Examples with PropertyVetoException java.beans.PropertyVetoException used on opensource projects

Example 76 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class MathVerifier method testMathGeneration.

public MathGenerationResults testMathGeneration(KeyValue simContextKey) throws SQLException, ObjectNotFoundException, DataAccessException, XmlParseException, MappingException, MathException, MatrixException, ExpressionException, ModelException, PropertyVetoException {
    User adminUser = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new org.vcell.util.document.KeyValue(PropertyLoader.ADMINISTRATOR_ID));
    if (lg.isTraceEnabled())
        lg.trace("Testing SimContext with key '" + simContextKey + "'");
    // get biomodel refs
    java.sql.Connection con = null;
    java.sql.Statement stmt = null;
    con = conFactory.getConnection(new Object());
    cbit.vcell.modeldb.BioModelSimContextLinkTable bmscTable = cbit.vcell.modeldb.BioModelSimContextLinkTable.table;
    cbit.vcell.modeldb.BioModelTable bmTable = cbit.vcell.modeldb.BioModelTable.table;
    cbit.vcell.modeldb.UserTable userTable = cbit.vcell.modeldb.UserTable.table;
    String sql = "SELECT " + bmscTable.bioModelRef.getQualifiedColName() + "," + bmTable.ownerRef.getQualifiedColName() + "," + userTable.userid.getQualifiedColName() + " FROM " + bmscTable.getTableName() + "," + bmTable.getTableName() + "," + userTable.getTableName() + " WHERE " + bmscTable.simContextRef.getQualifiedColName() + " = " + simContextKey + " AND " + bmTable.id.getQualifiedColName() + " = " + bmscTable.bioModelRef.getQualifiedColName() + " AND " + bmTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
    ArrayList<KeyValue> bioModelKeys = new ArrayList<KeyValue>();
    stmt = con.createStatement();
    User owner = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            KeyValue key = new KeyValue(rset.getBigDecimal(bmscTable.bioModelRef.getUnqualifiedColName()));
            bioModelKeys.add(key);
            KeyValue ownerRef = new KeyValue(rset.getBigDecimal(bmTable.ownerRef.getUnqualifiedColName()));
            String userid = rset.getString(userTable.userid.getUnqualifiedColName());
            owner = new User(userid, ownerRef);
        }
    } finally {
        if (stmt != null) {
            stmt.close();
        }
        con.close();
    }
    // use the first biomodel...
    if (bioModelKeys.size() == 0) {
        throw new RuntimeException("zombie simContext ... no biomodels");
    }
    BioModelInfo bioModelInfo = dbServerImpl.getBioModelInfo(owner, bioModelKeys.get(0));
    // 
    // read in the BioModel from the database
    // 
    BigString bioModelXML = dbServerImpl.getBioModelXML(owner, bioModelInfo.getVersion().getVersionKey());
    BioModel bioModelFromDB = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    BioModel bioModelNewMath = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    bioModelFromDB.refreshDependencies();
    bioModelNewMath.refreshDependencies();
    // 
    // get all Simulations for this model
    // 
    Simulation[] modelSimsFromDB = bioModelFromDB.getSimulations();
    // 
    // ---> only for the SimContext we started with...
    // recompute mathDescription, and verify it is equivalent
    // then check each associated simulation to ensure math overrides are applied in an equivalent manner also.
    // 
    SimulationContext[] simContextsFromDB = bioModelFromDB.getSimulationContexts();
    SimulationContext[] simContextsNewMath = bioModelNewMath.getSimulationContexts();
    SimulationContext simContextFromDB = null;
    SimulationContext simContextNewMath = null;
    for (int k = 0; k < simContextsFromDB.length; k++) {
        // find it...
        if (simContextsFromDB[k].getKey().equals(simContextKey)) {
            simContextFromDB = simContextsFromDB[k];
            simContextNewMath = simContextsNewMath[k];
            break;
        }
    }
    if (simContextFromDB == null) {
        throw new RuntimeException("BioModel referred to by this SimContext does not contain this SimContext");
    } else {
        MathDescription origMathDesc = simContextFromDB.getMathDescription();
        // 
        try {
            if (simContextNewMath.getGeometry().getDimension() > 0 && simContextNewMath.getGeometry().getGeometrySurfaceDescription().getGeometricRegions() == null) {
                simContextNewMath.getGeometry().getGeometrySurfaceDescription().updateAll();
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
        // 
        // updated mathDescription loaded into copy of bioModel, then test for equivalence.
        // 
        cbit.vcell.mapping.MathMapping mathMapping = simContextNewMath.createNewMathMapping();
        MathDescription mathDesc_latest = mathMapping.getMathDescription();
        MathMapping_4_8 mathMapping_4_8 = new MathMapping_4_8(simContextNewMath);
        MathDescription mathDesc_4_8 = mathMapping_4_8.getMathDescription();
        String issueString = null;
        org.vcell.util.Issue[] issues = mathMapping.getIssues();
        if (issues != null && issues.length > 0) {
            StringBuffer buffer = new StringBuffer("Issues(" + issues.length + "):\n");
            for (int l = 0; l < issues.length; l++) {
                buffer.append(" <<" + issues[l].toString() + ">>\n");
            }
            issueString = buffer.toString();
        }
        simContextNewMath.setMathDescription(mathDesc_latest);
        MathCompareResults mathCompareResults_latest = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, mathDesc_latest);
        MathCompareResults mathCompareResults_4_8 = null;
        try {
            mathCompareResults_4_8 = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), origMathDesc, mathDesc_4_8);
        } catch (Exception e) {
            e.printStackTrace(System.out);
            mathCompareResults_4_8 = new MathCompareResults(Decision.MathDifferent_FAILURE_UNKNOWN, e.getMessage());
        }
        return new MathGenerationResults(bioModelFromDB, simContextFromDB, origMathDesc, mathDesc_latest, mathCompareResults_latest, mathDesc_4_8, mathCompareResults_4_8);
    }
}

