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Posted to commits@airavata.apache.org by sh...@apache.org on 2015/12/04 22:02:13 UTC
[48/54] [abbrv] airavata git commit: fixing test failures
fixing test failures
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/242a4033
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/242a4033
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/242a4033
Branch: refs/heads/master
Commit: 242a40331bf321feccd559f0f1e6a0bc339625e7
Parents: bd1cc2f
Author: scnakandala <su...@gmail.com>
Authored: Fri Dec 4 14:44:08 2015 -0500
Committer: scnakandala <su...@gmail.com>
Committed: Fri Dec 4 14:44:08 2015 -0500
----------------------------------------------------------------------
.../data/manager/DataManagerFactoryTest.java | 10 +-
.../data/manager/DataManagerImplTest.java | 4 +
.../airavata/data/manager/utils/AppCatInit.java | 320 +++++++++++++++++++
3 files changed, 332 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/242a4033/modules/data-manager/src/test/java/org/apache/airavata/data/manager/DataManagerFactoryTest.java
----------------------------------------------------------------------
diff --git a/modules/data-manager/src/test/java/org/apache/airavata/data/manager/DataManagerFactoryTest.java b/modules/data-manager/src/test/java/org/apache/airavata/data/manager/DataManagerFactoryTest.java
index 365c250..a7bf204 100644
--- a/modules/data-manager/src/test/java/org/apache/airavata/data/manager/DataManagerFactoryTest.java
+++ b/modules/data-manager/src/test/java/org/apache/airavata/data/manager/DataManagerFactoryTest.java
@@ -21,6 +21,10 @@
package org.apache.airavata.data.manager;
import junit.framework.Assert;
+import org.apache.airavata.data.manager.utils.ssh.SSHKeyAuthentication;
+import org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory;
+import org.apache.airavata.registry.cpi.DataCatalog;
+import org.apache.airavata.registry.cpi.DataCatalogException;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -29,8 +33,10 @@ public class DataManagerFactoryTest {
private final static Logger logger = LoggerFactory.getLogger(DataManagerFactoryTest.class);
@Test
- public void testCreateDataManager() throws DataManagerException {
- DataManager dataManager = DataManagerFactory.getDataManager();
+ public void testCreateDataManager() throws DataManagerException, DataCatalogException {
+ DataCatalog dataCatalog = RegistryFactory.getDataCatalog();
+ SSHKeyAuthentication sshKeyAuthentication = new SSHKeyAuthentication();
+ DataManager dataManager = new DataManagerImpl(dataCatalog, sshKeyAuthentication);
Assert.assertNotNull(dataManager);
}
}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/242a4033/modules/data-manager/src/test/java/org/apache/airavata/data/manager/DataManagerImplTest.java
----------------------------------------------------------------------
diff --git a/modules/data-manager/src/test/java/org/apache/airavata/data/manager/DataManagerImplTest.java b/modules/data-manager/src/test/java/org/apache/airavata/data/manager/DataManagerImplTest.java
index ecab2af..795daef 100644
--- a/modules/data-manager/src/test/java/org/apache/airavata/data/manager/DataManagerImplTest.java
+++ b/modules/data-manager/src/test/java/org/apache/airavata/data/manager/DataManagerImplTest.java
@@ -20,6 +20,7 @@
*/
package org.apache.airavata.data.manager;
+import org.apache.airavata.data.manager.utils.AppCatInit;
import org.apache.airavata.data.manager.utils.DataCatInit;
import org.apache.airavata.data.manager.utils.ssh.SSHKeyAuthentication;
import org.apache.airavata.model.data.resource.DataReplicaLocationModel;
@@ -41,6 +42,7 @@ import java.util.UUID;
public class DataManagerImplTest {
private final static Logger logger = LoggerFactory.getLogger(DataManagerImplTest.class);
+ private static AppCatInit appCatInit;
private static DataCatInit dataCatInit;
private static DataManager dataManager;
private static DataResourceModel dataResourceModel;
@@ -50,6 +52,8 @@ public class DataManagerImplTest {
public static void setUp() {
try {
System.out.println("********** SET UP ************");
+ appCatInit = new AppCatInit("appcatalog-derby.sql");
+ appCatInit.initializeDB();
dataCatInit = new DataCatInit("datacatalog-derby.sql");
dataCatInit.initializeDB();
DataCatalog dataCatalog = RegistryFactory.getDataCatalog();
