Examples with GeometryInfo cbit.vcell.geometry.GeometryInfo used on opensource projects

Example 16 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class DbDriver method getVCInfoContainer.

/**
 * Insert the method's description here.
 * Creation date: (9/24/2003 12:54:32 PM)
 * @return cbit.vcell.modeldb.VCInfoContainer
 */
public static VCInfoContainer getVCInfoContainer(User user, Connection con, DatabaseSyntax dbSyntax, int whichExtraInfo) throws SQLException, DataAccessException {
    VCInfoContainer results = null;
    // 
    VCImageInfo[] vcImageInfos = null;
    GeometryInfo[] geometryInfos = null;
    MathModelInfo[] mathModelInfos = null;
    BioModelInfo[] bioModelInfos = null;
    PublicationInfo[] publicationInfos = null;
    // 
    StringBuffer sql = null;
    String special = null;
    ResultSet rset = null;
    boolean enableSpecial = true;
    boolean enableDistinct = true;
    Statement stmt = con.createStatement();
    stmt.setFetchSize(500);
    try {
        String aliasSimName = "aliasSimName";
        String aliasSimID = "aliasSimID";
        String aliasSCName = "aliasSCName";
        String aliasSVName = "aliasSVName";
        // 
        // BioModelInfos
        // 
        {
            double beginTime = System.currentTimeMillis();
            special = " ORDER BY " + BioModelTable.table.name.getQualifiedColName() + "," + BioModelTable.table.versionBranchID.getQualifiedColName() + "," + BioModelTable.table.versionDate.getQualifiedColName();
            sql = new StringBuffer(BioModelTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), dbSyntax));
            sql.insert(7, Table.SQL_GLOBAL_HINT);
            rset = stmt.executeQuery(sql.toString());
            TreeMap<BigDecimal, BioModelInfo> mapBmToBioModelInfo = new TreeMap<BigDecimal, BioModelInfo>();
            while (rset.next()) {
                BigDecimal bmID = rset.getBigDecimal(VersionTable.id_ColumnName);
                if (!mapBmToBioModelInfo.containsKey(bmID)) {
                    BioModelInfo versionInfo = (BioModelInfo) BioModelTable.table.getInfo(rset, con, dbSyntax);
                    mapBmToBioModelInfo.put(bmID, versionInfo);
                }
            }
            rset.close();
            if (whichExtraInfo != 0) {
                // Add mapping simName->SimID
                try {
                    // String aliasUserKey = "aliasUserKey";
                    sql = new StringBuffer("SELECT " + SimContextTable.table.id.getQualifiedColName() + "," + SimContextTable.table.name.getQualifiedColName() + " " + aliasSCName + "," + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + "," + SimulationTable.table.name.getQualifiedColName() + " " + aliasSimName + "," + SimulationTable.table.id.getQualifiedColName() + " " + aliasSimID + (whichExtraInfo == 0xFF ? "," + ApplicationMathTable.table.outputFuncLarge.getQualifiedColName() + "," + ApplicationMathTable.table.outputFuncSmall.getQualifiedColName() + "," + SimulationTable.table.mathOverridesSmall + "," + SimulationTable.table.mathOverridesLarge + "," + SubVolumeTable.table.handle.getQualifiedColName() + "," + SubVolumeTable.table.name.getQualifiedColName() + " " + aliasSVName : // SubVolumeTable.table.ordinal.getQualifiedColName()+
                    "") + " FROM " + SimContextTable.table.getTableName() + "," + BioModelSimContextLinkTable.table.getTableName() + "," + BioModelSimulationLinkTable.table.getTableName() + "," + SimulationTable.table.getTableName() + (whichExtraInfo == 0xFF ? "," + ApplicationMathTable.table.getTableName() + "," + // GeometricRegionTable.table.getTableName()+","+
                    SubVolumeTable.table.getTableName() : "") + " WHERE " + BioModelSimContextLinkTable.table.simContextRef.getQualifiedColName() + " = " + SimContextTable.table.id.getQualifiedColName() + " AND " + SimulationTable.table.id.getQualifiedColName() + " = " + BioModelSimulationLinkTable.table.simRef.getQualifiedColName() + " AND " + BioModelSimulationLinkTable.table.bioModelRef.getQualifiedColName() + " = " + BioModelSimContextLinkTable.table.bioModelRef.getQualifiedColName() + " AND " + SimContextTable.table.mathRef.getQualifiedColName() + " = " + SimulationTable.table.mathRef.getQualifiedColName() + (whichExtraInfo == 0xFF ? " AND " + SimContextTable.table.id.getQualifiedColName() + " = " + ApplicationMathTable.table.simContextRef.getQualifiedColName() + " (+)" + // " AND "+SubVolumeTable.table.geometryRef.getQualifiedColName()+" = "+GeometricRegionTable.table.geometryRef.getQualifiedColName()
