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updated maven project structure

This commit is contained in:
Claudio Atzori 2018-10-18 11:56:26 +02:00
parent 72ebf7c0f3
commit 1b46966383
3 changed files with 220 additions and 20 deletions
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30
dnet-pace-core/pom.xml
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@ -1,70 +1,60 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet45-parent</artifactId>
<version>1.0.0</version>
<relativePath />
<artifactId>dnet-dedup</artifactId>
<version>3.0.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-pace-core</artifactId>
<packaging>jar</packaging>
<version>2.6.8-SNAPSHOT</version>
<scm>
<developerConnection>scm:svn:https://svn.driver.research-infrastructures.eu/driver/dnet45/modules/dnet-pace-core/trunk</developerConnection>
</scm>
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>edu.cmu</groupId>
<artifactId>secondstring</artifactId>
<version>1.0.0</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>15.0</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>${google.gson.version}</version>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>${commons.lang.version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons.io.version}</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>${commons.collections.version}</version>
</dependency>
<dependency>
<groupId>com.googlecode.protobuf-java-format</groupId>
<artifactId>protobuf-java-format</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>stringtemplate</artifactId>
<version>3.2</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>${commons.logging.version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>

199
dnet-pace-core/src/main/java/eu/dnetlib/pace/util/BlockProcessor.java Normal file
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package eu.dnetlib.pace.util;
import com.google.common.collect.Lists;
import eu.dnetlib.pace.clustering.NGramUtils;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.config.WfConfig;
import eu.dnetlib.pace.distance.PaceDocumentDistance;
import eu.dnetlib.pace.distance.eval.ScoreResult;
import eu.dnetlib.pace.model.Field;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.model.MapDocumentComparator;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import java.util.*;
public class BlockProcessor {
public static final List<String> accumulators= new ArrayList<>();
private static final Log log = LogFactory.getLog(BlockProcessor.class);
private DedupConfig dedupConf;
public static void constructAccumulator( final DedupConfig dedupConf) {
accumulators.add(String.format("%s::%s",dedupConf.getWf().getEntityType(), "records per hash key = 1"));
accumulators.add(String.format("%s::%s",dedupConf.getWf().getEntityType(), "missing " + dedupConf.getWf().getOrderField()));
accumulators.add(String.format("%s::%s",dedupConf.getWf().getEntityType(), String.format("Skipped records for count(%s) >= %s", dedupConf.getWf().getOrderField(), dedupConf.getWf().getGroupMaxSize())));
accumulators.add(String.format("%s::%s",dedupConf.getWf().getEntityType(), "skip list"));
accumulators.add(String.format("%s::%s",dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)"));
accumulators.add(String.format("%s::%s",dedupConf.getWf().getEntityType(), "d < " + dedupConf.getWf().getThreshold()));
}
public BlockProcessor(DedupConfig dedupConf) {
this.dedupConf = dedupConf;
}
public void process(final String key, final Iterable<MapDocument> documents, final Reporter context) {
final Queue<MapDocument> q = prepare(documents);
if (q.size() > 1) {
log.info("reducing key: '" + key + "' records: " + q.size());
//process(q, context);
process(simplifyQueue(q, key, context), context);
} else {
context.incrementCounter(dedupConf.getWf().getEntityType(), "records per hash key = 1", 1);
}
}
private Queue<MapDocument> prepare(final Iterable<MapDocument> documents) {
final Queue<MapDocument> queue = new PriorityQueue<>(100, new MapDocumentComparator(dedupConf.getWf().getOrderField()));
final Set<String> seen = new HashSet<String>();
final int queueMaxSize = dedupConf.getWf().getQueueMaxSize();
documents.forEach(doc -> {
if (queue.size() <= queueMaxSize) {
final String id = doc.getIdentifier();
if (!seen.contains(id)) {
