From: Sasha <Main-laptop2>
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;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<JobStat> RUNTIME = new Comparator<JobStat>() {
-		@Override
-		public int compare(JobStat o1, JobStat o2) {
-			return new Integer(o2.getRuntime()).compareTo(o1.getRuntime());
-		}
-	};
-
-	static final Comparator<JobStat> STARTTIME = new Comparator<JobStat>() {
-		@Override
-		public int compare(JobStat o1, JobStat o2) {
-			return new Long(o1.start).compareTo(o2.start);
-		}
-	};
-
-	static final Comparator<JobStat> RESULTSIZE = new Comparator<JobStat>() {
-		@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<JobStat> RUNTIME = new Comparator<JobStat>() {
+		@Override
+		public int compare(JobStat o1, JobStat o2) {
+			return new Integer(o2.getRuntime()).compareTo(o1.getRuntime());
+		}
+	};
+
+	static final Comparator<JobStat> STARTTIME = new Comparator<JobStat>() {
+		@Override
+		public int compare(JobStat o1, JobStat o2) {
+			return new Long(o1.start).compareTo(o2.start);
+		}
+	};
+
+	static final Comparator<JobStat> RESULTSIZE = new Comparator<JobStat>() {
+		@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);