Example 21 with VCSimulationDataIdentifier
use of cbit.vcell.solver.VCSimulationDataIdentifier in project vcell by virtualcell.
the class RestDatabaseService method getDataSetMetadata.
public DataSetMetadata getDataSetMetadata(SimDataServerResource resource, User vcellUser) throws ObjectNotFoundException, DataAccessException, SQLException {
if (vcellUser == null) {
vcellUser = VCellApiApplication.DUMMY_USER;
}
UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
// resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
String simId = resource.getAttribute(VCellApiApplication.SIMDATAID);
KeyValue simKey = new KeyValue(simId);
SimulationRep simRep = getSimulationRep(simKey);
if (simRep == null) {
throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
}
User owner = simRep.getOwner();
int jobIndex = 0;
VCMessageSession rpcSession = vcMessagingService.createProducerSession();
try {
RpcDataServerProxy rpcDataServerProxy = new RpcDataServerProxy(userLoginInfo, rpcSession);
VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
VCDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
DataSetMetadata dataSetMetadata = rpcDataServerProxy.getDataSetMetadata(vcdID);
return dataSetMetadata;
} finally {
rpcSession.close();
}
}
Also used :
VCSimulationIdentifier(cbit.vcell.solver.VCSimulationIdentifier)
KeyValue(org.vcell.util.document.KeyValue)
User(org.vcell.util.document.User)
VCMessageSession(cbit.vcell.message.VCMessageSession)
BigString(org.vcell.util.BigString)
VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier)
RpcDataServerProxy(org.vcell.rest.rpc.RpcDataServerProxy)
DataSetMetadata(cbit.vcell.simdata.DataSetMetadata)
ObjectNotFoundException(org.vcell.util.ObjectNotFoundException)
UserLoginInfo(org.vcell.util.document.UserLoginInfo)
VCDataIdentifier(org.vcell.util.document.VCDataIdentifier)
SimulationRep(cbit.vcell.modeldb.SimulationRep)
Example 22 with VCSimulationDataIdentifier
use of cbit.vcell.solver.VCSimulationDataIdentifier in project vcell by virtualcell.
the class SimResultsViewer method initialize.
/**
* Insert the method's description here.
* Creation date: (10/17/2005 11:37:52 PM)
* @exception org.vcell.util.DataAccessException The exception description.
*/
private void initialize() throws DataAccessException {
// create main viewer for jobIndex 0 and wire it up
if (isODEData) {
setMainViewer(createODEDataViewer());
} else {
setMainViewer(createPDEDataViewer());
}
java.beans.PropertyChangeListener pcl = new java.beans.PropertyChangeListener() {
public void propertyChange(java.beans.PropertyChangeEvent evt) {
if (evt.getSource() == SimResultsViewer.this && (evt.getPropertyName().equals("dataViewerManager"))) {
try {
getMainViewer().setDataViewerManager(getDataViewerManager());
} catch (java.beans.PropertyVetoException exc) {
exc.printStackTrace();
}
}
if (evt.getSource() == SimResultsViewer.this && (evt.getPropertyName().equals("simulationModelInfo"))) {
getMainViewer().setSimulationModelInfo(getSimulationModelInfo());
}
}
};
addPropertyChangeListener(pcl);
// if necessarry, create parameter choices panel and wire it up
if (getSimulation().getScanCount() > 1) {
JPanel panel = new JPanel();
panel.setLayout(new BorderLayout(5, 0));
panel.setBorder(BorderFactory.createEtchedBorder());
JLabel label = new JLabel("<html><b>Choose Parameter Values</b></html>");
label.setHorizontalAlignment(SwingConstants.CENTER);
