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Diff for: ‎.gitignore

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# Built application files
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*.apk
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*.ap_
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# Files for the Dalvik VM
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*.dex
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# Java class files
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*.class
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# Generated files
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bin/
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gen/
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# Gradle files
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.gradle/
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build/
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/*/build/
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# Local configuration file (sdk path, etc)
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local.properties
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# Proguard folder generated by Eclipse
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proguard/
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# Log Files
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*.log
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app/crashlytics.properties
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/.idea/*
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/captures
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.DS_Store
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/tmp/
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*.gz
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com_crashlytics_export_strings.xml
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*.iml
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app/*.properties

Diff for: ‎LICENSE

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same "printed page" as the copyright notice for easier
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identification within third-party archives.
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Copyright {yyyy} {name of copyright owner}
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Copyright 2016 Open mHealth
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.

Diff for: ‎README.md

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# Introduction
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MoleMapper Android is an open source port of the [Mole Mapper](https://github.com/Sage-Bionetworks/MoleMapper) ResearchKit(TM) melanoma research study to ResearchStack.
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This implementation of MoleMapper on Android was created to serve as an open source example of best practices for creating a production-ready ResearchStack application. Initial funding was generous provided by a grant from the Robert Wood Johnson Foundation.
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Oregon Health & Science University will be posting their public fork of Mole Mapper for Android in the near future, which will more closely follow the Mole Mapper Android app (being released soon by OHSU on Google Play). We will prove links to that project and the app on Google Play as they become available.
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# About MoleMapper
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MoleMapper is a personalized tool to help you map, measure, and monitor the moles on your skin. Using a familiar Maps-like interface, you can measure the size of a mole using the camera and a common reference object like a coin.
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If you are 18 or older, MoleMapper also gives you the option to participate in a research study developed in partnership with researchers at Oregon Health & Science University and Sage Bionetworks, a 501 (c)(3) nonprofit research organization to better understand skin biology and melanoma risks.
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The MoleMapper research study was created in partnership with researchers at Oregon Health & Science University and Sage Bionetworks. Unless otherwise noted, it should be assumed that all images, logos, and trademarks are copyrighted and should be used only with permission of the original copyright owners.
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### 3<sup>rd</sup>-party library disclosures
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<b>
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com.android.support:appcompat-v7<br />
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com.android.support:cardview-v7<br />
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com.android.support:design
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</b>
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- Used for theming and styling views within the app. Libraries also provide backward-compatible versions of Android framework APIs (e.g. vector icon support)
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<b>com.android.support:support-v13:23.2.0</b>
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- Support is a set of code libraries that provide backward-compatible versions of Android framework APIs. We use support for FragmentCompat and its use in receiving the results for permission requests.
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<b>com.android.support:multidex</b>
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- The Android MultiDex support library enables us to go past the default 65K method limit for an android project.
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<b>com.davemorrissey.labs:subsampling-scale-image-view</b>
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- Used within the MoleMeasurementActivity, allows user to zoom and pan an image with subsampling for low impact on memory
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<b>co.touchlab.squeaky:squeaky-processor:0.4.0.0</b>
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- Annotation processor for the Squeaky ORMLite database library. The library creates auto-generated code at compile time for our database pojos (see Mole or Measurement classes)
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<b>
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pl.charmas.android:android-reactive-location<br />
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com.google.android.gms:play-services-location<br />
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</b>
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- play-services-location allows the app to get the user's location while being conscious of battery life. Android-reactive-location library wraps the location services API’s in Rx Observables.
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<b>com.crashlytics.sdk.android:crashlytics</b>
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- Crash / Logging library being used during the QA period. This library will be removed at v1.0 release.

