Examples with ObjectNotFoundException org.vcell.util.ObjectNotFoundException used on opensource projects

Example 51 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class GeomDbDriver method getPixelClass.

/**
 * This method was created in VisualAge.
 * @param vcImage cbit.image.VCImage
 */
private VCPixelClass getPixelClass(QueryHashtable dbc, Connection con, KeyValue imageRegionKey) throws SQLException, DataAccessException {
    // 
    // check object cache first
    // 
    VCPixelClass vcPixelClass = (VCPixelClass) dbc.get(imageRegionKey);
    if (vcPixelClass != null) {
        return vcPixelClass;
    }
    String sql;
    sql = " SELECT *" + " FROM  " + imageRegionTable.getTableName() + " WHERE " + imageRegionTable.id + " = " + imageRegionKey;
    // 
    // System.out.println(sql);
    // 
    // Connection con = conFact.getConnection();
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        // 
        if (rset.next()) {
            KeyValue vcpcKey = new KeyValue(rset.getBigDecimal(imageRegionTable.id.toString()));
            String rName = rset.getString(imageRegionTable.regionName.toString()).trim();
            int pixValue = rset.getInt(imageRegionTable.pixelValue.toString());
            vcPixelClass = new VCPixelClass(vcpcKey, rName, pixValue);
            dbc.put(vcpcKey, vcPixelClass);
        } else {
            throw new ObjectNotFoundException("ImageRegion(" + imageRegionKey + ") not found");
        }
        return vcPixelClass;
    } finally {
        // Release resources include resultset
        stmt.close();
    }
}

Example 52 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class GeomDbDriver method getGeometry.

/**
 * getModel method comment.
 */
private Geometry getGeometry(QueryHashtable dbc, Connection con, User user, KeyValue geomKey, boolean bCheckPermission) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (user == null || geomKey == null) {
        throw new IllegalArgumentException("Improper parameters for getGeometry");
    }
    // log.print("GeomDbDriver.getGeometry(user="+user+", id="+geomKey+")");
    String sql;
    Field[] f = { new StarField(geomTable), userTable.userid, extentTable.extentX, extentTable.extentY, extentTable.extentZ };
    Table[] t = { geomTable, userTable, extentTable };
    String condition = geomTable.id.getQualifiedColName() + " = " + geomKey + " AND " + userTable.id.getQualifiedColName() + " = " + geomTable.ownerRef.getQualifiedColName() + " AND " + extentTable.id.getQualifiedColName() + " = " + geomTable.extentRef.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax, bCheckPermission);
    // System.out.println(sql);
    Geometry geom = null;
    // Connection con = conFact.getConnection();
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            // This geometry privacy flag gives this user permission to access
            geom = getGeometry(dbc, con, user, rset);
        } else {
            // see if at least 1 geometry parents (Mathmodels and/or BioModels) are shared with this user
            if (bCheckPermission) {
                rset.close();
                String parentSQL = GeometryTable.getParentsPermissionSQL(geomKey, user);
                rset = stmt.executeQuery(parentSQL);
                if (rset.next()) {
                    // At least 1 parent of the geometry exists that's shared to this user so give them the geometry
                    rset.close();
                    // Get the geometry without checking the geometry permission
                    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax, false);
                    rset = stmt.executeQuery(sql);
                    if (rset.next()) {
                        geom = getGeometry(dbc, con, user, rset);
                    }
                }
            }
            if (geom == null) {
                throw new ObjectNotFoundException("Geometry id=" + geomKey + " not found for user '" + user + "'");
            }
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    return geom;
}

Example 53 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class ServerDocumentManager method saveSimulation.

/**
 * Insert the method's description here.
 * Creation date: (10/28/00 12:08:30 AM)
 * @deprecated for testing purposes only.
 */
public String saveSimulation(QueryHashtable dbc, User user, String simulationXML, boolean bForceIndependent) throws DataAccessException, java.sql.SQLException, java.beans.PropertyVetoException, cbit.vcell.xml.XmlParseException {
    // 
    // this invokes "update" on the database layer
    // 
    Simulation simulation = XmlHelper.XMLToSim(simulationXML);
    forceDeepDirtyIfForeign(user, simulation);
    Version oldVersion = simulation.getVersion();
    Simulation origSimulation = null;
    if (oldVersion != null) {
        try {
            origSimulation = dbServer.getDBTopLevel().getSimulation(dbc, user, oldVersion.getVersionKey());
        } catch (ObjectNotFoundException e) {
        }
    }
    boolean bSomethingChanged = false;
    // 
    // UPDATE AND SUBSTITUTE FROM BOTTOM UP
    // 
    // Image->Geometry
    // Geometry->MathDescription
    // MathDescription->Simulation
    // 
    // 
    // if this simulation has an image:
    // save if necessary (only once) and store saved instance in hashTable
    // 
    Hashtable<Versionable, Versionable> memoryToDatabaseHash = new Hashtable<Versionable, Versionable>();
    {
        VCImage memoryImage = simulation.getMathDescription().getGeometry().getGeometrySpec().getImage();
        if (memoryImage != null) {
            // defaults to unchanged
            memoryToDatabaseHash.put(memoryImage, memoryImage);
            if (memoryImage.getKey() != null && memoryImage.getVersion().getName().equals(memoryImage.getName())) {
                // 
                // if image had previously been saved, not been forced 'dirty', and name not changed
                // compare with original image to see if "update" is required.
