Merge remote-tracking branch 'upstream/master' into resource_consolid…

…ation
google · Oct 9, 2023 · f81fb89 · f81fb89
2 parents a5d7f34 + 0818bd0
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diff --git a/.github/dependabot.yaml b/.github/dependabot.yaml
@@ -0,0 +1,20 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+    # Gotta Catch 'Em All! (i.e. don't wait and propose them only "trickled")
+    open-pull-requests-limit: 99
+
+  - package-ecosystem: gradle
+    directory: /
+    schedule:
+      interval: weekly
+      day: monday
+      time: "04:00"
+
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+      day: monday
+      time: "04:00"
diff --git a/.github/workflows/codeql.yaml b/.github/workflows/codeql.yaml
@@ -0,0 +1,51 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "master" ]
+  schedule:
+    - cron: '32 13 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-22.04-64core
+    timeout-minutes: 60
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java' ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    - name: Switch to Java 17 from Eclipse Temurin distro
+      uses: actions/setup-java@v3
+      with:
+        java-version: 17
+        distribution: temurin
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+
+    # TODO: use Autobuild instead of ./gradlew after https://github.com/github/codeql-action/issues/1417 is fixed
+    # - name: Autobuild
+    #   uses: github/codeql-action/autobuild@v2
+    - name: Build with Gradle
+      run: ./gradlew --scan --full-stacktrace -Dorg.gradle.dependency.verification=off compileDebugAndroidTestSources
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Android FHIR SDK
 
-[![master](https://github.com/google/android-fhir/actions/workflows/build.yml/badge.svg?branch=master)](https://github.com/google/android-fhir/actions/workflows/build.yml) [![master](https://storage.googleapis.com/android-fhir-build-badges/build.svg)](https://storage.googleapis.com/android-fhir-build-badges/build.html) [![codecov](https://codecov.io/gh/google/android-fhir/branch/master/graph/badge.svg?token=PDSC4WRDTQ)](https://codecov.io/gh/google/android-fhir/branch/master) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) [![project chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://chat.fhir.org/#narrow/stream/276344-android)
+[![master](https://github.com/google/android-fhir/actions/workflows/build.yml/badge.svg?branch=master)](https://github.com/google/android-fhir/actions/workflows/build.yml) [![codecov](https://codecov.io/gh/google/android-fhir/branch/master/graph/badge.svg?token=PDSC4WRDTQ)](https://codecov.io/gh/google/android-fhir/branch/master) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) [![project chat](https://img.shields.io/badge/zulip-join_chat-brightgreen.svg)](https://chat.fhir.org/#narrow/stream/276344-android)
 
 The Android FHIR SDK is a set of Kotlin libraries for building offline-capable, mobile-first
 healthcare applications using the [HL7® FHIR® standard](https://www.hl7.org/fhir/) on Android. It
@@ -15,7 +15,7 @@ The SDK contains the following libraries:
 | -------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------- | ----------------------------------------------------------------------------------- |----------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | Data Capture Library | [![Google Maven](https://badgen.net/maven/v/metadata-url/dl.google.com/dl/android/maven2/com/google/android/fhir/data-capture/maven-metadata.xml)](https://maven.google.com/web/index.html?#com.google.android.fhir:data-capture) | [code](https://github.com/google/android-fhir/tree/master/datacapture)| [wiki](https://github.com/google/android-fhir/wiki/Structured-Data-Capture-Library) | Android 7.0 (API level 24) | Collect, validate, and process healthcare data on Android                                                                                                  |
 | FHIR Engine Library  | [![Google Maven](https://badgen.net/maven/v/metadata-url/dl.google.com/dl/android/maven2/com/google/android/fhir/engine/maven-metadata.xml)](https://maven.google.com/web/index.html?#com.google.android.fhir:engine)             | [code](https://github.com/google/android-fhir/tree/master/engine)     | [wiki](https://github.com/google/android-fhir/wiki/FHIR-Engine-Library)             | Android 7.0 (API level 24) | Store and manage FHIR resources locally on Android and synchronize with FHIR server                                                                        |
-| Workflow Library     | [![Google Maven](https://badgen.net/maven/v/metadata-url/dl.google.com/dl/android/maven2/com/google/android/fhir/workflow/maven-metadata.xml)](https://maven.google.com/web/index.html?#com.google.android.fhir:workflow)         | [code](https://github.com/google/android-fhir/tree/master/workflow)   | [wiki](https://github.com/google/android-fhir/wiki/Workflow-Library)                | Android 8.0 (API level 26) | Provide decision support and analytics in clinical workflow on Android including implementation of specific FHIR operations ($measure_evaluate and $apply) |
+| Workflow Library     | [![Google Maven](https://badgen.net/maven/v/metadata-url/dl.google.com/dl/android/maven2/com/google/android/fhir/workflow/maven-metadata.xml)](https://maven.google.com/web/index.html?#com.google.android.fhir:workflow)         | [code](https://github.com/google/android-fhir/tree/master/workflow)   | [wiki](https://github.com/google/android-fhir/wiki/Workflow-Library)                | Android 7.0 (API level 24) | Provide decision support and analytics in clinical workflow on Android including implementation of specific FHIR operations ($measure_evaluate and $apply) |
 
