From: Sasha Date: Mon, 29 Jul 2013 11:55:21 +0000 (+0100) Subject: Refactoring and code style improving X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a9d68d14dd391010e0a9e3b02a590f36db8e2e47;hp=b4563866bd1a84e8e79790ce533f2a84bc5d188e;p=jabaws.git Refactoring and code style improving --- diff --git a/engine/compbio/engine/local/ExecutableWrapper.java b/engine/compbio/engine/local/ExecutableWrapper.java index 597af4e..9e652f9 100644 --- a/engine/compbio/engine/local/ExecutableWrapper.java +++ b/engine/compbio/engine/local/ExecutableWrapper.java @@ -75,17 +75,14 @@ public final class ExecutableWrapper implements pbuilder = new ProcessBuilder(params); if (executable.getEnvironment() != null) { - log.debug("Setting command environment variables: " - + pbuilder.environment()); - Util.mergeEnvVariables(pbuilder.environment(), executable - .getEnvironment()); + log.debug("Setting command environment variables: " + pbuilder.environment()); + Util.mergeEnvVariables(pbuilder.environment(), executable.getEnvironment()); log.debug("Process environment:" + pbuilder.environment()); } log.debug("Setting command: " + pbuilder.command()); PathValidator.validateDirectory(workDirectory); pbuilder.directory(new File(workDirectory)); - log.debug("Current working directory is " - + SysPrefs.getCurrentDirectory()); + log.debug("Current working directory is " + SysPrefs.getCurrentDirectory()); log.debug("Setting working directory: " + workDirectory); // Initialize private executor to dump processes output if any to the // file system @@ -98,8 +95,7 @@ public final class ExecutableWrapper implements // get access to the thread efficiently deadlocking the // proccess! this.es = Executors.newCachedThreadPool(); - log - .debug("Initializing executor for local processes output dump"); + log.debug("Initializing executor for local processes output dump"); // Make sure that the executors are going to be properly closed Runtime.getRuntime().addShutdownHook(new Thread() { @Override @@ -119,7 +115,7 @@ public final class ExecutableWrapper implements */ public static final void shutdownService() { if (es != null) { - es.shutdownNow(); + es.shutdownNow(); } } diff --git a/webservices/compbio/stat/collector/JobStat.java b/webservices/compbio/stat/collector/JobStat.java index 72c7ae1..2ad48ff 100644 --- a/webservices/compbio/stat/collector/JobStat.java +++ b/webservices/compbio/stat/collector/JobStat.java @@ -1,281 +1,285 @@ -/* Copyright (c) 2011 Peter Troshin - * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 - * - * This library is free software; you can redistribute it and/or modify it under the terms of the - * Apache License version 2 as published by the Apache Software Foundation - * - * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without - * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache - * License for more details. - * - * A copy of the license is in apache_license.txt. It is also available here: - * @see: http://www.apache.org/licenses/LICENSE-2.0.txt - * - * Any republication or derived work distributed in source code form - * must include this copyright and license notice. - */ -package compbio.stat.collector; - -import java.sql.Timestamp; -import java.text.DateFormat; -import java.text.SimpleDateFormat; -import java.util.Comparator; -import java.util.Date; -import java.util.Locale; - -import compbio.engine.client.ConfExecutable; -import compbio.util.Util; -import compbio.ws.client.Services; - -public class JobStat { - - static final Comparator RUNTIME = new Comparator() { - @Override - public int compare(JobStat o1, JobStat o2) { - return new Integer(o2.getRuntime()).compareTo(o1.getRuntime()); - } - }; - - static final Comparator STARTTIME = new Comparator() { - @Override - public int compare(JobStat o1, JobStat o2) { - return new Long(o1.start).compareTo(o2.start); - } - }; - - static final Comparator RESULTSIZE = new Comparator() { - @Override - public int compare(JobStat o1, JobStat o2) { - return new Long(o2.resultSize).compareTo(o1.resultSize); - } - }; - - private static DateFormat DATE_TIME = SimpleDateFormat.getDateTimeInstance( - DateFormat.DEFAULT, DateFormat.DEFAULT, Locale.UK); - - Services webService; - String clusterJobId; - String jobname; - long start; - long finish; - long inputSize; - long resultSize; - boolean isCollected; - boolean isCancelled; - - private JobStat(Services webService, String clusterJobId, String jobname, - long start, long finish, long inputSize, long resultSize, - boolean isCancelled, boolean isCollected) { - super(); - this.webService = webService; - this.clusterJobId = clusterJobId; - this.jobname = jobname; - this.start = start; - this.finish = finish; - this.inputSize = inputSize; - this.resultSize = resultSize; - this.isCancelled = isCancelled; - this.isCollected = isCollected; - validate(); - } - - static JobStat newInstance(Services webService, String clusterJobId, - String jobname, long start, long finish, long inputSize, - long resultSize, boolean isCancelled, boolean isCollected) { - return new JobStat(webService, clusterJobId, jobname, start, finish, - inputSize, resultSize, isCancelled, isCollected); - } - - static JobStat newInstance(Services webService, String clusterJobId, - String jobname, Timestamp start, Timestamp finish, long inputSize, - long resultSize, boolean isCancelled, boolean isCollected) { - long startm = ExecutionStatCollector.UNDEFINED; - long stopm = ExecutionStatCollector.UNDEFINED; - if (start != null) { - startm = start.getTime(); - } - if (finish != null) { - stopm = finish.getTime(); - } - return new JobStat(webService, clusterJobId, jobname, startm, stopm, - inputSize, resultSize, isCancelled, isCollected); - } - - void validate() { - if (webService == null) { - throw new AssertionError("webService must be defined!:\n " + this); - } - if (Util.isEmpty(jobname)) { - throw new AssertionError("jobname must be defined!:\n" + this); - } - } - - private JobStat(String jobId) { - assert !Util.isEmpty(jobname); - this.jobname = jobId; - } - - static JobStat newIncompleteStat(String jobname) { - return new JobStat(jobname); - } - - public boolean isClusterJob() { - return jobname.startsWith(ConfExecutable.CLUSTER_TASK_ID_PREFIX); - } - - @Override - public int hashCode() { - final int prime = 31; - int result = 1; - result = prime * result + ((jobname == null) ? 0 : jobname.hashCode()); - return result; - } - - @Override - public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; - JobStat other = (JobStat) obj; - if (jobname == null) { - if (other.jobname != null) - return false; - } else if (!jobname.equals(other.jobname)) - return false; - return true; - } - - public int getRuntime() { - if (start != ExecutionStatCollector.UNDEFINED - && finish != ExecutionStatCollector.UNDEFINED) { - return (int) (finish - start) / 1000; - } - return ExecutionStatCollector.UNDEFINED; - } - - @Override - public String toString() { - return getJobReport(); - } - - String getJobReport() { - String report = "WS: " + webService + "\n"; - report += "JOB: " + jobname + "\n"; - if (start != ExecutionStatCollector.UNDEFINED) { - report += "Started " + new Date(start) + "\n"; - } - if (finish != ExecutionStatCollector.UNDEFINED) { - report += "Finished " + new Date(finish) + "\n"; - } - if (start != ExecutionStatCollector.UNDEFINED - && finish != ExecutionStatCollector.UNDEFINED) { - report += "Runtime " + getRuntime() + "\n"; - } - report += "Input size " + inputSize + "\n"; - report += "Result size " + resultSize + "\n"; - report += "ClusterJobID " + clusterJobId + "\n"; - report += "Collected? " + isCollected + "\n"; - report += "Cancelled? " + isCancelled + "\n"; - return report; - } - - /** - * Header Job Started Finished Runtime Input Result - */ - String getJobReportTabulated() { - String report = webService + "\t"; - report += jobname + "\t"; - if (start != ExecutionStatCollector.UNDEFINED) { - report += ExecutionStatCollector.DF.format(new Date(start)) + "\t"; - } else { - report += ExecutionStatCollector.UNDEFINED + "\t"; - } - if (finish != ExecutionStatCollector.UNDEFINED) { - report += ExecutionStatCollector.DF.format(new Date(finish)) + "\t"; - } else { - report += ExecutionStatCollector.UNDEFINED + "\t"; - } - if (start != ExecutionStatCollector.UNDEFINED - && finish != ExecutionStatCollector.UNDEFINED) { - report += getRuntime() + "\t"; - } else { - report += ExecutionStatCollector.UNDEFINED + "\t"; - } - report += inputSize + "\t"; - report += resultSize + "\t"; - report += clusterJobId + "\t"; - report += isCollected + "\t"; - report += isCancelled + "\t"; - return report; - } - - public Services getWebService() { - return webService; - } - - public String getClusterJobId() { - return clusterJobId; - } - - public String getJobname() { - return jobname; - } - - public String getEscJobname() { - String[] parts = jobname.split("#"); - return parts[0] + "%23" + parts[1]; - } - - public String getStart() { - if (start != ExecutionStatCollector.UNDEFINED) { - return DATE_TIME.format(new Date(start)); - } - return "?"; - } - - public String getFinish() { - if (finish != ExecutionStatCollector.UNDEFINED) { - return DATE_TIME.format(new Date(finish)); - } - return "?"; - } - - public long getInputSize() { - if (inputSize != ExecutionStatCollector.UNDEFINED) { - return inputSize; - } - return 0; - } - - public long getResultSize() { - if (resultSize > 0) { - return resultSize; - } - return 