label.setBorder(BorderFactory.createEmptyBorder(2, 2, 0, 2));
panel.add(label, BorderLayout.NORTH);
String[] scanParams = getSimulation().getMathOverrides().getScannedConstantNames();
Arrays.sort(scanParams);
JPanel tablePanel = new JPanel();
tablePanel.setLayout(new BoxLayout(tablePanel, BoxLayout.X_AXIS));
for (int i = 0; i < scanParams.length; i++) {
Constant[] scanConstants = getSimulation().getMathOverrides().getConstantArraySpec(scanParams[i]).getConstants();
String[][] values = new String[scanConstants.length][1];
for (int j = 0; j < scanConstants.length; j++) {
values[j][0] = scanConstants[j].getExpression().infix();
}
class ScanChoicesTableModel extends javax.swing.table.AbstractTableModel {
String[] columnNames;
Object[][] rowData;
ScanChoicesTableModel(Object[][] argData, String[] argNames) {
columnNames = argNames;
rowData = argData;
}
public String getColumnName(int column) {
return columnNames[column].toString();
}
public int getRowCount() {
return rowData.length;
}
public int getColumnCount() {
return columnNames.length;
}
public Object getValueAt(int row, int col) {
return rowData[row][col];
}
public boolean isCellEditable(int row, int column) {
return false;
}
public void setValueAt(Object value, int row, int col) {
rowData[row][col] = value;
fireTableCellUpdated(row, col);
}
}
;
ScanChoicesTableModel tm = new ScanChoicesTableModel(values, new String[] { scanParams[i] });
final JTable table = new JTable(tm);
choicesHash.put(scanParams[i], table);
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
table.getSelectionModel().setSelectionInterval(0, 0);
final ListSelectionListener[] nextListSelectionListener = new ListSelectionListener[1];
nextListSelectionListener[0] = new javax.swing.event.ListSelectionListener() {
public void valueChanged(javax.swing.event.ListSelectionEvent e) {
if (!e.getValueIsAdjusting()) {
DefaultListSelectionModel list = (DefaultListSelectionModel) e.getSource();
int selected = list.getAnchorSelectionIndex();
final int previous = (selected == e.getFirstIndex() ? e.getLastIndex() : e.getFirstIndex());
ListReset listReset = new ListReset() {
@Override
public void reset(VCDataIdentifier myVcDataIdentifier) {
if (myVcDataIdentifier instanceof VCSimulationDataIdentifier) {
int paramScanIndex = ((VCSimulationDataIdentifier) myVcDataIdentifier).getJobIndex();
table.getSelectionModel().removeListSelectionListener(nextListSelectionListener[0]);
try {
table.setRowSelectionInterval(paramScanIndex, paramScanIndex);
} finally {
table.getSelectionModel().addListSelectionListener(nextListSelectionListener[0]);
}
} else {
table.setRowSelectionInterval(previous, previous);
}
}
};
updateScanParamChoices("SimResultsViewer set paramScan index=" + getSelectedParamScanJobIndex(), listReset);
}
}
};
table.getSelectionModel().addListSelectionListener(nextListSelectionListener[0]);
JScrollPane scr = new JScrollPane(table);
JPanel p = new JPanel();
scr.setPreferredSize(new java.awt.Dimension(100, Math.min(150, table.getPreferredSize().height + table.getTableHeader().getPreferredSize().height + 5)));
p.setLayout(new java.awt.BorderLayout());
p.add(scr, java.awt.BorderLayout.CENTER);
p.setBorder(BorderFactory.createEmptyBorder(4, 4, 4, 4));
tablePanel.add(p);
}
panel.add(tablePanel, BorderLayout.CENTER);
if (isODEData) {
JPanel buttonPanel = new JPanel(new FlowLayout());
