Examples with Diagram cbit.vcell.model.Diagram used on opensource projects

Example 11 with Diagram

use of cbit.vcell.model.Diagram in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * Outputs a XML version of a Model object
 * Creation date: (2/15/2001 11:39:27 AM)
 * @return Element
 * @param param cbit.vcell.model.Model
 */
private Element getXML(Model param) throws XmlParseException /*, cbit.vcell.parser.ExpressionException */
{
    Element modelnode = new Element(XMLTags.ModelTag);
    String versionName = (param.getName() != null) ? mangle(param.getName()) : "unnamed_model";
    // get Attributes
    modelnode.setAttribute(XMLTags.NameAttrTag, versionName);
    // modelnode.setAttribute(XMLTags.AnnotationAttrTag, this.mangle(param.getDescription()));
    if (param.getDescription() != null && param.getDescription().length() > 0) {
        Element annotationElem = new Element(XMLTags.AnnotationTag);
        annotationElem.setText(mangle(param.getDescription()));
        modelnode.addContent(annotationElem);
    }
    // get global parameters
    ModelParameter[] modelGlobals = param.getModelParameters();
    if (modelGlobals != null && modelGlobals.length > 0) {
        modelnode.addContent(getXML(modelGlobals));
    }
    // Get Species
    Species[] array = param.getSpecies();
    for (int i = 0; i < array.length; i++) {
        modelnode.addContent(getXML(array[i]));
    }
    // Get Structures(Features and Membranes). Add them in an ordered fashion, but it does not matter who comes first.
    try {
        ArrayList<Element> list = new ArrayList<Element>();
        Structure[] structarray = param.getStructures();
        for (int i = 0; i < structarray.length; i++) {
            Element structure = getXML(structarray[i], param);
            if (structarray[i] instanceof Feature)
                modelnode.addContent(structure);
            else
                list.add(structure);
        }
        for (int i = 0; i < list.size(); i++) {
            modelnode.addContent((Element) list.get(i));
        }
    } catch (XmlParseException e) {
        e.printStackTrace();
        throw new XmlParseException("An error occurred while procesing a Structure for the model " + versionName, e);
    }
    // Process SpeciesContexts
    SpeciesContext[] specarray = param.getSpeciesContexts();
    for (int i = 0; i < specarray.length; i++) {
        modelnode.addContent(getXML(specarray[i]));
    }
    // Get reaction Steps(Simple Reactions and Fluxtep)
    ReactionStep[] reactarray = param.getReactionSteps();
    for (int i = 0; i < reactarray.length; i++) {
        modelnode.addContent(getXML(reactarray[i]));
    }
    // add the rbmModelContainer elements
    RbmModelContainer rbmModelContainer = param.getRbmModelContainer();
    if (rbmModelContainer != null && !rbmModelContainer.isEmpty()) {
        Element rbmModelContainerElement = getXML(rbmModelContainer);
        {
            // for testing purposes only
            Document doc = new Document();
            Element clone = (Element) rbmModelContainerElement.clone();
            doc.setRootElement(clone);
            String xmlString = XmlUtil.xmlToString(doc, false);
            System.out.println(xmlString);
        }
        modelnode.addContent(rbmModelContainerElement);
    }
    // // Add rate rules
    // if (param.getRateRuleVariables()!=null && param.getRateRuleVariables().length>0){
    // modelnode.addContent( getXML(param.getRateRuleVariables()) );
    // }
    // Get Diagrams
    Diagram[] diagarray = param.getDiagrams();
    for (int i = 0; i < diagarray.length; i++) {
        modelnode.addContent(getXML(diagarray[i]));
    }
    // Add Metadata information
    if (param.getVersion() != null) {
        modelnode.addContent(getXML(param.getVersion(), param));
    }
    // add model UnitSystem
    ModelUnitSystem unitSystem = param.getUnitSystem();
    if (unitSystem != null) {
        modelnode.addContent(getXML(unitSystem));
    }
    return modelnode;
}

Example 12 with Diagram

use of cbit.vcell.model.Diagram in project vcell by virtualcell.

the class DiagramTable method getDiagram.

