// 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
- .currentTimeMillis()).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
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
* par.getOptionName() + "=" + par.getPossibleValues().get(0); } //\r
* separate options options.add(option); } return options; }\r
*/\r
- \r
- public static <T> LimitsManager<T> getLimits(Class<Executable<T>> clazz) {\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(\r
- "No limits are found for " + clazz + " executable! "\r
- + e.getLocalizedMessage(), e.getCause());\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