Fix build and added alternate authentication strategy

.gitignore

@@ -0,0 +1,10 @@
+.idea/**
+*.swp
+*.swo
+target/**
+.project
+.classpath
+*.iml
+*.ipr
+*.iws
+out

README.md

@@ -39,3 +39,10 @@ Instances exist for the following ontologies:
 * [ENVO TermGenie](http://envo.termgenie.org)
 
 To get write access to any of these TG instances, contact the administrators of the ontology (list available from obofoundry.org)
+
+#Updates to TermeGene
+Need to install https://github.com/RitwikSaikia/jsonrpc/ locally and maven install the server code.
+
+Add user here:
+
+https://github.com/geneontology/go-site/blob/master/metadata/users.yaml

TermGenie/TermGenieCore/src/main/java/org/bbop/termgenie/core/ioc/IOCModule.java

@@ -336,7 +336,7 @@ protected void bind(String name, File value) {
 	}
 
 	/**
-	 * Convenience method for binding a Map<IRI, String> parameter. Check system
+	 * Convenience method for binding a Map&lt;IRI, String&gt; parameter. Check system
 	 * properties for overwrites.
 	 * 
 	 * @param name

TermGenie/TermGenieOntologyCommit/TermGenieOntologyCommit-API/src/main/java/org/bbop/termgenie/ontology/CommitObject.java

@@ -18,7 +18,7 @@ public enum Modification {
 	}
 
 	/**
-	 * Mark a new object of type <T> as added for the commit.
+	 * Mark a new object of type &lt;T&gt; as added for the commit.
 	 * 
 	 * @param <T> type
 	 * @param object the object to be committed
@@ -29,7 +29,7 @@ public static <T> CommitObject<T> add(T object) {
 	}
 
 	/**
-	 * Mark a new object of type <T> as modified for the commit.
+	 * Mark a new object of type &lt;T&gt; as modified for the commit.
 	 * 
 	 * @param <T> type
 	 * @param object the object to be committed
@@ -40,7 +40,7 @@ public static <T> CommitObject<T> modify(T object) {
 	}
 
 	/**
-	 * Mark a new object of type <T> as to be deleted for the commit.
+	 * Mark a new object of type &lt;T&gt; as to be deleted for the commit.
 	 * 
 	 * @param <T> type
 	 * @param object the object to be committed

TermGenie/TermGenieOntologyCommit/TermGenieOntologyCommit-SVN/pom.xml

@@ -18,7 +18,15 @@
 		<dependency>
 			<groupId>org.tmatesoft.svnkit</groupId>
 			<artifactId>svnkit</artifactId>
-			<version>1.3.8</version>
+			<version>1.8.14</version>
+			<!--<version>1.9.0-r10609-atlassian-hosted</version>-->
+			<exclusions>
+				<exclusion>
+					<groupId>com.trilead</groupId>
+					<artifactId>trilead-ssh2</artifactId>
+				</exclusion>
+			</exclusions>
+
 		</dependency>
 		<dependency>
 			<groupId>org.bbop.termgenie</groupId>

TermGenie/WebApplications/TermGenieJQuery/pom.xml

@@ -12,12 +12,6 @@
 
 	<name>TermGenieJQuery</name>
 
-	<repositories>
-		<repository>
-			<id>json-rpc</id>
-			<url>http://json-rpc.googlecode.com/svn/mavenrepo</url>
-		</repository>
-	</repositories>
 
 	<dependencies>
 		<dependency>
@@ -30,17 +24,11 @@
 			<artifactId>TermGenieRulesDynamic</artifactId>
 			<version>${project.parent.version}</version>
 		</dependency>
-		<dependency>
-			<groupId>org.json.rpc</groupId>
-			<artifactId>jsonrpc</artifactId>
-			<version>1.0</version>
-			<exclusions>
-				<exclusion>
-					<artifactId>slf4j-api</artifactId>
-					<groupId>org.slf4j</groupId>
-				</exclusion>
-			</exclusions>
-   		</dependency>
+        <dependency>
+            <groupId>org.json.rpc</groupId>
+            <artifactId>jsonrpc</artifactId>
+            <version>1.1</version>
+        </dependency>
 		<dependency>
 			<groupId>org.bbop.termgenie</groupId>
 			<artifactId>TermGenieOntologyCommit-Core</artifactId>

TermGenie/WebApplications/TermGenieJQuery/src/main/java/org/bbop/termgenie/services/authenticate/BrowserIdHandlerImpl.java

@@ -39,7 +39,8 @@ public class BrowserIdHandlerImpl implements BrowserIdHandler {
 	public BrowserIdHandlerImpl(@Named("BrowserIdVerificationUrl") String browserIdVerificationUrl,
 			@Named("TermGenieBrowserIdAudience") String termgenieBrowserIdAudience,
 			InternalSessionHandler sessionHandler,
-			UserDataProvider userDataProvider)
+			UserDataProvider userDataProvider
+	)
 	{
 		super();
 		this.browserIdVerificationUrl = browserIdVerificationUrl;

