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

Example 1 with SimulationRepresentation

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

the class BiomodelSimulationServerResource method get_json.

@Override
public SimulationRepresentation get_json() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.prohibitInvalidCredentials);
    SimulationRepresentation simulationRep = getBiomodelSimulationRepresentation(vcellUser);
    if (simulationRep != null) {
        return simulationRep;
    }
    throw new RuntimeException("simulation not found");
}

Example 2 with SimulationRepresentation

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

the class RestDatabaseService method query.

public SimulationRepresentation query(BiomodelSimulationServerResource resource, User vcellUser) throws SQLException, DataAccessException, ExpressionException, XmlParseException, MappingException, MathException, MatrixException, ModelException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    ArrayList<String> conditions = new ArrayList<String>();
    String bioModelID = (String) resource.getRequestAttributes().get(VCellApiApplication.BIOMODELID);
    if (bioModelID != null) {
        conditions.add("(" + BioModelTable.table.id.getQualifiedColName() + " = " + bioModelID + ")");
    } else {
        throw new RuntimeException(VCellApiApplication.BIOMODELID + " not specified");
    }
    StringBuffer conditionsBuffer = new StringBuffer();
    for (String condition : conditions) {
        if (conditionsBuffer.length() > 0) {
            conditionsBuffer.append(" AND ");
        }
        conditionsBuffer.append(condition);
    }
    int startRow = 1;
    int maxRows = 1;
    BioModelRep[] bioModelReps = databaseServerImpl.getBioModelReps(vcellUser, conditionsBuffer.toString(), null, startRow, maxRows);
    for (BioModelRep bioModelRep : bioModelReps) {
        KeyValue[] simContextKeys = bioModelRep.getSimContextKeyList();
        for (KeyValue scKey : simContextKeys) {
            SimContextRep scRep = getSimContextRep(scKey);
            if (scRep != null) {
                bioModelRep.addSimContextRep(scRep);
            }
        }
        KeyValue[] simulationKeys = bioModelRep.getSimKeyList();
        for (KeyValue simKey : simulationKeys) {
            SimulationRep simulationRep = getSimulationRep(simKey);
            if (simulationRep != null) {
                bioModelRep.addSimulationRep(simulationRep);
            }
        }
    }
    if (bioModelReps == null || bioModelReps.length != 1) {
        // 
        // try to determine if the current credentials are insufficient, try to fetch BioModel again with administrator privilege.
        // 
        User adminUser = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new KeyValue(PropertyLoader.ADMINISTRATOR_ID));
        BioModelRep[] allBioModelReps = databaseServerImpl.getBioModelReps(adminUser, conditionsBuffer.toString(), null, startRow, 1);
        if (allBioModelReps != null && allBioModelReps.length >= 0) {
            throw new PermissionException("insufficient privilege to retrive BioModel " + bioModelID);
        } else {
            throw new RuntimeException("failed to get biomodel");
        }
    }
    String simulationId = (String) resource.getRequestAttributes().get(VCellApiApplication.SIMULATIONID);
    if (simulationId == null) {
        throw new RuntimeException(VCellApiApplication.SIMULATIONID + " not specified");
    }
    SimulationRep simRep = getSimulationRep(new KeyValue(simulationId));
    BigString bioModelXML = databaseServerImpl.getBioModelXML(vcellUser, bioModelReps[0].getBmKey());
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    return new SimulationRepresentation(simRep, bioModel);
}

Example 3 with SimulationRepresentation

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

the class RestDatabaseService method query.