                // 
                VCImage databaseImage = null;
                if (origSimulation != null) {
                    VCImage origImage = origSimulation.getMathDescription().getGeometry().getGeometrySpec().getImage();
                    if (origImage != null && origImage.getKey().equals(memoryImage.getKey())) {
                        databaseImage = origImage;
                    }
                }
                if (databaseImage == null) {
                    // 
                    // saved image not found in origMathModel (too bad), get from database.
                    // 
                    databaseImage = dbServer.getDBTopLevel().getVCImage(dbc, user, memoryImage.getKey(), false);
                }
                if (databaseImage != null && !databaseImage.compareEqual(memoryImage)) {
                    KeyValue updatedImageKey = dbServer.getDBTopLevel().updateVersionable(user, memoryImage, false, true);
                    VCImage updatedImage = dbServer.getDBTopLevel().getVCImage(dbc, user, updatedImageKey, false);
                    memoryToDatabaseHash.put(memoryImage, updatedImage);
                    bSomethingChanged = true;
                }
            } else {
                // 
                // Image hasn't been saved, has been renamed, or has been forced 'dirty'
                // insert it with a unique name
                // 
                int count = 0;
                fixNullImageName(memoryImage);
                while (dbServer.getDBTopLevel().isNameUsed(user, VersionableType.VCImage, memoryImage.getName(), true)) {
                    try {
                        memoryImage.setName(TokenMangler.getNextRandomToken(memoryImage.getName()));
                    } catch (java.beans.PropertyVetoException e) {
                        e.printStackTrace(System.out);
                    }
                    if (count++ > 5) {
                        throw new DataAccessException("failed to find unique image name '" + memoryImage.getName() + "' is last name tried");
                    }
                }
                KeyValue updatedImageKey = dbServer.getDBTopLevel().insertVersionable(user, memoryImage, memoryImage.getName(), false, true);
                VCImage updatedImage = dbServer.getDBTopLevel().getVCImage(dbc, user, updatedImageKey, false);
                memoryToDatabaseHash.put(memoryImage, updatedImage);
                bSomethingChanged = true;
            }
        }
    }
    // 
    // for the Geometry:
    // substitute saved Image into Geometry and
    // save Geometry if necessary (only once) and store saved instance in hashtable.
    // 
    {
        Geometry memoryGeometry = simulation.getMathDescription().getGeometry();
        // defaults to unchanged
        memoryToDatabaseHash.put(memoryGeometry, memoryGeometry);
        boolean bMustSaveGeometry = false;
        VCImage geometryImage = memoryGeometry.getGeometrySpec().getImage();
        if (geometryImage != null && memoryToDatabaseHash.get(geometryImage) != geometryImage) {
            // 
            // image had changed and was saved, load saved image into geometry and force a save of this geometry.
            // 
            memoryGeometry.getGeometrySpec().setImage((VCImage) memoryToDatabaseHash.get(geometryImage));
            geometryImage = (VCImage) memoryToDatabaseHash.get(geometryImage);
            bMustSaveGeometry = true;
        }
        if (memoryGeometry.getKey() != null && memoryGeometry.getVersion().getName().equals(memoryGeometry.getName())) {
            if (!bMustSaveGeometry) {
                // 
                // if geometry had previously been saved, not been forced 'dirty', and name not changed
                // compare with original geometry to see if "update" is required.
                // 
                Geometry databaseGeometry = null;
                if (origSimulation != null) {
                    Geometry origGeometry = origSimulation.getMathDescription().getGeometry();
                    if (origGeometry.getKey().equals(memoryGeometry.getKey())) {
                        databaseGeometry = origGeometry;
                    }
                }
                if (databaseGeometry == null) {
                    // 
                    // saved geometry not found in origMathModel (too bad), get from database.
