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

Example 11 with VCellApiApplication

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

the class TestRestServerBlinov method getVCellApiApplication.

public static VCellApiApplication getVCellApiApplication() throws DataAccessException {
    return new VCellApiApplication(getRestDatabaseService(), null, null, null, null, new Configuration(), null, null) {

        @Override
        public Restlet createInboundRoot() {
            // TODO Auto-generated method stub
            Router rootRouter = new Router(getContext());
            // rootRouter.setDefaultMatchingMode(Template.MODE_STARTS_WITH);
            rootRouter.attach("/" + BIOMODEL, BiomodelsServerResource.class);
            rootRouter.attach("/" + BIOMODEL + "/{" + BIOMODELID + "}", BiomodelServerResource.class);
            rootRouter.attach("/" + BIOMODEL + "/{" + BIOMODELID + "}/" + SBML_DOWNLOAD, BiomodelSBMLServerResource.class);
            rootRouter.attach("/" + BIOMODEL + "/{" + BIOMODELID + "}/" + VCML_DOWNLOAD, BiomodelVCMLServerResource.class);
            return rootRouter;
        }

        @Override
        public User getVCellUser(ChallengeResponse response, AuthenticationPolicy authPolicy) {
            // TODO Auto-generated method stub
            return new User("gsoc", new KeyValue("0"));
        }
    };
}

Example 12 with VCellApiApplication

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

the class LostPasswordRestlet method handle.

@Override
public void handle(Request request, Response response) {
    if (request.getMethod().equals(Method.POST)) {
        System.out.println("in LostPasswordRestlet.handle()");
        String userid = request.getEntityAsText();
        if (userid == null || userid.length() == 0) {
            response.setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
            response.setEntity("expecting username in body", MediaType.TEXT_PLAIN);
            return;
        }
        // first line of defense against sql insertion attacks.
        if (!TokenMangler.fixTokenStrict(userid).equals(userid)) {
            response.setStatus(Status.CLIENT_ERROR_BAD_REQUEST);
            response.setEntity("unexpected characters in userid '" + userid + "'", MediaType.TEXT_PLAIN);
            return;
        }
        try {
            VCellApiApplication vcellApiApplication = (VCellApiApplication) getApplication();
            vcellApiApplication.getRestDatabaseService().sendLostPassword(userid);
        } catch (Exception e) {
            e.printStackTrace();
            response.setStatus(Status.SERVER_ERROR_INTERNAL);
            response.setEntity("we failed to send a verification email for account '" + userid + "': " + e.getMessage(), MediaType.TEXT_PLAIN);
            return;
        }
        response.setStatus(Status.SUCCESS_ACCEPTED);
        response.setEntity("we sent you a lost password email, please follow the link in that email", MediaType.TEXT_PLAIN);
    }
}

Example 13 with VCellApiApplication

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

the class SimulationTasksServerResource method getSimulationTaskRepresentations.

private SimulationTaskRepresentation[] getSimulationTaskRepresentations(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    ArrayList<SimulationTaskRepresentation> simTaskReps = new ArrayList<SimulationTaskRepresentation>();
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        SimpleJobStatus[] simJobStatusList = restDatabaseService.query(this, vcellUser);
        for (SimpleJobStatus simpleJobStatus : simJobStatusList) {
            SimulationTaskRepresentation simTaskRep = new SimulationTaskRepresentation(simpleJobStatus);
            simTaskReps.add(simTaskRep);
        }
    } catch (PermissionException ee) {
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "permission denied to requested resource");
    } catch (DataAccessException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to retrieve active jobs from VCell Database : " + e.getMessage());
    } catch (SQLException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to retrieve active jobs from VCell Database : " + e.getMessage());
    }
    return simTaskReps.toArray(new SimulationTaskRepresentation[0]);
// }
}

Example 14 with VCellApiApplication

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

the class EmailTokenVerifyRestlet method handle.

@Override
public void handle(Request request, Response response) {
    if (request.getMethod().equals(Method.GET)) {
        Form form = request.getResourceRef().getQueryAsForm();
        String emailverify_token = form.getFirstValue(VCellApiApplication.EMAILVERIFYTOKEN_FORMNAME);
        VCellApiApplication vcellApiApplication = (VCellApiApplication) getApplication();
        UnverifiedUser unverifiedUser = vcellApiApplication.getUserVerifier().getUnverifiedUser(emailverify_token);
        if (unverifiedUser != null) {
            if (unverifiedUser.verificationTimeoutDate.after(new Date())) {
                // 
                try {
                    vcellApiApplication.getRestDatabaseService().addUser(unverifiedUser.submittedUserInfo);
                } catch (SQLException e1) {
                    e1.printStackTrace();
                    throw new RuntimeException(e1.getMessage(), e1);
                } catch (DataAccessException e1) {
                    e1.printStackTrace();
                    throw new RuntimeException(e1.getMessage(), e1);
                } catch (UseridIDExistsException e1) {
                    e1.printStackTrace();
                    throw new RuntimeException(e1.getMessage(), e1);
                }
                // 
                // make default redirect after login (/biomodel).
                // 
                Reference successRedirectRef = new Reference(request.getResourceRef().getHostIdentifier() + "/" + VCellApiApplication.BIOMODEL);
                // 
                // redirect to login page for user to log in
                // 
                Form newform = new Form();
                newform.add(VCellApiApplication.REDIRECTURL_FORMNAME, successRedirectRef.toUrl().toString());
                newform.add(VCellApiApplication.IDENTIFIER_FORMNAME, unverifiedUser.submittedUserInfo.userid);
                newform.add(VCellApiApplication.SECRET_FORMNAME, "");
                Reference redirectRef;
                try {
                    redirectRef = new Reference(request.getResourceRef().getHostIdentifier() + "/" + VCellApiApplication.LOGINFORM + "?" + newform.encode());
                } catch (IOException e) {
                    throw new RuntimeException(e.getMessage());
                }
                response.redirectSeeOther(redirectRef);
                return;
            } else {
                response.setStatus(Status.CLIENT_ERROR_NOT_FOUND);
                response.setEntity("email verification expired, please register again at " + request.getResourceRef().getHostIdentifier() + "/" + VCellApiApplication.REGISTRATIONFORM, MediaType.TEXT_PLAIN);
            }
        } else {
            response.setStatus(Status.CLIENT_ERROR_NOT_FOUND);
            response.setEntity("email verification not found, please register again at " + request.getResourceRef().getHostIdentifier() + "/" + VCellApiApplication.REGISTRATIONFORM, MediaType.TEXT_PLAIN);
        }
    }
}

Example 15 with VCellApiApplication

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

the class LoginRestlet method handle.

@Override
public void handle(Request request, Response response) {
    // String html =
    // "<html>" +
    // "/login ... should have been redirected."+
    // "</html>";
    // response.setEntity(html, MediaType.TEXT_HTML);
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(request.getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
    String jsonString = "{}";
    if (vcellUser != null) {
        jsonString = "{user: \"" + vcellUser.getName() + "\"}";
    }
    response.setEntity(new JsonRepresentation(jsonString));
}