JAutodoc

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

@@ -47,23 +47,31 @@ import com.fasterxml.jackson.databind.node.ObjectNode;
 import com.fasterxml.jackson.databind.node.TextNode;
 
 /**
- * Simple command line interface to Genesys
- * 
+ * Simple command line interface to Genesys.
+ *
  * @author matijaobreza
- * 
  */
 public class CLI {
+	
+	/** The Constant _log. */
 	private static final Logger _log = LogManager.getLogger(CLI.class);
 
+	/** The properties file. */
 	private File propertiesFile;
+	
+	/** The properties. */
 	private Properties properties;
 
+	/** The in. */
 	private Scanner in = new Scanner(System.in);
 
+	/** The mapper. */
 	private static ObjectMapper mapper = new ObjectMapper();
 
+	/** The genesys client. */
 	private GenesysClient genesysClient = new GenesysClient();
 
+	/** The ignored fields. */
 	private static Set<String> ignoredFields;
 
 	static {
@@ -76,6 +84,11 @@ public class CLI {
 		ignoredFields.add("version");
 	}
 
+	/**
+	 * The main method.
+	 *
+	 * @param args the arguments
+	 */
 	public static void main(String[] args) {
 		_log.info("Hello World!");
 
@@ -84,6 +97,9 @@ public class CLI {
 		cli.run();
 	}
 
+	/**
+	 * Run.
+	 */
 	private void run() {
 		checkPreconditions();
 
@@ -115,6 +131,13 @@ public class CLI {
 		}
 	}
 
+	/**
+	 * Do work.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 * @throws PleaseRetryException the please retry exception
+	 * @throws IOException Signals that an I/O exception has occurred.
+	 */
 	private void doWork() throws GenesysApiException, PleaseRetryException, IOException {
 		String line = null;
 		do {
@@ -136,6 +159,12 @@ public class CLI {
 		} while (!"Q".equalsIgnoreCase(line));
 	}
 
+	/**
+	 * Update json data.
+	 *
+	 * @param label the label
+	 * @param n the n
+	 */
 	private void updateJsonData(String label, JsonNode n) {
 		if (n.isArray()) {
 			updateJsonArray(label, (ArrayNode) n);
@@ -144,6 +173,12 @@ public class CLI {
 		}
 	}
 
+	/**
+	 * Update json object.
+	 *
+	 * @param label the label
+	 * @param n the n
+	 */
 	private void updateJsonObject(String label, JsonNode n) {
 		Iterator<Entry<String, JsonNode>> f = n.fields();
 
@@ -182,6 +217,12 @@ public class CLI {
 		System.out.println("Done editing " + label);
 	}
 
+	/**
+	 * Update json array.
+	 *
+	 * @param label the label
+	 * @param n the n
+	 */
 	private void updateJsonArray(String label, ArrayNode n) {
 		System.out.println("Array: " + n);
 		ArrayNode na = n.arrayNode();
@@ -221,6 +262,11 @@ public class CLI {
 		System.out.println("Done editing array " + label);
 	}
 
+	/**
+	 * Do custom.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 */
 	private void doCustom() throws GenesysApiException {
 		System.out.print("URL: ");
 		String url = in.nextLine();
@@ -233,6 +279,11 @@ public class CLI {
 		System.out.println(genesysClient.query(Verb.valueOf(method), url, null, data));
 	}
 
+	/**
+	 * Do crops.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 */
 	private void doCrops() throws GenesysApiException {
 		String line = null;
 		do {
@@ -255,6 +306,11 @@ public class CLI {
 		} while (!("0".equalsIgnoreCase(line)));
 	}
 
+	/**
+	 * Update crop rules.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 */
 	private void updateCropRules() throws GenesysApiException {
 		System.out.println("Crop shortName: ");
 		String shortName = in.nextLine().trim();
@@ -283,6 +339,11 @@ public class CLI {
 				+ genesysClient.query(Verb.POST, "/crops/" + shortName + "/rules", null, arr.toString()));
 	}
 
+	/**
+	 * Update crop.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 */
 	private void updateCrop() throws GenesysApiException {
 		System.out.println("Crop shortName: ");
 		String shortName = in.nextLine().trim();
@@ -313,6 +374,11 @@ public class CLI {
 		System.out.println("Put method: " + genesysClient.query(Verb.PUT, "/crops", null, cropJson.toString()));
 	}
 
+	/**
+	 * Do traits.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 */
 	private void doTraits() throws GenesysApiException {
 		String line = null;
 		do {
@@ -336,6 +402,11 @@ public class CLI {
 		} while (!("0".equalsIgnoreCase(line)));
 	}
 