JButton button = new JButton("Time Plot with Multiple Parameter Value Sets");
buttonPanel.add(button);
panel.add(buttonPanel, BorderLayout.SOUTH);
button.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
mainViewer.showTimePlotMultipleScans(dataManager);
}
});
} else {
pdeDataViewer.setSimNameSimDataID(new ExportSpecs.SimNameSimDataID(getSimulation().getName(), getSimulation().getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), SimResultsViewer.getParamScanInfo(getSimulation(), getSelectedParamScanJobIndex())));
}
setParamChoicesPanel(panel);
}
// put things together
setLayout(new java.awt.BorderLayout());
add(getMainViewer(), java.awt.BorderLayout.CENTER);
if (getSimulation().getScanCount() > 1) {
add(getParamChoicesPanel(), java.awt.BorderLayout.SOUTH);
}
}
Also used :
JPanel(javax.swing.JPanel)
FlowLayout(java.awt.FlowLayout)
Constant(cbit.vcell.math.Constant)
ActionEvent(java.awt.event.ActionEvent)
ExportSpecs(cbit.vcell.export.server.ExportSpecs)
BoxLayout(javax.swing.BoxLayout)
JButton(javax.swing.JButton)
DefaultListSelectionModel(javax.swing.DefaultListSelectionModel)
BorderLayout(java.awt.BorderLayout)
BorderLayout(java.awt.BorderLayout)
JScrollPane(javax.swing.JScrollPane)
JLabel(javax.swing.JLabel)
VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier)
ListSelectionListener(javax.swing.event.ListSelectionListener)
ActionListener(java.awt.event.ActionListener)
JTable(javax.swing.JTable)
ListSelectionListener(javax.swing.event.ListSelectionListener)
VCDataIdentifier(org.vcell.util.document.VCDataIdentifier)
Example 23 with VCSimulationDataIdentifier
use of cbit.vcell.solver.VCSimulationDataIdentifier in project vcell by virtualcell.
the class VCellClientDataServiceImpl method getVtkManager.
@Override
public VtkManager getVtkManager(SimulationDataSetRef simulationDataSetRef) throws FileNotFoundException, DataAccessException {
VCSimulationDataIdentifier vcSimulationDataIdentifier = getVCSimulationDataIdentifier(simulationDataSetRef);
VtkManager vtkManager = null;
if (!simulationDataSetRef.isLocal) {
vtkManager = vcellClient.getRequestManager().getVtkManager(null, vcSimulationDataIdentifier);
} else {
// ---- preliminary : construct the localDatasetControllerProvider
File primaryDir = ResourceUtil.getLocalRootDir();
User usr = User.tempUser;
DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
LocalDataSetControllerProvider localDSCProvider = new LocalDataSetControllerProvider(usr, dataSetControllerImpl, localExportServiceImpl);
VCDataManager vcDataManager = new VCDataManager(localDSCProvider);
vtkManager = new VtkManager(null, vcDataManager, vcSimulationDataIdentifier);
}
return vtkManager;
}
Also used :
LocalDataSetControllerProvider(cbit.vcell.client.LocalDataSetControllerProvider)
User(org.vcell.util.document.User)
DataSetControllerImpl(cbit.vcell.simdata.DataSetControllerImpl)
ExportServiceImpl(cbit.vcell.export.server.ExportServiceImpl)
VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier)
LocalVCSimulationDataIdentifier(cbit.vcell.client.ClientSimManager.LocalVCSimulationDataIdentifier)
VtkManager(cbit.vcell.simdata.VtkManager)
File(java.io.File)
VCDataManager(cbit.vcell.simdata.VCDataManager)
Example 24 with VCSimulationDataIdentifier
use of cbit.vcell.solver.VCSimulationDataIdentifier in project vcell by virtualcell.
the class SimulationStateMachine method onWorkerEvent.
