Merge pull request #222 from google/jt/sdc-extraction

Prototype definition-based extraction

datacapture/src/main/java/com/google/android/fhir/datacapture/mapping/ResourceMapper.kt

@@ -0,0 +1,182 @@
+/*
+ * Copyright 2020 Google LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *       http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package com.google.android.fhir.datacapture.mapping
+
+import com.google.fhir.r4.core.Boolean
+import com.google.fhir.r4.core.Date
+import com.google.fhir.r4.core.DateTime
+import com.google.fhir.r4.core.Decimal
+import com.google.fhir.r4.core.Integer
+import com.google.fhir.r4.core.Questionnaire
+import com.google.fhir.r4.core.QuestionnaireItemTypeCode
+import com.google.fhir.r4.core.QuestionnaireResponse
+import com.google.fhir.r4.core.Time
+import com.google.fhir.r4.core.Url
+import com.google.fhir.shaded.protobuf.Message
+
+/**
+ * Maps [QuestionnaireResponse]s to FHIR resources and vice versa.
+ *
+ * The process of converting [QuestionnaireResponse]s to other FHIR resources is called
+ * [extraction](http://build.fhir.org/ig/HL7/sdc/extraction.html). The reverse process of converting
+ * existing FHIR resources to [QuestionnaireResponse]s to be used to pre-fill the UI is called
+ * [population](http://build.fhir.org/ig/HL7/sdc/populate.html).
+ *
+ * [Definition-based extraction](http://build.fhir.org/ig/HL7/sdc/extraction.html#definition-based-extraction)
+ * and [expression-based population](http://build.fhir.org/ig/HL7/sdc/populate.html#expression-based-population)
+ * are used because these approaches are generic enough to work with any FHIR resource types, and at
+ * the same time relatively easy to implement.
+ *
+ * WARNING: This is not production-ready.
+ */
+internal object ResourceMapper {
+
+    /**
+     * Extract a FHIR resource from the `questionnaire` and `questionnaireResponse`.
+     *
+     * This method assumes there is only one FHIR resource to be extracted from the given
+     * `questionnaire` and `questionnaireResponse`.
+     */
+    fun extract(
+        questionnaire: Questionnaire,
+        questionnaireResponse: QuestionnaireResponse
+    ): Message {
+        val builder = questionnaire.itemContextNameToExpressionMap.values.first().let {
+            Class.forName("com.google.fhir.r4.core.$it")
+                .getMethod("newBuilder")
+                .invoke(null) as Message.Builder
+        }
+        return builder
+            .extractFields(questionnaire.itemList, questionnaireResponse.itemList)
+            .build()
+    }
+}
+
+/**
+ * Extracts values for fields in the builder from the corresponding questions and answers in
+ * [questionnaireItemList] and [questionnaireResponseItemList].
+ */
+private fun Message.Builder.extractFields(
+    questionnaireItemList: List<Questionnaire.Item>,
+    questionnaireResponseItemList: List<QuestionnaireResponse.Item>
+): Message.Builder {
+    val questionnaireItemListIterator = questionnaireItemList.iterator()
+    val questionnaireResponseItemListIterator = questionnaireResponseItemList.iterator()
+    while (
+        questionnaireItemListIterator.hasNext() &&
+        questionnaireResponseItemListIterator.hasNext()
+    ) {
+        val questionnaireItem = questionnaireItemListIterator.next()
+        val questionnaireResponseItem = questionnaireResponseItemListIterator.next()
+        this.extractField(questionnaireItem, questionnaireResponseItem)
+        extractFields(questionnaireItem.itemList, questionnaireResponseItem.itemList)
+    }
+    return this
+}
+
+/**
+ * Extracts value for field in the builder from the corresponding question and answer in
+ * [questionnaireItem] and [questionnaireResponseItem].
+ *
+ * NOTE: Nested fields are not handled. See https://github.com/google/android-fhir/issues/240.
+ */
+private fun Message.Builder.extractField(