+	/**
+	 * Do datasets.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 */
 	private void doDatasets() throws GenesysApiException {
 		String line = null;
 		do {
@@ -359,6 +430,11 @@ public class CLI {
 		} while (!("0".equalsIgnoreCase(line)));
 	}
 
+	/**
+	 * Adds the method.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 */
 	private void addMethod() throws GenesysApiException {
 		ObjectNode datasetJson = mapper.createObjectNode();
 		System.out.println("Method description: ");
@@ -392,6 +468,11 @@ public class CLI {
 
 	}
 
+	/**
+	 * Adds the dataset.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 */
 	private void addDataset() throws GenesysApiException {
 		ObjectNode datasetJson = mapper.createObjectNode();
 		System.out.println("WIEWS Code: ");
@@ -410,6 +491,11 @@ public class CLI {
 
 	}
 
+	/**
+	 * Adds the dataset data.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 */
 	private void addDatasetData() throws GenesysApiException {
 		ObjectNode datasetJson = mapper.createObjectNode();
 
@@ -428,6 +514,11 @@ public class CLI {
 				+ genesysClient.query(Verb.PUT, "/datasets/" + datasetId + "/data", null, datasetJson.toString()));
 	}
 
+	/**
+	 * Adds the dataset raw.
+	 *
+	 * @throws GenesysApiException the genesys api exception
+	 */
 	private void addDatasetRaw() throws GenesysApiException {
 		System.out.println("Dataset ID: ");
 		long datasetId = Long.parseLong(in.nextLine());
@@ -442,6 +533,9 @@ public class CLI {
 				+ genesysClient.query(Verb.PUT, "/datasets/" + datasetId + "/data", null, json));
 	}
 
+	/**
+	 * Check preconditions.
+	 */
 	private void checkPreconditions() {
 		boolean restart = false;
 		if (StringUtils.isBlank(properties.getProperty("client.key"))) {
@@ -469,6 +563,9 @@ public class CLI {
 		}
 	}
 
+	/**
+	 * Authenticate.
+	 */
 	private void authenticate() {
 		String authorizationUrl = genesysClient.getAuthorizationUrl();
 
@@ -487,6 +584,9 @@ public class CLI {
 		saveProperties();
 	}
 
+	/**
+	 * Save properties.
+	 */
 	private void saveProperties() {
 		FileOutputStream fis = null;
 		try {
@@ -499,6 +599,11 @@ public class CLI {
 		}
 	}
 
+	/**
+	 * Load properties.
+	 *
+	 * @param propertiesFileName the properties file name
+	 */
 	private void loadProperties(String propertiesFileName) {
 		// .properties file location
 		propertiesFile = new File(propertiesFileName);

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

@@ -21,6 +21,7 @@ package org.genesys2.client.oauth;
  */
 public class GenesysApiException extends Exception {
 	
+	/** The Constant serialVersionUID. */
 	private static final long serialVersionUID = -6008425446284829953L;
 
 	/**

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

@@ -49,6 +49,7 @@ import com.fasterxml.jackson.databind.SerializationFeature;
 import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 
+// TODO: Auto-generated Javadoc
 /**
  * Genesys API client using Scribe.
  */
@@ -66,7 +67,7 @@ public class GenesysClient {
 	/** The service. */
 	private OAuthService service;
 
-	/** GenesysTokens: access- and refreshToken */
+	/**  GenesysTokens: access- and refreshToken. */
 	private GenesysTokens tokens = new GenesysTokens();
 
 	/** The genesys api. */
@@ -78,10 +79,10 @@ public class GenesysClient {
 	/** The api secret. */
 	private String apiSecret;
 
-	/** Socket connect timeout */
+	/**  Socket connect timeout. */
 	private int connectTimeout = 20;
 
-	/** Socket read timeout */
+	/**  Socket read timeout. */
 	private int readTimeout = 120;
 
 	static {
@@ -97,18 +98,38 @@ public class GenesysClient {
 	public GenesysClient() {
 	}
 
+	/**
+	 * Sets the read timeout.
+	 *
+	 * @param readTimeout the new read timeout
+	 */
 	public void setReadTimeout(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(int connectTimeout) {
 		this.connectTimeout = connectTimeout;
 	}
 
+	/**
+	 * Gets the connect timeout.
+	 *
+	 * @return the connect timeout
+	 */
 	public int getConnectTimeout() {
 		return connectTimeout;
 	}
@@ -188,10 +209,20 @@ public class GenesysClient {
 				.callback(callback).scope(SCOPE).build();
 	}
 
+	/**
+	 * Sets the tokens.
+	 *
+	 * @param tokens the new tokens
+	 */
 	public void setTokens(GenesysTokens tokens) {
 		this.tokens = tokens;
 	}
 
