Examples with BioModelsQuerySpec org.vcell.api.client.query.BioModelsQuerySpec used on opensource projects

Example 1 with BioModelsQuerySpec

use of org.vcell.api.client.query.BioModelsQuerySpec in project vcell by virtualcell.

the class VCSchedulerPanel method refresh.

private void refresh() throws IOException {
    if (vcellApiClient != null) {
        StringBuffer buffer = new StringBuffer();
        BiomodelRepresentation[] biomodelReps = vcellApiClient.getBioModels(new BioModelsQuerySpec());
        for (BiomodelRepresentation biomodelRep : biomodelReps) {
            buffer.append("biomodel : " + biomodelRep.getBmKey() + " : " + biomodelRep.getName() + "\n");
            for (ApplicationRepresentation appRep : biomodelRep.getApplications()) {
                buffer.append("   app : " + appRep.getName() + "\n");
            }
            for (SimulationRepresentation simRep : biomodelRep.getSimulations()) {
                buffer.append("   sim : " + simRep.getName() + "\n");
            }
        }
        setText(buffer.toString());
    } else {
        setText("vcellApiClient is null");
    }
}

Example 2 with BioModelsQuerySpec

use of org.vcell.api.client.query.BioModelsQuerySpec in project vcell by virtualcell.

the class VCellApiClientTest method main.

/**
 * @param args
 */
public static void main(String[] args) {
    VCellApiClient vcellApiClient = null;
    try {
        if (args.length != 4 && args.length != 5) {
            System.out.println("usage: VCellApiClient host port userid password [clientID]");
            System.exit(1);
        }
        String host = args[0];
        int port = Integer.parseInt(args[1]);
        String username = args[2];
        String password = args[3];
        boolean bIgnoreCertProblems = true;
        boolean bIgnoreHostMismatch = true;
        vcellApiClient = new VCellApiClient(host, port, bIgnoreCertProblems, bIgnoreHostMismatch);
        vcellApiClient.authenticate(username, password, false);
        // test /biomodel[? query string]
        BiomodelRepresentation[] biomodelReps = vcellApiClient.getBioModels(new BioModelsQuerySpec());
        for (BiomodelRepresentation biomodelRep : biomodelReps) {
            System.out.println("biomodel : " + biomodelRep.getBmKey() + " : " + biomodelRep.getName());
            for (ApplicationRepresentation appRep : biomodelRep.getApplications()) {
                System.out.println("   app : " + appRep.getName());
            }
            for (SimulationRepresentation simRep : biomodelRep.getSimulations()) {
                System.out.println("   sim : " + simRep.getName());
            }
        }
        boolean bFirstSimulationToStartStop = true;
        if (biomodelReps.length > 0) {
            // test /biomodel/[bmkey]
            System.out.println(" ... re-fetching first biomodel owned by me ...");
            BioModelsQuerySpec bioModelsQuerySpec = new BioModelsQuerySpec();
            bioModelsQuerySpec.owner = username;
            BiomodelRepresentation firstBiomodelRep = vcellApiClient.getBioModels(bioModelsQuerySpec)[0];
            System.out.println("biomodel : " + firstBiomodelRep.getBmKey() + " : " + firstBiomodelRep.getName());
            for (ApplicationRepresentation appRep : firstBiomodelRep.getApplications()) {
                System.out.println("   appRep : " + appRep.getName());
            }
            for (SimulationRepresentation simRep : firstBiomodelRep.getSimulations()) {
                System.out.println("   simRep (returned with BioModelRep) : " + simRep.getKey() + " : " + simRep.getName());
                // test /biomodel/[bmkey]/simulation/simkey
                SimulationRepresentation simulation = vcellApiClient.getSimulation(firstBiomodelRep.getBmKey(), simRep.getKey());
                System.out.println("   simRep (retrieved separately) : " + simulation.getKey() + " : " + simulation.getName());
                if (bFirstSimulationToStartStop) {
                    bFirstSimulationToStartStop = false;
                    // test /biomodel/[bmkey]/simulation/[simkey]/startSimulation
                    SimTasksQuerySpec simTasksQuerySpec = new SimTasksQuerySpec();
                    simTasksQuerySpec.simId = simRep.getKey();
                    SimulationTaskRepresentation[] beforeStartSimTasks = vcellApiClient.getSimTasks(simTasksQuerySpec);
                    System.out.println("SENDING START SIMULATION");
                    SimulationTaskRepresentation[] justAfterStartSimTasks = vcellApiClient.startSimulation(firstBiomodelRep.getBmKey(), simRep.getKey());
                    System.out.println("SENT START SIMULATION");
                    System.out.println("WAITING 5 seconds");
                    try {
                        Thread.sleep(5000);
                    } catch (Exception e) {
                    }
                    SimulationTaskRepresentation[] longAfterStartSimTasks = vcellApiClient.getSimTasks(simTasksQuerySpec);
                    System.out.println("SENDING STOP SIMULATION");
                    SimulationTaskRepresentation[] justAfterStopSimTasks = vcellApiClient.stopSimulation(firstBiomodelRep.getBmKey(), simRep.getKey());
                    System.out.println("SENT STOP SIMULATION");
                    System.out.println("WAITING 5 seconds");
                    try {
                        Thread.sleep(5000);
                    } catch (Exception e) {
                    }
                    SimulationTaskRepresentation[] longAfterStopSimTasks = vcellApiClient.getSimTasks(simTasksQuerySpec);
                    System.out.println("\n\nsimulation status:");
                    for (SimulationTaskRepresentation simTaskRep : beforeStartSimTasks) {
                        System.out.println("    BEFORE START Job = " + simTaskRep.getJobIndex() + ", Task = " + simTaskRep.getTaskId() + ", Status = " + simTaskRep.getStatus());
                    }
                    for (SimulationTaskRepresentation simTaskRep : justAfterStartSimTasks) {
                        System.out.println("    JUST AFTER START Job = " + simTaskRep.getJobIndex() + ", Task = " + simTaskRep.getTaskId() + ", Status = " + simTaskRep.getStatus());
                    }
                    for (SimulationTaskRepresentation simTaskRep : longAfterStartSimTasks) {
                        System.out.println("    LONG AFTER START Job = " + simTaskRep.getJobIndex() + ", Task = " + simTaskRep.getTaskId() + ", Status = " + simTaskRep.getStatus());
                    }
                    for (SimulationTaskRepresentation simTaskRep : justAfterStopSimTasks) {
                        System.out.println("    JUST AFTER STOP Job = " + simTaskRep.getJobIndex() + ", Task = " + simTaskRep.getTaskId() + ", Status = " + simTaskRep.getStatus());
                    }
                    for (SimulationTaskRepresentation simTaskRep : longAfterStopSimTasks) {
                        System.out.println("    LONG AFTER STOP Job = " + simTaskRep.getJobIndex() + ", Task = " + simTaskRep.getTaskId() + ", Status = " + simTaskRep.getStatus());
                    }
                    System.out.println("\n\n");
                }
                System.out.println("\n");
            }
        }
        // test /simtask
        SimulationTaskRepresentation[] simTaskReps = vcellApiClient.getSimTasks(new SimTasksQuerySpec());
        for (SimulationTaskRepresentation simTaskRep : simTaskReps) {
            System.out.println("simTask : " + simTaskRep.getSimKey() + " : " + simTaskRep.getSimName());
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    } finally {
        if (vcellApiClient != null) {
            try {
                vcellApiClient.close();
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    }
}

