Examples with MathModelMetaData cbit.vcell.mathmodel.MathModelMetaData used on opensource projects

Example 1 with MathModelMetaData

use of cbit.vcell.mathmodel.MathModelMetaData in project vcell by virtualcell.

the class LocalUserMetaDbServerMessaging method getMathModelMetaData.

/**
 * getVersionInfo method comment.
 * @throws RemoteException
 */
public MathModelMetaData getMathModelMetaData(KeyValue mathModelKey) throws DataAccessException {
    try {
        log.print("LocalUserMetaDbServerMessaging.getMathModelMetaData(key=" + mathModelKey + ")");
        MathModelMetaData mathModelMetaData = dbServerProxy.getMathModelMetaData(mathModelKey);
        return mathModelMetaData;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 2 with MathModelMetaData

use of cbit.vcell.mathmodel.MathModelMetaData in project vcell by virtualcell.

the class LocalUserMetaDbServerMessaging method getMathModelMetaDatas.

/**
 * getVersionInfo method comment.
 * @throws RemoteException
 */
public MathModelMetaData[] getMathModelMetaDatas(boolean bAll) throws DataAccessException {
    try {
        log.print("LocalUserMetaDbServerMessaging.getMathModelMetaDatas(bAll=" + bAll + ")");
        MathModelMetaData[] mathModelMetaDataArray = dbServerProxy.getMathModelMetaDatas(bAll);
        return mathModelMetaDataArray;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 3 with MathModelMetaData

use of cbit.vcell.mathmodel.MathModelMetaData 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;
}

Example 4 with MathModelMetaData

use of cbit.vcell.mathmodel.MathModelMetaData in project vcell by virtualcell.

the class MathModelTable method getMathModelMetaData.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.math.MathDescription
 * @param user cbit.vcell.server.User
 * @param rset java.sql.ResultSet
 */
public MathModelMetaData getMathModelMetaData(ResultSet rset, Connection con, KeyValue[] simulationKeys, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
    // 
    // Get Version
    // 
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version mathModelVersion = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    KeyValue mathDescrRef = new KeyValue(rset.getBigDecimal(table.mathRef.toString()));
    // MathModelMetaData mathModelMetaData = new MathModelMetaData(version,mathRef,simulationKeys);
    MathModelMetaData mathModelMetaData = populateOutputFunctions(con, mathDescrRef, mathModelVersion, simulationKeys, dbSyntax);
    return mathModelMetaData;
}

Example 5 with MathModelMetaData

use of cbit.vcell.mathmodel.MathModelMetaData in project vcell by virtualcell.

the class DbDriver method updateVersionableInit.

/**
 * This method was created in VisualAge.
 * @return cbit.image.VCImage
 * @param user cbit.vcell.server.User
 * @param image cbit.image.VCImage
 */
protected Version updateVersionableInit(InsertHashtable hash, Connection con, User user, Versionable versionable, boolean bVersion) throws DataAccessException, SQLException, RecordChangedException {
    if (hash.getDatabaseKey(versionable) != null) {
        throw new DataAccessException(versionable + " already inserted in this transaction");
    }
    if (versionable.getVersion() == null || versionable.getVersion().getVersionKey() == null) {
        throw new DataAccessException(versionable + " Not expecting null key before update.  Update Failed");
    }
    // Can only update things we own
    if (!versionable.getVersion().getOwner().equals(user)) {
        throw new PermissionException("Versionable name=" + versionable.getName() + " type=" + VersionTable.versionableTypeFromVersionable(versionable) + "\nuser=" + versionable.getVersion().getOwner() + " Not Equal to client user=" + user);
    }
    // 
    // get new Version info
    // 
    User owner = user;
    GroupAccess accessInfo = versionable.getVersion().getGroupAccess();
    // 
    if (versionable instanceof BioModelMetaData || versionable instanceof MathModelMetaData || versionable instanceof Geometry) {
        Statement stmt = null;
        try {
            stmt = con.createStatement();
            String sql = "SELECT " + VersionTable.privacy_ColumnName + " FROM " + VersionTable.getVersionTable(versionable).getTableName() + " WHERE " + VersionTable.id_ColumnName + " = " + versionable.getVersion().getVersionKey();
            ResultSet rset = stmt.executeQuery(sql);
            BigDecimal dbgrpid = null;
            if (rset.next()) {
                dbgrpid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
            }
            rset.close();
            if (!dbgrpid.equals(versionable.getVersion().getGroupAccess().getGroupid())) {
                accessInfo = getGroupAccessFromGroupID(con, dbgrpid);
            }
        } catch (Throwable e) {
        // Don't fail, just keep the permission versionable came in with
        } finally {
            if (stmt != null) {
                stmt.close();
            }
        }
    }
    KeyValue versionKey = keyFactory.getNewKey(con);
    java.util.Date date = getNewDate(con);
    // 
    // always use the previous BranchPointReference unless branching
    // 
    KeyValue branchPointRefKey = versionable.getVersion().getBranchPointRefKey();
    // Check for Archive and Publish not needed in update because versionflag is always forced to Current
    VersionFlag versionFlag = null;
    // if (bVersion){
    // versionFlag = VersionFlag.Archived;
    // }else{
    versionFlag = VersionFlag.Current;
    // }
    String versionName = versionable.getVersion().getName();
    java.math.BigDecimal branchID = versionable.getVersion().getBranchID();
    String annot = versionable.getDescription();
    // 
    // Insert Software Version
    // 
    insertSoftwareVersion(con, versionKey);
    // 
    return new Version(versionKey, versionName, owner, accessInfo, branchPointRefKey, branchID, date, versionFlag, annot);
}