merge recent revision from trunk
This commit is contained in:
brianjlowe
parent
b480cb2eea
commit
101de4614b
6 changed files with 1632 additions and 259 deletions
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@ -0,0 +1,40 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils;
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import java.lang.reflect.Constructor;
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import java.util.HashMap;
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import java.util.Map;
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import javax.servlet.ServletContext;
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import net.sf.json.JSONObject;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessDataGetterN3;
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import edu.cornell.mannlib.vitro.webapp.utils.dataGetter.DataGetter;
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/*
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* This class determines what n3 should be returned for a particular data getter and can be overwritten or extended in VIVO.
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*/
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public class ProcessDataGetterN3Map {
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private static final Log log = LogFactory.getLog(ProcessDataGetterN3Map.class);
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public static HashMap<String, String> getDataGetterTypeToProcessorMap() {
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HashMap<String, String> map = new HashMap<String, String>();
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map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessSparqlDataGetterN3");
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map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessClassGroupDataGetterN3");
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map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessIndividualsForClassesDataGetterN3");
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map.put("edu.cornell.mannlib.vitro.webapp.utils.dataGetter.FixedHTMLDataGetter", "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.utils.ProcessFixedHTMLN3");
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return map;
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}
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}
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File diff suppressed because it is too large
Load diff
564
webapp/src/edu/ucsf/vitro/opensocial/OpenSocialSmokeTests.java
Normal file
564
webapp/src/edu/ucsf/vitro/opensocial/OpenSocialSmokeTests.java
Normal file
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@ -0,0 +1,564 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.ucsf.vitro.opensocial;
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import java.io.File;
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import java.io.InputStream;
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import java.net.Socket;
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import java.net.SocketTimeoutException;
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import java.net.URL;
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import java.sql.Connection;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Statement;
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import java.util.ArrayList;
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import java.util.List;
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import javax.servlet.ServletContext;
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import javax.servlet.ServletContextEvent;
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import javax.servlet.ServletContextListener;
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import org.apache.commons.dbcp.BasicDataSource;
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import org.apache.commons.httpclient.HttpClient;
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import org.apache.commons.httpclient.HttpStatus;
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import org.apache.commons.httpclient.methods.GetMethod;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
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import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
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import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
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/**
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* Do some quick checks to see whether the OpenSocial stuff is configured and
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* working.
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*/
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public class OpenSocialSmokeTests implements ServletContextListener {
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private static final String PROPERTY_SHINDIG_URL = "OpenSocial.shindigURL";
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private static final String PROPERTY_SHINDIG_TOKEN_KEY_FILE = "OpenSocial.tokenKeyFile";
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private static final String PROPERTY_SHINDIG_TOKEN_SERVICE = "OpenSocial.tokenService";
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private static final String PROPERTY_DB_DRIVER = "VitroConnection.DataSource.driver";
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private static final String PROPERTY_DB_JDBC_URL = "VitroConnection.DataSource.url";
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private static final String PROPERTY_DB_USERNAME = "VitroConnection.DataSource.username";
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private static final String PROPERTY_DB_PASSWORD = "VitroConnection.DataSource.password";
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private static final String FILENAME_SHINDIG_PROPERTIES = "shindig.orng.properties";
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/*
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* If a connection fails in the tester thread, how long do we wait before
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* trying again?
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*/
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private static final long SLEEP_INTERVAL = 10000; // 10 seconds
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private ServletContext ctx;
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private ConfigurationProperties configProps;
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private List<Warning> warnings = new ArrayList<Warning>();
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private String shindigBaseUrl;
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private String tokenServiceHost;
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private int tokenServicePort;
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/**
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* When the system starts up, run the tests.
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*/
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@Override
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public void contextInitialized(ServletContextEvent sce) {
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ctx = sce.getServletContext();
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StartupStatus ss = StartupStatus.getBean(ctx);
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configProps = ConfigurationProperties.getBean(ctx);
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/*
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* If OpenSocial is not configured in deploy.properties, skip the tests.
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*/
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if (!configurationPresent()) {
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ss.info(this, "The OpenSocial connection is not configured.");
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return;
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}
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/*
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* Run all of the non-threaded tests. If any fail, skip the threaded
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* tests.