TermGenie/WebApplications/TermGenieJQuery/src/main/java/org/bbop/termgenie/services/info/ConfigurationHandler.java

@@ -0,0 +1,33 @@
+package org.bbop.termgenie.services.info;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Properties;
+
+/**
+ * Created by nathandunn on 11/22/16.
+ */
+public class ConfigurationHandler {
+
+    private static ConfigurationHandler configurationHandler ;
+    private Properties properties = new Properties();
+
+    private ConfigurationHandler(){
+        ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+        InputStream input = classLoader.getResourceAsStream("termgenie.properties");
+        try {
+            properties.load(input);
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    public static ConfigurationHandler getConfigurationHandler() {
+        if(configurationHandler==null) configurationHandler = new ConfigurationHandler();
+        return configurationHandler;
+    }
+
+    public String getValue(String key){
+        return properties.getProperty(key);
+    }
+}

TermGenie/WebApplications/TermGenieJQuery/src/main/java/org/bbop/termgenie/servlets/AbstractTermGenieContextListener.java

@@ -54,6 +54,8 @@ protected final class TermGenieServletModule extends ServletModule {
 		protected void configureServlets() {
 			serve("/jsonrpc").with(TermGenieJsonRPCServlet.class);
 			serve("/termlookup").with(TermLookupServlet.class);
+			serve("/gh-request").with(GHAuthenticationRequestServlet.class);
+			serve("/gh-access").with(GHAuthenticationAccessServlet.class);  // configured in GH
 		}
 
 		@Provides
@@ -114,6 +116,7 @@ protected final synchronized Injector getInjector() {
 	private IOCModule[] getConfiguration() {
 		List<IOCModule> modules = new ArrayList<IOCModule>();
 		modules.add(new ManagementServiceModule(applicationProperties));
+		modules.add(new GHAuthenticationModule(applicationProperties));
 		add(modules, getServiceModule(), true, "ServiceModule");
 		add(modules, getAuthenticationModule(), true, "Authentication");
 		add(modules, getUserPermissionModule(), true, "UserPermission");

TermGenie/WebApplications/TermGenieJQuery/src/main/java/org/bbop/termgenie/servlets/GHAuthenticationAccessServlet.java

