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

Example 26 with VCSimulationIdentifier

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

the class SimulationJobTable method getSimulationJobStatus.

/**
 * This method was created in VisualAge.
 * @return VCImage
 * @param rset ResultSet
 * @param log SessionLog
 */
public SimulationJobStatusPersistent getSimulationJobStatus(ResultSet rset) throws SQLException {
    // serverid
    String serID = rset.getString(this.serverID.toString());
    if (rset.wasNull()) {
        serID = null;
    }
    // simRef
    KeyValue parsedSimKey = new KeyValue(rset.getBigDecimal(simRef.toString()));
    // userKey
    KeyValue userKey = new KeyValue(rset.getBigDecimal(SimulationTable.table.ownerRef.toString()));
    // userKey
    String userid = rset.getString(UserTable.table.userid.toString());
    org.vcell.util.document.User owner = new org.vcell.util.document.User(userid, userKey);
    // submitDate
    java.util.Date parsedSubmitDate = rset.getTimestamp(submitDate.toString());
    // taskID
    int parsedTaskID = rset.getInt(taskID.toString());
    // schedulerStatus
    int parsedSchedulerStatusInt = rset.getInt(schedulerStatus.toString());
    SchedulerStatus parsedSchedulerStatus = SchedulerStatus.fromDatabaseNumber(parsedSchedulerStatusInt);
    // statusMsg
    String parsedStatusMsg = TokenMangler.getSQLRestoredString(rset.getString(statusMsg.toString()));
    SimulationMessagePersistent simulationMessage = SimulationMessagePersistent.fromSerialized(parsedSchedulerStatus, parsedStatusMsg);
    // 
    // read queue stuff
    // 
    // queueDate
    java.util.Date parsedQueuedDate = rset.getTimestamp(queueDate.toString());
    // queuePriority
    int parsedQueuePriority = rset.getInt(queuePriority.toString());
    if (rset.wasNull()) {
        parsedQueuePriority = -1;
    }
    // queueID
    int parsedQueueID = rset.getInt(queueID.toString());
    if (rset.wasNull()) {
        parsedQueueID = -1;
    }
    SimulationJobStatusPersistent.SimulationQueueID simulationQueueID = SimulationJobStatusPersistent.SimulationQueueID.fromDatabaseNumber(parsedQueueID);
    SimulationQueueEntryStatusPersistent simQueueEntryStatus = new SimulationQueueEntryStatusPersistent(parsedQueuedDate, parsedQueuePriority, simulationQueueID);
    // 
    // read solver stuff
    // 
    // startDate
    java.util.Date parsedStartDate = rset.getTimestamp(startDate.toString());
    // computeHost
    String parsedComputeHost = rset.getString(computeHost.toString());
    // latestUpdateDate
    java.util.Date parsedLatestUpdateDate = rset.getTimestamp(latestUpdateDate.toString());
    // endDate
    java.util.Date parsedEndDate = rset.getTimestamp(endDate.toString());
    // hasData
    String parsedHasData = rset.getString(hasData.toString());
    HtcJobID parsedHtcJobID = null;
    String htcJobIDString = rset.getString(pbsJobID.toString());
    if (!rset.wasNull() && htcJobIDString != null && htcJobIDString.length() > 0) {
        parsedHtcJobID = SimulationJobTable.fromDatabase(htcJobIDString);
    }
    SimulationExecutionStatusPersistent simExeStatus = new SimulationExecutionStatusPersistent(parsedStartDate, parsedComputeHost, parsedLatestUpdateDate, parsedEndDate, parsedHasData != null, parsedHtcJobID);
    VCSimulationIdentifier parsedVCSimID = new VCSimulationIdentifier(parsedSimKey, owner);
    // jobIndex
    int parsedJobIndex = rset.getInt(jobIndex.toString());
    SimulationJobStatusPersistent simulationJobStatus = new SimulationJobStatusPersistent(VCellServerID.getServerID(serID), parsedVCSimID, parsedJobIndex, parsedSubmitDate, parsedSchedulerStatus, parsedTaskID, simulationMessage, simQueueEntryStatus, simExeStatus);
    // sysDate
    java.util.Date parsedSysDate = rset.getTimestamp(DatabaseConstants.SYSDATE_COLUMN_NAME);
    if (!rset.wasNull()) {
        simulationJobStatus.setTimeDateStamp(parsedSysDate);
    }
    return simulationJobStatus;
}

