Merge branch 'master' into sp/988-landing-page

README.md

@@ -1,100 +1,44 @@
-# Android FHIR SDK (Pre-beta release) [![master](https://github.com/google/android-fhir/workflows/CI/badge.svg?branch=master)](https://github.com/google/android-fhir/actions?query=workflow%3ACI) [![codecov](https://codecov.io/gh/google/android-fhir/branch/master/graph/badge.svg?token=PDSC4WRDTQ)](https://codecov.io/gh/google/android-fhir/branch/master)
+# Android FHIR SDK
 
-The Android FHIR SDK (the SDK) is an Android library for building
-offline-capable, mobile-first healthcare applications using
-[FHIR](https://www.hl7.org/fhir/) resources on Android. The overall goal is to
-simplify the process of incorporating support for FHIR into new or existing
-mobile solutions and to accelerate the adoption of FHIR standards as part of
-broader interoperability efforts in healthcare.
+[![master](https://github.com/google/android-fhir/workflows/CI/badge.svg?branch=master)](https://github.com/google/android-fhir/actions?query=workflow%3ACI) [![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)
 
-## Usage
+The Android FHIR SDK (the SDK) is a set of Kotlin libraries for building offline-capable,
+mobile-first healthcare applications using [FHIR](https://www.hl7.org/fhir/) resources on Android.
+It aims to accelerate the adoption of FHIR by making it easy to incorporate FHIR into new and
+existing mobile applications.
 
-The SDK is designed to support Android 21 (lollipop) and above. Android Studio
-4.0 is required for [Java 8 library
-desugaring](https://developer.android.com/studio/preview/features#j8-desugar).
+## Requirements
 
-## Libraries
-
-The repository is organised into the following libraries:
-
-| Library | Status | Notes |
-| -------------------- | -------------- | -------------------------------------------------------- |
-| Data Capture Library | Stable | Approaching beta release |
-| FHIR Engine | Mostly stable | Finalizing sync API subject to change. Other APIs stable |
-| Workflow Library | In development | Pending alpha release |
-
-
-### 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)
-
-This is the main library for building a mobile based clinical data repository
-using FHIR. It provides:
-
-- SQLite database for FHIR resources
-- APIs for accessing (create, read, update, and delete) FHIR resources in the
- database
-- APIs for searching FHIR resources in the database
-- Sync API for synchronization of resources with a FHIR server
-
-To use this library in your Android application, see [FHIR Engine Library User's
-Guide](https://github.com/google/android-fhir/wiki/FHIR-Engine-Library-User's-Guide).
-
-### Structured data capture (SDC) 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)
-
-This library is a partial implementation of the [Structured Data Capture FHIR
-IG](http:https://build.fhir.org/ig/HL7/sdc/) on Android. It includes the UI components
-and APIs to capture healthcare data using FHIR questionnaires.
+The SDK supports Android 21 (lollipop) and above. Android Studio 4.0 or above is required for
+[Java 8 library desugaring](https://developer.android.com/studio/preview/features#j8-desugar).
 
-To use this library in your Android application, see [Structured Data Capture
-Library User's
-Guide](https://github.com/google/android-fhir/wiki/Structured-Data-Capture-Library-User's-Guide).
-
-### Workflow library
-
-This library provides APIs that use digital clinical guidelines to support decision making and analytics in clinical workflows.
-
-It supports the following operations:
-
-| Operation | Status | Notes |
-| -------------------------- | -------------- | -------------------------------------------------------------------- |
-| Measure/$evaluate-measure | Alpha | See https://www.hl7.org/fhir/measure-operation-evaluate-measure.html |
-| PlanDefinition/$apply | In development | See https://www.hl7.org/fhir/plandefinition-operation-apply.html |
-
-Future features of the library will provide support for Tasking and other Workflow related requirements
-
-## Sample Applications
-
-Two sample applications are provided that demonstrate different features of the
-SDK.
-
-**These applications are provided for demonstration purposes only and are not
-for use in production. Do NOT use in production.**
-
-### Reference Application
+## Libraries
 
