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package de.lmu.ifi.dbs.elki.datasource;
/*
This file is part of ELKI:
Environment for Developing KDD-Applications Supported by Index-Structures
Copyright (C) 2011
Ludwig-Maximilians-Universität München
Lehr- und Forschungseinheit für Datenbanksysteme
ELKI Development Team
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import de.lmu.ifi.dbs.elki.data.ExternalID;
import de.lmu.ifi.dbs.elki.data.type.TypeUtil;
import de.lmu.ifi.dbs.elki.datasource.bundle.MultipleObjectsBundle;
import de.lmu.ifi.dbs.elki.datasource.filter.ObjectFilter;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.utilities.FormatUtil;
import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.Parameterizable;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParameter;
/**
* Joins multiple data sources by their label
*
* @author Erich Schubert
*/
public class ExternalIDJoinDatabaseConnection extends AbstractDatabaseConnection implements Parameterizable {
/**
* Logger
*/
private static final Logging logger = Logging.getLogger(ExternalIDJoinDatabaseConnection.class);
/**
* The filters to invoke
*/
final protected List<DatabaseConnection> sources;
/**
* Constructor.
*
* @param filters Filters to use.
* @param sources Data sources to join.
*/
public ExternalIDJoinDatabaseConnection(List<ObjectFilter> filters, List<DatabaseConnection> sources) {
super(filters);
this.sources = sources;
}
@Override
public MultipleObjectsBundle loadData() {
List<MultipleObjectsBundle> bundles = new ArrayList<MultipleObjectsBundle>(sources.size());
for(DatabaseConnection dbc : sources) {
bundles.add(dbc.loadData());
}
MultipleObjectsBundle first = bundles.get(0);
Map<ExternalID, Integer> labelmap = new HashMap<ExternalID, Integer>(first.dataLength());
// Process first bundle
{
// Identify a label column
final int lblcol;
{
int lblc = -1;
for(int i = 0; i < first.metaLength(); i++) {
if(TypeUtil.EXTERNALID.isAssignableFromType(first.meta(i))) {
lblc = i;
break;
}
}
lblcol = lblc; // make static
}
if(lblcol == -1) {
throw new AbortException("No external ID column found in primary source.");
}
for(int i = 0; i < first.dataLength(); i++) {
ExternalID data = (ExternalID) first.data(i, lblcol);
if(data == null) {
logger.warning("Object without ID encountered.");
continue;
}
Integer old = labelmap.put(data, i);
if(old != null) {
logger.warning("Duplicate id encountered: " + data + " in rows " + old + " and " + i);
}
}
}
// Process additional columns
for(int c = 1; c < sources.size(); c++) {
MultipleObjectsBundle cur = bundles.get(c);
final int lblcol;
{
int lblc = -1;
for(int i = 0; i < cur.metaLength(); i++) {
if(TypeUtil.EXTERNALID.isAssignableFromType(cur.meta(i))) {
lblc = i;
break;
}
}
lblcol = lblc; // make static
}
if(lblcol == -1) {
StringBuffer buf = new StringBuffer();
for(int i = 0; i < cur.metaLength(); i++) {
if(buf.length() > 0) {
buf.append(",");
}
buf.append(cur.meta(i));
}
throw new AbortException("No external ID column found in source " + (c + 1) + " to join with. Got: " + buf.toString());
}
// Destination columns
List<ArrayList<Object>> dcol = new ArrayList<ArrayList<Object>>(cur.metaLength());
for(int i = 0; i < cur.metaLength(); i++) {
// Skip the label columns
if(i == lblcol) {
dcol.add(null);
continue;
}
ArrayList<Object> newcol = new ArrayList<Object>(first.dataLength());
// Pre-fill with nulls.
for(int j = 0; j < first.dataLength(); j++) {
newcol.add(null);
}
first.appendColumn(cur.meta(i), newcol);
dcol.add(newcol);
}
for(int i = 0; i < cur.dataLength(); i++) {
ExternalID data = (ExternalID) cur.data(i, lblcol);
if(data == null) {
logger.warning("Object without label encountered.");
continue;
}
Integer row = labelmap.get(data);
if(row == null) {
logger.warning("ID not found for join: " + data + " in row " + i);
continue;
}
for(int d = 0; d < cur.metaLength(); d++) {
if(d == lblcol) {
continue;
}
List<Object> col = dcol.get(d);
assert (col != null);
col.set(row, cur.data(i, d));
}
}
}
for(int i = 0; i < first.dataLength(); i++) {
for(int d = 0; d < first.metaLength(); d++) {
if(first.data(i, d) == null) {
StringBuffer buf = new StringBuffer();
for(int d2 = 0; d2 < first.metaLength(); d2++) {
if(buf.length() > 0) {
buf.append(", ");
}
if(first.data(i, d2) == null) {
buf.append("null");
}
else {
buf.append(first.data(i, d2));
}
}
logger.warning("null value in joined data, row " + i + " column " + d + FormatUtil.NEWLINE + "[" + buf.toString() + "]");
break;
}
}
}
return first;
}
@Override
protected Logging getLogger() {
return logger;
}
/**
* Parameterization class.
*
* @author Erich Schubert
*
* @apiviz.exclude
*/
public static class Parameterizer extends AbstractDatabaseConnection.Parameterizer {
/**
* The static option ID
*/
public static final OptionID SOURCES_ID = OptionID.getOrCreateOptionID("join.sources", "The data sources to join.");
/**
* The data souces to use.
*/
protected List<DatabaseConnection> sources;
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
super.configFilters(config);
final ObjectListParameter<DatabaseConnection> sourcesParam = new ObjectListParameter<DatabaseConnection>(SOURCES_ID, DatabaseConnection.class);
if(config.grab(sourcesParam)) {
sources = sourcesParam.instantiateClasses(config);
}
}
@Override
protected ExternalIDJoinDatabaseConnection makeInstance() {
return new ExternalIDJoinDatabaseConnection(filters, sources);
}
}
}
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