http://git-wip-us.apache.org/repos/asf/airavata/blob/242a4033/modules/data-manager/src/test/java/org/apache/airavata/data/manager/utils/AppCatInit.java
----------------------------------------------------------------------
diff --git a/modules/data-manager/src/test/java/org/apache/airavata/data/manager/utils/AppCatInit.java b/modules/data-manager/src/test/java/org/apache/airavata/data/manager/utils/AppCatInit.java
new file mode 100644
index 0000000..2433b78
--- /dev/null
+++ b/modules/data-manager/src/test/java/org/apache/airavata/data/manager/utils/AppCatInit.java
@@ -0,0 +1,320 @@
+/*
+ *
+ * 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.data.manager.utils;
+
+import org.apache.airavata.common.exception.ApplicationSettingsException;
+import org.apache.airavata.common.utils.ServerSettings;
+import org.apache.derby.drda.NetworkServerControl;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.InetAddress;
+import java.net.URI;
+import java.sql.*;
+import java.util.StringTokenizer;
+
+public class AppCatInit {
+ private static final Logger logger = LoggerFactory.getLogger(AppCatInit.class);
+ public static final String DERBY_SERVER_MODE_SYS_PROPERTY = "derby.drda.startNetworkServer";
+ public String scriptName = "appcatalog-derby.sql";
+ private NetworkServerControl server;
+ private static final String delimiter = ";";
+ public static final String COMPUTE_RESOURCE_TABLE = "COMPUTE_RESOURCE";
+ private String jdbcUrl = null;
+ private String jdbcDriver = null;
+ private String jdbcUser = null;
+ private String jdbcPassword = null;
+
+ public AppCatInit(String scriptName) {
+ this.scriptName = scriptName;
+ }
+
+ public static boolean checkStringBufferEndsWith(StringBuffer buffer, String suffix) {
+ if (suffix.length() > buffer.length()) {
+ return false;
+ }
+ // this loop is done on purpose to avoid memory allocation performance
+ // problems on various JDKs
+ // StringBuffer.lastIndexOf() was introduced in jdk 1.4 and
+ // implementation is ok though does allocation/copying
+ // StringBuffer.toString().endsWith() does massive memory
+ // allocation/copying on JDK 1.5
+ // See http://issues.apache.org/bugzilla/show_bug.cgi?id=37169
+ int endIndex = suffix.length() - 1;
+ int bufferIndex = buffer.length() - 1;
+ while (endIndex >= 0) {
+ if (buffer.charAt(bufferIndex) != suffix.charAt(endIndex)) {
+ return false;
+ }
+ bufferIndex--;
+ endIndex--;
+ }
+ return true;
+ }
+
+ private static boolean isServerStarted(NetworkServerControl server, int ntries)
+ {
+ for (int i = 1; i <= ntries; i ++)
+ {
+ try {
+ Thread.sleep(500);
+ server.ping();
+ return true;
+ }
+ catch (Exception e) {
+ if (i == ntries)
+ return false;
+ }
+ }
+ return false;
+ }
+
+ public void initializeDB() {
+
+ try{
+ jdbcDriver = ServerSettings.getSetting("appcatalog.jdbc.driver");
+ jdbcUrl = ServerSettings.getSetting("appcatalog.jdbc.url");
+ jdbcUser = ServerSettings.getSetting("appcatalog.jdbc.user");
+ jdbcPassword = ServerSettings.getSetting("appcatalog.jdbc.password");
+ jdbcUrl = jdbcUrl + "?" + "user=" + jdbcUser + "&" + "password=" + jdbcPassword;
+ } catch (ApplicationSettingsException e) {
+ logger.error("Unable to read properties", e);
+ }
+
+ startDerbyInServerMode();
+ if(!isServerStarted(server, 20)){
+ throw new RuntimeException("Derby server cound not started within five seconds...");
+ }
+// startDerbyInEmbeddedMode();
+
+ Connection conn = null;
+ try {
+ Class.forName(jdbcDriver).newInstance();
+ conn = DriverManager.getConnection(jdbcUrl, jdbcUser, jdbcPassword);
+ if (!isDatabaseStructureCreated(COMPUTE_RESOURCE_TABLE, conn)) {
+ executeSQLScript(conn);
+ logger.info("New Database created for App Catalog !!!");
+ } else {
+ logger.debug("Database already created for App Catalog!");
+ }
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw new RuntimeException("Database failure", e);
+ } finally {
+ try {
+ if (conn != null){
+ if (!conn.getAutoCommit()) {
+ conn.commit();
+ }
+ conn.close();
+ }
+ } catch (SQLException e) {
+ logger.error(e.getMessage(), e);
+ }
+ }
+ }
+
+ public static boolean isDatabaseStructureCreated(String tableName, Connection conn) {
+ try {
+ System.out.println("Running a query to test the database tables existence.");
+ // check whether the tables are already created with a query
+ Statement statement = null;
+ try {
+ statement = conn.createStatement();
+ ResultSet rs = statement.executeQuery("select * from " + tableName);