Example 27 with VCSimulationIdentifier

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

the class EstParams_ReacBindingPanel method simulateWithCurrentParameters.

private // used by reaction binding panel only. not used by VFRAP 1.1 though
void simulateWithCurrentParameters() {
    fStudy = getFrapWorkspace().getWorkingFrapStudy();
    // save external files if needed
    AsynchClientTask saveTask = new AsynchClientTask("Preparing to run simulation ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // check external data before running simulation
            if (!FRAPWorkspace.areExternalDataOK(getLocalWorkspace(), fStudy.getFrapDataExternalDataInfo(), fStudy.getRoiExternalDataInfo())) {
                // if external files are missing/currupt or ROIs are changed, create keys and save them
                fStudy.setFrapDataExternalDataInfo(FRAPStudy.createNewExternalDataInfo(getLocalWorkspace(), FRAPStudy.IMAGE_EXTDATA_NAME));
                fStudy.setRoiExternalDataInfo(FRAPStudy.createNewExternalDataInfo(getLocalWorkspace(), FRAPStudy.ROI_EXTDATA_NAME));
                try {
                    fStudy.saveROIsAsExternalData(getLocalWorkspace(), fStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), fStudy.getStartingIndexForRecovery());
                    fStudy.saveImageDatasetAsExternalData(getLocalWorkspace(), fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), fStudy.getStartingIndexForRecovery());
                } catch (Exception e) {
                    // TODO Auto-generated catch block
                    e.printStackTrace();
                }
            }
        }
    };
    // run simulation task
    AsynchClientTask runSimTask = new AsynchClientTask("Running simulation ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            BioModel bioModel = null;
            KeyValue simKey = null;
            // }
            try {
                bioModel = FRAPStudy.createNewSimBioModel(fStudy, getCurrentParameters(), null, LocalWorkspace.createNewKeyValue(), LocalWorkspace.getDefaultOwner(), fStudy.getStartingIndexForRecovery());
                // we don't have to set the bioModel to frap study, we just need the results.
                // change time bound and time step
                // Simulation sim = bioModel.getSimulations()[0];
                // sim.getSolverTaskDescription().setTimeBounds(getRefTimeBounds());
                // sim.getSolverTaskDescription().setTimeStep(getRefTimeStep());
                // sim.getSolverTaskDescription().setOutputTimeSpec(getRefTimeSpec());
                // System.out.println("run FRAP Reference Simulation...");
                // final double RUN_REFSIM_PROGRESS_FRACTION = 1.0;
                // DataSetControllerImpl.ProgressListener runRefSimProgressListener =
                // new DataSetControllerImpl.ProgressListener(){
                // public void updateProgress(double progress) {
                // if(progressListener != null){
                // //To run to the steady state the time length is unpredictable. Progress increase 10 times
                // //because we manually set ending time to 1000 and usually it will reach steady state in less than 100 seconds.
                // //max allowed progress is 80%. this is heuristic.
                // progressListener.updateProgress(Math.min(0.8, (progress*10)*RUN_REFSIM_PROGRESS_FRACTION));
                // }
                // }
                // public void updateMessage(String message){
                // if(progressListener != null){
                // progressListener.updateMessage(message);
                // }
                // }
                // };
                // run simulation
                FRAPStudy.runFVSolverStandalone(new File(getLocalWorkspace().getDefaultSimDataDirectory()), bioModel.getSimulation(0), fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), fStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), this.getClientTaskStatusSupport(), false);
                /*//prepare to run native FV solver
					Simulation simulation = bioModel.getSimulations()[0];
					// clone and resample geometry
					Geometry resampledGeometry = null;
					try {
						resampledGeometry = (Geometry) BeanUtils.cloneSerializable(simulation.getMathDescription().getGeometry());
						GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
						ISize newSize = simulation.getMeshSpecification().getSamplingSize();
						geoSurfaceDesc.setVolumeSampleSize(newSize);
						geoSurfaceDesc.updateAll();		
					} catch (Exception e) {
						e.printStackTrace();
						throw new SolverException(e.getMessage());
					}	
					
