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

Example 41 with VCellApiApplication

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

the class BiomodelBNGLServerResource method get_xml.

@Override
@Get(BiomodelBNGLResource.APPLICATION_BNGL_XML)
public StringRepresentation get_xml() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
    String vcml = getBiomodelBNGL(vcellUser);
    if (vcml != null) {
        String bioModelID = (String) getRequestAttributes().get(VCellApiApplication.BIOMODELID);
        setAttribute("Content-Disposition", "attachment; filename=\"VCBioModel_" + bioModelID + ".vcml\"");
        return new StringRepresentation(vcml, BiomodelBNGLResource.VCDOC_MEDIATYPE);
    }
    throw new RuntimeException("biomodel not found");
}

Example 42 with VCellApiApplication

use of org.vcell.rest.VCellApiApplication 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 43 with VCellApiApplication

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

Example 44 with VCellApiApplication

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

the class BiomodelVCMLServerResource method get_xml.

@Override
@Get(BiomodelVCMLResource.APPLICATION_VCML_XML)
public StringRepresentation get_xml() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
    String vcml = getBiomodelVCML(vcellUser);
    if (vcml != null) {
        String bioModelID = (String) getRequestAttributes().get(VCellApiApplication.BIOMODELID);
        // setAttribute("Content-type", "application/vcml+xml");
        setAttribute("Content-Disposition", "attachment; filename=\"VCBioModel_" + bioModelID + ".vcml\"");
        return new StringRepresentation(vcml, BiomodelVCMLResource.VCDOC_MEDIATYPE);
    }
    throw new RuntimeException("biomodel not found");
}

Example 45 with VCellApiApplication

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

the class BiomodelsServerResource method get_html.

@Override
public Representation get_html() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
    BiomodelRepresentation[] biomodels = new BiomodelRepresentation[0];
    boolean bFormatErr = false;
    try {
        biomodels = getBiomodelRepresentations(vcellUser);
    } catch (ParseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        bFormatErr = true;
    }
    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("bmName", getQueryValue(PARAM_BM_NAME));
    dataModel.put("bmId", getQueryValue(PARAM_BM_ID));
    dataModel.put("savedLow", (bFormatErr ? "Error" : getQueryValue(PARAM_SAVED_LOW)));
    dataModel.put("savedHigh", (bFormatErr ? "Error" : getQueryValue(PARAM_SAVED_HIGH)));
    dataModel.put("ownerName", getQueryValue(PARAM_BM_OWNER));
    dataModel.put("category", getQueryValue(PARAM_CATEGORY));
    dataModel.put("orderBy", getQueryValue(PARAM_ORDERBY));
    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("biomodels", Arrays.asList(biomodels));
    Gson gson = new Gson();
    dataModel.put("jsonResponse", gson.toJson(biomodels));
    Configuration templateConfiguration = application.getTemplateConfiguration();
    Representation formFtl = new ClientResource(LocalReference.createClapReference("/biomodels.ftl")).get();
    TemplateRepresentation templateRepresentation = new TemplateRepresentation(formFtl, templateConfiguration, dataModel, MediaType.TEXT_HTML);
    return templateRepresentation;
}