 ## Demo apps
 
@@ -38,7 +38,7 @@ To contribute to the project, please see [Contributing](https://github.com/googl
 
 You can create a [GitHub issue](https://github.com/google/android-fhir/issues) for bugs and feature requests.
 
-In case you find any security bug, please do NOT create a Github issue. Instead, email us at <[email protected]>.
+In case you find any security bug, please do NOT create a GitHub issue. Instead, email us at <[email protected]>.
 
 If you want to provide any feedback or discuss use cases you can: 
 * email us at <[email protected]>

diff --git a/buildSrc/src/main/kotlin/Dependencies.kt b/buildSrc/src/main/kotlin/Dependencies.kt
@@ -159,6 +159,9 @@ object Dependencies {
     "$androidFhirGroup:$androidFhirEngineModule:${Versions.androidFhirEngine}"
   const val androidFhirKnowledge = "$androidFhirGroup:knowledge:${Versions.androidFhirKnowledge}"
 
+  const val apacheCommonsCompress =
+    "org.apache.commons:commons-compress:${Versions.apacheCommonsCompress}"
+
   const val desugarJdkLibs = "com.android.tools:desugar_jdk_libs:${Versions.desugarJdkLibs}"
   const val fhirUcum = "org.fhir:ucum:${Versions.fhirUcum}"
   const val gson = "com.google.code.gson:gson:${Versions.gson}"
@@ -243,6 +246,7 @@ object Dependencies {
     const val androidFhirCommon = "0.1.0-alpha04"
     const val androidFhirEngine = "0.1.0-beta03"
     const val androidFhirKnowledge = "0.1.0-alpha01"
+    const val apacheCommonsCompress = "1.21"
     const val desugarJdkLibs = "2.0.3"
     const val caffeine = "2.9.1"
     const val fhirUcum = "1.0.3"

diff --git a/catalog/src/main/assets/component_open_choice.json b/catalog/src/main/assets/component_open_choice.json
@@ -20,7 +20,7 @@
           }
         }
       ],
-      "text": "Do you have any pre-existing health conditions?",
+      "text": "Do you have any preexisting health conditions?",
       "item": [
         {
           "linkId": "1.1",

diff --git a/catalog/src/main/assets/component_open_choice_with_validation.json b/catalog/src/main/assets/component_open_choice_with_validation.json
@@ -18,7 +18,7 @@
         }
       ],
       "linkId": "1",
-      "text": "Do you have any pre-existing health conditions?",
+      "text": "Do you have any preexisting health conditions?",
       "required": true,
       "item": [
         {

diff --git a/...datacapture/test/views/QuestionnaireItemDialogMultiSelectViewHolderFactoryEspressoTest.kt b/...datacapture/test/views/QuestionnaireItemDialogMultiSelectViewHolderFactoryEspressoTest.kt
@@ -29,6 +29,7 @@ import androidx.test.espresso.matcher.ViewMatchers
 import androidx.test.espresso.matcher.ViewMatchers.isDisplayed
 import androidx.test.espresso.matcher.ViewMatchers.withId
 import androidx.test.ext.junit.rules.ActivityScenarioRule
+import androidx.test.filters.SdkSuppress
 import androidx.test.platform.app.InstrumentationRegistry
 import com.google.android.fhir.datacapture.R
 import com.google.android.fhir.datacapture.extensions.DisplayItemControlType
@@ -261,6 +262,7 @@ class QuestionnaireItemDialogMultiSelectViewHolderFactoryEspressoTest {
   }
 
   @Test
+  @SdkSuppress(minSdkVersion = 33) // TODO https://github.com/google/android-fhir/issues/1482 FIXME
   fun selectOther_shouldScrollDownToShowAddAnotherAnswer() {
     val questionnaireItem =
       answerOptions(
@@ -327,6 +329,7 @@ class QuestionnaireItemDialogMultiSelectViewHolderFactoryEspressoTest {
   }
 