					SimulationJob simJob = new SimulationJob(simulation, 0, null); //fielddata ID?
					
					StringWriter simulationInputStringWriter = new StringWriter();
					FiniteVolumeFileWriter fvFileWriter = new FiniteVolumeFileWriter(new PrintWriter(simulationInputStringWriter,true), simJob, resampledGeometry, new File(getLocalWorkspace().getDefaultSimDataDirectory())); //need dir?		
					fvFileWriter.write(null); //what are parameter names?
					simulationInputStringWriter.close();
					String fvInputStr = simulationInputStringWriter.getBuffer().toString();
					
					//run simulation with native FV solver
					double[][][] rawSimResults = new NativeFVSolver().solve(fvInputStr);*/
                simKey = bioModel.getSimulations()[0].getVersion().getVersionKey();
            } catch (Exception e) {
                if (bioModel != null && bioModel.getSimulations() != null) {
                    FRAPStudy.removeExternalDataAndSimulationFiles(bioModel.getSimulations()[0].getVersion().getVersionKey(), null, null, getLocalWorkspace());
                }
                throw e;
            }
            // push sim key into hash table
            // for all loaded file
            hashTable.put(FRAPStudyPanel.SIMULATION_KEY, simKey);
        }
    };
    // generate dimension reduced sim data
    AsynchClientTask readDataTask = new AsynchClientTask("Reading simulation data ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            KeyValue simulationKey = (KeyValue) hashTable.get(FRAPStudyPanel.SIMULATION_KEY);
            if (simulationKey != null) {
                VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simulationKey, LocalWorkspace.getDefaultOwner());
                VCSimulationDataIdentifier vcSimDataID = new VCSimulationDataIdentifier(vcSimID, FieldDataFileOperationSpec.JOBINDEX_DEFAULT);
                double[] rawSimTimePoints = getLocalWorkspace().getVCDataManager().getDataSetTimes(vcSimDataID);
                // to store time points in frap model (simulation time points may be slightly different with exp time points)
                setCurrentRawSimTimePoints(rawSimTimePoints);
                // refDataTimePoints = timeShiftForBaseDiffRate(rawRefDataTimePoints);
                // System.out.println("simulation done...");
                // DataSetControllerImpl.ProgressListener reducedRefDataProgressListener =
                // new DataSetControllerImpl.ProgressListener(){
                // public void updateProgress(double progress) {
                // if(progressListener != null){
                // progressListener.setProgress((int)((.5+progress*(1-RUNSIM_PROGRESS_FRACTION))*100));
                // }
                // }
                // public void updateMessage(String message){
                // if(progressListener != null){
                // progressListener.setMessage(message);
                // }
                // }
                // };
                double[][] results = FRAPOptimizationUtils.dataReduction(getLocalWorkspace().getVCDataManager(), vcSimDataID, rawSimTimePoints, fStudy.getFrapData().getRois(), this.getClientTaskStatusSupport(), false);
                // to store data in frap model.
                setCurrentSimResults(results);
                System.out.println("generating dimension reduced ref data, done ....");
                // remove reference simulation files
                FRAPStudy.removeSimulationFiles(simulationKey, getLocalWorkspace());
            }
        }
    };
    // plot task
    AsynchClientTask plotTask = new AsynchClientTask("Generating plots ...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            try {
                setData(fStudy.getFrapData(), getCurrentParameters(), fStudy.getFrapData().getImageDataset().getImageTimeStamps(), fStudy.getStartingIndexForRecovery(), fStudy.getSelectedROIsForErrorCalculation());
            } catch (Exception e) {
                // TODO Auto-generated catch block
                e.printStackTrace(System.out);
            }
        }
    };
    // dispatch
    ClientTaskDispatcher.dispatch(EstParams_ReacBindingPanel.this, new Hashtable<String, Object>(), new AsynchClientTask[] { saveTask, runSimTask, readDataTask, plotTask }, false);
}

