<session-timeout>20</session-timeout>\r
</session-config>\r
\r
+ <servlet>\r
+ <display-name>This is a standard tomcat 'default' servlet for making listings</display-name>\r
+ <servlet-name>listings</servlet-name>\r
+ <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>\r
+ <init-param>\r
+ <param-name>debug</param-name>\r
+ <param-value>0</param-value>\r
+ </init-param>\r
+ <init-param>\r
+ <param-name>readonly</param-name>\r
+ <param-value>true</param-value>\r
+ </init-param>\r
+ <init-param>\r
+ <param-name>listings</param-name>\r
+ <param-value>true</param-value>\r
+ </init-param>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
<servlet>\r
<description>Display pre-calculated accounting info</description>\r
<servlet-name>DisplayStat</servlet-name>\r
<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
<load-on-startup>1</load-on-startup>\r
</servlet>\r
- \r
+ \r
+ <servlet-mapping>\r
+ <servlet-name>listings</servlet-name>\r
+ <url-pattern>/</url-pattern>\r
+ </servlet-mapping>\r
+ \r
<servlet-mapping>\r
<servlet-name>DisplayStat</servlet-name>\r
<url-pattern>/DisplayStat</url-pattern>\r
<web-resource-collection>\r
<web-resource-name>Administrator pages</web-resource-name>\r
<!-- Prohibit access to any resources -->\r
+ <url-pattern>/</url-pattern>\r
<url-pattern>/DisplayStat</url-pattern>\r
<url-pattern>/Joblist</url-pattern>\r
<url-pattern>/AnnualStat</url-pattern>\r
package compbio.stat.collector;\r
\r
import static org.testng.Assert.assertEquals;\r
+import static org.testng.Assert.assertFalse;\r
+import static org.testng.Assert.assertTrue;\r
\r
import java.io.File;\r
+import java.util.Date;\r
+import java.util.concurrent.Executors;\r
+import java.util.concurrent.ScheduledExecutorService;\r
+import java.util.concurrent.ScheduledFuture;\r
+import java.util.concurrent.TimeUnit;\r
\r
+import org.testng.Assert;\r
import org.testng.annotations.Test;\r
\r
import compbio.metadata.AllTestSuit;\r
+import compbio.stat.collector.ExecutionStatCollector.JobDirectory;\r
\r
public class ExecutionStatCollectorTester {\r
\r
+ final static String LOCAL_JOBS = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
+ + File.separator + "ljobs";\r
+ final static String CLUSTER_JOBS = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
+ + File.separator + "jobs";\r
@Test\r
public void testCollectStat() {\r
ExecutionStatCollector local_jobs = new ExecutionStatCollector(\r
- AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator + "ljobs");\r
+ LOCAL_JOBS, 1);\r
ExecutionStatCollector cl_jobs = new ExecutionStatCollector(\r
- AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator + "jobs");\r
+ CLUSTER_JOBS, 24);\r
+\r
StatProcessor local_stats = local_jobs.getStats();\r
StatProcessor cl_stats = cl_jobs.getStats();\r
// System.out.println("L: " + local_stats.stats);\r
assertEquals(2, local_stats.getAbandonedJobs().size());\r
\r
}\r
- public void testUpdateStat() {\r
+\r
+ @Test\r
+ public void testUpdateStatTester() {\r
+\r
+ ScheduledExecutorService executor = Executors.newScheduledThreadPool(1);\r
+ ScheduledFuture<?> sf = executor.scheduleAtFixedRate(\r
+ new ExecutionStatCollector(LOCAL_JOBS, 1), 1, 10,\r
+ TimeUnit.SECONDS);\r
+\r
+ try {\r
+ Thread.sleep(1000 * 35);\r
+ executor.shutdown();\r
+ executor.awaitTermination(300, TimeUnit.SECONDS);\r
+ } catch (InterruptedException e) {\r
+ e.printStackTrace();\r