                    " AND " + SimContextTable.table.geometryRef.getQualifiedColName() + " = " + SubVolumeTable.table.geometryRef.getQualifiedColName() + " (+)" : ""));
                    final BigDecimal[] array = mapBmToBioModelInfo.keySet().toArray(new BigDecimal[0]);
                    final int MAX_LIST = 500;
                    for (int i = 0; i < array.length; i += MAX_LIST) {
                        StringBuffer bmListStr = new StringBuffer();
                        for (int j = 0; (i + j) < array.length && j < MAX_LIST; j++) {
                            bmListStr.append((j != 0 ? "," : "") + array[i + j].toString());
                        }
                        final String sql2 = sql.toString() + " AND " + BioModelSimulationLinkTable.table.bioModelRef.getQualifiedColName() + " IN (" + bmListStr.toString() + ")" + " ORDER BY " + BioModelSimulationLinkTable.table.bioModelRef.getQualifiedColName() + "," + SimContextTable.table.id.getQualifiedColName() + "," + SimulationTable.table.id.getQualifiedColName();
                        rset = stmt.executeQuery(sql2);
                        BioModelInfo bmInfo = null;
                        while (rset.next()) {
                            final BigDecimal bmID = rset.getBigDecimal(BioModelSimContextLinkTable.table.bioModelRef.toString());
                            bmInfo = mapBmToBioModelInfo.get(bmID);
                            if (bmInfo != null) {
                                final BigDecimal scID = rset.getBigDecimal(SimContextTable.table.id.toString());
                                final String scName = rset.getString(aliasSCName);
                                bmInfo.addSCID(scName, scID);
                                if ((whichExtraInfo & EXTRAINFO_ANNOTFUNC) != 0) {
                                    if (!bmInfo.hasSCIDForAnnotFunc(scID)) {
                                        String outputFunctionsXML = DbDriver.varchar2_CLOB_get(rset, ApplicationMathTable.table.outputFuncSmall, ApplicationMathTable.table.outputFuncLarge, dbSyntax);
                                        if (outputFunctionsXML != null) {
                                            bmInfo.addAnnotatedFunctionsStr(scName, scID, outputFunctionsXML);
                                        }
                                    }
                                }
                                final String simName = rset.getString(aliasSimName);
                                if (bmInfo.getSimID(simName) == null) {
                                    final BigDecimal simID = rset.getBigDecimal(aliasSimID);
                                    bmInfo.addSimID(simName, simID);
                                    if ((whichExtraInfo & EXTRAINFO_MATHOVERRIDES) != 0) {
                                        CommentStringTokenizer mathOverridesTokenizer = SimulationTable.getMathOverridesTokenizer(rset, dbSyntax);
                                        List<Element> mathOverrideElements = MathOverrides.parseOverrideElementsFromVCML(mathOverridesTokenizer);
                                        // int scanCount=1;
                                        // for(Element ele:mathOverrideElements) {
                                        // if(ele.getSpec() != null) {
                                        // scanCount*=ele.getSpec().getNumValues();
                                        // //										if(scanCount==0) {
                                        // //											scanCount=ele.getSpec().getNumValues();
                                        // //										}else {
                                        // //											scanCount*=ele.getSpec().getNumValues();
                                        // //										}
                                        // }
                                        // }
                                        // //							if(scanCount > 1) {
                                        // //								System.out.println("bmid="+bmID+" simid="+simID+" scans="+scanCount+" "+simName);
                                        // //							}
                                        bmInfo.addMathOverrides(simName, mathOverrideElements);
                                    }
                                }
                                if ((whichExtraInfo & EXTRAINFO_SUBVOLUMES) != 0) {
                                    final int subVolumeID = rset.getInt(SubVolumeTable.table.handle.toString());
                                    if (bmInfo.getSubVolumeName(subVolumeID) == null) {
                                        bmInfo.addSubVolume(subVolumeID, rset.getString(aliasSVName));
