Examples with SimulationRep cbit.vcell.modeldb.SimulationRep used on opensource projects

Example 11 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep in project vcell by virtualcell.

the class RestDatabaseService method getBioModelRep.

public BioModelRep getBioModelRep(KeyValue bmKey, User vcellUser) throws SQLException, ObjectNotFoundException, DataAccessException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    ArrayList<String> conditions = new ArrayList<String>();
    if (bmKey != null) {
        conditions.add("(" + BioModelTable.table.id.getQualifiedColName() + " = " + bmKey.toString() + ")");
    } else {
        throw new RuntimeException("bioModelID not specified");
    }
    StringBuffer conditionsBuffer = new StringBuffer();
    for (String condition : conditions) {
        if (conditionsBuffer.length() > 0) {
            conditionsBuffer.append(" AND ");
        }
        conditionsBuffer.append(condition);
    }
    int startRow = 1;
    int maxRows = 1;
    BioModelRep[] bioModelReps = databaseServerImpl.getBioModelReps(vcellUser, conditionsBuffer.toString(), null, startRow, maxRows);
    for (BioModelRep bioModelRep : bioModelReps) {
        KeyValue[] simContextKeys = bioModelRep.getSimContextKeyList();
        for (KeyValue scKey : simContextKeys) {
            SimContextRep scRep = getSimContextRep(scKey);
            if (scRep != null) {
                bioModelRep.addSimContextRep(scRep);
            }
        }
        KeyValue[] simulationKeys = bioModelRep.getSimKeyList();
        for (KeyValue simKey : simulationKeys) {
            SimulationRep simulationRep = getSimulationRep(simKey);
            if (simulationRep != null) {
                bioModelRep.addSimulationRep(simulationRep);
            }
        }
    }
    if (bioModelReps == null || bioModelReps.length != 1) {
        throw new ObjectNotFoundException("failed to get biomodel");
    }
    return bioModelReps[0];
}

Example 12 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep in project vcell by virtualcell.

the class RestDatabaseService method stopSimulation.

public SimulationRep stopSimulation(BiomodelSimulationStopServerResource resource, User vcellUser) throws PermissionException, ObjectNotFoundException, DataAccessException, SQLException {
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String simId = resource.getAttribute(VCellApiApplication.SIMULATIONID);
    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();
    if (!owner.compareEqual(vcellUser)) {
        throw new PermissionException("not authorized to stop simulation");
    }
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
        try {
            userLoginInfo.setUser(vcellUser);
        } catch (Exception e) {
            e.printStackTrace();
            throw new DataAccessException(e.getMessage());
        }
        RpcSimServerProxy rpcSimServerProxy = new RpcSimServerProxy(userLoginInfo, rpcSession);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        rpcSimServerProxy.stopSimulation(vcellUser, vcSimID);
        return simRep;
    } finally {
        rpcSession.close();
    }
}

Example 13 with SimulationRep

use of cbit.vcell.modeldb.SimulationRep in project vcell by virtualcell.

the class SimDataServerResource method getSimDataRepresentation.

private SimDataRepresentation getSimDataRepresentation(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        DataSetMetadata dataSetMetadata = restDatabaseService.getDataSetMetadata(this, vcellUser);
        SimulationRep simRep = restDatabaseService.getSimulationRep(dataSetMetadata.getSimKey());
        SimDataRepresentation simDataRepresentation = new SimDataRepresentation(dataSetMetadata, simRep.getScanCount());
        return simDataRepresentation;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "not authorized");
    } catch (ObjectNotFoundException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "simulation metadata not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}