                    // 
                    databaseGeometry = dbServer.getDBTopLevel().getGeometry(dbc, user, memoryGeometry.getKey(), false);
                }
                if (databaseGeometry != null && !databaseGeometry.compareEqual(memoryGeometry)) {
                    bMustSaveGeometry = true;
                }
            }
            if (bMustSaveGeometry) {
                KeyValue updatedImageKey = (geometryImage != null) ? (geometryImage.getKey()) : (null);
                KeyValue updatedGeometryKey = dbServer.getDBTopLevel().updateVersionable(dbc, user, memoryGeometry, updatedImageKey, false, true);
                Geometry updatedGeometry = dbServer.getDBTopLevel().getGeometry(dbc, user, updatedGeometryKey, false);
                memoryToDatabaseHash.put(memoryGeometry, updatedGeometry);
                bSomethingChanged = true;
            }
        } else {
            // 
            // Geometry hasn't been saved, has been renamed, or has been forced 'dirty'
            // insert it with a unique name
            // 
            int count = 0;
            while (dbServer.getDBTopLevel().isNameUsed(user, VersionableType.Geometry, memoryGeometry.getName(), true)) {
                try {
                    memoryGeometry.setName(TokenMangler.getNextRandomToken(memoryGeometry.getName()));
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                }
                if (count++ > 5) {
                    throw new DataAccessException("failed to find unique geometry name '" + memoryGeometry.getName() + "' is last name tried");
                }
            }
            KeyValue updatedImageKey = (geometryImage != null) ? (geometryImage.getKey()) : (null);
            KeyValue updatedGeometryKey = dbServer.getDBTopLevel().insertVersionable(dbc, user, memoryGeometry, updatedImageKey, memoryGeometry.getName(), false, true);
            Geometry updatedGeometry = dbServer.getDBTopLevel().getGeometry(dbc, user, updatedGeometryKey, false);
            memoryToDatabaseHash.put(memoryGeometry, updatedGeometry);
            bSomethingChanged = true;
        }
    }
    // 
    // for the MathDescription:
    // substitute saved geometry into MathDescription
    // save MathDescription if necessary (only once) and store saved instance in hashtable.
    // 
    MathCompareResults mathCompareResults = null;
    {
        MathDescription memoryMathDescription = simulation.getMathDescription();
        // defaults to unchanged
        memoryToDatabaseHash.put(memoryMathDescription, memoryMathDescription);
        boolean bMustSaveMathDescription = false;
        Geometry scGeometry = memoryMathDescription.getGeometry();
        if (scGeometry != null && memoryToDatabaseHash.get(scGeometry) != scGeometry) {
            // 
            // geometry had changed and was saved, load saved geometry into SimulationContext (and it's MathDescription) and force a save of this SimulationContext.
            // 
            memoryMathDescription.setGeometry((Geometry) memoryToDatabaseHash.get(scGeometry));
            bMustSaveMathDescription = true;
        }
        if (memoryMathDescription.getKey() != null && memoryMathDescription.getVersion().getName().equals(memoryMathDescription.getName())) {
            if (!bMustSaveMathDescription) {
                // 
                // if MathDescription had previously been saved, not been forced 'dirty', and name not changed
                // compare with original MathDescription to see if "update" is required.
                // 
                MathDescription databaseMathDescription = null;
                if (origSimulation != null) {
                    MathDescription origMathDescription = origSimulation.getMathDescription();
                    if (origMathDescription.getKey().equals(memoryMathDescription.getKey())) {
                        databaseMathDescription = origMathDescription;
                    }
                }
                if (databaseMathDescription == null) {
                    // 
                    // saved mathDescription not found in origMathModel (too bad), get from database.
                    // 
                    databaseMathDescription = dbServer.getDBTopLevel().getMathDescription(dbc, user, memoryMathDescription.getKey());
                }
                if (databaseMathDescription != null) {
                    mathCompareResults = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), memoryMathDescription, databaseMathDescription);
                    if (!mathCompareResults.decision.equals(Decision.MathEquivalent_SAME_MATHDESC_AS_IN_DB)) {
                        bMustSaveMathDescription = true;
                    }
                }
            }
            if (bMustSaveMathDescription) {
                KeyValue updatedGeometryKey = memoryMathDescription.getGeometry().getKey();
                KeyValue updatedMathDescriptionKey = dbServer.getDBTopLevel().updateVersionable(user, memoryMathDescription, updatedGeometryKey, false, true);
                MathDescription updatedMathDescription = dbServer.getDBTopLevel().getMathDescription(dbc, user, updatedMathDescriptionKey);
                memoryToDatabaseHash.put(memoryMathDescription, updatedMathDescription);
                bSomethingChanged = true;
            }
        } else {
            // 
            // MathDescription hasn't been saved, has been renamed, or has been forced 'dirty'
            // insert it with a any name (doens't have to be unique ... mathDescription is not a top-level versionable).
            // 
            KeyValue updatedGeometryKey = memoryMathDescription.getGeometry().getKey();
            KeyValue updatedMathDescriptionKey = dbServer.getDBTopLevel().insertVersionable(user, memoryMathDescription, updatedGeometryKey, memoryMathDescription.getName(), false, true);
            MathDescription updatedMathDescription = dbServer.getDBTopLevel().getMathDescription(dbc, user, updatedMathDescriptionKey);
            memoryToDatabaseHash.put(memoryMathDescription, updatedMathDescription);
            bSomethingChanged = true;
        }
    }
    // 
    // for each Simulation in document:
    // substitute saved MathDescriptions into Simulation and
    // save Simulation if necessary (only once) and store saved instance in hashtable.
