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From scnakand...@apache.org
Subject [14/51] [partial] airavata-php-gateway git commit: removing files from wrong merge
Date Tue, 13 Dec 2016 22:14:38 GMT
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/commons/src/main/java/org/apache/airavata/common/utils/SecurityUtil.java
----------------------------------------------------------------------
diff --git a/modules/commons/src/main/java/org/apache/airavata/common/utils/SecurityUtil.java b/modules/commons/src/main/java/org/apache/airavata/common/utils/SecurityUtil.java
deleted file mode 100644
index 845a040..0000000
--- a/modules/commons/src/main/java/org/apache/airavata/common/utils/SecurityUtil.java
+++ /dev/null
@@ -1,180 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you 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.apache.airavata.common.utils;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.crypto.Cipher;
-import javax.crypto.spec.IvParameterSpec;
-import java.io.*;
-import java.security.*;
-import java.security.cert.CertificateException;
-
-/**
- * Class which includes security utilities.
- */
-public class SecurityUtil {
-
-    public static final String PASSWORD_HASH_METHOD_PLAINTEXT = "PLAINTEXT";
-
-    public static final String CHARSET_ENCODING = "UTF-8";
-    public static final String ENCRYPTION_ALGORITHM = "AES";
-    public static final String PADDING_MECHANISM = "AES/CBC/PKCS5Padding";
-
-    private static final Logger logger = LoggerFactory.getLogger(SecurityUtil.class);
-
-    /**
-     * Creates a hash of given string with the given hash algorithm.
-     * 
-     * @param stringToDigest
-     *            The string to digest.
-     * @param digestingAlgorithm
-     *            Hash algorithm.
-     * @return The digested string.
-     * @throws NoSuchAlgorithmException
-     *             If given hash algorithm doesnt exists.
-     */
-    public static String digestString(String stringToDigest, String digestingAlgorithm) throws NoSuchAlgorithmException {
-
-        if (digestingAlgorithm == null || digestingAlgorithm.equals(PASSWORD_HASH_METHOD_PLAINTEXT)) {
-            return stringToDigest;
-        }
-
-        MessageDigest messageDigest = MessageDigest.getInstance(digestingAlgorithm);
-        try {
-            return new String(messageDigest.digest(stringToDigest.getBytes("UTF-8")));
-        } catch (UnsupportedEncodingException e) {
-            logger.error("Error encoding password string when creating digest", e);
-            throw new RuntimeException("Error encoding password string when creating digest", e);
-        }
-    }
-
-    /**
-     * Sets the truststore for application. Useful when communicating over HTTPS.
-     * 
-     * @param trustStoreFilePath
-     *            Where trust store is located.
-     * @param trustStorePassword
-     *            The trust store password.
-     */
-    public static void setTrustStoreParameters(String trustStoreFilePath, String trustStorePassword) {
-
-        if (System.getProperty("javax.net.ssl.trustStrore") == null) {
-            logger.info("Setting Java trust store to " + trustStoreFilePath);
-            System.setProperty("javax.net.ssl.trustStrore", trustStoreFilePath);
-        }
-
-        if (System.getProperty("javax.net.ssl.trustStorePassword") == null) {
-            System.setProperty("javax.net.ssl.trustStorePassword", trustStoreFilePath);
-        }
-
-    }
-
-    public static byte[] encryptString(String keyStorePath, String keyAlias,
-                                 KeyStorePasswordCallback passwordCallback, String value)
-            throws GeneralSecurityException, IOException {
-        return encrypt(keyStorePath, keyAlias, passwordCallback, value.getBytes(CHARSET_ENCODING));
-    }
-
-    public static byte[] encrypt(String keyStorePath, String keyAlias,
-                                 KeyStorePasswordCallback passwordCallback, byte[] value)
-            throws GeneralSecurityException, IOException {
-
-        Key secretKey = getSymmetricKey(keyStorePath, keyAlias, passwordCallback);
-
-        Cipher cipher = Cipher.getInstance(PADDING_MECHANISM);
-        cipher.init(Cipher.ENCRYPT_MODE, secretKey,
-                new IvParameterSpec(new byte[16]));
-        return cipher.doFinal(value);
-    }
-
-    private static Key getSymmetricKey(String keyStorePath, String keyAlias,
-                                       KeyStorePasswordCallback passwordCallback)
-            throws CertificateException, NoSuchAlgorithmException, KeyStoreException, IOException,
-            UnrecoverableKeyException {
-
-        KeyStore ks = SecurityUtil.loadKeyStore(keyStorePath, "jceks", passwordCallback);
-
-        if (ks == null) {
-            throw new IOException("Unable to load Java keystore " + keyStorePath);
-        }
-
-        return ks.getKey(keyAlias, passwordCallback.getSecretKeyPassPhrase(keyAlias));
-
-    }
-
-    public static byte[] decrypt(String keyStorePath, String keyAlias,
-                                 KeyStorePasswordCallback passwordCallback, byte[] encrypted)
-            throws GeneralSecurityException, IOException {
-
-        Key secretKey = getSymmetricKey(keyStorePath, keyAlias, passwordCallback);
-
-        Cipher cipher = Cipher.getInstance(PADDING_MECHANISM);
-        cipher.init(Cipher.DECRYPT_MODE, secretKey,
-                new IvParameterSpec(new byte[16]));
-
-        return cipher.doFinal(encrypted);
-    }
-
-    public static String decryptString(String keyStorePath, String keyAlias,
-                                       KeyStorePasswordCallback passwordCallback, byte[] encrypted)
-            throws GeneralSecurityException, IOException {
-
-        byte[] decrypted = decrypt(keyStorePath, keyAlias, passwordCallback, encrypted);
-        return new String(decrypted, CHARSET_ENCODING);
-    }
-
-    public static KeyStore loadKeyStore(String keyStoreFilePath, String keyStoreType,
-                                        KeyStorePasswordCallback passwordCallback)
-            throws KeyStoreException, IOException, CertificateException, NoSuchAlgorithmException {
-
-        java.io.FileInputStream fis = null;
-        try {
-            fis = new java.io.FileInputStream(keyStoreFilePath);
-            return loadKeyStore(fis, keyStoreType, passwordCallback);
-        } finally {
-            if (fis != null) {
-                fis.close();
-            }
-        }
-    }
-
-    public static KeyStore loadKeyStore(InputStream inputStream, String keyStoreType,
-                                        KeyStorePasswordCallback passwordCallback)
-            throws KeyStoreException, IOException, CertificateException, NoSuchAlgorithmException {
-
-        if (keyStoreType == null) {
-            keyStoreType = KeyStore.getDefaultType();
-        }
-
-        KeyStore ks = KeyStore.getInstance(keyStoreType);
-        ks.load(inputStream, passwordCallback.getStorePassword());
-
-        return ks;
-    }
-
-
-
-
-
-}

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/commons/src/main/java/org/apache/airavata/common/utils/ServerSettings.java
----------------------------------------------------------------------
diff --git a/modules/commons/src/main/java/org/apache/airavata/common/utils/ServerSettings.java b/modules/commons/src/main/java/org/apache/airavata/common/utils/ServerSettings.java
deleted file mode 100644
index 46b1ebb..0000000
--- a/modules/commons/src/main/java/org/apache/airavata/common/utils/ServerSettings.java
+++ /dev/null
@@ -1,468 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you 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.apache.airavata.common.utils;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.net.InetAddress;
-import java.net.UnknownHostException;
-import java.util.HashMap;
-import java.util.Map;
-
-public class ServerSettings extends ApplicationSettings {
-
-    private static final Logger log = LoggerFactory.getLogger(ServerSettings.class);
-
-    private static final String DEFAULT_USER = "default.registry.user";
