+++ /dev/null
-\r
-## CHANGE THIS (The root directory where to store all the log files) \r
-#logDir = .\r
-\r
-## Uncomment to enable JWS2 activity logging to standard out (to the console if available)\r
-## for possible log levels please refer to Log4j documentation http://logging.apache.org/log4j/1.2/manual.html \r
-## Valid log levels are:\r
-## TRACE - log everything from below including very detailed messages (useful for debugging only)\r
-## DEBUG - log everything from below including some minor events (useful for debugging only)\r
-## INFO - log everything from below including some information messages\r
-## WARN - log error and warnings\r
-## ERROR - log errors and fatal events only \r
-## FATAL - log fatal events only\r
-\r
-## Uncomment this if you would like the system to log messages into stdout\r
-#log4j.rootLogger=TRACE, rootfile\r
-#log4j.appender.rootfile=org.apache.log4j.RollingFileAppender\r
-#log4j.appender.rootfile.File=JABAWSLogFilename.log\r
-#log4j.appender.rootfile.Target=System.out\r
-#log4j.appender.rootfile.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.rootfile.layout.ConversionPattern=%t %d %m%n\r
-\r
-## Uncomment to enable JWS2 activity logging to the file\r
-#log4j.logger.compbio=TRACE, ACTIVITY\r
-#log4j.appender.ACTIVITY=org.apache.log4j.RollingFileAppender\r
-################log4j.appender.ACTIVITY.File=${logDir}/activity.log\r
-#log4j.appender.ACTIVITY.File=${catalina.base}/logs/JABAWSLogFilename.log\r
-#log4j.appender.ACTIVITY.MaxFileSize=10MB\r
-#log4j.appender.ACTIVITY.MaxBackupIndex=10000\r
-#log4j.appender.ACTIVITY.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.ACTIVITY.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p %3x - %m%n\r
-\r
-## Uncomment for separate local engine execution log (debugging only)\r
-#log4j.logger.compbio.engine.local.LocalExecutorService=INFO, C\r
-#log4j.appender.C=org.apache.log4j.FileAppender\r
-#log4j.appender.C.File=LocalExecutorService.log\r
-#log4j.appender.C.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.C.layout.ConversionPattern=%m%n\r
-\r
-##################################################################################################################################\r
-# log4j.properties from runner/\r
-\r
-#log4j.appender.stdout=org.apache.log4j.ConsoleAppender\r
-#log4j.appender.stdout.Target=System.out\r
-#log4j.appender.stdout.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.stdout.layout.ConversionPattern=%m%n\r
-#log4j.rootLogger=info, stdout\r
-\r
-log4j.rootLogger=TRACE, rootfile\r
-log4j.appender.rootfile=org.apache.log4j.FileAppender\r
-log4j.appender.rootfile.File=${catalina.base}/logs/JABAWSLogFilename.log1\r
-log4j.appender.rootfile.Target=System.out\r
-log4j.appender.rootfile.layout=org.apache.log4j.PatternLayout\r
-log4j.appender.rootfile.layout.ConversionPattern=%t %d %m%n\r
-\r
-# %d{ABSOLUTE} %5p %c{1}:%L -\r
-log4j.logger.compbio=TRACE, B\r
-log4j.appender.B=org.apache.log4j.FileAppender\r
-#log4j.appender.B.File=engine.log\r
-log4j.appender.B.File=${catalina.base}/logs/engine.log\r
-log4j.appender.B.layout=org.apache.log4j.PatternLayout\r
-log4j.appender.B.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - \r
-\r
-# %d{ABSOLUTE} %5p %c{1}:%L -\r
-#log4j.logger.compbio.engine.local.LocalExecutorService=INFO, C\r
-#log4j.appender.C=org.apache.log4j.FileAppender\r
-#log4j.appender.C.File=LocalExecutorService.log\r
-#log4j.appender.C.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.C.layout.ConversionPattern=%m%n\r
-# %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - \r
-\r
-#log4j.logger.RunnerLogger=ERROR, D\r
-#log4j.appender.D=org.apache.log4j.ConsoleAppender \r
-#log4j.appender.D.layout=org.apache.log4j.PatternLayout\r
-#log4j.appender.D.layout.ConversionPattern=%r [%t] %p %c %x - %m%n\r
-/* Copyright (c) 2011 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-package compbio.stat.collector;\r