-This is the initial demo application for showcasing core SDK features and CQL
-proof of concept. The demo uses synthea generated data that has been loaded into
-the HAPI FHIR server public demo site.
+The SDK contains the following libraries:
 
-To run this application, clone the codebase and
-[run](https://developer.android.com/studio/run) the `reference` module.
+| Library | Latest release | Code | Wiki | Summary |
+| -------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------- | ----------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------- |
+| 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) | Store and manage FHIR resources locally on Android and synchronize with FHIR server |
+| 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) | Collect, validate, and process healthcare data on Android |
+| 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) | Provide decision support and analytics in clinical workflow on Android |
 
-### SDC Gallery App
+## Demo apps
 
-This app includes a number of pre-loaded sample FHIR Questionnaires.
+This repository also contains the following demo apps:
 
-It uses the SDC library to create data capture forms using FHIR questionnaires.
-For supported widgets, features and known bugs, see the latest release notes.
+| Demo app | Code | Wiki |
+| ----------------------------------- | ------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------- |
+| FHIR Engine Demo App | [code](https://github.com/google/android-fhir/tree/master/demo) | [wiki](https://github.com/google/android-fhir/wiki/FHIR-Engine-Library#demo-app) |
+| Structured Data Capture Catalog App | [code](https://github.com/google/android-fhir/tree/master/catalog) | [wiki](https://github.com/google/android-fhir/wiki/Structured-Data-Capture-Library#catalog-app) |
 
-To run this application, clone the codebase and run the `datacapturegallery`
-module.
+**These applications are provided for demo purposes only. Do NOT use in production.**
 
 ## Contributing
 
 The SDK is being developed by a consortium of application developers. We welcome
 contributions. Please see [How to
 Contribute](https://github.com/google/android-fhir/blob/master/docs/contributing.md)
-and [Developer's
-Guide](https://github.com/google/android-fhir/wiki/Developer's-Guide) for more
+and [Contributing](https://github.com/google/android-fhir/wiki/Contributing) for more
 information.
 
 ## Feedback

buildSrc/src/main/kotlin/Dependencies.kt

@@ -21,6 +21,7 @@ object Dependencies {
  const val appCompat = "androidx.appcompat:appcompat:${Versions.Androidx.appCompat}"
  const val constraintLayout =
  "androidx.constraintlayout:constraintlayout:${Versions.Androidx.constraintLayout}"
+ const val coreKtx = "androidx.core:core-ktx:${Versions.Androidx.coreKtx}"
  const val datastorePref =
  "androidx.datastore:datastore-preferences:${Versions.Androidx.datastorePref}"
  const val fragmentKtx = "androidx.fragment:fragment-ktx:${Versions.Androidx.fragmentKtx}"
@@ -30,17 +31,30 @@ object Dependencies {
  }
 
  object Cql {
- const val cqlEngine = "org.opencds.cqf:cql-engine:${Versions.Cql.cqlEngine}"
- const val cqlEngineFhir = "org.opencds.cqf:cql-engine-fhir:${Versions.Cql.cqlEngine}"
+ const val evaluator = "org.opencds.cqf.cql:evaluator:${Versions.Cql.evaluator}"
+ const val evaluatorBuilder = "org.opencds.cqf.cql:evaluator.builder:${Versions.Cql.evaluator}"
+ const val evaluatorDagger = "org.opencds.cqf.cql:evaluator.dagger:${Versions.Cql.evaluator}"
  }
 
  object HapiFhir {
  const val structuresR4 = "ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${Versions.hapiFhir}"
  const val validation = "ca.uhn.hapi.fhir:hapi-fhir-validation:${Versions.hapiFhir}"
  }
 
