Examples with SimulationInfo cbit.vcell.solver.SimulationInfo used on opensource projects

Example 1 with SimulationInfo

use of cbit.vcell.solver.SimulationInfo in project vcell by virtualcell.

the class ClientRequestManager method stopSimulations.

public void stopSimulations(final ClientSimManager clientSimManager, final Simulation[] simulations) {
    // stop is single step operation, don't bother with tasks, thread inline
    AsynchClientTask task1 = new AsynchClientTask("stopping simulations", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Hashtable<Simulation, Throwable> failures = new Hashtable<Simulation, Throwable>();
            if (simulations != null && simulations.length > 0) {
                for (int i = 0; i < simulations.length; i++) {
                    try {
                        SimulationInfo simInfo = simulations[i].getSimulationInfo();
                        if (simInfo != null) {
                            // check for running once more... directly from job status
                            SimulationStatus serverSimulationStatus = getServerSimulationStatus(simInfo);
                            if (serverSimulationStatus != null && serverSimulationStatus.numberOfJobsDone() < simulations[i].getScanCount()) {
                                SimulationStatus simStatus = getClientServerManager().getJobManager().stopSimulation(simInfo.getAuthoritativeVCSimulationIdentifier());
                                // updateStatus
                                clientSimManager.updateStatusFromStopRequest(simulations[i], simStatus);
                            }
                        } else {
                            // this should really not happen...
                            throw new RuntimeException(">>>>>>>>>> trying to stop an unsaved simulation...");
                        }
                    } catch (Throwable exc) {
                        exc.printStackTrace(System.out);
                        failures.put(simulations[i], exc);
                    }
                }
                hashTable.put("failures", failures);
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("stopping simulations", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            @SuppressWarnings("unchecked") Hashtable<Simulation, Throwable> failures = (Hashtable<Simulation, Throwable>) hashTable.get("failures");
            if (failures != null && !failures.isEmpty()) {
                Enumeration<Simulation> en = failures.keys();
                while (en.hasMoreElements()) {
                    Simulation sim = (Simulation) en.nextElement();
                    Throwable exc = (Throwable) failures.get(sim);
                    // notify user
                    PopupGenerator.showErrorDialog(clientSimManager.getDocumentWindowManager(), "Failed to dispatch stop request for simulation'" + sim.getName() + "'\n" + exc.getMessage(), exc);
                }
            }
        }
    };
    ClientTaskDispatcher.dispatch(clientSimManager.getDocumentWindowManager().getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 2 with SimulationInfo

use of cbit.vcell.solver.SimulationInfo in project vcell by virtualcell.

the class TestingFrameworkWindowManager method selectSimInfoPrivate.

/**
 * Insert the method's description here.
 * Creation date: (11/13/2004 1:52:50 PM)
 * @return cbit.vcell.solver.SimulationInfo
 * @param sims cbit.vcell.solver.Simulation[]
 */
private SimulationInfo selectSimInfoPrivate(Simulation[] sims) {
    // Sort
    if (sims.length > 0) {
        java.util.Arrays.sort(sims, new java.util.Comparator<Simulation>() {

            public int compare(Simulation si1, Simulation si2) {
                return si1.getName().compareTo(si2.getName());
            }

            public boolean equals(Object obj) {
                return false;
            }
        });
    }
    String[] simInfoNames = new String[sims.length];
    for (int i = 0; i < simInfoNames.length; i++) {
        simInfoNames[i] = sims[i].getSimulationInfo().getName();
    }
    // Display the list of simInfo names in a list for user to choose the simulationInfo to compare with
    // in the case of regression testing.
    String selectedRefSimInfoName = (String) PopupGenerator.showListDialog(this, simInfoNames, "Please select reference simulation");
    if (selectedRefSimInfoName == null) {
        // PopupGenerator.showErrorDialog("Reference SimInfo not selected");
        return null;
    }
    int simIndex = -1;
    for (int i = 0; i < simInfoNames.length; i++) {
        if (simInfoNames[i].equals(selectedRefSimInfoName)) {
            simIndex = i;
        }
    }
    if (simIndex == -1) {
        PopupGenerator.showErrorDialog(TestingFrameworkWindowManager.this, "No such SimInfo Exists : " + selectedRefSimInfoName);
        return null;
    }
    SimulationInfo simInfo = (SimulationInfo) sims[simIndex].getSimulationInfo();
    return simInfo;
}

Example 3 with SimulationInfo

use of cbit.vcell.solver.SimulationInfo in project vcell by virtualcell.

the class TestingFrameworkWindowManager method updateTestCriteria.

