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

Example 1 with BiomodelRepresentation

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

the class BiomodelsServerResource method get_json.

@Override
public BiomodelRepresentation[] get_json() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.prohibitInvalidCredentials);
    BiomodelRepresentation[] bmReps = new BiomodelRepresentation[0];
    try {
        bmReps = getBiomodelRepresentations(vcellUser);
    } catch (ParseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    return bmReps;
}

Example 2 with BiomodelRepresentation

use of org.vcell.rest.common.BiomodelRepresentation 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;
}

Example 3 with BiomodelRepresentation

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

the class BiomodelsServerResource method getBiomodelRepresentations.

private BiomodelRepresentation[] getBiomodelRepresentations(User vcellUser) throws ParseException {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    ArrayList<BiomodelRepresentation> biomodelReps = new ArrayList<BiomodelRepresentation>();
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        BioModelRep[] bioModelReps = restDatabaseService.query(this, vcellUser);
        for (BioModelRep bioModelRep : bioModelReps) {
            BiomodelRepresentation biomodelRep = new BiomodelRepresentation(bioModelRep);
            biomodelReps.add(biomodelRep);
        }
    } 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 biomodelReps.toArray(new BiomodelRepresentation[0]);
// }
}

Example 4 with BiomodelRepresentation

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

the class BiomodelServerResource method getBiomodelRepresentation.

private BiomodelRepresentation getBiomodelRepresentation(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        BioModelRep bioModelRep = restDatabaseService.query(this, vcellUser);
        BiomodelRepresentation biomodelRep = new BiomodelRepresentation(bioModelRep);
        return biomodelRep;
    } 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 5 with BiomodelRepresentation

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

the class BiomodelServerResource method get_html.

@Override
public Representation get_html() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
    BiomodelRepresentation biomodel = getBiomodelRepresentation(vcellUser);
    if (biomodel == null) {
        throw new RuntimeException("biomodel not found");
    }
    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("bmId", getQueryValue(VCellApiApplication.BIOMODELID));
    dataModel.put("biomodel", biomodel);
    Gson gson = new Gson();
    dataModel.put("jsonResponse", gson.toJson(biomodel));
    Configuration templateConfiguration = application.getTemplateConfiguration();
    Representation formFtl = new ClientResource(LocalReference.createClapReference("/biomodel.ftl")).get();
    TemplateRepresentation templateRepresentation = new TemplateRepresentation(formFtl, templateConfiguration, dataModel, MediaType.TEXT_HTML);
    return templateRepresentation;
}