Introduce S4H PDF upload

.github/workflows/app.yml

@@ -48,6 +48,11 @@ jobs:
       - run: flutter pub get
       - run: flutter pub run build_runner build
       - run: flutter build apk
+        env:
+          GPR_USER: ${{ secrets.GPR_USER }}
+          GPR_TOKEN: ${{ secrets.GPR_TOKEN }}
+          D4L_CLIENT_ID: ${{ secrets.D4L_CLIENT_ID }}
+          D4L_CLIENT_SECRET: ${{ secrets.D4L_CLIENT_SECRET }}
 
   build-ios:
     name: Build iOS Package

.gitignore

@@ -1,2 +1,3 @@
 node_modules
 *.log
+.idea/

app/CONTRIBUTING.md

@@ -16,6 +16,27 @@ Please also see the [contribution guide in the root folder](../CONTRIBUTING.md).
 You should now be able to run the app by opening the debug panel on the left and
 pressing the green triangle at the top (or using the shortcut <kbd>F5</kbd>).
 
+### `secrets.properties`
+
+The CHDP libraries require a few secrets to build. In
+[`android/secrets.properties`](android/secrets.properties) (gitignored) add the
+following keys and appropriate values:
+
+```properties
+gpr.user=
+gpr.token=
+
+d4l.clientId=
+d4l.clientSecret=
+```
+
+The first two are a Github username and Personal Access Token with the
+`read:packages` scope. This is used by gradle to download the SDK from D4L's
+private repositories.
+
+The next two are secrets given by D4L.  Ask Thomas at Thomas.Harris (at) hpi.de
+for them.
+
 ## Architecture
 
 The app consists of multiple so-called modules. Our main modules correspond to

app/android/.gitignore

@@ -11,3 +11,4 @@ GeneratedPluginRegistrant.java
 key.properties
 **/*.keystore
 **/*.jks
+secrets.properties

app/android/app/build.gradle

@@ -25,6 +25,21 @@ apply plugin: 'com.android.application'
 apply plugin: 'kotlin-android'
 apply from: "$flutterRoot/packages/flutter_tools/gradle/flutter.gradle"
 
+def secrets = new Properties()
+def secretsPropertiesFile = new File(rootProject.projectDir, "secrets.properties")
+if (secretsPropertiesFile.isFile()) {
+    secretsPropertiesFile.withReader("UTF-8") { reader -> secrets.load(reader) }
+} else {
+    assert System.getenv('GPR_USER')
+    assert System.getenv('GPR_TOKEN')
+    assert System.getenv('D4L_CLIENT_ID')
+    assert System.getenv('D4L_CLIENT_SECRET')
+    secrets.setProperty("gpr.user", System.getenv('GPR_USER'))
+    secrets.setProperty("gpr.token", System.getenv('GPR_TOKEN'))
+    secrets.setProperty("d4l.clientId", System.getenv('D4L_CLIENT_ID'))
+    secrets.setProperty("d4l.clientSecret", System.getenv('D4L_CLIENT_SECRET'))
+}
+
 android {
     compileSdkVersion 31
 
@@ -44,13 +59,27 @@ android {
     defaultConfig {
         // TODO: Specify your own unique Application ID (https://developer.android.com/studio/build/application-id.html).
         applicationId "de.hpi.pharme"
-        minSdkVersion 19
+        minSdkVersion 23
         targetSdkVersion 30
         versionCode flutterVersionCode.toInteger()
         versionName flutterVersionName
+
+        manifestPlaceholders += [
+                platform      : "s4h",
+                environment   : "staging",
+                clientId      : secrets.getProperty("d4l.clientId"),
+                clientSecret  : secrets.getProperty("d4l.clientSecret"),
+                redirectScheme: "eu.smart4health.7cf2befc-a010-4290-996c-a94426b5ce65",
+                debug         : "false"
+        ]
     }
 
     buildTypes {
+
+        debug {
+            matchingFallbacks = ["release", "debug"]
+        }
+
         release {
             // TODO: Add your own signing config for the release build.
             // Signing with the debug keys for now, so `flutter run --release` works.
@@ -65,4 +94,8 @@ flutter {
 
 dependencies {
     implementation "org.jetbrains.kotlin:kotlin-stdlib-jdk7:$kotlin_version"
+
+    implementation "care.data4life.hc-sdk-kmp:sdk-android:1.15.1"
+    implementation "care.data4life.hc-fhir-sdk-java:fhir-java:1.6.2"
+    implementation "com.jakewharton.threetenabp:threetenabp:1.4.0"
 }

app/android/app/src/main/AndroidManifest.xml

@@ -6,7 +6,9 @@
    <application
         android:label="PharMe"
         android:icon="@mipmap/launcher_icon"
+       android:theme="@style/NormalTheme"
         android:usesCleartextTraffic="false"
+       android:name="${applicationName}"
    >
         <activity
             android:name=".MainActivity"