    // 
    Simulation memorySimulation = simulation;
    // 
    // didn't evaluate this Simulation yet.
    // 
    // defaults to unchanged
    memoryToDatabaseHash.put(memorySimulation, memorySimulation);
    boolean bMustSaveSimulation = false;
    MathDescription simMathDescription = memorySimulation.getMathDescription();
    if (simMathDescription != null && memoryToDatabaseHash.get(simMathDescription) != simMathDescription) {
        if (memoryToDatabaseHash.get(simMathDescription) != null) {
            // make sure mathDescription hasn't already propagated (newer math won't be in hashtable)
            // 
            // mathDescription had changed and was saved, load saved mathDescription into SimulationContext (and force a save)
            // 
            memorySimulation.setMathDescription((MathDescription) memoryToDatabaseHash.get(simMathDescription));
            bMustSaveSimulation = true;
        }
    }
    Simulation databaseSimulation = null;
    // 
    if (memorySimulation.getKey() != null) {
        databaseSimulation = origSimulation;
        if (databaseSimulation != null && !databaseSimulation.compareEqual(memorySimulation)) {
            bMustSaveSimulation = true;
        }
        if (!memorySimulation.getVersion().getName().equals(memorySimulation.getName())) {
            // name was changed.
            bMustSaveSimulation = true;
        }
    } else {
        // never been saved.
        bMustSaveSimulation = true;
    }
    if (bMustSaveSimulation) {
        KeyValue updatedMathDescriptionKey = memorySimulation.getMathDescription().getKey();
        KeyValue updatedSimulationKey = null;
        boolean bMathEquivalent = false;
        if (origSimulation != null) {
            bMathEquivalent = !bForceIndependent && Simulation.testEquivalency(memorySimulation, origSimulation, mathCompareResults);
        }
        if (memorySimulation.getKey() != null && memorySimulation.getVersion().getName().equals(memorySimulation.getName())) {
            // name not changed, update simulation (but pass in database Simulation to check for parent-equivalence)
            updatedSimulationKey = dbServer.getDBTopLevel().updateVersionable(user, memorySimulation, updatedMathDescriptionKey, false, bMathEquivalent, true);
        } else {
            // name changed, insert simulation (but pass in database Simulation to check for parent-equivalence)
            updatedSimulationKey = dbServer.getDBTopLevel().insertVersionable(user, memorySimulation, updatedMathDescriptionKey, memorySimulation.getName(), false, bMathEquivalent, true);
        }
        Simulation updatedSimulation = dbServer.getDBTopLevel().getSimulation(dbc, user, updatedSimulationKey);
        memoryToDatabaseHash.put(memorySimulation, updatedSimulation);
        bSomethingChanged = true;
        simulationXML = XmlHelper.simToXML(updatedSimulation);
        return simulationXML;
    } else {
        return simulationXML;
    }
}

Example 54 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class ServerDocumentManager method saveMathModel.

/**
 * Insert the method's description here.
 * Creation date: (10/28/00 12:08:30 AM)
 */
public String saveMathModel(QueryHashtable dbc, User user, String mathModelXML, String newName, String[] independentSims) throws DataAccessException, java.sql.SQLException, java.beans.PropertyVetoException, cbit.vcell.xml.XmlParseException {
    // 
    // this invokes "update" on the database layer
    // 
    MathModel mathModel = XmlHelper.XMLToMathModel(new XMLSource(mathModelXML));
    forceDeepDirtyIfForeign(user, mathModel);
    boolean isSaveAsNew = true;
    // 
    if (newName != null) {
        try {
            mathModel.setName(newName);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException("couldn't set new name for MathModel: " + e.getMessage());
        }
    } else {
        isSaveAsNew = false;
    }
    Version oldVersion = mathModel.getVersion();
    MathModel origMathModel = null;
    if (oldVersion != null) {
        try {
            String origMathModelXML = getMathModelXML(dbc, user, oldVersion.getVersionKey(), false);
            origMathModel = XmlHelper.XMLToMathModel(new XMLSource(origMathModelXML));
        } catch (ObjectNotFoundException nfe) {
            if (isSaveAsNew) {
                User foceClearVersionUser = new User("foceClearVersionUser", new KeyValue("0"));
                forceDeepDirtyIfForeign(foceClearVersionUser, mathModel);
            } else {
                throw new DataAccessException("Stored model has been changed or removed, please use 'Save As..'");
            }
        }
    }
    boolean bSomethingChanged = false;
    // 
    // UPDATE AND SUBSTITUTE FROM BOTTOM UP
    // 
    // Image->Geometry
    // Geometry->MathDescription
    // MathDescription->Simulation,MathModel
    // Simulation->MathModel
    // 
    Simulation[] simArray = mathModel.getSimulations();
    // 
    // if this mathModel has an image:
    // save if necessary (only once) and store saved instance in hashTable
    // 
    Hashtable<Versionable, Versionable> memoryToDatabaseHash = new Hashtable<Versionable, Versionable>();
    {
        VCImage memoryImage = mathModel.getMathDescription().getGeometry().getGeometrySpec().getImage();
        if (memoryImage != null) {
            // defaults to unchanged
            memoryToDatabaseHash.put(memoryImage, memoryImage);
            if (memoryImage.getKey() != null && memoryImage.getVersion().getName().equals(memoryImage.getName())) {
                // 
                // if image had previously been saved, not been forced 'dirty', and name not changed
                // compare with original image to see if "update" is required.
