Merge branch '3-migrate-to-scribe-4-2' into 'master'

Resolve "Migrate to scribe:4.2"

Closes #3

See merge request !3

pom.xml

-<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">
+<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>
 	<groupId>org.genesys-pgr</groupId>
@@ -41,7 +42,6 @@
 		<nexus-staging-maven-plugin.version>1.6.8</nexus-staging-maven-plugin.version>
 
 		<show.deprecations>true</show.deprecations>
-		<scribe.version>1.3.7</scribe.version>
 	</properties>
 
 
@@ -88,9 +88,9 @@
 
 	<dependencies>
 		<dependency>
-			<groupId>org.scribe</groupId>
-			<artifactId>scribe</artifactId>
-			<version>${scribe.version}</version>
+			<groupId>com.github.scribejava</groupId>
+			<artifactId>scribejava-core</artifactId>
+			<version>4.2.0</version>
 		</dependency>
 		<dependency>
 			<groupId>log4j</groupId>
@@ -134,6 +134,7 @@
 			<groupId>org.apache.httpcomponents</groupId>
 			<artifactId>httpclient</artifactId>
 			<version>4.3.6</version>
+			<scope>test</scope>
 		</dependency>
 	</dependencies>
 

src/main/java/org/genesys2/client/oauth/CLI.java

@@ -21,7 +21,6 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
-import java.net.SocketException;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.Map.Entry;
@@ -38,13 +37,12 @@ import com.fasterxml.jackson.databind.node.IntNode;
 import com.fasterxml.jackson.databind.node.NullNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import com.fasterxml.jackson.databind.node.TextNode;
+import com.github.scribejava.core.model.Verb;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.LogManager;
 import org.apache.log4j.Logger;
-import org.scribe.exceptions.OAuthConnectionException;
-import org.scribe.model.Verb;
 
 /**
  * Simple command line interface to Genesys.
@@ -69,7 +67,7 @@ public class CLI {
 	private static ObjectMapper mapper = new ObjectMapper();
 
 	/** The genesys client. */
-	private final GenesysClient genesysClient = new GenesysClient();
+	private GenesysClient genesysClient;
 
 	/** The ignored fields. */
 	private static Set<String> ignoredFields;
@@ -93,7 +91,7 @@ public class CLI {
 		_log.info("Hello World!");
 
 		final CLI cli = new CLI();
-		cli.loadProperties("client.properties");
+		cli.genesysClient = GenesysClient.build(cli.loadProperties("client.properties"));
 		cli.run();
 	}
 
@@ -111,13 +109,11 @@ public class CLI {
 
 		} catch (final OAuthAuthenticationException e) {
 			_log.error("Failed to fetch /me", e);
-			authenticate();
-		} catch (final OAuthConnectionException e) {
-			if (e.getCause() != null && e.getCause() instanceof SocketException) {
-				_log.error("Could not connect to host");
+			try {
+				authenticate();
+			} catch (OAuthAuthenticationException e1) {
+				_log.error("Failed to authenticate", e1);
 				return;
-			} else {
-				_log.error(e.getMessage(), e);
 			}
 		} catch (final Throwable e) {
 			_log.error(e.getMessage(), e);
@@ -566,8 +562,10 @@ public class CLI {
 
 	/**
 	 * Authenticate.
+	 * 
+	 * @throws OAuthAuthenticationException
 	 */
-	private void authenticate() {
+	private void authenticate() throws OAuthAuthenticationException {
 		final String authorizationUrl = genesysClient.getAuthorizationUrl();
 
 		System.out.println("Authorization URL: \n" + authorizationUrl);
@@ -604,8 +602,9 @@ public class CLI {
 	 * Load properties.
 	 *
 	 * @param propertiesFileName the properties file name
+	 * @return
 	 */
-	private void loadProperties(final String propertiesFileName) {
+	private Properties loadProperties(final String propertiesFileName) {
 		// .properties file location
 		propertiesFile = new File(propertiesFileName);
 
@@ -626,7 +625,7 @@ public class CLI {
 			IOUtils.closeQuietly(fis);
 		}
 
-		genesysClient.loadProperties(properties);
+		return properties;
 	}
 
 }

src/main/java/org/genesys2/client/oauth/GenesysClient.java

@@ -19,8 +19,6 @@ package org.genesys2.client.oauth;
 import java.io.File;
 import java.io.IOException;
 import java.io.Serializable;
-import java.net.Authenticator;
-import java.net.PasswordAuthentication;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.nio.charset.Charset;
@@ -31,7 +29,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Properties;
 import java.util.UUID;
-import java.util.concurrent.TimeUnit;
+import java.util.concurrent.ExecutionException;
 
