import compbio.engine.conf.DirectoryManager;\r
import compbio.engine.conf.PropertyHelperManager;\r
import compbio.metadata.JobStatus;\r
+import compbio.metadata.LimitsManager;\r
import compbio.metadata.ResultNotAvailableException;\r
import compbio.util.FileUtil;\r
import compbio.util.PropertyHelper;\r
// Work directory could be null for cancelled or incomplete jobs, just\r
// ignore\r
if (!compbio.util.Util.isEmpty(workDirectory)) {\r
- writeFile(workDirectory, fileAndEventName, new Long(System\r
- .nanoTime()).toString(), false);\r
+ writeFile(workDirectory, fileAndEventName,\r
+ new Long(System.currentTimeMillis()).toString(), false);\r
}\r
}\r
\r
String content, boolean override) {\r
File file = null;\r
if (compbio.util.Util.isEmpty(workDirectory)) {\r
- log\r
- .debug("Calling compbio.engine.Util.writeFile() with not work directory."\r
- + " Skipping writing statistics!");\r
+ log.debug("Calling compbio.engine.Util.writeFile() with not work directory."\r
+ + " Skipping writing statistics!");\r
return;\r
}\r
assert !compbio.util.Util.isEmpty(content) : "Content expected!";\r
return sfile.createNewFile();\r
}\r
} catch (IOException e) {\r
- log.error("Could not record stat marker file " + fileType\r
- + " into the directory " + workDirectory + " ! "\r
- + e.getMessage(), e.getCause());\r
+ log.error(\r
+ "Could not record stat marker file " + fileType\r
+ + " into the directory " + workDirectory + " ! "\r
+ + e.getMessage(), e.getCause());\r
}\r
return false;\r
}\r
String absolute = relativePath;\r
if (!PathValidator.isAbsolutePath(relativePath)) {\r
absolute = PropertyHelperManager.getLocalPath() + relativePath;\r
- Util.log\r
- .trace("Changing local path in enviromental variable to absolute: FROM "\r
- + relativePath + " TO " + absolute);\r
+ Util.log.trace("Changing local path in enviromental variable to absolute: FROM "\r
+ + relativePath + " TO " + absolute);\r
}\r
return absolute;\r
}\r
} else {\r
bin = ph.getProperty("local." + execCommandName + ".bin");\r
}\r
+ // For executable Jar files the location of Java executable is not\r
+ // required for local execution. If it is not provided, JABAWS will\r
+ // attempt to use Java from JAVA_HOME env variable\r
+ if (isJavaLibrary(clazz)) {\r
+ if (compbio.util.Util.isEmpty(bin)) {\r
+ bin = getJava();\r
+ }\r
+ }\r
// If path to executable defined in the properties is not absolute,\r
// then make it so\r
// as setting working directory of ProcessBuilder will make it\r
// to find an executable otherwise\r
if (!compbio.util.Util.isEmpty(bin)\r
&& !PathValidator.isAbsolutePath(bin)) {\r
- bin = PropertyHelperManager.getLocalPath() + bin;\r
+ bin = bin.trim();\r
+ if (bin.equalsIgnoreCase("java")\r
+ || bin.equalsIgnoreCase("java.exe")) {\r
+ // do not make path absolute to the java executable if\r
+ // relative path is provided. Java executable is not a part\r
+ // of JABAWS distribution!\r
+ } else {\r
+ bin = PropertyHelperManager.getLocalPath() + bin;\r
+ }\r
}\r
} else {\r
bin = ph.getProperty("cluster." + execCommandName + ".bin");\r
}\r
+ // Could have done: Set executable flag if not set\r
+ // but - do not because in some cases more than one file must be made\r
+ // executable!\r
+ /*\r
+ * if (!compbio.util.Util.isEmpty(bin)) { File command = new File(bin);\r
+ * if (!command.canExecute()) { log.debug(\r
+ * "The command line binary is not executable! (just unpacked from war file? )"\r
+ * ); log.debug("Attempting to set executable flag for command: " +\r
+ * bin); command.setExecutable(true, false); } }\r
+ */\r
+ log.debug("Using executable: " + bin);\r
return bin; // File.separator\r
}\r
+ /**\r
+ * Returns true of executableName.jar.file property has some value in the\r
+ * Executable.properties file, false otherwise.\r
+ * \r
+ * @param clazz\r
+ * @return\r
+ */\r
+ public static boolean isJavaLibrary(Class<?> clazz) {\r
+ String execCommandName = clazz.getSimpleName().toLowerCase();\r
+ String java_lib = ph.getProperty(execCommandName + ".jar.file");\r
+ return !compbio.util.Util.isEmpty(java_lib);\r
+ }\r
+\r
+ /**\r
+ * Returns the absolute path to the Java executable from JAVA_HOME\r