+ object Jackson {
+ const val annotations = "com.fasterxml.jackson.core:jackson-annotations:${Versions.jackson}"
+ const val core = "com.fasterxml.jackson.core:jackson-core:${Versions.jackson}"
+ const val databind = "com.fasterxml.jackson.core:jackson-databind:${Versions.jackson}"
+ }
+
+ object JavaJsonTools {
+ const val jacksonCoreUtils =
+ "com.github.java-json-tools:jackson-coreutils:${Versions.JavaJsonTools.jacksonCoreUtils}"
+ const val msgSimple =
+ "com.github.java-json-tools:msg-simple:${Versions.JavaJsonTools.msgSimple}"
+ }
+
  object Kotlin {
- const val androidxCoreKtx = "androidx.core:core-ktx:${Versions.Kotlin.androidxCoreKtx}"
  const val kotlinCoroutinesAndroid =
  "org.jetbrains.kotlinx:kotlinx-coroutines-android:${Versions.Kotlin.kotlinCoroutinesCore}"
  const val kotlinCoroutinesCore =
@@ -82,10 +96,13 @@ object Dependencies {
  const val guava = "com.google.guava:guava:${Versions.guava}"
  const val httpInterceptor = "com.squareup.okhttp3:logging-interceptor:${Versions.http}"
  const val http = "com.squareup.okhttp3:okhttp:${Versions.http}"
+ const val stax = "javax.xml.stream:stax-api:${Versions.stax}"
  const val jsonToolsPatch = "com.github.java-json-tools:json-patch:${Versions.jsonToolsPatch}"
  const val kotlinPoet = "com.squareup:kotlinpoet:${Versions.kotlinPoet}"
  const val material = "com.google.android.material:material:${Versions.material}"
  const val sqlcipher = "net.zetetic:android-database-sqlcipher:${Versions.sqlcipher}"
+ const val woodstox = "org.codehaus.woodstox:woodstox-core-asl:${Versions.woodstox}"
+ const val xerces = "xerces:xercesImpl:${Versions.xerces}"
 
  // Dependencies for testing go here
  object AndroidxTest {
@@ -115,6 +132,7 @@ object Dependencies {
  const val activity = "1.2.1"
  const val appCompat = "1.1.0"
  const val constraintLayout = "1.1.3"
+ const val coreKtx = "1.2.0"
  const val datastorePref = "1.0.0"
  const val fragmentKtx = "1.3.1"
  const val lifecycle = "2.2.0"
@@ -127,10 +145,15 @@ object Dependencies {
 
  object Cql {
  const val cqlEngine = "1.3.14-SNAPSHOT"
+ const val evaluator = "1.3.1-SNAPSHOT"
+ }
+
+ object JavaJsonTools {
+ const val jacksonCoreUtils = "2.0"
+ const val msgSimple = "1.2"
  }
 
  object Kotlin {
- const val androidxCoreKtx = "1.2.0"
  const val kotlinCoroutinesCore = "1.4.2"
  const val stdlib = "1.5.31"
  }
@@ -144,12 +167,16 @@ object Dependencies {
  // TODO: The next release of HAPI FHIR will hopefully have
  // https://github.com/hapifhir/hapi-fhir/pull/3043 merged in. If it does, when we update, we
  // should remove any excludes directives for "net.sf.saxon" across our build.gradle files.
+ const val jackson = "2.12.2"
  const val jsonToolsPatch = "1.13"
  const val kotlinPoet = "1.9.0"
  const val material = "1.4.0"
  const val retrofit = "2.7.2"
+ const val stax = "1.0-2"
  const val sqlcipher = "4.5.0"
  const val truth = "1.0.1"
+ const val woodstox = "4.4.1"
+ const val xerces = "2.11.0"
 
