Examples with Table cbit.sql.Table used on opensource projects

Example 11 with Table

use of cbit.sql.Table in project vcell by virtualcell.

the class GeomDbDriver method getVCImage.

/**
 * getModel method comment.
 */
private VCImage getVCImage(QueryHashtable dbc, Connection con, User user, KeyValue imageKey, boolean bCheckPermission) throws SQLException, DataAccessException, ObjectNotFoundException {
    // log.print("GeomDbDriver.getImage(user="+user+", id="+imageKey+")");
    String sql;
    Field[] f = { new StarField(imageTable), userTable.userid, imageDataTable.data, new StarField(extentTable) };
    Table[] t = { imageTable, userTable, imageDataTable, extentTable };
    String condition = imageTable.id.getQualifiedColName() + " = " + imageKey + " AND " + imageTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName() + " AND " + imageTable.id.getQualifiedColName() + " = " + imageDataTable.imageRef.getQualifiedColName() + " AND " + imageTable.extentRef.getQualifiedColName() + " = " + extentTable.id.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax, bCheckPermission);
    // System.out.println(sql);
    // Connection con = conFact.getConnection();
    VCImage vcImage = null;
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            vcImage = imageTable.getImage(rset, con, imageDataTable, dbSyntax);
            getImageRegionsForVCImage(dbc, con, vcImage);
        } else {
            throw new ObjectNotFoundException("Image id=" + imageKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    return vcImage;
}

Example 12 with Table

use of cbit.sql.Table in project vcell by virtualcell.

the class SimulationContextDbDriver method getSimulationContextSQL.

/**
 * getModel method comment.
 */
private SimulationContext getSimulationContextSQL(QueryHashtable dbc, Connection con, User user, KeyValue simContextKey) throws /*, ReactStepDbDriver reactStepDB*/
SQLException, DataAccessException, IllegalMappingException, PropertyVetoException {
    SimulationContext simContext = null;
    String sql;
    Field[] f = { new cbit.sql.StarField(simContextTable), userTable.userid };
    Table[] t = { simContextTable, userTable };
    String condition = simContextTable.id.getQualifiedColName() + " = " + simContextKey + " AND " + simContextTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    // System.out.println(sql);
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            simContext = simContextTable.getSimContext(dbc, con, user, rset, geomDB, modelDB, mathDescDB);
        } else {
            throw new ObjectNotFoundException("SimulationContext id=" + simContextKey + " not found for user '" + user + "'");
        }
    } finally {
        stmt.close();
    }
    DataSymbolTable.table.populateDataSymbols(con, simContextKey, simContext.getDataContext(), user, simContext.getModel().getUnitSystem());
    ArrayList<AnnotatedFunction> outputFunctionList = ApplicationMathTable.table.getOutputFunctionsSimcontext(con, simContextKey, dbSyntax);
    if (outputFunctionList != null) {
        OutputFunctionContext outputFnContext = simContext.getOutputFunctionContext();
        outputFnContext.setOutputFunctions(outputFunctionList);
    }
    SimContextTable.table.readAppComponents(con, simContext, dbSyntax);
    assignStimuliSQL(con, simContextKey, simContext);
    assignStructureMappingsSQL(dbc, con, simContextKey, simContext);
    assignSpeciesContextSpecsSQL(con, simContextKey, simContext);
    assignReactionSpecsSQL(con, simContextKey, simContext);
    for (GeometryClass gc : simContext.getGeometry().getGeometryClasses()) {
        try {
            StructureSizeSolver.updateUnitStructureSizes(simContext, gc);
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
    }
    simContext.getGeometryContext().enforceHierarchicalBoundaryConditions(simContext.getModel().getStructureTopology());
    simContext.getModel().refreshDependencies();
    assignAnalysisTasksSQL(con, simContextKey, simContext);
    // really needed to calculate MembraneMapping parameters that are not stored (inside/outside flux correction factors).
    simContext.refreshDependencies();
    return simContext;
}

Example 13 with Table

use of cbit.sql.Table in project vcell by virtualcell.

the class BioModelDbDriver method getBioModelMetaDatas.