   @Test
+  @SdkSuppress(minSdkVersion = 33) // TODO https://github.com/google/android-fhir/issues/1482 FIXME
   fun clickAddAnotherAnswer_shouldScrollDownToShowAddAnotherAnswer() {
     val questionnaireItem =
       answerOptions(

diff --git a/...in/java/com/google/android/fhir/datacapture/extensions/MoreQuestionnaireItemComponents.kt b/...in/java/com/google/android/fhir/datacapture/extensions/MoreQuestionnaireItemComponents.kt
@@ -845,7 +845,7 @@ fun Questionnaire.QuestionnaireItemComponent.createQuestionnaireResponseItem():
 }
 
 /**
- * Returns a list of answers from the initial values of the questionnaire item. `null` if no intial
+ * Returns a list of answers from the initial values of the questionnaire item. `null` if no initial
  * value.
  */
 private fun Questionnaire.QuestionnaireItemComponent.createQuestionnaireResponseItemAnswers():

diff --git a/datacapture/src/test/java/com/google/android/fhir/datacapture/mapping/ResourceMapperTest.kt b/datacapture/src/test/java/com/google/android/fhir/datacapture/mapping/ResourceMapperTest.kt
@@ -1078,7 +1078,7 @@ class ResourceMapperTest {
     }
 
   @Test
-  fun `extract_updateIntegerObservationForDecimalDefination_shouldUpdateAsDecimal() `() =
+  fun `extract_updateIntegerObservationForDecimalDefinition_shouldUpdateAsDecimal() `() =
     runBlocking {
       @Language("JSON")
       val questionnaireJson =

diff --git a/docs/data-capture/scripts/navigation-loader.js b/docs/data-capture/scripts/navigation-loader.js
@@ -52,8 +52,8 @@ revealParents = (part) => {
 };
 
 /*
-    This is a work-around for safari being IE of our times.
-    It doesn't fire a DOMContentLoaded, presumabely because eventListener is added after it wants to do it
+    This is a workaround for safari being IE of our times.
+    It doesn't fire a DOMContentLoaded, presumably because eventListener is added after it wants to do it
 */
 if (document.readyState == 'loading') {
     window.addEventListener('DOMContentLoaded', () => {

diff --git a/...ne/engine/com.google.android.fhir.sync/-periodic-sync-configuration/sync-constraints.html b/...ne/engine/com.google.android.fhir.sync/-periodic-sync-configuration/sync-constraints.html
@@ -28,7 +28,7 @@ <h1 class="cover"><span>sync</span><wbr></wbr><span>Constraints</span></h1>
   <div>
     <div class="platform-hinted " data-platform-hinted="data-platform-hinted"><div class="content sourceset-depenent-content" data-active="" data-togglable=":engine:dokkaHtml/release"><div class="symbol monospace">val <a href="sync-constraints.html">syncConstraints</a>: <a href="https://developer.android.com/reference/kotlin/androidx/work/Constraints.html">Constraints</a><span class="top-right-position"><span class="copy-icon"></span><div class="copy-popup-wrapper popup-to-left"><span class="copy-popup-icon"></span><span>Content copied to clipboard</span></div></span></div></div></div>
   </div>
-<p class="paragraph">Constraints that specify the requirements needed before the synchronisation is triggered. E.g. network type (Wifi, 3G etc), the device should be charging etc.</p></div>
+<p class="paragraph">Constraints that specify the requirements needed before the synchronisation is triggered. E.g. network type (WiFi, 3G etc), the device should be charging etc.</p></div>
           <h2 class="">Sources</h2>
           <div class="table" data-togglable="Sources"><a data-name="-1831107255%2FSource%2F-2001932064" anchor-label="https://github.com/google/android-fhir/tree/master/engine/src/main/java/com/google/android/fhir/sync/Config.kt#L51" id="-1831107255%2FSource%2F-2001932064" data-filterable-set=":engine:dokkaHtml/main"></a>
             <div class="table-row" data-filterable-current=":engine:dokkaHtml/main" data-filterable-set=":engine:dokkaHtml/main">

diff --git a/docs/engine/scripts/navigation-loader.js b/docs/engine/scripts/navigation-loader.js
@@ -52,8 +52,8 @@ revealParents = (part) => {
 };
 