-    private static final String DEFAULT_USER_PASSWORD = "default.registry.password";
-    private static final String DEFAULT_USER_GATEWAY = "default.registry.gateway";
-    private static final String ENABLE_SHARING = "enable.sharing";
-
-    public static final String IP = "ip";
-
-    private static final String API_SERVER_TLS_ENABLED = "apiserver.tls.enabled";
-    private static final String API_SERVER_KEYSTORE = "apiserver.keystore";
-    private static final String API_SERVER_KEYSTORE_PASSWD = "apiserver.keystore.password";
-
-    // Orchestrator Constants
-    public static final String ORCHESTRATOR_SERVER_HOST = "orchestrator.server.host";
-    public static final String ORCHESTRATOR_SERVER_PORT = "orchestrator.server.port";
-    public static final String ORCHESTRATOR_SERVER_NAME = "orchestrator.server.name";
-    // Gfac constants
-    public static final String GFAC_SERVER_HOST = "gfac.server.host";
-    public static final String GFAC_SERVER_PORT = "gfac.server.port";
-    public static final String GFAC_SERVER_NAME = "gfac.server.name";
-    public static final String GFAC_THREAD_POOL_SIZE = "gfac.thread.pool.size";
-    public static final int DEFAULT_GFAC_THREAD_POOL_SIZE = 50;
-    public static final String GFAC_CONFIG_XML = "gfac-config.xml";
-    // Credential Store constants
-    public static final String CREDENTIAL_SERVER_HOST = "credential.store.server.host";
-    public static final String CREDENTIAL_SERVER_PORT = "credential.store.server.port";
-    // Zookeeper + curator constants
-    public static final String EMBEDDED_ZK = "embedded.zk";
-    public static final String ZOOKEEPER_SERVER_CONNECTION = "zookeeper.server.connection";
-    public static final String ZOOKEEPER_TIMEOUT = "zookeeper.timeout";
-
-    // Aurora Scheduler Constants
-    public static final String AURORA_SCHEDULER_HOSTS = "aurora.scheduler.hosts";
-	public static final String AURORA_EXECUTOR_NAME = "aurora.executor.name";
-	public static final String MESOS_CLUSTER_NAME = "mesos.cluster.name";
-	public static final String AURORA_SCHEDULER_CONNECT_TIMEOUT_MS = "aurora.scheduler.timeoutms";
-	public static final String AURORA_EXECUTOR_CONFIG_TEMPLATE_FILE = "aurora.executor.config.template.filename";
-
-    private static final String CREDENTIAL_STORE_DB_URL = "credential.store.jdbc.url";
-    private static final String CREDENTIAL_STORE_DB_USER = "credential.store.jdbc.user";
-    private static final String CREDENTIAL_STORE_DB_PASSWORD = "credential.store.jdbc.password";
-    private static final String CREDENTIAL_STORE_DB_DRIVER = "credential.store.jdbc.driver";
-
-    private static String USER_PROFILE_MONGODB_HOST = "userprofile.mongodb.host";
-    private static String USER_PROFILE_MONGODB_PORT = "userprofile.mongodb.port";
-
-    private static final String REGISTRY_DB_URL = "registry.jdbc.url";
-    private static final String REGISTRY_DB_USER = "registry.jdbc.user";
-    private static final String REGISTRY_DB_PASSWORD = "registry.jdbc.password";
-    private static final String REGISTRY_DB_DRIVER = "registry.jdbc.driver";
-    private static final String HOST_SCHEDULER = "host.scheduler";
-    private static final String MY_PROXY_SERVER = "myproxy.server";
-    private static final String MY_PROXY_USER = "myproxy.user";
-    private static final String MY_PROXY_PASSWORD = "myproxy.password";
-    private static final String MY_PROXY_LIFETIME = "myproxy.life";
-    public static final String JOB_NOTIFICATION_ENABLE = "job.notification.enable";
-    public static final String JOB_NOTIFICATION_EMAILIDS = "job.notification.emailids";
-    public static final String JOB_NOTIFICATION_FLAGS = "job.notification.flags";
-
-    public static final String RABBITMQ_BROKER_URL = "rabbitmq.broker.url";
-    public static final String RABBITMQ_STATUS_EXCHANGE_NAME = "rabbitmq.status.exchange.name";
-    public static final String RABBITMQ_PROCESS_EXCHANGE_NAME = "rabbitmq.process.exchange.name";
-    public static final String RABBITMQ_EXPERIMENT_EXCHANGE_NAME = "rabbitmq.experiment.exchange.name";
-    public static final String RABBITMQ_PROCESS_LAUNCH_QUEUE_NAME = "process.launch.queue.name";
-    public static final String RABBITMQ_EXPERIMENT_LAUNCH_QUEUE_NAME = "experiment.launch.queue.name";
-    public static final String RABBITMQ_DURABLE_QUEUE="durable.queue";
-    public static final String RABBITMQ_PREFETCH_COUNT="prefetch.count";
-
-
-    //    Workflow Enactment Service component configuration.
-    private static final String ENACTMENT_THREAD_POOL_SIZE = "enactment.thread.pool.size";
-    private static final int DEFAULT_ENACTMENT_THREAD_POOL_SIZE = 10;
-    private static final String WORKFLOW_PARSER = "workflow.parser";
-
-    // email based monitoring configurations
-    private static final String EMAIL_BASED_MONITORING_PERIOD = "email.based.monitoring.period";
-    private static final String EMAIL_BASED_MONITOR_HOST = "email.based.monitor.host";
-    private static final String EMAIL_BASED_MONITOR_ADDRESS = "email.based.monitor.address";
-    private static final String EMAIL_BASED_MONITOR_PASSWORD = "email.based.monitor.password";
-    private static final String EMAIL_BASED_MONITOR_FOLDER_NAME = "email.based.monitor.folder.name";
-    private static final String EMAIL_BASED_MONITOR_STORE_PROTOCOL = "email.based.monitor.store.protocol";
-    private static final String ENABLE_EMAIL_BASED_MONITORING = "enable.email.based.monitoring";
-
-    private static final String IS_RUNNING_ON_AWS = "isRunningOnAws";
-    private static final String ENABLE_KAFKA_LOGGING = "enable.kafka.logging";
-    private static final String KAFKA_BROKER_LIST = "kafka.broker.list";
-    private static final String KAFKA_TOPIC_PREFIX = "kafka.topic.prefix";
-    private static final String SERVER_ROLES = "server.roles";
-
-    // todo until AIRAVATA-2066 is finished, keep server side list configurations here.
-    private static Map<String, String[]> listConfigurations = new HashMap<>();
-
-    private static boolean stopAllThreads = false;
-    private static boolean emailBaseNotificationEnable;
-    private static String outputLocation;
-
-    public static String getDefaultUser() throws ApplicationSettingsException {
-        return getSetting(DEFAULT_USER);
-    }
-
-    public static String getRabbitmqProcessLaunchQueueName() {
-        return getSetting(RABBITMQ_PROCESS_LAUNCH_QUEUE_NAME, "process.launch.queue");
-    }
-
-    public static String getRabbitmqExperimentLaunchQueueName() {
-        return getSetting(RABBITMQ_EXPERIMENT_EXCHANGE_NAME, "experiment.launch.queue");
-    }
-
-    public static String getRabbitmqBrokerUrl() {
-        return getSetting(RABBITMQ_BROKER_URL, "amqp://localhost:5672");
-    }
-
-    public static String getRabbitmqStatusExchangeName(){
-        return getSetting(RABBITMQ_STATUS_EXCHANGE_NAME, "status_exchange");
-    }
-
-    public static String getRabbitmqProcessExchangeName(){
-        return getSetting(RABBITMQ_PROCESS_EXCHANGE_NAME, "process_exchange");
-    }
-
-    public static String getRabbitmqExperimentExchangeName() {
-        return getSetting(RABBITMQ_EXPERIMENT_EXCHANGE_NAME, "experiment_exchange");
-    }
-
-    public static boolean getRabbitmqDurableQueue(){
-        return Boolean.valueOf(getSetting(RABBITMQ_DURABLE_QUEUE, "false"));
-    }
-
-    public static int getRabbitmqPrefetchCount(){
-        return Integer.valueOf(getSetting(RABBITMQ_PREFETCH_COUNT, "200"));
-    }
-
-    public static String getDefaultUserPassword() throws ApplicationSettingsException {
-        return getSetting(DEFAULT_USER_PASSWORD);
-    }
-
-    public static String getDefaultUserGateway() throws ApplicationSettingsException {
-        return getSetting(DEFAULT_USER_GATEWAY);
-    }
-
-    public static String getCredentialStoreDBUser() throws ApplicationSettingsException {
-        try {
-            return getSetting(CREDENTIAL_STORE_DB_USER);
-        } catch (ApplicationSettingsException e) {
-            return getSetting(REGISTRY_DB_USER);
