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

Example 1 with PermissionException

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

the class BiomodelBNGLServerResource method getBiomodelBNGL.

private String getBiomodelBNGL(User vcellUser) {
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        // Make temporary resource compatible with restDatabaseService so we can re-use
        BiomodelVCMLServerResource bmsr = new BiomodelVCMLServerResource() {

            @Override
            public Map<String, Object> getRequestAttributes() {
                HashMap<String, Object> hashMap = new HashMap<String, Object>();
                hashMap.put(VCellApiApplication.BIOMODELID, BiomodelBNGLServerResource.this.biomodelid);
                return hashMap;
            }

            @Override
            public Request getRequest() {
                // TODO Auto-generated method stub
                return BiomodelBNGLServerResource.this.getRequest();
            }
        };
        StringWriter bnglStringWriter = new StringWriter();
        PrintWriter pw = new PrintWriter(bnglStringWriter);
        String biomodelVCML = restDatabaseService.query(bmsr, vcellUser);
        BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(biomodelVCML));
        SimulationContext chosenSimContext = bioModel.getSimulationContext(0);
        RbmNetworkGenerator.writeBngl(chosenSimContext, pw, false, true);
        String resultString = bnglStringWriter.toString();
        return resultString;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "permission denied to requested resource");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
}

Example 2 with PermissionException

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

the class PublicationServerResource method getPublicationRepresentation.

private static PublicationRepresentation getPublicationRepresentation(RestDatabaseService restDatabaseService, User vcellUser, KeyValue pubID) {
    // RestDatabaseService restDatabaseService = ((VCellApiApplication)getApplication()).getRestDatabaseService();
    try {
        PublicationRep publicationRep = restDatabaseService.getPublicationRep(pubID, vcellUser);
        PublicationRepresentation publicationRepresentation = new PublicationRepresentation(publicationRep);
        return publicationRepresentation;
    } 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, "publication not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}

Example 3 with PermissionException

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

the class RestDatabaseService method query.

public SimulationRepresentation query(BiomodelSimulationServerResource resource, User vcellUser) throws SQLException, DataAccessException, ExpressionException, XmlParseException, MappingException, MathException, MatrixException, ModelException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    ArrayList<String> conditions = new ArrayList<String>();
    String bioModelID = (String) resource.getRequestAttributes().get(VCellApiApplication.BIOMODELID);
    if (bioModelID != null) {
        conditions.add("(" + BioModelTable.table.id.getQualifiedColName() + " = " + bioModelID + ")");
    } else {
        throw new RuntimeException(VCellApiApplication.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) {
        // 
        // try to determine if the current credentials are insufficient, try to fetch BioModel again with administrator privilege.
        // 
        User adminUser = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new KeyValue(PropertyLoader.ADMINISTRATOR_ID));
        BioModelRep[] allBioModelReps = databaseServerImpl.getBioModelReps(adminUser, conditionsBuffer.toString(), null, startRow, 1);
        if (allBioModelReps != null && allBioModelReps.length >= 0) {
            throw new PermissionException("insufficient privilege to retrive BioModel " + bioModelID);
        } else {
            throw new RuntimeException("failed to get biomodel");
        }
    }
    String simulationId = (String) resource.getRequestAttributes().get(VCellApiApplication.SIMULATIONID);
    if (simulationId == null) {
        throw new RuntimeException(VCellApiApplication.SIMULATIONID + " not specified");
    }
    SimulationRep simRep = getSimulationRep(new KeyValue(simulationId));
    BigString bioModelXML = databaseServerImpl.getBioModelXML(vcellUser, bioModelReps[0].getBmKey());
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    return new SimulationRepresentation(simRep, bioModel);
}

Example 4 with PermissionException

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

the class SimDataValuesServerResource method getSimDataValuesRepresentation.

private SimDataValuesRepresentation getSimDataValuesRepresentation(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        DataSetTimeSeries dataSetTimeSeries = restDatabaseService.getDataSetTimeSeries(this, vcellUser);
        SimDataValuesRepresentation simDataRepresentation = new SimDataValuesRepresentation(dataSetTimeSeries);
        return simDataRepresentation;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "not authorized to stop simulation");
    } catch (ObjectNotFoundException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "simulation not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}

Example 5 with PermissionException

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

the class SimulationTasksServerResource method getSimulationTaskRepresentations.

private SimulationTaskRepresentation[] getSimulationTaskRepresentations(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    ArrayList<SimulationTaskRepresentation> simTaskReps = new ArrayList<SimulationTaskRepresentation>();
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        SimpleJobStatus[] simJobStatusList = restDatabaseService.query(this, vcellUser);
        for (SimpleJobStatus simpleJobStatus : simJobStatusList) {
            SimulationTaskRepresentation simTaskRep = new SimulationTaskRepresentation(simpleJobStatus);
            simTaskReps.add(simTaskRep);
        }
    } catch (PermissionException ee) {
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "permission denied to requested resource");
    } catch (DataAccessException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to retrieve active jobs from VCell Database : " + e.getMessage());
    } catch (SQLException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to retrieve active jobs from VCell Database : " + e.getMessage());
    }
    return simTaskReps.toArray(new SimulationTaskRepresentation[0]);
// }
}