Examples with OverrideRepresentation org.vcell.rest.common.OverrideRepresentation used on opensource projects

Example 1 with OverrideRepresentation

use of org.vcell.rest.common.OverrideRepresentation in project vcell by virtualcell.

the class RestDatabaseService method saveSimulation.

public SimulationSaveResponse saveSimulation(BiomodelSimulationSaveServerResource resource, User vcellUser, List<OverrideRepresentation> overrideRepresentations) throws PermissionException, ObjectNotFoundException, DataAccessException, SQLException, XmlParseException, PropertyVetoException, MappingException, ExpressionException {
    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");
    }
    boolean myModel = simRep.getOwner().compareEqual(vcellUser);
    // get the bioModel
    String biomodelId = resource.getAttribute(VCellApiApplication.BIOMODELID);
    KeyValue biomodelKey = new KeyValue(biomodelId);
    BigString bioModelXML = this.databaseServerImpl.getBioModelXML(vcellUser, biomodelKey);
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    // copy the simulation as new
    Simulation origSimulation = null;
    for (Simulation sim : bioModel.getSimulations()) {
        if (sim.getKey().equals(simKey)) {
            origSimulation = sim;
        }
    }
    if (origSimulation == null) {
        throw new RuntimeException("cannot find original Simulation");
    }
    SimulationContext simContext = bioModel.getSimulationContext(origSimulation);
    Simulation newUnsavedSimulation = simContext.copySimulation(origSimulation);
    // make appropriate changes
    // MATH OVERRIDES
    MathOverrides mathOverrides = new MathOverrides(newUnsavedSimulation);
    for (OverrideRepresentation overrideRep : overrideRepresentations) {
        overrideRep.applyMathOverrides(mathOverrides);
    }
    newUnsavedSimulation.setMathOverrides(mathOverrides);
    // save bioModel
    String editedBioModelXML = XmlHelper.bioModelToXML(bioModel);
    ServerDocumentManager serverDocumentManager = new ServerDocumentManager(this.databaseServerImpl);
    String modelName = bioModel.getName();
    if (!myModel) {
        modelName = modelName + "_" + Math.abs(new Random().nextInt());
    }
    String newBioModelXML = serverDocumentManager.saveBioModel(new QueryHashtable(), vcellUser, editedBioModelXML, modelName, null);
    BioModel savedBioModel = XmlHelper.XMLToBioModel(new XMLSource(newBioModelXML));
    Simulation savedSimulation = null;
    for (Simulation sim : savedBioModel.getSimulations()) {
        if (sim.getName().equals(newUnsavedSimulation.getName())) {
            savedSimulation = sim;
        }
    }
    if (savedSimulation == null) {
        throw new RuntimeException("cannot find new Simulation");
    }
    return new SimulationSaveResponse(savedBioModel, savedSimulation);
}

Example 2 with OverrideRepresentation

use of org.vcell.rest.common.OverrideRepresentation in project vcell by virtualcell.

the class BiomodelSimulationSaveServerResource method save.

@Override
public void save(JsonRepresentation jsonOverrides) throws JSONException {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.prohibitInvalidCredentials);
    ArrayList<OverrideRepresentation> overrideRepresentations = new ArrayList<OverrideRepresentation>();
    if (jsonOverrides != null && jsonOverrides.getMediaType().isCompatible(MediaType.APPLICATION_JSON)) {
        JSONObject obj = jsonOverrides.getJsonObject();
        JSONArray overrideArray = obj.getJSONArray("overrides");
        for (int i = 0; i < overrideArray.length(); i++) {
            JSONObject overrideObj = overrideArray.getJSONObject(i);
            String name = overrideObj.getString("name");
            String type = overrideObj.getString("type");
            int cardinality = overrideObj.getInt("cardinality");
            double[] values = new double[0];
            if (overrideObj.has("values")) {
                JSONArray valuesArray = overrideObj.getJSONArray("values");
                values = new double[valuesArray.length()];
                for (int j = 0; j < valuesArray.length(); j++) {
                    values[j] = valuesArray.getDouble(j);
                }
            }
            String expression = null;
            if (overrideObj.has("expression")) {
                expression = overrideObj.getString("expression");
            }
            OverrideRepresentation overrideRep = new OverrideRepresentation(name, type, cardinality, values, expression);
            overrideRepresentations.add(overrideRep);
        }
    }
    RestDatabaseService restDatabaseService = application.getRestDatabaseService();
    try {
        if (vcellUser == null) {
            throw new PermissionException("must be authenticated to copy simulation");
        }
        SimulationSaveResponse simulationSavedResponse = restDatabaseService.saveSimulation(this, vcellUser, overrideRepresentations);
        JSONObject responseJson = new JSONObject();
        String redirectURL = "/" + VCellApiApplication.BIOMODEL + "/" + simulationSavedResponse.newBioModel.getVersion().getVersionKey() + "/" + VCellApiApplication.SIMULATION + "/" + simulationSavedResponse.newSimulation.getKey().toString();
        responseJson.put("redirect", redirectURL);
        responseJson.put("status", "simulation saved");
        JsonRepresentation representation = new JsonRepresentation(responseJson);
        redirectSeeOther(redirectURL);
    // return representation;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "not authorized to save simulation");
    } catch (ObjectNotFoundException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "simulation not found");
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
}