/**
 * This method was created in VisualAge.
 * @return Model
 * @param rset ResultSet
 * @param log SessionLog
 */
public Diagram getDiagram(ResultSet rset, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    KeyValue key = new KeyValue(rset.getBigDecimal(id.toString()));
    String mName = rset.getString(name.toString());
    Diagram diagram = new Diagram(null, mName);
    String languageString = DbDriver.varchar2_CLOB_get(rset, DiagramTable.table.diagramSmall, DiagramTable.table.diagramLarge, dbSyntax);
    if (languageString == null || languageString.length() == 0) {
        throw new DataAccessException("no data stored for Diagram");
    }
    // Is this needed?
    // if (languageString.endsWith(";}\n")){
    // StringBuffer buffer = new StringBuffer(languageString.substring(0,languageString.length()-2));
    // buffer.append("\n}\n");
    // languageString = buffer.toString();
    // }
    org.vcell.util.CommentStringTokenizer tokens = new org.vcell.util.CommentStringTokenizer(languageString);
    try {
        diagram.fromTokens(tokens);
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
    return diagram;
}

Example 13 with Diagram

use of cbit.vcell.model.Diagram in project vcell by virtualcell.

the class ModelDbDriver method insertModel.

/**
 * This method was created in VisualAge.
 * @param model cbit.vcell.model.Model
 */
private void insertModel(InsertHashtable hash, Connection con, User user, Model model, Version newVersion) throws SQLException, DataAccessException, RecordChangedException {
    // 
    // insert model record
    // 
    insertModelSQL(con, user, model, newVersion);
    hash.put(model, newVersion.getVersionKey());
    // 
    // make sure all species are in the database and the hashtable
    // 
    StructureTopology structureTopology = model.getStructureTopology();
    ElectricalTopology electricalTopology = model.getElectricalTopology();
    Species[] speciesArray = model.getSpecies();
    for (int i = 0; i < speciesArray.length; i++) {
        // speciesArray[i].getKey();
        KeyValue speciesKey = null;
        // if (speciesKey == null) {
        speciesKey = reactStepDB.insertSpecies(hash, con, speciesArray[i], user);
        // throw new DataAccessException("Database error: species "+species.getName()+" has null key");
        // }else if (speciesArray[i].getOwnerKey()!=null && speciesArray[i].getOwnerKey()==user.getID()){
        // reactStepDB.updateSpecies(con,speciesArray[i],user);
        // }
        // if (hash.getDatabaseKey(speciesArray[i])==null){
        hash.put(speciesArray[i], speciesKey);
    // }
    }
    // 
    // make sure all structures are in the database and the hashtable (add entry to link table)
    // this does not populate the parent, negativeFeature, and positiveFeature columns ... done later with updateStructureKeys()
    // 
    Structure[] structures = model.getStructures();
    for (int i = 0; i < structures.length; i++) {
        Structure structure = (Structure) structures[i];
        KeyValue structureKey = null;
        if (hash.getDatabaseKey(structure) == null) {
            structureKey = reactStepDB.insertStructure(hash, con, structure);
        }
        KeyValue linkKey = keyFactory.getNewKey(con);
        insertModelStructLinkSQL(con, linkKey, newVersion.getVersionKey(), /*modelKey*/
        hash.getDatabaseKey(structure));
    }
    // 
    for (Structure structure : structures) {
        KeyValue structKey = hash.getDatabaseKey(structure);
        KeyValue parentKey = null;
        Structure parentStruct = structureTopology.getParentStructure(structure);
        if (parentStruct != null) {
            parentKey = hash.getDatabaseKey(parentStruct);
        }
        KeyValue negKey = null;
        KeyValue posKey = null;
        if (structure instanceof Membrane) {
            Membrane membrane = (Membrane) structure;
            Feature negFeature = electricalTopology.getNegativeFeature(membrane);
            if (negFeature != null) {
                negKey = hash.getDatabaseKey(negFeature);
            }
            Feature posFeature = electricalTopology.getPositiveFeature(membrane);
            if (posFeature != null) {
                posKey = hash.getDatabaseKey(posFeature);
            }
        }
        StructureKeys structureKeys = new StructureKeys(structKey, parentKey, posKey, negKey);
        reactStepDB.updateStructureKeys(con, structureKeys);
    }
    // 
    // make sure all speciesContexts are in database and the hashtable
    // 
    SpeciesContext[] speciesContexts = model.getSpeciesContexts();
    for (int i = 0; i < speciesContexts.length; i++) {
        SpeciesContext sc = speciesContexts[i];
        if (hash.getDatabaseKey(sc) == null) {
            insertSpeciesContextSQL(hash, con, keyFactory.getNewKey(con), sc, newVersion.getVersionKey());
        }
    }
    // 
    // insert all reactionSteps
    // 
    ReactionStep[] reactionSteps = model.getReactionSteps();
    for (int i = 0; i < reactionSteps.length; i++) {
        ReactionStep rs = reactionSteps[i];
        if (hash.getDatabaseKey(rs) == null) {
            reactStepDB.insertReactionStep(hash, con, user, rs, newVersion.getVersionKey());
        }
    }
    // 
    // insert diagrams
    // 
    Diagram[] diagrams = model.getDiagrams();
    for (int i = 0; i < diagrams.length; i++) {
        Diagram diagram = diagrams[i];
        KeyValue key = keyFactory.getNewKey(con);
        KeyValue structKey = hash.getDatabaseKey(diagram.getStructure());
        if (structKey != null) {
            insertDiagramSQL(con, key, diagram, newVersion.getVersionKey(), /*modelKey*/
            hash.getDatabaseKey(diagram.getStructure()));
        } else {
            if (lg.isWarnEnabled())
                lg.warn("ModelDbDriver.insertModel(),  diagram " + diagram.toString() + " is orphaned, check Model logic");
        }
    }
    // 
    // insert GlobalModelParameters
    // 
    // //-----------------testing remove
    // try{
    // Model.ModelParameter testParam = model.new ModelParameter("test",new Expression("1.0"),Model.ROLE_UserDefined,VCUnitDefinition.UNIT_molecules);
    // model.setModelParameters(new Model.ModelParameter[] {testParam});
    // }catch(Exception e){
    // e.printStackTrace();
    // }
    // //-----------------
    GlobalModelParameterTable.table.insertModelParameters(con, keyFactory, model.getModelParameters(), newVersion.getVersionKey());
}