 /*
-    This is a work-around for safari being IE of our times.
-    It doesn't fire a DOMContentLoaded, presumabely because eventListener is added after it wants to do it
+    This is a workaround for safari being IE of our times.
+    It doesn't fire a DOMContentLoaded, presumably because eventListener is added after it wants to do it
 */
 if (document.readyState == 'loading') {
     window.addEventListener('DOMContentLoaded', () => {

diff --git a/docs/index.html b/docs/index.html
@@ -0,0 +1,15 @@
+<!DOCTYPE html>
+<html lang="en">
+<body>
+
+<h1>Android FHIR SDK Technical Documentation</h1>
+
+<h2>API Docs</h2>
+<ul>
+  <li><a href="engine/">engine</a></li>
+  <li><a href="data-capture/">data-capture</a></li>
+  <li><a href="workflow/">workflow</a></li>
+</ul>  
+
+</body>
+</html>
diff --git a/docs/workflow/scripts/navigation-loader.js b/docs/workflow/scripts/navigation-loader.js
@@ -52,8 +52,8 @@ revealParents = (part) => {
 };
 
 /*
-    This is a work-around for safari being IE of our times.
-    It doesn't fire a DOMContentLoaded, presumabely because eventListener is added after it wants to do it
+    This is a workaround for safari being IE of our times.
+    It doesn't fire a DOMContentLoaded, presumably because eventListener is added after it wants to do it
 */
 if (document.readyState == 'loading') {
     window.addEventListener('DOMContentLoaded', () => {

diff --git a/engine/benchmark/build.gradle.kts b/engine/benchmark/build.gradle.kts
@@ -56,19 +56,16 @@ configurations {
 }
 
 dependencies {
+  androidTestImplementation(Dependencies.Androidx.workRuntimeKtx)
   androidTestImplementation(Dependencies.AndroidxTest.benchmarkJunit)
   androidTestImplementation(Dependencies.AndroidxTest.extJunit)
   androidTestImplementation(Dependencies.AndroidxTest.runner)
-  androidTestImplementation(Dependencies.Cql.engineJackson)
-  androidTestImplementation(Dependencies.Cql.evaluator)
-  androidTestImplementation(Dependencies.Cql.evaluatorBuilder)
-  androidTestImplementation(Dependencies.junit)
-  androidTestImplementation(Dependencies.Kotlin.kotlinCoroutinesAndroid)
-  androidTestImplementation(Dependencies.truth)
-  androidTestImplementation(Dependencies.Androidx.workRuntimeKtx)
   androidTestImplementation(Dependencies.AndroidxTest.workTestingRuntimeKtx)
-  androidTestImplementation(Dependencies.mockWebServer)
+  androidTestImplementation(Dependencies.Kotlin.kotlinCoroutinesAndroid)
   androidTestImplementation(Dependencies.Retrofit.coreRetrofit)
+  androidTestImplementation(Dependencies.junit)
+  androidTestImplementation(Dependencies.mockWebServer)
+  androidTestImplementation(Dependencies.truth)
 