+ Assert.fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ /**\r
+ * This test will fail in time as it relies on last access time for file in\r
+ * the filesystem! This OK as it has been tested by then.\r
+ * \r
+ */\r
+ @Test\r
+ public void testHasTimedOut() {\r
+ ExecutionStatCollector ecol = new ExecutionStatCollector(LOCAL_JOBS, 1);\r
+ File f = new File(LOCAL_JOBS + File.separator\r
+ + "ClustalW#1015373448154965");\r
+ File timedOut = new File(LOCAL_JOBS + File.separator\r
+ + "Mafft#7868649707286965");\r
+\r
+ JobDirectory jd = new JobDirectory(f);\r
+ JobDirectory timedOutDir = new JobDirectory(timedOut);\r
+ System.out.println("! " + new Date(f.lastModified()));\r
+\r
+ assertTrue((System.currentTimeMillis() - f.lastModified())\r
+ / (1000 * 60 * 60) < 1);\r
+ assertFalse((System.currentTimeMillis() - timedOut.lastModified())\r
+ / (1000 * 60 * 60) < 1);\r
+ assertFalse(ecol.hasTimedOut(jd));\r
+ assertTrue(ecol.hasTimedOut(timedOutDir));\r
+ }\r
+\r
+ @Test\r
+ public void testHasCompleted() {\r
+ ExecutionStatCollector ecol_no_timeout = new ExecutionStatCollector(\r
+ LOCAL_JOBS, 10000000);\r
+ ExecutionStatCollector ecol = new ExecutionStatCollector(LOCAL_JOBS, 1);\r
+\r
+ File normal = new File(LOCAL_JOBS + File.separator\r
+ + "ClustalW#100368900075204");\r
+ File finished = new File(LOCAL_JOBS + File.separator\r
+ + "ClustalW#1015373448154965");\r
+ File cancelled = new File(LOCAL_JOBS + File.separator\r
+ + "Mafft#7918237850044965");\r
+ File noresult = new File(LOCAL_JOBS + File.separator\r
+ + "ClustalW#1015343425414965");\r
+\r
+ JobDirectory dnormal = new JobDirectory(normal);\r
+ JobDirectory dfinished = new JobDirectory(finished);\r
+ JobDirectory dcancelled = new JobDirectory(cancelled);\r
+\r
+ JobDirectory dnoresult = new JobDirectory(noresult);\r
+\r
+ assertTrue(ecol.hasCompleted(dnormal));\r
+ assertTrue(ecol.hasCompleted(dfinished));\r
+ assertTrue(ecol.hasCompleted(dcancelled));\r
+\r
+ assertTrue(ecol.hasCompleted(dnoresult));\r
+ assertFalse(ecol_no_timeout.hasCompleted(dnoresult));\r
\r
}\r
}\r
\r
import org.apache.log4j.Logger;\r
\r
-import compbio.engine.client.ConfExecutable;\r
import compbio.engine.client.Executable;\r
import compbio.metadata.JobStatus;\r
-import compbio.runner.msa.ClustalW;\r
import compbio.util.FileUtil;\r
import compbio.ws.client.Services;\r
\r
return ftime;\r
}\r
\r
- @SuppressWarnings("unchecked")\r
- Class<Executable<?>> getWSRunnerName() {\r
- String name = jobdir.getName().split("#")[0];\r
- try {\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
- name = ClustalW.class.getPackage().getName() + "." + name;\r
- return (Class<Executable<?>>) Class.forName(name);\r
- } catch (ClassNotFoundException e) {\r
- e.printStackTrace();\r
- throw new RuntimeException(\r
- "Cannot match the directory name to the executable! Executable name is "\r
- + name);\r
- }\r
- }\r
-\r
private Services getService() {\r
- return Services.getService(getWSRunnerName());\r
+ return Services.getServiceByJobDirectory(jobdir);\r
}\r
\r
// Mafft, Muscle, Tcoffee, Clustal task:fasta.in result:fasta.out\r
* TODO replace with Universal names for WS!\r
*/\r
long getResultSize() {\r
- Class<Executable<?>> name = getWSRunnerName();\r
+ Class<? extends Executable<?>> name = Services\r
+ .getRunnerByJobDirectory(jobdir);\r
+\r
File f = null;\r