public synchronized void onWorkerEvent(WorkerEvent workerEvent, SimulationDatabase simulationDatabase, VCMessageSession session) throws DataAccessException, VCMessagingException, SQLException {
updateSolverProcessTimestamp();
WorkerEventMessage workerEventMessage = new WorkerEventMessage(workerEvent);
VCMongoMessage.sendWorkerEvent(workerEventMessage);
// as the filter of the client
String userName = workerEvent.getUserName();
int workerEventTaskID = workerEvent.getTaskID();
if (lg.isTraceEnabled())
lg.trace("onWorkerEventMessage[" + workerEvent.getEventTypeID() + "," + workerEvent.getSimulationMessage() + "][simid=" + workerEvent.getVCSimulationDataIdentifier() + ",job=" + jobIndex + ",task=" + workerEventTaskID + "]");
VCSimulationDataIdentifier vcSimDataID = workerEvent.getVCSimulationDataIdentifier();
if (vcSimDataID == null) {
VCMongoMessage.sendInfo("onWorkerEvent() ignoring WorkerEvent - no SimID in message): " + workerEvent.show());
return;
}
KeyValue simKey = vcSimDataID.getSimulationKey();
SimulationJobStatus oldSimulationJobStatus = simulationDatabase.getLatestSimulationJobStatus(simKey, jobIndex);
if (oldSimulationJobStatus == null) {
VCMongoMessage.sendInfo("onWorkerEvent() ignoring WorkerEvent, no current SimulationJobStatus: " + workerEvent.show());
return;
}
if (oldSimulationJobStatus == null || oldSimulationJobStatus.getSchedulerStatus().isDone() || oldSimulationJobStatus.getTaskID() > workerEventTaskID) {
VCMongoMessage.sendInfo("onWorkerEvent() ignoring outdated WorkerEvent, (currState=" + oldSimulationJobStatus.getSchedulerStatus().getDescription() + "): " + workerEvent.show());
return;
}
int taskID = oldSimulationJobStatus.getTaskID();
SchedulerStatus oldSchedulerStatus = oldSimulationJobStatus.getSchedulerStatus();
//
// status information (initialized as if new record)
//
Date startDate = null;
Date lastUpdateDate = null;
Date endDate = null;
boolean hasData = false;
HtcJobID htcJobID = null;
String computeHost = null;
VCellServerID vcServerID = VCellServerID.getSystemServerID();
Date submitDate = null;
Date queueDate = null;
int queuePriority = PRIORITY_DEFAULT;
SimulationJobStatus.SimulationQueueID simQueueID = SimulationJobStatus.SimulationQueueID.QUEUE_ID_WAITING;
//
// update using previously stored status (if available).
//
SimulationExecutionStatus oldSimExeStatus = oldSimulationJobStatus.getSimulationExecutionStatus();
if (oldSimExeStatus != null && oldSimExeStatus.getStartDate() != null) {
startDate = oldSimExeStatus.getStartDate();
}
if (oldSimExeStatus != null && oldSimExeStatus.getLatestUpdateDate() != null) {
lastUpdateDate = oldSimExeStatus.getLatestUpdateDate();
}
if (oldSimExeStatus != null && oldSimExeStatus.getEndDate() != null) {
endDate = oldSimExeStatus.getEndDate();
}
if (oldSimExeStatus != null && oldSimExeStatus.hasData()) {
hasData = true;
}
if (oldSimExeStatus != null && oldSimExeStatus.getComputeHost() != null) {
computeHost = oldSimExeStatus.getComputeHost();
}
if (oldSimExeStatus != null && oldSimExeStatus.getHtcJobID() != null) {
htcJobID = oldSimExeStatus.getHtcJobID();
}
vcServerID = oldSimulationJobStatus.getServerID();
submitDate = oldSimulationJobStatus.getSubmitDate();
SimulationQueueEntryStatus oldQueueStatus = oldSimulationJobStatus.getSimulationQueueEntryStatus();
if (oldQueueStatus != null && oldQueueStatus.getQueueDate() != null) {
queueDate = oldQueueStatus.getQueueDate();
}
if (oldQueueStatus != null) {
queuePriority = oldQueueStatus.getQueuePriority();
}
if (oldQueueStatus != null && oldQueueStatus.getQueueID() != null) {
simQueueID = oldQueueStatus.getQueueID();
}
//
if (workerEvent.getHtcJobID() != null) {
htcJobID = workerEvent.getHtcJobID();
}
if (workerEvent.getHostName() != null) {
computeHost = workerEvent.getHostName();
}
SimulationMessage workerEventSimulationMessage = workerEvent.getSimulationMessage();
if (workerEventSimulationMessage.getHtcJobId() != null) {
htcJobID = workerEventSimulationMessage.getHtcJobId();
}
SimulationJobStatus newJobStatus = null;
if (workerEvent.isAcceptedEvent()) {
//
if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued()) {
// new queue status
SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
// new exe status
lastUpdateDate = new Date();
startDate = lastUpdateDate;
endDate = null;
SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.DISPATCHED, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
}
} else if (workerEvent.isStartingEvent()) {
// only update database when the job event changes from started to running. The later progress event will not be recorded.
