23andMe API & google oauth2 - round trip working example w/ sickle cell anemia

tutorials/oauth2-with-23andme-in-java/index.md

@@ -0,0 +1,31 @@
+---
+title: Authenticating to the 23andMe API with the Google Java OAuth 2.0 Client
+description: Authenticate to the 23andMe API with the Google Java OAuth 2.0 client and pull a single genotype for i3003137, a SNP associated with Sickle Cell Anemia.
+author: dennisbyrne
+tags: OAuth, OAuth2, Java, 23andMe, genomics
+date_published: 2017-04-26
+---
+
+This sample app uses Google's OAuth 2.0 java lib to authenticate with 23andMe. Once authenticated the app pulls a single genotype for i3003137, a SNP associated with Sickle Cell Anemia.
+
+## Create a 23andMe client
+
+Follow the instructions at https://api.23andme.com/apply/ to create a 23andMe Oauth client. Make sure to set your `redirect_uri` to http://127.0.0.1:8080/Callback . You will be given a `client_id` and a `client_secret`.
+
+## Clone the community repo
+
+      git clone https://github.com/GoogleCloudPlatform/community.git
+
+## Run the sample app
+
+      cd community/tutorials/oauth2-with-23andMe-in-java/java/
+
+Make sure you have [maven installed][install_maven], then run the app:
+
+      mvn compile && mvn -q exec:java -Dexec.args="`client_id` `client_secret`"
+
+[install_maven]: https://maven.apache.org/install.html
+
+## Example output
+
+`Genotype @ i3003137, a SNP associated with Sickle Cell Anemia: TT`

tutorials/oauth2-with-23andme-in-java/java/pom.xml

@@ -0,0 +1,86 @@
+<!--
+Copyright 2015 Google Inc. All Rights Reserved.
+
+ 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.
+-->
+
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <parent>
+    <groupId>com.google.oauth-client</groupId>
+    <artifactId>google-oauth-client-parent</artifactId>
+    <version>1.23.0-SNAPSHOT</version>
+    <relativePath>../../pom.xml</relativePath>
+  </parent>
+  <artifactId>simple-example-23andMe</artifactId>
+  <name>23andMe API Example using OAuth2</name>
+
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>exec-maven-plugin</artifactId>
+        <version>1.1</version>
+        <executions>
+          <execution>
+            <goals>
+              <goal>java</goal>
+            </goals>
+          </execution>
+        </executions>
+        <configuration>
+          <mainClass>com.google.api.services.samples.ttam.SimpleExample</mainClass>
+        </configuration>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-deploy-plugin</artifactId>
+        <version>2.5</version>
+        <configuration>
+          <skip>true</skip>
+        </configuration>
+      </plugin>
+      <plugin>
+        <artifactId>maven-checkstyle-plugin</artifactId>
+        <version>2.6</version>
+        <configuration>
+          <configLocation>../checkstyle.xml</configLocation>
+          <consoleOutput>true</consoleOutput>
+          <failOnViolation>false</failOnViolation>
+        </configuration>
+        <executions>
+          <execution>
+            <goals>
+              <goal>check</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+    <finalName>${project.artifactId}-${project.version}</finalName>
+  </build>
+  <dependencies>
+    <dependency>
+      <groupId>com.google.oauth-client</groupId>
+      <artifactId>google-oauth-client-jetty</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>com.google.http-client</groupId>
+      <artifactId>google-http-client-jackson2</artifactId>
+    </dependency>
+  </dependencies>
+  <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  </properties>
+</project>

tutorials/oauth2-with-23andme-in-java/java/src/main/java/com/google/api/services/samples/ttam/Account.java

@@ -0,0 +1,27 @@
+/*
+ * Copyright (c) 2011 Google Inc.
+ *
+ * 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.api.services.samples.ttam;
+
+import com.google.api.client.util.Key;
+
+import java.util.List;
+
+public class Account {
+
+    @Key
+    public List<Profile> profiles;
+
+}

tutorials/oauth2-with-23andme-in-java/java/src/main/java/com/google/api/services/samples/ttam/Genotype.java

@@ -0,0 +1,25 @@
+/*
+ * Copyright (c) 2011 Google Inc.
+ *
+ * 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.api.services.samples.ttam;
+
+import com.google.api.client.util.Key;
+
+public class Genotype {
+
+    @Key
+    public String i3003137;
+
+}

tutorials/oauth2-with-23andme-in-java/java/src/main/java/com/google/api/services/samples/ttam/Profile.java

@@ -0,0 +1,25 @@
+/*
+ * Copyright (c) 2011 Google Inc.
+ *
+ * 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.api.services.samples.ttam;
+
+import com.google.api.client.util.Key;
+
+public class Profile {
+
+    @Key
+    public String id;
+
+}

tutorials/oauth2-with-23andme-in-java/java/src/main/java/com/google/api/services/samples/ttam/SimpleExample.java