-\r
-import java.sql.Timestamp;\r
-import java.text.DateFormat;\r
-import java.text.SimpleDateFormat;\r
-import java.util.Comparator;\r
-import java.util.Date;\r
-import java.util.Locale;\r
-\r
-import compbio.engine.client.ConfExecutable;\r
-import compbio.util.Util;\r
-import compbio.ws.client.Services;\r
-\r
-public class JobStat {\r
-\r
- static final Comparator<JobStat> RUNTIME = new Comparator<JobStat>() {\r
- @Override\r
- public int compare(JobStat o1, JobStat o2) {\r
- return new Integer(o2.getRuntime()).compareTo(o1.getRuntime());\r
- }\r
- };\r
-\r
- static final Comparator<JobStat> STARTTIME = new Comparator<JobStat>() {\r
- @Override\r
- public int compare(JobStat o1, JobStat o2) {\r
- return new Long(o1.start).compareTo(o2.start);\r
- }\r
- };\r
-\r
- static final Comparator<JobStat> RESULTSIZE = new Comparator<JobStat>() {\r
- @Override\r
- public int compare(JobStat o1, JobStat o2) {\r
- return new Long(o2.resultSize).compareTo(o1.resultSize);\r
- }\r
- };\r
-\r
- private static DateFormat DATE_TIME = SimpleDateFormat.getDateTimeInstance(\r
- DateFormat.DEFAULT, DateFormat.DEFAULT, Locale.UK);\r
-\r
- Services webService;\r
- String clusterJobId;\r
- String jobname;\r
- long start;\r
- long finish;\r
- long inputSize;\r
- long resultSize;\r
- boolean isCollected;\r
- boolean isCancelled;\r
-\r
- private JobStat(Services webService, String clusterJobId, String jobname,\r
- long start, long finish, long inputSize, long resultSize,\r
- boolean isCancelled, boolean isCollected) {\r
- super();\r
- this.webService = webService;\r
- this.clusterJobId = clusterJobId;\r
- this.jobname = jobname;\r
- this.start = start;\r
- this.finish = finish;\r
- this.inputSize = inputSize;\r
- this.resultSize = resultSize;\r
- this.isCancelled = isCancelled;\r
- this.isCollected = isCollected;\r
- validate();\r
- }\r
-\r
- static JobStat newInstance(Services webService, String clusterJobId,\r
- String jobname, long start, long finish, long inputSize,\r
- long resultSize, boolean isCancelled, boolean isCollected) {\r
- return new JobStat(webService, clusterJobId, jobname, start, finish,\r
- inputSize, resultSize, isCancelled, isCollected);\r
- }\r
-\r
- static JobStat newInstance(Services webService, String clusterJobId,\r
- String jobname, Timestamp start, Timestamp finish, long inputSize,\r
- long resultSize, boolean isCancelled, boolean isCollected) {\r
- long startm = ExecutionStatCollector.UNDEFINED;\r
- long stopm = ExecutionStatCollector.UNDEFINED;\r
- if (start != null) {\r
- startm = start.getTime();\r
- }\r
- if (finish != null) {\r
- stopm = finish.getTime();\r
- }\r
- return new JobStat(webService, clusterJobId, jobname, startm, stopm,\r
- inputSize, resultSize, isCancelled, isCollected);\r
- }\r
-\r
- void validate() {\r
- if (webService == null) {\r
- throw new AssertionError("webService must be defined!:\n " + this);\r
- }\r
- if (Util.isEmpty(jobname)) {\r
- throw new AssertionError("jobname must be defined!:\n" + this);\r
- }\r
- }\r
-\r
- private JobStat(String jobId) {\r
- assert !Util.isEmpty(jobname);\r
- this.jobname = jobId;\r
- }\r
-\r
- static JobStat newIncompleteStat(String jobname) {\r
- return new JobStat(jobname);\r
- }\r
-\r
- public boolean isClusterJob() {\r
- return jobname.startsWith(ConfExecutable.CLUSTER_TASK_ID_PREFIX);\r
- }\r
-\r
- @Override\r
- public int hashCode() {\r
- final int prime = 31;\r
- int result = 1;\r
- result = prime * result + ((jobname == null) ? 0 : jobname.hashCode());\r
- return result;\r
- }\r
-\r
- @Override\r
- public boolean equals(Object obj) {\r
- if (this == obj)\r
- return true;\r
- if (obj == null)\r
- return false;\r
- if (getClass() != obj.getClass())\r
- return false;\r
- JobStat other = (JobStat) obj;\r
- if (jobname == null) {\r
- if (other.jobname != null)\r
- return false;\r