@@ -0,0 +1,153 @@
+package org.bbop.termgenie.servlets;
+
+import com.google.gson.Gson;
+import com.google.inject.Inject;
+import com.google.inject.Singleton;
+import com.google.inject.name.Named;
+import org.apache.http.HttpResponse;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.message.BasicNameValuePair;
+import org.apache.log4j.Logger;
+import org.bbop.termgenie.services.InternalSessionHandler;
+import org.bbop.termgenie.services.info.ConfigurationHandler;
+import org.bbop.termgenie.user.UserData;
+import org.bbop.termgenie.user.UserDataProvider;
+
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import javax.servlet.http.HttpSession;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * https://developer.github.com/v3/oauth/#2-github-redirects-back-to-your-site
+ */
+@Singleton
+public class GHAuthenticationAccessServlet extends HttpServlet {
+
+	private static final Logger logger = Logger.getLogger(GHAuthenticationAccessServlet.class);
+
+	// generated
+	private static final long serialVersionUID = 4604786454943166862L;
+
+	private final Gson gson;
+	private final UserDataProvider userDataProvider;
+	private final InternalSessionHandler sessionHandler;
+	private final String clientId ;
+	private final String clientSecret ;
+
+	@Inject
+	public GHAuthenticationAccessServlet(
+			InternalSessionHandler sessionHandler,
+			UserDataProvider userDataProvider,
+			@Named("github_client_id")
+			String clientId,
+			@Named("github_client_secret")
+			String clientSecret
+	) {
+		super();
+//		this.lookupService = lookupService;
+		this.gson = new Gson();
+		this.userDataProvider = userDataProvider;
+		this.sessionHandler = sessionHandler;
+		this.clientId = clientId ;
+		this.clientSecret = clientSecret;
+	}
+
+
+
+	@Override
+	protected void doGet(HttpServletRequest req, HttpServletResponse resp)
+			throws ServletException, IOException
+	{
+		String code = req.getParameter("code");
+
+		String accessToken = getAccessToken(code);
+
+		HttpClient httpClient = HttpClientBuilder.create().build();
+		HttpGet getRequest = new HttpGet("https://api.github.com/user?access_token="+accessToken);
+		HttpResponse response = httpClient.execute(getRequest);
+
+		BufferedReader rd = new BufferedReader(
+				new InputStreamReader(response.getEntity().getContent()));
+
+		StringBuilder result = new StringBuilder();
+		String line = "";
+		while ((line = rd.readLine()) != null) {
+			result.append(line);
+		}
+		GHUserResponse ghUserResponse = gson.fromJson(result.toString(), GHUserResponse.class);
+
+		boolean isAuthenticated = ghUserResponse.email!=null;
+
+		if(isAuthenticated){
+			UserData userData  = userDataProvider.getUserDataPerEMail(ghUserResponse.email);
+			HttpSession httpSession = req.getSession();
+			sessionHandler.setAuthenticated(userData, httpSession);
+		}
+		else{
+			throw new RuntimeException("Failed to authenticate");
+		}
+	}
+
+	private String getAccessToken(String code) throws IOException{
+		// we have to pull the returned "code" off of the server
+		// and then do a post to github to get the access_code
+//		String clientId= ConfigurationHandler.getConfigurationHandler().getValue("client_id");
+//		String clientSecret = ConfigurationHandler.getConfigurationHandler().getValue("github.client_secret");
+
+		// https://developer.github.com/v3/oauth/#2-github-redirects-back-to-your-site
+		// TODO: 1 post to the client to get the acces token
+
+		List<NameValuePair> urlParameters = new ArrayList<NameValuePair>();
+		urlParameters.add(new BasicNameValuePair("client_id",this.clientId));
+		urlParameters.add(new BasicNameValuePair("client_secret",this.clientSecret));
+		urlParameters.add(new BasicNameValuePair("code",code));
+
+		HttpClient httpClient = HttpClientBuilder.create().build();
+		HttpPost postRequest = new HttpPost("https://github.com/login/oauth/access_token");
+		postRequest.addHeader("User-Agent", "TermGenie/1.0");
+		postRequest.addHeader("Accept","application/json");
+		postRequest.addHeader("Accept","application/xml");
+
+		System.out.println("posting '${urlParameters}'");
+
+		postRequest.setEntity(new UrlEncodedFormEntity(urlParameters));
+
+		HttpResponse response = httpClient.execute(postRequest);
+
+		BufferedReader rd = new BufferedReader(
+				new InputStreamReader(response.getEntity().getContent()));
+
+		StringBuffer result = new StringBuffer();
+		String line = "";
+		while ((line = rd.readLine()) != null) {
+			result.append(line);
+		}
+
+		GHAccessResponse ghAccessResponse = gson.fromJson(result.toString(), GHAccessResponse.class);
+
+		String accessToken = ghAccessResponse.access_token;
+		return accessToken ;
+	}
+
+	static class GHUserResponse {
+		String email;
+		String username;
+	}
+
+	static class GHAccessResponse {
+		String access_token;
+	}
+
+}

TermGenie/WebApplications/TermGenieJQuery/src/main/java/org/bbop/termgenie/servlets/GHAuthenticationModule.java

@@ -0,0 +1,21 @@
+package org.bbop.termgenie.servlets;
+
+import org.bbop.termgenie.core.ioc.IOCModule;
+
+import java.util.Properties;
+
+/**
+ * Created by nathandunn on 11/28/16.
+ */
+public class GHAuthenticationModule extends IOCModule{
+
+    public GHAuthenticationModule(Properties properties){
+        super(properties);
+    }
+
+    @Override
+    protected void configure() {
+        bindSecret("github_client_id");
+        bindSecret("github_client_secret");
+    }
+}

TermGenie/WebApplications/TermGenieJQuery/src/main/java/org/bbop/termgenie/servlets/GHAuthenticationRequestServlet.java

@@ -0,0 +1,49 @@
+package org.bbop.termgenie.servlets;
+
+import com.google.gson.Gson;
+import com.google.inject.Inject;
+import com.google.inject.Singleton;
+import com.google.inject.name.Named;
+import org.apache.log4j.Logger;
+import org.bbop.termgenie.services.info.ConfigurationHandler;
+import org.bbop.termgenie.services.lookup.TermLookupService;
+
+import javax.servlet.ServletException;
+import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.io.IOException;
+
+/**
+ * https://developer.github.com/v3/oauth/#1-redirect-users-to-request-github-access
+ */
+@Singleton
+public class GHAuthenticationRequestServlet extends HttpServlet {
+
+	private static final Logger logger = Logger.getLogger(GHAuthenticationRequestServlet.class);
+
+	// generated
+	private static final long serialVersionUID = 4604786454943166862L;
+
+	private final String clientId ;
+
+	@Inject
+	public GHAuthenticationRequestServlet(
+			@Named("github_client_id")
+                String clientId
+	) {
+		super();
+		this.clientId = clientId ;
+	}
+
+	@Override
+	protected void doGet(HttpServletRequest req, HttpServletResponse resp)
+			throws ServletException, IOException
+	{
+//		String clientId = ConfigurationHandler.getConfigurationHandler().getValue("client_id");
+		String url="https://github.com/login/oauth/authorize?client_id="+clientId+"&scope=user:email";
+		resp.sendRedirect(url);
+	}
+
+
+}