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*/
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checkDatabaseTables();
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checkShindigConfigFile();
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checkTokenKeyFile();
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checkTokenServiceInfo();
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if (!warnings.isEmpty()) {
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for (Warning w : warnings) {
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w.warn(ss);
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}
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return;
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}
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/*
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* Run the threaded tests.
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*/
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ss.info(this, "Starting threads for OpenSocial smoke tests");
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new ShindigTestThread(this, ss, shindigBaseUrl).start();
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new TokenServiceTestThread(this, ss, tokenServiceHost, tokenServicePort)
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.start();
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}
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/**
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* Get the base URL for the Shindig server. If none, then the whole thing is
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* disabled.
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*/
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private boolean configurationPresent() {
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String shindigUrl = configProps.getProperty(PROPERTY_SHINDIG_URL);
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if (StringUtils.isNotEmpty(shindigUrl)) {
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this.shindigBaseUrl = shindigUrl;
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return true;
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} else {
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return false;
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}
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}
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/**
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* Check that we can connect to the database, and query one of the Shindig
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* tables.
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*/
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private void checkDatabaseTables() {
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BasicDataSource dataSource = null;
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Connection conn = null;
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Statement stmt = null;
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ResultSet rset = null;
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try {
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dataSource = new BasicDataSource();
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dataSource.setDriverClassName(getProperty(PROPERTY_DB_DRIVER));
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dataSource.setUrl(getProperty(PROPERTY_DB_JDBC_URL));
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dataSource.setUsername(getProperty(PROPERTY_DB_USERNAME));
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dataSource.setPassword(getProperty(PROPERTY_DB_PASSWORD));
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conn = dataSource.getConnection();
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stmt = conn.createStatement();
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rset = stmt.executeQuery("select * from shindig_apps");
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} catch (NoSuchPropertyException e) {
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warnings.add(new Warning(e.getMessage()));
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} catch (SQLException e) {
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if (e.getMessage().contains("doesn't exist")) {
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warnings.add(new Warning("The Shindig tables don't exist "
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+ "in the database. Was shindig_orng_tables.sql "
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+ "run to set them up?", e));
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} else {
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warnings.add(new Warning(
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"Can't access the Shindig database tables", e));
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}
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} finally {
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try {
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if (rset != null) {
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rset.close();
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}
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} catch (Exception e) {
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e.printStackTrace();
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}
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try {
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if (stmt != null) {
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stmt.close();
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}
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} catch (Exception e) {
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e.printStackTrace();
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}
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try {
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if (conn != null) {
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conn.close();
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}
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} catch (Exception e) {
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e.printStackTrace();
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}
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}
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}
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/**
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* Check that the Shindig configuration file is present in the classpath.
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*/
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private void checkShindigConfigFile() {
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URL url = this.getClass()
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.getResource("/" + FILENAME_SHINDIG_PROPERTIES);
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if (url == null) {
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String message = "Can't find the '" + FILENAME_SHINDIG_PROPERTIES
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+ "' file in the classpath. ";
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message += "Has the Tomcat classpath been set to include the "
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+ "Shindig config directory? "
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+ "(inside the Vitro home directory) ";
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message += "Was the openSocial build script run? "
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+ "('ant -file openSocialBuild.xml')";
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warnings.add(new Warning(message));
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}
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}
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/**
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* Check that the Token Key file has been specified in deploy.properties,
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* and that it actually does exist.
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*/
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private void checkTokenKeyFile() {
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try {
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String tokenFilename = getProperty(PROPERTY_SHINDIG_TOKEN_KEY_FILE);
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File tokenFile = new File(tokenFilename);
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if (!tokenFile.exists()) {
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warnings.add(new Warning(
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"Token key file for Shindig does not exist: '"
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+ tokenFilename + "'"));
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} else if (!tokenFile.isFile()) {
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warnings.add(new Warning(
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"Token key file for Shindig is not a file: '"
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+ tokenFilename + "'"));
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}
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} catch (NoSuchPropertyException e) {
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warnings.add(new Warning(e.getMessage()));
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}
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}
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/**
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* Get the Token Service info from deploy.properties. It must be in the form
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* of host:port, and may not refer to localhost.