-        }
-    }
-
-    public static String getCredentialStoreDBPassword() throws ApplicationSettingsException {
-        try {
-            return getSetting(CREDENTIAL_STORE_DB_PASSWORD);
-        } catch (ApplicationSettingsException e) {
-            return getSetting(REGISTRY_DB_PASSWORD);
-        }
-    }
-
-    public static String getCredentialStoreDBDriver() throws ApplicationSettingsException {
-        try {
-            return getSetting(CREDENTIAL_STORE_DB_DRIVER);
-        } catch (ApplicationSettingsException e) {
-            return getSetting(REGISTRY_DB_DRIVER);
-        }
-    }
-
-    public static String getCredentialStoreDBURL() throws ApplicationSettingsException {
-        try {
-            return getSetting(CREDENTIAL_STORE_DB_URL);
-        } catch (ApplicationSettingsException e) {
-            return getSetting(REGISTRY_DB_URL);
-        }
-
-    }
-
-    public static boolean isAPIServerTLSEnabled() {
-        try {
-            return Boolean.parseBoolean(getSetting(API_SERVER_TLS_ENABLED));
-        } catch (ApplicationSettingsException e) {
-            return false;
-        }
-    }
-
-    public static String getApiServerKeystorePasswd() throws ApplicationSettingsException{
-        return getSetting(API_SERVER_KEYSTORE_PASSWD);
-    }
-
-    public static String getApiServerKeystore() throws ApplicationSettingsException{
-        return getSetting(API_SERVER_KEYSTORE);
-    }
-
-    public static String getHostScheduler() throws ApplicationSettingsException {
-        return getSetting(HOST_SCHEDULER);
-    }
-
-    public static boolean isStopAllThreads() {
-        return stopAllThreads;
-    }
-
-    public static void setStopAllThreads(boolean stopAllThreads) {
-        ServerSettings.stopAllThreads = stopAllThreads;
-    }
-
-    public static String getMyProxyServer() throws ApplicationSettingsException {
-        return getSetting(MY_PROXY_SERVER);
-    }
-
-    public static String getMyProxyUser() throws ApplicationSettingsException {
-        return getSetting(MY_PROXY_USER);
-    }
-
-    public static String getMyProxyPassword() throws ApplicationSettingsException {
-        return getSetting(MY_PROXY_PASSWORD);
-    }
-
-    public static int getMyProxyLifetime() throws ApplicationSettingsException {
-        return Integer.parseInt(getSetting(MY_PROXY_LIFETIME));
-    }
-
-    public static boolean isEmbeddedZK() {
-        return Boolean.parseBoolean(getSetting(EMBEDDED_ZK, "true"));
-    }
-
-    public static String getIp() {
-        try {
-            return getSetting(IP);
-        } catch (ApplicationSettingsException e) {
-            try {
-                return InetAddress.getLocalHost().getHostAddress();
-            } catch (UnknownHostException e1) {
-                e1.printStackTrace();
-            }
-        }
-        return null;
-    }
-
-    public static int getEnactmentThreadPoolSize() {
-        String threadPoolSize = null;
-        try {
-            threadPoolSize = getSetting(ENACTMENT_THREAD_POOL_SIZE);
-        } catch (ApplicationSettingsException e) {
-            return DEFAULT_ENACTMENT_THREAD_POOL_SIZE;
-        }
-        return Integer.valueOf(threadPoolSize);
-    }
-
-    public static String getWorkflowParser() throws ApplicationSettingsException {
-        return getSetting(WORKFLOW_PARSER);
-    }
-
-
-    public static int getEmailMonitorPeriod() throws ApplicationSettingsException {
-        return Integer.valueOf(getSetting(EMAIL_BASED_MONITORING_PERIOD, "100000"));
-
-    }
-
-    public static String getEmailBasedMonitorHost() throws ApplicationSettingsException {
-        return getSetting(EMAIL_BASED_MONITOR_HOST);
-    }
-
-    public static String getEmailBasedMonitorAddress() throws ApplicationSettingsException {
-        return getSetting(EMAIL_BASED_MONITOR_ADDRESS);
-    }
-
-    public static String getEmailBasedMonitorPassword() throws ApplicationSettingsException {
-        return getSetting(EMAIL_BASED_MONITOR_PASSWORD);
-    }
-
-    public static String getEmailBasedMonitorFolderName() throws ApplicationSettingsException {
-        return getSetting(EMAIL_BASED_MONITOR_FOLDER_NAME);
-    }
-
-    public static String getEmailBasedMonitorStoreProtocol() throws ApplicationSettingsException {
-        return getSetting(EMAIL_BASED_MONITOR_STORE_PROTOCOL);
-    }
-
-    public static boolean isEmailBasedNotificationEnable() {
-        return Boolean.valueOf(getSetting(ENABLE_EMAIL_BASED_MONITORING, "false"));
-    }
-
-    public static boolean isAPISecured() throws ApplicationSettingsException {
-        return Boolean.valueOf(getSetting(Constants.IS_API_SECURED));
-    }
-
-    public static String getRemoteAuthzServerUrl() throws ApplicationSettingsException {
-        return getSetting(Constants.REMOTE_OAUTH_SERVER_URL);
-    }
-
-    public static String getAuthorizationPoliyName() throws ApplicationSettingsException {
-        return getSetting(Constants.AUTHORIZATION_POLICY_NAME);
-    }
-
-    public static String getZookeeperConnection() throws ApplicationSettingsException {
-        return getSetting(ZOOKEEPER_SERVER_CONNECTION, "localhost:2181");
-    }
-
-    public static int getZookeeperTimeout() {
-        return Integer.valueOf(getSetting(ZOOKEEPER_TIMEOUT, "3000"));
-    }
-
-    public static String getGFacServerName() throws ApplicationSettingsException {
-        return getSetting(GFAC_SERVER_NAME);
-    }
-
-    public static String getGfacServerHost() throws ApplicationSettingsException {
-        return getSetting(GFAC_SERVER_HOST);
-    }
-
-    public static String getGFacServerPort() throws ApplicationSettingsException {
-        return getSetting(GFAC_SERVER_PORT);
-    }
-
-    public static int getGFacThreadPoolSize() {
-        try {
-            String threadPoolSize = getSetting(GFAC_THREAD_POOL_SIZE);
-            if (threadPoolSize != null && !threadPoolSize.isEmpty()) {
-                return Integer.valueOf(threadPoolSize);
-            } else {
-                log.warn("Thread pool size is not configured, use default gfac thread pool size " +
-                        DEFAULT_GFAC_THREAD_POOL_SIZE);
-            }
-        } catch (ApplicationSettingsException e) {
-            log.warn("Couldn't read thread pool size from configuration on exception, use default gfac thread pool " +
-                    "size " + DEFAULT_GFAC_THREAD_POOL_SIZE);
-        }
-        return DEFAULT_GFAC_THREAD_POOL_SIZE;
-    }
-
-    public static String getOrchestratorServerName() throws ApplicationSettingsException {
-        return getSetting(ORCHESTRATOR_SERVER_NAME);
-    }
-
-    public static String getOrchestratorServerHost() throws ApplicationSettingsException {
-        return getSetting(ORCHESTRATOR_SERVER_HOST);
-    }
-
-    public static int getOrchestratorServerPort() throws ApplicationSettingsException {
-        return Integer.valueOf(getSetting(ORCHESTRATOR_SERVER_PORT));
-    }
-
-    public static boolean isTLSEnabled() throws ApplicationSettingsException {
-        return Boolean.valueOf(getSetting(Constants.IS_TLS_ENABLED));
-    }
-
-    public static int getTLSServerPort() throws ApplicationSettingsException {
-        return Integer.valueOf(getSetting(Constants.TLS_SERVER_PORT));
-    }
-
-    public static String getKeyStorePath() throws ApplicationSettingsException {
-        return getSetting(Constants.KEYSTORE_PATH);
-    }
-
-    public static String getKeyStorePassword() throws ApplicationSettingsException {
-        return getSetting(Constants.KEYSTORE_PASSWORD);
-    }
-
-    public static int getTLSClientTimeout() throws ApplicationSettingsException {
-        return Integer.valueOf(getSetting(Constants.TLS_CLIENT_TIMEOUT));
-    }
-
-    public static String getSecurityManagerClassName() throws ApplicationSettingsException {
-        return getSetting(Constants.SECURITY_MANAGER_CLASS);
-    }
-
-    public static String getAuthzCacheManagerClassName() throws ApplicationSettingsException {
-        return getSetting(Constants.AUTHZ_CACHE_MANAGER_CLASS);