                // 
                VCImage databaseImage = null;
                if (origMathModel != null) {
                    VCImage origImage = origMathModel.getMathDescription().getGeometry().getGeometrySpec().getImage();
                    if (origImage != null && origImage.getKey().equals(memoryImage.getKey())) {
                        databaseImage = origImage;
                    }
                }
                if (databaseImage == null) {
                    // 
                    // saved image not found in origMathModel (too bad), get from database.
                    // 
                    databaseImage = dbServer.getDBTopLevel().getVCImage(dbc, user, memoryImage.getKey(), false);
                }
                if (databaseImage != null && !databaseImage.compareEqual(memoryImage)) {
                    KeyValue updatedImageKey = dbServer.getDBTopLevel().updateVersionable(user, memoryImage, false, true);
                    VCImage updatedImage = dbServer.getDBTopLevel().getVCImage(dbc, user, updatedImageKey, false);
                    memoryToDatabaseHash.put(memoryImage, updatedImage);
                    bSomethingChanged = true;
                }
            } else {
                // 
                // Image hasn't been saved, has been renamed, or has been forced 'dirty'
                // insert it with a unique name
                // 
                int count = 0;
                fixNullImageName(memoryImage);
                while (dbServer.getDBTopLevel().isNameUsed(user, VersionableType.VCImage, memoryImage.getName(), true)) {
                    try {
                        memoryImage.setName(TokenMangler.getNextRandomToken(memoryImage.getName()));
                    } catch (java.beans.PropertyVetoException e) {
                        e.printStackTrace(System.out);
                    }
                    if (count++ > 5) {
                        throw new DataAccessException("failed to find unique image name '" + memoryImage.getName() + "' is last name tried");
                    }
                }
                KeyValue updatedImageKey = dbServer.getDBTopLevel().insertVersionable(user, memoryImage, memoryImage.getName(), false, true);
                VCImage updatedImage = dbServer.getDBTopLevel().getVCImage(dbc, user, updatedImageKey, false);
                memoryToDatabaseHash.put(memoryImage, updatedImage);
                bSomethingChanged = true;
            }
        }
    }
    // 
    // for the Geometry:
    // substitute saved Image into Geometry and
    // save Geometry if necessary (only once) and store saved instance in hashtable.
    // 
    {
        Geometry memoryGeometry = mathModel.getMathDescription().getGeometry();
        // defaults to unchanged
        memoryToDatabaseHash.put(memoryGeometry, memoryGeometry);
        boolean bMustSaveGeometry = false;
        VCImage geometryImage = memoryGeometry.getGeometrySpec().getImage();
        if (geometryImage != null && memoryToDatabaseHash.get(geometryImage) != geometryImage) {
            // 
            // image had changed and was saved, load saved image into geometry and force a save of this geometry.
            // 
            memoryGeometry.getGeometrySpec().setImage((VCImage) memoryToDatabaseHash.get(geometryImage));
            geometryImage = (VCImage) memoryToDatabaseHash.get(geometryImage);
            bMustSaveGeometry = true;
        }
        if (memoryGeometry.getKey() != null && memoryGeometry.getVersion().getName().equals(memoryGeometry.getName())) {
            if (!bMustSaveGeometry) {
                // 
                // if geometry had previously been saved, not been forced 'dirty', and name not changed
                // compare with original geometry to see if "update" is required.
                // 
                Geometry databaseGeometry = null;
                if (origMathModel != null) {
                    Geometry origGeometry = origMathModel.getMathDescription().getGeometry();
                    if (origGeometry.getKey().equals(memoryGeometry.getKey())) {
                        databaseGeometry = origGeometry;
                    }
                }
                if (databaseGeometry == null) {
                    // 
                    // saved geometry not found in origMathModel (too bad), get from database.
