DedupConfig as json file

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java

@@ -18,8 +18,6 @@ import org.apache.spark.util.LongAccumulator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.broker.model.Event;
 import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher;
@@ -27,9 +25,6 @@ import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
 import eu.dnetlib.dhp.broker.oa.util.EventFinder;
 import eu.dnetlib.dhp.broker.oa.util.EventGroup;
 import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup;
-import eu.dnetlib.dhp.utils.ISLookupClientFactory;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import eu.dnetlib.pace.config.DedupConfig;
 
 public class GenerateEventsJob {
 
@@ -52,12 +47,6 @@ public class GenerateEventsJob {
 		final String workingPath = parser.get("workingPath");
 		log.info("workingPath: {}", workingPath);
 
-		final String isLookupUrl = parser.get("isLookupUrl");
-		log.info("isLookupUrl: {}", isLookupUrl);
-
-		final String dedupConfigProfileId = parser.get("dedupConfProfile");
-		log.info("dedupConfigProfileId: {}", dedupConfigProfileId);
-
 		final String eventsPath = workingPath + "/events";
 		log.info("eventsPath: {}", eventsPath);
 
@@ -72,10 +61,6 @@ public class GenerateEventsJob {
 
 		final SparkConf conf = new SparkConf();
 
-		// TODO UNCOMMENT
-		// final DedupConfig dedupConfig = loadDedupConfig(isLookupUrl, dedupConfigProfileId);
-		final DedupConfig dedupConfig = null;
-
 		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
 
 			ClusterUtils.removeDir(spark, eventsPath);
@@ -90,7 +75,7 @@ public class GenerateEventsJob {
 			final Dataset<Event> dataset = groups
 				.map(
 					g -> EventFinder
-						.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, dedupConfig, accumulators),
+						.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators),
 					Encoders
 						.bean(EventGroup.class))
 				.flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class));
@@ -112,23 +97,4 @@ public class GenerateEventsJob {
 
 	}
 
-	private static DedupConfig loadDedupConfig(final String isLookupUrl, final String profId) throws Exception {
-
-		final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
-
-		final String conf = isLookUpService
-			.getResourceProfileByQuery(
-				String
-					.format(
-						"for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()",
-						profId));
-
-		final DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class);
-		dedupConfig.getPace().initModel();
-		dedupConfig.getPace().initTranslationMap();
-		// dedupConfig.getWf().setConfigurationId("???");
-
-		return dedupConfig;
-	}
-
 }

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java

@@ -17,7 +17,6 @@ import org.apache.spark.util.LongAccumulator;
 import eu.dnetlib.broker.objects.OaBrokerMainEntity;
 import eu.dnetlib.dhp.broker.model.Topic;
 import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
-import eu.dnetlib.pace.config.DedupConfig;
 
 public abstract class UpdateMatcher<T> {
 
@@ -37,7 +36,6 @@ public abstract class UpdateMatcher<T> {
 
 	public Collection<UpdateInfo<T>> searchUpdatesForRecord(final OaBrokerMainEntity res,
 		final Collection<OaBrokerMainEntity> others,
-		final DedupConfig dedupConfig,
 		final Map<String, LongAccumulator> accumulators) {
 
 		final Map<String, UpdateInfo<T>> infoMap = new HashMap<>();
@@ -49,7 +47,7 @@ public abstract class UpdateMatcher<T> {
 					if (topic != null) {
 						final UpdateInfo<T> info = new UpdateInfo<>(topic, hl, source, res,
 							getCompileHighlightFunction(),
-							getHighlightToStringFunction(), dedupConfig);
+							getHighlightToStringFunction());
 
 						final String s = DigestUtils.md5Hex(info.getHighlightValueAsString());
 						if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) {

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java

@@ -37,7 +37,6 @@ import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreOpenAccess;
 import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMorePid;
 import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSubject;
 import eu.dnetlib.dhp.broker.oa.util.aggregators.simple.ResultGroup;
-import eu.dnetlib.pace.config.DedupConfig;
 
 public class EventFinder {
 
@@ -76,7 +75,6 @@ public class EventFinder {
 		final Set<String> dsIdWhitelist,
 		final Set<String> dsIdBlacklist,
 		final Set<String> dsTypeWhitelist,
-		final DedupConfig dedupConfig,
 		final Map<String, LongAccumulator> accumulators) {
 
 		final List<UpdateInfo<?>> list = new ArrayList<>();
@@ -84,7 +82,7 @@ public class EventFinder {
 		for (final OaBrokerMainEntity target : results.getData()) {
 			if (verifyTarget(target, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
 				for (final UpdateMatcher<?> matcher : matchers) {
-					list.addAll(matcher.searchUpdatesForRecord(target, results.getData(), dedupConfig, accumulators));
+					list.addAll(matcher.searchUpdatesForRecord(target, results.getData(), accumulators));
 				}
 			}
 		}