-    }
-
-    public static boolean isAuthzCacheEnabled() throws ApplicationSettingsException {
-        return Boolean.valueOf(getSetting(Constants.AUTHZ_CACHE_ENABLED));
-    }
-
-    public static int getCacheSize() throws ApplicationSettingsException {
-        return Integer.valueOf(getSetting(Constants.IN_MEMORY_CACHE_SIZE));
-    }
-
-    public static String getUserProfileMongodbHost() throws ApplicationSettingsException{
-        return getSetting(USER_PROFILE_MONGODB_HOST);
-    }
-
-    public static int getUserProfileMongodbPort() throws ApplicationSettingsException{
-        return Integer.parseInt(getSetting(USER_PROFILE_MONGODB_PORT));
-    }
-
-    public static String getLocalDataLocation() {
-        return System.getProperty("java.io.tmpdir");
-    }
-
-    public static Boolean isEnableSharing() throws ApplicationSettingsException {
-        return Boolean.parseBoolean(getSetting(ENABLE_SHARING));
-    }
-    public static boolean isRunningOnAws() {
-        return Boolean.valueOf(getSetting(IS_RUNNING_ON_AWS, "false"));
-    }
-
-    public static String getKafkaBrokerList() {
-        return getSetting(KAFKA_BROKER_LIST, null);
-    }
-
-    public static String getKafkaTopicPrefix() {
-        return getSetting(KAFKA_TOPIC_PREFIX, "all");
-    }
-
-    public static boolean isEnabledKafkaLogging() {
-        return Boolean.valueOf(getSetting(ENABLE_KAFKA_LOGGING, "false"));
-    }
-
-    public static void setServerRoles(String[] roles) {
-        listConfigurations.put(SERVER_ROLES, roles);
-    }
-
-    public static String[] getServerRoles() {
-        return listConfigurations.get(SERVER_ROLES);
-    }
-    
-    public static String getAuroraSchedulerHosts() throws ApplicationSettingsException {
-    	return getSetting(AURORA_SCHEDULER_HOSTS);
-    }
-    
-    public static String getMesosClusterName() throws ApplicationSettingsException {
-    	return getSetting(MESOS_CLUSTER_NAME);
-    }
-    
-    public static String getAuroraExecutorName() throws ApplicationSettingsException {
-    	return getSetting(AURORA_EXECUTOR_NAME);
-    }
-    
-    public static String getAuroraExecutorConfigTemplateFileName() throws ApplicationSettingsException {
-    	return getSetting(AURORA_EXECUTOR_CONFIG_TEMPLATE_FILE);
-    }
-    
-    public static int getAuroraSchedulerTimeout() throws ApplicationSettingsException {
-    	return Integer.valueOf(getSetting(AURORA_SCHEDULER_CONNECT_TIMEOUT_MS));
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/commons/src/main/java/org/apache/airavata/common/utils/ServiceUtils.java
----------------------------------------------------------------------
diff --git a/modules/commons/src/main/java/org/apache/airavata/common/utils/ServiceUtils.java b/modules/commons/src/main/java/org/apache/airavata/common/utils/ServiceUtils.java
deleted file mode 100644
index 0c54053..0000000
--- a/modules/commons/src/main/java/org/apache/airavata/common/utils/ServiceUtils.java
+++ /dev/null
@@ -1,93 +0,0 @@
-///*
-// *
-// * Licensed to the Apache Software Foundation (ASF) under one
-// * or more contributor license agreements.  See the NOTICE file
-// * distributed with this work for additional information
-// * regarding copyright ownership.  The ASF licenses this file
-// * to you 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.apache.airavata.common.utils;
-//
-//import java.io.IOException;
-//import java.net.SocketException;
-//
-//import org.apache.airavata.common.exception.ApplicationSettingsException;
-//import org.apache.axis2.context.ConfigurationContext;
-//import org.apache.axis2.description.TransportInDescription;
-//import org.apache.axis2.util.Utils;
-//import org.slf4j.Logger;
-//import org.slf4j.LoggerFactory;
-//
-//public class ServiceUtils {
-//    private static final Logger log = LoggerFactory.getLogger(ServiceUtils.class);
-////    private static final String REPOSITORY_PROPERTIES = "airavata-server.properties";
-//    public static final String IP = "ip";
-//    public static final String PORT = "port";
-//
-//	public static String generateServiceURLFromConfigurationContext(
-//			ConfigurationContext context, String serviceName) throws IOException, ApplicationSettingsException {
-////		URL url = ServiceUtils.class.getClassLoader()
-////				.getResource(REPOSITORY_PROPERTIES);
-//		 String localAddress = null;
-//        String port = null;
-////        Properties properties = new Properties();
-//        try {
-//            localAddress = ServerSettings.getSetting(IP);
-//        } catch (ApplicationSettingsException e) {
-//			//we will ignore this exception since the properties file will not contain the values
-//			//when it is ok to retrieve them from the axis2 context
-//		}
-//        if(localAddress == null){
-//	        try {
-//	            localAddress = Utils.getIpAddress(context
-//	                    .getAxisConfiguration());
-//	        } catch (SocketException e) {
-//	            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
-//	        }
-//        }
-//        String protocol="http";
-//        if(ServerSettings.isEnableHttps()){
-//            protocol="https";
-//        }
-//
-//        try {
-//            port = ServerSettings.getTomcatPort(protocol);
-//        } catch (ApplicationSettingsException e) {
-//            //we will ignore this exception since the properties file will not contain the values
-//            //when it is ok to retrieve them from the axis2 context
-//        }
-//        if (port == null) {
-//            TransportInDescription transportInDescription = context
-//                .getAxisConfiguration().getTransportsIn()
-//                .get(protocol);
-//            if (transportInDescription != null
-//                && transportInDescription.getParameter(PORT) != null) {
-//                port = (String) transportInDescription
-//                    .getParameter(PORT).getValue();
-//            }
-//        }
-//        localAddress = protocol+"://" + localAddress + ":" + port;
-//        localAddress = localAddress + "/"
-//    		//We are not using axis2 config context to get the context root because it is invalid
-//            //+ context.getContextRoot() + "/"
-//    		//FIXME: the context root will be correct after updating the web.xml 
-//            + ServerSettings.getServerContextRoot() + "/"
-//            + context.getServicePath() + "/"
-//            + serviceName;
-//        log.debug("Service Address Configured:" + localAddress);
-//        return localAddress;
-//	}
-//}

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/commons/src/main/java/org/apache/airavata/common/utils/StringUtil.java
----------------------------------------------------------------------
diff --git a/modules/commons/src/main/java/org/apache/airavata/common/utils/StringUtil.java b/modules/commons/src/main/java/org/apache/airavata/common/utils/StringUtil.java
deleted file mode 100644
index 3ce5cda..0000000
--- a/modules/commons/src/main/java/org/apache/airavata/common/utils/StringUtil.java
+++ /dev/null
@@ -1,480 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you 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.apache.airavata.common.utils;
-
-import java.io.ByteArrayOutputStream;
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.ListIterator;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-
-public class StringUtil {
-	public static final String DELIMETER=",";
-	public static final String QUOTE="\"";
-	
-	public static Map<Integer, String> getContainedParameters(String s) {
-		Map<Integer,String> parameterMap=new HashMap<Integer,String>();
-		int i=0;
-		for(i=0;i<s.length();i++){
-			if (s.charAt(i)=='$' && (i+1)<s.length() && s.charAt(i+1)=='{'){
-				int i2=s.indexOf('{', i+2);
-				int e=s.indexOf('}', i+2);
-				if (e!=-1){
-					if (i2==-1 || e<i2){
-						parameterMap.put(i, s.substring(i,e+1));
-						i=e;
-					}
-				}
-			}
-		}
-		return parameterMap;
-	}
-	
-	// Merits for the following function should go to 
-	// http://blog.houen.net/java-get-url-from-string/ 