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*/
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private void checkTokenServiceInfo() {
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String tsInfo = configProps.getProperty(PROPERTY_SHINDIG_TOKEN_SERVICE);
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if (StringUtils.isEmpty(tsInfo)) {
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warnings.add(new Warning("There is no value for '"
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+ PROPERTY_SHINDIG_TOKEN_SERVICE + "' in deploy.properties"));
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return;
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}
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/*
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* If the parameter is invalid, use this message.
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*/
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String warningText = "The '" + PROPERTY_SHINDIG_TOKEN_SERVICE
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+ "' parameter is set to \"" + tsInfo
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+ "\". It must be in the form [hostname]:[port]. "
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+ "For example, \"myhost.mydomain.edu:8777\". "
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+ "The hostname may be an IP address, "
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+ "but it may not be \"localhost\" or \"127.0.0.1\"";
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int firstColon = tsInfo.indexOf(':');
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if (firstColon <= 0) {
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warnings.add(new Warning(warningText));
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return;
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}
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int lastColon = tsInfo.lastIndexOf(':');
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if (firstColon != lastColon) {
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warnings.add(new Warning(warningText));
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return;
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}
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tokenServiceHost = tsInfo.substring(0, firstColon);
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if (("localhost".equals(tokenServiceHost))
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|| ("127.0.0.1".equals(tokenServiceHost))) {
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warnings.add(new Warning(warningText));
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return;
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}
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try {
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tokenServicePort = Integer.parseInt(tsInfo
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.substring(firstColon + 1));
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} catch (Exception e) { // probably a NumberFormatException
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warnings.add(new Warning(warningText, e));
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}
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}
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private String getProperty(String key) throws NoSuchPropertyException {
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String value = configProps.getProperty(key);
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if (StringUtils.isEmpty(value)) {
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throw new NoSuchPropertyException(key);
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} else {
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return value;
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}
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}
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@Override
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public void contextDestroyed(ServletContextEvent sce) {
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// nothing to destroy
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}
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// ----------------------------------------------------------------------
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// Helper classes
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// ----------------------------------------------------------------------
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private static class NoSuchPropertyException extends Exception {
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NoSuchPropertyException(String key) {
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super("There is no value for '" + key + "' in deploy.properties");
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}
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}
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private class Warning {
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private final String message;
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private final Throwable cause;
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Warning(String message) {
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this.message = message;
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this.cause = null;
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}
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Warning(String message, Throwable cause) {
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this.message = message;
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this.cause = cause;
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}
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void warn(StartupStatus ss) {
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if (cause == null) {
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ss.warning(OpenSocialSmokeTests.this, message);
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} else {
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ss.warning(OpenSocialSmokeTests.this, message, cause);
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}
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}
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}
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private static class ShindigTestThread extends VitroBackgroundThread {
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private final OpenSocialSmokeTests listener;
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private final StartupStatus ss;
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private final String shindigBaseUrl;
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public ShindigTestThread(OpenSocialSmokeTests listener,
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StartupStatus ss, String shindigBaseUrl) {
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super("OpenSocialSmokeTest.ShindigTestThread");
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this.listener = listener;
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this.ss = ss;
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this.shindigBaseUrl = shindigBaseUrl;
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}
|
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|
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@Override
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public void run() {
|
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try {
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new ShindigTester(shindigBaseUrl).connect();
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ss.info(listener, "Shindig service responds to a REST query.");
|
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} catch (ShindigTesterException e) {
|
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String message = e.getMessage();
|
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Throwable cause = e.getCause();
|
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if (cause == null) {
|
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ss.warning(listener, message);
|
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} else {
|
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ss.warning(listener, message, cause);
|
||||
}
|
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return;
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}
|
||||
}
|
||||
}
|
||||
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private static class ShindigTester {
|
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// Use the parent's log
|
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private static final Log log = LogFactory
|
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.getLog(OpenSocialSmokeTests.class);
|
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|
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/** Pretend that there is an HTTP status code for this. */
|
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private static final int SOCKET_TIMEOUT_STATUS = -500;
|
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|
||||
private final String shindigBaseUrl;
|
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private final HttpClient httpClient = new HttpClient();
|
||||
|
||||
private int statusCode = Integer.MIN_VALUE;
|
||||
|
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public ShindigTester(String shindigBaseUrl) {
|
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this.shindigBaseUrl = shindigBaseUrl;
|
||||
}
|
||||
|
||||
public void connect() throws ShindigTesterException {
|
||||
testConnection();
|
||||
|
||||
if (!isDone()) {
|
||||
sleep();
|
||||
testConnection();
|
||||
}
|
||||
|
||||
if (!isDone()) {
|
||||
sleep();
|
||||
testConnection();
|
||||
}
|
||||
|
||||
if (statusCode != HttpStatus.SC_OK) {
|
||||
throw new ShindigTesterException(statusCode);
|
||||
}
|
||||
}
|
||||
|
||||
private void testConnection() throws ShindigTesterException {
|
||||
String shindigTestUrl = shindigBaseUrl + "/rest/activities";
|
||||
GetMethod method = new GetMethod(shindigTestUrl);
|
||||
try {
|
||||
log.debug("Trying to connect to Shindig");
|
||||
statusCode = httpClient.executeMethod(method);
|
||||
log.debug("HTTP status was " + statusCode);
|
||||
|
||||
// clear the buffer.
