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Bridging the gap between ResearchStack and i2b2 with FHIR
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README.md

C3-PRO Android Framework

C3-PRO uses the HAPI FHIR library and ResearchStack in an attempt to bring the C3-PRO functionality to Android.

Combining 🔥 FHIR and ResearchStack, usually for data storage into i2b2, this framework allows you to use FHIR Questionnaire resources directly with a ResearchStack ViewTaskActivity and will return FHIR QuestionnaireResponse that you can send to your server.

Usage

The library is hosted at bintray.

To set up a project to use the C3PRO framework, the library is available on jCenter and can simply be added as a dependency:

dependencies {
    compile ('ch.usz.c3pro:c3-pro-android-framework:1.0'){
        exclude module: 'javax.servlet-api'
        exclude module: 'hapi-fhir-base'
    }

}

Some packages of third party dependencies need to be excluded to avoid duplicate class names.

#####The setup

A sample application to demonstrate the setup is available here

A subclass of Application is needed and set as main application in the AndroidManifest. Most setup methods are best put in the onCreate() method of the C3PROApplication class to make sure they survive Activities' lifecycles. The DataQueue or EncryptedDataQueue is best set up here with the FHIR url. There are also some ResearchStack settings. More details about that can be found on the ResearchStack website.

The Applicationfile should look something like this:

public class C3PROApplication extends Application {

    @Override
    public void onCreate() {
        super.onCreate();

        // TODO: initialize C3-PRO
        /**
         * Initialize DataQueue:
         * You have to provide a context (your application) and an URL to the FHIR Server.
         * Once initialized, DataQueue can write and read Resources from your server in a
         * background thread.
         * */
        DataQueue.init(this, "http://fhirtest.uhn.ca/baseDstu3");

        /**
         * Or initialize EncryptedDataQueue. It can do everything the DataQueue can do plus it can
         * send jsonObjects containing encrypted FHIR resources to a special C3-PRO server.
         * */
        try {
            EncryptedDataQueue.init(this, "http://fhirtest.uhn.ca/baseDstu3", "http://encrypted.c3-pro.org", "enc/public.crt", "");
        } catch (CertificateException e) {
            e.printStackTrace();
        }catch (NoSuchAlgorithmException e) {
            e.printStackTrace();
        } catch (InvalidKeySpecException e) {
            e.printStackTrace();
        }

        // TODO: following are some ResearchStack settings. For more info, visit http://researchstack.org
        // ResearchStack: Customize your pin code preferences
        PinCodeConfig pinCodeConfig = new PinCodeConfig(); // default pin config (4-digit, 1 min lockout)

        // ResearchStack: Customize encryption preferences
        EncryptionProvider encryptionProvider = new UnencryptedProvider(); // No pin, no encryption

        // ResearchStack: If you have special file handling needs, implement FileAccess
        FileAccess fileAccess = new SimpleFileAccess();

        // ResearchStack: If you have your own custom database, implement AppDatabase
        AppDatabase database = new DatabaseHelper(this,
                DatabaseHelper.DEFAULT_NAME,
                null,
                DatabaseHelper.DEFAULT_VERSION);

        StorageAccess.getInstance().init(pinCodeConfig, encryptionProvider, fileAccess, database);
    }
}

The AndroidManifest:

<manifest xmlns:android="http://schemas.android.com/apk/res/android"
    package="ch.usz.c3pro.demo.android">

    <application
        android:name=".C3PROApplication"
        android:allowBackup="true"
        android:icon="@mipmap/ic_launcher"
        android:label="@string/app_name"
        android:supportsRtl="true"
        android:theme="@style/AppTheme">

        <activity android:name=".MainActivity">
            <intent-filter>
                <action android:name="android.intent.action.MAIN" />

                <category android:name="android.intent.category.LAUNCHER" />
            </intent-filter>
        </activity>

    </application>

</manifest>

The build.gradle:

apply plugin: 'com.android.application'

android {
    compileSdkVersion 23
    buildToolsVersion "23.0.3"

    defaultConfig {
        applicationId "ch.usz.c3pro.demo.android"
        minSdkVersion 16
        targetSdkVersion 23
        versionCode 1
        versionName "1.0"
    }
    buildTypes {
        release {
            minifyEnabled false
            proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
        }
    }
    dexOptions {
        javaMaxHeapSize "3g"
    }
}

dependencies {
    compile fileTree(include: ['*.jar'], dir: 'libs')
    testCompile 'junit:junit:4.12'

    // TODO: include C3PRO framework, but exclude some of the hapi library
    compile('ch.usz.c3pro:c3-pro-android-framework:1.0') {
        exclude module: 'javax.servlet-api'
        exclude module: 'hapi-fhir-base'
    }
}

Versions

The library uses HAPI FHIR 1.6 for dstu3. Questionnaires in dstu2 (with group and question elements) will not work with this demo setup. Target Android sdk is 23, minimum sdk 16 due to ResearchStack.

Issues

Implementation is ongoing, not everything is complete and nothing has been tested systematically.

  • EnableWhen conditions have only been tested with boolean and singlechoice answertypes
  • The encrypted DataQueue is not tested yet and still has some testing artefacts in the framework code
  • Proper error handling not thoroughly implemented as of yet.

Modules

The framework will consist of several modules that complement each other, similar to the C3-PRO ios framework.

Questionnaires

Enables the conversion of a FHIR Questionnaire resource to a ResearchSTack task that can be presented to the user using a ViewTaskActivity and conversion back from a TaskResult to a FHIR QuestionnaireResponse resource.

DataQueue

This module provides a FHIR server implementation used to move FHIR resources, created on device, to a FHIR server, without the need for user interaction nor -confirmation. An EncryptedDataQueue is available to send jsonObjects containing encrypted FHIR resources to a special C3-PRO server.

GoogleFit

Supports easy interaction with the Google Fit API. Step count, height and latest weight of the user can be read and returned as FHIR Quantity and Observation. It can also write new height and weight data into the Fit history.

Licence

This work will be Apache 2 licensed. A NOTICE.txt file will follow at some point, and don't forget to also add the licensing information of the submodules somewhere in your product:

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