Examples with SBMLDocument org.sbml.jsbml.SBMLDocument used on opensource projects

Example 6 with SBMLDocument

use of org.sbml.jsbml.SBMLDocument in project vcell by virtualcell.

the class SBMLUnitTranslatorTest method testSBMLtoVCell.

@Test
public void testSBMLtoVCell() throws XMLStreamException, IOException, SbmlException {
    File[] sbmlFiles = getBiomodelsCuratedSBMLFiles();
    // };
    for (File sbmlFile : sbmlFiles) {
        if (sbmlFile.getName().equals("BIOMD0000000539.xml")) {
            System.err.println("skipping this model, seems like a bug in jsbml  RenderParser.processEndDocument() ... line 403 ... wrong constant for extension name");
            continue;
        }
        SBMLDocument doc = SBMLReader.read(sbmlFile);
        BioModel bioModel = new BioModel(null);
        VCUnitSystem unitSystem = bioModel.getModel().getUnitSystem();
        Model sbmlModel = doc.getModel();
        ListOf<UnitDefinition> listOfUnitDefinitions = sbmlModel.getListOfUnitDefinitions();
        for (UnitDefinition sbmlUnitDef : listOfUnitDefinitions) {
            VCUnitDefinition vcUnit = SBMLUnitTranslator.getVCUnitDefinition(sbmlUnitDef, unitSystem);
            UnitDefinition new_sbmlUnitDef = SBMLUnitTranslator.getSBMLUnitDefinition(vcUnit, 3, 1, unitSystem);
            VCUnitDefinition new_vcUnit = SBMLUnitTranslator.getVCUnitDefinition(new_sbmlUnitDef, unitSystem);
            if (!vcUnit.getSymbol().equals(new_vcUnit.getSymbol())) {
                System.err.println("orig vcUnit '" + vcUnit.getSymbol() + "' doesn't match new vcUnit '" + new_vcUnit.getSymbol() + "'");
            }
            // System.out.println("sbmlUnit = "+sbmlUnitDef.toString()+", vcUnit = "+vcUnit.getSymbol());
            System.out.println("sbmlUnit(" + sbmlUnitDef.getClass().getName() + ", builtin=" + sbmlUnitDef.isVariantOfSubstance() + ") = " + sbmlUnitDef.toString() + ", id=" + sbmlUnitDef.getId() + ",  name=" + sbmlUnitDef.getName() + ",   vcUnit = " + vcUnit.getSymbol());
            if (sbmlUnitDef.getNumUnits() > 1) {
                System.out.println("vcUnit = " + vcUnit.getSymbol());
                for (Unit unit : sbmlUnitDef.getListOfUnits()) {
                    try {
                        // VCUnitDefinition vcUnit = unitSystem.getInstance(unit.getKind().getName());
                        System.out.println("    vcUnit = " + unit);
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                }
                System.out.println("found bigger unit, " + sbmlUnitDef);
            }
        }
        if (sbmlFile == sbmlFiles[0]) {
            System.out.println("sbml length unit = " + sbmlModel.getLengthUnitsInstance() + ", idref=" + sbmlModel.getLengthUnits());
            System.out.println("sbml area unit = " + sbmlModel.getAreaUnitsInstance() + ", idref=" + sbmlModel.getAreaUnits());
            System.out.println("sbml volume unit = " + sbmlModel.getVolumeUnitsInstance() + ", idref=" + sbmlModel.getVolumeUnits());
            System.out.println("sbml time unit = " + sbmlModel.getTimeUnitsInstance() + ", idref=" + sbmlModel.getTimeUnits());
            System.out.println("sbml extent unit = " + sbmlModel.getExtentUnitsInstance() + ", idref=" + sbmlModel.getExtentUnits());
            System.out.println("sbml substance unit = " + sbmlModel.getSubstanceUnitsInstance() + ", idref=" + sbmlModel.getSubstanceUnits());
            for (UnitDefinition sbmlUnitDef : sbmlModel.getListOfPredefinedUnitDefinitions()) {
                if (sbmlUnitDef.getNumUnits() == 1 && sbmlUnitDef.getUnit(0).isAvogadro()) {
                    continue;
                }
                if (sbmlUnitDef.getNumUnits() == 1 && sbmlUnitDef.getUnit(0).isKatal()) {
                    continue;
                }
                VCUnitDefinition vcUnit = SBMLUnitTranslator.getVCUnitDefinition(sbmlUnitDef, unitSystem);
                // System.out.println("sbmlUnit = "+sbmlUnitDef.toString()+", vcUnit = "+vcUnit.getSymbol());
                System.out.println("sbmlUnit(" + sbmlUnitDef.getClass().getName() + ", builtin=" + sbmlUnitDef.isVariantOfSubstance() + ") = " + sbmlUnitDef.toString() + ", id=" + sbmlUnitDef.getId() + ",  name=" + sbmlUnitDef.getName() + ",   vcUnit = " + vcUnit.getSymbol());
            // for (Unit unit : sbmlUnitDef.getListOfUnits()){
            // try {
            // VCUnitDefinition vcUnit = unitSystem.getInstance(unit.getKind().getName());
            // System.out.println("    vcUnit = "+vcUnit.getSymbol());
            // }catch (Exception e){
            // e.printStackTrace();
            // }
            // }
            }
        }
    }
}