Example 77 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class ModelDbDriver method getModel.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.Model
 * @param rset java.sql.ResultSet
 */
private Model getModel(QueryHashtable dbc, ResultSet rset, Connection con, User user) throws SQLException, DataAccessException {
    // User owner = new User(ownerName, ownerRef);
    try {
        Model model = modelTable.getModel(rset, con);
        // model.setOwner(owner);
        KeyValue modelKey = model.getVersion().getVersionKey();
        // 
        // set structures for this model
        // 
        StructureTopology structureTopology = model.getStructureTopology();
        Structure[] structures = reactStepDB.getStructuresFromModel(dbc, con, modelKey);
        if (structures != null && structures.length > 0) {
            model.setStructures(structures);
        }
        HashMap<KeyValue, StructureKeys> structureKeysMap = reactStepDB.getStructureParentMapByModel(dbc, con, modelKey);
        ReactStepDbDriver.populateStructureAndElectricalTopology(model, structureKeysMap);
        // 
        // set species for this model
        // 
        SpeciesContext[] speciesContexts = getSpeciesContextFromModel(dbc, con, user, modelKey, structureTopology);
        if (speciesContexts != null) {
            Vector<Species> speciesList = new Vector<Species>();
            for (int i = 0; i < speciesContexts.length; i++) {
                if (!speciesList.contains(speciesContexts[i].getSpecies())) {
                    speciesList.addElement(speciesContexts[i].getSpecies());
                }
            }
            Species[] speciesArray = new Species[speciesList.size()];
            speciesList.copyInto(speciesArray);
            model.setSpecies(speciesArray);
        }
        // 
        if (speciesContexts != null) {
            model.setSpeciesContexts(speciesContexts);
        }
        // 
        // Add global parameters to the model
        // 
        GlobalModelParameterTable.table.setModelParameters(con, model);
        // 
        // add reactionSteps for this model
        // 
        ReactionStep[] reactSteps = reactStepDB.getReactionStepsFromModel(dbc, con, model, modelKey);
        if (reactSteps != null) {
            model.setReactionSteps(reactSteps);
            for (int i = 0; i < reactSteps.length; i++) {
                try {
                    // 
                    // fix any improperly defined reactionSteps (which have parameters that should be catalysts)
                    // name space of kinetic parameters should be unique with respect to SpeciesContexts (so if they overlap, should be a catalyst).
                    // 
                    Kinetics.KineticsParameter[] params = reactSteps[i].getKinetics().getKineticsParameters();
                    for (int j = 0; j < params.length; j++) {
                        SpeciesContext speciesContext = model.getSpeciesContext(params[j].getName());
                        if (speciesContext != null) {
                            reactSteps[i].addCatalyst(speciesContext);
                            if (lg.isWarnEnabled())
                                lg.warn("ModelDbDriver.getModel(), Parameter '" + params[j].getName() + "' in Reaction " + reactSteps[i].getName() + " in Model(" + model.getKey() + ") conflicts with SpeciesContext, added as a catalyst");
                        }
                    }
                } catch (Throwable e) {
                    lg.error(e.getMessage(), e);
                }
                try {
                    reactSteps[i].rebindAllToModel(model);
                } catch (cbit.vcell.parser.ExpressionBindingException e) {
                    throw new DataAccessException("bindingException: " + e.getMessage());
                } catch (cbit.vcell.parser.ExpressionException e) {
                    throw new DataAccessException(e.getMessage());
                } catch (PropertyVetoException e) {
                    throw new DataAccessException("PropertyVetoException: " + e.getMessage());
                } catch (cbit.vcell.model.ModelException e) {
                    throw new DataAccessException(e.getMessage());
                }
            }
        }
        // 
        // add diagrams for this model
        // 
        Diagram[] diagrams = getDiagramsFromModel(dbc, con, modelKey, structureTopology, dbSyntax);
        model.setDiagrams(diagrams);
        // 
        // add rbm
        // 
        ModelTable.readRbmElement(con, model, dbSyntax);
        if (!model.getRbmModelContainer().isEmpty()) {
            for (SpeciesContext sc : model.getSpeciesContexts()) {
                sc.parseSpeciesPatternString(model);
            }
        }
        return model;
    } catch (PropertyVetoException e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 78 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class ModelTable method readRbmElement.