Example 14 with Diagram

use of cbit.vcell.model.Diagram in project vcell by virtualcell.

the class ModelDbDriver method getDiagram.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.Diagram
 * @param rset java.sql.ResultSet
 */
private Diagram getDiagram(QueryHashtable dbc, Connection con, ResultSet rset, StructureTopology structureTopology) throws SQLException, DataAccessException {
    KeyValue structKey = new KeyValue(rset.getBigDecimal(diagramTable.structRef.toString()));
    Diagram diagram = diagramTable.getDiagram(rset, dbSyntax);
    diagram.setStructure(reactStepDB.getStructure(dbc, con, structKey));
    return diagram;
}

Example 15 with Diagram

use of cbit.vcell.model.Diagram in project vcell by virtualcell.

the class ModelDbDriver method getDiagramsFromModel.

/**
 * getModels method comment.
 */
private cbit.vcell.model.Diagram[] getDiagramsFromModel(QueryHashtable dbc, Connection con, KeyValue modelKey, StructureTopology structureTopology, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    // log.print("ModelDbDriver.getDiagramsFromModel(modelKey=" + modelKey + ")");
    String sql;
    switch(dbSyntax) {
        case ORACLE:
            {
                sql = " SELECT *" + " FROM " + diagramTable.getTableName() + "," + SoftwareVersionTable.table.getTableName() + " WHERE " + diagramTable.modelRef + " = " + modelKey + " AND " + diagramTable.modelRef + " = " + SoftwareVersionTable.table.versionableRef.getUnqualifiedColName() + "(+)" + " ORDER BY " + diagramTable.id.getQualifiedColName();
                break;
            }
        case POSTGRES:
            {
                sql = " SELECT *" + " FROM " + diagramTable.getTableName() + " LEFT OUTER JOIN " + SoftwareVersionTable.table.getTableName() + " ON " + diagramTable.modelRef + " = " + SoftwareVersionTable.table.versionableRef.getUnqualifiedColName() + " WHERE " + diagramTable.modelRef + " = " + modelKey + // " AND " + diagramTable.modelRef + " = " + SoftwareVersionTable.table.versionableRef.getUnqualifiedColName() +"(+)" +
                " ORDER BY " + diagramTable.id.getQualifiedColName();
                break;
            }
        default:
            {
                throw new RuntimeException("unexpected DatabaseSyntax " + dbSyntax);
            }
    }
    Statement stmt = con.createStatement();
    Vector<Diagram> diagramList = new Vector<Diagram>();
    String softwareVersion = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        // 
        while (rset.next()) {
            Diagram diagram = getDiagram(dbc, con, rset, structureTopology);
            diagramList.addElement(diagram);
            softwareVersion = rset.getString(SoftwareVersionTable.table.softwareVersion.getUnqualifiedColName());
            if (rset.wasNull()) {
                softwareVersion = null;
            }
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    // 
    // put results in an array
    // 
    Diagram[] diagramArray = new Diagram[diagramList.size()];
    diagramList.copyInto(diagramArray);
    VCellSoftwareVersion vCellSoftwareVersion = VCellSoftwareVersion.fromString(softwareVersion);
    XmlReader.reorderDiagramsInPlace_UponRead(vCellSoftwareVersion, diagramArray, structureTopology);
    // //----------------------------------------
    return diagramArray;
}