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.core.JsonParseException;
@@ -43,25 +41,20 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;
 import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.github.scribejava.core.builder.ServiceBuilder;
+import com.github.scribejava.core.model.OAuth2AccessToken;
+import com.github.scribejava.core.model.OAuthRequest;
+import com.github.scribejava.core.model.Response;
+import com.github.scribejava.core.model.Verb;
+import com.github.scribejava.core.oauth.OAuth20Service;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang.StringUtils;
-import org.apache.http.HttpHeaders;
-import org.apache.http.entity.ContentType;
 import org.apache.log4j.LogManager;
 import org.apache.log4j.Logger;
 import org.genesys2.client.oauth.api.GenesysApi;
 import org.genesys2.client.oauth.api.accession.AccessionJson;
 import org.genesys2.client.oauth.api.images.RepositoryImage;
-import org.scribe.builder.ServiceBuilder;
-import org.scribe.exceptions.OAuthConnectionException;
-import org.scribe.exceptions.OAuthException;
-import org.scribe.model.OAuthRequest;
-import org.scribe.model.Response;
-import org.scribe.model.Token;
-import org.scribe.model.Verb;
-import org.scribe.model.Verifier;
-import org.scribe.oauth.OAuthService;
 
 /**
  * Genesys API client using Scribe.
@@ -71,32 +64,17 @@ public class GenesysClient {
 	/** The Constant _log. */
 	private static final Logger _log = LogManager.getLogger(GenesysClient.class);
 
-	/** The Constant SCOPE. */
-	private static final String SCOPE = "read,write";
-
 	/** The mapper. */
 	private static ObjectMapper objectMapper;
 
 	/** The service. */
-	private OAuthService service;
+	private final OAuth20Service service;
 
 	/** GenesysTokens: access- and refreshToken. */
 	private GenesysTokens tokens = new GenesysTokens();
 
-	/** The genesys api. */
-	private GenesysApi genesysApi;
-
-	/** The api key. */
-	private String apiKey;
-
-	/** The api secret. */
-	private String apiSecret;
-
-	/** Socket connect timeout. */
-	private int connectTimeout = 20;
-
-	/** Socket read timeout. */
-	private int readTimeout = 120;
+	/** Base URL of Genesys */
+	private String baseUrl;
 
 	/** UTF8 charset */
 	private static Charset CHARSET_UTF8 = Charset.forName("UTF8");
@@ -112,72 +90,9 @@ public class GenesysClient {
 	/**
 	 * Instantiates a new genesys client.
 	 */
-	public GenesysClient() {
-	}
-
-	/**
-	 * Sets the read timeout.
-	 *
-	 * @param readTimeout the new read timeout
-	 */
-	public void setReadTimeout(final int readTimeout) {
-		this.readTimeout = readTimeout;
-	}
-
-	/**
-	 * Gets the read timeout.
-	 *
-	 * @return the read timeout
-	 */
-	public int getReadTimeout() {
-		return readTimeout;
-	}
-
-	/**
-	 * Sets the connect timeout.
-	 *
-	 * @param connectTimeout the new connect timeout
-	 */
-	public void setConnectTimeout(final int connectTimeout) {
-		this.connectTimeout = connectTimeout;
-	}
-
-	/**
-	 * Gets the connect timeout.
-	 *
-	 * @return the connect timeout
-	 */
-	public int getConnectTimeout() {
-		return connectTimeout;
-	}
-
-	/**
-	 * Sets the base url.
-	 *
-	 * @param baseUrl the base url
-	 * @return the genesys client
-	 */
-	public GenesysClient setBaseUrl(final String baseUrl) {
-		genesysApi.setBaseUrl(baseUrl);
-		return this;
-	}
-
-	/**
-	 * Sets the genesys api.
-	 *
-	 * @param genesysApi the new genesys api
-	 */
-	public void setGenesysApi(final GenesysApi genesysApi) {
-		this.genesysApi = genesysApi;
-	}
-
-	/**
-	 * Gets the genesys api.
-	 *
-	 * @return the genesys api
-	 */
-	public GenesysApi getGenesysApi() {
-		return genesysApi;
+	public GenesysClient(final String baseUrl, final String clientId, final String clientSecret, final String callbackUrl, String scope) {
+		this.baseUrl = baseUrl;
+		service = new ServiceBuilder(clientId).apiSecret(clientSecret).callback(callbackUrl).scope(scope).build(new GenesysApi(baseUrl));
 	}
 