Diff for: ‎app/.gitignore

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/build

Diff for: ‎app/build.gradle

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apply plugin: 'com.android.application'
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apply plugin: 'me.tatarka.retrolambda'
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apply plugin: 'com.neenbedankt.android-apt'
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apply plugin: 'io.fabric'
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android {
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compileSdkVersion 23
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buildToolsVersion "23.0.2"
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defaultConfig {
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applicationId "org.researchstack.molemapper"
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minSdkVersion 16
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targetSdkVersion 23
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versionCode 9
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versionName "0.9.4"
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multiDexEnabled true
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// Enables use of vector drawable for projects using Gradle 2.0.+. Please see
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// http://android-developers.blogspot.com/2016/02/android-support-library-232.html if you
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// are running Gradle 1.5 for other necessary steps
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vectorDrawables.useSupportLibrary = true
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}
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buildTypes {
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release {
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minifyEnabled false
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proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
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buildConfigField 'String', 'STUDY_BASE_URL', "\"https://webservices.sagebridge.org/\""
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// Define STUDY_ID, STUDY_NAME, STUDY_PEM can be defined here or in your local.properties
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// file. These variables are needed for upload to properly work.
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// RELEASE_STUDY_ID is of type String (e.g. "id-mole-mapper-study")
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// RELEASE_STUDY_NAME is of type String (e.g. "MoleMapper Study")
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// RELEASE_STUDY_PEM_FILE_NAME is of type String, (e.g. "molemapper"). The pem file should
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// be located at the root directory of your assets folder.
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buildConfigField 'String', 'STUDY_ID', RELEASE_STUDY_ID
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buildConfigField 'String', 'STUDY_NAME', RELEASE_STUDY_NAME
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buildConfigField 'String', 'STUDY_PEM', RELEASE_STUDY_PEM_FILE_NAME
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}
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debug {
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debuggable true
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minifyEnabled false
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proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
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buildConfigField 'String', 'STUDY_BASE_URL', "\"https://webservices.sagebridge.org/\""
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// Define STUDY_ID, STUDY_NAME, STUDY_PEM can be defined here or in your local.properties
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// file. These variables are needed for upload to properly work.
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// RELEASE_STUDY_ID is of type String (e.g. "id-mole-mapper-study")
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// RELEASE_STUDY_NAME is of type String (e.g. "MoleMapper Study")
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// RELEASE_STUDY_PEM_FILE_NAME is of type String, (e.g. "molemapper"). The pem file should
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// be located at the root directory of your assets folder.
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buildConfigField 'String', 'STUDY_ID', DEBUG_STUDY_ID
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buildConfigField 'String', 'STUDY_NAME', DEBUG_STUDY_NAME
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buildConfigField 'String', 'STUDY_PEM', DEBUG_STUDY_PEM_FILE_NAME
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}
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}
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compileOptions {
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sourceCompatibility JavaVersion.VERSION_1_8
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targetCompatibility JavaVersion.VERSION_1_8
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}
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packagingOptions {
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exclude 'META-INF/LICENSE.txt'
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exclude 'META-INF/NOTICE.txt'
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}
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dexOptions {
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javaMaxHeapSize "4g" //specify the heap size for the dex process
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}
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}
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dependencies {
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compile fileTree(dir: 'libs', include: ['*.jar'])
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testCompile 'junit:junit:4.12'
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compile 'com.android.support:appcompat-v7:23.2.1'
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compile 'com.android.support:cardview-v7:23.2.1'
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compile 'com.android.support:support-v13:23.2.1'
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compile 'com.android.support:design:23.2.1'
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compile 'com.android.support:multidex:1.0.1'
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compile 'org.researchstack:skin:1.0.0.rc1-tl'
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compile 'com.davemorrissey.labs:subsampling-scale-image-view:3.4.1'
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apt 'co.touchlab.squeaky:squeaky-processor:0.4.0.0'
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compile 'com.madgag.spongycastle:core:1.54.0.0'
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compile 'com.madgag.spongycastle:prov:1.54.0.0'
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compile 'com.madgag.spongycastle:pkix:1.54.0.0'
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compile 'pl.charmas.android:android-reactive-location:0.8@aar'
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compile 'com.google.android.gms:play-services-location:8.4.0'
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compile('com.crashlytics.sdk.android:crashlytics:2.5.5@aar') {
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transitive = true;
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}
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}

Diff for: ‎app/lint.xml

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<lint>
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<issue id="InvalidPackage">
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<ignore regexp="okio-1.6.0.jar"/>
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<ignore regexp="retrofit-2.0.0-beta3.jar"/>
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<ignore regexp="pkix-1.54.0.0.jar"/>
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</issue>
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</lint>

Diff for: ‎app/proguard-rules.pro

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# Add project specific ProGuard rules here.
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# By default, the flags in this file are appended to flags specified
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# in /Users/wdziemia/Library/Android/sdk/tools/proguard/proguard-android.txt
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# You can edit the include path and order by changing the proguardFiles
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# directive in build.gradle.
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#
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# For more details, see
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# http://developer.android.com/guide/developing/tools/proguard.html
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# Add any project specific keep options here:
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# If your project uses WebView with JS, uncomment the following
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# and specify the fully qualified class name to the JavaScript interface
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# class:
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#-keepclassmembers class fqcn.of.javascript.interface.for.webview {
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# public *;
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#}

Diff for: ‎app/src/androidTest/java/org/researchstack/molemapper/ApplicationTest.java

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package org.researchstack.molemapper;
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import android.app.Application;
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import android.test.ApplicationTestCase;
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/**
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* <a href="http://d.android.com/tools/testing/testing_android.html">Testing Fundamentals</a>
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*/
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public class ApplicationTest extends ApplicationTestCase<Application>
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{
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public ApplicationTest()
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{
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super(Application.class);
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}
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}

