From 5b8f68c132f6df1dc4e1567ade0ab2d1dc8de317 Mon Sep 17 00:00:00 2001
From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Mon, 5 Sep 2011 15:11:23 +0000
Subject: [PATCH] Adding listener for setting executable flag on the web
 application start up

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4563 e3abac25-378b-4346-85de-24260fe3988d
---
 WEB-INF/web.xml                                    |    7 +-
 binaries/src/setexecflag.sh                        |    2 +-
 .../compbio/ws/server/SetExecutableFlag.java       |   89 ++++++++++++++++++++
 3 files changed, 95 insertions(+), 3 deletions(-)
 create mode 100644 webservices/compbio/ws/server/SetExecutableFlag.java

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index 794c4cb..3bf22cf 100644
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -12,9 +12,12 @@
     <listener>
         <listener-class>compbio.stat.servlet.StatisticCollector</listener-class>
      </listener>
-    <listener>
+     <listener>
+        <listener-class>compbio.ws.server.SetExecutableFlag</listener-class>
+     </listener>
+     <listener>
         <listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>
-    </listener>
+     </listener>
     
  	<!-- Session timeout in minutes -->
 	<session-config>
diff --git a/binaries/src/setexecflag.sh b/binaries/src/setexecflag.sh
index e4d11a0..aa82b3d 100644
--- a/binaries/src/setexecflag.sh
+++ b/binaries/src/setexecflag.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 
 echo ""
 echo "Setting executable flag for Clustalw..."
diff --git a/webservices/compbio/ws/server/SetExecutableFlag.java b/webservices/compbio/ws/server/SetExecutableFlag.java
new file mode 100644
index 0000000..dea7cbe
--- /dev/null
+++ b/webservices/compbio/ws/server/SetExecutableFlag.java
@@ -0,0 +1,89 @@
+package compbio.ws.server;
+
+import java.io.File;
+import java.io.IOException;
+
+import javax.servlet.ServletContextEvent;
+import javax.servlet.ServletContextListener;
+
+import org.apache.log4j.Logger;
+
+import compbio.engine.client.Executable.ExecProvider;
+import compbio.engine.client.Util;
+import compbio.engine.conf.PropertyHelperManager;
+import compbio.runner.disorder.IUPred;
+import compbio.runner.msa.Muscle;
+import compbio.util.SysPrefs;
+
+/**
+ * Run setexecflag.sh script if executable flag is not set
+ * 
+ * @author pvtroshin
+ * 
+ */
+public class SetExecutableFlag implements ServletContextListener {
+
+	private final Logger log = Logger.getLogger(SetExecutableFlag.class);
+
+	@Override
+	public void contextDestroyed(ServletContextEvent arg0) {
+		// do nothing
+	}
+
+	/**
+	 * This listener is designed to run only once when the web application is
+	 * deployed to set executable flag for binaries.
+	 * 
+	 * @param arg0
+	 *            - ignored
+	 */
+	@Override
+	public void contextInitialized(ServletContextEvent arg0) {
+		// Assume at least one of these is configured
+		// Do not even bother with cluster execution, sysadmins set the flag
+		// themselves
+		String command = Util.getCommand(ExecProvider.Local, Muscle.class);
+		if (compbio.util.Util.isEmpty(command)) {
+			command = Util.getCommand(ExecProvider.Local, IUPred.class);
+		}
+		boolean isExec = true;
+		if (!compbio.util.Util.isEmpty(command)) {
+			File file = new File(command);
+			isExec = file.canExecute();
+		}
+
+		String workDir = PropertyHelperManager.getLocalPath() + "binaries/src";
+		String script = "setexecflag.sh";
+
+		// Run only one once if not on Windows
+		if (!SysPrefs.isWindows && !isExec) {
+
+			// verify script exist
+			File scriptFile = new File(workDir, script);
+			if (!scriptFile.exists()) {
+				log.debug("Setexecflag.sh script is NOT found in "
+						+ scriptFile.getAbsolutePath());
+				return;
+			} else {
+				scriptFile.setExecutable(true);
+				log.debug("Setexecflag.sh script is found");
+			}
+
+			try {
+				log.debug("Executable flag is NOT set for the binaries - attemping to set it");
+				ProcessBuilder pb = new ProcessBuilder(scriptFile.getAbsolutePath());
+				pb.directory(new File(workDir));
+				Process process = pb.start();
+				process.waitFor();
+				process.destroy();
+			} catch (IOException e) {
+				log.debug("Failed to execute set executable flag script due to IOException! Please run it manually!");
+				log.debug(e.getMessage(), e);
+			} catch (InterruptedException e) {
+				log.debug("Failed to execute set executable flag script due to Interruption! Please run it manually!");
+			}
+		} else {
+			log.debug("Executable flag is already set for the binaries.");
+		}
+	}
+}
-- 
1.7.10.2