app/android/app/src/main/kotlin/de/hpi/frasecys/MainActivity.kt

@@ -1,6 +1,151 @@
 package de.hpi.pharme
 
 import io.flutter.embedding.android.FlutterActivity
+import com.jakewharton.threetenabp.AndroidThreeTen
+import care.data4life.sdk.Data4LifeClient
+import io.flutter.embedding.engine.FlutterEngine
+import io.flutter.plugin.common.MethodChannel
+import android.os.Bundle
+import care.data4life.sdk.listener.ResultListener
+import care.data4life.sdk.lang.D4LException
+import care.data4life.fhir.r4.model.Attachment
+import care.data4life.fhir.r4.model.CodeSystemDocumentReferenceStatus
+import care.data4life.fhir.r4.model.DocumentReference
+import android.util.Base64
+import java.io.File
+import java.security.MessageDigest
+import care.data4life.sdk.call.Fhir4Record
+import java.util.Calendar
+import care.data4life.fhir.r4.util.FhirDateTimeConverter
 
-class MainActivity: FlutterActivity() {
+class MainActivity : FlutterActivity() {
+
+    override fun onCreate(savedInstanceState: Bundle?) {
+        super.onCreate(savedInstanceState)
+
+        AndroidThreeTen.init(this.applicationContext)
+        Data4LifeClient.init(applicationContext)
+    }
+
+
+    override fun configureFlutterEngine(flutterEngine: FlutterEngine) {
+        super.configureFlutterEngine(flutterEngine)
+
+        MethodChannel(flutterEngine.dartExecutor.binaryMessenger, "chdp")
+            .setMethodCallHandler { call, result ->
+                when (call.method) {
+                    "isLoggedIn" -> Data4LifeClient.getInstance().isUserLoggedIn(
+                        object : ResultListener<Boolean> {
+                            override fun onSuccess(t: Boolean) = result.success(t)
+
+                            override fun onError(exception: D4LException) =
+                                result.error(
+                                    "D4LException",
+                                    "Failed to check login status",
+                                    exception
+                                )
+                        }
+                    )
+                    "login" -> {
+                        val intent = Data4LifeClient.getInstance().getLoginIntent(
+                            this@MainActivity,
+                            setOf(
+                                "perm:r",
+                                "rec:r",
+                                "rec:w",
+                                "attachment:r",
+                                "attachment:w",
+                                "user:r",
+                                "user:w",
+                                "user:q",
+                            )
+                        )
+
+                        [email protected](intent, Data4LifeClient.D4L_AUTH)
+
+                        result.success(0)
+                    }
+                    "logout" -> {
+                        Data4LifeClient.getInstance().logout(
+                            object : care.data4life.sdk.listener.Callback {
+                                override fun onSuccess() = result.success(0)
+
+                                override fun onError(exception: D4LException) =
+                                    result.error(
+                                        "D4LException",
+                                        "Failed to logout",
+                                        exception
+                                    )
+                            }
+                        )
+
+                    }
+                    "upload" -> {
+                        val path: String = call.argument("path")!!
+                        val title: String = call.argument("title")!!
+                        val docRef = makeDocumentReference(path, title)
+
+                        Data4LifeClient.getInstance().fhir4.create(
+                            resource = docRef,
+                            annotations = listOf("pharme"),
+                            callback = object :
+                                care.data4life.sdk.call.Callback<Fhir4Record<DocumentReference>> {
+                                override fun onSuccess(_result: Fhir4Record<DocumentReference>) {
+                                    result.success(true)
+                                }
+
+                                override fun onError(exception: D4LException) {
+                                    result.success(false)
+                                }
+                            }
+                        )
+                    }
+                    "toast" -> {
+                        val msg: String = call.argument("msg")!!
+
+                        android.widget.Toast.makeText(this, msg, android.widget.Toast.LENGTH_SHORT).show()
+                    }
+                    else -> result.notImplemented()
+                }
+            }
+    }
+
+    override fun onActivityResult(
+        requestCode: Int,
+        resultCode: Int,
+        data: android.content.Intent?,
+    ) {
+        super.onActivityResult(requestCode, resultCode, data)
+
+        if (requestCode == Data4LifeClient.D4L_AUTH) {
+            if (resultCode == android.app.Activity.RESULT_OK) {
+                android.util.Log.i("PHARME", "login successful")
+            }
+        }
+    }
 }
+
+fun makeDocumentReference(path: String, title: String): DocumentReference {
+    val bytes = File(path).readBytes()
+    return DocumentReference(
+        CodeSystemDocumentReferenceStatus.CURRENT,
+        listOf(
+            DocumentReference.DocumentReferenceContent(
+                Attachment().apply {
+                    contentType = "application/pdf"
+                    data = Base64.encodeToString(
+                        bytes,
+                        Base64.NO_WRAP,
+                    )
+                    size = bytes.size
+                    hash = with(MessageDigest.getInstance("SHA-1")) {
+                        Base64.encodeToString(digest(bytes), Base64.NO_WRAP)
+                    }
+                },
+            ),
+        ),
+    ).apply {
+        description = title
+        date = FhirDateTimeConverter.toFhirInstant(Calendar.getInstance().time)
+    }
+}

