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

Example 1 with Table

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

the class MigrateDbManager method main.

public static void main(String[] args) throws SQLException {
    ConnectionFactory conFactory_Oracle = null;
    ConnectionFactory conFactory_Postgres = null;
    try {
        String driverName_Oracle = "oracle.jdbc.driver.OracleDriver";
        String connectionURL_Oracle = "jdbc:oracle:thin:@VCELL-DB.cam.uchc.edu:1521/vcelldborcl.cam.uchc.edu";
        String userid_Oracle = "vcell";
        String password_Oracle = "cbittech";
        conFactory_Oracle = DatabaseService.getInstance().createConnectionFactory(driverName_Oracle, connectionURL_Oracle, userid_Oracle, password_Oracle);
        String driverName_Postgres = "org.postgresql.Driver";
        String connectionURL_Postgres = "jdbc:postgresql://localhost:5432/schaff";
        String userid_Postgres = "schaff";
        String password_Postgres = "cbittech";
        conFactory_Postgres = DatabaseService.getInstance().createConnectionFactory(driverName_Postgres, connectionURL_Postgres, userid_Postgres, password_Postgres);
        int retryCount = 0;
        boolean done = false;
        while (!done && retryCount < 100) {
            try {
                Table[] tables = SQLCreateAllTables.getVCellTables();
                for (Table table : tables) {
                    if (!table.getTableName().toUpperCase().startsWith("VC_")) {
                        continue;
                    }
                    if (table == SimContextStatTable.table || table == SimContextStat2Table.table) {
                        continue;
                    }
                    migrate(table, conFactory_Oracle, conFactory_Postgres);
                }
                done = true;
            } catch (Exception e) {
                e.printStackTrace();
                // sleep 10 seconds
                Thread.sleep(10000);
                retryCount++;
            }
        }
        System.out.println("done");
        System.exit(0);
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    } finally {
        if (conFactory_Oracle != null) {
            conFactory_Oracle.close();
        }
        if (conFactory_Postgres != null) {
            conFactory_Postgres.close();
        }
    }
}

Example 2 with Table

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

the class GeometryTable method getInfoSQL.

/**
 * This method was created in VisualAge.
 * @return java.lang.String
 */
public String getInfoSQL(User user, String extraConditions, String special, boolean bCheckPermission, DatabaseSyntax dbSyntax) {
    UserTable userTable = UserTable.table;
    GeometryTable gTable = this;
    ExtentTable eTable = ExtentTable.table;
    SoftwareVersionTable swvTable = SoftwareVersionTable.table;
    String sql;
    Field[] f = { userTable.userid, new cbit.sql.StarField(gTable), eTable.extentX, eTable.extentY, eTable.extentZ, swvTable.softwareVersion };
    Table[] t = { gTable, userTable, eTable, swvTable };
    switch(dbSyntax) {
        case ORACLE:
            {
                String condition = // links in the extent table
                eTable.id.getQualifiedColName() + " = " + gTable.extentRef.getQualifiedColName() + " AND " + userTable.id.getQualifiedColName() + " = " + // links in the userTable
                gTable.ownerRef.getQualifiedColName() + " AND " + gTable.id.getQualifiedColName() + " = " + swvTable.versionableRef.getQualifiedColName() + "(+) ";
                if (extraConditions != null && extraConditions.trim().length() > 0) {
                    condition += " AND " + extraConditions;
                }
                sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, special, dbSyntax, bCheckPermission);
                return sql;
            }
        case POSTGRES:
            {
                String condition = // links in the extent table
                eTable.id.getQualifiedColName() + " = " + gTable.extentRef.getQualifiedColName() + " AND " + userTable.id.getQualifiedColName() + " = " + gTable.ownerRef.getQualifiedColName() + // links in the userTable
                " ";
                // " AND " + gTable.id.getQualifiedColName() + " = " + swvTable.versionableRef.getQualifiedColName()+"(+) ";
                if (extraConditions != null && extraConditions.trim().length() > 0) {
                    condition += " AND " + extraConditions;
                }
                OuterJoin outerJoin = new OuterJoin(gTable, swvTable, JoinOp.LEFT_OUTER_JOIN, gTable.id, swvTable.versionableRef);
                sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, outerJoin, condition, special, dbSyntax, bCheckPermission);
                return sql;
            }
        default:
            {
                throw new RuntimeException("unexpected DatabaseSyntax " + dbSyntax);
            }
    }
}

Example 3 with Table

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

the class MathDescTable method getInfoSQL.