- } else if (!jobname.equals(other.jobname))\r
- return false;\r
- return true;\r
- }\r
-\r
- public int getRuntime() {\r
- if (start != ExecutionStatCollector.UNDEFINED\r
- && finish != ExecutionStatCollector.UNDEFINED) {\r
- return (int) (finish - start) / 1000;\r
- }\r
- return ExecutionStatCollector.UNDEFINED;\r
- }\r
-\r
- @Override\r
- public String toString() {\r
- return getJobReport();\r
- }\r
-\r
- String getJobReport() {\r
- String report = "WS: " + webService + "\n";\r
- report += "JOB: " + jobname + "\n";\r
- if (start != ExecutionStatCollector.UNDEFINED) {\r
- report += "Started " + new Date(start) + "\n";\r
- }\r
- if (finish != ExecutionStatCollector.UNDEFINED) {\r
- report += "Finished " + new Date(finish) + "\n";\r
- }\r
- if (start != ExecutionStatCollector.UNDEFINED\r
- && finish != ExecutionStatCollector.UNDEFINED) {\r
- report += "Runtime " + getRuntime() + "\n";\r
- }\r
- report += "Input size " + inputSize + "\n";\r
- report += "Result size " + resultSize + "\n";\r
- report += "ClusterJobID " + clusterJobId + "\n";\r
- report += "Collected? " + isCollected + "\n";\r
- report += "Cancelled? " + isCancelled + "\n";\r
- return report;\r
- }\r
-\r
- /**\r
- * Header Job Started Finished Runtime Input Result\r
- */\r
- String getJobReportTabulated() {\r
- String report = webService + "\t";\r
- report += jobname + "\t";\r
- if (start != ExecutionStatCollector.UNDEFINED) {\r
- report += ExecutionStatCollector.DF.format(new Date(start)) + "\t";\r
- } else {\r
- report += ExecutionStatCollector.UNDEFINED + "\t";\r
- }\r
- if (finish != ExecutionStatCollector.UNDEFINED) {\r
- report += ExecutionStatCollector.DF.format(new Date(finish)) + "\t";\r
- } else {\r
- report += ExecutionStatCollector.UNDEFINED + "\t";\r
- }\r
- if (start != ExecutionStatCollector.UNDEFINED\r
- && finish != ExecutionStatCollector.UNDEFINED) {\r
- report += getRuntime() + "\t";\r
- } else {\r
- report += ExecutionStatCollector.UNDEFINED + "\t";\r
- }\r
- report += inputSize + "\t";\r
- report += resultSize + "\t";\r
- report += clusterJobId + "\t";\r
- report += isCollected + "\t";\r
- report += isCancelled + "\t";\r
- return report;\r
- }\r
-\r
- public Services getWebService() {\r
- return webService;\r
- }\r
-\r
- public String getClusterJobId() {\r
- return clusterJobId;\r
- }\r
-\r
- public String getJobname() {\r
- return jobname;\r
- }\r
-\r
- public String getEscJobname() {\r
- String[] parts = jobname.split("#");\r
- return parts[0] + "%23" + parts[1];\r
- }\r
-\r
- public String getStart() {\r
- if (start != ExecutionStatCollector.UNDEFINED) {\r
- return DATE_TIME.format(new Date(start));\r
- }\r
- return "?";\r
- }\r
-\r
- public String getFinish() {\r
- if (finish != ExecutionStatCollector.UNDEFINED) {\r
- return DATE_TIME.format(new Date(finish));\r
- }\r
- return "?";\r
- }\r
-\r
- public long getInputSize() {\r
- if (inputSize != ExecutionStatCollector.UNDEFINED) {\r
- return inputSize;\r
- }\r
- return 0;\r
- }\r
-\r
- public long getResultSize() {\r
- if (resultSize > 0) {\r
- return resultSize;\r
- }\r
- return 0;\r
- }\r
-\r
- public boolean hasResult() {\r
- return resultSize > 0;\r
- }\r
-\r
- public boolean hasStarted() {\r
- return start != ExecutionStatCollector.UNDEFINED;\r
- }\r
-\r
- public boolean getIsCollected() {\r
- return isCollected;\r
- }\r
-\r
- public boolean getIsCancelled() {\r
- return isCancelled;\r
- }\r
-\r
- public boolean getIsFinished() {\r
- return finish != ExecutionStatCollector.UNDEFINED;\r
- }\r
-\r
-}
\ No newline at end of file
+/* Copyright (c) 2011 Peter Troshin
+ *
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
+ *
+ * This library is free software; you can redistribute it and/or modify it under the terms of the
+ * Apache License version 2 as published by the Apache Software Foundation
+ *
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
+ * License for more details.
