Examples with OptRun org.vcell.optimization.thrift.OptRun used on opensource projects

Example 6 with OptRun

use of org.vcell.optimization.thrift.OptRun in project vcell by virtualcell.

the class OptServerImpl method runNextWaitingOptProblem.

public void runNextWaitingOptProblem() {
    OptRunContext optRunContext = null;
    synchronized (optRunContexts) {
        for (int i = 0; i < optRunContexts.size(); i++) {
            if (optRunContexts.get(i).optRunStatus == OptRunStatus.Queued) {
                optRunContext = optRunContexts.get(i);
                optRunContext.optRunStatus = OptRunStatus.Running;
                System.err.println("OptServerImpl - starting optimizationId " + optRunContext.optimizationId);
                break;
            }
        }
    }
    try {
        if (optRunContext != null) {
            OptProblem optProblem = CopasiServicePython.readOptProblem(optRunContext.getOptProblemBinaryFile());
            CopasiServicePython.writeOptProblem(optRunContext.getOptProblemBinaryFile(), optProblem);
            CopasiServicePython.runCopasiPython(optRunContext.getOptProblemBinaryFile(), optRunContext.getOptRunBinaryFile());
            OptRun optRun = CopasiServicePython.readOptRun(optRunContext.getOptRunBinaryFile());
            System.out.println("ran optRun id " + optRunContext.optimizationId + ": status=" + optRun.statusMessage + ": (" + optRun.getOptResultSet().toString() + ")");
            synchronized (optRunContexts) {
                optRunContext.optRunStatus = OptRunStatus.Complete;
                System.err.println("OptServerImpl - optimizationId " + optRunContext.optimizationId + " status=" + OptRunStatus.Complete);
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
        synchronized (optRunContexts) {
            optRunContext.optRunStatus = OptRunStatus.Failed;
            System.err.println("OptServerImpl - optimizationId " + optRunContext.optimizationId + " status=" + OptRunStatus.Failed);
        }
    }
}

Example 7 with OptRun

use of org.vcell.optimization.thrift.OptRun in project vcell by virtualcell.

the class OptimizationServerResource method getOptRun.

private OptRun getOptRun(User vcellUser) {
    // }else{
    try {
        String optimizationId = (String) getRequestAttributes().get(VCellApiApplication.OPTIMIZATIONID);
        VCellApiApplication application = ((VCellApiApplication) getApplication());
        OptRunContext optRunContext = application.getOptServerImpl().getOptRunContextByOptimizationId(optimizationId);
        if (optRunContext == null) {
            throw new ObjectNotFoundException("optimization id '" + optimizationId + "' not found");
        }
        switch(optRunContext.getStatus()) {
            case Complete:
                {
                    OptRun optRun = CopasiServicePython.readOptRun(optRunContext.getOptRunBinaryFile());
                    return optRun;
                }
            case Queued:
            case Running:
            case Failed:
                {
                    OptProblem optProblem = CopasiServicePython.readOptProblem(optRunContext.getOptProblemBinaryFile());
                    OptRun optRun = new OptRun();
                    optRun.setOptProblem(optProblem);
                    optRun.setStatus(optRunContext.getStatus());
                    optRun.setStatusMessage(optRunContext.getStatus().name());
                    return optRun;
                }
            default:
                {
                    throw new RuntimeException("unexpected optimization status '" + optRunContext.getStatus() + "'");
                }
        }
    } 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, "optimization not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}

Example 8 with OptRun

use of org.vcell.optimization.thrift.OptRun in project vcell by virtualcell.

the class OptimizationServerResource method get_html.

@Override
public Representation get_html() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
    OptRun optRun = getOptRun(vcellUser);
    if (optRun == null) {
        throw new RuntimeException("optimization not found");
    }
    try {
        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("optId", getQueryValue(VCellApiApplication.OPTIMIZATIONID));
        TSerializer serializer = new TSerializer(new TJSONProtocol.Factory());
        String optRunJson = new String(serializer.serialize(optRun));
        dataModel.put("optimization", new JSONObject(optRunJson));
        dataModel.put("jsonResponse", optRunJson);
        Configuration templateConfiguration = application.getTemplateConfiguration();
        Representation formFtl = new ClientResource(LocalReference.createClapReference("/optimization.ftl")).get();
        TemplateRepresentation templateRepresentation = new TemplateRepresentation(formFtl, templateConfiguration, dataModel, MediaType.TEXT_HTML);
        return templateRepresentation;
    } catch (Exception e) {
        e.printStackTrace();
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
}

Example 9 with OptRun

use of org.vcell.optimization.thrift.OptRun in project vcell by virtualcell.

the class OptimizationServerResource method get_json.

@Override
public JsonRepresentation get_json() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.prohibitInvalidCredentials);
    OptRun optRun = getOptRun(vcellUser);
    try {
        TSerializer serializer = new TSerializer(new TJSONProtocol.Factory());
        String optRunJson = new String(serializer.serialize(optRun));
        JsonRepresentation optRunJsonRep = new JsonRepresentation(optRunJson);
        return optRunJsonRep;
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
}