 	/**
@@ -185,45 +100,23 @@ public class GenesysClient {
 	 *
 	 * @param properties the properties
 	 */
-	public void loadProperties(final Properties properties) {
+	public static GenesysClient build(final Properties properties) {
 
 		final String baseUrl = properties.getProperty("base.url");
-		genesysApi.setBaseUrl(baseUrl);
 
-		final String httpAuth = properties.getProperty("http.auth");
-
-		if (StringUtils.isNotBlank(httpAuth) && httpAuth.contains(":")) {
-			_log.warn("Using HTTP AUTH " + httpAuth);
-			Authenticator.setDefault(new Authenticator() {
-				@Override
-				protected PasswordAuthentication getPasswordAuthentication() {
-					return new PasswordAuthentication(httpAuth.split(":", 2)[0], httpAuth.split(":", 2)[1].toCharArray());
-				}
-			});
-		}
-
-		tokens = new GenesysTokens();
+		GenesysTokens tokens = new GenesysTokens();
 		tokens.setAccessToken(properties.getProperty("access.token"));
 		tokens.setRefreshToken(properties.getProperty("refresh.token"));
 
-		// CropHub auth service
-		connect(properties.getProperty("client.key"), properties.getProperty("client.secret"), properties.getProperty("client.callback"));
+		// Genesys client instance auth service
+		return new GenesysClient(baseUrl, properties.getProperty("client.key"), properties.getProperty("client.secret"), properties.getProperty("client.callback"),
+				properties.getProperty("client.scope"));
 	}
 
-	/**
-	 * Connect.
-	 *
-	 * @param clientId the client id
-	 * @param clientSecret the client secret
-	 * @param callbackUrl the callback URL for web-based clients. Use "oob" for out-of-band
-	 *        authentication.
-	 */
-	public void connect(final String clientId, final String clientSecret, final String callbackUrl) {
-		apiKey = clientId;
-		apiSecret = clientSecret;
-		service = new ServiceBuilder().provider(genesysApi).apiKey(clientId).apiSecret(clientSecret).callback(callbackUrl).scope(SCOPE).build();
+	public String getAuthorizationUrl() {
+		return service.getAuthorizationUrl();
 	}
-
+	
 	/**
 	 * Sets the tokens.
 	 *
@@ -288,7 +181,7 @@ public class GenesysClient {
 		if (StringUtils.isBlank(postBody)) {
 			return query(method, url, queryString, null, null);
 		} else {
-			return query(method, url, queryString, ContentType.APPLICATION_JSON.withCharset(CHARSET_UTF8).getMimeType(), postBody.getBytes(CHARSET_UTF8));
+			return query(method, url, queryString, HttpConstants.APPLICATION_JSON_UTF8, postBody.getBytes(CHARSET_UTF8));
 		}
 	}
 
@@ -305,7 +198,7 @@ public class GenesysClient {
 	 */
 	private String query(final Verb method, final String url, final Map<String, String> queryString, final Serializable object)
 			throws GenesysApiException, JsonProcessingException {
-		return query(method, url, queryString, ContentType.APPLICATION_JSON.withCharset(CHARSET_UTF8).getMimeType(), objectMapper.writeValueAsBytes(object));
+		return query(method, url, queryString, HttpConstants.APPLICATION_JSON_UTF8, objectMapper.writeValueAsBytes(object));
 	}
 
 	private String query(final Verb method, final String url, final Map<String, String> queryString, final String contentType, final byte[] postBody) throws GenesysApiException {
@@ -335,55 +228,54 @@ public class GenesysClient {
 				if (_log.isTraceEnabled()) {
 					_log.trace("Body: " + new String(postBody));
 				}
-				request.addPayload(postBody);
+				request.setPayload(postBody);
 			}
 
-			service.signRequest(tokens.accessToken(), request);
-			request.setConnectionKeepAlive(true);
-			request.setConnectTimeout(connectTimeout, TimeUnit.SECONDS);
-			request.setReadTimeout(readTimeout, TimeUnit.SECONDS);
-			request.setCharset("UTF-8");
+			request.setCharset("UTF-8");			
 			Response response = null;
 
 			try {
-				response = request.send();
-			} catch (final OAuthConnectionException e) {
-				throw e;
-			}
+				service.signRequest(tokens.accessToken(), request);
+				response = service.execute(request);
 
-			final String responseBody = response.getBody();
+				final String responseBody = response.getBody();
 
-			_log.debug("HTTP status code " + response.getCode());
+				_log.debug("HTTP status code " + response.getCode());
 
