Merge branch 'master' into sp/issue-2188-m3-theme

google · Oct 9, 2023 · 48952f2 · 48952f2
2 parents cf62bca + 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/build.gradle.kts b/buildSrc/build.gradle.kts
@@ -11,7 +11,7 @@ repositories {
 dependencies {
   implementation("com.diffplug.spotless:spotless-plugin-gradle:6.21.0")
 
-  implementation("com.android.tools.build:gradle:8.1.1")
+  implementation("com.android.tools.build:gradle:8.1.2")
 
   implementation("app.cash.licensee:licensee-gradle-plugin:1.3.0")
   implementation("com.osacky.flank.gradle:fladle:0.17.4")

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/build.gradle.kts b/catalog/build.gradle.kts
@@ -56,6 +56,7 @@ dependencies {
   implementation(Dependencies.Navigation.navUiKtx)
 
   implementation(project(path = ":datacapture"))
+  implementation(project(path = ":engine"))
   implementation(project(path = ":contrib:barcode"))
 
   testImplementation(Dependencies.junit)

diff --git a/catalog/src/main/AndroidManifest.xml b/catalog/src/main/AndroidManifest.xml
@@ -24,6 +24,7 @@
     />
 
     <application
+        android:name=".CatalogApplication"
         android:allowBackup="true"
         android:icon="@mipmap/ic_card_file_box"
         android:label="@string/app_name"

diff --git a/catalog/src/main/assets/behavior_answer_expression.json b/catalog/src/main/assets/behavior_answer_expression.json
@@ -0,0 +1,34 @@
+{
+  "resourceType": "Questionnaire",
+  "item": [
+    {
+      "extension": [
+        {
+          "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-answerExpression",
+          "valueExpression": {
+            "language": "application/x-fhir-query",
+            "expression": "Task?subject=Patient/P1&code=33879002&status=ready&_sort=period"
+          }
+        },
+        {
+          "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-choiceColumn",
+          "extension": [
+            {
+              "url": "path",
+              "valueString": "description + ' - ' + reasonCode.coding.where(system='http://snomed.info/sct').display"
+            },
+            {
+              "url": "forDisplay",
+              "valueBoolean": true
+            }
+          ]
+        }
+      ],
+      "linkId": "vaccines",
+      "text": "Which vaccine tasks were completed?",
+      "type": "reference",
+      "required": true,
+      "repeats": true
+    }
+  ]
+}
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/catalog/src/main/assets/resource_data_bundle.json b/catalog/src/main/assets/resource_data_bundle.json
@@ -0,0 +1,116 @@
+{
+  "resourceType": "Bundle",
+  "entry": [
+    {
+      "resource": {
+        "resourceType" : "Patient",
+        "id" : "P1"
+      }
+    },
+    {
+      "resource": {
+        "resourceType": "Task",
+        "id": "b8e13d21-1a62-4172-a9ef-57670e6ac238",
+        "status": "ready",
+        "code": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "33879002",
+              "display": "Vaccination routine"
+            }
+          ]
+        },
+        "description": "BCG at birth",
+        "for": {
+          "reference": "Patient/P1"
+        },
+        "reasonCode": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "42284007",
+              "display": "BCG vaccine"
+            },
+            {
+              "system": "https://smartregister.org/immunization/vaccine-codes",
+              "code": "bcg",
+              "display": "BCG"
+            }
+          ],
+          "text": "BCG"
+        }
+      }
+    },
+    {
+      "resource": {
+        "resourceType": "Task",
+        "id": "4090ba9a-fbbb-4634-a06d-0cbe938ab090",
+        "status": "cancelled",
+        "code": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "33879002",
+              "display": "Vaccination routine"
+            }
+          ]
+        },
+        "description": "OPV 0 at birth",
+        "for": {
+          "reference": "Patient/P1"
+        },
+        "reasonCode": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "111164008",
+              "display": "Poliovirus vaccine"
+            },
+            {
+              "system": "https://smartregister.org/immunization/vaccine-codes",
+              "code": "opv0",
+              "display": "OPV 0"
+            }
+          ],
+          "text": "OPV 0"
+        }
+      }
+    },
+    {
+      "resource": {
+        "resourceType": "Task",
+        "id": "087e82c6-e346-4725-8db1-7e10aec99be9",
+        "status": "ready",
+        "code": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "33879002",
+              "display": "Vaccination routine"
+            }
+          ]
+        },
+        "description": "OPV 1 at 6 weeks",
+        "for": {
+          "reference": "Patient/P1"
+        },
+        "reasonCode": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "111164008",
+              "display": "Poliovirus vaccine"
+            },
+            {
+              "system": "https://smartregister.org/immunization/vaccine-codes",
+              "code": "opv1",
+              "display": "OPV 1"
+            }
+          ],
+          "text": "OPV 1"
+        }
+      }
+    }
+  ]
+}
diff --git a/catalog/src/main/java/com/google/android/fhir/catalog/BehaviorListViewModel.kt b/catalog/src/main/java/com/google/android/fhir/catalog/BehaviorListViewModel.kt
@@ -38,6 +38,11 @@ class BehaviorListViewModel(application: Application) : AndroidViewModel(applica
       R.string.behavior_name_calculated_expression,
       "behavior_calculated_expression.json",
     ),
+    ANSWER_EXPRESSION(
+      R.drawable.ic_answers_behavior,
+      R.string.behavior_name_answer_expression,
+      "behavior_answer_expression.json",
+    ),
     CONTEXT_VARIABLES(
       R.drawable.ic_context,
       R.string.behavior_name_context_variables,

diff --git a/catalog/src/main/java/com/google/android/fhir/catalog/CatalogApplication.kt b/catalog/src/main/java/com/google/android/fhir/catalog/CatalogApplication.kt
@@ -0,0 +1,60 @@
+/*
+ * Copyright 2022-2023 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.catalog
+
+import android.app.Application
+import ca.uhn.fhir.context.FhirContext
+import com.google.android.fhir.FhirEngine
+import com.google.android.fhir.FhirEngineConfiguration
+import com.google.android.fhir.FhirEngineProvider
+import com.google.android.fhir.datacapture.DataCaptureConfig
+import com.google.android.fhir.search.search
+import kotlinx.coroutines.CoroutineScope
+import kotlinx.coroutines.Dispatchers
+import kotlinx.coroutines.launch
+import org.hl7.fhir.r4.model.Bundle
+
+class CatalogApplication : Application(), DataCaptureConfig.Provider {
+  // Only initiate the FhirEngine when used for the first time, not when the app is created.
+  private val fhirEngine: FhirEngine by lazy { FhirEngineProvider.getInstance(this) }
+
+  private lateinit var dataCaptureConfig: DataCaptureConfig
+
+  override fun onCreate() {
+    super.onCreate()
+
+    FhirEngineProvider.init(FhirEngineConfiguration())
+
+    dataCaptureConfig =
+      DataCaptureConfig(xFhirQueryResolver = { fhirEngine.search(it).map { it.resource } })
+
+    CoroutineScope(Dispatchers.IO).launch {
+      assets
+        .open("resource_data_bundle.json")
+        .bufferedReader()
+        .use { bufferedReader -> bufferedReader.readText() }
+        .let { stringValue ->
+          FhirContext.forR4Cached().newJsonParser().parseResource(stringValue) as Bundle
+        }
+        .entry
+        .map { bundleEntryComponent -> bundleEntryComponent.resource }
+        .let { resources -> fhirEngine.create(*resources.toTypedArray()) }
+    }
+  }
+
+  override fun getDataCaptureConfig(): DataCaptureConfig = dataCaptureConfig
+}