+ *
+ * A copy of the license is in apache_license.txt. It is also available here:
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ * Any republication or derived work distributed in source code form
+ * must include this copyright and license notice.
+ */
+package compbio.stat.collector;
+
+import java.sql.Timestamp;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Comparator;
+import java.util.Date;
+import java.util.Locale;
+
+import compbio.engine.client.ConfExecutable;
+import compbio.util.Util;
+import compbio.ws.client.Services;
+
+public class JobStat {
+
+ static final Comparator<JobStat> RUNTIME = new Comparator<JobStat>() {
+ @Override
+ public int compare(JobStat o1, JobStat o2) {
+ return new Integer(o2.getRuntime()).compareTo(o1.getRuntime());
+ }
+ };
+
+ static final Comparator<JobStat> STARTTIME = new Comparator<JobStat>() {
+ @Override
+ public int compare(JobStat o1, JobStat o2) {
+ return new Long(o1.start).compareTo(o2.start);
+ }
+ };
+
+ static final Comparator<JobStat> RESULTSIZE = new Comparator<JobStat>() {
+ @Override
+ public int compare(JobStat o1, JobStat o2) {
+ return new Long(o2.resultSize).compareTo(o1.resultSize);
+ }
+ };
+
+ private static DateFormat DATE_TIME = SimpleDateFormat.getDateTimeInstance(
+ DateFormat.DEFAULT, DateFormat.DEFAULT, Locale.UK);
+
+ Services webService;
+ String clusterJobId;
+ String jobname;
+ long start;
+ long finish;
+ long inputSize;
+ long resultSize;
+ boolean isCollected;
+ boolean isCancelled;
+
+ private JobStat(Services webService, String clusterJobId, String jobname,
+ long start, long finish, long inputSize, long resultSize,
+ boolean isCancelled, boolean isCollected) {
+ super();
+ this.webService = webService;
+ this.clusterJobId = clusterJobId;
+ this.jobname = jobname;
+ this.start = start;
+ this.finish = finish;
+ this.inputSize = inputSize;
+ this.resultSize = resultSize;
+ this.isCancelled = isCancelled;
+ this.isCollected = isCollected;
+ validate();
+ }
+
+ public static JobStat newInstance(Services webService, String clusterJobId,
+ String jobname, long start, long finish, long inputSize,
+ long resultSize, boolean isCancelled, boolean isCollected) {
+ return new JobStat(webService, clusterJobId, jobname, start, finish,
+ inputSize, resultSize, isCancelled, isCollected);
+ }
+
+ public static JobStat newInstance(Services webService, String clusterJobId,
+ String jobname, Timestamp start, Timestamp finish, long inputSize,
+ long resultSize, boolean isCancelled, boolean isCollected) {
+ long startm = ExecutionStatCollector.UNDEFINED;
+ long stopm = ExecutionStatCollector.UNDEFINED;
+ if (start != null) {
+ startm = start.getTime();
+ }
+ if (finish != null) {
+ stopm = finish.getTime();
+ }
+ return new JobStat(webService, clusterJobId, jobname, startm, stopm,
+ inputSize, resultSize, isCancelled, isCollected);
+ }
+
+ void validate() {
+ if (webService == null) {
+ throw new AssertionError("webService must be defined!:\n " + this);
+ }
+ if (Util.isEmpty(jobname)) {
+ throw new AssertionError("jobname must be defined!:\n" + this);
+ }
+ }
+
+ private JobStat(String jobId) {
+ assert !Util.isEmpty(jobname);
+ this.jobname = jobId;
+ }
+
+ public static JobStat newIncompleteStat(String jobname) {
+ return new JobStat(jobname);
+ }
+
+ public boolean isClusterJob() {
+ return jobname.startsWith(ConfExecutable.CLUSTER_TASK_ID_PREFIX);
+ }
+
+ @Override
+ public int hashCode() {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + ((jobname == null) ? 0 : jobname.hashCode());
