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

Example 61 with Version

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

the class SimulationDbDriver method updateVersionableInit.

/**
 * This method was created in VisualAge.
 * @return cbit.image.VCImage
 * @param user cbit.vcell.server.User
 * @param image cbit.image.VCImage
 */
protected SimulationVersion updateVersionableInit(InsertHashtable hash, Connection con, User user, Versionable versionable, boolean bVersion, boolean bMathematicallyEquivalent) throws DataAccessException, SQLException, RecordChangedException {
    SimulationVersion dbSimulationVersion = ((Simulation) versionable).getSimulationVersion();
    Version newVersion = updateVersionableInit(hash, con, user, versionable, bVersion);
    // 
    // point to oldest mathematically equivalent ancestor, this will be used for all identification (status/data).
    // 
    KeyValue parentSimRef = null;
    if (bMathematicallyEquivalent) {
        if (dbSimulationVersion == null) {
            throw new RuntimeException("Simulation must have been saved for bMathematicallyEquivalent to be true");
        }
        if (dbSimulationVersion.getParentSimulationReference() != null) {
            // //
            // // mathematically equivalent, prior link is transitive  (B->C and A==B, then A->C)
            // //
            parentSimRef = dbSimulationVersion.getParentSimulationReference();
        } else {
            // //
            // // mathematically equivalent, no prior link (A==B, then A->B)
            // //
            parentSimRef = dbSimulationVersion.getVersionKey();
        }
    }
    return new SimulationVersion(newVersion.getVersionKey(), newVersion.getName(), newVersion.getOwner(), newVersion.getGroupAccess(), newVersion.getBranchPointRefKey(), newVersion.getBranchID(), newVersion.getDate(), newVersion.getFlag(), newVersion.getAnnot(), parentSimRef);
}

Example 62 with Version

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

the class SimulationTable 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) throws SQLException, DataAccessException {
    KeyValue mathRef = new KeyValue(rset.getBigDecimal(SimulationTable.table.mathRef.toString()));
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    SimulationVersion simulationVersion = (SimulationVersion) version;
    String softwareVersion = rset.getString(SoftwareVersionTable.table.softwareVersion.toString());
    return new SimulationInfo(mathRef, simulationVersion, VCellSoftwareVersion.fromString(softwareVersion));
}

Example 63 with Version

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

the class VersionTable method getVersion.

/**
 * This method was created in VisualAge.
 * @return cbit.util.Version
 * @param rset ResultSet
 * @param log SessionLog
 */
public static Version getVersion(ResultSet rset, GroupAccess groupAccess) throws SQLException, DataAccessException {
    KeyValue vBranchPointRef = null;
    java.math.BigDecimal vBranchID = null;
    java.util.Date vDate = null;
    VersionFlag vFlag = null;
    String vAnnot = null;
    // 
    java.math.BigDecimal vBranchPointRefDB = rset.getBigDecimal(versionBranchPointRef_ColumnName);
    if (rset.wasNull()) {
        vBranchPointRef = null;
    } else {
        vBranchPointRef = new KeyValue(vBranchPointRefDB);
    }
    java.math.BigDecimal vBranchIDDB = rset.getBigDecimal(versionBranchID_ColumnName);
    if (rset.wasNull()) {
        vBranchID = null;
    } else {
        vBranchID = vBranchIDDB;
    }
    vDate = getDate(rset, versionDate_ColumnName);
    if (vDate == null) {
        throw new DataAccessException("could not parse date");
    }
    // 
    vFlag = VersionFlag.fromInt(rset.getInt(VersionTable.versionFlag_ColumnName));
    // 
    String vAnnotDB = rset.getString(versionAnnot_ColumnName);
    if (rset.wasNull()) {
        vAnnot = null;
    } else {
        vAnnot = org.vcell.util.TokenMangler.getSQLRestoredString(vAnnotDB);
    }
    boolean bFoundParentSimRefColumn = false;
    KeyValue parentSimRef = null;
    try {
        java.sql.ResultSetMetaData rsetMetaData = rset.getMetaData();
        int numColumns = rsetMetaData.getColumnCount();
        for (int i = 0; i < numColumns; i++) {
            if (rsetMetaData.getColumnName(i + 1).toUpperCase().endsWith(SimulationTable.table.versionParentSimRef.toString().toUpperCase())) {
                bFoundParentSimRefColumn = true;
                break;
            }
        }
        if (bFoundParentSimRefColumn) {
            java.math.BigDecimal parentSimRefDB = rset.getBigDecimal(SimulationTable.table.versionParentSimRef.toString());
            if (rset.wasNull()) {
                parentSimRef = null;
            } else {
                parentSimRef = new KeyValue(parentSimRefDB);
            }
        }
    } catch (SQLException e) {
        e.printStackTrace(System.out);
        lg.warn("VersionTable.getVersion(): consuming exception for missing column " + versionParentSimRef_ColumnName + ": " + e.getMessage(), e);
    }
    // 
    KeyValue key = new KeyValue(rset.getBigDecimal(Table.id_ColumnName));
    String name = TokenMangler.getSQLRestoredString(rset.getString(VersionTable.name_ColumnName));
    String ownerName = rset.getString(UserTable.table.userid.toString());
    KeyValue ownerID = new KeyValue(rset.getBigDecimal(VersionTable.ownerRef_ColumnName));
    User owner = new User(ownerName, ownerID);
    // 
    if (bFoundParentSimRefColumn) {
        return new SimulationVersion(key, name, owner, groupAccess, vBranchPointRef, vBranchID, vDate, vFlag, vAnnot, parentSimRef);
    } else {
        return new Version(key, name, owner, groupAccess, vBranchPointRef, vBranchID, vDate, vFlag, vAnnot);
    }
}