@@ -0,0 +1,128 @@
+/*
+ * Copyright (c) 2011 Google Inc.
+ *
+ * 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.api.services.samples.ttam;
+
+import com.google.api.client.auth.oauth2.AuthorizationCodeFlow;
+import com.google.api.client.auth.oauth2.ClientParametersAuthentication;
+import com.google.api.client.auth.oauth2.Credential;
+import com.google.api.client.extensions.java6.auth.oauth2.AuthorizationCodeInstalledApp;
+import com.google.api.client.extensions.java6.auth.oauth2.VerificationCodeReceiver;
+import com.google.api.client.extensions.jetty.auth.oauth2.LocalServerReceiver;
+import com.google.api.client.http.*;
+import com.google.api.client.http.javanet.NetHttpTransport;
+import com.google.api.client.json.JsonFactory;
+import com.google.api.client.json.JsonObjectParser;
+import com.google.api.client.json.jackson2.JacksonFactory;
+import com.google.api.client.util.store.DataStoreFactory;
+import com.google.api.client.util.store.FileDataStoreFactory;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collection;
+
+import static com.google.api.client.auth.oauth2.BearerToken.authorizationHeaderAccessMethod;
+
+
+/**
+ * 23andMe API Example with Sickle Cell Anemia, using OAuth2
+ *
+ * Instructions:
+ * 1) Create a 23andMe client at https://api.23andme.com/apply/ with a redirect_uri of http://127.0.0.1:8080/Callback
+ * 2) Run this java application with two arguments: the client_id followed by the client_secret
+ * 3) Authenticate, using your 23andMe credentials
+ *
+ * @author Dennis Byrne <[email protected]>
+ */
+public class SimpleExample {
+
+    /**
+     * The client_id field value at https://api.23andme.com/dev/
+     */
+    private final String clientId;
+    /**
+     * The client_secret field value at https://api.23andme.com/dev/
+     */
+    private final String clientSecret;
+    private final DataStoreFactory dataStoreFactory;
+    private final HttpTransport httpTransport;
+    private final JsonFactory jsonFactory;
+
+    private static final Collection<String> SCOPES = Arrays.asList("basic", "i3003137");
+
+    private static final String DOMAIN = "127.0.0.1";
+    private static final int PORT = 8080;
+    private static final String BASE_URL = "https://api.23andme.com/";
+    private static final String AUTHORIZATION_SERVER_URL = BASE_URL + "authorize/";
+    private static final String TOKEN_SERVER_URL = BASE_URL + "token/";
+
+    public SimpleExample(FileDataStoreFactory dataStoreFactory, String clientId, String clientSecret) {
+        this.clientId = clientId;
+        this.dataStoreFactory = dataStoreFactory;
+        this.clientSecret = clientSecret;
+        this.httpTransport = new NetHttpTransport();
+        this.jsonFactory = new JacksonFactory();
+    }
+
+    public static void main(String[] args) throws Throwable {
+        File directory = new File(System.getProperty("user.home"), ".store/ttam");
+        if (args.length != 2) {
+            throw new AssertionError("client_id and client_secret are required");
+        }
+        SimpleExample simpleExample = new SimpleExample(new FileDataStoreFactory(directory), args[0], args[1]);
+        Genotype genotype = simpleExample.retrieveGenotype();
+        System.out.println("Genotype @ i3003137, a SNP associated with Sickle Cell Anemia: " + genotype.i3003137);
+    }
+
+    public Genotype retrieveGenotype() throws Exception {
+        final Credential credential = authorize();
+
+        HttpRequestInitializer initializer = new HttpRequestInitializer() {
+            public void initialize(HttpRequest request) throws IOException {
+                credential.initialize(request);
+                request.setParser(new JsonObjectParser(jsonFactory));
+            }
+        };
+        HttpRequestFactory requestFactory = httpTransport.createRequestFactory(initializer);
+
+        GenericUrl userUrl = new GenericUrl(BASE_URL + "/1/user/");
+        HttpRequest userRequest = requestFactory.buildGetRequest(userUrl);
+        HttpResponse userResponse = userRequest.execute();
+        Account account = userResponse.parseAs(Account.class);
+        Profile profile = account.profiles.get(0);
+
+        GenericUrl genotypesUrl = new GenericUrl(BASE_URL + "1/genotypes/" + profile.id + "/?locations=i3003137");
+        HttpRequest genotypesRequest = requestFactory.buildGetRequest(genotypesUrl);
+        HttpResponse genotypesResponse = genotypesRequest.execute();
+        return genotypesResponse.parseAs(Genotype.class);
+    }
+
+    private Credential authorize() throws Exception {
+        HttpExecuteInterceptor credentials = new ClientParametersAuthentication(this.clientId, this.clientSecret);
+        AuthorizationCodeFlow flow = new AuthorizationCodeFlow.Builder(authorizationHeaderAccessMethod(),
+                                                             httpTransport,
+                                                             jsonFactory,
+                                                             new GenericUrl(TOKEN_SERVER_URL),
+                                                             credentials,
+                                                             this.clientId,
+                                                             AUTHORIZATION_SERVER_URL)
+                                                            .setScopes(SCOPES)
+                                                            .setDataStoreFactory(dataStoreFactory).build();
+        LocalServerReceiver.Builder builder = new LocalServerReceiver.Builder();
+        VerificationCodeReceiver receiver = builder.setHost(DOMAIN)
+                                                   .setPort(PORT).build();
+        return new AuthorizationCodeInstalledApp(flow, receiver).authorize("user");
+    }
+}