Example 3 with BioModelsQuerySpec

use of org.vcell.api.client.query.BioModelsQuerySpec in project vcell by virtualcell.

the class RemoteProxyVCellConnectionFactoryTest method test.

@Test
public void test() throws IOException {
    BiomodelRepresentation[] biomodelReps = apiClient.getBioModels(new BioModelsQuerySpec());
    assertNotNull(biomodelReps);
    VCInfoContainer vcInfoContainer = null;
    try {
        vcInfoContainer = vcConn.getUserMetaDbServer().getVCInfoContainer();
    } catch (DataAccessException | RemoteProxyException e) {
        e.printStackTrace();
        fail("exception");
    }
    assertNotNull(vcInfoContainer);
}

Example 4 with BioModelsQuerySpec

use of org.vcell.api.client.query.BioModelsQuerySpec in project vcell by virtualcell.

the class VCellModelService method getModels.

public Task<List<VCellModel>, String> getModels(VCellService vCellService) {
    final Task<List<VCellModel>, String> task = new Task<List<VCellModel>, String>() {

        @Override
        protected List<VCellModel> doInBackground() throws Exception {
            boolean bIgnoreCertProblems = true;
            boolean bIgnoreHostMismatch = true;
            VCellApiClient vCellApiClient = null;
            List<VCellModel> vCellModels = new ArrayList<VCellModel>();
            try {
                vCellApiClient = new VCellApiClient(HOST, PORT, bIgnoreCertProblems, bIgnoreHostMismatch);
                vCellApiClient.authenticate("ImageJ", "richarddberlin", false);
                BioModelsQuerySpec querySpec = new BioModelsQuerySpec();
                querySpec.owner = "tutorial";
                final BiomodelRepresentation[] biomodelReps = vCellApiClient.getBioModels(querySpec);
                final int modelsToLoad = biomodelReps.length;
                int modelsLoaded = 0;
                for (BiomodelRepresentation biomodelRep : biomodelReps) {
                    setSubtask(biomodelRep.getName());
                    ApplicationRepresentation[] applicationReps = biomodelRep.getApplications();
                    if (applicationReps.length > 0) {
                        String vcml = getVCML(biomodelRep);
                        if (vcml != null) {
                            SBMLDocument sbml = vCellService.getSBML(vcml, applicationReps[0].getName());
                            VCellModel vCellModel = new VCellModel(biomodelRep.getName(), biomodelRep.getBmKey(), sbml);
                            vCellModels.add(vCellModel);
                            modelsLoaded++;
                            setProgress(modelsLoaded * 100 / modelsToLoad);
                        } else {
                            System.err.println("failed to return VCML for " + biomodelRep.bmKey);
                        }
                    }
                }
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
            return vCellModels;
        }
    };
    return task;
}