-			if (response.getCode() >= 200 && response.getCode() < 300) {
-				_log.debug("Returning response body");
-				return responseBody;
-			} else {
-				if (response.getCode() == 301 || response.getCode() == 302) {
-					_log.debug("Redirect: " + response.getHeader(HttpHeaders.LOCATION));
-					throw new HttpRedirectException(response.getHeader(HttpHeaders.LOCATION));
-				}
-				if (response.getCode() == 401) {
-					_log.warn("Response error: " + response.getCode());
-					System.err.println(responseBody);
-					if (i == 0) {
-						refreshAccessToken();
-					} else {
-						throw new OAuthAuthenticationException("Unauthorized");
-					}
+				if (response.getCode() >= 200 && response.getCode() < 300) {
+					_log.debug("Returning response body");
+					return responseBody;
 				} else {
-					_log.error(method + " " + request.getCompleteUrl());
-					_log.error(postBody);
-					_log.error("HTTP response code: " + response.getCode());
-					_log.error("Response: " + responseBody);
-					if (responseBody.contains("Deadlock found when trying to get lock; try restarting transaction")
-							|| responseBody.contains("nested exception is org.hibernate.exception.LockAcquisitionException: could not execute statement")
-							|| responseBody.contains("nested exception is org.hibernate.exception.LockTimeoutException: could not execute statement")) {
-						throw new PleaseRetryException(responseBody);
+					if (response.getCode() == 301 || response.getCode() == 302) {
+						_log.debug("Redirect: " + response.getHeader(HttpConstants.LOCATION));
+						throw new HttpRedirectException(response.getHeader(HttpConstants.LOCATION));
+					}
+					if (response.getCode() == 401) {
+						_log.warn("Response error: " + response.getCode());
+						System.err.println(responseBody);
+						if (i == 0) {
+							refreshAccessToken();
+						} else {
+							throw new OAuthAuthenticationException("Unauthorized");
+						}
 					} else {
-						throw new GenesysApiException("Unexpected error: " + responseBody);
+						_log.error(method + " " + request.getCompleteUrl());
+						_log.error(new String(postBody));
+						_log.error("HTTP response code: " + response.getCode());
+						_log.error("Response: " + responseBody);
+						if (responseBody.contains("Deadlock found when trying to get lock; try restarting transaction")
+								|| responseBody.contains("nested exception is org.hibernate.exception.LockAcquisitionException: could not execute statement")
+								|| responseBody.contains("nested exception is org.hibernate.exception.LockTimeoutException: could not execute statement")) {
+							throw new PleaseRetryException(responseBody);
+						} else {
+							throw new GenesysApiException("Unexpected error: " + responseBody);
+						}
 					}
 				}
+
+			} catch (final Throwable e) {
+				e.printStackTrace();
+				throw new GenesysApiException(e.getMessage());
 			}
 		}
 		return null;
@@ -396,7 +288,7 @@ public class GenesysClient {
 	 * @return the api url
 	 */
 	private String getApiUrl(final String url) {
-		return genesysApi.getBaseUrl().concat("/api/v0").concat(url);
+		return baseUrl.concat("/api/v0").concat(url);
 	}
 
 	/**
@@ -408,11 +300,11 @@ public class GenesysClient {
 		if (tokens.hasRefreshToken()) {
 			_log.info("Using Refresh Token to get new access token");
 			try {
-				final Token accessToken = genesysApi.getAccessToken(apiKey, apiSecret, tokens.getRefreshToken());
-				tokens.setAccessToken(accessToken.getToken());
-
+				OAuth2AccessToken accessToken = service.refreshAccessToken(tokens.getRefreshToken());
+				tokens.setAccessToken(accessToken.getAccessToken());
 				_log.info("Got new Access Token!");
-			} catch (final OAuthException e) {
+
+			} catch (Throwable e) {
 				_log.info("Refresh token didn't work: " + e.getMessage());
 				throw new OAuthAuthenticationException("Refresh token not valid, please re-authenticate");
 			}
@@ -484,8 +376,8 @@ public class GenesysClient {
 
 	/**
 	 * Update accession information with new values provided in the JSON string. In case of
-	 * {@link PleaseRetryException}, this method will attempt to re-send the data 5 times before
-	 * giving up.
+	 * {@link PleaseRetryException}, this method will attempt to re-send the data 5 times before giving
+	 * up.
 	 *
 	 * @param instCode the WIEWS institute code
 	 * @param jsonAccessionList the JSON array of accessions
@@ -648,31 +540,28 @@ public class GenesysClient {
 		return query(Verb.POST, "/acn/" + instCode + "/delete", null, jsonAccessionIdList);
 	}
 