|
||||
InputStream stream = method.getResponseBodyAsStream();
|
||||
stream.close();
|
||||
} catch (SocketTimeoutException e) {
|
||||
// Catch the exception so we can retry this.
|
||||
// Save the status so we know why we failed.
|
||||
statusCode = SOCKET_TIMEOUT_STATUS;
|
||||
} catch (Exception e) {
|
||||
throw new ShindigTesterException(e);
|
||||
} finally {
|
||||
method.releaseConnection();
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Stop trying to connect if we succeed, or if we receive an error that
|
||||
* won't change on retry.
|
||||
*/
|
||||
private boolean isDone() {
|
||||
return (statusCode == HttpStatus.SC_OK)
|
||||
|| (statusCode == HttpStatus.SC_FORBIDDEN);
|
||||
}
|
||||
|
||||
private void sleep() {
|
||||
try {
|
||||
Thread.sleep(SLEEP_INTERVAL);
|
||||
} catch (InterruptedException e) {
|
||||
e.printStackTrace(); // Should never happen
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
protected static class ShindigTesterException extends Exception {
|
||||
private final int httpStatusCode;
|
||||
|
||||
protected ShindigTesterException(Integer httpStatusCode) {
|
||||
super("Failed to connect to the Shindig service. "
|
||||
+ "status code was " + httpStatusCode);
|
||||
this.httpStatusCode = httpStatusCode;
|
||||
}
|
||||
|
||||
protected ShindigTesterException(Throwable cause) {
|
||||
super("Failed to connect to the Shindig service.", cause);
|
||||
this.httpStatusCode = Integer.MIN_VALUE;
|
||||
}
|
||||
|
||||
protected int getHttpStatusCode() {
|
||||
return httpStatusCode;
|
||||
}
|
||||
}
|
||||
|
||||
private static class TokenServiceTestThread extends VitroBackgroundThread {
|
||||
private final OpenSocialSmokeTests listener;
|
||||
private final StartupStatus ss;
|
||||
private final String tokenServiceHost;
|
||||
private final int tokenServicePort;
|
||||
|
||||
public TokenServiceTestThread(OpenSocialSmokeTests listener,
|
||||
StartupStatus ss, String tokenServiceHost, int tokenServicePort) {
|
||||
super("OpenSocialSmokeTest.TokenServiceTestThread");
|
||||
this.listener = listener;
|
||||
this.ss = ss;
|
||||
this.tokenServiceHost = tokenServiceHost;
|
||||
this.tokenServicePort = tokenServicePort;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void run() {
|
||||
try {
|
||||
new TokenServiceTester(tokenServiceHost, tokenServicePort)
|
||||
.connect();
|
||||
ss.info(listener,
|
||||
"Shindig security token service responds to a request.");
|
||||
} catch (TokenServiceTesterException e) {
|
||||
String message = e.getMessage();
|
||||
Throwable cause = e.getCause();
|
||||
if (cause == null) {
|
||||
ss.warning(listener, message);
|
||||
} else {
|
||||
ss.warning(listener, message, cause);
|
||||
}
|
||||
return;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
protected static class TokenServiceTester {
|
||||
// Use the parent's log
|
||||
private static final Log log = LogFactory
|
||||
.getLog(OpenSocialSmokeTests.class);
|
||||
|
||||
private final String host;
|
||||
private final int port;
|
||||
|
||||
private Object problem;
|
||||
|
||||
public TokenServiceTester(String host, int port) {
|
||||
this.host = host;
|
||||
this.port = port;
|
||||
}
|
||||
|
||||
public void connect() throws TokenServiceTesterException {
|
||||
testConnection();
|
||||
|
||||
if (!isDone()) {
|
||||
sleep();
|
||||
testConnection();
|
||||
}
|
||||
|
||||
if (!isDone()) {
|
||||
sleep();
|
||||
testConnection();
|
||||
}
|
||||
|
||||
if (problem instanceof Throwable) {
|
||||
throw new TokenServiceTesterException(
|
||||
"Test of the Shindig token service failed.",
|
||||
(Throwable) problem);
|
