Examples with Version org.vcell.util.document.Version used on opensource projects

Example 41 with Version

use of org.vcell.util.document.Version in project vcell by virtualcell.

the class XmlReader method getBioModel.

/**
 * This method returns a Biomodel object from a XML Element.
 * Creation date: (3/13/2001 12:35:00 PM)
 * @return cbit.vcell.biomodel.BioModel
 * @param param org.jdom.Element
 */
public BioModel getBioModel(Element param, VCellSoftwareVersion docVcellSoftwareVersion) throws XmlParseException {
    this.docVCellSoftwareVersion = docVcellSoftwareVersion;
    // long l1 = System.currentTimeMillis();
    // Get metadata information Version (if available)
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // Create new biomodel
    BioModel biomodel = new BioModel(version);
    // Set name
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    try {
        biomodel.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // biomodel.setDescription(unMangle(annotation));
        // }
        // get annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            biomodel.setDescription(unMangle(annotationText));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException(e);
    }
    // long l2 = System.currentTimeMillis();
    // System.out.println("biomodel-------- "+((double)(l2-l1))/1000);
    // ***Add biomodel to the dictionnary***
    // dictionnary.put(simcontext.getClass().getName()+":"+simcontext.getName(), simcontext);
    // Set model
    Model newmodel = getModel(param.getChild(XMLTags.ModelTag, vcNamespace));
    biomodel.setModel(newmodel);
    // Set simulation contexts
    java.util.List<Element> children = param.getChildren(XMLTags.SimulationSpecTag, vcNamespace);
    java.util.Iterator<Element> iterator = children.iterator();
    // System.out.println("model-------- "+((double)(l3-l2))/1000);
    while (iterator.hasNext()) {
        // long l4 = System.currentTimeMillis();
        Element tempElement = iterator.next();
        SimulationContext simContext = getSimulationContext(tempElement, biomodel);
        try {
            biomodel.addSimulationContext(simContext);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace();
            throw new XmlParseException("An error occurred while trying to add the SimContext " + simContext.getName() + " to the BioModel Object!", e);
        }
        // process the simulations within this Simspec
        Iterator<Element> simIterator = tempElement.getChildren(XMLTags.SimulationTag, vcNamespace).iterator();
        // System.out.println("simcontext-------- "+((double)(l5-l4))/1000);
        while (simIterator.hasNext()) {
            try {
                biomodel.addSimulation(getSimulation((Element) simIterator.next(), simContext.getMathDescription()));
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace();
                throw new XmlParseException("A PropertyVetoException occurred when adding a Simulation entity to the BioModel " + name, e);
            }
        }
    // long l6 = System.currentTimeMillis();
    // System.out.println("sims-------- "+((double)(l6-l5))/1000);
    }
    // biomodel.getVCMetaData().setAnnotation(biomodel, param);
    // biomodel.getVCMetaData().setNotes(biomodel, param);
    boolean bMetaDataPopulated = false;
    List<Element> elementsMetaData = param.getChildren(XMLMetaData.VCMETADATA_TAG, VCMetaData.nsVCML);
    if (elementsMetaData != null && elementsMetaData.size() > 0) {
        for (Element elementMetaData : elementsMetaData) {
            XMLMetaDataReader.readFromElement(biomodel.getVCMetaData(), biomodel, elementMetaData);
        }
        bMetaDataPopulated = true;
    } else {
        // no metadata was found, populate vcMetaData from biomodel (mainly free text annotation for identifiables)
        if (!bMetaDataPopulated) {
            biomodel.populateVCMetadata(bMetaDataPopulated);
        }
    }
    Element pathwayElement = param.getChild(XMLTags.PathwayModelTag, vcNamespace);
    if (pathwayElement != null) {
        Element rdfElement = pathwayElement.getChild(XMLRDF.tagRDF, XMLRDF.nsRDF);
        if (rdfElement != null) {
            PathwayReaderBiopax3 pathwayReader = new PathwayReaderBiopax3(new RDFXMLContext());
            PathwayModel pathwayModel = pathwayReader.parse(rdfElement, false);
            // ??? is this needed ???
            pathwayModel.reconcileReferences(null);
            // we keep as lvl 1 only the objects which we want to show in the diagram
            pathwayModel.filterDiagramObjects();
            biomodel.getPathwayModel().merge(pathwayModel);
        } else {
            throw new XmlParseException("expecting RDF element as child of pathwayModel within VCML document");
        }
    }
    Element relationshipElement = param.getChild(XMLTags.RelationshipModelTag, vcNamespace);
    if (relationshipElement != null) {
        Element rmnsElement = relationshipElement.getChild("RMNS", vcNamespace);
        if (rmnsElement != null) {
            RelationshipReader relationshipReader = new RelationshipReader();
            RelationshipModel relationshipModel = relationshipReader.parse(rmnsElement, biomodel);
            biomodel.getRelationshipModel().merge(relationshipModel);
        } else {
        // throw new XmlParseException("expecting RMNS element as child of pathwayModel within VCML document");
        }
    }
    return biomodel;
}

Example 42 with Version

use of org.vcell.util.document.Version in project vcell by virtualcell.

the class XmlReader method getModel.

