Examples with KeyValue org.vcell.util.document.KeyValue used on opensource projects

Example 86 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class GeomDbDriver method getGeometry.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.Model
 * @param rset java.sql.ResultSet
 */
private Geometry getGeometry(QueryHashtable dbc, Connection con, User user, ResultSet rset) throws SQLException, DataAccessException {
    // 
    // get Image reference
    // 
    java.math.BigDecimal bigD = rset.getBigDecimal(geomTable.imageRef.toString());
    KeyValue imageRef = null;
    if (!rset.wasNull()) {
        imageRef = new KeyValue(bigD);
    }
    // 
    // get geometry object
    // 
    Geometry tempGeometry = null;
    try {
        tempGeometry = geomTable.getGeometry(rset, con);
    } catch (PropertyVetoException e) {
        throw new DataAccessException(e.getMessage());
    }
    Geometry geom = null;
    // 
    // get image for this geometry
    // 
    VCImage vcImage = null;
    if (imageRef != null) {
        // permission checking for the image is disabled because it is a child of this geometry
        vcImage = getVCImage(dbc, con, user, imageRef, false);
    }
    if (vcImage != null) {
        geom = new Geometry(tempGeometry, vcImage);
    } else {
        geom = tempGeometry;
    }
    // 
    // get SubVolumes for this geometry
    // 
    SubVolume[] subVolumes = getSubVolumesFromGeometry(dbc, con, geom.getVersion().getVersionKey());
    if (subVolumes != null) {
        try {
            geom.getGeometrySpec().setSubVolumes(subVolumes);
        } catch (java.beans.PropertyVetoException e) {
            lg.error(e.getMessage(), e);
            throw new DataAccessException(e.getMessage());
        }
    }
    // 
    if (geom.getDimension() > 0) {
        getSurfaceDescription(con, geom);
    }
    // 
    if (geom.getDimension() > 0) {
        getFilaments(con, geom);
    }
    // 
    // get SurfaceClasses for this geometry
    // 
    SurfaceClass[] surfaceClasses = getSurfaceClassesFromGeometry(dbc, con, geom.getVersion().getVersionKey());
    if (surfaceClasses != null) {
        try {
            geom.getGeometrySurfaceDescription().setSurfaceClasses(surfaceClasses);
        } catch (java.beans.PropertyVetoException e) {
            lg.error(e.getMessage(), e);
            throw new DataAccessException(e.getMessage());
        }
    }
    return geom;
}

Example 87 with KeyValue

use of org.vcell.util.document.KeyValue 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 88 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class MathModelDbDriver method getSimulationEntriesFromMathModel.

/**
 * getModels method comment.
 */
KeyValue[] getSimulationEntriesFromMathModel(Connection con, KeyValue mathModelKey) throws SQLException, DataAccessException {
    // if (lg.isTraceEnabled()) lg.trace("MathModelDbDriver.getSimulationEntriesFromMathModel(mathModelKey=" + mathModelKey + ")");
    String sql;
    sql = " SELECT " + mathModelSimLinkTable.simRef + " FROM " + mathModelSimLinkTable.getTableName() + " WHERE " + mathModelSimLinkTable.mathModelRef + " = " + mathModelKey + " ORDER BY " + mathModelSimLinkTable.id;
    Statement stmt = con.createStatement();
    java.util.Vector<KeyValue> keyList = new Vector<KeyValue>();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        // 
        while (rset.next()) {
            KeyValue key = mathModelSimLinkTable.getSimulationKey(rset);
            keyList.addElement(key);
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    // 
    // put results in an array
    // 
    KeyValue[] keyArray = new KeyValue[keyList.size()];
    keyList.copyInto(keyArray);
    return keyArray;
}

Example 89 with KeyValue

use of org.vcell.util.document.KeyValue 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 90 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class MathModelTable method getInfo.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.geometry.GeometryInfo
 * @param rset java.sql.ResultSet
 * @param log cbit.vcell.server.SessionLog
 */
public VersionInfo getInfo(ResultSet rset, Connection con, DatabaseSyntax dbSyntax) throws SQLException, org.vcell.util.DataAccessException {
    KeyValue mathRef = new KeyValue(rset.getBigDecimal(table.mathRef.toString()));
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    String serialDbChildSummary = DbDriver.varchar2_CLOB_get(rset, MathModelTable.table.childSummarySmall, MathModelTable.table.childSummaryLarge, dbSyntax);
    String softwareVersion = rset.getString(SoftwareVersionTable.table.softwareVersion.toString());
    return new MathModelInfo(version, mathRef, serialDbChildSummary, VCellSoftwareVersion.fromString(softwareVersion));
}