                    // 
                    databaseGeometry = dbServer.getDBTopLevel().getGeometry(dbc, user, memoryGeometry.getKey(), false);
                }
                if (databaseGeometry != null && !databaseGeometry.compareEqual(memoryGeometry)) {
                    bMustSaveGeometry = true;
                }
            }
            if (bMustSaveGeometry) {
                KeyValue updatedImageKey = (geometryImage != null) ? (geometryImage.getKey()) : (null);
                KeyValue updatedGeometryKey = dbServer.getDBTopLevel().updateVersionable(dbc, user, memoryGeometry, updatedImageKey, false, true);
                Geometry updatedGeometry = dbServer.getDBTopLevel().getGeometry(dbc, user, updatedGeometryKey, false);
                memoryToDatabaseHash.put(memoryGeometry, updatedGeometry);
                bSomethingChanged = true;
            }
        } else {
            // 
            // Geometry hasn't been saved, has been renamed, or has been forced 'dirty'
            // insert it with a unique name
            // 
            int count = 0;
            while (dbServer.getDBTopLevel().isNameUsed(user, VersionableType.Geometry, memoryGeometry.getName(), true)) {
                try {
                    memoryGeometry.setName(TokenMangler.getNextRandomToken(memoryGeometry.getName()));
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                }
                if (count++ > 5) {
                    throw new DataAccessException("failed to find unique geometry name '" + memoryGeometry.getName() + "' is last name tried");
                }
            }
            KeyValue updatedImageKey = (geometryImage != null) ? (geometryImage.getKey()) : (null);
            KeyValue updatedGeometryKey = dbServer.getDBTopLevel().insertVersionable(dbc, user, memoryGeometry, updatedImageKey, memoryGeometry.getName(), false, true);
            Geometry updatedGeometry = dbServer.getDBTopLevel().getGeometry(dbc, user, updatedGeometryKey, false);
            memoryToDatabaseHash.put(memoryGeometry, updatedGeometry);
            bSomethingChanged = true;
        }
    }
    // 
    // for the MathDescription:
    // substitute saved geometry into MathDescription
    // save MathDescription if necessary (only once) and store saved instance in hashtable.
    // 
    MathCompareResults mathCompareResults = null;
    {
        MathDescription memoryMathDescription = mathModel.getMathDescription();
        // defaults to unchanged
        memoryToDatabaseHash.put(memoryMathDescription, memoryMathDescription);
        boolean bMustSaveMathDescription = false;
        Geometry scGeometry = memoryMathDescription.getGeometry();
        if (scGeometry != null && memoryToDatabaseHash.get(scGeometry) != scGeometry) {
            // 
            // geometry had changed and was saved, load saved geometry into SimulationContext (and it's MathDescription) and force a save of this SimulationContext.
            // 
            memoryMathDescription.setGeometry((Geometry) memoryToDatabaseHash.get(scGeometry));
            bMustSaveMathDescription = true;
        }
        MathDescription databaseMathDescription = null;
        if (memoryMathDescription.getKey() != null) {
            // 
            if (origMathModel != null) {
                MathDescription origMathDescription = origMathModel.getMathDescription();
                if (origMathDescription.getKey().equals(memoryMathDescription.getKey())) {
                    databaseMathDescription = origMathDescription;
                }
            }
            if (databaseMathDescription == null) {
                // 
                // saved mathDescription not found in origMathModel (too bad), get from database.
                // 
                databaseMathDescription = dbServer.getDBTopLevel().getMathDescription(dbc, user, memoryMathDescription.getKey());
            }
            if (databaseMathDescription != null) {
                if (!memoryMathDescription.compareEqual(databaseMathDescription)) {
                    bMustSaveMathDescription = true;
                }
            }
        } else {
            bMustSaveMathDescription = true;
        }
        if (bMustSaveMathDescription) {
            // 
            if (databaseMathDescription != null) {
                try {
                    mathCompareResults = MathDescription.testEquivalency(SimulationSymbolTable.createMathSymbolTableFactory(), memoryMathDescription, databaseMathDescription);
                } catch (Exception e) {
                    e.printStackTrace(System.out);
                    mathCompareResults = new MathCompareResults(Decision.MathDifferent_FAILURE_UNKNOWN, "Exception: '" + e.getMessage() + "'");
                    System.out.println("FAILED TO COMPARE THE FOLLOWING MATH DESCRIPTIONS");
                    try {
                        System.out.println("MemoryMathDescription:\n" + ((memoryMathDescription != null) ? (memoryMathDescription.getVCML_database()) : ("null")));
                        System.out.println("DatabaseMathDescription:\n" + ((databaseMathDescription != null) ? (databaseMathDescription.getVCML_database()) : ("null")));
                    } catch (Exception e2) {
                        System.out.println("couldn't print math descriptions");
                    }
                }
            } else {
                mathCompareResults = new MathCompareResults(Decision.MathDifferent_NOT_SAVED);
            }
            KeyValue updatedGeometryKey = memoryMathDescription.getGeometry().getKey();
            KeyValue updatedMathDescriptionKey = null;
            if (memoryMathDescription.getVersion() != null && memoryMathDescription.getVersion().getName().equals(memoryMathDescription.getName())) {
                updatedMathDescriptionKey = dbServer.getDBTopLevel().updateVersionable(user, memoryMathDescription, updatedGeometryKey, false, true);
            } else {
                updatedMathDescriptionKey = dbServer.getDBTopLevel().insertVersionable(user, memoryMathDescription, updatedGeometryKey, memoryMathDescription.getName(), false, true);
            }
            MathDescription updatedMathDescription = dbServer.getDBTopLevel().getMathDescription(dbc, user, updatedMathDescriptionKey);
            memoryToDatabaseHash.put(memoryMathDescription, updatedMathDescription);
            bSomethingChanged = true;
        } else {
            mathCompareResults = new MathCompareResults(Decision.MathEquivalent_SAME_MATHDESC_AS_IN_DB);
        }
    }
    // 
    for (int i = 0; simArray != null && i < simArray.length; i++) {
        Simulation memorySimulation = simArray[i];
        if (!memoryToDatabaseHash.containsKey(memorySimulation)) {
            // 
            // didn't evaluate this Simulation yet.