Example 28 with VCSimulationIdentifier

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

the class IMGExporter method main.

public static void main(String[] args) throws Exception {
    if (args.length < 7) {
        System.out.println("Usage: IMGExporter username userkey simulationkey userdatadir beginTimeIndex endTimeIndex {varName1 varName2 ...}");
        System.exit(0);
    }
    String userName = args[0];
    String userKey = args[1];
    String SimulationKey = args[2];
    String primaryDirStr = args[3];
    int beginTimeIndex = Integer.valueOf(args[4]);
    int endTimeIndex = Integer.valueOf(args[5]);
    String[] varNames = new String[args.length - 6];
    if (args.length > 6) {
        for (int i = 6; i < args.length; i++) {
            varNames[i - 6] = args[i];
        }
    }
    PropertyLoader.loadProperties();
    User user = new User(userName, new KeyValue(userKey));
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(new KeyValue(SimulationKey), user);
    VCSimulationDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, 0);
    class PrintingExportServiceImpl extends ExportServiceImpl {

        public PrintingExportServiceImpl() {
            super();
        }

        @Override
        protected void fireExportEvent(ExportEvent event) {
            super.fireExportEvent(event);
            System.out.println("Event type=" + event.getEventTypeID() + " JobID=" + event.getJobID() + " progress=" + event.getProgress());
        }
    }
    ExportServiceImpl exportServiceImpl = new PrintingExportServiceImpl();
    Cachetable cachetable = new Cachetable(10 * Cachetable.minute);
    File primaryDir = new File(primaryDirStr);
    DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cachetable, primaryDir, null);
    DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, exportServiceImpl);
    double[] allTimes = dataSetControllerImpl.getDataSetTimes(vcdID);
    TimeSpecs timeSpecs = new TimeSpecs(beginTimeIndex, endTimeIndex, allTimes, ExportConstants.TIME_RANGE);
    VariableSpecs variableSpecs = new VariableSpecs(varNames, ExportConstants.VARIABLE_MULTI);
    GeometrySpecs geometrySpecs = new GeometrySpecs(null, 0, 0, ExportConstants.GEOMETRY_SLICE);
    DisplayPreferences displayPreferences = new DisplayPreferences(DisplayAdapterService.BLUERED, new Range(0, 1), DisplayAdapterService.createBlueRedSpecialColors());
    MovieSpecs movieSpecs = new MovieSpecs(// /
    1000.0, // /
    false, // /
    new DisplayPreferences[] { displayPreferences }, // /
    ExportFormat.FORMAT_JPEG, // /
    0, // /
    1, // /
    1, // /
    1, ImagePaneModel.MESH_MODE, FormatSpecificSpecs.CODEC_JPEG, 1.0f, false, FormatSpecificSpecs.PARTICLE_SELECT);
    ExportSpecs exportSpecs = new ExportSpecs(vcdID, ExportFormat.QUICKTIME, variableSpecs, timeSpecs, geometrySpecs, movieSpecs, "IMGExporterTest", null);
    exportServiceImpl.makeRemoteFile(null, user, dataServerImpl, exportSpecs);
}

Example 29 with VCSimulationIdentifier

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

the class SimulationJobStatusEvent method fromJsonRep.