Example 7 with SBMLDocument

use of org.sbml.jsbml.SBMLDocument in project vcell by virtualcell.

the class ProjectService method load.

public Task<Project, String> load(File root) {
    final Task<Project, String> task = new Task<Project, String>() {

        @Override
        protected Project doInBackground() throws Exception {
            Project project = new Project(root.getName());
            String rootPath = root.getAbsolutePath();
            File[] dataFiles = Paths.get(rootPath, "data").toFile().listFiles();
            File[] geometryFiles = Paths.get(rootPath, "geometry").toFile().listFiles();
            File[] modelDirectories = Paths.get(rootPath, "models").toFile().listFiles();
            File[] resultsFiles = Paths.get(rootPath, "results").toFile().listFiles();
            int numFiles = dataFiles.length + geometryFiles.length + modelDirectories.length + resultsFiles.length;
            int numLoaded = 0;
            if (dataFiles != null) {
                for (File dataFile : dataFiles) {
                    try {
                        setSubtask(dataFile.getName());
                        Dataset data = datasetIOService.open(dataFile.getAbsolutePath());
                        project.getData().add(data);
                        numLoaded++;
                        setProgress(numLoaded * 100 / numFiles);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
            if (geometryFiles != null) {
                for (File geometryFile : geometryFiles) {
                    try {
                        setSubtask(geometryFile.getName());
                        Dataset geometry = datasetIOService.open(geometryFile.getAbsolutePath());
                        // Geometry datasets are saved as 8-bit images so we must convert back to 1-bit
                        if (geometry.firstElement() instanceof UnsignedByteType) {
                            @SuppressWarnings("unchecked") Img<UnsignedByteType> img = (Img<UnsignedByteType>) geometry.getImgPlus().getImg();
                            Img<BitType> converted = opService.convert().bit(img);
                            ImgPlus<BitType> convertedImgPlus = new ImgPlus<>(converted, geometry.getName());
                            geometry.setImgPlus(convertedImgPlus);
                        }
                        project.getGeometry().add(geometry);
                        numLoaded++;
                        setProgress(numLoaded * 100 / numFiles);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
            if (modelDirectories != null) {
                for (File modelDirectory : modelDirectories) {
                    setSubtask(modelDirectory.getName());
                    SBMLDocument sbmlDocument = null;
                    BufferedImage image = null;
                    File[] modelFiles = modelDirectory.listFiles();
                    System.out.println(modelFiles.length);
                    // Invalid model directory
                    if (modelFiles.length > 2)
                        continue;
                    for (File modelFile : modelFiles) {
                        System.out.println(modelFile.getName());
                        if (FilenameUtils.getExtension(modelFile.getName()).equals("xml")) {
                            sbmlDocument = new SBMLReader().readSBML(modelFile);
                            System.out.println("Loaded sbml");
                        } else if (FilenameUtils.getExtension(modelFile.getName()).equals("png")) {
                            image = ImageIO.read(modelFile);
                            System.out.println("Loaded image");
                        }
                    }
                    if (sbmlDocument != null) {
                        VCellModel vCellModel = new VCellModel(modelDirectory.getName(), null, sbmlDocument);
                        vCellModel.setImage(image);
                        project.getModels().add(vCellModel);
                        System.out.println("Added model");
                    }
                    numLoaded++;
                    setProgress(numLoaded * 100 / numFiles);
                }
            }
            if (resultsFiles != null) {
                for (File resultsFile : resultsFiles) {
                    try {
                        setSubtask(resultsFile.getName());
                        Dataset results = datasetIOService.open(resultsFile.getAbsolutePath());
                        // Loading 1-dimensional tif images adds a dimension
                        // so must crop out empty dimensions
                        @SuppressWarnings("unchecked") ImgPlus<T> imgPlus = (ImgPlus<T>) results.getImgPlus();
                        int numDimensions = imgPlus.numDimensions();
                        long[] dimensions = new long[2 * imgPlus.numDimensions()];
                        for (int i = 0; i < numDimensions; i++) {
                            dimensions[i] = 0;
                            dimensions[i + numDimensions] = imgPlus.dimension(i) - 1;
                        }
                        FinalInterval interval = Intervals.createMinMax(dimensions);
                        ImgPlus<T> cropped = opService.transform().crop(imgPlus, interval, true);
                        results.setImgPlus(cropped);
                        project.getResults().add(results);
                        numLoaded++;
                        setProgress(numLoaded * 100 / numFiles);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                }
            }
            currentProjectRoot = root;
            return project;
        }
    };
    return task;
}

Example 8 with SBMLDocument

use of org.sbml.jsbml.SBMLDocument 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;
}

Example 9 with SBMLDocument

use of org.sbml.jsbml.SBMLDocument in project vcell by virtualcell.

the class VCellService method getSBML.

private static SBMLDocument getSBML(final SimulationServiceImpl client, final String vcml, final String applicationName) throws ThriftDataAccessException, XMLStreamException, IOException {
    final String sbml;
    try {
        sbml = client.getSBML(vcml, applicationName);
    } catch (final TException e) {
        throw new IOException(e);
    }
    final SBMLReader reader = new SBMLReader();
    final SBMLDocument document = reader.readSBMLFromString(sbml);
    return document;
}