public static void readRbmElement(Connection con, Model model, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    Statement stmt = null;
    try {
        stmt = con.createStatement();
        ResultSet rset = stmt.executeQuery("SELECT * FROM " + ModelTable.table.getTableName() + " WHERE " + ModelTable.table.id.getUnqualifiedColName() + " = " + model.getVersion().getVersionKey().toString());
        if (rset.next()) {
            String rbmXMLStr = DbDriver.varchar2_CLOB_get(rset, ModelTable.table.rbmSmall, ModelTable.table.rbmLarge, dbSyntax);
            rset.close();
            if (rbmXMLStr != null) {
                Element rbmElement = XmlUtil.stringToXML(rbmXMLStr, null).getRootElement();
                XmlReader reader = new XmlReader(false);
                try {
                    reader.getRbmModelContainer(rbmElement, model);
                } catch (ModelException | PropertyVetoException | XmlParseException e) {
                    throw new DataAccessException(e.getMessage(), e);
                }
            }
        }
    } finally {
        if (stmt != null) {
            try {
                stmt.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Example 79 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class ReactStepDbDriver method getReactionParticipant.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.ReactionParticipant
 * @param rset java.sql.ResultSet
 * @exception java.sql.SQLException The exception description.
 */
private ReactionParticipant getReactionParticipant(QueryHashtable dbc, Connection con, ResultSet rset, ReactionStep rs) throws SQLException, DataAccessException {
    // 
    // try to get ReactionParticipant from object cache
    // 
    KeyValue rpKey = new KeyValue(rset.getBigDecimal(ReactPartTable.table.id.toString()));
    ReactionParticipant rp = (ReactionParticipant) dbc.get(rpKey);
    if (rp != null) {
        return rp;
    }
    // 
    // get foreign keys
    // 
    KeyValue speciesContextKey = new KeyValue(rset.getBigDecimal(ReactPartTable.table.scRef.toString()));
    // 
    // get ReactionParticipant
    // 
    rp = reactPartTable.getReactionParticipant(rpKey, rset);
    // 
    // get referenced Objects (Species and Structure)
    // 
    SpeciesContext speciesContext = modelDB.getSpeciesContext(dbc, con, speciesContextKey);
    try {
        rp.setSpeciesContext(speciesContext);
    } catch (PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("PropertyVetoException: " + e.getMessage());
    }
    rp.setReactionStep(rs);
    // ========== Since there is no flux carrier in fluxReaction, this is not required?? ===========
    // if (rp instanceof Flux && rs instanceof FluxReaction) {
    // try {
    // ((FluxReaction) rs).setFluxCarrier(speciesContext.getSpecies(), null);
    // }catch (ModelException e){
    // e.printStackTrace(System.out);
    // throw new DataAccessException("ModelException: "+e.getMessage());
    // }catch (PropertyVetoException e){
    // e.printStackTrace(System.out);
    // throw new DataAccessException("PropertyVetoException: "+e.getMessage());
    // }
    // }
    // 
    // stick ReactionParticipant in object cache
    // 
    dbc.put(rpKey, rp);
    return rp;
}