public static SimulationJobStatusEvent fromJsonRep(Object eventSource, SimulationJobStatusEventRepresentation eventRep) {
    String simid = Simulation.createSimulationID(new KeyValue(eventRep.jobStatus.simulationKey));
    int jobIndex = eventRep.jobStatus.jobIndex;
    int taskID = eventRep.jobStatus.taskID;
    VCellServerID serverID = VCellServerID.getServerID(eventRep.jobStatus.vcellServerID);
    KeyValue simkey = new KeyValue(eventRep.jobStatus.simulationKey);
    User owner = new User(eventRep.jobStatus.owner_userid, new KeyValue(eventRep.jobStatus.onwer_userkey));
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simkey, owner);
    Date submitDate = eventRep.jobStatus.submitDate;
    SchedulerStatus schedulerStatus = null;
    if (eventRep.jobStatus.schedulerStatus != null) {
        schedulerStatus = SchedulerStatus.valueOf(eventRep.jobStatus.schedulerStatus.name());
    }
    HtcJobID htcJobID = null;
    Long htcJobNumber = eventRep.jobStatus.htcJobNumber;
    SimulationJobStatusRepresentation.BatchSystemType htcBatchSystemType = eventRep.jobStatus.htcBatchSystemType;
    if (htcJobNumber != null) {
        htcJobID = new HtcJobID(htcJobNumber.toString(), BatchSystemType.valueOf(htcBatchSystemType.name()));
    }
    SimulationMessage simMessage = null;
    DetailedState detailedState = DetailedState.valueOf(eventRep.jobStatus.detailedState.name());
    String message = eventRep.jobStatus.detailedStateMessage;
    if (detailedState != null) {
        simMessage = SimulationMessage.create(detailedState, message, htcJobID);
    }
    SimulationQueueEntryStatus simQueueStatus = null;
    Date queueDate = eventRep.jobStatus.queueDate;
    Integer queuePriority = eventRep.jobStatus.queuePriority;
    SimulationJobStatusRepresentation.SimulationQueueID queueId2 = eventRep.jobStatus.queueId;
    if (queueDate != null && queuePriority != null) {
        simQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationQueueID.valueOf(queueId2.name()));
    }
    SimulationExecutionStatus simExeStatus = null;
    Date startDate = eventRep.jobStatus.simexe_startDate;
    String computeHost = eventRep.jobStatus.computeHost;
    Date latestUpdateDate = eventRep.jobStatus.simexe_latestUpdateDate;
    Date endDate = eventRep.jobStatus.simexe_endDate;
    Boolean hasData = eventRep.jobStatus.hasData;
    if (latestUpdateDate != null) {
        simExeStatus = new SimulationExecutionStatus(startDate, computeHost, latestUpdateDate, endDate, hasData, htcJobID);
    }
    SimulationJobStatus jobStatus = new SimulationJobStatus(serverID, vcSimID, jobIndex, submitDate, schedulerStatus, taskID, simMessage, simQueueStatus, simExeStatus);
    Double progress = eventRep.progress;
    Double timepoint = eventRep.timePoint;
    String username = eventRep.username;
    SimulationJobStatusEvent event = new SimulationJobStatusEvent(eventSource, simid, jobStatus, progress, timepoint, username);
    return event;
}

Example 30 with VCSimulationIdentifier

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

the class ClientDocumentManager method getBioModel.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 4:02:44 PM)
 * @return cbit.vcell.biomodel.BioModel
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
public BioModel getBioModel(KeyValue bioModelKey) throws DataAccessException {
    XMLHolder<BioModel> bioModelXML = getBioModelXML(bioModelKey);
    BioModel bioModel = getBioModelFromDatabaseXML(bioModelXML);
    // if the positive & negative features for the membranes are not already set, set them using struct topology.
    bioModel.getModel().getElectricalTopology().populateFromStructureTopology();
    // 
    // preload SimulationJobStatus for all simulations if any missing from hash.
    // 
    Simulation[] simulations = bioModel.getSimulations();
    KeyValue[] simKeys = new KeyValue[simulations.length];
    for (int i = 0; i < simulations.length; i++) {
        VCSimulationIdentifier vcSimulationIdentifier = simulations[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
        simKeys[i] = vcSimulationIdentifier.getSimulationKey();
    }
    preloadSimulationStatus(simKeys);
    return bioModel;
}