if (name.getSimpleName().equalsIgnoreCase("Probcons")) {\r
f = files.get("alignment.out");\r
+ ";create=false");\r
\r
conn.setAutoCommit(true);\r
-\r
- Runtime.getRuntime().addShutdownHook(new Thread() {\r
- @Override\r
- public void run() {\r
- shutdownDBServer();\r
- }\r
- });\r
+ /*\r
+ * Runtime.getRuntime().addShutdownHook(new Thread() {\r
+ * \r
+ * @Override public void run() { shutdownDBServer(); } });\r
+ */\r
}\r
return conn;\r
}\r
}\r
\r
void insertData(Set<JobStat> jobstatus) throws SQLException {\r
- System.out.println("Inserting " + jobstatus.size());\r
+ log.info("Inserting " + jobstatus.size()\r
+ + " new records into the statistics database");\r
\r
conn.setAutoCommit(false);\r
String insert = "insert into exec_stat (service_name, cluster_job_id, job_id, start, finish, "\r
package compbio.stat.servlet;\r
\r
+import java.io.File;\r
import java.io.IOException;\r
import java.sql.SQLException;\r
import java.sql.Timestamp;\r
PropertyHelper helper = PropertyHelperManager.getPropertyHelper();\r
String clusterTempDir = helper.getProperty("cluster.tmp.directory")\r
.trim();\r
+ clusterTempDir = new File(clusterTempDir).getName();\r
String localTempDir = helper.getProperty("local.tmp.directory").trim();\r
// TODO include the time slice\r
Timestamp startDate = new Timestamp(Long.parseLong(fromDate));\r
import compbio.stat.collector.ExecutionStatCollector;\r
import compbio.stat.collector.StatDB;\r
import compbio.util.PropertyHelper;\r
+import compbio.util.Util;\r
\r
public class StatisticCollector implements ServletContextListener {\r
\r
int clusterMaxRuntime = getClusterJobTimeOut();\r
\r
int localMaxRuntime = getLocalJobTimeOut();\r
- String localWorkDir = getLocalJobDir();\r
+ String localWorkDir = compbio.engine.client.Util\r
+ .convertToAbsolute(getLocalJobDir());\r
\r
log.info("Initializing statistics collector");\r
- executor = Executors.newScheduledThreadPool(1);\r
+ executor = Executors.newScheduledThreadPool(2);\r
\r
if (collectClusterStats()) {\r
+ // TODO remove work out of the constructor Tomcat takes ages to\r
+ // start!\r
ExecutionStatCollector clusterCollector = new ExecutionStatCollector(\r
clusterWorkDir, clusterMaxRuntime);\r
clustercf = executor.scheduleAtFixedRate(clusterCollector, 60,\r
24 * 60, TimeUnit.MINUTES);\r
+ // clustercf = executor.scheduleAtFixedRate(clusterCollector, 15,\r
+ // 30,\r
+ // TimeUnit.SECONDS);\r
log.info("Collecting cluster statistics ");\r
+ } else {\r
+ log.info("Cluster statistics collector is disabled or not configured! ");\r
}\r
if (collectLocalStats()) {\r
ExecutionStatCollector localCollector = new ExecutionStatCollector(\r
localWorkDir, localMaxRuntime);\r
+ // localcf = executor.scheduleAtFixedRate(localCollector, 100, 60,\r
+ // TimeUnit.SECONDS);\r
+\r
localcf = executor.scheduleAtFixedRate(localCollector, 10, 24 * 60,\r
TimeUnit.MINUTES);\r
log.info("Collecting local statistics ");\r
+ } else {\r
+ log.info("Local statistics collector is disabled or not configured! ");\r
}\r
\r
}\r
}\r
\r
private static String getStringProperty(String propName) {\r
- String locdir = ph.getProperty(propName);\r
- if (locdir != null) {\r
- locdir = locdir.trim();\r
+ if (propName != null) {\r
+ propName = propName.trim();\r
}\r
- return locdir;\r
+ return propName;\r
}\r
\r
static boolean collectClusterStats() {\r
return getBooleanProperty(ph\r
.getProperty("cluster.stat.collector.enable"));\r