-	public static List<String> getURLS(String text) {
-		List<String> links = new ArrayList<String>();
-		String regex = "\\(?\\b((http|https|ftp)://|www[.])[-A-Za-z0-9+&@#/%?=~_()|!:,.;]*[-A-Za-z0-9+&@#/%=~_()|]";
-		Pattern p = Pattern.compile(regex);
-		Matcher m = p.matcher(text);
-		while (m.find()) {
-			String urlStr = m.group();
-			if (urlStr.startsWith("(") && urlStr.endsWith(")")) {
-				urlStr = urlStr.substring(1, urlStr.length() - 1);
-			}
-			if (!links.contains(urlStr)) {
-				links.add(urlStr);
-			}
-		}
-		return links;
-	}
-
-	public static String createHTMLUrlTaggedString2(String value, List<String> pullLinks) {
-		for (String url : pullLinks) {
-			String hyperlinkString="<a href='"+url+"'>"+url+"</a>";
-			value=value.replaceAll(Pattern.quote(url), hyperlinkString);
-		}
-		return value;
-	}
-	public static String createHTMLUrlTaggedString(String value) {
-		String urledString = "";
-		int lastIndex=0,index=0;
-		while(index!=-1){
-			index=value.toLowerCase().indexOf("://",lastIndex);
-			if (index!=-1){
-				int beginIndex=value.lastIndexOf(" ",index);
-				urledString+=value.substring(lastIndex,beginIndex+1);
-				int endIndex=value.indexOf(" ",index);
-				if (beginIndex==-1){
-					beginIndex=0;
-				}else{
-					beginIndex++;
-				}
-				if (endIndex==-1){
-					endIndex=value.length();
-				}
-				String url=value.substring(beginIndex, endIndex);
-				urledString+="<a href='"+url+"'>"+url+"</a>";
-				lastIndex=endIndex;
-			}
-		}
-		urledString+=value.substring(lastIndex, value.length());
-		return urledString;
-	}
-	
-	private static boolean isQuoted(String s, String delimiter){
-		//Check if we need quotes
-		if (s.contains(delimiter)){
-			//Check if its already quoted
-			s=s.replaceAll("\"\"", "");
-			return (s.substring(0,1).equals(QUOTE) && s.subSequence(s.length()-1, s.length()).equals(QUOTE));
-		}
-		//no delimiters present, so already in proper form
-		return true;
-	}
-	
-	private static boolean isQuoted(String s){
-		return isQuoted(s, DELIMETER);
-	}
-	
-	/**
-	 * Create a delimiter separated string out of a list
-	 * @param list
-	 * @return
-	 */
-	public static String createDelimiteredString(String[] list) {
-        return createDelimiteredString(list, DELIMETER);
-    }
-
-
-    /**
-	 * Create a delimiter separated string out of a list
-	 * @param list
-	 * @return
-	 */
-	public static String createDelimiteredString(String[] list,String delimiter){
-		String s=null;
-		for (String ss : list) {
-			ss=quoteString(ss, delimiter);
-			if (s==null){
-				s=ss;
-			}else{
-				s+=delimiter +ss;
-			}
-		}
-		return s;
-	}
-
-	/**
-	 * Return a proper quoted string if the string contains the delimiter character
-	 * @param s
-	 * @return
-	 */
-	public static String quoteString(String s) {
-        return quoteString(s, DELIMETER);
-    }
-
-
-    /**
-	 * Return a proper quoted string if the string contains the delimiter character
-	 * @param s
-	 * @return
-	 */
-	public static String quoteString(String s,String delimiter){
-		if (isQuoted(s,delimiter)){
-			return s;
-		}else{
-			return QUOTE+s.replaceAll(QUOTE, QUOTE+QUOTE)+QUOTE;
-		}
-	}
-
-	/**
-	 * Parse the delimitered string and return elements as a string array 
-	 * @param s
-	 * @return
-	 */
-	public static String[] getElementsFromString(String s, String delimeter, String quote) {
-		List<String> list=new ArrayList<String>();
-		String currentItem="";
-		String previousChar=null;
-		boolean insideQuote=false;
-		for(int i=0;i<s.length();i++){
-			String c=s.substring(i,i+1);
-			if (c.equals(delimeter)){
-				//if not inside a quoted string ignore the delimiter character
-				if (insideQuote) {
-					currentItem+=c;
-				}else{
-					list.add(currentItem);
-					currentItem = "";
-				}
-			}else if (c.equals(quote)){
-				if (quote.equals(previousChar)){
-					//which means previousChar was an escape character, not a quote for the string
-					currentItem+=quote;
-					if (insideQuote){
-						//mistakenly thought previous char was opening quote char, thus need to make this false
-						insideQuote=false;
-					}else{
-						//mistakenly thought previous char was closing quote char, thus need to make this true
-						insideQuote=true;
-					}
-				} else{
-					if (insideQuote){
-						//quote ended
-						insideQuote=false;
-					}else{
-						//quote beginning
-						insideQuote=true;
-					}
-				}
-			}else{
-				currentItem+=c;
-			}
-			previousChar=c;
-		}
-		list.add(currentItem);
-		return list.toArray(new String[]{});
-	}
-	
-	/**
-	 * Parse the delimitered string and return elements as a string array 
-	 * @param s
-	 * @return
-	 */
-	public static String[] getElementsFromString(String s) {
-		return getElementsFromString(s, DELIMETER, QUOTE);
-	}
-
-    /**
-     * Converts object to String without worrying about null check.
-     * 
-     * @param object
-     * @return The object.toString if object is not null; "" otherwise.
-     */
-    public static String toString(Object object) {
-        if (object == null) {
-            return "";
-        } else {
-            return object.toString();
-        }
-    }
-
-    /**
-     * Trims a specified string, and makes it null if the result is empty string.
-     * 
-     * @param string
-     * @return the string processed
-     */
-    public static String trimAndNullify(String string) {
-        if (string != null) {
-            string = string.trim();
-            if (string.equals("")) {
-                string = null;
-            }
-        }
-        return string;
-    }
-
-    /**
-     * @param oldName
-     * @return Trimmed String
-     */
-    public static String trimSpaceInString(String oldName) {
-        if (oldName == null) {
-            return "";
-        }
-        return oldName.replace(" ", "");
-    }
-
-    /**
-     * Converts a specified string to a Java identifier.
-     * 
-     * @param name
-     * @return the Java identifier
-     */
-    public static String convertToJavaIdentifier(String name) {
-
-        final char REPLACE_CHAR = '_';
-
-        if (name == null || name.length() == 0) {
-            return "" + REPLACE_CHAR;
-        }
-
-        StringBuilder buf = new StringBuilder();
-
-        char c = name.charAt(0);
-        if (!Character.isJavaIdentifierStart(c)) {
-            // Add _ at the beggining instead of replacing it to _. This is
-            // more readable if the name is like 3D_Model.
-            buf.append(REPLACE_CHAR);
-        }
-
-        for (int i = 0; i < name.length(); i++) {
-            c = name.charAt(i);
-            if (Character.isJavaIdentifierPart(c)) {
-                buf.append(c);
-            } else {
-                buf.append(REPLACE_CHAR);
-            }
-        }
-
-        return buf.toString();
-    }
-
-    /**
-     * Creates a new name by incrementing the number after the underscore at the end of the old name. If there is no
-     * underscore and number at the end, put "_2" at the end.
-     * 
-     * @param oldName
-     * @return the new name
-     */
-    public static String incrementName(String oldName) {
-
-        final char PREFIX = '_';
-
-        String newName;
-        if (oldName == null || oldName.length() == 0) {
-            newName = "noName";
-        } else {
-            int lastDashIndex = oldName.lastIndexOf(PREFIX);
-            if (lastDashIndex < 0) {
-                newName = oldName + PREFIX + 2;
-            } else {
-                String suffix = oldName.substring(lastDashIndex + 1);
-                try {
-                    int number = Integer.parseInt(suffix);
-                    int newNumber = number + 1;
-                    newName = oldName.substring(0, lastDashIndex + 1) + newNumber;
-                } catch (RuntimeException e) {
-                    // It was not a number
-                    newName = oldName + PREFIX + 2;
-                }
-            }
-        }
-        return newName;
-    }
-
-    /**
-     * Returns the local class name of a specified class.
