Examples with User org.vcell.util.document.User used on opensource projects

Example 1 with User

use of org.vcell.util.document.User in project vcell by virtualcell.

the class RunRefSimulationFastOp method createNewExternalDataInfo.

private ExternalDataInfo createNewExternalDataInfo(LocalContext localWorkspace, String extDataIDName) {
    File targetDir = new File(localWorkspace.getDefaultSimDataDirectory());
    KeyValue key = LocalWorkspace.createNewKeyValue();
    User owner = LocalWorkspace.getDefaultOwner();
    ExternalDataIdentifier newImageDataExtDataID = new ExternalDataIdentifier(key, owner, extDataIDName);
    String filename = new File(targetDir, newImageDataExtDataID.getID() + SimDataConstants.LOGFILE_EXTENSION).getAbsolutePath();
    ExternalDataInfo newImageDataExtDataInfo = new ExternalDataInfo(newImageDataExtDataID, filename);
    return newImageDataExtDataInfo;
}

Example 2 with User

use of org.vcell.util.document.User in project vcell by virtualcell.

the class RunRefSimulationOp method createNewExternalDataInfo.

private static ExternalDataInfo createNewExternalDataInfo(LocalWorkspace localWorkspace, String extDataIDName) {
    File targetDir = new File(localWorkspace.getDefaultSimDataDirectory());
    KeyValue key = LocalWorkspace.createNewKeyValue();
    User owner = LocalWorkspace.getDefaultOwner();
    ExternalDataIdentifier newImageDataExtDataID = new ExternalDataIdentifier(key, owner, extDataIDName);
    String filename = new File(targetDir, newImageDataExtDataID.getID() + SimDataConstants.LOGFILE_EXTENSION).getAbsolutePath();
    ExternalDataInfo newImageDataExtDataInfo = new ExternalDataInfo(newImageDataExtDataID, filename);
    return newImageDataExtDataInfo;
}

Example 3 with User

use of org.vcell.util.document.User in project vcell by virtualcell.

the class AccessTokenServerResource method get_json.

@Override
public AccessTokenRepresentation get_json() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    String clientId = getQueryValue(PARAM_CLIENT_ID);
    String userId = getQueryValue(PARAM_USER_ID);
    String userPassword = getQueryValue(PARAM_USER_PASSWORD);
    try {
        ApiClient apiClient = application.getUserVerifier().getApiClient(clientId);
        if (apiClient == null) {
            throw new RuntimeException("client not found");
        }
        User authenticatedUser = application.getUserVerifier().authenticateUser(userId, userPassword.toCharArray());
        if (authenticatedUser == null) {
            throw new RuntimeException("unable to authenticate user");
        }
        ApiAccessToken apiAccessToken = application.getUserVerifier().generateApiAccessToken(apiClient.getKey(), authenticatedUser);
        AccessTokenRepresentation tokenRep = new AccessTokenRepresentation(apiAccessToken);
        // 
        // indicate no caching of response.
        // 
        ArrayList<CacheDirective> cacheDirectives = new ArrayList<CacheDirective>();
        cacheDirectives.add(CacheDirective.noCache());
        getResponse().setCacheDirectives(cacheDirectives);
        return tokenRep;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage(), e);
    }
}

Example 4 with User

use of org.vcell.util.document.User in project vcell by virtualcell.

the class BatchScheduler method schedule.

/**
 * Insert the method's description here.
 * Creation date: (5/11/2006 9:32:58 AM)
 */
public static WaitingJob[] schedule(SimulationJobStatus[] activeJobsThisSite, Map<KeyValue, SimulationRequirements> simulationRequirementsMap, int siteJobQuota, int userQuotaOde, int userQuotaPde, VCellServerID systemID) {
    Hashtable<User, Integer> userPdeRunningJobsThisSite = new Hashtable<User, Integer>();
    Hashtable<User, Integer> userOdeRunningJobsThisSite = new Hashtable<User, Integer>();
    cbit.vcell.server.SimulationJobStatus jobStatus = null;
    int numRunningJobsThisSite = 0;
    for (int i = 0; i < activeJobsThisSite.length; i++) {
        jobStatus = activeJobsThisSite[i];
        if (!jobStatus.getSchedulerStatus().isActive()) {
            continue;
        }
        if (jobStatus.getSchedulerStatus().isWaiting()) {
            // we only do statistics on running jobs;
            continue;
        }
        numRunningJobsThisSite++;
        if (jobStatus.getServerID().equals(systemID)) {
            // the number of running jobs on this site
            User user = activeJobsThisSite[i].getVCSimulationIdentifier().getOwner();
            SimulationRequirements simRequirements = simulationRequirementsMap.get(jobStatus.getVCSimulationIdentifier().getSimulationKey());
            if (simRequirements != null && simRequirements.isPDE()) {
                Integer numUserPdeJobs = userPdeRunningJobsThisSite.get(user);
                if (numUserPdeJobs == null) {
                    userPdeRunningJobsThisSite.put(user, 1);
                } else {
                    userPdeRunningJobsThisSite.put(user, numUserPdeJobs.intValue() + 1);
                }
            } else {
                Integer numUserOdeJobs = userOdeRunningJobsThisSite.get(user);
                if (numUserOdeJobs == null) {
                    userOdeRunningJobsThisSite.put(user, 1);
                } else {
                    userOdeRunningJobsThisSite.put(user, numUserOdeJobs.intValue() + 1);
                }
            }
        }
    }
    ArrayList<WaitingJob> waitingJobs = new ArrayList<WaitingJob>();
    for (int i = 0; i < activeJobsThisSite.length; i++) {
        jobStatus = activeJobsThisSite[i];
        if (!jobStatus.getSchedulerStatus().isWaiting()) {
            // ignore non-waiting job
            continue;
        }
        if (!jobStatus.getServerID().equals(systemID)) {
            // doesn't belong
            continue;
        }
        User user = activeJobsThisSite[i].getVCSimulationIdentifier().getOwner();
        Integer numRunningPDEsThisSite = userPdeRunningJobsThisSite.get(user);
        if (numRunningPDEsThisSite == null) {
            numRunningPDEsThisSite = new Integer(0);
        }
        Integer numRunningODEsThisSite = userOdeRunningJobsThisSite.get(user);
        if (numRunningODEsThisSite == null) {
            numRunningODEsThisSite = new Integer(0);
        }
        long waitingTimeStamp = jobStatus.getSimulationQueueEntryStatus().getQueueDate().getTime();
        KeyValue simKey = jobStatus.getVCSimulationIdentifier().getSimulationKey();
        waitingJobs.add(new WaitingJob(user, numRunningPDEsThisSite, numRunningODEsThisSite, waitingTimeStamp, jobStatus, simulationRequirementsMap.get(simKey)));
    }
    Collections.sort(waitingJobs, new Comparator<WaitingJob>() {

        @Override
        public int compare(WaitingJob o1, WaitingJob o2) {
            // 
            if (!o1.getNumRunningJobs().equals(o2.getNumRunningJobs())) {
                return o1.getNumRunningJobs().compareTo(o2.getNumRunningJobs());
            }
            // 
            if (o1.simRequirements.isPDE() != o2.simRequirements.isPDE()) {
                if (o1.simRequirements.isPDE()) {
                    return 1;
                } else {
                    return -1;
                }
            }
            // 
            return o1.waitingTimeStamp.compareTo(o2.waitingTimeStamp);
        }
    });
    // 
    // enforce quota for each user
    // 
    HashSet<User> users = new HashSet<User>();
    users.addAll(userPdeRunningJobsThisSite.keySet());
    users.addAll(userOdeRunningJobsThisSite.keySet());
    for (User user : users) {
        Integer numRunningPDEsThisSite = userPdeRunningJobsThisSite.get(user);
        int numRunningPDEs = 0;
        if (numRunningPDEsThisSite != null) {
            numRunningPDEs = numRunningPDEsThisSite;
        }
        Integer numRunningODEsThisSite = userOdeRunningJobsThisSite.get(user);
        int numRunningODEs = 0;
        if (numRunningODEsThisSite != null) {
            numRunningODEs = numRunningODEsThisSite;
        }
        // 
        // go full list and remove any jobs that would exceed this users quota
        // 
        Iterator<WaitingJob> waitingJobIter = waitingJobs.iterator();
        while (waitingJobIter.hasNext()) {
            WaitingJob waitingJob = waitingJobIter.next();
            if (waitingJob.user.equals(user)) {
                if (waitingJob.simRequirements.isPDE()) {
                    if (numRunningPDEs < userQuotaPde) {
                        numRunningPDEs++;
                    } else {
                        waitingJobIter.remove();
                    }
                } else {
                    if (numRunningODEs < userQuotaOde) {
                        numRunningODEs++;
                    } else {
                        waitingJobIter.remove();
                    }
                }
            }
        }
    }
    // 
    // enforce site quota (keep only first N jobs) where currentRunning + N <= quota
    // 
    int numJobsSlotsAvailable = Math.max(0, siteJobQuota - numRunningJobsThisSite);
    int numJobsEligible = waitingJobs.size();
    int numJobsToDispatch = Math.min(numJobsSlotsAvailable, numJobsEligible);
    if (numJobsToDispatch == 0) {
        return new WaitingJob[0];
    } else {
        return waitingJobs.subList(0, numJobsToDispatch).toArray(new WaitingJob[0]);
    }
}

Example 5 with User

use of org.vcell.util.document.User in project vcell by virtualcell.

the class SolverPostprocessor method main.

public static void main(java.lang.String[] args) {
    if (args.length < NUM_STD_ARGS) {
        System.out.println("Usage: " + SolverPostprocessor.class.getName() + " simKey username userKey jobindex taskid solverExitCode [postProcessorCommandFile]");
        System.exit(1);
    }
    Logging.init();
    Log4jSessionLog log = new Log4jSessionLog(LOG_NAME);
    Logger lg = log.getLogger();
    VCMessagingService vcMessagingService = null;
    try {
        PropertyLoader.loadProperties(POST_PROCESSOR_PROPERTIES);
        ResourceUtil.setNativeLibraryDirectory();
        NativeLoader.setOsType(OsType.LINUX);
        KeyValue simKey = new KeyValue(args[0]);
        String userName = args[1];
        KeyValue userKey = new KeyValue(args[2]);
        int jobIndex = Integer.parseInt(args[3]);
        int taskID = Integer.parseInt(args[4]);
        int solverExitCode = Integer.parseInt(args[5]);
        User owner = new User(userName, userKey);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        String hostName = ManageUtils.getHostName();
        VCMongoMessage.serviceStartup(ServiceName.solverPostprocessor, Integer.valueOf(simKey.toString()), args);
        // 
        // JMX registration
        // 
        MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
        mbs.registerMBean(new VCellServiceMXBeanImpl(), new ObjectName(VCellServiceMXBean.jmxObjectName));
        vcMessagingService = VCellServiceHelper.getInstance().loadService(VCMessagingService.class);
        vcMessagingService.setDelegate(new ServerMessagingDelegate());
        VCMessageSession session = vcMessagingService.createProducerSession();
        WorkerEventMessage workerEventMessage;
        if (solverExitCode == 0) {
            Exception postProcessingException = null;
            if (args.length > NUM_STD_ARGS) {
                String fname = args[NUM_STD_ARGS];
                if (lg.isDebugEnabled()) {
                    lg.debug("processing " + fname);
                }
                postProcessingException = runPostprocessingCommands(fname, lg);
            }
            if (lg.isDebugEnabled()) {
                lg.debug("postProcessingException is " + postProcessingException);
            }
            if (postProcessingException == null) {
                lg.debug("sendWorkerExitNormal");
                workerEventMessage = WorkerEventMessage.sendWorkerExitNormal(session, SolverPostprocessor.class.getName(), hostName, vcSimID, jobIndex, taskID, solverExitCode);
            } else {
                lg.debug("sendWorkerExitError postprocessing");
                workerEventMessage = WorkerEventMessage.sendWorkerExitError(session, postProcessingException, hostName, vcSimID, jobIndex, taskID, SimulationMessage.WorkerExited(postProcessingException));
            }
        } else {
            // solverExitCode != 0
            lg.debug("sendWorkerExitError solverExitCode");
            workerEventMessage = WorkerEventMessage.sendWorkerExitError(session, SolverPostprocessor.class.getName(), hostName, vcSimID, jobIndex, taskID, solverExitCode);
        }
        lg.debug(workerEventMessage);
        VCMongoMessage.sendWorkerEvent(workerEventMessage);
    } catch (Throwable e) {
        log.exception(e);
    } finally {
        if (vcMessagingService != null) {
            try {
                vcMessagingService.close();
            } catch (VCMessagingException e) {
                e.printStackTrace();
            }
        }
        ApplicationTerminator.beginCountdown(TimeUnit.SECONDS, 10, 0);
        VCMongoMessage.shutdown();
        System.exit(0);
    }
}