||||
} else if (problem instanceof String) {
|
||||
throw new TokenServiceTesterException((String) problem);
|
||||
}
|
||||
}
|
||||
|
||||
private void testConnection() {
|
||||
try {
|
||||
log.debug("Connecting to the token service");
|
||||
Socket s = new Socket(host, port);
|
||||
|
||||
s.getOutputStream().write("c=default\n".getBytes());
|
||||
|
||||
int byteCount = 0;
|
||||
int totalBytecount = 0;
|
||||
byte[] buffer = new byte[8192];
|
||||
|
||||
// The following will block until the page is transmitted.
|
||||
InputStream inputStream = s.getInputStream();
|
||||
while ((byteCount = inputStream.read(buffer)) > 0) {
|
||||
totalBytecount += byteCount;
|
||||
}
|
||||
|
||||
if (totalBytecount == 0) {
|
||||
log.debug("Received an empty response.");
|
||||
problem = "The Shindig security token service responded to a test, but the response was empty.";
|
||||
} else {
|
||||
log.debug("Recieved the token.");
|
||||
problem = null;
|
||||
}
|
||||
} catch (Exception e) {
|
||||
log.debug("Problem with the token service", e);
|
||||
problem = e;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Stop trying to connect if we succeed, or if we receive an error that
|
||||
* won't change on retry.
|
||||
*/
|
||||
private boolean isDone() {
|
||||
return ((problem == null) || (problem instanceof String));
|
||||
}
|
||||
|
||||
private void sleep() {
|
||||
try {
|
||||
Thread.sleep(SLEEP_INTERVAL);
|
||||
} catch (InterruptedException e) {
|
||||
e.printStackTrace(); // Should never happen
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
protected static class TokenServiceTesterException extends Exception {
|
||||
protected TokenServiceTesterException(String message) {
|
||||
super(message);
|
||||
}
|
||||
|
||||
protected TokenServiceTesterException(String message, Throwable cause) {
|
||||
super(message, cause);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -18,7 +18,7 @@ import com.hp.hpl.jena.rdf.model.Resource;
|
|||
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
|
||||
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
|
||||
|
||||
public class SimpleReasonerPropertyTest extends AbstractTestClass {
|
||||
public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
|
||||
|
||||
long delay = 50;
|
||||
|
||||
|
|
@ -439,8 +439,6 @@ public class SimpleReasonerPropertyTest extends AbstractTestClass {
|
|||
|
||||
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
|
||||
aBox.register(simpleReasoner);
|
||||
SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
|
||||
tBox.register(simpleReasonerTBoxListener);
|
||||
// Individuals a, b, c and d
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
|
|
@ -460,8 +458,6 @@ public class SimpleReasonerPropertyTest extends AbstractTestClass {
|
|||
// Verify inferences
|
||||
Assert.assertTrue(inf.contains(b,Q,a));
|
||||
Assert.assertTrue(inf.contains(d,Y,c));
|
||||
|
||||
simpleReasonerTBoxListener.setStopRequested();
|
||||
}
|
||||
|
||||
//==================================== Utility methods ====================
|
||||
|
|
@ -0,0 +1,430 @@
|
|||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
|
||||
package edu.cornell.mannlib.vitro.webapp.reasoner;
|
||||
|
||||
import org.apache.log4j.Level;
|
||||
import org.junit.Assert;
|
||||
import org.junit.Before;
|
||||
import org.junit.Test;
|
||||
import org.mindswap.pellet.jena.PelletReasonerFactory;
|
||||
|
||||
import com.hp.hpl.jena.ontology.OntClass;
|
||||
import com.hp.hpl.jena.ontology.OntModel;
|
||||
import com.hp.hpl.jena.ontology.OntModelSpec;
|
||||
import com.hp.hpl.jena.ontology.OntProperty;
|
||||