-     * 
-     * @param klass
-     *            The specified class
-     * @return The local class name
-     */
-    public static String getClassName(Class klass) {
-        String fullName = klass.getName();
-        int index = fullName.lastIndexOf(".");
-        if (index < 0) {
-            return fullName;
-        } else {
-            return fullName.substring(index + 1);
-        }
-    }
-
-    /**
-     * @param throwable
-     * @return The stackTrace in String
-     */
-    public static String getStackTraceInString(Throwable throwable) {
-        ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
-        PrintStream printStream = new PrintStream(byteArrayOutputStream);
-        throwable.printStackTrace(printStream);
-        printStream.flush();
-        return byteArrayOutputStream.toString();
-    }
-    
-    private static Options deriveCommandLineOptions(String[] args){
-    	Options options = new Options();
-    	String[] argCopy = getChangedList(args);
-    	int i=0;
-        for (String arg : argCopy) {
-            if (arg.startsWith("--")){
-            	arg=arg.substring(2);
-                int pos = arg.indexOf('=');
-                String opt;
-                boolean hasArgs=true;
-	            if (pos==-1){ //if not of the form --arg=value
-	            	if (i==argCopy.length-1 || argCopy[i+1].startsWith("-")){ // no value specified 
-	            		hasArgs=false;
-	            	}
-	            	opt=arg;
-	            }else{
-	            	opt=arg.substring(0, pos);
-	            }
-                options.addOption(opt, hasArgs, "");
-            }
-            i++;
-        }
-        return options;
-    }
-    
-	public static Map<String, String> parseCommandLineOptions(String[] args) {
-		Map<String,String> commandLineOptions=new HashMap<String,String>();
-		try {
-			CommandLineParameters cmdParameters = getCommandLineParser(args);
-			Map<String, String> parameters = cmdParameters.getParameters();
-			for (String s : parameters.keySet()) {
-				commandLineOptions.put(s, parameters.get(s)==null? "":parameters.get(s));
-			}
-		} catch (ParseException e1) {
-			e1.printStackTrace();
-		}
-		return commandLineOptions;
-	}
-
-	public static CommandLineParameters getCommandLineParser(String[] args)
-			throws ParseException {
-		String[] argCopy = getChangedList(args);
-		CommandLineParser parser = new DynamicOptionPosixParser();
-		CommandLine cmdLine = parser.parse(deriveCommandLineOptions(argCopy), argCopy);
-		return new CommandLineParameters(cmdLine);
-	}
-
-	
-	//commons-cli does not support arg names having the period (".")
-	private static final String ARG_DOT_REPLACE="dot_replacement_value";
-	
-	private static String[] getChangedList(String[] args) {
-		String[] argCopy = Arrays.asList(args).toArray(new String []{});
-		for (int i=0;i<argCopy.length; i++) {
-			argCopy[i]=changeOption(argCopy[i]);
-		}
-		return argCopy;
-	}
-	
-	private static String revertOption(String option){
-		return option==null? option : option.replaceAll(Pattern.quote(ARG_DOT_REPLACE), ".");
-	}
-	
-	private static String changeOption(String option){
-		return option==null? option : option.replaceAll(Pattern.quote("."), ARG_DOT_REPLACE);
-	}
-	
-	private static class DynamicOptionPosixParser extends PosixParser{
-		@Override
-		protected void processOption(String arg0, @SuppressWarnings("rawtypes") ListIterator arg1)
-				throws ParseException {
-			if (getOptions().hasOption(arg0)){
-				super.processOption(arg0, arg1);
-			}
-		}
-	}
-	
-	public static class CommandLineParameters{
-		private Map<String,String> parameters=new HashMap<String, String>();
-		private List<String> arguments=new ArrayList<String>();
-		protected CommandLineParameters(CommandLine cmd){
-			for(Option opt:cmd.getOptions()){
-				parameters.put(revertOption(opt.getOpt()), revertOption(opt.getValue()));
-			}
-			for(String arg:cmd.getArgs()){
-				arguments.add(revertOption(arg));
-			}
-		}
-		public List<String> getArguments() {
-			return arguments;
-		}
-		public void setArguments(List<String> arguments) {
-			this.arguments = arguments;
-		}
-		public Map<String,String> getParameters() {
-			return parameters;
-		}
-		public void setParameters(Map<String,String> parameters) {
-			this.parameters = parameters;
-		}
-	}
-
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/commons/src/main/java/org/apache/airavata/common/utils/SwingUtil.java
----------------------------------------------------------------------
diff --git a/modules/commons/src/main/java/org/apache/airavata/common/utils/SwingUtil.java b/modules/commons/src/main/java/org/apache/airavata/common/utils/SwingUtil.java
deleted file mode 100644
index dc9a7e2..0000000
--- a/modules/commons/src/main/java/org/apache/airavata/common/utils/SwingUtil.java
+++ /dev/null
@@ -1,358 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you 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.apache.airavata.common.utils;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Cursor;
-import java.awt.Dimension;
-import java.awt.Frame;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Image;
-import java.awt.Insets;
-import java.awt.Toolkit;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.net.URL;
-import java.util.List;
-
-import javax.swing.ImageIcon;
-import javax.swing.JTextField;
-import javax.swing.Spring;
-import javax.swing.SpringLayout;
-
-public class SwingUtil {
-
-    /**
-     * Minimum size, zero.
-     */
-    public static final Dimension MINIMUM_SIZE = new Dimension(0, 0);
-
-    /**
-     * The default distance between components.
-     */
-    public static final int PAD = 6;
-
-    /**
-     * Default cursor.
-     */
-    public static final Cursor DEFAULT_CURSOR = new Cursor(Cursor.DEFAULT_CURSOR);
-
-    /**
-     * Hand cursor.
-     */
-    public static final Cursor HAND_CURSOR = new Cursor(Cursor.HAND_CURSOR);
-
-    /**
-     * Cross hair cursor.
-     */
-    public static final Cursor CROSSHAIR_CURSOR = new Cursor(Cursor.CROSSHAIR_CURSOR);
-
-    /**
-     * Move cursor.
-     */
-    public static final Cursor MOVE_CURSOR = new Cursor(Cursor.MOVE_CURSOR);
-
-    /**
-     * Wait cursor.
-     */
-    public static final Cursor WAIT_CURSOR = new Cursor(Cursor.WAIT_CURSOR);
-
-    /**
-     * Creates an icon from an image contained in the "images" directory.
-     * 
-     * @param filename
-     * @return the ImageIcon created
-     */
-    public static ImageIcon createImageIcon(String filename) {
-        ImageIcon icon = null;
-        URL imgURL = getImageURL(filename);
-        if (imgURL != null) {
-            icon = new ImageIcon(imgURL);
-        }
-        return icon;
-    }
-
-    /**
-     * Creates an image from an image contained in the "images" directory.
-     * 
-     * @param filename
-     * @return the Image created
-     */
-    public static Image createImage(String filename) {
-    	Image icon = null;
-        URL imgURL = getImageURL(filename);
-        if (imgURL != null) {
-            icon = Toolkit.getDefaultToolkit().getImage(imgURL);
-        }
-        return icon;
-    }
-
-	public static URL getImageURL(String filename) {
-		String path = "/images/" + filename;
-        URL imgURL = SwingUtil.class.getResource(path);
-		return imgURL;
-	}
-    
-    /**
-     * Return the Frame of a specified component if any.
-     * 
-     * @param component
-     *            the specified component
-     * 
-     * @return the Frame of a specified component if any; otherwise null
-     */
-    public static Frame getFrame(Component component) {
-        Frame frame;
-        Component parent;
-        while ((parent = component.getParent()) != null) {
-            component = parent;
-        }
-        if (component instanceof Frame) {
-            frame = (Frame) component;
-        } else {
-            frame = null;
-        }
-        return frame;
-    }
-
-    /**
-     * Wight none of rows or eolumns. Used by layoutToGrid().
-     */
-    public final static int WEIGHT_NONE = -1;
-
-    /**
-     * Weight all rows or columns equally. Used by layoutToGrid().
-     */
-    public final static int WEIGHT_EQUALLY = -2;
-
-    /**
-     * Layouts the child components of a specified parent component using GridBagLayout.