app/android/app/src/main/res/values-night/styles.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <resources>
     <!-- Theme applied to the Android Window while the process is starting when the OS's Dark Mode setting is on -->
-    <style name="LaunchTheme" parent="@android:style/Theme.Black.NoTitleBar">
+    <style name="LaunchTheme" parent="Theme.AppCompat.DayNight.NoActionBar">
         <!-- Show a splash screen on the activity. Automatically removed when
              Flutter draws its first frame -->
         <item name="android:windowBackground">@drawable/launch_background</item>
@@ -12,7 +12,7 @@
          running.
 
          This Theme is only used starting with V2 of Flutter's Android embedding. -->
-    <style name="NormalTheme" parent="@android:style/Theme.Black.NoTitleBar">
+    <style name="NormalTheme" parent="Theme.AppCompat.DayNight.NoActionBar">
         <item name="android:windowBackground">?android:colorBackground</item>
     </style>
 </resources>

app/android/app/src/main/res/values/styles.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <resources>
     <!-- Theme applied to the Android Window while the process is starting when the OS's Dark Mode setting is off -->
-    <style name="LaunchTheme" parent="@android:style/Theme.Light.NoTitleBar">
+    <style name="LaunchTheme" parent="Theme.AppCompat.Light.NoActionBar">
         <!-- Show a splash screen on the activity. Automatically removed when
              Flutter draws its first frame -->
         <item name="android:windowBackground">@drawable/launch_background</item>
@@ -12,7 +12,7 @@
          running.
 
          This Theme is only used starting with V2 of Flutter's Android embedding. -->
-    <style name="NormalTheme" parent="@android:style/Theme.Light.NoTitleBar">
+    <style name="NormalTheme" parent="Theme.AppCompat.Light.NoActionBar">
         <item name="android:windowBackground">?android:colorBackground</item>
     </style>
 </resources>

app/android/build.gradle

@@ -11,10 +11,50 @@ buildscript {
     }
 }
 
+def secrets = new Properties()
+def secretsPropertiesFile = new File(rootProject.projectDir, "secrets.properties")
+if (secretsPropertiesFile.isFile()) {
+    secretsPropertiesFile.withReader("UTF-8") { reader -> secrets.load(reader) }
+} else {
+    assert System.getenv('GPR_USER')
+    assert System.getenv('GPR_TOKEN')
+    assert System.getenv('D4L_CLIENT_ID')
+    assert System.getenv('D4L_CLIENT_SECRET')
+    secrets.setProperty("gpr.user", System.getenv('GPR_USER'))
+    secrets.setProperty("gpr.token", System.getenv('GPR_TOKEN'))
+    secrets.setProperty("d4l.clientId", System.getenv('D4L_CLIENT_ID'))
+    secrets.setProperty("d4l.clientSecret", System.getenv('D4L_CLIENT_SECRET'))
+}
+
 allprojects {
     repositories {
         google()
         mavenCentral()
+
+        // tried to loop over a list of urls like in kotlin but no dice
+        maven {
+            url "https://maven.pkg.github.com/d4l-data4life/hc-util-sdk-kmp"
+            credentials {
+                username secrets.getProperty("gpr.user")
+                password secrets.getProperty("gpr.token")
+            }
+        }
+
+        maven {
+            url "https://maven.pkg.github.com/d4l-data4life/hc-fhir-sdk-java"
+            credentials {
+                username secrets.getProperty("gpr.user")
+                password secrets.getProperty("gpr.token")
+            }
+        }
+
+        maven {
+            url "https://maven.pkg.github.com/d4l-data4life/hc-fhir-helper-sdk-kmp"
+            credentials {
+                username secrets.getProperty("gpr.user")
+                password secrets.getProperty("gpr.token")
+            }
+        }
     }
 }
 

app/lib/common/models/medication/guideline.dart

@@ -1,8 +1,6 @@
 import 'package:freezed_annotation/freezed_annotation.dart';
 import 'package:hive/hive.dart';
 
-import '../../module.dart';
-
 part 'guideline.g.dart';
 
 @HiveType(typeId: 9)
@@ -70,7 +68,7 @@ class Guideline {
 
   @override
   int get hashCode {
-    return hashValues(
+    return Object.hash(
       implication,
       recommendation,
       warningLevel,
@@ -115,7 +113,7 @@ class Phenotype {
   }
 
   @override
-  int get hashCode => hashValues(geneResult.name, geneSymbol.name);
+  int get hashCode => Object.hash(geneResult.name, geneSymbol.name);
 }
 
 @HiveType(typeId: 11)