Diff for: ‎app/src/main/AndroidManifest.xml

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<manifest
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package="org.researchstack.molemapper"
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xmlns:android="http://schemas.android.com/apk/res/android"
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>
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<uses-permission android:name="android.permission.INTERNET"/>
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<uses-permission android:name="android.permission.CAMERA"/>
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<uses-feature android:name="android.hardware.camera"/>
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<uses-feature android:name="android.hardware.camera.autofocus"/>
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<application
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android:name="org.researchstack.molemapper.MoleMapperApplication"
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android:allowBackup="true"
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android:icon="@mipmap/ic_launcher"
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android:label="@string/app_name"
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android:supportsRtl="true"
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android:theme="@style/Theme.MoleMapper"
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>
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<activity
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android:name="org.researchstack.skin.ui.SplashActivity"
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android:theme="@style/Theme.MoleMapper.Splash"
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android:windowSoftInputMode="adjustNothing"
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>
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<intent-filter>
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<action android:name="android.intent.action.MAIN"/>
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<category android:name="android.intent.category.LAUNCHER"/>
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</intent-filter>
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</activity>
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<activity
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android:name="org.researchstack.skin.ui.MainActivity"
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android:label="@string/app_name"
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android:screenOrientation="portrait"
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android:theme="@style/Theme.MoleMapper.Main"
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/>
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<activity
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android:name="org.researchstack.molemapper.PhotoCaptureActivity"
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android:screenOrientation="portrait"
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android:theme="@style/Theme.MoleMapper.TransparentStatusBar"
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/>
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<activity
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android:name="org.researchstack.molemapper.BodyMapActivity"
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/>
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<activity
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android:name="org.researchstack.molemapper.BodyZoneActivity"
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/>
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<activity
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android:name="org.researchstack.molemapper.MoleHistoryActivity"
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android:theme="@style/Theme.MoleMapper.TransparentStatusBar"
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/>
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<activity
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android:name="org.researchstack.molemapper.MoleMeasurementActivity"
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android:theme="@style/Theme.MoleMapper.TransparentStatusBar"
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/>
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<activity
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android:name="org.researchstack.skin.ui.OnboardingActivity"
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android:label="@string/app_name"
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android:theme="@style/Theme.MoleMapper.Onboarding"
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/>
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<activity
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android:name="org.researchstack.backbone.ui.ViewTaskActivity"
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android:label="@string/app_name"
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android:windowSoftInputMode="adjustResize"
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android:theme="@style/Theme.MoleMapper.Survey"
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/>
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<activity
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android:name="org.researchstack.skin.ui.ConsentTaskActivity"
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android:label="@string/app_name"
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android:windowSoftInputMode="adjustResize"
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android:theme="@style/Theme.MoleMapper.Survey"
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/>
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<activity
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android:name="org.researchstack.skin.ui.SignUpTaskActivity"
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android:label="@string/app_name"
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android:theme="@style/Theme.MoleMapper.Survey"
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/>
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<activity
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android:name="org.researchstack.skin.ui.EmailVerificationActivity"
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android:label="@string/rss_confirm"
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android:theme="@style/Theme.MoleMapper.Survey"
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/>
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<activity
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android:name="org.researchstack.backbone.ui.ViewWebDocumentActivity"
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android:label="@string/app_name"
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android:theme="@style/Theme.MoleMapper.Survey"
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/>
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<activity
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android:name="org.researchstack.backbone.ui.ViewVideoActivity"
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android:configChanges="orientation|keyboard|keyboardHidden|screenSize|screenLayout|uiMode"
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android:label="@string/app_name"
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android:theme="@style/Theme.MoleMapper.Video"
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/>
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<activity
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android:name="org.researchstack.molemapper.MoleMapperSettingsActivity"
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android:label="@string/rss_settings"
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android:theme="@style/Theme.MoleMapper.Settings"/>
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<activity
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android:name="org.researchstack.molemapper.ui.MoleLearnActivity"
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android:label="@string/learn_more"
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android:theme="@style/Theme.MoleMapper.Settings"
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/>
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<receiver
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android:name="org.researchstack.skin.notification.TaskNotificationReceiver"
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android:enabled="true"
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/>
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<receiver
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android:name="org.researchstack.skin.notification.DeviceBootReceiver"
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android:enabled="true"
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android:exported="false"
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>
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<intent-filter>
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<action android:name="android.intent.action.BOOT_COMPLETED"/>
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</intent-filter>
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</receiver>
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<receiver
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android:name="org.researchstack.skin.notification.TaskAlertReceiver"
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android:enabled="true"
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android:exported="false"
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>
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<intent-filter>
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<action android:name="org.researchstack.skin.notification.ALERT_CREATE"/>
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<action android:name="org.researchstack.skin.notification.ALERT_CREATE_ALL"/>
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<action android:name="org.researchstack.skin.notification.ALERT_DELETE"/>
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<action android:name="org.researchstack.skin.notification.ALERT_DELETE_ALL"/>
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</intent-filter>
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</receiver>
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<meta-data
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android:name="io.fabric.ApiKey"
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android:value="XXXXXXXXXXXXXX"/>
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</application>
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</manifest>

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