            // 
            // defaults to unchanged
            memoryToDatabaseHash.put(memorySimulation, memorySimulation);
            boolean bMustSaveSimulation = false;
            MathDescription simMathDescription = memorySimulation.getMathDescription();
            if (simMathDescription != null && memoryToDatabaseHash.get(simMathDescription) != simMathDescription) {
                if (memoryToDatabaseHash.get(simMathDescription) != null) {
                    // make sure mathDescription hasn't already propagated (newer math won't be in hashtable)
                    // 
                    // mathDescription had changed and was saved, load saved mathDescription into SimulationContext (and force a save)
                    // 
                    memorySimulation.setMathDescription((MathDescription) memoryToDatabaseHash.get(simMathDescription));
                    bMustSaveSimulation = true;
                }
            }
            Simulation databaseSimulation = null;
            // 
            if (memorySimulation.getKey() != null) {
                if (origMathModel != null) {
                    for (int j = 0; j < origMathModel.getNumSimulations(); j++) {
                        if (origMathModel.getSimulations(j).getKey().equals(memorySimulation.getKey())) {
                            databaseSimulation = origMathModel.getSimulations(j);
                            break;
                        }
                    }
                }
                if (databaseSimulation == null) {
                    // 
                    // saved simulation not found in origBioModel (too bad), get from database.
                    // 
                    databaseSimulation = dbServer.getDBTopLevel().getSimulation(dbc, user, memorySimulation.getKey());
                }
                if (databaseSimulation != null && !databaseSimulation.compareEqual(memorySimulation)) {
                    bMustSaveSimulation = true;
                }
                if (!memorySimulation.getVersion().getName().equals(memorySimulation.getName())) {
                    // name was changed.
                    bMustSaveSimulation = true;
                }
            } else {
                // never been saved.
                bMustSaveSimulation = true;
            }
            if (bMustSaveSimulation) {
                KeyValue updatedMathDescriptionKey = memorySimulation.getMathDescription().getKey();
                KeyValue updatedSimulationKey = null;
                boolean bSimMathematicallyEquivalent = false;
                if (databaseSimulation != null) {
                    // 
                    // if to be forced "independent", then set equivalent to false
                    // 
                    boolean bForceIndependent = false;
                    for (int j = 0; independentSims != null && j < independentSims.length; j++) {
                        if (independentSims[j].equals(memorySimulation.getName())) {
                            bForceIndependent = true;
                        }
                    }
                    // check for math equivalency
                    try {
                        bSimMathematicallyEquivalent = !bForceIndependent && Simulation.testEquivalency(memorySimulation, databaseSimulation, mathCompareResults);
                    } catch (Exception e) {
                        e.printStackTrace(System.out);
                        throw new DataAccessException(e.getMessage());
                    }
                    // 
                    if (bSimMathematicallyEquivalent) {
                        VCSimulationIdentifier vcSimulationIdentifier = databaseSimulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
                        SimulationStatusPersistent simStatus = dbServer.getSimulationStatus(vcSimulationIdentifier.getSimulationKey());
                        if (simStatus == null || !simStatus.getHasData()) {
                            bSimMathematicallyEquivalent = false;
                        }
                    }
                }
                if (memorySimulation.getKey() != null && memorySimulation.getVersion().getName().equals(memorySimulation.getName())) {
                    // name not changed, update simulation (but pass in database Simulation to check for parent-equivalence)
                    updatedSimulationKey = dbServer.getDBTopLevel().updateVersionable(user, memorySimulation, updatedMathDescriptionKey, false, bSimMathematicallyEquivalent, true);
                } else {
                    // name changed, insert simulation (but pass in database Simulation to check for parent-equivalence)
                    updatedSimulationKey = dbServer.getDBTopLevel().insertVersionable(user, memorySimulation, updatedMathDescriptionKey, memorySimulation.getName(), false, bSimMathematicallyEquivalent, true);
