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

Example 21 with PermissionException

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

the class BiomodelsServerResource method getBiomodelRepresentations.

private BiomodelRepresentation[] getBiomodelRepresentations(User vcellUser) throws ParseException {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    ArrayList<BiomodelRepresentation> biomodelReps = new ArrayList<BiomodelRepresentation>();
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        BioModelRep[] bioModelReps = restDatabaseService.query(this, vcellUser);
        for (BioModelRep bioModelRep : bioModelReps) {
            BiomodelRepresentation biomodelRep = new BiomodelRepresentation(bioModelRep);
            biomodelReps.add(biomodelRep);
        }
    } catch (PermissionException ee) {
        ee.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "not authorized");
    } catch (DataAccessException | SQLException | ExpressionException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to retrieve biomodels from VCell Database : " + e.getMessage());
    }
    return biomodelReps.toArray(new BiomodelRepresentation[0]);
// }
}

Example 22 with PermissionException

use of org.vcell.util.PermissionException 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 23 with PermissionException

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

the class BiomodelServerResource method getBiomodelRepresentation.

private BiomodelRepresentation getBiomodelRepresentation(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        BioModelRep bioModelRep = restDatabaseService.query(this, vcellUser);
        BiomodelRepresentation biomodelRep = new BiomodelRepresentation(bioModelRep);
        return biomodelRep;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "permission denied to requested resource");
    } catch (ObjectNotFoundException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "biomodel not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}

Example 24 with PermissionException

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

the class SimulationControllerImpl method getOrCreateSolverController.

/**
 * This method was created by a SmartGuide.
 * @throws SolverException
 * @throws DataAccessException
 * @throws ConfigurationException
 * @exception java.rmi.RemoteException The exception description.
 * @throws JMSException
 * @throws AuthenticationException
 * @throws SQLException
 * @throws FileNotFoundException
 */
LocalSolverController getOrCreateSolverController(SimulationTask simTask) throws FileNotFoundException, ConfigurationException, DataAccessException, AuthenticationException, SQLException, SolverException {
    Simulation simulation = simTask.getSimulation();
    VCSimulationIdentifier vcSimID = simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
    if (vcSimID == null) {
        throw new IllegalArgumentException("cannot run an unsaved simulation");
    }
    if (!simulation.getVersion().getOwner().equals(localVCellConnection.getUserLoginInfo().getUser())) {
        throw new PermissionException("insufficient privilege: startSimulation()");
    }
    SimulationTaskID simTaskInfo = new SimulationTaskID(simTask);
    LocalSolverController solverController = solverControllerHash.get(simTaskInfo);
    if (solverController == null) {
        solverController = createNewSolverController(simTask);
        solverControllerHash.put(simTaskInfo, solverController);
    }
    return solverController;
}

Example 25 with PermissionException

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

the class SimulationContextDbDriver method deleteSimContextSQL.

/**
 * removeModel method comment.
 */
private void deleteSimContextSQL(Connection con, User user, KeyValue simContextKey) throws SQLException, PermissionException, DataAccessException, DependencyException {
    // log.print("deleteSimContextSQL(user=" + user + ", simContextKey=" + simContextKey + ")");
    // 
    // check for external references (from BioModel)
    // 
    failOnExternalRefs(con, BioModelSimContextLinkTable.table.simContextRef, BioModelSimContextLinkTable.table, simContextKey, SimContextTable.table);
    KeyValue mathKey = getDeletableMathKeyFromSimContext(con, user, simContextKey);
    // 
    // delete SimulationContext (Model and Geometry link tables are ON DELETE CASCADE)
    // 
    String sql;
    sql = DatabasePolicySQL.enforceOwnershipDelete(user, simContextTable, simContextTable.id.getQualifiedColName() + " = " + simContextKey);
    updateCleanSQL(con, sql);
    // 
    try {
        mathDescDB.deleteVersionable(con, user, VersionableType.MathDescription, mathKey);
        if (lg.isTraceEnabled()) {
            lg.trace("SimulationContextDbDriver.delete(" + simContextKey + ") deletion of MathDescription(" + mathKey + ") succeeded");
        }
    } catch (PermissionException | DependencyException e) {
        if (lg.isWarnEnabled()) {
            lg.warn("SimulationContextDbDriver.delete(" + simContextKey + ") deletion of MathDescription(" + mathKey + ") failed: " + e.getMessage());
        }
    }
}