-     * 
-     * @param parent
-     *            The specified parent component
-     * @param numRow
-     *            The number of rows
-     * @param numColumn
-     *            The number of columns
-     * @param weightedRow
-     *            The row to weight
-     * @param weightedColumn
-     *            The column to weight
-     */
-    public static void layoutToGrid(Container parent, int numRow, int numColumn, int weightedRow, int weightedColumn) {
-        GridBagLayout layout = new GridBagLayout();
-        parent.setLayout(layout);
-        GridBagConstraints constraints = new GridBagConstraints();
-
-        constraints.fill = GridBagConstraints.BOTH;
-        constraints.insets = new Insets(SwingUtil.PAD, SwingUtil.PAD, SwingUtil.PAD, SwingUtil.PAD);
-
-        for (int row = 0; row < numRow; row++) {
-            constraints.gridy = row;
-            if (weightedRow == WEIGHT_EQUALLY) {
-                constraints.weighty = 1;
-            } else if (row == weightedRow) {
-                constraints.weighty = 1;
-            } else {
-                constraints.weighty = 0;
-            }
-            for (int column = 0; column < numColumn; column++) {
-                constraints.gridx = column;
-                if (weightedColumn == WEIGHT_EQUALLY) {
-                    constraints.weightx = 1;
-                } else if (column == weightedColumn) {
-                    constraints.weightx = 1;
-                } else {
-                    constraints.weightx = 0;
-                }
-                Component component = parent.getComponent(row * numColumn + column);
-                layout.setConstraints(component, constraints);
-            }
-        }
-    }
-
-    /**
-     * @param parent
-     * @param rowWeights
-     * @param columnWeights
-     */
-    public static void layoutToGrid(Container parent, double[] rowWeights, double[] columnWeights) {
-        GridBagLayout layout = new GridBagLayout();
-        parent.setLayout(layout);
-        GridBagConstraints constraints = new GridBagConstraints();
-
-        constraints.fill = GridBagConstraints.BOTH;
-        constraints.insets = new Insets(SwingUtil.PAD, SwingUtil.PAD, SwingUtil.PAD, SwingUtil.PAD);
-
-        for (int row = 0; row < rowWeights.length; row++) {
-            constraints.gridy = row;
-            constraints.weighty = rowWeights[row];
-            for (int column = 0; column < columnWeights.length; column++) {
-                constraints.gridx = column;
-                constraints.weightx = columnWeights[column];
-                Component component = parent.getComponent(row * columnWeights.length + column);
-                layout.setConstraints(component, constraints);
-            }
-        }
-    }
-
-    /**
-     * @param parent
-     * @param rowWeights
-     * @param columnWeights
-     */
-    @SuppressWarnings("boxing")
-    public static void layoutToGrid(Container parent, List<Double> rowWeights, List<Double> columnWeights) {
-        GridBagLayout layout = new GridBagLayout();
-        parent.setLayout(layout);
-        GridBagConstraints constraints = new GridBagConstraints();
-
-        constraints.fill = GridBagConstraints.BOTH;
-        constraints.insets = new Insets(SwingUtil.PAD, SwingUtil.PAD, SwingUtil.PAD, SwingUtil.PAD);
-
-        for (int row = 0; row < rowWeights.size(); row++) {
-            constraints.gridy = row;
-            constraints.weighty = rowWeights.get(row);
-            for (int column = 0; column < columnWeights.size(); column++) {
-                constraints.gridx = column;
-                constraints.weightx = columnWeights.get(column);
-                Component component = parent.getComponent(row * columnWeights.size() + column);
-                layout.setConstraints(component, constraints);
-            }
-        }
-    }
-
-    /**
-     * Aligns the first <code>rows</code> * <code>cols</code> components of <code>parent</code> in a grid. Each
-     * component in a column is as wide as the maximum preferred width of the components in that column; height is
-     * similarly determined for each row. The parent is made just big enough to fit them all.
-     * 
-     * @param parent
-     * 
-     * @param rows
-     *            number of rows
-     * @param cols
-     *            number of columns
-     */
-    public static void makeSpringCompactGrid(Container parent, int rows, int cols) {
-        makeSpringCompactGrid(parent, rows, cols, PAD, PAD, PAD, PAD);
-    }
-
-    /**
-     * Aligns the first <code>rows</code> * <code>cols</code> components of <code>parent</code> in a grid. Each
-     * component in a column is as wide as the maximum preferred width of the components in that column; height is
-     * similarly determined for each row. The parent is made just big enough to fit them all.
-     * 
-     * @param parent
-     * 
-     * @param rows
-     *            number of rows
-     * @param cols
-     *            number of columns
-     * @param initialX
-     *            x location to start the grid at
-     * @param initialY
-     *            y location to start the grid at
-     * @param xPad
-     *            x padding between cells
-     * @param yPad
-     *            y padding between cells
-     */
-    private static void makeSpringCompactGrid(Container parent, int rows, int cols, int initialX, int initialY,
-            int xPad, int yPad) {
-
-        SpringLayout layout = new SpringLayout();
-        parent.setLayout(layout);
-
-        // Align all cells in each column and make them the same width.
-        Spring x = Spring.constant(initialX);
-        for (int c = 0; c < cols; c++) {
-            Spring width = Spring.constant(0);
-            for (int r = 0; r < rows; r++) {
-                width = Spring.max(width, getConstraintsForCell(r, c, parent, cols).getWidth());
-            }
-            for (int r = 0; r < rows; r++) {
-                SpringLayout.Constraints constraints = getConstraintsForCell(r, c, parent, cols);
-                constraints.setX(x);
-                constraints.setWidth(width);
-            }
-            x = Spring.sum(x, Spring.sum(width, Spring.constant(xPad)));
-        }
-
-        // Align all cells in each row and make them the same height.
-        Spring y = Spring.constant(initialY);
-        for (int r = 0; r < rows; r++) {
-            Spring height = Spring.constant(0);
-            for (int c = 0; c < cols; c++) {
-                height = Spring.max(height, getConstraintsForCell(r, c, parent, cols).getHeight());
-            }
-            for (int c = 0; c < cols; c++) {
-                SpringLayout.Constraints constraints = getConstraintsForCell(r, c, parent, cols);
-                constraints.setY(y);
-                constraints.setHeight(height);
-            }
-            y = Spring.sum(y, Spring.sum(height, Spring.constant(yPad)));
-        }
-
-        // Set the parent's size.
-        SpringLayout.Constraints pCons = layout.getConstraints(parent);
-        pCons.setConstraint(SpringLayout.SOUTH, y);
-        pCons.setConstraint(SpringLayout.EAST, x);
-    }
-
-    /* Used by makeCompactGrid. */
-    private static SpringLayout.Constraints getConstraintsForCell(int row, int col, Container parent, int cols) {
-        SpringLayout layout = (SpringLayout) parent.getLayout();
-        Component c = parent.getComponent(row * cols + col);
-        return layout.getConstraints(c);
-    }
-    
-    public static void addPlaceHolder(final JTextField field,final String placeHolderText){
-    	field.addFocusListener(new FocusListener(){
-    		private Color fontColor=field.getForeground();
-//    		private String previousText=field.getText();
-    		
-			public void focusGained(FocusEvent arg0) {
-				if (field.getText().equals(placeHolderText)){
-					field.setText("");
-				}
-				field.setForeground(fontColor);
-			}
-
-			public void focusLost(FocusEvent arg0) {
-				if (field.getText().trim().equals("")){
-					fontColor=field.getForeground();
-					field.setForeground(Color.GRAY);
-					field.setText(placeHolderText);
-				}
-			}
-    	});
-    	if (field.getText().trim().equals("")){
-    		field.setText(placeHolderText);
-    		field.setForeground(Color.GRAY);
-    	}
-    }
-    
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/commons/src/main/java/org/apache/airavata/common/utils/ThriftUtils.java
----------------------------------------------------------------------
diff --git a/modules/commons/src/main/java/org/apache/airavata/common/utils/ThriftUtils.java b/modules/commons/src/main/java/org/apache/airavata/common/utils/ThriftUtils.java
deleted file mode 100644
index c30527e..0000000
--- a/modules/commons/src/main/java/org/apache/airavata/common/utils/ThriftUtils.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you 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.apache.airavata.common.utils;
-
-import org.apache.airavata.model.task.*;
-import org.apache.thrift.TBase;
