--- /dev/null
+package compbio.engine;\r
+\r
+import java.io.File;\r
+import java.io.FileFilter;\r
+import java.io.IOException;\r
+import java.util.Date;\r
+import java.util.HashMap;\r
+import java.util.Map;\r
+\r
+import org.apache.log4j.Level;\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.engine.client.ConfExecutable;\r
+import compbio.engine.conf.PropertyHelperManager;\r
+import compbio.metadata.JobStatus;\r
+import compbio.util.FileUtil;\r
+import compbio.util.PropertyHelper;\r
+\r
+/**\r
+ * Number of runs of each WS = number of folders with name\r
+ * \r
+ * Number of successful runs = all runs with no result file\r
+ * \r
+ * Per period of time = limit per file creating time Runtime (avg/max) =\r
+ * \r
+ * started time - finished time Task & result size = result.size\r
+ * \r
+ * Abandoned runs - not collected runs\r
+ * \r
+ * Cancelled runs - cancelled\r
+ * \r
+ * Cluster vs local runs\r
+ * \r
+ * Reasons for failure = look in the err out?\r
+ * \r
+ * \r
+ * Metadata required:\r
+ * \r
+ * work directory for local and cluster tasks = from Helper or cmd parameter. WS\r
+ * names - enumeration. Status file names and content.\r
+ * \r
+ * @author pvtroshin\r
+ * \r
+ */\r
+public class ExecutionStatCollector {\r
+\r
+ private static final Logger log = Logger\r
+ .getLogger(ExecutionStatCollector.class);\r
+\r
+ static PropertyHelper ph = PropertyHelperManager.getPropertyHelper();\r
+\r
+ static String getClusterJobDir() {\r
+ String clusterdir = ph.getProperty("cluster.tmp.directory");\r
+ if (clusterdir != null) {\r
+ clusterdir.trim();\r
+ }\r
+ return clusterdir;\r
+ }\r
+\r
+ static String getLocalJobDir() {\r
+ String locdir = ph.getProperty("local.tmp.directory");\r
+ if (locdir != null) {\r
+ locdir.trim();\r
+ }\r
+ return locdir;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param args\r
+ */\r
+ public static void main(String[] args) {\r
+\r
+ String workDir = PropertyHelperManager.getLocalPath()\r
+ + getLocalJobDir().trim();\r
+ System.out.println(workDir);\r
+ File[] files = FileUtil.getFiles("H:/www-jws2/job_dir/jobsout",\r
+ directories);\r
+ for (File file : files) {\r
+ JobDirectory jd = new JobDirectory(file);\r
+ System.out.println(jd.getJobReport());\r
+ }\r
+ }\r
+\r
+ static FileFilter directories = new FileFilter() {\r
+ @Override\r
+ public boolean accept(File pathname) {\r
+ return pathname.isDirectory();\r
+ }\r
+ };\r
+\r
+ static class JobDirectory {\r
+ static final int UNDEFINED = -1;\r
+\r
+ File jobdir;\r
+ Map<String, File> files = new HashMap<String, File>();\r
+\r
+ public JobDirectory(File directory) {\r
+ this.jobdir = directory;\r
+ for (File f : jobdir.listFiles()) {\r
+ files.put(f.getName(), f);\r
+ }\r
+ }\r
+\r
+ public boolean hasStatus(JobStatus status) {\r
+ return files.containsKey(status.toString());\r
+ }\r
+\r
+ long getStartTime() {\r
+ long starttime = UNDEFINED;\r
+ try {\r
+ File startfile = files.get(JobStatus.STARTED.toString());\r
+ if (startfile == null) {\r
+ startfile = files.get(JobStatus.SUBMITTED.toString());\r
+ }\r
+ if (startfile != null) {\r
+ String start = FileUtil.readFileToString(startfile);\r
+ starttime = Long.parseLong(start.trim());\r
+ }\r
+ } catch (IOException e) {\r
+ log.log(Level.WARN,\r
+ "Cannot parse start time: " + e.getMessage(), e);\r
+ } catch (NumberFormatException e) {\r
+ log.log(Level.WARN,\r
+ "Cannot parse start time: " + e.getMessage(), e);\r
+ }\r
+ return starttime;\r
+ }\r
+ long getFinishedTime() {\r
+ long ftime = UNDEFINED;\r
+ try {\r
+ File finished = files.get(JobStatus.FINISHED.toString());\r
+ if (finished != null) {\r
+ String start = FileUtil.readFileToString(finished);\r
+ ftime = Long.parseLong(start.trim());\r
+ // System.out.println("f " + ftime);\r
+ }\r
+ } catch (IOException e) {\r
+ log.log(Level.WARN,\r
+ "Cannot parse finished time: " + e.getMessage(), e);\r
+ } catch (NumberFormatException e) {\r
+ log.log(Level.WARN,\r
+ "Cannot parse finished time: " + e.getMessage(), e);\r
+ }\r
+ return ftime;\r
+ }\r
+\r
+ public int getRuntime() {\r
+ return (int) (getFinishedTime() - getStartTime());\r
+ }\r
+\r
+ String getWSName() {\r
+ String name = jobdir.getName().split("#")[0];\r
+ if (name.startsWith(ConfExecutable.CLUSTER_TASK_ID_PREFIX)) {\r
+ assert ConfExecutable.CLUSTER_TASK_ID_PREFIX.length() == 1;\r
+ name = name.substring(1);\r
+ }\r
+ return name;\r
+ }\r
+\r
+ // Mafft, Muscle, Tcoffee, Clustal task:fasta.in result:fasta.out\r
+ // Probcons task:fasta.in result:alignment.out\r
+ /*\r
+ * TODO replace with Universal names for WS!\r
+ */\r
+ long getResultSize() {\r
+ String name = getWSName();\r
+ File f = null;\r
+ if (name.equalsIgnoreCase("Probcons")) {\r
+ f = files.get("alignment.out");\r
+ }\r
+ f = files.get("fasta.out");\r
+ if (f != null) {\r
+ return f.length();\r
+ }\r
+ return UNDEFINED;\r
+ }\r
+\r
+ long getInputSize() {\r
+ File input = files.get("fasta.in");\r
+ if (input != null) {\r
+ return input.length();\r
+ }\r
+ return UNDEFINED;\r
+ }\r
+\r
+ String getJobReport() {\r
+ String report = "JOB: " + jobdir.getName() + "\n";\r
+ if (getStartTime() != UNDEFINED) {\r
+ report += "Started " + new Date(getStartTime()) + "\n";\r
+ }\r
+ if (getFinishedTime() != UNDEFINED) {\r
+ report += "Finished " + new Date(getFinishedTime()) + "\n";\r
+ }\r
+ if (getStartTime() != UNDEFINED && getFinishedTime() != UNDEFINED) {\r
+ report += "Runtime " + getRuntime() + "\n";\r
+ }\r
+ report += "Input size " + getInputSize() + "\n";\r
+ report += "Result size " + getResultSize() + "\n";\r
+ return report;\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jabaws.git / commitdiff