+    questionnaireItem: Questionnaire.Item,
+    questionnaireResponseItem: QuestionnaireResponse.Item
+) {
+    val targetFieldName = questionnaireItem.definitionFieldName
+    if (targetFieldName.isEmpty()) {
+        return
+    }
+
+    questionnaireItem.type.getClass()?.let {
+        this.javaClass.getMethod("set${targetFieldName.capitalize()}", it).invoke(
+            this,
+            questionnaireResponseItem.answerList.single().getValueForType(questionnaireItem.type)
+        )
+    }
+}
+
+/**
+ * Returns the field name for the [Questionnaire.Item]'s definition.
+ *
+ * For example, if the definition URI is
+ * `"http://hl7.org/fhir/StructureDefinition/Patient#Patient.birthDate"`, this function will return
+ * `"birthDate"`.
+ */
+private val Questionnaire.Item.definitionFieldName
+    get() = this.definition.value.substringAfterLast(".")
+
+/**
+ * Returns the [Class] for the answer to the [Questionnaire.Item].
+ *
+ * Used to retrieve the method to invoke to set the field in the extracted FHIR resource.
+ */
+private fun Questionnaire.Item.TypeCode.getClass(): Class<out Message>? = when (this.value) {
+    QuestionnaireItemTypeCode.Value.DATE -> Date::class.java
+    QuestionnaireItemTypeCode.Value.BOOLEAN -> Boolean::class.java
+    QuestionnaireItemTypeCode.Value.DECIMAL -> Decimal::class.java
+    QuestionnaireItemTypeCode.Value.INTEGER -> Integer::class.java
+    QuestionnaireItemTypeCode.Value.DATE_TIME -> DateTime::class.java
+    QuestionnaireItemTypeCode.Value.TIME -> Time::class.java
+    QuestionnaireItemTypeCode.Value.STRING, QuestionnaireItemTypeCode.Value.TEXT ->
+        com.google.fhir.r4.core.String::class.java
+    QuestionnaireItemTypeCode.Value.URL -> Url::class.java
+    else -> null
+}
+
+/**
+ * Returns the value of the [QuestionnaireResponse.Item.Answer] for the [type].
+ *
+ * Used to retrieve the value to set the field in the extracted FHIR resource.
+ *
+ * @throws IllegalArgumentException if [type] is not supported (for example, questions of type
+ * [QuestionnaireItemTypeCode.Value.GROUP] do not collect any answer).
+ */
+private fun QuestionnaireResponse.Item.Answer.getValueForType(
+    type: Questionnaire.Item.TypeCode
+): Message = when (val value = type.value) {
+    QuestionnaireItemTypeCode.Value.DATE -> this.value.date
+    QuestionnaireItemTypeCode.Value.BOOLEAN -> this.value.boolean
+    QuestionnaireItemTypeCode.Value.DECIMAL -> this.value.decimal
+    QuestionnaireItemTypeCode.Value.INTEGER -> this.value.integer
+    QuestionnaireItemTypeCode.Value.DATE_TIME -> this.value.dateTime
+    QuestionnaireItemTypeCode.Value.TIME -> this.value.time
+    QuestionnaireItemTypeCode.Value.STRING, QuestionnaireItemTypeCode.Value.TEXT ->
+        this.value.stringValue
+    QuestionnaireItemTypeCode.Value.URL -> this.value.uri
+    else -> throw IllegalArgumentException("Unsupported value type $value")
+}
+
+/**
+ * The map from the `name`s to `expression`s in the [item extraction context extension](http://build.fhir.org/ig/HL7/sdc/StructureDefinition-sdc-questionnaire-itemExtractionContext.html)s.
+ */
+private val Questionnaire.itemContextNameToExpressionMap: Map<String, String>
+    get() {
+        return this.extensionList.filter {
+            it.url.value == ITEM_CONTEXT_EXTENSION_URL
+        }.map {
+            val expression = it.value.expression
+            expression.name.value to expression.expression.value
+        }.toMap()
+    }
+
+/**
+ * See [Extension: item extraction context](http://build.fhir.org/ig/HL7/sdc/StructureDefinition-sdc-questionnaire-itemExtractionContext.html).
+ */
+private const val ITEM_CONTEXT_EXTENSION_URL: String =
+    "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemContext"

datacapture/src/test/java/com/google/android/fhir/datacapture/mapping/ResourceMapperTest.kt