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ JobStat other = (JobStat) obj;
+ if (jobname == null) {
+ if (other.jobname != null)
+ return false;
+ } else if (!jobname.equals(other.jobname))
+ return false;
+ return true;
+ }
+
+ public int getRuntime() {
+ if (start != ExecutionStatCollector.UNDEFINED && finish != ExecutionStatCollector.UNDEFINED) {
+ return (int) (finish - start) / 1000;
+ }
+ return ExecutionStatCollector.UNDEFINED;
+ }
+
+ @Override
+ public String toString() {
+ return getJobReport();
+ }
+
+ String getJobReport() {
+ String report = "WS: " + webService + "\n";
+ report += "JOB: " + jobname + "\n";
+ if (start != ExecutionStatCollector.UNDEFINED) {
+ report += "Started " + new Date(start) + "\n";
+ }
+ if (finish != ExecutionStatCollector.UNDEFINED) {
+ report += "Finished " + new Date(finish) + "\n";
+ }
+ if (start != ExecutionStatCollector.UNDEFINED && finish != ExecutionStatCollector.UNDEFINED) {
+ report += "Runtime " + getRuntime() + "\n";
+ }
+ report += "Input size " + inputSize + "\n";
+ report += "Result size " + resultSize + "\n";
+ report += "ClusterJobID " + clusterJobId + "\n";
+ report += "Collected? " + isCollected + "\n";
+ report += "Cancelled? " + isCancelled + "\n";
+ return report;
+ }
+
+ /**
+ * Header Job Started Finished Runtime Input Result
+ */
+ String getJobReportTabulated() {
+ String report = webService + "\t";
+ report += jobname + "\t";
+ if (start != ExecutionStatCollector.UNDEFINED) {
+ report += ExecutionStatCollector.DF.format(new Date(start)) + "\t";
+ } else {
+ report += ExecutionStatCollector.UNDEFINED + "\t";
+ }
+ if (finish != ExecutionStatCollector.UNDEFINED) {
+ report += ExecutionStatCollector.DF.format(new Date(finish)) + "\t";
+ } else {
+ report += ExecutionStatCollector.UNDEFINED + "\t";
+ }
+ if (start != ExecutionStatCollector.UNDEFINED && finish != ExecutionStatCollector.UNDEFINED) {
+ report += getRuntime() + "\t";
+ } else {
+ report += ExecutionStatCollector.UNDEFINED + "\t";
+ }
+ report += inputSize + "\t";
+ report += resultSize + "\t";
+ report += clusterJobId + "\t";
+ report += isCollected + "\t";
+ report += isCancelled + "\t";
+ return report;
+ }
+
+ public Services getWebService() {
+ return webService;
+ }
+
+ public String getClusterJobId() {
+ return clusterJobId;
+ }
+
+ public String getJobname() {
+ return jobname;
+ }
+
+ public String getEscJobname() {
+ String[] parts = jobname.split("#");
+ return parts[0] + "%23" + parts[1];
+ }
+
+ public String getStart() {
+ if (start != ExecutionStatCollector.UNDEFINED) {
+ return DATE_TIME.format(new Date(start));
+ }
+ return "?";
+ }
+
+ public long getNumericalStart() {
+ return start;
+ }
+
+ public long getNumericalFinish() {
+ return finish;
+ }
+
+ public String getFinish() {
+ if (finish != ExecutionStatCollector.UNDEFINED) {
+ return DATE_TIME.format(new Date(finish));
+ }
+ return "?";
+ }
+
+ public long getInputSize() {
+ if (inputSize != ExecutionStatCollector.UNDEFINED) {
+ return inputSize;
+ }
+ return 0;
+ }
+
+ public long getResultSize() {
+ if (resultSize > 0) {
+ return resultSize;
+ }
+ return 0;
+ }
+
+ public boolean hasResult() {
+ return resultSize > 0;
+ }
+
+ public boolean hasStarted() {
+ return start != ExecutionStatCollector.UNDEFINED;
+ }
+
+ public boolean getIsCollected() {
+ return isCollected;
+ }
+
+ public boolean getIsCancelled() {
+ return isCancelled;
+ }
+
+ public boolean getIsFinished() {
+ return finish != ExecutionStatCollector.UNDEFINED;
+ }
+}
git://source.jalview.org / jabaws.git / commitdiff