seen.add(id);
queue.add(doc);
}
}
});
return queue;
}
private Queue<MapDocument> simplifyQueue(final Queue<MapDocument> queue, final String ngram, final Reporter context) {
final Queue<MapDocument> q = new LinkedList<>();
String fieldRef = "";
final List<MapDocument> tempResults = Lists.newArrayList();
while (!queue.isEmpty()) {
final MapDocument result = queue.remove();
final String orderFieldName = dedupConf.getWf().getOrderField();
final Field orderFieldValue = result.values(orderFieldName);
if (!orderFieldValue.isEmpty()) {
final String field = NGramUtils.cleanupForOrdering(orderFieldValue.stringValue());
if (field.equals(fieldRef)) {
tempResults.add(result);
} else {
populateSimplifiedQueue(q, tempResults, context, fieldRef, ngram);
tempResults.clear();
tempResults.add(result);
fieldRef = field;
}
} else {
context.incrementCounter(dedupConf.getWf().getEntityType(), "missing " + dedupConf.getWf().getOrderField(), 1);
}
}
populateSimplifiedQueue(q, tempResults, context, fieldRef, ngram);
return q;
}
private void populateSimplifiedQueue(final Queue<MapDocument> q,
final List<MapDocument> tempResults,
final Reporter context,
final String fieldRef,
final String ngram) {
WfConfig wf = dedupConf.getWf();
if (tempResults.size() < wf.getGroupMaxSize()) {
q.addAll(tempResults);
} else {
context.incrementCounter(wf.getEntityType(), String.format("Skipped records for count(%s) >= %s", wf.getOrderField(), wf.getGroupMaxSize()), tempResults.size());
log.info("Skipped field: " + fieldRef + " - size: " + tempResults.size() + " - ngram: " + ngram);
}
}
private void process(final Queue<MapDocument> queue, final Reporter context) {
final PaceDocumentDistance algo = new PaceDocumentDistance();
while (!queue.isEmpty()) {
final MapDocument pivot = queue.remove();
final String idPivot = pivot.getIdentifier();
WfConfig wf = dedupConf.getWf();
final Field fieldsPivot = pivot.values(wf.getOrderField());
final String fieldPivot = (fieldsPivot == null) || fieldsPivot.isEmpty() ? null : fieldsPivot.stringValue();
if (fieldPivot != null) {
// System.out.println(idPivot + " --> " + fieldPivot);
int i = 0;
for (final MapDocument curr : queue) {
final String idCurr = curr.getIdentifier();
if (mustSkip(idCurr)) {
context.incrementCounter(wf.getEntityType(), "skip list", 1);
break;
}
if (i > wf.getSlidingWindowSize()) {
break;
}
final Field fieldsCurr = curr.values(wf.getOrderField());
final String fieldCurr = (fieldsCurr == null) || fieldsCurr.isEmpty() ? null : fieldsCurr.stringValue();
if (!idCurr.equals(idPivot) && (fieldCurr != null)) {
final ScoreResult sr = similarity(algo, pivot, curr);
log.info(sr.toString()+"SCORE "+ sr.getScore());
emitOutput(sr, idPivot, idCurr, context);
i++;
}
}
}
}
}
private void emitOutput(final ScoreResult sr, final String idPivot, final String idCurr, final Reporter context) {
final double d = sr.getScore();
if (d >= dedupConf.getWf().getThreshold()) {
writeSimilarity(context, idPivot, idCurr);
context.incrementCounter(dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)", 1);
} else {
context.incrementCounter(dedupConf.getWf().getEntityType(), "d < " + dedupConf.getWf().getThreshold(), 1);
}
}
private ScoreResult similarity(final PaceDocumentDistance algo, final MapDocument a, final MapDocument b) {
try {
return algo.between(a, b, dedupConf);
} catch(Throwable e) {
log.error(String.format("\nA: %s\n----------------------\nB: %s", a, b), e);
throw new IllegalArgumentException(e);
}
}
private boolean mustSkip(final String idPivot) {
return dedupConf.getWf().getSkipList().contains(getNsPrefix(idPivot));
}
private String getNsPrefix(final String id) {
return StringUtils.substringBetween(id, "|", "::");
}
private void writeSimilarity(final Reporter context, final String from, final String to) {
final String type = dedupConf.getWf().getEntityType();
context.emit(type, from, to);
context.emit(type, to, from);
}
}

11
dnet-pace-core/src/main/java/eu/dnetlib/pace/util/Reporter.java Normal file
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package eu.dnetlib.pace.util;
import java.io.Serializable;
public interface Reporter extends Serializable {
void incrementCounter(String counterGroup, String counterName, long delta);
void emit(String type, String from, String to);
}