Examples with VCellApiApplication org.vcell.rest.VCellApiApplication used on opensource projects

Example 21 with VCellApiApplication

use of org.vcell.rest.VCellApiApplication in project vcell by virtualcell.

the class PublicationsServerResource method getPublicationRepresentations.

private PublicationRepresentation[] getPublicationRepresentations(User vcellUser) {
    ArrayList<PublicationRepresentation> publicationRepresentations = new ArrayList<PublicationRepresentation>();
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        PublicationRep[] publicationReps = restDatabaseService.query(this, vcellUser);
        for (PublicationRep publicationRep : publicationReps) {
            PublicationRepresentation publicationRepresentation = new PublicationRepresentation(publicationRep);
            publicationRepresentations.add(publicationRepresentation);
        }
    } 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 publicationRepresentations.toArray(new PublicationRepresentation[0]);
}

Example 22 with VCellApiApplication

use of org.vcell.rest.VCellApiApplication in project vcell by virtualcell.

the class PublicationsServerResource method get_json.

@Override
public PublicationRepresentation[] get_json() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.prohibitInvalidCredentials);
    return getPublicationRepresentations(vcellUser);
}

Example 23 with VCellApiApplication

use of org.vcell.rest.VCellApiApplication in project vcell by virtualcell.

the class SimDataServerResource method get_html.

@Override
public Representation get_html() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
    SimDataRepresentation simData = null;
    try {
        simData = getSimDataRepresentation(vcellUser);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
    Map<String, Object> dataModel = new HashMap<String, Object>();
    // +"?"+VCellApiApplication.REDIRECTURL_FORMNAME+"="+getRequest().getResourceRef().toUrl());
    dataModel.put("loginurl", "/" + VCellApiApplication.LOGINFORM);
    dataModel.put("logouturl", "/" + VCellApiApplication.LOGOUT + "?" + VCellApiApplication.REDIRECTURL_FORMNAME + "=" + Reference.encode(getRequest().getResourceRef().toUrl().toString()));
    if (vcellUser != null) {
        dataModel.put("userid", vcellUser.getName());
    }
    dataModel.put("userId", getAttribute(PARAM_USER));
    dataModel.put("simId", getQueryValue(PARAM_SIM_ID));
    Long startRowParam = getLongQueryValue(PARAM_START_ROW);
    if (startRowParam != null) {
        dataModel.put("startRow", startRowParam);
    } else {
        dataModel.put("startRow", 1);
    }
    Long maxRowsParam = getLongQueryValue(PARAM_MAX_ROWS);
    if (maxRowsParam != null) {
        dataModel.put("maxRows", maxRowsParam);
    } else {
        dataModel.put("maxRows", 10);
    }
    dataModel.put("simdata", simData);
    Gson gson = new Gson();
    dataModel.put("jsonResponse", gson.toJson(simData));
    Configuration templateConfiguration = application.getTemplateConfiguration();
    Representation formFtl = new ClientResource(LocalReference.createClapReference("/simdata.ftl")).get();
    TemplateRepresentation templateRepresentation = new TemplateRepresentation(formFtl, templateConfiguration, dataModel, MediaType.TEXT_HTML);
    return templateRepresentation;
}

Example 24 with VCellApiApplication

use of org.vcell.rest.VCellApiApplication in project vcell by virtualcell.

the class SimDataServerResource method get_json.

@Override
public SimDataRepresentation get_json() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.prohibitInvalidCredentials);
    return getSimDataRepresentation(vcellUser);
}

Example 25 with VCellApiApplication

use of org.vcell.rest.VCellApiApplication 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());
    }
// }
}