-import org.apache.thrift.TDeserializer;
-import org.apache.thrift.TException;
-import org.apache.thrift.TSerializer;
-
-public class ThriftUtils {
-	public static byte[] serializeThriftObject(TBase object) throws TException {
-		return new TSerializer().serialize(object);
-	}
-
-	public static void createThriftFromBytes(byte[] bytes, TBase object) throws TException {
-		new TDeserializer().deserialize(object, bytes);
-	}
-
-	public static Object getSubTaskModel(TaskModel taskModel) throws TException {
-		switch (taskModel.getTaskType()) {
-			case DATA_STAGING:
-				DataStagingTaskModel dataStagingTaskModel = new DataStagingTaskModel();
-				ThriftUtils.createThriftFromBytes(taskModel.getSubTaskModel(), dataStagingTaskModel);
-				return dataStagingTaskModel;
-			case ENV_SETUP:
-                EnvironmentSetupTaskModel environmentSetupTaskModel = new EnvironmentSetupTaskModel();
-                ThriftUtils.createThriftFromBytes(taskModel.getSubTaskModel(), environmentSetupTaskModel);
-                return environmentSetupTaskModel;
-			case JOB_SUBMISSION:
-                JobSubmissionTaskModel jobSubmissionTaskModel = new JobSubmissionTaskModel();
-                ThriftUtils.createThriftFromBytes(taskModel.getSubTaskModel(), jobSubmissionTaskModel);
-                return jobSubmissionTaskModel;
-            case MONITORING:
-                MonitorTaskModel monitorTaskModel = new MonitorTaskModel();
-                ThriftUtils.createThriftFromBytes(taskModel.getSubTaskModel(), monitorTaskModel);
-                return monitorTaskModel;
-			case ENV_CLEANUP:
-				// TODO return Environment Clean up task  model
-			default:
-				return null;
-		}
-	}
-}

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/commons/src/main/java/org/apache/airavata/common/utils/Version.java
----------------------------------------------------------------------
diff --git a/modules/commons/src/main/java/org/apache/airavata/common/utils/Version.java b/modules/commons/src/main/java/org/apache/airavata/common/utils/Version.java
deleted file mode 100644
index fe34bb1..0000000
--- a/modules/commons/src/main/java/org/apache/airavata/common/utils/Version.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you 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.apache.airavata.common.utils;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlRootElement;
-
-@XmlAccessorType(XmlAccessType.FIELD)
-@XmlRootElement
-public class Version {
-	public String PROJECT_NAME;
-	private Integer majorVersion=0;
-	private Integer minorVersion=0;
-	private Integer maintenanceVersion;
-	private String versionData;
-	private BuildType buildType;
-	
-	public static enum BuildType{
-		ALPHA,
-		BETA,
-		RC
-	}
-	
-	public Version() {
-	}
-	
-	public Version(String PROJECT_NAME,Integer majorVersion,Integer minorVersion,Integer maintenanceVersion,String versionData,BuildType buildType) {
-		this.PROJECT_NAME=PROJECT_NAME;
-		this.majorVersion=majorVersion;
-		this.minorVersion=minorVersion;
-		this.maintenanceVersion=maintenanceVersion;
-		this.versionData=versionData;
-		this.buildType=buildType;
-	}
-	
-	public Integer getMajorVersion() {
-		return majorVersion;
-	}
-
-	public Integer getMinorVersion() {
-		return minorVersion;
-	}
-
-	public Integer getMaintenanceVersion() {
-		return maintenanceVersion;
-	}
-
-	public String getVersionData() {
-		return versionData;
-	}
-
-	public BuildType getBuildType() {
-		return buildType;
-	}
-	
-	public String getVersion(){
-		String version = getBaseVersion();
-		version = attachVersionData(version);
-		return version;
-	}
-
-	private String attachVersionData(String version) {
-		if (getVersionData()!=null){
-			version+="-"+getVersionData();
-		}
-		return version;
-	}
-
-	public String getBaseVersion() {
-		String version=getMajorVersion().toString()+"."+getMinorVersion();
-		return version;
-	}
-	
-	public String getFullVersion(){
-		String version = getBaseVersion();
-		version = attachMaintainanceVersion(version);
-		version = attachVersionData(version);
-		version = attachBuildType(version);
-		return version;
-	}
-
-	private String attachMaintainanceVersion(String version) {
-		if (getMaintenanceVersion()!=null){
-			version+="."+getMaintenanceVersion();
-		}
-		return version;
-	}
-	
-	private String attachBuildType(String version) {
-		if (getBuildType()!=null){
-			version+="-"+getBuildType().name();
-		}
-		return version;
-	}
-	
-	@Override
-	public String toString() {
-		return getVersion();
-	}
-}

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/commons/src/main/java/org/apache/airavata/common/utils/WSConstants.java
----------------------------------------------------------------------
diff --git a/modules/commons/src/main/java/org/apache/airavata/common/utils/WSConstants.java b/modules/commons/src/main/java/org/apache/airavata/common/utils/WSConstants.java
deleted file mode 100644
index 9737ac4..0000000
--- a/modules/commons/src/main/java/org/apache/airavata/common/utils/WSConstants.java
+++ /dev/null
@@ -1,187 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you 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.apache.airavata.common.utils;
-
-import javax.xml.namespace.QName;
-
-import org.xmlpull.infoset.XmlNamespace;
-
-public interface WSConstants {
-
-    /**
-     * xmlns
-     */
-    public final static String XMLNS = "xmlns";
-
-    /**
-     * XML Schema prefix, xsd
-     */
-    public static final String XSD_NS_PREFIX = "xsd";
-
-    /**
-     * XML Schema URI.
-     */
-    public static final String XSD_NS_URI = "http://www.w3.org/2001/XMLSchema";
-
-//    /**
-//     * XML Schema Namespace
-//     */
-//    public static final XmlNamespace XSD_NS = XmlConstants.BUILDER.newNamespace(XSD_NS_PREFIX, XSD_NS_URI);
-
-    /**
-     * The any type.
-     */
-    public static final QName XSD_ANY_TYPE = new QName(XSD_NS_URI, "any", XSD_NS_PREFIX);
-
-    /**
-     * xsd:anyURI
-     */
-    public static final QName XSD_ANY_URI = new QName(XSD_NS_URI, "anyURI", XSD_NS_PREFIX);
-
-    /**
-     * tns
-     */
-    public static final String TARGET_NS_PREFIX = "tns";
-
-    /**
-     * typens
-     */
-    public static final String TYPE_NS_PREFIX = "typens";
-
-    /**
-     * schema
-     */
-    public static final String SCHEMA_TAG = "schema";
-
-    /**
-     * Element name for annotation, annotation
-     */
-    public static final String ANNOTATION_TAG = "annotation";
-
-    /**
-     * Element name for documentation, documentation
-     */
-    public static final String DOCUMENTATION_TAG = "documentation";
-
-    /**
-     * appinfo
-     */
-    public static final String APPINFO_TAG = "appinfo";
-
-    /**
-     * element
-     */
-    public static final String ELEMENT_TAG = "element";
-
-    /**
-     * sequence
-     */
-    public static final String SEQUENCE_TAG = "sequence";
-
-    /**
-     * complexType
-     */
-    public static final String COMPLEX_TYPE_TAG = "complexType";
-
-    /**
-     * simpleType
-     */
-    public static final String SIMPLE_TYPE_TAG = "simpleType";
-
-    /**
-     * name
-     */
-    public static final String NAME_ATTRIBUTE = "name";
-
-    /**
-     * type
-     */
-    public static final String TYPE_ATTRIBUTE = "type";
-
-    /**
-     * targetNamespace
-     */
-    public static final String TARGET_NAMESPACE_ATTRIBUTE = "targetNamespace";
-
-    /**
-     * elementFormDefault
-     */
-    public final static String ELEMENT_FORM_DEFAULT_ATTRIBUTE = "elementFormDefault";
-
-    /**
-     * unqualified
-     */
-    public final static String UNQUALIFIED_VALUE = "unqualified";
-
-    /**
-     * default
-     */
-    public static final String DEFAULT_ATTRIBUTE = "default";
-
-    /**
-     * UsingAddressing
-     */
-    public static final String USING_ADDRESSING_TAG = "UsingAddressing";
-
-    /**
-     * <appinfo xmlns="http://www.w3.org/2001/XMLSchema">
-     * 
-     * </appinfo>
-     */
-//    public static final String EMPTY_APPINFO = "<appinfo xmlns=\"http://www.w3.org/2001/XMLSchema\">\n\n</appinfo>";
-    public static final String EMPTY_APPINFO = "{'appinfo': '' }";
-
-    /**
-     * minOccurs
-     */
-    public static final String MIN_OCCURS_ATTRIBUTE = "minOccurs";
-
-    /**
-     * maxOccurs
-     */
-    public static final String MAX_OCCURS_ATTRIBUTE = "maxOccurs";
-
-    /**
-     * unbounded
-     */
-    public static final String UNBOUNDED_VALUE = "unbounded";
-
-    /**
-     * import
-     */
-    public static final String IMPORT_TAG = "import";
-
-    /**
-     * schemaLocation
-     */
-    public static final String SCHEMA_LOCATION_ATTRIBUTE = "schemaLocation";
-
-    public static final String LEAD_NS_URI = "http://www.extreme.indiana.edu/lead";
-
-    /**
-     * The any type.
-     */
-    public static final QName LEAD_ANY_TYPE = new QName(LEAD_NS_URI, "any",
-            XSD_NS_PREFIX);
-
-
-}
\ No newline at end of file


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