                                    }
                                }
                            }
                        }
                        rset.close();
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                // ignore
                }
            }
            if (mapBmToBioModelInfo.size() > 0) {
                bioModelInfos = new BioModelInfo[mapBmToBioModelInfo.size()];
                mapBmToBioModelInfo.values().toArray(bioModelInfos);
            }
            // }
            if (lg.isInfoEnabled()) {
                lg.info("BioModelInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
            }
        }
        // 
        // MathModelInfos
        // 
        {
            double beginTime = System.currentTimeMillis();
            special = " ORDER BY " + MathModelTable.table.name.getQualifiedColName() + "," + MathModelTable.table.versionBranchID.getQualifiedColName() + "," + MathModelTable.table.versionDate.getQualifiedColName();
            sql = new StringBuffer(MathModelTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), dbSyntax));
            sql.insert(7, Table.SQL_GLOBAL_HINT);
            TreeMap<BigDecimal, MathModelInfo> mapMmToMathModelInfo = new TreeMap<BigDecimal, MathModelInfo>();
            rset = stmt.executeQuery(sql.toString());
            ArrayList<MathModelInfo> tempInfos = new ArrayList<MathModelInfo>();
            Set<String> distinctV = new HashSet<String>();
            while (rset.next()) {
                MathModelInfo versionInfo = (MathModelInfo) MathModelTable.table.getInfo(rset, con, dbSyntax);
                if (!distinctV.contains(versionInfo.getVersion().getVersionKey().toString())) {
                    tempInfos.add(versionInfo);
                    distinctV.add(versionInfo.getVersion().getVersionKey().toString());
                    mapMmToMathModelInfo.put(BigDecimal.valueOf(Long.parseLong(versionInfo.getVersion().getVersionKey().toString())), versionInfo);
                }
            }
            rset.close();
            if (whichExtraInfo != 0) {
                // Add mapping simName->SimID
                try {
                    // String aliasUserKey = "aliasUserKey";
                    sql = new StringBuffer("SELECT " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + "," + ApplicationMathTable.table.outputFuncLarge.getQualifiedColName() + "," + ApplicationMathTable.table.outputFuncSmall.getQualifiedColName() + "," + SimulationTable.table.name.getQualifiedColName() + " " + aliasSimName + "," + SimulationTable.table.id.getQualifiedColName() + " " + aliasSimID + "," + SimulationTable.table.mathOverridesSmall + "," + SimulationTable.table.mathOverridesLarge + "," + SubVolumeTable.table.handle.getQualifiedColName() + "," + SubVolumeTable.table.name.getQualifiedColName() + " " + aliasSVName + " FROM " + MathModelTable.table.getTableName() + "," + MathDescTable.table.getTableName() + "," + MathModelSimulationLinkTable.table.getTableName() + "," + ApplicationMathTable.table.getTableName() + "," + SimulationTable.table.getTableName() + "," + SubVolumeTable.table.getTableName() + " WHERE " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + " = " + ApplicationMathTable.table.mathModelRef.getQualifiedColName() + " (+)" + " AND " + MathModelTable.table.id.getQualifiedColName() + " = " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + " AND " + SimulationTable.table.id.getQualifiedColName() + " = " + MathModelSimulationLinkTable.table.simRef.getQualifiedColName() + " AND " + MathDescTable.table.id.getQualifiedColName() + " = " + MathModelTable.table.mathRef.getQualifiedColName() + " AND " + MathDescTable.table.geometryRef.getQualifiedColName() + " = " + SubVolumeTable.table.geometryRef.getQualifiedColName() + " (+)");
                    final BigDecimal[] array = mapMmToMathModelInfo.keySet().toArray(new BigDecimal[0]);
                    final int MAX_LIST = 500;
                    for (int i = 0; i < array.length; i += MAX_LIST) {
                        StringBuffer mmListStr = new StringBuffer();
                        for (int j = 0; (i + j) < array.length && j < MAX_LIST; j++) {
                            mmListStr.append((j != 0 ? "," : "") + array[i + j].toString());
                        }
                        final String sql2 = sql.toString() + " AND " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + " IN (" + mmListStr.toString() + ")" + " ORDER BY " + MathModelSimulationLinkTable.table.mathModelRef.getQualifiedColName() + "," + SimulationTable.table.id.getQualifiedColName();