0; - } - - public boolean hasResult() { - return resultSize > 0; - } - - public boolean hasStarted() { - return start != ExecutionStatCollector.UNDEFINED; - } - - public boolean getIsCollected() { - return isCollected; - } - - public boolean getIsCancelled() { - return isCancelled; - } - - public boolean getIsFinished() { - return finish != ExecutionStatCollector.UNDEFINED; - } - -} \ No newline at end of file +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ +package compbio.stat.collector; + +import java.sql.Timestamp; +import java.text.DateFormat; +import java.text.SimpleDateFormat; +import java.util.Comparator; +import java.util.Date; +import java.util.Locale; + +import compbio.engine.client.ConfExecutable; +import compbio.util.Util; +import compbio.ws.client.Services; + +public class JobStat { + + static final Comparator RUNTIME = new Comparator() { + @Override + public int compare(JobStat o1, JobStat o2) { + return new Integer(o2.getRuntime()).compareTo(o1.getRuntime()); + } + }; + + static final Comparator STARTTIME = new Comparator() { + @Override + public int compare(JobStat o1, JobStat o2) { + return new Long(o1.start).compareTo(o2.start); + } + }; + + static final Comparator RESULTSIZE = new Comparator() { + @Override + public int compare(JobStat o1, JobStat o2) { + return new Long(o2.resultSize).compareTo(o1.resultSize); + } + }; + + private static DateFormat DATE_TIME = SimpleDateFormat.getDateTimeInstance( + DateFormat.DEFAULT, DateFormat.DEFAULT, Locale.UK); + + Services webService; + String clusterJobId; + String jobname; + long start; + long finish; + long inputSize; + long resultSize; + boolean isCollected; + boolean isCancelled; + + private JobStat(Services webService, String clusterJobId, String jobname, + long start, long finish, long inputSize, long resultSize, + boolean isCancelled, boolean isCollected) { + super(); + this.webService = webService; + this.clusterJobId = clusterJobId; + this.jobname = jobname; + this.start = start; + this.finish = finish; + this.inputSize = inputSize; + this.resultSize = resultSize; + this.isCancelled = isCancelled; + this.isCollected = isCollected; + validate(); + } + + public static JobStat newInstance(Services webService, String clusterJobId, + String jobname, long start, long finish, long inputSize, + long resultSize, boolean isCancelled, boolean isCollected) { + return new JobStat(webService, clusterJobId, jobname, start, finish, + inputSize, resultSize, isCancelled, isCollected); + } + + public static JobStat newInstance(Services webService, String clusterJobId, + String jobname, Timestamp start, Timestamp finish, long inputSize, + long resultSize, boolean isCancelled, boolean isCollected) { + long startm = ExecutionStatCollector.UNDEFINED; + long stopm = ExecutionStatCollector.UNDEFINED; + if (start != null) { + startm = start.getTime(); + } + if (finish != null) { + stopm = finish.getTime(); + } + return new JobStat(webService, clusterJobId, jobname, startm, stopm, + inputSize, resultSize, isCancelled, isCollected); + } + + void validate() { + if (webService == null) { + throw new AssertionError("webService must be defined!:\n " + this); + } + if (Util.isEmpty(jobname)) { + throw new AssertionError("jobname must be defined!:\n" + this); + } + } + + private JobStat(String jobId) { + assert !Util.isEmpty(jobname); + this.jobname = jobId; + } + + public static JobStat newIncompleteStat(String jobname) { + return new JobStat(jobname); + } + + public boolean isClusterJob() { + return jobname.startsWith(ConfExecutable.CLUSTER_TASK_ID_PREFIX); + } + + @Override + public int hashCode() { + final int prime = 31; + int result = 1; + result = prime * result + ((jobname == null) ? 0 : jobname.hashCode()); + return result; + } + + @Override + public boolean equals(Object obj) { + if (this == obj) + return true; + if (obj == null) + return false; + if (getClass() != obj.getClass()) + return false; + JobStat other = (JobStat) obj; + if (jobname == null) { + if (other.jobname != null) + return false; + } else if (!jobname.equals(other.jobname)) + return false; + return true; + } + + public int getRuntime() { + if (start != ExecutionStatCollector.UNDEFINED && finish != ExecutionStatCollector.UNDEFINED) { + return (int) (finish - start) / 1000; + } + return ExecutionStatCollector.UNDEFINED; + } + + @Override + public String toString() { + return getJobReport(); + } + + String getJobReport() { + String report = "WS: " + webService + "\n"; + report += "JOB: " + jobname + "\n"; + if (start != ExecutionStatCollector.UNDEFINED) { + report += "Started " + new Date(start) + "\n"; + } + if (finish != ExecutionStatCollector.UNDEFINED) { + report += "Finished " + new