/**
 * Insert the method's description here.
 * Creation date: (4/9/2003 1:31:08 PM)
 * @return cbit.vcell.numericstestingframework.TestSuiteInfo
 */
public void updateTestCriteria(TestCriteriaNew origTestCriteria, TestCriteriaNew newTestCriteria) throws DataAccessException {
    EditTestCriteriaOP testCriteriaOP = null;
    if (newTestCriteria instanceof TestCriteriaNewMathModel) {
        MathModelInfo regrMMInfo = ((TestCriteriaNewMathModel) newTestCriteria).getRegressionMathModelInfo();
        SimulationInfo regrsimInfo = ((TestCriteriaNewMathModel) newTestCriteria).getRegressionSimInfo();
        testCriteriaOP = new EditTestCriteriaOPMathModel(origTestCriteria.getTCritKey(), (regrMMInfo != null ? regrMMInfo.getVersion().getVersionKey() : null), (regrsimInfo != null ? regrsimInfo.getVersion().getVersionKey() : null), newTestCriteria.getMaxAbsError(), newTestCriteria.getMaxRelError());
    } else if (newTestCriteria instanceof TestCriteriaNewBioModel) {
        BioModelInfo regrBMInfo = ((TestCriteriaNewBioModel) newTestCriteria).getRegressionBioModelInfo();
        SimulationInfo regrsimInfo = ((TestCriteriaNewBioModel) newTestCriteria).getRegressionSimInfo();
        testCriteriaOP = new EditTestCriteriaOPBioModel(origTestCriteria.getTCritKey(), (regrBMInfo != null ? regrBMInfo.getVersion().getVersionKey() : null), (regrsimInfo != null ? regrsimInfo.getVersion().getVersionKey() : null), newTestCriteria.getMaxAbsError(), newTestCriteria.getMaxRelError());
    }
    getRequestManager().getDocumentManager().doTestSuiteOP(testCriteriaOP);
    RemoveTestResultsOP removeTestResults = new RemoveTestResultsOP(new BigDecimal[] { origTestCriteria.getTCritKey() });
    getRequestManager().getDocumentManager().doTestSuiteOP(removeTestResults);
}

Example 4 with SimulationInfo

use of cbit.vcell.solver.SimulationInfo in project vcell by virtualcell.

the class TestCriteriaNewBioModel method describe.

@Override
public String describe() {
    StringBuilder sb = new StringBuilder();
    if (regrBioModelInfo != null) {
        Version v = regrBioModelInfo.getVersion();
        if (v != null) {
            sb.append(v.getName());
            sb.append(' ');
        } else {
            sb.append("unversioned ");
        }
    } else {
        sb.append("no model info");
    }
    SimulationInfo si = getSimInfo();
    if (si != null) {
        sb.append(si.getName());
    } else {
        sb.append("no simulation");
    }
    return sb.toString();
}

Example 5 with SimulationInfo

use of cbit.vcell.solver.SimulationInfo in project vcell by virtualcell.

the class CheckBeforeDelete method checkLostResults.

/**
 * Insert the method's description here.
 * Creation date: (6/1/2004 3:44:03 PM)
 * @return cbit.vcell.solver.SolverResultSetInfo[]
 * @param bioModel cbit.vcell.biomodel.BioModel
 */
private Simulation[] checkLostResults(BioModel oldBioModel, BioModel newlySavedBioModel, cbit.vcell.clientdb.DocumentManager documentManager, Simulation[] submittedSimulations) throws Exception {
    // 
    // before deleting old version, prompt user if old simulation results will not be availlable in new edition
    // 
    Vector<Simulation> lostResultsSimulationList = new Vector<Simulation>();
    Simulation[] oldSimulations = oldBioModel.getSimulations();
    for (int i = 0; i < oldSimulations.length; i++) {
        Simulation oldSimulation = oldSimulations[i];
        SimulationStatus simStatus = null;
        SimulationInfo oldSimInfo = oldSimulation.getSimulationInfo();
        if (oldSimInfo != null) {
            // 
            // we need to ask for previous sim results (here we need possible translation to ask for parent's results).
            // 
            simStatus = documentManager.getServerSimulationStatus(oldSimInfo.getAuthoritativeVCSimulationIdentifier());
        }
        if (simStatus != null && simStatus.getHasData()) {
            // 
            // results exist in old version (the BioModel to be deleted) for SimulationInfo "oldSimInfo"
            // Users should be warned when they are going to loose any simulation results in any unexpected way.
            // 
            // WARN if the lost data is because new simulation is not mathematically equivalent to old edition
            // (different MathDescription key)
            // 
            // IGNORE if the lost data is from edits of a Simulation only (same MathDescription)
            // (same MathDescription key, different Simulation key)
            // 
            // IGNORE if Simulation has been deleted
            // (Simulation not found in current BioModel)
            // 
            // IGNORE if Simulation has been submitted for running
            // 
            boolean bDataInNewEdition = false;
            Simulation[] newSimulations = newlySavedBioModel.getSimulations();
            Simulation correspondingSimulation = null;
            for (int j = 0; j < newSimulations.length; j++) {
                if (newSimulations[j].getName().equals(oldSimulation.getName())) {
                    correspondingSimulation = newSimulations[j];
                    if (correspondingSimulation.getKey().equals(oldSimulation.getKey())) {
                        // 
                        // exactly same simulation (same key), so no lost data
                        // 
                        bDataInNewEdition = true;
                    } else if (correspondingSimulation.getSimulationVersion().getParentSimulationReference() != null) {
                        // 
                        // new simulation changed but points to same results
                        // 
                        bDataInNewEdition = true;
                    }
                    break;
                }
            }
            if (!bDataInNewEdition && correspondingSimulation != null) {
                // 
                // result set (for "rsInfo") will be lost, should we ignore this fact?
                // 
                boolean bIgnore = false;
                // 
                if (correspondingSimulation.getMathDescription().getKey().equals(oldSimulation.getMathDescription().getKey())) {
                    bIgnore = true;
                }
                // 
                for (int j = 0; submittedSimulations != null && j < submittedSimulations.length; j++) {
                    if (correspondingSimulation.getName().equals(submittedSimulations[j].getName())) {
                        bIgnore = true;
                    }
                }
                // 
                if (!bIgnore) {
                    lostResultsSimulationList.add(correspondingSimulation);
                }
            }
        }
    }
    return (Simulation[]) BeanUtils.getArray(lostResultsSimulationList, Simulation.class);
}