/**
 * This method was created in VisualAge.
 * @return java.lang.String
 */
public String getInfoSQL(User user, String extraConditions, String special, DatabaseSyntax dbSyntax) {
    UserTable userTable = UserTable.table;
    MathDescTable vTable = MathDescTable.table;
    SoftwareVersionTable swvTable = SoftwareVersionTable.table;
    String sql;
    // Field[] f = {userTable.userid,new cbit.sql.StarField(vTable)};
    Field[] f = new Field[] { vTable.id, userTable.userid, swvTable.softwareVersion };
    f = (Field[]) org.vcell.util.BeanUtils.addElements(f, vTable.versionFields);
    f = (Field[]) org.vcell.util.BeanUtils.addElement(f, vTable.geometryRef);
    Table[] t = { vTable, userTable, swvTable };
    switch(dbSyntax) {
        case ORACLE:
            {
                String condition = // links in the userTable
                userTable.id.getQualifiedColName() + " = " + vTable.ownerRef.getQualifiedColName() + " AND " + vTable.id.getQualifiedColName() + " = " + swvTable.versionableRef.getQualifiedColName() + "(+) ";
                if (extraConditions != null && extraConditions.trim().length() > 0) {
                    condition += " AND " + extraConditions;
                }
                sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, special, dbSyntax);
                return sql;
            }
        case POSTGRES:
            {
                // links in the userTable
                String condition = userTable.id.getQualifiedColName() + " = " + vTable.ownerRef.getQualifiedColName() + " ";
                // " AND " + vTable.id.getQualifiedColName() + " = " + swvTable.versionableRef.getQualifiedColName()+"(+) ";
                if (extraConditions != null && extraConditions.trim().length() > 0) {
                    condition += " AND " + extraConditions;
                }
                OuterJoin outerJoin = new OuterJoin(vTable, swvTable, JoinOp.LEFT_OUTER_JOIN, vTable.id, swvTable.versionableRef);
                sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, outerJoin, condition, special, dbSyntax);
                return sql;
            }
        default:
            {
                throw new RuntimeException("unexpected DatabaseSyntax " + dbSyntax);
            }
    }
}

Example 4 with Table

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

the class MathDescriptionDbDriver method getMathDescriptionSQL.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.math.MathDescription
 * @param user cbit.vcell.server.User
 * @param mathDescKey cbit.sql.KeyValue
 */
private MathDescription getMathDescriptionSQL(QueryHashtable dbc, Connection con, User user, KeyValue mathDescKey) throws SQLException, DataAccessException, ObjectNotFoundException {
    String sql;
    Field[] f = { userTable.userid, new cbit.sql.StarField(mathDescTable) };
    Table[] t = { mathDescTable, userTable };
    String condition = mathDescTable.id.getQualifiedColName() + " = " + mathDescKey + " AND " + userTable.id.getQualifiedColName() + " = " + mathDescTable.ownerRef.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    // System.out.println(sql);
    MathDescription mathDescription = null;
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            // 
            // note: must call mathDescTable.getMathDescription() first (rset.getBytes(language) must be called first)
            // 
            mathDescription = mathDescTable.getMathDescription(rset, con, dbSyntax);
            // 
            // get Geometry reference and assign to mathDescription
            // 
            java.math.BigDecimal bigD = rset.getBigDecimal(MathDescTable.table.geometryRef.toString());
            KeyValue geomRef = null;
            if (!rset.wasNull()) {
                geomRef = new KeyValue(bigD);
            } else {
                throw new DataAccessException("Error:  Geometry Reference Cannot be Null for MathDescription");
            }
            Geometry geom = (Geometry) geomDB.getVersionable(dbc, con, user, VersionableType.Geometry, geomRef, false);
            try {
                mathDescription.setGeometry(geom);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new DataAccessException("DataAccess Exception: " + e.getMessage());
            }
        } else {
            throw new ObjectNotFoundException("MathDescription id=" + mathDescKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    return mathDescription;
}

Example 5 with Table

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

the class MathModelDbDriver method getMathModelMetaDatas.

/**
 * getModel method comment.
 */
MathModelMetaData[] getMathModelMetaDatas(Connection con, User user, boolean bAll) throws SQLException, DataAccessException, ObjectNotFoundException {
    if (user == null) {
        throw new IllegalArgumentException("Improper parameters for getMathModelMetaDatas");
    }
    if (lg.isTraceEnabled())
        lg.trace("MathModelDbDriver.getMathModelMetaData(user=" + user + ", bAll=" + bAll + ")");
    // 
    // to construct a MathModelMetaData 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(mathModelTable), userTable.userid };
    Table[] t = { mathModelTable, userTable };
    String condition = userTable.id.getQualifiedColName() + " = " + mathModelTable.ownerRef.getQualifiedColName();
    if (!bAll) {
        condition += " AND " + userTable.id.getQualifiedColName() + " = " + user.getID();
    }
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax, true);
    // 
    StringBuffer newSQL = new StringBuffer(sql);
    newSQL.insert(7, Table.SQL_GLOBAL_HINT);
    sql = newSQL.toString();
    // 
    Statement stmt = con.createStatement();
    Vector<MathModelMetaData> mathModelMetaDataList = new Vector<MathModelMetaData>();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            MathModelMetaData mathModelMetaData = mathModelTable.getMathModelMetaData(rset, this, con, dbSyntax);
            mathModelMetaDataList.addElement(mathModelMetaData);
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    MathModelMetaData[] mathModelMetaDataArray = new MathModelMetaData[mathModelMetaDataList.size()];
    mathModelMetaDataList.copyInto(mathModelMetaDataArray);
    return mathModelMetaDataArray;
}