+	/**
+	 * Gets the tokens.
+	 *
+	 * @return the tokens
+	 */
 	public GenesysTokens getTokens() {
 		return tokens;
 	}
@@ -219,6 +250,7 @@ public class GenesysClient {
 	 * @return the string
 	 * @throws OAuthAuthenticationException the o auth authentication exception
 	 * @throws PleaseRetryException the please retry exception
+	 * @throws HttpRedirectException the http redirect exception
 	 * @throws GenesysApiException the genesys api exception
 	 */
 	public String query(Verb method, String url, Map<String, String> queryString, String postBody)
@@ -311,8 +343,8 @@ public class GenesysClient {
 
 	/**
 	 * Refresh accessToken with refreshToken.
-	 * 
-	 * @throws GenesysApiException
+	 *
+	 * @throws GenesysApiException the genesys api exception
 	 */
 	public void refreshAccessToken() throws GenesysApiException {
 		if (tokens.hasRefreshToken()) {
@@ -371,15 +403,14 @@ public class GenesysClient {
 	}
 
 	/**
-	 * Update MLS status of accessions
+	 * Update MLS status of accessions.
 	 *
 	 * @param instCode the inst code
 	 * @param accns the accns
 	 * @return the string
 	 * @throws GenesysApiException the genesys api exception
-	 * @throws JsonProcessingException
-	 * @throws PleaseRetryException
-	 * 
+	 * @throws PleaseRetryException the please retry exception
+	 * @throws JsonProcessingException the json processing exception
 	 * @deprecated Please use {@link #updateAccessions(String, Collection)} with
 	 *             only the instCode, acceNumb, (genus, ) and mlsStat provided.
 	 */
@@ -422,6 +453,16 @@ public class GenesysClient {
 		throw new RuntimeException("All retries failed");
 	}
 
+	/**
+	 * Update accessions.
+	 *
+	 * @param instCode the inst code
+	 * @param accns the accns
+	 * @return the string
+	 * @throws GenesysApiException the genesys api exception
+	 * @throws InterruptedException the interrupted exception
+	 * @throws JsonProcessingException the json processing exception
+	 */
 	public String updateAccessions(String instCode, Collection<AccessionJson> accns) throws GenesysApiException,
 			InterruptedException, JsonProcessingException {
 
@@ -496,11 +537,11 @@ public class GenesysClient {
 
 	/**
 	 * Delete accessions from Genesys by ID-triplet (INSTCODE, ACCENUMB, GENUS).
-	 * 
-	 * @param instCode
-	 * @param jsonAccessionId3List
-	 * @return
-	 * @throws GenesysApiException
+	 *
+	 * @param instCode the inst code
+	 * @param jsonAccessionId3List the json accession id3 list
+	 * @return the string
+	 * @throws GenesysApiException the genesys api exception
 	 */
 	public String deleteAccessionsByName(String instCode, String jsonAccessionId3List) throws GenesysApiException {
 		return query(Verb.POST, "/acn/" + instCode + "/delete-named", null, jsonAccessionId3List);
@@ -525,14 +566,14 @@ public class GenesysClient {
 	}
 
 	/**
-	 * Delete accessions from Genesys
-	 * 
-	 * @param instCode
-	 * @param jsonAccessionIdList
-	 * @return
-	 * @throws OAuthAuthenticationException
-	 * @throws PleaseRetryException
-	 * @throws GenesysApiException
+	 * Delete accessions from Genesys.
+	 *
+	 * @param instCode the inst code
+	 * @param jsonAccessionIdList the json accession id list
+	 * @return the string
+	 * @throws OAuthAuthenticationException the o auth authentication exception
+	 * @throws PleaseRetryException the please retry exception
+	 * @throws GenesysApiException the genesys api exception
 	 */
 	public String deleteAccessionsByGenesysId(String instCode, String jsonAccessionIdList)
 			throws OAuthAuthenticationException, PleaseRetryException, GenesysApiException {

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

 /**
- * Copyright 2014 Global Crop Diversity Trust
+ * Copyright 2015 Global Crop Diversity Trust
  * 
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -25,38 +25,79 @@ import org.scribe.model.Token;
  * A place to keep the tokens for the session.
  */
 public class GenesysTokens implements Serializable {
+	
+	/** The Constant serialVersionUID. */
 	private static final long serialVersionUID = 3022586353518887500L;
 
+	/** The access token. */
 	private String accessToken = null;
+	
+	/** The refresh token. */
 	private String refreshToken = null;
 
+	/** The _access token. */
 	private Token _accessToken = null;
 