  // Test dependencies
 

buildSrc/src/main/kotlin/LicenseeConfig.kt

@@ -63,6 +63,33 @@ fun Project.configureLicensee() {
  allowDependency("net.zetetic", "android-database-sqlcipher", "4.5.0") {
  because("Custom license, essentially BSD-3. https://www.zetetic.net/sqlcipher/license/")
  }
+
+ // JAXB https://github.com/eclipse-ee4j/jaxb-ri
+ allowDependency("jakarta.xml.bind", "jakarta.xml.bind-api", "2.3.3") {
+ because("BSD 3-clause.")
+ }
+
+ // 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.")
+ }
+
+ // Streaming API for XML (StAX)
+ allowDependency("javax.xml.stream", "stax-api", "1.0-2") {
+ because("Dual-licensed under CDDL 1.0 and GPL v3.")
+ }
+
+ // ANTLR 4
+ allowDependency("org.antlr", "antlr4-runtime", "4.9.1") {
+ because("BSD 3-clause. http:https://www.antlr.org/license.html")
+ }
+
+ // JSON-P https://javaee.github.io/jsonp/
+ allowDependency("org.glassfish", "javax.json", "1.1.4") {
+ because(
+ "Dual-licensed under CDDL 1.1 and GPL v2 with classpath exception. https://oss.oracle.com/licenses/CDDL+GPL-1.1"
+ )
+ }
  }
 }
 

datacapturegallery/build.gradle.kts → catalog/build.gradle.kts

@@ -9,7 +9,7 @@ android {
  buildToolsVersion = Plugins.Versions.buildTools
 
  defaultConfig {
- applicationId = "com.google.android.fhir.datacapture.gallery"
+ applicationId = "com.google.android.fhir.catalog"
  minSdk = Sdk.minSdk
  targetSdk = Sdk.targetSdk
  versionCode = 1
@@ -54,9 +54,9 @@ dependencies {
 
  implementation(Dependencies.Androidx.appCompat)
  implementation(Dependencies.Androidx.constraintLayout)
+ implementation(Dependencies.Androidx.coreKtx)
  implementation(Dependencies.Androidx.fragmentKtx)
  implementation(Dependencies.material)
- implementation(Dependencies.Kotlin.androidxCoreKtx)
  implementation(Dependencies.Kotlin.stdlib)
  implementation(Dependencies.Navigation.navFragmentKtx)
  implementation(Dependencies.Navigation.navUiKtx)

datacapturegallery/src/androidTest/java/com/google/android/fhir/datacapture/gallery/ExampleInstrumentedTest.kt → catalog/src/androidTest/java/com/google/android/fhir/catalog/ExampleInstrumentedTest.kt

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.google.android.fhir.datacapture.gallery
+package com.google.android.fhir.catalog
 
 import androidx.test.ext.junit.runners.AndroidJUnit4
 import androidx.test.platform.app.InstrumentationRegistry
@@ -33,6 +33,6 @@ class ExampleInstrumentedTest {
  fun useAppContext() {
  // Context of the app under test.
  val appContext = InstrumentationRegistry.getInstrumentation().targetContext
- Assert.assertEquals("com.google.android.fhir.datacapture.gallery", appContext.packageName)
+ Assert.assertEquals("com.google.android.fhir.catalog", appContext.packageName)
  }
 }

datacapturegallery/src/main/AndroidManifest.xml → catalog/src/main/AndroidManifest.xml

@@ -16,7 +16,7 @@
 -->
 <manifest
  xmlns:android="http:https://schemas.android.com/apk/res/android"
- package="com.google.android.fhir.datacapture.gallery"
+ package="com.google.android.fhir.catalog"
 >
 
  <application
@@ -27,7 +27,10 @@
  android:supportsRtl="true"
  android:theme="@style/Theme.Androidfhir"
  >
- <activity android:name=".MainActivity" android:exported="true">
+ <activity
+ android:name="com.google.android.fhir.catalog.MainActivity"
+ android:exported="true"
+ >
  <intent-filter>
  <action android:name="android.intent.action.MAIN" />
  <category android:name="android.intent.category.LAUNCHER" />

datacapturegallery/src/main/java/com/google/android/fhir/datacapture/gallery/CustomNumberPickerFactory.kt → catalog/src/main/java/com/google/android/fhir/catalog/CustomNumberPickerFactory.kt