import com.hp.hpl.jena.rdf.model.Literal;
|
||||
import com.hp.hpl.jena.rdf.model.Model;
|
||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||
import com.hp.hpl.jena.rdf.model.Resource;
|
||||
import com.hp.hpl.jena.vocabulary.OWL;
|
||||
import com.hp.hpl.jena.vocabulary.RDF;
|
||||
|
||||
import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
|
||||
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
|
||||
|
||||
public class SimpleReasonerSameAsTest extends AbstractTestClass {
|
||||
|
||||
long delay = 50;
|
||||
|
||||
@Before
|
||||
public void suppressErrorOutput() {
|
||||
suppressSyserr();
|
||||
//Turn off log messages to console
|
||||
setLoggerLevel(SimpleReasoner.class, Level.OFF);
|
||||
setLoggerLevel(SimpleReasonerTBoxListener.class, Level.OFF);
|
||||
}
|
||||
|
||||
/*
|
||||
* basic scenario of adding an abox sameAs assertion
|
||||
//*/
|
||||
@Test
|
||||
public void addSameAsABoxAssertion1() {
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
S.setLabel("property S", "en-US");
|
||||
|
||||
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
T.setLabel("property T", "en-US");
|
||||
|
||||
Literal literal1 = tBox.createLiteral("Literal value 1");
|
||||
Literal literal2 = tBox.createLiteral("Literal value 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
// Individuals a, b, c and d
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
Resource c = aBox.createResource("http://test.vivo/c");
|
||||
Resource d = aBox.createResource("http://test.vivo/d");
|
||||
|
||||
aBox.add(a,P,c);
|
||||
aBox.add(a,S,literal1);
|
||||
aBox.add(b,Q,d);
|
||||
aBox.add(b,T,literal2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,P,c));
|
||||
Assert.assertTrue(inf.contains(b,S,literal1));
|
||||
Assert.assertTrue(inf.contains(a,Q,d));
|
||||
Assert.assertTrue(inf.contains(a,T,literal2));
|
||||
|
||||
Assert.assertFalse(aBox.contains(b,OWL.sameAs,a));
|
||||
Assert.assertFalse(aBox.contains(b,P,c));
|
||||
Assert.assertFalse(aBox.contains(b,S,literal1));
|
||||
Assert.assertFalse(aBox.contains(a,Q,d));
|
||||
Assert.assertFalse(aBox.contains(a,T,literal2));
|
||||
}
|
||||
|
||||
/*
|
||||
* basic scenario of removing an abox sameAs assertion
|
||||
*/
|
||||
@Test
|
||||
public void removeSameAsABoxAssertion1() {
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
S.setLabel("property S", "en-US");
|
||||
|
||||
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
T.setLabel("property T", "en-US");
|
||||
|
||||
Literal literal1 = tBox.createLiteral("Literal value 1");
|
||||
Literal literal2 = tBox.createLiteral("Literal value 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
// Individuals a, b, c and d
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
Resource c = aBox.createResource("http://test.vivo/c");
|
||||
Resource d = aBox.createResource("http://test.vivo/d");
|
||||
|
||||
aBox.add(a,P,c);
|
||||
aBox.add(a,S,literal1);
|
||||
aBox.add(b,Q,d);
|
||||
aBox.add(b,T,literal2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,P,c));
|
||||
Assert.assertTrue(inf.contains(b,S,literal1));
|
||||
Assert.assertTrue(inf.contains(a,Q,d));
|
||||
Assert.assertTrue(inf.contains(a,T,literal2));
|
||||
|
||||
aBox.remove(a,OWL.sameAs,b);
|
||||
|
||||
Assert.assertFalse(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertFalse(inf.contains(b,P,c));
|
||||
Assert.assertFalse(inf.contains(b,S,literal1));
|
||||
Assert.assertFalse(inf.contains(a,Q,d));
|
||||
Assert.assertFalse(inf.contains(a,T,literal2));
|
||||
}
|
||||
|
||||
/*
|
||||
* basic scenario of adding an abox assertion for
|
||||
* an individual is sameAs another.