                        rset = stmt.executeQuery(sql2);
                        MathModelInfo mmInfo = null;
                        while (rset.next()) {
                            final BigDecimal mmID = rset.getBigDecimal(MathModelSimulationLinkTable.table.mathModelRef.toString());
                            mmInfo = mapMmToMathModelInfo.get(mmID);
                            if (mmInfo != null) {
                                if (mmInfo.getAnnotatedFunctionsStr() == null) {
                                    String outputFunctionsXML = DbDriver.varchar2_CLOB_get(rset, ApplicationMathTable.table.outputFuncSmall, ApplicationMathTable.table.outputFuncLarge, dbSyntax);
                                    if (outputFunctionsXML != null) {
                                        mmInfo.setAnnotatedFunctionsStr(outputFunctionsXML);
                                    }
                                }
                                final String simName = rset.getString(aliasSimName);
                                if (mmInfo.getSimID(simName) == null) {
                                    final BigDecimal simID = rset.getBigDecimal(aliasSimID);
                                    CommentStringTokenizer mathOverridesTokenizer = SimulationTable.getMathOverridesTokenizer(rset, dbSyntax);
                                    List<Element> mathOverrideElements = MathOverrides.parseOverrideElementsFromVCML(mathOverridesTokenizer);
                                    // int scanCount=1;
                                    // for(Element ele:mathOverrideElements) {
                                    // if(ele.getSpec() != null) {
                                    // scanCount*=ele.getSpec().getNumValues();
                                    // }
                                    // }
                                    mmInfo.addSimID(simName, simID, mathOverrideElements);
                                }
                                final int subVolumeID = rset.getInt(SubVolumeTable.table.handle.toString());
                                if (mmInfo.getSubVolumeName(subVolumeID) == null) {
                                    mmInfo.addSubVolume(subVolumeID, rset.getString(aliasSVName));
                                }
                            }
                        }
                        rset.close();
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                // ignore
                }
            }
            if (tempInfos.size() > 0) {
                mathModelInfos = new MathModelInfo[tempInfos.size()];
                tempInfos.toArray(mathModelInfos);
            }
            if (lg.isInfoEnabled()) {
                lg.info("MathModelInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
            }
        }
        // 
        // VCImageInfos
        // 
        {
            double beginTime = System.currentTimeMillis();
            special = " ORDER BY " + ImageTable.table.name.getQualifiedColName() + "," + ImageTable.table.versionBranchID.getQualifiedColName() + "," + ImageTable.table.versionDate.getQualifiedColName();
            sql = new StringBuffer(ImageTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), true, dbSyntax));
            sql.insert(7, Table.SQL_GLOBAL_HINT);
            rset = stmt.executeQuery(sql.toString());
            ArrayList<VCImageInfo> tempInfos = new ArrayList<VCImageInfo>();
            Set<String> distinctV = new HashSet<String>();
            while (rset.next()) {
                VCImageInfo versionInfo = (VCImageInfo) ImageTable.table.getInfo(rset, con, dbSyntax);
                if (!distinctV.contains(versionInfo.getVersion().getVersionKey().toString())) {
                    tempInfos.add(versionInfo);
                    distinctV.add(versionInfo.getVersion().getVersionKey().toString());
                }
            }
            rset.close();
            if (tempInfos.size() > 0) {
                vcImageInfos = new VCImageInfo[tempInfos.size()];
                tempInfos.toArray(vcImageInfos);
            }
            if (lg.isInfoEnabled()) {
                lg.info("ImageInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
            }
        }
        // 
        // GeometeryInfos
        // 
        {
            double beginTime = System.currentTimeMillis();
            special = " ORDER BY " + GeometryTable.table.name.getQualifiedColName() + "," + GeometryTable.table.versionBranchID.getQualifiedColName() + "," + GeometryTable.table.versionDate.getQualifiedColName();
