webservices/compbio/ws/server/SetExecutableFlag.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.io.File;\r
   4 import java.io.IOException;\r
   5 \r
   6 import javax.servlet.ServletContextEvent;\r
   7 import javax.servlet.ServletContextListener;\r
   8 \r
   9 import org.apache.log4j.Logger;\r
  10 \r
  11 import compbio.engine.client.Executable.ExecProvider;\r
  12 import compbio.engine.client.Util;\r
  13 import compbio.engine.conf.PropertyHelperManager;\r
  14 import compbio.runner.disorder.IUPred;\r
  15 import compbio.runner.msa.Muscle;\r
  16 import compbio.util.SysPrefs;\r
  17 \r
  18 /**\r
  19  * Run setexecflag.sh script if executable flag is not set\r
  20  * \r
  21  * @author pvtroshin\r
  22  * \r
  23  */\r
  24 public class SetExecutableFlag implements ServletContextListener {\r
  25 \r
  26         private final Logger log = Logger.getLogger(SetExecutableFlag.class);\r
  27 \r
  28         @Override\r
  29         public void contextDestroyed(ServletContextEvent arg0) {\r
  30                 // do nothing\r
  31         }\r
  32 \r
  33         /**\r
  34          * This listener is designed to run only once when the web application is\r
  35          * deployed to set executable flag for binaries.\r
  36          * \r
  37          * @param arg0\r
  38          *            - ignored\r
  39          */\r
  40         @Override\r
  41         public void contextInitialized(ServletContextEvent arg0) {\r
  42                 // Assume at least one of these is configured\r
  43                 // Do not even bother with cluster execution, sysadmins set the flag\r
  44                 // themselves\r
  45                 String command = Util.getCommand(ExecProvider.Local, Muscle.class);\r
  46                 if (compbio.util.Util.isEmpty(command)) {\r
  47                         command = Util.getCommand(ExecProvider.Local, IUPred.class);\r
  48                 }\r
  49                 boolean isExec = true;\r
  50                 if (!compbio.util.Util.isEmpty(command)) {\r
  51                         File file = new File(command);\r
  52                         isExec = file.canExecute();\r
  53                 }\r
  54 \r
  55                 String workDir = PropertyHelperManager.getLocalPath() + "binaries/src";\r
  56                 String script = "setexecflag.sh";\r
  57 \r
  58                 // Run only one once if not on Windows\r
  59                 if (!SysPrefs.isWindows && !isExec) {\r
  60 \r
  61                         // verify script exist\r
  62                         File scriptFile = new File(workDir, script);\r
  63                         if (!scriptFile.exists()) {\r
  64                                 log.debug("Setexecflag.sh script is NOT found in "\r
  65                                                 + scriptFile.getAbsolutePath());\r
  66                                 return;\r
  67                         } else {\r
  68                                 scriptFile.setExecutable(true);\r
  69                                 log.debug("Setexecflag.sh script is found");\r
  70                         }\r
  71 \r
  72                         try {\r
  73                                 log.debug("Executable flag is NOT set for the binaries - attemping to set it");\r
  74                                 ProcessBuilder pb = new ProcessBuilder(scriptFile.getAbsolutePath());\r
  75                                 pb.directory(new File(workDir));\r
  76                                 Process process = pb.start();\r
  77                                 process.waitFor();\r
  78                                 process.destroy();\r
  79                         } catch (IOException e) {\r
  80                                 log.debug("Failed to execute set executable flag script due to IOException! Please run it manually!");\r
  81                                 log.debug(e.getMessage(), e);\r
  82                         } catch (InterruptedException e) {\r
  83                                 log.debug("Failed to execute set executable flag script due to Interruption! Please run it manually!");\r
  84                         }\r
  85                 } else {\r
  86                         log.debug("Executable flag is already set for the binaries.");\r
  87                 }\r
  88         }\r
  89 }\r