled, read-only will take precedence.
@@ -385,6 +389,9 @@ class QuestionnaireFragment : Fragment() {
      */
     internal const val EXTRA_QUESTIONNAIRE_RESPONSE_JSON_STRING = "questionnaire-response"
 
+    /** A JSON encoded string extra for questionnaire context. */
+    internal const val EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_JSON_STRING =
+      "questionnaire-launch-context"
     /**
      * A [URI][android.net.Uri] extra for streaming a JSON encoded questionnaire response.
      *

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

@@ -26,6 +26,7 @@ import ca.uhn.fhir.context.FhirContext
 import ca.uhn.fhir.context.FhirVersionEnum
 import ca.uhn.fhir.parser.IParser
 import com.google.android.fhir.datacapture.enablement.EnablementEvaluator
+import com.google.android.fhir.datacapture.extensions.EXTENSION_SDC_QUESTIONNAIRE_LAUNCH_CONTEXT
 import com.google.android.fhir.datacapture.extensions.EntryMode
 import com.google.android.fhir.datacapture.extensions.addNestedItemsToAnswer
 import com.google.android.fhir.datacapture.extensions.allItems
@@ -41,7 +42,11 @@ import com.google.android.fhir.datacapture.extensions.isHidden
 import com.google.android.fhir.datacapture.extensions.isPaginated
 import com.google.android.fhir.datacapture.extensions.isXFhirQuery
 import com.google.android.fhir.datacapture.extensions.localizedTextSpanned
+import com.google.android.fhir.datacapture.extensions.packRepeatedGroups
 import com.google.android.fhir.datacapture.extensions.shouldHaveNestedItemsUnderAnswers
+import com.google.android.fhir.datacapture.extensions.unpackRepeatedGroups
+import com.google.android.fhir.datacapture.extensions.validateLaunchContext
+import com.google.android.fhir.datacapture.fhirpath.ExpressionEvaluator
 import com.google.android.fhir.datacapture.fhirpath.ExpressionEvaluator.detectExpressionCyclicDependency
 import com.google.android.fhir.datacapture.fhirpath.ExpressionEvaluator.evaluateCalculatedExpressions
 import com.google.android.fhir.datacapture.fhirpath.fhirPathEngine
@@ -66,6 +71,7 @@ import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemComponent
 import org.hl7.fhir.r4.model.QuestionnaireResponse
 import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemAnswerComponent
 import org.hl7.fhir.r4.model.QuestionnaireResponse.QuestionnaireResponseItemComponent
+import org.hl7.fhir.r4.model.Resource
 import org.hl7.fhir.r4.model.ResourceType
 import org.hl7.fhir.r4.model.ValueSet
 import timber.log.Timber
@@ -143,6 +149,33 @@ internal class QuestionnaireViewModel(application: Application, state: SavedStat
         }
       }
     }
+    questionnaireResponse.packRepeatedGroups()
+  }
+
+  /**
+   * The launch context allows information to be passed into questionnaire based on the context in
+   * which he questionnaire is being evaluated. For example, what patient, what encounter, what
+   * user, etc. is "in context" at the time the questionnaire response is being completed.
+   * Currently, we support at most one launch context.The supported launch contexts are defined in:
+   * https://build.fhir.org/ig/HL7/sdc/StructureDefinition-sdc-questionnaire-launchContext.html
+   */
+  private val questionnaireLaunchContext: Resource?
+
+  init {
+    questionnaireLaunchContext =
+      if (state.contains(QuestionnaireFragment.EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_JSON_STRING)) {
+        val questionnaireLaunchContextJson: String =
+          state[QuestionnaireFragment.EXTRA_QUESTIONNAIRE_LAUNCH_CONTEXT_JSON_STRING]!!
+        questionnaire.extension
+          .firstOrNull { it.url == EXTENSION_SDC_QUESTIONNAIRE_LAUNCH_CONTEXT }
+          ?.let {
+            val resource = parser.parseResource(questionnaireLaunchContextJson) as Resource
+            validateLaunchContext(it, resource.resourceType.name)
+            resource
+          }
+      } else {
+        null
+      }
   }
 
   /** The map from each item in the [Questionnaire] to its parent. */
@@ -305,7 +338,15 @@ internal class QuestionnaireViewModel(application: Application, state: SavedStat
    */
   fun getQuestionnaireResponse(): QuestionnaireResponse {
     return questionnaireResponse.copy().apply {
-      item = getEnabledResponseItems(this@QuestionnaireViewModel.questionnaire.item, item)
+      // Use the view model's questionnaire and questionnaire response for calculating enabled items
+      // because the calculation relies on references to the questionnaire response items.
+      item =
+        getEnabledResponseItems(
+            this@QuestionnaireViewModel.questionnaire.item,
+            questionnaireResponse.item
+          )
+          .map { it.copy() }
+      unpackRepeatedGroups(this@QuestionnaireViewModel.questionnaire)
     }
   }
 