Date(finish) + "\n"; + } + if (start != ExecutionStatCollector.UNDEFINED && finish != ExecutionStatCollector.UNDEFINED) { + report += "Runtime " + getRuntime() + "\n"; + } + report += "Input size " + inputSize + "\n"; + report += "Result size " + resultSize + "\n"; + report += "ClusterJobID " + clusterJobId + "\n"; + report += "Collected? " + isCollected + "\n"; + report += "Cancelled? " + isCancelled + "\n"; + return report; + } + + /** + * Header Job Started Finished Runtime Input Result + */ + String getJobReportTabulated() { + String report = webService + "\t"; + report += jobname + "\t"; + if (start != ExecutionStatCollector.UNDEFINED) { + report += ExecutionStatCollector.DF.format(new Date(start)) + "\t"; + } else { + report += ExecutionStatCollector.UNDEFINED + "\t"; + } + if (finish != ExecutionStatCollector.UNDEFINED) { + report += ExecutionStatCollector.DF.format(new Date(finish)) + "\t"; + } else { + report += ExecutionStatCollector.UNDEFINED + "\t"; + } + if (start != ExecutionStatCollector.UNDEFINED && finish != ExecutionStatCollector.UNDEFINED) { + report += getRuntime() + "\t"; + } else { + report += ExecutionStatCollector.UNDEFINED + "\t"; + } + report += inputSize + "\t"; + report += resultSize + "\t"; + report += clusterJobId + "\t"; + report += isCollected + "\t"; + report += isCancelled + "\t"; + return report; + } + + public Services getWebService() { + return webService; + } + + public String getClusterJobId() { + return clusterJobId; + } + + public String getJobname() { + return jobname; + } + + public String getEscJobname() { + String[] parts = jobname.split("#"); + return parts[0] + "%23" + parts[1]; + } + + public String getStart() { + if (start != ExecutionStatCollector.UNDEFINED) { + return DATE_TIME.format(new Date(start)); + } + return "?"; + } + + public long getNumericalStart() { + return start; + } + + public long getNumericalFinish() { + return finish; + } + + public String getFinish() { + if (finish != ExecutionStatCollector.UNDEFINED) { + return DATE_TIME.format(new Date(finish)); + } + return "?"; + } + + public long getInputSize() { + if (inputSize != ExecutionStatCollector.UNDEFINED) { + return inputSize; + } + return 0; + } + + public long getResultSize() { + if (resultSize > 0) { + return resultSize; + } + return 0; + } + + public boolean hasResult() { + return resultSize > 0; + } + + public boolean hasStarted() { + return start != ExecutionStatCollector.UNDEFINED; + } + + public boolean getIsCollected() { + return isCollected; + } + + public boolean getIsCancelled() { + return isCancelled; + } + + public boolean getIsFinished() { + return finish != ExecutionStatCollector.UNDEFINED; + } +} diff --git a/webservices/compbio/stat/collector/StatDB.java b/webservices/compbio/stat/collector/StatDB.java index b469c44..3af1b14 100644 --- a/webservices/compbio/stat/collector/StatDB.java +++ b/webservices/compbio/stat/collector/StatDB.java @@ -52,22 +52,19 @@ public class StatDB { static Connection conn; - private synchronized static Connection getDBConnection() - throws SQLException { + private synchronized static Connection getDBConnection() throws SQLException { if (conn != null && !conn.isClosed()) { return conn; } else { try { String dbpath = PropertyHelperManager.getLocalPath(); - log.info("Looking for JABAWS access statistics database at: " - + dbpath); + log.info("Looking for JABAWS access statistics database at: " + dbpath); System.setProperty("derby.system.home", dbpath); // Apparently under Tomcat webapp you cannot rely on Java // auto discovery and have to register the driver explicitly Class.forName(driver); - conn = DriverManager.getConnection(protocol + statDBName - + ";create=false"); + conn = DriverManager.getConnection(protocol + statDBName + ";create=false"); conn.setAutoCommit(true); /* @@ -81,6 +78,7 @@ public class StatDB { } return conn; } + public StatDB() throws SQLException { this.conn = getDBConnection(); } diff --git a/webservices/compbio/ws/server/SetExecutableFlag.java b/webservices/compbio/ws/server/SetExecutableFlag.java index dea7cbe..a04e547 100644 --- a/webservices/compbio/ws/server/SetExecutableFlag.java +++ b/webservices/compbio/ws/server/SetExecutableFlag.java @@ -58,11 +58,10 @@ public class SetExecutableFlag implements ServletContextListener { // Run only one once if not on Windows if (!SysPrefs.isWindows && !isExec) { - // verify script exist + // verify script exists File scriptFile = new File(workDir, script); if (!scriptFile.exists()) { - log.debug("Setexecflag.sh script is NOT found in " - + scriptFile.getAbsolutePath()); + log.debug("Setexecflag.sh script is NOT found in " + scriptFile.getAbsolutePath()); return; } else { scriptFile.setExecutable(true);