                }
                Simulation updatedSimulation = dbServer.getDBTopLevel().getSimulation(dbc, user, updatedSimulationKey);
                memoryToDatabaseHash.put(memorySimulation, updatedSimulation);
                bSomethingChanged = true;
            }
        }
    }
    if (bSomethingChanged || origMathModel == null || !mathModel.compareEqual(origMathModel)) {
        // 
        // create new MathModelMetaData and save to server
        // 
        KeyValue mathDescriptionKey = ((MathDescription) memoryToDatabaseHash.get(mathModel.getMathDescription())).getKey();
        KeyValue[] simKeys = new KeyValue[mathModel.getNumSimulations()];
        for (int i = 0; i < mathModel.getNumSimulations(); i++) {
            simKeys[i] = ((Simulation) memoryToDatabaseHash.get(mathModel.getSimulations(i))).getKey();
        }
        MathModelMetaData mathModelMetaData = null;
        if (oldVersion == null) {
            mathModelMetaData = new MathModelMetaData(mathDescriptionKey, simKeys, mathModel.getName(), mathModel.getDescription(), mathModel.getOutputFunctionContext().getOutputFunctionsList());
        } else {
            mathModelMetaData = new MathModelMetaData(oldVersion, mathDescriptionKey, simKeys, mathModel.getOutputFunctionContext().getOutputFunctionsList());
            if (!mathModel.getDescription().equals(oldVersion.getAnnot())) {
                try {
                    mathModelMetaData.setDescription(mathModel.getDescription());
                } catch (java.beans.PropertyVetoException e) {
                    e.printStackTrace(System.out);
                }
            }
        }
        MathModelMetaData updatedMathModelMetaData = null;
        if (mathModel.getVersion() == null || !mathModel.getVersion().getName().equals(mathModel.getName())) {
            KeyValue updatedMathModelKey = dbServer.getDBTopLevel().insertVersionable(user, mathModelMetaData, null, /*hack*/
            mathModel.getName(), false, true);
            updatedMathModelMetaData = dbServer.getDBTopLevel().getMathModelMetaData(dbc, user, updatedMathModelKey);
        } else {
            KeyValue updatedMathModelKey = dbServer.getDBTopLevel().updateVersionable(user, mathModelMetaData, null, /*hack*/
            false, true);
            updatedMathModelMetaData = dbServer.getDBTopLevel().getMathModelMetaData(dbc, user, updatedMathModelKey);
        }
        // 
        // (THIS IS THE REALLY SCARY PART...NOT GETTING A FRESH VIEW OF EVERYTING FROM THE DATABASE FOR CREATING THE XML)
        // 
        // mathModelXML = getMathModelXML(user,updatedMathModelMetaData.getVersion().getVersionKey());
        MathModel updatedMathModel = new MathModel(updatedMathModelMetaData.getVersion());
        updatedMathModel.setMathDescription((MathDescription) memoryToDatabaseHash.get(mathModel.getMathDescription()));
        for (int i = 0; i < mathModel.getNumSimulations(); i++) {
            updatedMathModel.addSimulation((Simulation) memoryToDatabaseHash.get(mathModel.getSimulations(i)));
        }
        updatedMathModel.getOutputFunctionContext().setOutputFunctions(mathModel.getOutputFunctionContext().getOutputFunctionsList());
        mathModelXML = cbit.vcell.xml.XmlHelper.mathModelToXML(updatedMathModel);
        dbServer.insertVersionableChildSummary(user, VersionableType.MathModelMetaData, updatedMathModel.getVersion().getVersionKey(), updatedMathModel.createMathModelChildSummary().toDatabaseSerialization());
        dbServer.insertVersionableXML(user, VersionableType.MathModelMetaData, updatedMathModel.getVersion().getVersionKey(), mathModelXML);
        return mathModelXML;
    } else {
        return mathModelXML;
    }
}

Example 55 with ObjectNotFoundException

use of org.vcell.util.ObjectNotFoundException in project vcell by virtualcell.

the class ServerDocumentManager method isChanged.

/**
 * Insert the method's description here.
 * Creation date: (10/28/00 12:08:30 AM)
 */
boolean isChanged(QueryHashtable dbc, User user, Geometry geometry) throws DataAccessException {
    // 
    // identify versionable as it was last loaded from the database
    // 
    KeyValue key = (geometry.getVersion() != null) ? (geometry.getVersion().getVersionKey()) : null;
    if (key == null) {
        return true;
    }
    Versionable savedVersionable = null;
    // 
    try {
        savedVersionable = dbServer.getDBTopLevel().getGeometry(dbc, user, key, true);
    } catch (ObjectNotFoundException e) {
        // 
        return true;
    } catch (Throwable e) {
        // 
        // loaded version has been deleted
        // 
        e.printStackTrace(System.out);
        return true;
    }
    return isChanged0(user, geometry, savedVersionable);
}