Example 64 with Version

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

the class GeomDbDriver method updateVersionable.

/**
 * This method was created in VisualAge.
 * @return cbit.image.VCImage
 * @param user cbit.vcell.server.User
 * @param image cbit.image.VCImage
 */
public KeyValue updateVersionable(InsertHashtable hash, Connection con, User user, VCImage vcImage, boolean bVersion) throws DataAccessException, SQLException, RecordChangedException {
    Version newVersion = null;
    try {
        newVersion = updateVersionableInit(hash, con, user, vcImage, bVersion);
        insertVCImage(hash, con, user, vcImage, newVersion);
    } catch (ImageException e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("ImageException: " + e.getMessage());
    }
    return newVersion.getVersionKey();
}

Example 65 with Version

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

the class GeometryTable 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) throws SQLException, DataAccessException {
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    int dim = rset.getInt(GeometryTable.table.dimension.toString());
    double oX = rset.getBigDecimal(GeometryTable.table.originX.toString()).doubleValue();
    double oY = rset.getBigDecimal(GeometryTable.table.originY.toString()).doubleValue();
    double oZ = rset.getBigDecimal(GeometryTable.table.originZ.toString()).doubleValue();
    org.vcell.util.Origin origin = new org.vcell.util.Origin(oX, oY, oZ);
    double extentX = rset.getBigDecimal(ExtentTable.table.extentX.toString()).doubleValue();
    double extentY = rset.getBigDecimal(ExtentTable.table.extentY.toString()).doubleValue();
    double extentZ = rset.getBigDecimal(ExtentTable.table.extentZ.toString()).doubleValue();
    org.vcell.util.Extent extent = new org.vcell.util.Extent(extentX, extentY, extentZ);
    KeyValue imgRef = null;
    java.math.BigDecimal bigDecimal = rset.getBigDecimal(GeometryTable.table.imageRef.toString());
    if (!rset.wasNull()) {
        imgRef = new KeyValue(bigDecimal);
    }
    String softwareVersion = rset.getString(SoftwareVersionTable.table.softwareVersion.toString());
    GeometryInfo geomInfo = new GeometryInfo(version, dim, extent, origin, imgRef, VCellSoftwareVersion.fromString(softwareVersion));
    return geomInfo;
/*GeometryInfo geomInfo = new GeometryInfo();

	geomInfo.dimension = rset.getInt(GeometryTable.dimension.toString());
	geomInfo.originX = rset.getDouble(GeometryTable.originX.toString());
	geomInfo.originY = rset.getDouble(GeometryTable.originY.toString());
	geomInfo.originZ = rset.getDouble(GeometryTable.originZ.toString());
	geomInfo.extentRef = new KeyValue(rset.getBigDecimal(GeometryTable.extentRef.toString(), 0));
	geomInfo.imageRef = new KeyValue(rset.getBigDecimal(GeometryTable.imageRef.toString(), 0));

	geomInfo.version = getVersion(rset,log);
	
	return geomInfo;
	*/
}