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.google.android.fhir.datacapture.gallery
+package com.google.android.fhir.catalog
 
 import android.view.View
 import android.widget.NumberPicker

datacapturegallery/src/main/java/com/google/android/fhir/datacapture/gallery/CustomQuestionnaireFragment.kt → catalog/src/main/java/com/google/android/fhir/catalog/CustomQuestionnaireFragment.kt

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.google.android.fhir.datacapture.gallery
+package com.google.android.fhir.catalog
 
 import com.google.android.fhir.datacapture.QuestionnaireFragment
 

datacapturegallery/src/main/java/com/google/android/fhir/datacapture/gallery/MainActivity.kt → catalog/src/main/java/com/google/android/fhir/catalog/MainActivity.kt

@@ -14,13 +14,14 @@
  * limitations under the License.
  */
 
-package com.google.android.fhir.datacapture.gallery
+package com.google.android.fhir.catalog
 
 import android.os.Bundle
 import androidx.appcompat.app.AppCompatActivity
 import androidx.navigation.Navigation
 import androidx.navigation.ui.NavigationUI
 import com.google.android.material.bottomnavigation.BottomNavigationView
+import com.google.android.fhir.catalog.databinding.ActivityMainBinding
 
 class MainActivity : AppCompatActivity(R.layout.activity_main) {
  override fun onCreate(savedInstanceState: Bundle?) {

datacapturegallery/src/main/java/com/google/android/fhir/datacapture/gallery/QuestionnaireContainerFragment.kt → catalog/src/main/java/com/google/android/fhir/catalog/QuestionnaireContainerFragment.kt

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.google.android.fhir.datacapture.gallery
+package com.google.android.fhir.catalog
 
 import android.os.Bundle
 import android.view.LayoutInflater
@@ -32,11 +32,11 @@ import androidx.lifecycle.lifecycleScope
 import androidx.navigation.fragment.NavHostFragment
 import androidx.navigation.fragment.navArgs
 import ca.uhn.fhir.context.FhirContext
+import com.google.android.fhir.catalog.databinding.FragmentQuestionnaireContainerBinding
 import com.google.android.fhir.datacapture.QuestionnaireFragment
 import com.google.android.fhir.datacapture.QuestionnaireFragment.Companion.EXTRA_QUESTIONNAIRE_JSON_STRING
 import com.google.android.fhir.datacapture.QuestionnaireFragment.Companion.EXTRA_QUESTIONNAIRE_JSON_URI
 import com.google.android.fhir.datacapture.QuestionnaireFragment.Companion.EXTRA_QUESTIONNAIRE_RESPONSE_JSON_STRING
-import com.google.android.fhir.datacapture.gallery.databinding.FragmentQuestionnaireContainerBinding
 import kotlinx.coroutines.launch
 import org.hl7.fhir.r4.model.QuestionnaireResponse
 

datacapturegallery/src/main/java/com/google/android/fhir/datacapture/gallery/QuestionnaireListAdapter.kt → catalog/src/main/java/com/google/android/fhir/catalog/QuestionnaireListAdapter.kt

@@ -14,14 +14,14 @@
  * limitations under the License.
  */
 
-package com.google.android.fhir.datacapture.gallery
+package com.google.android.fhir.catalog
 
 import android.view.LayoutInflater
 import android.view.ViewGroup
 import androidx.navigation.findNavController
 import androidx.recyclerview.widget.RecyclerView
 import androidx.recyclerview.widget.RecyclerView.Adapter
-import com.google.android.fhir.datacapture.gallery.databinding.QuestionnaireListItemViewBinding
+import com.google.android.fhir.catalog.databinding.QuestionnaireListItemViewBinding
 
 class QuestionnaireListAdapter(private val questionnaireList: List<QuestionnaireListItem>) :
  Adapter<QuestionnaireListAdapter.ViewHolder>() {