@@ -501,7 +542,10 @@ internal class QuestionnaireViewModel(application: Application, state: SavedStat
         checkNotNull(xFhirQueryResolver) {
           "XFhirQueryResolver cannot be null. Please provide the XFhirQueryResolver via DataCaptureConfig."
         }
-        xFhirQueryResolver!!.resolve(expression.expression)
+
+        val xFhirExpressionString =
+          ExpressionEvaluator.createXFhirQueryFromExpression(expression, questionnaireLaunchContext)
+        xFhirQueryResolver!!.resolve(xFhirExpressionString)
       } else if (expression.isFhirPath) {
         fhirPathEngine.evaluate(questionnaireResponse, expression.expression)
       } else {
@@ -728,60 +772,18 @@ internal class QuestionnaireViewModel(application: Application, state: SavedStat
           questionnaireResponseItem,
         )
       }
-      .flatMap { (questionnaireItem, questionnaireResponseItem) ->
-        val isRepeatedGroup =
-          questionnaireItem.type == Questionnaire.QuestionnaireItemType.GROUP &&
-            questionnaireItem.repeats
-        if (isRepeatedGroup) {
-          createRepeatedGroupResponse(questionnaireItem, questionnaireResponseItem)
-        } else {
-          listOf(
-            questionnaireResponseItem.apply {
-              text = questionnaireItem.localizedTextSpanned?.toString()
-              // Nested group items
-              item = getEnabledResponseItems(questionnaireItem.item, questionnaireResponseItem.item)
-              // Nested question items
-              answer.forEach { it.item = getEnabledResponseItems(questionnaireItem.item, it.item) }
-            }
-          )
+      .map { (questionnaireItem, questionnaireResponseItem) ->
+        questionnaireResponseItem.apply {
+          text = questionnaireItem.localizedTextSpanned?.toString()
+          // Nested group items
+          item = getEnabledResponseItems(questionnaireItem.item, questionnaireResponseItem.item)
+          // Nested question items
+          answer.forEach { it.item = getEnabledResponseItems(questionnaireItem.item, it.item) }
         }
       }
       .toList()
   }
 
-  /**
-   * Repeated groups need some massaging for their returned data-format; each instance of the group
-   * should be flattened out to be its own item in the parent, rather than an answer to the main
-   * item. See discussion:
-   * http://community.fhir.org/t/questionnaire-repeating-groups-what-is-the-correct-format/2276/3
-   *
-   * For example, if the group contains 2 questions, and the user answered the group 3 times, this
-   * function will return a list with 3 responses; each of those responses will have the linkId of
-   * the provided group, and each will contain an item array with 2 items (the answers to the
-   * individual questions within this particular group instance).
-   */
-  private fun createRepeatedGroupResponse(
-    questionnaireItem: QuestionnaireItemComponent,
-    questionnaireResponseItem: QuestionnaireResponseItemComponent,
-  ): List<QuestionnaireResponseItemComponent> {
-    val individualQuestions = questionnaireItem.item
-    return questionnaireResponseItem.answer.map { repeatedGroupInstance ->
-      val responsesToIndividualQuestions = repeatedGroupInstance.item
-      check(responsesToIndividualQuestions.size == individualQuestions.size) {
-        "Repeated groups responses must have the same # of responses as the group has questions"
-      }
-      QuestionnaireResponseItemComponent().apply {
-        linkId = questionnaireItem.linkId
-        text = questionnaireItem.localizedTextSpanned?.toString()
-        item =
-          getEnabledResponseItems(
-            questionnaireItemList = individualQuestions,
-            questionnaireResponseItemList = responsesToIndividualQuestions,
-          )
-      }
-    }
-  }
-
   /**
    * Gets a list of [QuestionnairePage]s for a paginated questionnaire, or `null` if the
    * questionnaire is not paginated.

datacapture/src/main/java/com/google/android/fhir/datacapture/enablement/EnablementEvaluator.kt

@@ -80,6 +80,11 @@ internal class EnablementEvaluator(val questionnaireResponse: QuestionnaireRespo
         questionnaireResponseItemParentMap[child] = item
         buildParentList(child)
       }
+      for (answer in item.answer) {
+        for (nestedItem in answer.item) {
+          buildParentList(nestedItem)
+        }
+      }
     }
 
     for (item in questionnaireResponse.item) {