   androidTestImplementation(project(":engine"))
   // for test json files only

diff --git a/engine/schemas/com.google.android.fhir.db.impl.ResourceDatabase/8.json b/engine/schemas/com.google.android.fhir.db.impl.ResourceDatabase/8.json
@@ -2,7 +2,7 @@
   "formatVersion": 1,
   "database": {
     "version": 8,
-    "identityHash": "81bc60d60855266f7fc233eb1c164a89",
+    "identityHash": "bf28146b530ec50ac067916072020d73",
     "entities": [
       {
         "tableName": "ResourceEntity",
@@ -990,6 +990,15 @@
             ],
             "orders": [],
             "createSql": "CREATE INDEX IF NOT EXISTS `index_LocalChangeResourceReferenceEntity_resourceReferenceValue` ON `${TABLE_NAME}` (`resourceReferenceValue`)"
+          },
+          {
+            "name": "index_LocalChangeResourceReferenceEntity_localChangeId",
+            "unique": false,
+            "columnNames": [
+              "localChangeId"
+            ],
+            "orders": [],
+            "createSql": "CREATE INDEX IF NOT EXISTS `index_LocalChangeResourceReferenceEntity_localChangeId` ON `${TABLE_NAME}` (`localChangeId`)"
           }
         ],
         "foreignKeys": [
@@ -1010,7 +1019,7 @@
     "views": [],
     "setupQueries": [
       "CREATE TABLE IF NOT EXISTS room_master_table (id INTEGER PRIMARY KEY,identity_hash TEXT)",
-      "INSERT OR REPLACE INTO room_master_table (id,identity_hash) VALUES(42, '81bc60d60855266f7fc233eb1c164a89')"
+      "INSERT OR REPLACE INTO room_master_table (id,identity_hash) VALUES(42, 'bf28146b530ec50ac067916072020d73')"
     ]
   }
 }
diff --git a/engine/src/androidTest/java/com/google/android/fhir/db/impl/DatabaseImplTest.kt b/engine/src/androidTest/java/com/google/android/fhir/db/impl/DatabaseImplTest.kt
@@ -40,6 +40,7 @@ import com.google.android.fhir.search.has
 import com.google.android.fhir.search.include
 import com.google.android.fhir.search.revInclude
 import com.google.android.fhir.sync.upload.LocalChangesFetchMode
+import com.google.android.fhir.sync.upload.UploadSyncResult
 import com.google.android.fhir.testing.assertJsonArrayEqualsIgnoringOrder
 import com.google.android.fhir.testing.assertResourceEquals
 import com.google.android.fhir.testing.readFromFile
@@ -49,7 +50,7 @@ import com.google.common.truth.Truth.assertThat
 import java.math.BigDecimal
 import java.time.Instant
 import java.util.Date
-import kotlinx.coroutines.flow.flowOf
+import kotlinx.coroutines.flow.collect
 import kotlinx.coroutines.runBlocking
 import org.hl7.fhir.r4.model.Address
 import org.hl7.fhir.r4.model.CarePlan
@@ -529,19 +530,23 @@ class DatabaseImplTest {
     database.insert(patient)
     // Delete the patient created in setup as we only want to upload the patient in this test
     database.deleteUpdates(listOf(TEST_PATIENT_1))
-    services.fhirEngine.syncUpload(LocalChangesFetchMode.AllChanges) {
-      it
-        .first { it.resourceId == "remote-patient-3" }
-        .let {
-          flowOf(
-            it.token to
-              Patient().apply {
-                id = it.resourceId
-                meta = remoteMeta
-              },
-          )
-        }
-    }
+    services.fhirEngine
+      .syncUpload(LocalChangesFetchMode.AllChanges) {
+        it
+          .first { it.resourceId == "remote-patient-3" }
+          .let {
+            UploadSyncResult.Success(
+              listOf(it),
+              listOf(
+                Patient().apply {
+                  id = it.resourceId
+                  meta = remoteMeta
+                },
+              ),
+            )
+          }
+      }
+      .collect()
     val selectedEntity = database.selectEntity(ResourceType.Patient, "remote-patient-3")
     assertThat(selectedEntity.versionId).isEqualTo(remoteMeta.versionId)
     assertThat(selectedEntity.lastUpdatedRemote).isEqualTo(remoteMeta.lastUpdated.toInstant())

diff --git a/engine/src/main/java/com/google/android/fhir/FhirEngine.kt b/engine/src/main/java/com/google/android/fhir/FhirEngine.kt
@@ -20,6 +20,8 @@ import com.google.android.fhir.db.ResourceNotFoundException
 import com.google.android.fhir.search.Search
 import com.google.android.fhir.sync.ConflictResolver
 import com.google.android.fhir.sync.upload.LocalChangesFetchMode
+import com.google.android.fhir.sync.upload.SyncUploadProgress
+import com.google.android.fhir.sync.upload.UploadSyncResult
 import java.time.OffsetDateTime
 import kotlinx.coroutines.flow.Flow
 import org.hl7.fhir.r4.model.Resource
@@ -49,14 +51,20 @@ interface FhirEngine {
   suspend fun <R : Resource> search(search: Search): List<SearchResult<R>>
 
   /**
-   * Synchronizes the [upload] result in the database. [upload] operation may result in multiple
-   * calls to the server to upload the data. Result of each call will be emitted by [upload] and the
-   * api caller should [Flow.collect] it.
+   * Synchronizes the upload results in the database.
+   *
+   * The [upload] function may initiate multiple server calls. Each call's result can then be used
+   * to emit [UploadSyncResult]. The caller should collect these results using [Flow.collect].
+   *
+   * @param localChangesFetchMode Specifies the mode to fetch local changes.
+   * @param upload A suspend function that takes a list of [LocalChange] and returns an
+   *   [UploadSyncResult].
+   * @return A [Flow] that emits the progress of the synchronization process.
    */
   suspend fun syncUpload(
     localChangesFetchMode: LocalChangesFetchMode,
-    upload: (suspend (List<LocalChange>) -> Flow<Pair<LocalChangeToken, Resource>>),
-  )
+    upload: (suspend (List<LocalChange>) -> UploadSyncResult),
+  ): Flow<SyncUploadProgress>
 
   /**
    * Synchronizes the [download] result in the database. The database will be updated to reflect the