Example 80 with PropertyVetoException

use of java.beans.PropertyVetoException in project vcell by virtualcell.

the class GeomDbDriver method insertGeometry.

/**
 * This method was created in VisualAge.
 */
private void insertGeometry(InsertHashtable hash, QueryHashtable dbc, Connection con, User user, Geometry geom, KeyValue updatedImageKey, Version newVersion, boolean bVersionChildren) throws ImageException, SQLException, DataAccessException, RecordChangedException {
    // log.print("GeomDbDriver.insertGeometry(" + geom + ")");
    // everybody needs to be in synch 'cause children may be manipulated...
    geom.refreshDependencies();
    KeyValue extentKey = null;
    GeometrySpec geometrySpec = geom.getGeometrySpec();
    if (geometrySpec.getImage() != null) {
        // //try {
        // imageVersionKey = hash.getDatabaseKey(geometrySpec.getImage());
        // if (imageVersionKey==null){
        // if(geometrySpec.getImage().getVersion()!=null && geometrySpec.getImage().getVersion().getVersionKey() != null){
        // imageVersionKey = updateVersionable(hash, con, user, geometrySpec.getImage(), bVersionChildren);
        // }else{
        // String imageName = geometrySpec.getImage().getName(); // + "_image";
        // while (isNameUsed(con,VersionableType.VCImage,user,imageName)){
        // imageName = cbit.util.TokenMangler.getNextRandomToken(imageName);
        // }
        // imageVersionKey = insertVersionable(hash, con, user, geometrySpec.getImage(),imageName ,bVersionChildren);
        // }
        // try{
        // geometrySpec.setImage(getVCImage(con,user,imageVersionKey));
        // }catch(PropertyVetoException e){
        // e.printStackTrace();
        // throw new DataAccessException(e.getMessage());
        // }
        // }
        // //} catch (RecordChangedException rce) {
        // //	throw rce;
        // //}
        extentKey = getExtentRefKeyFromImage(con, updatedImageKey);
    }
    // 
    if (extentKey == null) {
        extentKey = keyFactory.getNewKey(con);
        insertExtentSQL(con, extentKey, geometrySpec.getExtent().getX(), geometrySpec.getExtent().getY(), geometrySpec.getExtent().getZ());
    }
    // 
    insertGeometrySQL(con, geom, updatedImageKey, extentKey, newVersion, user);
    hash.put(geom, newVersion.getVersionKey());
    if (updatedImageKey != null && !updatedImageKey.equals(geom.getGeometrySpec().getImage().getKey())) {
        VCImage resavedImage = getVCImage(dbc, con, user, updatedImageKey, true);
        try {
            geom.getGeometrySpec().setImage(resavedImage);
        } catch (PropertyVetoException e) {
            e.printStackTrace();
            throw new DataAccessException(e.getMessage());
        }
    }
    insertSubVolumesSQL(hash, con, geom, newVersion.getVersionKey());
    insertSurfaceClassesSQL(hash, con, geom, newVersion.getVersionKey());
    if (geom.getDimension() > 0) {
        insertGeometrySurfaceDescriptionSQL(hash, con, geom, newVersion.getVersionKey());
        insertFilamentsSQL(con, geom, newVersion.getVersionKey());
    }
}