Java tutorial
/* * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute * Copyright [2016-2018] EMBL-European Bioinformatics Institute * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ /** * File: AbstractPerlModuleBasedTestCase.java * Created by: dstaines * Created on: Mar 23, 2010 * CVS: $$ */ package org.ensembl.healthcheck.testcase; import org.apache.commons.lang.StringUtils; import org.ensembl.healthcheck.DatabaseRegistryEntry; import org.ensembl.healthcheck.DatabaseServer; import org.ensembl.healthcheck.ReportManager; import org.ensembl.healthcheck.util.LogMapperPerl2Java; import org.ensembl.healthcheck.util.ActionAppendable; import org.ensembl.healthcheck.util.TemplateBuilder; import java.sql.Connection; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.logging.ConsoleHandler; import java.util.logging.Formatter; import java.util.logging.Handler; import java.util.logging.LogRecord; /** * @author dstaines * */ public abstract class AbstractPerlModuleBasedTestCase extends AbstractPerlBasedTestCase { private final LogMapperPerl2Java logMapper; private final Formatter perlLogMessagesFormatter; protected Map<Handler, Formatter> savedFormatter = new HashMap<Handler, Formatter>(); protected String pass = ""; public AbstractPerlModuleBasedTestCase() { super(); logMapper = new LogMapperPerl2Java(logger); perlLogMessagesFormatter = createPerlLogMessageFormatter(); setSpeciesIdAware(true); } /** * @return name of perl module used in this test */ protected abstract String getModule(); /* (non-Javadoc) * @see org.ensembl.healthcheck.testcase.AbstractPerlBasedTestCase#getPerlScript() */ @Override protected String getPerlScript(DatabaseRegistryEntry dbre, int speciesId) { DatabaseServer srv = dbre.getDatabaseServer(); if (srv.getPass() == null) { return TemplateBuilder.template( "./perl/run_healthcheck.pl -host $host$ -port $port$ -user $user$ -dbname $dbname$ -species_id $species_id$ -module $module$", "host", srv.getHost(), "port", srv.getPort(), "user", srv.getUser(), "dbname", dbre.getName(), "module", getModule(), "species_id", speciesId); } else { return TemplateBuilder.template( "./perl/run_healthcheck.pl -host $host$ -port $port$ -user $user$ -pass $pass$ -dbname $dbname$ -species_id $species_id$ -module $module$", "host", srv.getHost(), "port", srv.getPort(), "user", srv.getUser(), "pass", srv.getPass(), "dbname", dbre.getName(), "module", getModule(), "species_id", speciesId); } } protected Map<String, String> environmentVarsToSet() { Map<String, String> inheritedEnvironment = super.environmentVarsToSet(); if (!StringUtils.isEmpty(this.pass)) { inheritedEnvironment.put("pass", this.pass); } return inheritedEnvironment; } /** * @return formatter for log messages originating in a perl based healthcheck. */ protected Formatter createPerlLogMessageFormatter() { return new Formatter() { @Override public String formatMessage(LogRecord logRecord) { return logRecord.getMessage(); } @Override public String format(LogRecord logRecord) { return formatMessage(logRecord) + "\n"; } }; } /** * <p> * Forward a message received from the healthcheck to the ReportManager * or the logging system. * </p> * * @param message */ protected void dispatchMessage(final EnsTestCase e, final Connection c, String message) { // Parse output from the healthcheck with prefixes from // Bio::EnsEMBL::Healthcheck, forward to appropriate destinations. // if (message.startsWith("PROGRESS")) { // Progress messages go to the logger on the fine level. //Formatter savedFormatter = logger.getHandlers()[0].getFormatter(); logger.fine(message); return; } if (message.startsWith("LOG")) { // Log messages from perl get forwarded to the java logger. logMapper.log(message); return; } if (message.startsWith("PROBLEM")) { // Only count messages as a problem, if they are // prefixed with PROBLEM. The prefix is created by // Bio::EnsEMBL::Healthcheck. // ReportManager.problem(e, c, message); return; } if (message.startsWith("CORRECT")) { ReportManager.correct(e, c, message); return; } if (message.trim().length() == 0) { return; } // Otherwise pass this on as a warning. Definitely makes sense for the // API complaining about being run on the wrong version of a database. // logger.warning(message); } protected void setPerlFriendlyLogFormatters() { Handler[] configuredHandler = logger.getHandlers(); // It is possible that no Handler has been configured. In that case we // create and add one to the logger. // if (configuredHandler.length == 0) { logger.addHandler(new ConsoleHandler()); configuredHandler = logger.getHandlers(); } // Now there is at least one configuredHandler. // for (Handler h : configuredHandler) { savedFormatter.put(h, h.getFormatter()); h.setFormatter(perlLogMessagesFormatter); if (h.getFormatter() != perlLogMessagesFormatter) { throw new RuntimeException("Unable to set Formatter!"); } } } protected void removePerlFriendlyLogFormatters() { for (Handler h : logger.getHandlers()) { h.setFormatter(savedFormatter.get(h)); } } @Override public boolean run(final DatabaseRegistryEntry dbre) { setPerlFriendlyLogFormatters(); boolean savedUseParentHandler = logger.getUseParentHandlers(); logger.setUseParentHandlers(false); this.pass = dbre.getDatabaseServer().getPass(); boolean passes = super.run(dbre); removePerlFriendlyLogFormatters(); logger.setUseParentHandlers(savedUseParentHandler); return passes; } }