|
||||
*/
|
||||
@Test
|
||||
public void addABoxAssertion1() {
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
S.setLabel("property S", "en-US");
|
||||
|
||||
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
T.setLabel("property T", "en-US");
|
||||
|
||||
Literal literal1 = tBox.createLiteral("Literal value 1");
|
||||
Literal literal2 = tBox.createLiteral("Literal value 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
// Individuals a, b, c and d
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
Resource c = aBox.createResource("http://test.vivo/c");
|
||||
Resource d = aBox.createResource("http://test.vivo/d");
|
||||
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
|
||||
aBox.add(a,P,c);
|
||||
aBox.add(a,S,literal1);
|
||||
aBox.add(b,Q,d);
|
||||
aBox.add(b,T,literal2);
|
||||
|
||||
Assert.assertTrue(inf.contains(b,P,c));
|
||||
Assert.assertTrue(inf.contains(b,S,literal1));
|
||||
Assert.assertTrue(inf.contains(a,Q,d));
|
||||
Assert.assertTrue(inf.contains(a,T,literal2));
|
||||
}
|
||||
|
||||
/*
|
||||
* adding abox assertion for individuals that are sameAs
|
||||
* each other.
|
||||
*/
|
||||
@Test
|
||||
public void addABoxAssertion2() {
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntClass classA = tBox.createClass("http://test.vivo/A");
|
||||
classA.setLabel("class A", "en-US");
|
||||
|
||||
OntClass classB = tBox.createClass("http://test.vivo/B");
|
||||
classB.setLabel("class B", "en-US");
|
||||
|
||||
classA.addSubClass(classB);
|
||||
|
||||
OntProperty desc = tBox.createDatatypeProperty("http://test.vivo/desc");
|
||||
desc.setLabel("property desc", "en-US");
|
||||
|
||||
Literal desc1 = tBox.createLiteral("individual 1");
|
||||
Literal desc2 = tBox.createLiteral("individual 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
// Individuals a and b
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
|
||||
aBox.add(a,desc,desc1);
|
||||
aBox.add(b,desc,desc2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
aBox.add(a, RDF.type, classB);
|
||||
|
||||
Assert.assertTrue(inf.contains(a,desc,desc2));
|
||||
Assert.assertTrue(inf.contains(a,RDF.type,classA));
|
||||
Assert.assertTrue(inf.contains(b,desc,desc1));
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,RDF.type,classB));
|
||||
Assert.assertTrue(inf.contains(b,RDF.type,classA));
|
||||
}
|
||||
|
||||
/*
|
||||
* basic scenario of removing an abox assertion for
|
||||
* an individual is sameAs another.
|
||||
*/
|
||||
@Test
|
||||
public void removeABoxAssertion1() {
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
S.setLabel("property S", "en-US");
|
||||
|
||||
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
T.setLabel("property T", "en-US");
|
||||
|
||||
Literal literal1 = tBox.createLiteral("Literal value 1");
|
||||
Literal literal2 = tBox.createLiteral("Literal value 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
// Individuals a, b, c and d
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
Resource c = aBox.createResource("http://test.vivo/c");
|
||||
Resource d = aBox.createResource("http://test.vivo/d");
|
||||
|
||||
aBox.add(a,P,c);
|
||||
aBox.add(a,S,literal1);
|
||||
aBox.add(b,Q,d);
|
||||
aBox.add(b,T,literal2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
|
||||
aBox.remove(a,P,c);
|
||||
aBox.remove(a,S,literal1);
|
||||
|
||||
Assert.assertFalse(inf.contains(b,P,c));
|
||||
Assert.assertFalse(inf.contains(b,S,literal1));
|
||||
}
|
||||
|
||||
/*
|
||||
* adding an inverseOf assertion for individuals who are sameAs
|
||||
* each other.