if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
// new queue status
SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
// new exe status
lastUpdateDate = new Date();
if (startDate == null) {
startDate = lastUpdateDate;
}
SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.RUNNING, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
}
} else if (workerEvent.isNewDataEvent()) {
if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
if (!oldSchedulerStatus.isRunning() || simQueueID != SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL || hasData == false) {
// new queue status
SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
// new exe status
if (startDate == null) {
startDate = lastUpdateDate;
}
hasData = true;
SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.RUNNING, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
}
}
} else if (workerEvent.isProgressEvent() || workerEvent.isWorkerAliveEvent()) {
if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
if (!oldSchedulerStatus.isRunning() || simQueueID != SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL) {
// new queue status
SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
// new exe status
if (startDate == null) {
startDate = lastUpdateDate;
}
SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.RUNNING, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
} else if (oldSchedulerStatus.isRunning()) {
if (oldSimExeStatus != null) {
// Date latestUpdate = oldSimExeStatus.getLatestUpdateDate();
// if (System.currentTimeMillis() - latestUpdate.getTime() >= MessageConstants.INTERVAL_PING_SERVER_MS * 3 / 5) {
// new queue status
SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.RUNNING, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
}
// }
}
}
} else if (workerEvent.isCompletedEvent()) {
if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
// new queue status
SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
// new exe status
endDate = new Date();
hasData = true;
SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.COMPLETED, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
}
} else if (workerEvent.isFailedEvent()) {
if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
// new queue status
SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
// new exe status
endDate = new Date();
SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.FAILED, taskID, workerEventSimulationMessage, newQueueStatus, newExeStatus);
}
} else if (workerEvent.isWorkerExitErrorEvent()) {
if (oldSchedulerStatus.isWaiting() || oldSchedulerStatus.isQueued() || oldSchedulerStatus.isDispatched() || oldSchedulerStatus.isRunning()) {
// new queue status
SimulationQueueEntryStatus newQueueStatus = new SimulationQueueEntryStatus(queueDate, queuePriority, SimulationJobStatus.SimulationQueueID.QUEUE_ID_NULL);
// new exe status
endDate = new Date();
SimulationExecutionStatus newExeStatus = new SimulationExecutionStatus(startDate, computeHost, lastUpdateDate, endDate, hasData, htcJobID);
SimulationMessage simulationMessage = SimulationMessage.workerFailure("solver stopped unexpectedly, " + workerEventSimulationMessage.getDisplayMessage());
newJobStatus = new SimulationJobStatus(vcServerID, vcSimDataID.getVcSimID(), jobIndex, submitDate, SchedulerStatus.FAILED, taskID, simulationMessage, newQueueStatus, newExeStatus);
}
}
if (newJobStatus != null) {
if (!newJobStatus.compareEqual(oldSimulationJobStatus) || workerEvent.isProgressEvent() || workerEvent.isNewDataEvent()) {
Double progress = workerEvent.getProgress();
Double timepoint = workerEvent.getTimePoint();
RunningStateInfo runningStateInfo = null;
if (progress != null && timepoint != null) {
runningStateInfo = new RunningStateInfo(progress, timepoint);