/**
 * This method creates a Model object from a XML element.
 * Creation date: (3/14/2001 6:14:37 PM)
 * @return cbit.vcell.model.Model
 * @param param org.jdom.Element
 */
private Model getModel(Element param) throws XmlParseException {
    if (param == null) {
        throw new XmlParseException("Invalid 'NULL' XML 'model' element arrived!");
    }
    // Get version, if any
    Model newmodel = null;
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // if forcedModelUnitSystem has been set, ues that (could be overriding unit system for SBML export)
    if (forcedModelUnitSystem != null) {
        newmodel = new Model(version, forcedModelUnitSystem);
    } else {
        Element unitSystemNode = param.getChild(XMLTags.ModelUnitSystemTag, vcNamespace);
        if (unitSystemNode != null) {
            ModelUnitSystem modelUnitSystem = getUnitSystem(unitSystemNode);
            newmodel = new Model(version, modelUnitSystem);
        } else {
            newmodel = new Model(version);
        }
    }
    try {
        // Set attributes
        newmodel.setName(unMangle(param.getAttributeValue(XMLTags.NameAttrTag)));
        // Add annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            newmodel.setDescription(unMangle(annotationText));
        }
        // Add global parameters
        Element globalParamsElement = param.getChild(XMLTags.ModelParametersTag, vcNamespace);
        if (globalParamsElement != null) {
            ModelParameter[] modelParams = getModelParams(globalParamsElement, newmodel);
            // add global/model param to model - done inside getModelParam by passing newModel
            newmodel.setModelParameters(modelParams);
        }
        // Add Species (Compounds)
        Iterator<Element> iterator = param.getChildren(XMLTags.SpeciesTag, vcNamespace).iterator();
        ArrayList<Species> speciesList = new ArrayList<Species>();
        while (iterator.hasNext()) {
            org.jdom.Element temp = (Element) iterator.next();
            speciesList.add(getSpecies(temp));
        }
        newmodel.setSpecies(speciesList.toArray(new Species[speciesList.size()]));
        // Add Structures
        LinkedList<Structure> newstructures = new LinkedList<Structure>();
        // (features)
        List<Element> children = param.getChildren(XMLTags.FeatureTag, vcNamespace);
        for (Element featureElement : children) {
            newstructures.add(getFeature(featureElement));
        }
        // (Membrane)
        children = param.getChildren(XMLTags.MembraneTag, vcNamespace);
        for (Element memElement : children) {
            newstructures.add(getMembrane(newmodel, memElement, newstructures));
        }
        if (newstructures.size() > 0) {
            Structure[] structarray = new Structure[newstructures.size()];
            newstructures.toArray(structarray);
            // Add all the retrieved structures
            newmodel.setStructures(structarray);
        }
        // retrieve the RbmModelContainer, if present - must be done before we retrieve species context!
        Element element = param.getChild(XMLTags.RbmModelContainerTag, vcNamespace);
        if (element != null) {
            getRbmModelContainer(element, newmodel);
        } else {
            lg.info("RbmModelContainer is missing.");
        }
        // Add SpeciesContexts
        children = param.getChildren(XMLTags.SpeciesContextTag, vcNamespace);
        SpeciesContext[] newspeccon = new SpeciesContext[children.size()];
        int scCounter = 0;
        for (Element scElement : children) {
            newspeccon[scCounter] = getSpeciesContext(scElement, newmodel);
            scCounter++;
        }
        newmodel.setSpeciesContexts(newspeccon);
        // Retrieve rateRules and add to model
        // Element rateRuleVarsElement = param.getChild(XMLTags.RateRuleVariablesTag, vcNamespace);
        // if(rateRuleVarsElement != null){
        // RateRuleVariable[] rateRuleVars = getRateRuleVariables(rateRuleVarsElement, newmodel);
        // newmodel.setRateRuleVariables(rateRuleVars);
        // }
        // Add Reaction steps (if available)
        // (Simplereaction)
        // Create a varHash with reserved symbols and global parameters, if any, to pass on to Kinetics
        // must create new hash for each reaction and flux, since each kinetics uses new variables hash
        iterator = param.getChildren(XMLTags.SimpleReactionTag, vcNamespace).iterator();
        ArrayList<ReactionStep> reactionStepList = new ArrayList<ReactionStep>();
        while (iterator.hasNext()) {
            org.jdom.Element temp = iterator.next();
            reactionStepList.add(getSimpleReaction(temp, newmodel));
        }
        // (fluxStep)
        iterator = param.getChildren(XMLTags.FluxStepTag, vcNamespace).iterator();
        while (iterator.hasNext()) {
            org.jdom.Element temp = iterator.next();
            reactionStepList.add(getFluxReaction(temp, newmodel));
        }
        newmodel.setReactionSteps(reactionStepList.toArray(new ReactionStep[reactionStepList.size()]));
        // Add Diagrams
        children = param.getChildren(XMLTags.DiagramTag, vcNamespace);
        if (children.size() > 0) {
            Diagram[] newdiagrams = new Diagram[children.size()];
            int diagramCounter = 0;
            for (Element diagramElement : children) {
                newdiagrams[diagramCounter] = getDiagram(diagramElement, newmodel);
                diagramCounter++;
            }
            reorderDiagramsInPlace_UponRead(docVCellSoftwareVersion, newdiagrams, newmodel.getStructureTopology());
            // if(docVCellSoftwareVersion != null && !docVCellSoftwareVersion.isValid() && docVCellSoftwareVersion.getMajorVersion()<=5 && docVCellSoftwareVersion.getMinorVersion() <=2){
            // //In Vcell 5.2 and previous we need to order diagrams topologically, in 5.3 and later the diagrams are displayed as they are ordered when read from document
            // final StructureTopology structureTopology = newmodel.getStructureTopology();
            // Arrays.sort(newdiagrams, new Comparator<Diagram>() {
            // @Override
            // public int compare(Diagram o1, Diagram o2) {
            // return getStructureLevel(o1.getStructure(), structureTopology) - getStructureLevel(o2.getStructure(), structureTopology);
            // }
            // });
            // }
            newmodel.setDiagrams(newdiagrams);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException(e);
    } catch (ModelException e) {
        e.printStackTrace();
    }
    // model param expresions are not bound when they are read in, since they could be functions of each other or structures/speciesContexts.
    // Hence bind the model param exprs at the end, after reading all model level quantities.
    ModelParameter[] modelParameters = newmodel.getModelParameters();
    for (int i = 0; modelParameters != null && i < modelParameters.length; i++) {
        try {
            modelParameters[i].getExpression().bindExpression(newmodel);
        } catch (ExpressionBindingException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error binding global parameter '" + modelParameters[i].getName() + "' to model." + e.getMessage());
        }
    }
    return newmodel;
}