-\r
}\r
\r
static boolean collectLocalStats() {\r
return getBooleanProperty(ph.getProperty("local.stat.collector.enable"));\r
}\r
\r
- private static boolean getBooleanProperty(String propName) {\r
+ private static boolean getBooleanProperty(String propValue) {\r
boolean enabled = false;\r
- if (propName != null) {\r
- propName = propName.trim();\r
- enabled = Boolean.parseBoolean(propName);\r
+ if (!Util.isEmpty(propValue)) {\r
+ propValue = propValue.trim();\r
+ enabled = Boolean.parseBoolean(propValue);\r
}\r
return enabled;\r
}\r
\r
package compbio.ws.client;\r
\r
+import java.io.File;\r
import java.net.URL;\r
\r
import javax.xml.namespace.QName;\r
import compbio.data.msa.JABAService;\r
import compbio.data.msa.MsaWS;\r
import compbio.data.msa.SequenceAnnotation;\r
+import compbio.engine.client.ConfExecutable;\r
import compbio.engine.client.Executable;\r
+import compbio.runner.conservation.AACon;\r
+import compbio.runner.disorder.Disembl;\r
+import compbio.runner.disorder.GlobPlot;\r
+import compbio.runner.disorder.Jronn;\r
+import compbio.runner.msa.ClustalW;\r
+import compbio.runner.msa.Mafft;\r
+import compbio.runner.msa.Muscle;\r
+import compbio.runner.msa.Probcons;\r
+import compbio.runner.msa.Tcoffee;\r
\r
/**\r
* List of web services currently supported by JABAWS version 2\r
return null;\r
}\r
\r
- public static Services getService(Class<Executable<?>> runnerClassName) {\r
+ public static Services getServiceByRunner(\r
+ Class<Executable<?>> runnerClassName) {\r
assert runnerClassName != null;\r
String sname = runnerClassName.getSimpleName().toLowerCase();\r
for (Services service : Services.values()) {\r
return null;\r
}\r
\r
+ public Class<? extends Executable<?>> getServiceImpl() {\r
+ switch (this) {\r
+ case AAConWS :\r
+ return AACon.class;\r
+ case ClustalWS :\r
+ return ClustalW.class;\r
+ case MafftWS :\r
+ return Mafft.class;\r
+ case MuscleWS :\r
+ return Muscle.class;\r
+ case TcoffeeWS :\r
+ return Tcoffee.class;\r
+ case ProbconsWS :\r
+ return Probcons.class;\r
+ case DisemblWS :\r
+ return Disembl.class;\r
+ case GlobPlotWS :\r
+ return GlobPlot.class;\r
+ case JronnWS :\r
+ return Jronn.class;\r
+ default :\r
+ throw new RuntimeException(\r
+ "Unknown web service implementation class for service: "\r
+ + this);\r
+ }\r
+ }\r
+\r
+ public static Class<? extends Executable<?>> getRunnerByJobDirectory(File jobdir) {\r
+ Services service = getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
+ return service.getServiceImpl();\r
+ }\r
+\r
+ private static String getRunnerNameByJobDirectory(File jobdir) {\r
+ String name = jobdir.getName().split("#")[0];\r
+\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
+ public static Services getServiceByJobDirectory(File jobdir) {\r
+ return getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
+ }\r
+\r
+ private static Services getServiceByRunnerName(String name) {\r
+ for (Services service : Services.values()) {\r
+ String runnerName = service.getServiceImpl().getSimpleName()\r
+ .toLowerCase();\r
+ name = name.trim().toLowerCase();\r
+ if (name.startsWith(runnerName)) {\r
+ return service;\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+\r
Service getService(URL url, String sqname) {\r
QName qname = new QName(sqname, this.toString());\r
return Service.create(url, qname);\r
git://source.jalview.org / jabaws.git / commitdiff