From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Tue, 17 Jun 2014 06:57:43 +0000 (+0100)
Subject: New code update
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4825c5456a465ac3e13d0131f8e87f584b9871fa;p=jabaws.git

New code update
---

diff --git a/build.xml b/build.xml
index 6c7b389..fe7b271 100644
--- a/build.xml
+++ b/build.xml
@@ -83,7 +83,10 @@
 		<!-- Engines -->
 		<include name="compbio/engine/**"/>
 		<!-- Runners -->
+		<include name="compbio/runner/**"/>
+		<!-- Runners -->
 		<include name="compbio/stat/collector/**"/>
+		<include name="compbio/ws/client/**"/>
 		<!-- Logging configuration -->
 	</fileset>
 
@@ -343,14 +346,17 @@
 	<target name="stat-updater" depends="compile" description="Prepare executable jar for stat updater">
 		<echo>Jar file: StatUpdater jar</echo>
 		<delete file="${basedir}/${stat-updater}"></delete>
+		<copy file="${basedir}/log/log4j.properties.updater" tofile="${basedir}/log4j.properties"/>
 		<jar jarfile="${basedir}/${stat-updater}">
+			<fileset dir="${basedir}">
+				<include name="log4j.properties"/>
+			</fileset>
 			<fileset refid="statupdater"/>
 			<zipgroupfileset excludes="META-INF/*" dir="" includes="WEB-INF/lib/log4j-1.2.15.jar" />
 			<zipgroupfileset excludes="META-INF/*" dir="" includes="lib/jcommander-1.30.jar" />
 			<zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 				<include name="${compbio-util}"/>
-			</zipgroupfileset>
-			<manifest>
+			</zipgroupfileset>			<manifest>
 				<attribute name="Built-By" value="${author}" />
 				<attribute name="Main-Class" value="compbio.stat.collector.ExecutionStatUpdater" />
 				<attribute name="Class-Path" value="." />
@@ -359,6 +365,7 @@
 				<attribute name="Implementation-URL" value="${project.url}" />
 			</manifest>
 		</jar>
+		<delete file="${basedir}/log4j.properties"/>
 	</target>
 	
 	<target name="full-jabaws-client-jar" depends="compile" description="Pack datamodel, engine and runners">
diff --git a/log/log4j.properties.updater b/log/log4j.properties.updater
new file mode 100644
index 0000000..e6f4a06
--- /dev/null
+++ b/log/log4j.properties.updater
@@ -0,0 +1,20 @@
+
+## CHANGE THIS (The root directory where to store all the log files)  
+#logDir = .
+
+## Uncomment to enable JWS2 activity logging to standard out (to the console if available)
+## for possible log levels please refer to Log4j documentation http://logging.apache.org/log4j/1.2/manual.html 
+## Valid log levels are:
+## TRACE - log everything from below including very detailed messages (useful for debugging only)
+## DEBUG - log everything from below including some minor events (useful for debugging only)
+## INFO - log everything from below including some information messages
+## WARN - log error and warnings
+## ERROR - log errors and fatal events only 
+## FATAL - log fatal events only
+
+##################################################################################################################################
+log4j.rootLogger=DEBUG
+log4j.appender.R=org.apache.log4j.FileAppender
+log4j.appender.R.File=StatDBupdater.log
+log4j.appender.R.layout=org.apache.log4j.PatternLayout
+log4j.appender.R.layout.ConversionPattern=%m%n %d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - 
diff --git a/webservices/compbio/stat/collector/ExecutionStatUpdater.java b/webservices/compbio/stat/collector/ExecutionStatUpdater.java
index f26ecc3..a5d89d1 100644
--- a/webservices/compbio/stat/collector/ExecutionStatUpdater.java
+++ b/webservices/compbio/stat/collector/ExecutionStatUpdater.java
@@ -139,9 +139,9 @@ public class ExecutionStatUpdater {
 		return new StatProcessor(stats);
 	}
 
-	void writeStatToDB() throws SQLException {
+	void writeStatToDB(String dbname) throws SQLException {
 		Set<JobStat> rjobs = new HashSet<JobStat>(stats);
-		StatDB statdb = new StatDB();
+		StatDB statdb = new StatDB(dbname);
 		log.debug("Removing records that has already been recorded");
 		statdb.removeRecordedJobs(rjobs);
 		log.debug("New records left: " + rjobs.size());
@@ -155,18 +155,29 @@ public class ExecutionStatUpdater {
 	public static void main(String[] args) throws IOException, SQLException, ParseException {
 		mainJCommander jct = new mainJCommander();
 		new JCommander(jct, args);
-		String WorkingDir = jct.workingdir;
-		String dbname = jct.dbname;
-		Date ST = shortDF.parse(jct.starttime);
-		Date ET = shortDF.parse(jct.endtime);
-		long StartTime = 0;
-		if (null != ST) {
-			StartTime = ST.getTime();
-		}
+		String WorkingDir = "jobsout";
+		String DBname = "ExecutionStatistic";
+
+		long StartTime = 0L;
 		Date currDate = new Date();
 		long EndTime = currDate.getTime();
-		if (null != ET) {
-			EndTime = ET.getTime();
+		if (null != jct.starttime) {
+			Date ST = shortDF.parse(jct.starttime);
+			if (null != ST) {
+				StartTime = ST.getTime();
+			}
+		}
+		if (null != jct.endtime) {
+			Date ET = shortDF.parse(jct.endtime);
+			if (null != ET) {
+				EndTime = ET.getTime();
+			}
+		}
+		if (null != jct.dbname) {
+			DBname = jct.dbname;
+		}
+		if (null != jct.workingdir) {
+			WorkingDir = jct.workingdir;
 		}
 
 		System.out.println("Start time: " + jct.starttime + " = " + StartTime);
@@ -174,7 +185,7 @@ public class ExecutionStatUpdater {
 
 		ExecutionStatUpdater esu = new ExecutionStatUpdater(WorkingDir, 1);
 		esu.collectStatistics(StartTime, EndTime);
-		esu.writeStatToDB();
+		esu.writeStatToDB(DBname);
 	}
 
 	static FileFilter directories = new FileFilter() {
@@ -189,12 +200,14 @@ public class ExecutionStatUpdater {
 		// clear stats array;
 		stats.clear();
 		File[] dirs = workingDirectory.listFiles(directories);
+		log.debug("Start time = " + StartTime + ", end time = " + EndTime);
 		for (File dir : dirs) {
 			// skip work directory with test inputs and out of ordered time
 			// range
 			log.debug("check directory: " + dir.getName() + "...");
 			if (InputFilter.accept(new File(dir.getPath() + File.separator + SkeletalExecutable.INPUT)) && StartTime < dir.lastModified()
 					&& dir.lastModified() < EndTime) {
+				log.debug(", ACCEPTED");
 				JobDirectory jd = new JobDirectory(dir);
 				JobStat jstat = jd.getJobStat();
 				// Do not record stats on the job that has not completed yet
@@ -204,9 +217,11 @@ public class ExecutionStatUpdater {
 					log.debug("Skipping the job: " + jstat + " as it has not completed yet");
 				}
 			} else {
+				log.debug(", REJECTED");
 				log.trace("training input: " + dir.getName() + File.separator + SkeletalExecutable.INPUT);
 			}
 		}
+		log.debug("Statistics collected!");
 	}
 
 }