+ if (rs != null) {
+ rs.close();
+ }
+ } finally {
+ try {
+ if (statement != null) {
+ statement.close();
+ }
+ } catch (SQLException e) {
+ return false;
+ }
+ }
+ } catch (SQLException e) {
+ return false;
+ }
+
+ return true;
+ }
+
+ private void executeSQLScript(Connection conn) throws Exception {
+ StringBuffer sql = new StringBuffer();
+ BufferedReader reader = null;
+ try{
+
+ InputStream inputStream = this.getClass().getClassLoader().getResourceAsStream(scriptName);
+ reader = new BufferedReader(new InputStreamReader(inputStream));
+ String line;
+ while ((line = reader.readLine()) != null) {
+ line = line.trim();
+ if (line.startsWith("//")) {
+ continue;
+ }
+ if (line.startsWith("--")) {
+ continue;
+ }
+ StringTokenizer st = new StringTokenizer(line);
+ if (st.hasMoreTokens()) {
+ String token = st.nextToken();
+ if ("REM".equalsIgnoreCase(token)) {
+ continue;
+ }
+ }
+ sql.append(" ").append(line);
+
+ // SQL defines "--" as a comment to EOL
+ // and in Oracle it may contain a hint
+ // so we cannot just remove it, instead we must end it
+ if (line.indexOf("--") >= 0) {
+ sql.append("\n");
+ }
+ if ((checkStringBufferEndsWith(sql, delimiter))) {
+ executeSQL(sql.substring(0, sql.length() - delimiter.length()), conn);
+ sql.replace(0, sql.length(), "");
+ }
+ }
+ // Catch any statements not followed by ;
+ if (sql.length() > 0) {
+ executeSQL(sql.toString(), conn);
+ }
+ }catch (IOException e){
+ logger.error("Error occurred while executing SQL script for creating Airavata database", e);
+ throw new Exception("Error occurred while executing SQL script for creating Airavata database", e);
+ }finally {
+ if (reader != null) {
+ reader.close();
+ }
+
+ }
+
+ }
+
+ private static void executeSQL(String sql, Connection conn) throws Exception {
+ // Check and ignore empty statements
+ if ("".equals(sql.trim())) {
+ return;
+ }
+
+ Statement statement = null;
+ try {
+ logger.debug("SQL : " + sql);
+
+ boolean ret;
+ int updateCount = 0, updateCountTotal = 0;
+ statement = conn.createStatement();
+ ret = statement.execute(sql);
+ updateCount = statement.getUpdateCount();
+ do {
+ if (!ret) {
+ if (updateCount != -1) {
+ updateCountTotal += updateCount;
+ }
+ }
+ ret = statement.getMoreResults();
+ if (ret) {
+ updateCount = statement.getUpdateCount();
+ }
+ } while (ret);
+
+ logger.debug(sql + " : " + updateCountTotal + " rows affected");
+
+ SQLWarning warning = conn.getWarnings();
+ while (warning != null) {
+ logger.warn(warning + " sql warning");
+ warning = warning.getNextWarning();
+ }
+ conn.clearWarnings();
+ } catch (SQLException e) {
+ if (e.getSQLState().equals("X0Y32")) {
+ // eliminating the table already exception for the derby
+ // database
+ logger.info("Table Already Exists", e);
+ } else {
+ throw new Exception("Error occurred while executing : " + sql, e);
+ }
+ } finally {
+ if (statement != null) {
+ try {
+ statement.close();
+ } catch (SQLException e) {
+ logger.error("Error occurred while closing result set.", e);
+ }
+ }
+ }
+ }
+
+ private void startDerbyInServerMode() {
+ try {
+ System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "true");
+ server = new NetworkServerControl(InetAddress.getByName("0.0.0.0"),
+ 20000,
+ jdbcUser, jdbcPassword);
+ java.io.PrintWriter consoleWriter = new java.io.PrintWriter(System.out, true);
+ server.start(consoleWriter);
+ } catch (IOException e) {
+ logger.error("Unable to start Apache derby in the server mode! Check whether " +
+ "specified port is available");
+ } catch (Exception e) {
+ logger.error("Unable to start Apache derby in the server mode! Check whether " +
+ "specified port is available");
+ }
+
+ }
+
+ public static int getPort(String jdbcURL){
+ try{
+ String cleanURI = jdbcURL.substring(5);
+ URI uri = URI.create(cleanURI);
+ return uri.getPort();
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ return -1;
+ }
+ }
+
+ private void startDerbyInEmbeddedMode(){
+ try {
+ Class.forName("org.apache.derby.jdbc.EmbeddedDriver");
+ DriverManager.getConnection("jdbc:derby:memory:unit-testing-jpa;create=true").close();
+ } catch (ClassNotFoundException e) {
+ logger.error(e.getMessage(), e);
+ } catch (SQLException e) {
+ logger.error(e.getMessage(), e);
+ }
+ }
+
+ public void stopDerbyServer() {
+ try {
+ server.shutdown();
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ }
+ }
+}