Example 43 with Version

use of org.vcell.util.document.Version in project vcell by virtualcell.

the class CheckBeforeDelete method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws Exception {
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    // JFrame currentDocumentWindow = (JFrame)hashTable.get("currentDocumentWindow");
    VCDocument currentDocument = documentWindowManager.getVCDocument();
    if (!hashTable.containsKey(SaveDocument.DOC_KEY)) {
        throw new RuntimeException("CheckBeforeDelete task called although SaveDocument task did not complete - should have aborted!!");
    }
    // Don't delete ARCHIVE or PUBLISH  documents
    if (!currentDocument.getVersion().getFlag().compareEqual(VersionFlag.Current)) {
        hashTable.put("conditionalSkip", new String[] { DeleteOldDocument.class.getName() });
        return;
    }
    DocumentManager documentManager = (DocumentManager) hashTable.get(CommonTask.DOCUMENT_MANAGER.name);
    Simulation[] simulations = (Simulation[]) hashTable.get("simulations");
    VCDocument savedDocument = (VCDocument) hashTable.get(SaveDocument.DOC_KEY);
    // just to make sure, verify that we actually did save a new edition
    Version oldVersion = currentDocument.getVersion();
    Version newVersion = savedDocument.getVersion();
    if (newVersion.getVersionKey().compareEqual(oldVersion.getVersionKey())) {
        // throw new DataAccessException("CheckBeforeDelete task called but saved document has same version with current document");
        hashTable.put("conditionalSkip", new String[] { DeleteOldDocument.class.getName() });
        return;
    }
    // we saved a new one, now check for lost simulation data and warn the user
    Simulation[] simulationsWithLostResults = null;
    switch(currentDocument.getDocumentType()) {
        case BIOMODEL_DOC:
            {
                simulationsWithLostResults = checkLostResults((BioModel) currentDocument, (BioModel) savedDocument, documentManager, simulations);
                break;
            }
        case MATHMODEL_DOC:
            {
                simulationsWithLostResults = checkLostResults((MathModel) currentDocument, (MathModel) savedDocument, documentManager, simulations);
                break;
            }
        case GEOMETRY_DOC:
        default:
            // nothing to check for in this case
            return;
    }
    boolean bLost = simulationsWithLostResults != null && simulationsWithLostResults.length > 0;
    if (bLost) {
        String choice = PopupGenerator.showWarningDialog(documentWindowManager, documentWindowManager.getUserPreferences(), UserMessage.question_LostResults, null);
        if (choice.equals(UserMessage.OPTION_SAVE_AS_NEW_EDITION)) {
            // user canceled deletion
            throw UserCancelException.CANCEL_DELETE_OLD;
        }
        if (choice.equals(UserMessage.OPTION_CANCEL)) {
            throw UserCancelException.CANCEL_GENERIC;
        }
    }
}

