/**
* JobTracker.submitJob() kicks off a new job.
*
* <p>Create a 'JobInProgress' object, which contains both JobProfile and JobStatus. Those two
* sub-objects are sometimes shipped outside of the JobTracker. But JobInProgress adds info that's
* useful for the JobTracker alone.
*
* <p>We add the JIP to the jobInitQueue, which is processed asynchronously to handle
* split-computation and build up the right TaskTracker/Block mapping.
*/
public synchronized JobStatus submitJob(String jobFile) throws IOException {
totalSubmissions++;
JobInProgress job = new JobInProgress(jobFile, this, this.conf);
synchronized (jobs) {
synchronized (jobsByArrival) {
synchronized (jobInitQueue) {
jobs.put(job.getProfile().getJobId(), job);
jobsByArrival.add(job);
jobInitQueue.add(job);
jobInitQueue.notifyAll();
}
}
}
return job.getStatus();
}
public void doLayout() {
selections.clear();
if (points == null) {
points = new Vector<ExprPoint>();
}
points.clear();
for (Pair<Integer, Double> p : watsonProbes) {
ExprPoint ep = new ExprPoint(p.getFirst(), p.getLast(), '+');
points.add(ep);
}
for (Pair<Integer, Double> p : crickProbes) {
ExprPoint ep = new ExprPoint(p.getFirst(), p.getLast(), '-');
points.add(ep);
}
}
public void addString(String str) {
char[] array = str.toCharArray();
strings.add(new TreeString(strings.size(), array));
logger.log(Level.INFO, String.format("Adding string \"%s\"", str));
ukkonenExtendSuffixTree(strings.size() - 1);
// naiveExtendSuffixTree(strings.size()-1);
}
public synchronized TaskReport[] getReduceTaskReports(String jobid) {
JobInProgress job = (JobInProgress) jobs.get(jobid);
if (job == null) {
return new TaskReport[0];
} else {
Vector reports = new Vector();
Vector completeReduceTasks = job.reportTasksInProgress(false, true);
for (Iterator it = completeReduceTasks.iterator(); it.hasNext(); ) {
TaskInProgress tip = (TaskInProgress) it.next();
reports.add(tip.generateSingleReport());
}
Vector incompleteReduceTasks = job.reportTasksInProgress(false, false);
for (Iterator it = incompleteReduceTasks.iterator(); it.hasNext(); ) {
TaskInProgress tip = (TaskInProgress) it.next();
reports.add(tip.generateSingleReport());
}
return (TaskReport[]) reports.toArray(new TaskReport[reports.size()]);
}
}
public Vector completedJobs() {
Vector v = new Vector();
for (Iterator it = jobs.values().iterator(); it.hasNext(); ) {
JobInProgress jip = (JobInProgress) it.next();
JobStatus status = jip.getStatus();
if (status.getRunState() == JobStatus.SUCCEEDED) {
v.add(jip);
}
}
return v;
}
public Vector runningJobs() {
Vector v = new Vector();
for (Iterator it = jobs.values().iterator(); it.hasNext(); ) {
JobInProgress jip = (JobInProgress) it.next();
JobStatus status = jip.getStatus();
if (status.getRunState() == JobStatus.RUNNING) {
v.add(jip);
}
}
return v;
}
public void loadNetwork() throws IOException {
logger.log(Level.INFO, "Loading metabolism network...");
File file = props.getNetworkFile();
Mapper<String, MetabolicEntry> entryMapper = new MetabolicEntry.MetabolicMapper();
Parser<MetabolicEntry> parser = new Parser<MetabolicEntry>(file, entryMapper);
while (parser.hasNext()) {
MetabolicEntry entry = parser.next();
entries.add(entry);
Rxn rxn =
new Rxn(
props,
entry.getReaction(),
entry.getAbbreviation(),
entry.getReactionName(),
entry.getORF());
reactions.put(entry.getAbbreviation(), rxn);
locations.add(rxn.getLocation());
LogicalORFTree lot = new LogicalORFTree(entry.getORF());
ORFSet os = new ORFSet(entry.getORF());
totalORFs.addAll(os.getORFs());
orfSets.put(entry.getAbbreviation(), lot);
}
logger.log(Level.FINE, String.format("Loaded %d entries.", entries.size()));
abbrevs = new MetabolismAbbreviations(props);
abbrevs.loadAbbreviations();
logger.log(Level.FINEST, "Loaded abbrevations.");
}
public void testStatelessSearch()
throws org.jzkit.configuration.api.ConfigurationException, org.jzkit.search.SearchException,
org.jzkit.search.util.ResultSet.IRResultSetException,
org.jzkit.search.util.QueryModel.InvalidQueryException {
Logger log = Logger.getLogger(TestService.class.getName());
log.info("Starting jzkit2 server...");
RecordFormatSpecification request_spec = new ArchetypeRecordFormatSpecification("F");
ExplicitRecordFormatSpecification display_spec =
new ExplicitRecordFormatSpecification("text:html:F");
ApplicationContext app_context =
new ClassPathXmlApplicationContext("TestApplicationContext.xml");
log.info("JZKit server startup completed");
Vector collection_ids = new Vector();
collection_ids.add("LC/BOOKS");
QueryModel qm = new PrefixString("@attrset bib-1 @attr 1=4 Science");
System.err.println("Processing search......");
try {
Map additional_properties = new HashMap();
additional_properties.put("base_dir", "/a/b/c/d");
StatelessQueryService stateless_query_service =
(StatelessQueryService) app_context.getBean("StatelessQueryService");
org.jzkit.search.landscape.SimpleLandscapeSpecification landscape =
new org.jzkit.search.landscape.SimpleLandscapeSpecification(collection_ids);
// Test 1 - Kick off a search
StatelessSearchResultsPageDTO rp =
stateless_query_service.getResultsPageFor(
null, qm, landscape, 1, 5, request_spec, display_spec, additional_properties);
if (rp != null) {
System.err.println(
"Result Set Size....."
+ rp.total_hit_count
+ " records - result contains "
+ rp.number_of_records
+ " records");
System.err.println("Result Set ID : " + rp.result_set_id);
} else {
System.err.println("Results page was null");
}
if (rp.records != null) {
for (int i = 0; ((i < rp.records.length) && (i < 25)); i++) {
System.err.println(
"Getting next record (" + i + " out of " + rp.number_of_records + ").....");
InformationFragment frag = rp.records[i];
System.err.println(frag);
}
}
// Test 2 - use the result set ID to get a page of requests
rp =
stateless_query_service.getResultsPageFor(
rp.result_set_id,
qm,
landscape,
6,
5,
request_spec,
display_spec,
additional_properties);
if (rp.records != null) {
for (int i = 0; ((i < rp.records.length) && (i < 25)); i++) {
System.err.println(
"Getting next record (" + i + " out of " + rp.number_of_records + ").....");
InformationFragment frag = rp.records[i];
System.err.println(frag);
}
}
// Test 3 - Use the query to get a cache hit
rp =
stateless_query_service.getResultsPageFor(
null, qm, landscape, 6, 5, request_spec, display_spec, additional_properties);
if (rp.records != null) {
for (int i = 0; ((i < rp.records.length) && (i < 25)); i++) {
System.err.println(
"Getting next record (" + i + " out of " + rp.number_of_records + ").....");
InformationFragment frag = rp.records[i];
System.err.println(frag);
}
}
} catch (Exception e) {
e.printStackTrace();
}
}