            sql = new StringBuffer(GeometryTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), true, dbSyntax));
            sql.insert(7, Table.SQL_GLOBAL_HINT + (enableDistinct ? "DISTINCT " : ""));
            rset = stmt.executeQuery(sql.toString());
            ArrayList<GeometryInfo> tempInfos = new ArrayList<GeometryInfo>();
            Set<String> distinctV = new HashSet<String>();
            while (rset.next()) {
                GeometryInfo versionInfo = (GeometryInfo) GeometryTable.table.getInfo(rset, con);
                if (!distinctV.contains(versionInfo.getVersion().getVersionKey().toString())) {
                    tempInfos.add(versionInfo);
                    distinctV.add(versionInfo.getVersion().getVersionKey().toString());
                }
            }
            rset.close();
            if (tempInfos.size() > 0) {
                geometryInfos = new GeometryInfo[tempInfos.size()];
                tempInfos.toArray(geometryInfos);
            }
            if (lg.isInfoEnabled()) {
                lg.info("GeometryInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
            }
        }
        try {
            Vector<VersionInfo> bm_mm_VCDocumentInfos = new Vector<>();
            bm_mm_VCDocumentInfos.addAll(Arrays.asList((bioModelInfos != null ? bioModelInfos : new BioModelInfo[0])));
            bm_mm_VCDocumentInfos.addAll(Arrays.asList((mathModelInfos != null ? mathModelInfos : new MathModelInfo[0])));
            DbDriver.addPublicationInfos(con, stmt, bm_mm_VCDocumentInfos);
        } catch (Exception e) {
            e.printStackTrace();
        // Don't fail if something goes wrong with setting publication info
        }
    } finally {
        if (stmt != null) {
            stmt.close();
        }
    }
    results = new VCInfoContainer(user, vcImageInfos, geometryInfos, mathModelInfos, bioModelInfos);
    return results;
}

Example 17 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class ClientDocumentManager method reloadGeometryInfos.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 5:33:21 PM)
 * @return cbit.vcell.biomodel.BioModelInfo[]
 */
private void reloadGeometryInfos() throws DataAccessException {
    try {
        System.out.println("ClientDocumentManager.reloadGeometryInfos()");
        GeometryInfo[] geometryInfos = sessionManager.getUserMetaDbServer().getGeometryInfos(true);
        if (geometryInfos != null) {
            geoInfoHash.clear();
            for (int i = 0; i < geometryInfos.length; i++) {
                geoInfoHash.put(geometryInfos[i].getVersion().getVersionKey(), geometryInfos[i]);
            }
        }
    } catch (RemoteProxyException e) {
        handleRemoteProxyException(e);
        throw new DataAccessException("RemoteProxyException: " + e.getMessage());
    }
}

Example 18 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class ClientDocumentManager method addUserToGroup.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 5:43:44 PM)
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
public GeometryInfo addUserToGroup(GeometryInfo geometryInfo, String userToAdd) throws DataAccessException {
    try {
        // 
        // publish from database
        // 
        GeometryInfo newGeometryInfo = (GeometryInfo) addUserToGroup0(geometryInfo, VersionableType.Geometry, geoInfoHash, userToAdd);
        // //
        // // delete Geometry from cache
        // //
        // xmlHash.remove(geometryInfo.getVersion().getVersionKey());
        // //
        // // delete any MathModelMetaData's that use this GeometryInfo from cache
        // //
        // MathModelInfo referencedMathModelInfos[] = getMathModelReferences(geometryInfo);
        // for (int i = 0; i < referencedMathModelInfos.length; i++){
        // xmlHash.remove(referencedMathModelInfos[i].getVersion().getVersionKey());
        // }
        // //
        // // delete any BioModelMetaData's that use this GeometryInfo from cache
        // //
        // BioModelInfo referencedBioModelInfos[] = getBioModelReferences(geometryInfo);
        // for (int i = 0; i < referencedBioModelInfos.length; i++){
        // xmlHash.remove(referencedBioModelInfos[i].getVersion().getVersionKey());
        // }
        fireDatabaseUpdate(new DatabaseEvent(this, DatabaseEvent.UPDATE, geometryInfo, newGeometryInfo));
        return newGeometryInfo;
    } catch (RemoteProxyException e) {
        handleRemoteProxyException(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 19 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class ClientDocumentManager method updateGeometryRelatedHashes.