Example 44 with Version

use of org.vcell.util.document.Version in project vcell by virtualcell.

the class CheckUnchanged method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    DocumentManager documentManager = (DocumentManager) hashTable.get(CommonTask.DOCUMENT_MANAGER.name);
    // JFrame currentDocumentWindow = (JFrame)hashTable.get("currentDocumentWindow");
    if (documentWindowManager.getVCDocument().getDocumentType() == VCDocumentType.MATHMODEL_DOC) {
        if (((MathModelWindowManager) documentWindowManager).hasUnappliedChanges()) {
            String msg = "Changes have been made in VCML Editor, please click \"Apply Changes\" or \"Cancel\" to proceed.";
            PopupGenerator.showErrorDialog(documentWindowManager, msg);
            throw UserCancelException.CANCEL_UNAPPLIED_CHANGES;
        }
    }
    boolean isChanged = true;
    Version v = documentWindowManager.getVCDocument().getVersion();
    if (v == null || !v.getOwner().equals(documentManager.getSessionManager().getUser())) {
        isChanged = true;
    } else {
        try {
            isChanged = documentManager.isChanged(documentWindowManager.getVCDocument());
        } catch (DataAccessException exc) {
            String choice = PopupGenerator.showWarningDialog(documentWindowManager, documentWindowManager.getUserPreferences(), UserMessage.warn_UnableToCheckForChanges, null);
            if (!choice.equals(UserMessage.OPTION_CONTINUE)) {
                throw UserCancelException.WARN_UNABLE_CHECK;
            }
        }
    }
    if (!isChanged) {
        if (whileSavingForRunningSims) {
            // just skip the saves and go ahead
            hashTable.put("conditionalSkip", new String[] { SaveDocument.class.getName(), CheckBeforeDelete.class.getName(), DeleteOldDocument.class.getName() });
        } else {
            String choice = PopupGenerator.showWarningDialog(documentWindowManager, documentWindowManager.getUserPreferences(), UserMessage.warn_UnchangedDocument, null);
            if (choice.equals(UserMessage.OPTION_SAVE_AS_NEW)) {
                // user chose to Save As
                throw UserCancelException.CHOOSE_SAVE_AS;
            } else {
                // user canceled, just show existing document
                throw UserCancelException.WARN_NO_CHANGES;
            }
        }
    }
}

Example 45 with Version

use of org.vcell.util.document.Version in project vcell by virtualcell.

the class VCellBasicCellRenderer method setComponentProperties.

/**
 * Insert the method's description here.
 * Creation date: (5/8/01 8:35:45 AM)
 * @return javax.swing.Icon
 * @param nodeUserObject java.lang.Object
 */
protected void setComponentProperties(JLabel component, VCImageInfo imageInfo) {
    // component.setIcon(new ImageIcon(imageInfo.getBrowseGif().getGifEncodedData()));
    Version version = imageInfo.getVersion();
    String access = (version.getGroupAccess().getDescription());
    component.setToolTipText("Image");
    ISize size = imageInfo.getISize();
    String description = null;
    if (size.getZ() > 1) {
        description = "3D image (" + size.getX() + "," + size.getY() + "," + size.getZ() + ")";
    } else if (size.getY() > 1) {
        description = "2D image (" + size.getX() + "," + size.getY() + ")";
    } else {
        description = "1D image (" + size.getX() + ")";
    }
    component.setText(access + " " + description + " \"" + version.getName() + "\"" + "  (" + version.getDate() + ")");
}