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

Example 16 with PermissionException

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

the class BiomodelSimulationStartServerResource method start.

@Override
public Representation start() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.prohibitInvalidCredentials);
    RestDatabaseService restDatabaseService = application.getRestDatabaseService();
    try {
        SimulationRep simRep = restDatabaseService.startSimulation(this, vcellUser);
        Representation representation = new StringRepresentation("simulation started", MediaType.TEXT_PLAIN);
        redirectSeeOther("/" + VCellApiApplication.SIMTASK + "?" + SimulationTasksServerResource.PARAM_SIM_ID + "=" + simRep.getKey().toString() + "&" + SimulationTasksServerResource.PARAM_STATUS_COMPLETED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_DISPATCHED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_FAILED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_QUEUED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_RUNNING + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_STOPPED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_WAITING + "=on" + "&" + SimulationTasksServerResource.PARAM_START_ROW + "=1" + "&" + SimulationTasksServerResource.PARAM_MAX_ROWS + "=" + Integer.toString(simRep.getScanCount() * 4));
        return representation;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "not authorized to start 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 17 with PermissionException

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

the class BiomodelVCMLModelInfoResource method getBiomodel.

private BioModel getBiomodel(KeyValue bmKey, User vcellUser) {
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        // VCellApiApplication application = ((VCellApiApplication)getApplication());
        BigString cachedVcml = restDatabaseService.getBioModelXML(bmKey, vcellUser);
        BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(cachedVcml.toString()));
        return bioModel;
    } 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 18 with PermissionException

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

the class BiomodelVCMLModelInfoResource method getBiomodel.

private BioModel getBiomodel(String modelName, User vcellUser) {
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        // VCellApiApplication application = ((VCellApiApplication)getApplication());
        final VCInfoContainer vcInfoContainer = restDatabaseService.getVCInfoContainer(vcellUser);
        for (int i = 0; i < vcInfoContainer.getBioModelInfos().length; i++) {
            if (vcInfoContainer.getBioModelInfos()[i].getVersion().getName().equals(modelName)) {
                BigString cachedVcml = restDatabaseService.getBioModelXML(vcInfoContainer.getBioModelInfos()[i].getVersion().getVersionKey(), vcellUser);
                BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(cachedVcml.toString()));
                return bioModel;
            }
        }
        throw new Exception("VCDocument named '" + modelName + "'" + " not found");
    } 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 19 with PermissionException

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

the class BiomodelSimulationStopServerResource method stop.

@Override
public Representation stop() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.prohibitInvalidCredentials);
    RestDatabaseService restDatabaseService = application.getRestDatabaseService();
    try {
        SimulationRep simRep = restDatabaseService.stopSimulation(this, vcellUser);
        Representation representation = new StringRepresentation("simulation stopped", MediaType.TEXT_PLAIN);
        redirectSeeOther("/" + VCellApiApplication.SIMTASK + "?" + SimulationTasksServerResource.PARAM_SIM_ID + "=" + simRep.getKey().toString() + "&" + SimulationTasksServerResource.PARAM_STATUS_COMPLETED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_DISPATCHED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_FAILED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_QUEUED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_RUNNING + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_STOPPED + "=on" + "&" + SimulationTasksServerResource.PARAM_STATUS_WAITING + "=on" + "&" + SimulationTasksServerResource.PARAM_START_ROW + "=1" + "&" + SimulationTasksServerResource.PARAM_MAX_ROWS + "=" + Integer.toString(simRep.getScanCount() * 4));
        return representation;
    } 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 20 with PermissionException

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

the class BiomodelVCMLServerResource method getBiomodelVCML.

private String getBiomodelVCML(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        String cachedVcml = restDatabaseService.query(this, vcellUser);
        BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(cachedVcml));
        String latestVcml = XmlHelper.bioModelToXML(bioModel);
        return latestVcml;
    } 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());
    }
// }
}