|
||||
*/
|
||||
@Test
|
||||
public void addTBoxInverseAssertion1() throws InterruptedException {
|
||||
|
||||
// Create TBox, ABox and Inference models and register
|
||||
// the ABox reasoner listeners with the ABox and TBox
|
||||
// Pellet will compute TBox inferences
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createOntProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createOntProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
|
||||
aBox.register(simpleReasoner);
|
||||
SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
|
||||
tBox.register(simpleReasonerTBoxListener);
|
||||
|
||||
// Individuals a and b
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
|
||||
// abox statements
|
||||
aBox.add(a,P,b);
|
||||
aBox.add(a, OWL.sameAs,b);
|
||||
|
||||
// Assert P and Q as inverses and wait for SimpleReasoner TBox
|
||||
// thread to end
|
||||
|
||||
Q.addInverseOf(P);
|
||||
|
||||
tBox.rebind();
|
||||
tBox.prepare();
|
||||
|
||||
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
|
||||
Thread.sleep(delay);
|
||||
}
|
||||
|
||||
// Verify inferences
|
||||
Assert.assertTrue(inf.contains(b,Q,a));
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,P,b));
|
||||
Assert.assertTrue(inf.contains(a,Q,a));
|
||||
simpleReasonerTBoxListener.setStopRequested();
|
||||
}
|
||||
|
||||
/*
|
||||
* Basic scenario around recomputing the ABox inferences
|
||||
*/
|
||||
@Test
|
||||
public void recomputeABox1() throws InterruptedException {
|
||||
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
|
||||
P.setLabel("property P", "en-US");
|
||||
|
||||
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
|
||||
Q.setLabel("property Q", "en-US");
|
||||
|
||||
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
S.setLabel("property S", "en-US");
|
||||
|
||||
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
|
||||
T.setLabel("property T", "en-US");
|
||||
|
||||
Literal literal1 = tBox.createLiteral("Literal value 1");
|
||||
Literal literal2 = tBox.createLiteral("Literal value 2");
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
|
||||
aBox.register(simpleReasoner);
|
||||
|
||||
// Individuals a, b, c and d
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
Resource c = aBox.createResource("http://test.vivo/c");
|
||||
Resource d = aBox.createResource("http://test.vivo/d");
|
||||
|
||||
aBox.add(a,P,c);
|
||||
aBox.add(a,S,literal1);
|
||||
aBox.add(b,Q,d);
|
||||
aBox.add(b,T,literal2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
|
||||
simpleReasoner.recompute();
|
||||
|
||||
while (simpleReasoner.isRecomputing()) {
|
||||
Thread.sleep(delay);
|
||||
}
|
||||
|
||||
// Verify inferences
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,P,c));
|
||||
Assert.assertTrue(inf.contains(b,S,literal1));
|
||||
Assert.assertTrue(inf.contains(a,Q,d));
|
||||
Assert.assertTrue(inf.contains(a,T,literal2));
|
||||
}
|
||||
|
||||
//==================================== Utility methods ====================
|
||||
SimpleReasonerTBoxListener getTBoxListener(SimpleReasoner simpleReasoner) {
|
||||
return new SimpleReasonerTBoxListener(simpleReasoner, new Exception().getStackTrace()[1].getMethodName());
|
||||
}
|
||||
|
||||
// To help in debugging the unit test
|
||||
void printModel(Model model, String modelName) {
|
||||
|
||||
System.out.println("\nThe " + modelName + " model has " + model.size() + " statements:");
|
||||
System.out.println("---------------------------------------------------------------------");
|
||||
model.write(System.out);
|
||||
}
|
||||
|
||||
// To help in debugging the unit test
|
||||
void printModel(OntModel ontModel, String modelName) {
|
||||
|
||||
System.out.println("\nThe " + modelName + " model has " + ontModel.size() + " statements:");
|
||||
System.out.println("---------------------------------------------------------------------");
|
||||
ontModel.writeAll(System.out,"N3",null);
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -54,6 +54,8 @@ edu.cornell.mannlib.vitro.webapp.auth.policy.RestrictHomeMenuItemEditingPolicy$S
|
|||
|
||||
edu.cornell.mannlib.vitro.webapp.services.shortview.ShortViewServiceSetup
|
||||
|
||||
edu.ucsf.vitro.opensocial.OpenSocialSmokeTests
|
||||
|
||||
# The Solr index uses a "public" permission, so the PropertyRestrictionPolicyHelper
|
||||
# and the PermissionRegistry must already be set up.
|
||||
edu.cornell.mannlib.vitro.webapp.search.solr.SolrSetup
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue