Examples with BigString org.vcell.util.BigString used on opensource projects

Example 61 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class LocalUserMetaDbServerMessaging method saveBioModel.

/**
 * getVersionInfo method comment.
 * @throws RemoteException
 */
public BigString saveBioModel(BigString bioModelXML, String[] independentSims) throws DataAccessException {
    try {
        log.print("LocalUserMetaDbServerMessaging.saveBioModel()");
        BigString savedBioModelXML = dbServerProxy.saveBioModel(bioModelXML, independentSims);
        return savedBioModelXML;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 62 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class LocalUserMetaDbServerMessaging method getMathModelXML.

/**
 * getVersionInfo method comment.
 * @throws RemoteException
 */
public BigString getMathModelXML(KeyValue mathModelKey) throws DataAccessException, ObjectNotFoundException {
    try {
        log.print("LocalUserMetaDbServerMessaging.getMathModelXML(mathModelKey=" + mathModelKey + ")");
        BigString xml = dbServerProxy.getMathModelXML(mathModelKey);
        return xml;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 63 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class VCComprehensiveStatistics method collectBioModelStats.

private void collectBioModelStats(long startDateInMs, long endDateInMs) throws DataAccessException {
    retrieveUsers();
    for (User user : userList) {
        if (!userConstraintList.contains(user.getName())) {
            continue;
        }
        if (!internalDeveloper.contains(user.getName())) {
            boolean bInternal = internalUsers.contains(user.getName());
            ModelStat modelStat = bioModelStats[bInternal ? 0 : 1];
            BioModelInfo[] bioModelInfos = dbServerImpl.getBioModelInfos(user, false);
            for (BioModelInfo bmi : bioModelInfos) {
                Date createDate = bmi.getVersion().getDate();
                long t = createDate.getTime();
                // }
                if (t < startDateInMs || t > endDateInMs) {
                    continue;
                }
                // modelStat.count_model ++;
                try {
                    BigString bioModelXML = dbServerImpl.getBioModelXML(user, bmi.getVersion().getVersionKey());
                    BioModel bioModel = (BioModel) waitForModel(bioModelXML, false);
                    if (bioModel == null) {
                        System.out.println("----------          Skipped BioModel " + bmi.getVersion() + "          ----------");
                        continue;
                    }
                    modelStat.count_model++;
                    for (SimulationContext simContext : bioModel.getSimulationContexts()) {
                        modelStat.count_geoDimApplications[simContext.getGeometry().getDimension()]++;
                        if (simContext.isStoch()) {
                            modelStat.count_app_stochastic++;
                        } else {
                            modelStat.count_app_deterministic++;
                        }
                    }
                    boolean bHasCompletedSim = false;
                    for (Simulation sim : bioModel.getSimulations()) {
                        SimulationStatusPersistent ss = dbServerImpl.getSimulationStatus(sim.getKey());
                        if (ss != null) {
                            for (int scan = 0; scan < sim.getScanCount(); scan++) {
                                SimulationJobStatusPersistent jobStatus = ss.getJobStatus(scan);
                                if (jobStatus != null) {
                                    if (jobStatus.getSchedulerStatus() == SchedulerStatus.COMPLETED) {
                                        bHasCompletedSim = true;
                                        long elapsed = jobStatus.getEndDate().getTime() - jobStatus.getStartDate().getTime();
                                        if (elapsed < 2 * MINUTE_IN_MS) {
                                            modelStat.runningTimeHistogram[0]++;
                                        } else if (elapsed < 5 * MINUTE_IN_MS) {
                                            modelStat.runningTimeHistogram[1]++;
                                        } else if (elapsed < 20 * MINUTE_IN_MS) {
                                            modelStat.runningTimeHistogram[2]++;
                                        } else if (elapsed < HOUR_IN_MS) {
                                            modelStat.runningTimeHistogram[3]++;
                                        } else if (elapsed < DAY_IN_MS) {
                                            modelStat.runningTimeHistogram[4]++;
                                        } else {
                                            modelStat.runningTimeHistogram[5]++;
                                        }
                                    }
                                    int dimension = sim.getMathDescription().getGeometry().getDimension();
                                    modelStat.count_geoDimSim[dimension]++;
                                    if (sim.getMathDescription().isNonSpatialStoch() || sim.getMathDescription().isSpatialStoch()) {
                                        modelStat.count_sim_stochastic++;
                                    } else {
                                        modelStat.count_sim_deterministic++;
                                    }
                                    if (dimension > 0) {
                                        if (sim.getSolverTaskDescription().getSolverDescription().isSemiImplicitPdeSolver()) {
                                            modelStat.count_semiSim++;
                                        } else {
                                            modelStat.count_fullySim++;
                                        }
                                    }
                                }
                            }
                        }
                    }
                    if (bHasCompletedSim) {
                        modelStat.count_model_simcomplete++;
                    }
                } catch (Exception e2) {
                    e2.printStackTrace(System.out);
                }
            }
        }
    }
    itemCount++;
    statOutputPW.println(itemCount + ". BioModel Statistics ");
    statOutputPW.println("====================================================");
    for (ModelStat modelStat : bioModelStats) {
        statOutputPW.println("\t" + modelStat.title);
        statOutputPW.println("========================================");
        statOutputPW.println("number of biomodels saved :\t" + modelStat.count_model);
        statOutputPW.println("number of biomodels that has at least 1 completed simulation :\t" + modelStat.count_model_simcomplete);
        statOutputPW.println();
        statOutputPW.println("Application statistics :");
        statOutputPW.println("number of application ODE :\t" + modelStat.count_geoDimApplications[0]);
        statOutputPW.println("number of application 1D :\t" + modelStat.count_geoDimApplications[1]);
        statOutputPW.println("number of application 2D :\t" + modelStat.count_geoDimApplications[2]);
        statOutputPW.println("number of application 3D :\t" + modelStat.count_geoDimApplications[3]);
        statOutputPW.println("number of application stochastic :\t" + modelStat.count_app_stochastic);
        statOutputPW.println("number of application deterministic :\t" + modelStat.count_app_deterministic);
        statOutputPW.println();
        statOutputPW.println("Simulation statistics (including all simulations (stopped, failed, completed) :");
        statOutputPW.println("number of run simulation ODE :\t" + modelStat.count_geoDimSim[0]);
        statOutputPW.println("number of run simulation 1D :\t" + modelStat.count_geoDimSim[1]);
        statOutputPW.println("number of run simulation 2D :\t" + modelStat.count_geoDimSim[2]);
        statOutputPW.println("number of run simulation 3D :\t" + modelStat.count_geoDimSim[3]);
        statOutputPW.println("number of run simulation Semi-Implicit :\t" + modelStat.count_semiSim);
        statOutputPW.println("number of run simulation Fully-Implicit :\t" + modelStat.count_fullySim);
        statOutputPW.println("number of run simulation stochastic :\t" + modelStat.count_sim_stochastic);
        statOutputPW.println("number of run simulation deterministic :\t" + modelStat.count_sim_deterministic);
        statOutputPW.println();
        statOutputPW.println("Running time histogram for completed simulations only:");
        statOutputPW.println("0 ~ 2min:\t" + modelStat.runningTimeHistogram[0]);
        statOutputPW.println("2 ~ 5min:\t" + modelStat.runningTimeHistogram[1]);
        statOutputPW.println("5 ~ 20min:\t" + modelStat.runningTimeHistogram[2]);
        statOutputPW.println("20min ~ 1hr:\t" + modelStat.runningTimeHistogram[3]);
        statOutputPW.println("1hr ~ 1day:\t" + modelStat.runningTimeHistogram[4]);
        statOutputPW.println(">1day:\t" + modelStat.runningTimeHistogram[5]);
        statOutputPW.println();
        statOutputPW.println();
        statOutputPW.flush();
    }
}