@@ -0,0 +1,126 @@
+/*
+ * Copyright 2020 Google LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *       http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package com.google.android.fhir.datacapture.mapping
+
+import android.os.Build
+import com.google.common.truth.Truth.assertThat
+import com.google.fhir.common.JsonFormat
+import com.google.fhir.r4.core.Date
+import com.google.fhir.r4.core.Patient
+import com.google.fhir.r4.core.Questionnaire
+import com.google.fhir.r4.core.QuestionnaireResponse
+import java.time.LocalDate
+import java.time.ZoneId
+import org.junit.Test
+import org.junit.runner.RunWith
+import org.robolectric.RobolectricTestRunner
+import org.robolectric.annotation.Config
+
+@RunWith(RobolectricTestRunner::class)
+@Config(sdk = [Build.VERSION_CODES.P])
+class ResourceMapperTest {
+    @Test
+    fun extract() {
+        // https://developer.commure.com/docs/apis/sdc/examples#definition-based-extraction
+        val questionnaireJson = """
+            {
+              "resourceType": "Questionnaire",
+              "subjectType": [
+                "Patient"
+              ],
+              "extension": [
+                {
+                  "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemContext",
+                  "valueExpression": {
+                    "language": "application/x-fhir-query",
+                    "expression": "Patient",
+                    "name": "patient"
+                  }
+                }
+              ],
+              "item": [
+                {
+                  "linkId": "patient-0",
+                  "type": "group",
+                  "item": [
+                    {
+                      "linkId": "patient-0-birth-date",
+                      "definition": "http://hl7.org/fhir/StructureDefinition/Patient#Patient.birthDate",
+                      "type": "date"
+                    },
+                    {
+                      "linkId": "patient-0-active",
+                      "definition": "http://hl7.org/fhir/StructureDefinition/Patient#Patient.active",
+                      "type": "boolean"
+                    }
+                  ]
+                }
+              ]
+            }
+        """.trimIndent()
+        val questionnaireBuilder = Questionnaire.newBuilder()
+        JsonFormat.getParser().merge(questionnaireJson, questionnaireBuilder)
+
+        val questionnaireResponseJson = """
+            {
+              "resourceType": "QuestionnaireResponse",
+              "item": [
+                {
+                  "linkId": "patient-0",
+                  "item": [
+                    {
+                      "linkId": "patient-0-birth-date",
+                      "answer": [
+                        {
+                          "valueDate": "2021-01-01"
+                        }
+                      ]
+                    },
+                    {
+                      "linkId": "patient-0-active",
+                      "answer": [
+                        {
+                          "valueBoolean": true
+                        }
+                      ]
+                    }
+                  ]
+                }
+              ]
+            }
+        """.trimIndent()
+        val questionnaireResponseBuilder = QuestionnaireResponse.newBuilder()
+        JsonFormat.getParser().merge(questionnaireResponseJson, questionnaireResponseBuilder)
+
+        val patient = ResourceMapper.extract(
+            questionnaireBuilder.build(),
+            questionnaireResponseBuilder.build()
+        ) as Patient
+
+        assertThat(patient.birthDate).isEqualTo(
+            Date.newBuilder()
+                .setValueUs(
+                    LocalDate.of(2021, 1, 1)
+                        .atStartOfDay(ZoneId.systemDefault())
+                        .toEpochSecond() * 1000000)
+                .setTimezone(ZoneId.systemDefault().id)
+                .setPrecision(Date.Precision.DAY)
+                .build()
+        )
+        assertThat(patient.active.value).isTrue()
+    }
+}