public SimulationStatusRepresentation[] query(SimulationStatusServerResource resource, User vcellUser) throws SQLException, DataAccessException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    String userID = vcellUser.getName();
    SimpleJobStatusQuerySpec simQuerySpec = new SimpleJobStatusQuerySpec();
    simQuerySpec.userid = userID;
    simQuerySpec.simId = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_SIM_ID);
    String hasData = resource.getQueryValue(SimulationStatusServerResource.PARAM_HAS_DATA);
    if (hasData != null && hasData.equals("yes")) {
        simQuerySpec.hasData = true;
    } else if (hasData != null && hasData.equals("no")) {
        simQuerySpec.hasData = false;
    } else {
        simQuerySpec.hasData = null;
    }
    simQuerySpec.waiting = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_ACTIVE, false);
    simQuerySpec.queued = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_ACTIVE, false);
    simQuerySpec.dispatched = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_ACTIVE, false);
    simQuerySpec.running = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_ACTIVE, false);
    simQuerySpec.completed = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_COMPLETED, false);
    simQuerySpec.failed = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_FAILED, false);
    simQuerySpec.stopped = resource.getBooleanQueryValue(SimulationStatusServerResource.PARAM_STATUS_STOPPED, false);
    simQuerySpec.submitLowMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_SUBMIT_LOW);
    simQuerySpec.submitHighMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_SUBMIT_HIGH);
    simQuerySpec.startLowMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_START_LOW);
    simQuerySpec.startHighMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_START_HIGH);
    simQuerySpec.endLowMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_END_LOW);
    simQuerySpec.endHighMS = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_END_HIGH);
    Long startRowParam = resource.getLongQueryValue(SimulationStatusServerResource.PARAM_START_ROW);
    // default
    simQuerySpec.startRow = 1;
    if (startRowParam != null) {
        simQuerySpec.startRow = startRowParam.intValue();
    }
    Long maxRowsParam = resource.getLongQueryValue(SimulationTasksServerResource.PARAM_MAX_ROWS);
    // default
    simQuerySpec.maxRows = 10;
    if (maxRowsParam != null) {
        simQuerySpec.maxRows = maxRowsParam.intValue();
    }
    SimulationStatus[] simStatuses = null;
    HashMap<KeyValue, SimulationDocumentLink> simDocLinks = new HashMap<KeyValue, SimulationDocumentLink>();
    // 
    // ask server for simJobStatuses with above query spec.
    // find set of simulation IDs from the result set of simJobStatus
    // ask server for simulationStatuses from list of sim IDs.
    // 
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
        try {
            userLoginInfo.setUser(vcellUser);
        } catch (Exception e) {
            e.printStackTrace();
            throw new DataAccessException(e.getMessage());
        }
        RpcSimServerProxy rpcSimServerProxy = new RpcSimServerProxy(userLoginInfo, rpcSession);
        SimpleJobStatus[] simpleJobStatusArray = rpcSimServerProxy.getSimpleJobStatus(vcellUser, simQuerySpec);
        // gather unique simIDs and go back and ask server for SimulationStatuses
        for (SimpleJobStatus simpleJobStatus : simpleJobStatusArray) {
            KeyValue simulationKey = simpleJobStatus.jobStatus.getVCSimulationIdentifier().getSimulationKey();
            SimulationDocumentLink simulationDocumentLink = simpleJobStatus.simulationDocumentLink;
            simDocLinks.put(simulationKey, simulationDocumentLink);
        }
        KeyValue[] simKeys = simDocLinks.keySet().toArray(new KeyValue[0]);
        if (simKeys.length > 0) {
            simStatuses = rpcSimServerProxy.getSimulationStatus(vcellUser, simKeys);
        }
    } finally {
        rpcSession.close();
    }
    ArrayList<SimulationStatusRepresentation> simStatusReps = new ArrayList<SimulationStatusRepresentation>();
    for (int i = 0; simStatuses != null && i < simStatuses.length; i++) {
        KeyValue simulationKey = simStatuses[i].getVCSimulationIdentifier().getSimulationKey();
        SimulationRep simRep = getSimulationRep(simulationKey);
        try {
            SimulationRepresentation simRepresentation = new SimulationRepresentation(simRep, simDocLinks.get(simulationKey));
            simStatusReps.add(new SimulationStatusRepresentation(simRepresentation, simStatuses[i]));
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
        }
    }
    return simStatusReps.toArray(new SimulationStatusRepresentation[0]);
}

Example 4 with SimulationRepresentation

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

the class BiomodelSimulationServerResource method get_html.

@Override
public Representation get_html() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
    SimulationRepresentation simulation = getBiomodelSimulationRepresentation(vcellUser);
    if (simulation == null) {
        throw new RuntimeException("simulation not found");
    }
    Map<String, Object> dataModel = new HashMap<String, Object>();
    dataModel.put("simulation", simulation);
    // +"?"+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());
    }
    Gson gson = new Gson();
    dataModel.put("jsonResponse", gson.toJson(simulation));
    Configuration templateConfiguration = application.getTemplateConfiguration();
    Representation formFtl = new ClientResource(LocalReference.createClapReference("/simulation.ftl")).get();
    TemplateRepresentation templateRepresentation = new TemplateRepresentation(formFtl, templateConfiguration, dataModel, MediaType.TEXT_HTML);
    return templateRepresentation;
}