}
simulationDatabase.updateSimulationJobStatus(newJobStatus, runningStateInfo);
StatusMessage msgForClient = new StatusMessage(newJobStatus, userName, progress, timepoint);
msgForClient.sendToClient(session);
if (lg.isTraceEnabled())
lg.trace("Send status to client: " + msgForClient);
} else {
simulationDatabase.updateSimulationJobStatus(newJobStatus);
StatusMessage msgForClient = new StatusMessage(newJobStatus, userName, null, null);
msgForClient.sendToClient(session);
if (lg.isTraceEnabled())
lg.trace("Send status to client: " + msgForClient);
}
} else if (workerEvent.isProgressEvent() || workerEvent.isNewDataEvent()) {
Double progress = workerEvent.getProgress();
Double timepoint = workerEvent.getTimePoint();
RunningStateInfo runningStateInfo = null;
if (progress != null && timepoint != null) {
runningStateInfo = new RunningStateInfo(progress, timepoint);
}
simulationDatabase.updateSimulationJobStatus(oldSimulationJobStatus, runningStateInfo);
StatusMessage msgForClient = new StatusMessage(oldSimulationJobStatus, userName, progress, timepoint);
msgForClient.sendToClient(session);
if (lg.isTraceEnabled())
lg.trace("Send status to client: " + msgForClient);
} else {
VCMongoMessage.sendInfo("onWorkerEvent() ignoring WorkerEvent (currState=" + oldSchedulerStatus.getDescription() + "): " + workerEvent.show());
}
// addStateMachineTransition(new StateMachineTransition(new WorkerStateMachineEvent(taskID, workerEvent), oldSimulationJobStatus, newJobStatus));
}
Also used :
RunningStateInfo(cbit.vcell.server.RunningStateInfo)
SimulationExecutionStatus(cbit.vcell.server.SimulationExecutionStatus)
KeyValue(org.vcell.util.document.KeyValue)
SchedulerStatus(cbit.vcell.server.SimulationJobStatus.SchedulerStatus)
VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier)
SimulationQueueEntryStatus(cbit.vcell.server.SimulationQueueEntryStatus)
Date(java.util.Date)
StatusMessage(cbit.vcell.message.messages.StatusMessage)
VCellServerID(org.vcell.util.document.VCellServerID)
SimulationJobStatus(cbit.vcell.server.SimulationJobStatus)
SimulationMessage(cbit.vcell.solver.server.SimulationMessage)
WorkerEventMessage(cbit.vcell.message.messages.WorkerEventMessage)
HtcJobID(cbit.vcell.server.HtcJobID)
Example 25 with VCSimulationDataIdentifier
use of cbit.vcell.solver.VCSimulationDataIdentifier 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);
}
Also used :
AsynchClientTask(cbit.vcell.client.task.AsynchClientTask)
VCSimulationIdentifier(cbit.vcell.solver.VCSimulationIdentifier)
KeyValue(org.vcell.util.document.KeyValue)
Hashtable(java.util.Hashtable)
VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier)
BioModel(cbit.vcell.biomodel.BioModel)
FRAPStudy(cbit.vcell.microscopy.FRAPStudy)
File(java.io.File)
Aggregations
VCSimulationDataIdentifier (cbit.vcell.solver.VCSimulationDataIdentifier)47
VCSimulationIdentifier (cbit.vcell.solver.VCSimulationIdentifier)27
File (java.io.File)25
KeyValue (org.vcell.util.document.KeyValue)24
User (org.vcell.util.document.User)15
VCDataIdentifier (org.vcell.util.document.VCDataIdentifier)15
Simulation (cbit.vcell.solver.Simulation)11
BioModel (cbit.vcell.biomodel.BioModel)8
DataSetControllerImpl (cbit.vcell.simdata.DataSetControllerImpl)8
AsynchClientTask (cbit.vcell.client.task.AsynchClientTask)7
PDEDataManager (cbit.vcell.simdata.PDEDataManager)7
BigString (org.vcell.util.BigString)7
DataIdentifier (cbit.vcell.simdata.DataIdentifier)6
ODEDataManager (cbit.vcell.simdata.ODEDataManager)6
CartesianMesh (cbit.vcell.solvers.CartesianMesh)6
OutputContext (cbit.vcell.simdata.OutputContext)5
VCDataManager (cbit.vcell.simdata.VCDataManager)5
AnnotatedFunction (cbit.vcell.solver.AnnotatedFunction)5
IOException (java.io.IOException)5
Hashtable (java.util.Hashtable)5
