1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
|
package de.lmu.ifi.dbs.elki.datasource;
/*
This file is part of ELKI:
Environment for Developing KDD-Applications Supported by Index-Structures
Copyright (C) 2015
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 gnu.trove.impl.Constants;
import gnu.trove.map.hash.TObjectIntHashMap;
import java.util.ArrayList;
import java.util.List;
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.parameterization.Parameterization;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectListParameter;
/**
* Joins multiple data sources by their label
*
* @author Erich Schubert
* @since 0.4.0
*
* @apiviz.uses ExternalID
*/
public class ExternalIDJoinDatabaseConnection extends AbstractDatabaseConnection {
/**
* Logger
*/
private static final Logging LOG = 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<>(sources.size());
for (DatabaseConnection dbc : sources) {
bundles.add(dbc.loadData());
}
MultipleObjectsBundle first = bundles.get(0);
TObjectIntHashMap<ExternalID> labelmap = new TObjectIntHashMap<>(first.dataLength(), Constants.DEFAULT_LOAD_FACTOR, -1);
// 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) {
LOG.debug("Object without ID encountered.");
continue;
}
int old = labelmap.put(data, i);
if (old != -1) {
LOG.debug("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) {
StringBuilder buf = new StringBuilder();
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<>(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<>(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) {
LOG.warning("Object without label encountered.");
continue;
}
int row = labelmap.get(data);
if (row == -1) {
LOG.debug("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) {
StringBuilder buf = new StringBuilder();
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));
}
}
LOG.warning("null value in joined data, row " + i + " column " + d + FormatUtil.NEWLINE + "[" + buf.toString() + "]");
break;
}
}
}
return first;
}
@Override
protected Logging getLogger() {
return LOG;
}
/**
* Parameterization class.
*
* @author Erich Schubert
*
* @apiviz.exclude
*/
public static class Parameterizer extends AbstractDatabaseConnection.Parameterizer {
/**
* The static option ID
*/
public static final OptionID SOURCES_ID = new OptionID("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<>(SOURCES_ID, DatabaseConnection.class);
if (config.grab(sourcesParam)) {
sources = sourcesParam.instantiateClasses(config);
}
}
@Override
protected ExternalIDJoinDatabaseConnection makeInstance() {
return new ExternalIDJoinDatabaseConnection(filters, sources);
}
}
}
|
