Examples with VariableInfo org.vcell.sbmlsim.api.common.VariableInfo used on opensource projects

Example 1 with VariableInfo

use of org.vcell.sbmlsim.api.common.VariableInfo in project vcell by virtualcell.

the class SimulationServiceImpl method getVariableList.

@Override
public List<VariableInfo> getVariableList(SimulationInfo simInfo) throws Exception {
    SimulationServiceContext simServiceContext = sims.get(simInfo.getLocalId());
    if (simServiceContext == null) {
        throw new Exception("simulation results not found");
    }
    try {
        DataSetControllerImpl datasetController = getDataSetController(simServiceContext);
        OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
        final DataIdentifier[] dataIdentifiers;
        try {
            dataIdentifiers = datasetController.getDataIdentifiers(outputContext, simServiceContext.vcDataIdentifier);
        } catch (IOException | DataAccessException e) {
            e.printStackTrace();
            throw new RuntimeException("failed to retrieve variable information: " + e.getMessage(), e);
        }
        ArrayList<VariableInfo> varInfos = new ArrayList<VariableInfo>();
        for (DataIdentifier dataIdentifier : dataIdentifiers) {
            final DomainType domainType;
            if (dataIdentifier.getVariableType().equals(VariableType.VOLUME)) {
                domainType = DomainType.VOLUME;
            } else if (dataIdentifier.getVariableType().equals(VariableType.MEMBRANE)) {
                domainType = DomainType.MEMBRANE;
            } else {
                continue;
            }
            String domainName = "";
            if (dataIdentifier.getDomain() != null) {
                domainName = dataIdentifier.getDomain().getName();
            }
            VariableInfo varInfo = new VariableInfo(dataIdentifier.getName(), dataIdentifier.getDisplayName(), domainName, domainType);
            varInfos.add(varInfo);
        }
        return varInfos;
    } catch (Exception e) {
        e.printStackTrace();
        throw new Exception("failed to retrieve variable list: " + e.getMessage());
    }
}

Example 2 with VariableInfo

use of org.vcell.sbmlsim.api.common.VariableInfo in project vcell by virtualcell.

the class SimulationServiceImplTest method test.

@Test
public void test() throws URISyntaxException, Exception {
    SimulationServiceImpl simService = new SimulationServiceImpl();
    // TODO - Eliminate code duplication.
    URL sbmlFileUrl = SimulationServiceImplTest.class.getResource("../optoPlexin_PRG_rule_based.xml");
    File file = new File(sbmlFileUrl.toURI());
    VCMongoMessage.enabled = false;
    // TODO - Encapsulate this common setup stuff into VCellService initialization.
    // Then all VCell-based scripts can focus on the customization below.
    System.setProperty(PropertyLoader.installationRoot, new File("..").getAbsolutePath());
    ResourceUtil.setNativeLibraryDirectory();
    NativeLib.HDF5.load();
    file = new File("src/test/resources/org/vcell/sbmlsim/optoPlexin_PRG_rule_based.xml");
    Assert.assertTrue(file.exists());
    SBMLModel sbmlModel = new SBMLModel(file);
    SimulationSpec simSpec = new SimulationSpec();
    SimulationInfo simInfo = simService.computeModel(sbmlModel, simSpec);
    long timeMS = System.currentTimeMillis();
    while (simService.getStatus(simInfo).getSimState() != SimulationState.done && simService.getStatus(simInfo).getSimState() != SimulationState.failed) {
        try {
            Thread.sleep(1000);
        } catch (InterruptedException e) {
        }
        long time2MS = System.currentTimeMillis();
        if (time2MS - timeMS > 10000) {
            fail("timed out after 10 seconds");
        }
    }
    List<VariableInfo> vars = simService.getVariableList(simInfo);
    Assert.assertNotNull(vars);
    // TODO - Assert more things.
    final TimePoints timePoints = simService.getTimePoints(simInfo);
    vars.stream().forEach(var -> {
        try {
            System.out.println(// 
            var.getVariableDisplayName() + "[0] = " + simService.getData(simInfo, var, 0));
        } catch (Exception exc) {
            exc.printStackTrace();
        }
    });
}

Example 3 with VariableInfo

use of org.vcell.sbmlsim.api.common.VariableInfo in project vcell by virtualcell.

the class VCellSbmlSimCLI method process_simdata.

private void process_simdata() throws Exception {
    Gson gson = new Gson();
    SimulationInfo simInfo = null;
    if (simhandle != null) {
        simInfo = new SimulationInfo(simhandle);
    } else {
        throw new CliException("simhandle (simulation handle) not specified");
    }
    VariableInfo varInfo = null;
    if (varinfoJSON != null) {
        try {
            varInfo = gson.fromJson(varinfoJSON, VariableInfo.class);
        } catch (Exception e) {
            throw new CliException("failed to parse JSON text for varInfo: " + e.getMessage(), e);
        }
    } else {
        throw new CliException("varinfo (variableInfo) not specified");
    }
    if (timepointIndex == null) {
        throw new CliException("timepoint index not specified");
    }
    if (outputfile == null) {
        throw new CliException("outputfile not specified");
    }
    SimData simdata = simService.getData(simInfo, varInfo, timepointIndex);
    String simdataJSON = gson.toJson(simdata);
    FileUtils.write(outputfile, simdataJSON);
}