+	/**
+	 * Gets the access token.
+	 *
+	 * @return the access token
+	 */
 	public String getAccessToken() {
 		return accessToken;
 	}
 
+	/**
+	 * Sets the access token.
+	 *
+	 * @param accessToken the new access token
+	 */
 	public void setAccessToken(String accessToken) {
 		this.accessToken = accessToken;
 		this._accessToken = new Token(accessToken, "");
 	}
 
+	/**
+	 * Gets the refresh token.
+	 *
+	 * @return the refresh token
+	 */
 	public String getRefreshToken() {
 		return refreshToken;
 	}
 
+	/**
+	 * Sets the refresh token.
+	 *
+	 * @param refreshToken the new refresh token
+	 */
 	public void setRefreshToken(String refreshToken) {
 		this.refreshToken = refreshToken;
 	}
 
+	/**
+	 * Checks for refresh token.
+	 *
+	 * @return true, if successful
+	 */
 	public boolean hasRefreshToken() {
 		return StringUtils.isNotBlank(this.refreshToken);
 	}
 
+	/**
+	 * Checks for access token.
+	 *
+	 * @return true, if successful
+	 */
 	public boolean hasAccessToken() {
 		return StringUtils.isNotBlank(this.accessToken);
 	}
 
+	/**
+	 * Access token.
+	 *
+	 * @return the token
+	 */
 	public Token accessToken() {
 		return this._accessToken;
 	}

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

+/**
+ * Copyright 2015 Global Crop Diversity Trust
+ * 
+ * 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 org.genesys2.client.oauth;
 
+/**
+ * The Class HttpRedirectException.
+ */
 public class HttpRedirectException extends GenesysApiException {
+	
+	/** The Constant serialVersionUID. */
 	private static final long serialVersionUID = 1L;
 
+	/** The redirect url. */
 	private String redirectUrl;
 
+	/**
+	 * Instantiates a new http redirect exception.
+	 *
+	 * @param redirectUrl the redirect url
+	 */
 	public HttpRedirectException(String redirectUrl) {
 		this.redirectUrl = redirectUrl;
 	}
 
+	/**
+	 * Gets the redirect url.
+	 *
+	 * @return the redirect url
+	 */
 	public String getRedirectUrl() {
 		return redirectUrl;
 	}

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

@@ -21,6 +21,7 @@ package org.genesys2.client.oauth;
  */
 public class OAuthAuthenticationException extends GenesysApiException {
 	
+	/** The Constant serialVersionUID. */
 	private static final long serialVersionUID = -6008425446284829953L;
 
 	/**

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

@@ -16,6 +16,7 @@
 
 package org.genesys2.client.oauth;
 
+// TODO: Auto-generated Javadoc
 /**
  * API exception indicating that the operation failed due to concurrency issues
  * and should be retried by the client.
@@ -32,6 +33,7 @@ public class PleaseRetryException extends GenesysApiException {
 		super(message);
 	}
 
+	/** The Constant serialVersionUID. */
 	private static final long serialVersionUID = 3763066812749783171L;
 
 }

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

@@ -33,22 +33,25 @@ import org.scribe.model.Response;
 import org.scribe.model.Token;
 import org.scribe.utils.OAuthEncoder;
 
+// TODO: Auto-generated Javadoc
 /**
  * Genesys API v1.
  */
 public class GenesysApi extends DefaultApi20 {
+	
+	/** The Constant _log. */
 	private static final Logger _log = LogManager.getLogger(GenesysApi.class);
 
-	/** OAuth2 authorization endpoint that is appended to {@link #baseUrl} */
+	/**  OAuth2 authorization endpoint that is appended to {@link #baseUrl}. */
 	public static final String AUTHORIZE_URL = "/oauth/authorize?client_id=%s&client_secret=%s&response_type=code&redirect_uri=%s";
 
-	/** OAuth2 access token endpoint that is appended to {@link #baseUrl} */
+	/**  OAuth2 access token endpoint that is appended to {@link #baseUrl}. */
 	private static final String TOKEN_ENDPOINT = "/oauth/token";
 
 	/** The base URL of the Genesys server (e.g. https://www.genesys-pgr.org) */
 	private String baseUrl;
 
-	/** The complete authorization url */
+	/**  The complete authorization url. */
 	private String authorizeUrl;
 
 	/** The scoped authorize url. */
@@ -147,7 +150,7 @@ public class GenesysApi extends DefaultApi20 {
 	 * @param apiSecret the api secret
 	 * @param refreshToken the refresh token
 	 * @return the access token
-	 * @throws GenesysApiException 
+	 * @throws GenesysApiException the genesys api exception