/**
 * getModel method comment.
 */
BioModelMetaData[] getBioModelMetaDatas(Connection con, User user, boolean bAll, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (user == null) {
        throw new IllegalArgumentException("Improper parameters for getBioModelMetaDatas");
    }
    if (lg.isTraceEnabled())
        lg.trace("BioModelDbDriver.getBioModelMetaDatas(user=" + user + ", bAll=" + bAll + ")");
    // 
    // to construct a BioModelMetaData as an immutable object, lets collect all keys first
    // (even before authentication).  If the user doesn't authenticate, then throw away the
    // child keys (from link tables).
    // 
    // 
    // get BioModelMetaData object for bioModelKey
    // 
    String sql;
    Field[] f = { new cbit.sql.StarField(bioModelTable), userTable.userid };
    Table[] t = { bioModelTable, userTable };
    String condition = userTable.id.getQualifiedColName() + " = " + bioModelTable.ownerRef.getQualifiedColName();
    if (!bAll) {
        condition += " AND " + userTable.id.getQualifiedColName() + " = " + user.getID();
    }
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    // 
    StringBuffer newSQL = new StringBuffer(sql);
    newSQL.insert(7, Table.SQL_GLOBAL_HINT);
    sql = newSQL.toString();
    // 
    Statement stmt = con.createStatement();
    Vector<BioModelMetaData> bioModelMetaDataList = new Vector<BioModelMetaData>();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            BioModelMetaData bioModelMetaData = bioModelTable.getBioModelMetaData(rset, this, con, dbSyntax);
            bioModelMetaDataList.addElement(bioModelMetaData);
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    BioModelMetaData[] bioModelMetaDataArray = new BioModelMetaData[bioModelMetaDataList.size()];
    bioModelMetaDataList.copyInto(bioModelMetaDataArray);
    return bioModelMetaDataArray;
}

Example 14 with Table

use of cbit.sql.Table in project vcell by virtualcell.

the class BioModelDbDriver method getBioModelMetaData.

/**
 * getModel method comment.
 */
private BioModelMetaData getBioModelMetaData(Connection con, User user, KeyValue bioModelKey, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (user == null || bioModelKey == null) {
        throw new IllegalArgumentException("Improper parameters for getBioModelMetaData");
    }
    // if (lg.isTraceEnabled()) lg.trace("BioModelDbDriver.getBioModelMetaData(user=" + user + ", id=" + bioModelKey + ")");
    // 
    // to construct a BioModelMetaData as an immutable object, lets collect all keys first
    // (even before authentication).  If the user doesn't authenticate, then throw away the
    // child keys (from link tables).
    // 
    // 
    // get Simulation Keys for bioModelKey
    // 
    KeyValue[] simKeys = getSimulationEntriesFromBioModel(con, bioModelKey);
    // 
    // get SimulationContext Keys for bioModelKey
    // 
    KeyValue[] simContextKeys = getSimContextEntriesFromBioModel(con, bioModelKey);
    // 
    // get BioModelMetaData object for bioModelKey
    // 
    String sql;
    VCMetaDataTable vcMetadataTable = VCMetaDataTable.table;
    Field[] f = { new StarField(bioModelTable), userTable.userid, new StarField(vcMetadataTable) };
    Table[] t = { bioModelTable, userTable, vcMetadataTable };
    switch(dbSyntax) {
        case ORACLE:
            {
                String condition = bioModelTable.id.getQualifiedColName() + " = " + bioModelKey + " AND " + userTable.id.getQualifiedColName() + " = " + bioModelTable.ownerRef.getQualifiedColName() + " AND " + vcMetadataTable.bioModelRef.getQualifiedColName() + "(+) = " + bioModelTable.id.getQualifiedColName();
                sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, null, condition, null, dbSyntax, true);
                break;
            }
        case POSTGRES:
            {
                String condition = bioModelTable.id.getQualifiedColName() + " = " + bioModelKey + " AND " + userTable.id.getQualifiedColName() + " = " + bioModelTable.ownerRef.getQualifiedColName() + " ";
                // " AND "+ VCMetaDataTable.table.bioModelRef.getQualifiedColName() + "(+) = " + bioModelTable.id.getQualifiedColName();
                OuterJoin outerJoin = new OuterJoin(vcMetadataTable, bioModelTable, JoinOp.RIGHT_OUTER_JOIN, vcMetadataTable.bioModelRef, bioModelTable.id);
                sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, outerJoin, condition, null, dbSyntax, true);
                break;
            }
        default:
            {
                throw new RuntimeException("unexpected DatabaseSyntax " + dbSyntax);
            }
    }
    Statement stmt = con.createStatement();
    BioModelMetaData bioModelMetaData = null;
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            bioModelMetaData = bioModelTable.getBioModelMetaData(rset, con, simContextKeys, simKeys, dbSyntax);
        } else {
            throw new ObjectNotFoundException("BioModel id=" + bioModelKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    return bioModelMetaData;
}

Example 15 with Table

use of cbit.sql.Table 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;
}