private void updateGeometryRelatedHashes(Geometry savedGeometry) {
    if (savedGeometry == null || (savedGeometry.getVersion() != null && geoInfoHash.get(savedGeometry.getVersion().getVersionKey()) != null)) {
        return;
    }
    KeyValue imageRef = (savedGeometry.getGeometrySpec().getImage() != null) ? (savedGeometry.getGeometrySpec().getImage().getKey()) : (null);
    if (imageRef != null && imgInfoHash.get(imageRef) == null) {
        VCImage savedVCImage = savedGeometry.getGeometrySpec().getImage();
        ISize size = new ISize(savedVCImage.getNumX(), savedVCImage.getNumY(), savedVCImage.getNumZ());
        VCImageInfo savedVCImageInfo = new VCImageInfo(savedVCImage.getVersion(), size, savedVCImage.getExtent(), null, VCellSoftwareVersion.fromSystemProperty());
        imgInfoHash.put(savedVCImage.getVersion().getVersionKey(), savedVCImageInfo);
    }
    Version localTimeVersion = convertVersionToLocalTime(savedGeometry.getVersion());
    GeometryInfo savedGeometryInfo = new GeometryInfo(localTimeVersion, savedGeometry.getDimension(), savedGeometry.getExtent(), savedGeometry.getOrigin(), imageRef, VCellSoftwareVersion.fromSystemProperty());
    geoInfoHash.put(savedGeometry.getVersion().getVersionKey(), savedGeometryInfo);
    fireDatabaseInsert(new DatabaseEvent(this, DatabaseEvent.INSERT, null, geoInfoHash.get(savedGeometry.getVersion().getVersionKey())));
}

Example 20 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class ClientDocumentManager method setGroupPrivate.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 5:43:44 PM)
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
public GeometryInfo setGroupPrivate(GeometryInfo geometryInfo) throws DataAccessException {
    try {
        // 
        // unpublish from database
        // 
        GeometryInfo newGeometryInfo = (GeometryInfo) setGroupPrivate0(geometryInfo, VersionableType.Geometry, geoInfoHash);
        // //
        // // delete Geometry from cache
        // //
        // xmlHash.remove(geometryInfo.getVersion().getVersionKey());
        // //
        // // delete any MathModelMetaData's that use this GeometryInfo from cache
        // //
        // MathModelInfo referencedMathModelInfos[] = getMathModelReferences(geometryInfo);
        // for (int i = 0; i < referencedMathModelInfos.length; i++){
        // xmlHash.remove(referencedMathModelInfos[i].getVersion().getVersionKey());
        // }
        // //
        // // delete any BioModelMetaData's that use this GeometryInfo from cache
        // //
        // BioModelInfo referencedBioModelInfos[] = getBioModelReferences(geometryInfo);
        // for (int i = 0; i < referencedBioModelInfos.length; i++){
        // xmlHash.remove(referencedBioModelInfos[i].getVersion().getVersionKey());
        // }
        fireDatabaseUpdate(new DatabaseEvent(this, DatabaseEvent.UPDATE, geometryInfo, newGeometryInfo));
        return newGeometryInfo;
    } catch (RemoteProxyException e) {
        handleRemoteProxyException(e);
        throw new DataAccessException(e.getMessage());
    }
}