-	/**
-	 * Gets the authorization url.
-	 *
-	 * @return the authorization url
-	 */
-	public String getAuthorizationUrl() {
-		return service.getAuthorizationUrl(null);
-	}
-
 	/**
 	 * Obtain access and refresh tokens with verifier code.
 	 *
 	 * @param verifierCode the verifier code
+	 * @throws OAuthAuthenticationException 
 	 */
-	public void authenticate(final String verifierCode) {
-		final Verifier verifier = new Verifier(verifierCode);
-		final Token accessToken = service.getAccessToken(null, verifier);
+	public void authenticate(final String verifierCode) throws OAuthAuthenticationException {
+		try {
+			OAuth2AccessToken accessToken = service.getAccessToken(verifierCode);
+			
+			_log.info("ACCESS TOKEN: " + accessToken.getAccessToken() + " scope=" + accessToken.getScope() + " raw=" + accessToken.getRawResponse());
 
-		_log.info("ACCESS TOKEN: " + accessToken.getToken() + " sec=" + accessToken.getSecret() + " raw=" + accessToken.getRawResponse());
+			final String refreshToken = accessToken.getRefreshToken();
+			_log.info("REFRESH TOKEN: " + refreshToken);
 
-		final Token refreshToken = genesysApi.getRefreshToken(accessToken);
-		_log.info("REFRESH TOKEN: " + refreshToken.getToken() + " sec=" + refreshToken.getSecret() + " raw=" + refreshToken.getRawResponse());
+			tokens.setAccessToken(accessToken.getAccessToken());
+			tokens.setRefreshToken(refreshToken);
 
-		tokens.setAccessToken(accessToken.getToken());
-		tokens.setRefreshToken(refreshToken.getToken());
+		} catch (IOException | InterruptedException | ExecutionException e) {
+			_log.error("Auth error", e);
+			throw new OAuthAuthenticationException(e.getMessage());
+		}
 	}
 
 	/**
@@ -1105,8 +994,8 @@ public class GenesysClient {
 	}
 
 	/**
-	 * List existing image galleries for INSTCODE. The response is paginated, provide
-	 * <code>page</code> argument to request a specific page.
+	 * List existing image galleries for INSTCODE. The response is paginated, provide <code>page</code>
+	 * argument to request a specific page.
 	 *
 	 * @param instCode institute code (MCPD INSTCODE)
 	 * @param page 1 for first page

src/main/java/org/genesys2/client/oauth/GenesysTokens.java

@@ -18,8 +18,9 @@ package org.genesys2.client.oauth;
 
 import java.io.Serializable;
 
+import com.github.scribejava.core.model.OAuth2AccessToken;
+
 import org.apache.commons.lang.StringUtils;
-import org.scribe.model.Token;
 
 /**
  * A place to keep the tokens for the session.
@@ -36,7 +37,7 @@ public class GenesysTokens implements Serializable {
 	private String refreshToken = null;
 
 	/** The _access token. */
-	private Token _accessToken = null;
+	private OAuth2AccessToken _accessToken = null;
 
 	/**
 	 * Gets the access token.
@@ -54,7 +55,7 @@ public class GenesysTokens implements Serializable {
 	 */
 	public void setAccessToken(final String accessToken) {
 		this.accessToken = accessToken;
-		_accessToken = new Token(accessToken, "");
+		_accessToken = new OAuth2AccessToken(accessToken);
 	}
 
 	/**
@@ -98,7 +99,7 @@ public class GenesysTokens implements Serializable {
 	 *
 	 * @return the token
 	 */
-	public Token accessToken() {
+	public OAuth2AccessToken accessToken() {
 		return _accessToken;
 	}
 }

src/main/java/org/genesys2/client/oauth/HttpConstants.java

+package org.genesys2.client.oauth;
+
+public class HttpConstants {
+
+	public static final String APPLICATION_JSON_UTF8 = "application/json;charset=utf8";
+	
+	public static final String LOCATION = "Location"; 
+}

src/main/java/org/genesys2/client/oauth/api/GenesysApi.java

@@ -16,64 +16,25 @@
 
 package org.genesys2.client.oauth.api;
 
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.http.HttpHeaders;
-import org.apache.log4j.LogManager;
-import org.apache.log4j.Logger;
-import org.genesys2.client.oauth.GenesysApiException;
-import org.scribe.builder.api.DefaultApi20;
-import org.scribe.exceptions.OAuthException;
-import org.scribe.extractors.AccessTokenExtractor;
-import org.scribe.extractors.JsonTokenExtractor;
-import org.scribe.model.OAuthConfig;
-import org.scribe.model.OAuthConstants;
-import org.scribe.model.OAuthRequest;