+ * \r
+ * @return returns the absolute path to the Java executable from JAVA_HOME\r
+ */\r
+ public static String getJava() {\r
+ String javahome = System.getProperty("java.home");\r
+ if (compbio.util.Util.isEmpty(javahome)) {\r
+ javahome = System.getenv("JAVA_HOME");\r
+ }\r
+ if (compbio.util.Util.isEmpty(javahome)) {\r
+ log.warn("Cannot find Java in java.home system property "\r
+ + "or JAVA_HOME environment variable! ");\r
+ return null;\r
+ }\r
+ File jh = new File(javahome);\r
+ if (jh.exists() && jh.isDirectory()) {\r
+ String java = javahome + File.separator + "bin" + File.separator\r
+ + "java";\r
+ if (SysPrefs.isWindows) {\r
+ java += ".exe";\r
+ }\r
+ File jexe = new File(java);\r
+ if (jexe.exists() && jexe.isFile() && jexe.canExecute()) {\r
+ log.info("Using Java from: " + jexe.getAbsolutePath());\r
+ return jexe.getAbsolutePath();\r
+ } else {\r
+ log.warn("Cannot find java executable in the JAVA_HOME!");\r
+ }\r
+ } else {\r
+ log.warn("JAVA_HOME does not seems to point to a valid directory! Value: "\r
+ + javahome);\r
+ }\r
+ return null;\r
+ }\r
\r
public static ExecProvider getSupportedRuntimes(Class<?> clazz) {\r
boolean localRuntimeSupport = false;\r
if (!compbio.util.Util.isEmpty(localRuntime1)\r
|| !compbio.util.Util.isEmpty(localRuntime2)) {\r
localRuntimeSupport = true;\r
+ } else {\r
+ localRuntimeSupport = isJavaLibrary(clazz) && getJava() != null;\r
}\r
+\r
String clusterRuntime = ph.getProperty("cluster." + executableName\r
+ ".bin");\r
if (!compbio.util.Util.isEmpty(clusterRuntime)) {\r
throw new InvalidParameterException(\r
"Executable is not provided for any runtime environments");\r
}\r
-\r
public static ConfiguredExecutable<?> loadExecutable(String taskId)\r
throws ResultNotAvailableException {\r
String workDir = compbio.engine.Configurator.getWorkDirectory(taskId);\r
exec = ConfExecutable.newConfExecutable(rconf);\r
fileInStream.close();\r
} catch (FileNotFoundException e) {\r
- log.error("Could not find run configuration to load!"\r
- + e.getLocalizedMessage(), e.getCause());\r
+ log.error(\r
+ "Could not find run configuration to load!"\r
+ + e.getLocalizedMessage(), e.getCause());\r
throw new ResultNotAvailableException(\r
"Could not find run configuration to load!"\r
+ e.getMessage(), e.getCause());\r
} catch (IOException e) {\r
- log.error("IO Exception while reading run configuration file!"\r
- + e.getLocalizedMessage(), e.getCause());\r
+ log.error(\r
+ "IO Exception while reading run configuration file!"\r
+ + e.getLocalizedMessage(), e.getCause());\r
throw new ResultNotAvailableException(\r
- "Could not load run configuration!" + e.getMessage(), e\r
- .getCause());\r
+ "Could not load run configuration!" + e.getMessage(),\r
+ e.getCause());\r
} finally {\r
FileUtil.closeSilently(log, fileInStream);\r
}\r
return exec;\r
}\r
\r
+ /**\r
+ * For now just assume that all parameters which came in needs setting it\r
+ * will be a client responsibility to prepare RunnerConfig object then\r
+ * \r
+ * @param rconfig\r
+ * @return\r
+ * \r
+ * public static List<String> toOptionString(RunnerConfig<?>\r
+ * rconfig) { String option = ""; List<String> options = new\r
+ * ArrayList<String>(); for (Parameter<?> par :\r
+ * rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())\r
+ * { option = par.getOptionName(); } else { option =\r
+ * par.getOptionName() + "=" + par.getPossibleValues().get(0); } //\r
+ * separate options options.add(option); } return options; }\r
+ */\r
+\r
+ public static <T> LimitsManager<T> getLimits(Class<T> clazz) {\r
+ LimitsManager<T> limits = null;\r
+ try {\r
+ limits = ConfExecutable.getRunnerLimits(clazz);\r
+ } catch (FileNotFoundException e) {\r
+ Util.log.warn("No limits are found for " + clazz + " executable! "\r
+ + e.getLocalizedMessage(), e.getCause());\r
+ // its ok, limit may not be initialized\r
+ } catch (IOException e) {\r
+ Util.log.warn("IO exception while attempting to read limits for "\r
+ + clazz + " executable! " + e.getLocalizedMessage(),\r
+ e.getCause());\r
+ }\r
+ return limits;\r
+ }\r
+\r
}\r
git://source.jalview.org / jabaws.git / blobdiff