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/TrustUtils.java

@@ -1,8 +1,62 @@
 
 package eu.dnetlib.dhp.broker.oa.util;
 
+import java.io.IOException;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.broker.objects.OaBrokerMainEntity;
+import eu.dnetlib.pace.config.DedupConfig;
+import eu.dnetlib.pace.model.MapDocument;
+import eu.dnetlib.pace.tree.support.TreeProcessor;
+import eu.dnetlib.pace.util.MapDocumentUtil;
+
 public class TrustUtils {
 
+	private static final Logger log = LoggerFactory.getLogger(TrustUtils.class);
+
+	private static DedupConfig dedupConfig;
+
+	static {
+		final ObjectMapper mapper = new ObjectMapper();
+		try {
+			dedupConfig = mapper
+				.readValue(
+					DedupConfig.class.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/dedupConfig/dedupConfig.json"),
+					DedupConfig.class);
+		} catch (final IOException e) {
+			log.error("Error loading dedupConfig, e");
+		}
+
+	}
+
+	protected static float calculateTrust(final OaBrokerMainEntity r1, final OaBrokerMainEntity r2) {
+
+		if (dedupConfig == null) {
+			return BrokerConstants.MIN_TRUST;
+		}
+
+		try {
+			final ObjectMapper objectMapper = new ObjectMapper();
+			final MapDocument doc1 = MapDocumentUtil
+				.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r1));
+			final MapDocument doc2 = MapDocumentUtil
+				.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r2));
+
+			final double score = new TreeProcessor(dedupConfig).computeScore(doc1, doc2);
+
+			final double threshold = dedupConfig.getWf().getThreshold();
+
+			return TrustUtils.rescale(score, threshold);
+		} catch (final Exception e) {
+			log.error("Error computing score between results", e);
+			return BrokerConstants.MIN_TRUST;
+		}
+	}
+
 	public static float rescale(final double score, final double threshold) {
 		if (score >= BrokerConstants.MAX_TRUST) {
 			return BrokerConstants.MAX_TRUST;

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java

@@ -4,20 +4,11 @@ package eu.dnetlib.dhp.broker.oa.util;
 import java.util.function.BiConsumer;
 import java.util.function.Function;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
 import eu.dnetlib.broker.objects.OaBrokerEventPayload;
 import eu.dnetlib.broker.objects.OaBrokerInstance;
 import eu.dnetlib.broker.objects.OaBrokerMainEntity;
 import eu.dnetlib.broker.objects.OaBrokerProvenance;
 import eu.dnetlib.dhp.broker.model.Topic;
-import eu.dnetlib.pace.config.DedupConfig;
-import eu.dnetlib.pace.model.MapDocument;
-import eu.dnetlib.pace.tree.support.TreeProcessor;
-import eu.dnetlib.pace.util.MapDocumentUtil;
 
 public final class UpdateInfo<T> {
 
@@ -35,20 +26,17 @@ public final class UpdateInfo<T> {
 
 	private final float trust;
 
-	private static final Logger log = LoggerFactory.getLogger(UpdateInfo.class);
-
 	public UpdateInfo(final Topic topic, final T highlightValue, final OaBrokerMainEntity source,
 		final OaBrokerMainEntity target,
 		final BiConsumer<OaBrokerMainEntity, T> compileHighlight,
-		final Function<T, String> highlightToString,
+		final Function<T, String> highlightToString) {
-		final DedupConfig dedupConfig) {
 		this.topic = topic;
 		this.highlightValue = highlightValue;
 		this.source = source;
 		this.target = target;
 		this.compileHighlight = compileHighlight;
 		this.highlightToString = highlightToString;
-		this.trust = calculateTrust(dedupConfig, source, target);
+		this.trust = TrustUtils.calculateTrust(source, target);
 	}
 
 	public T getHighlightValue() {
@@ -63,31 +51,6 @@ public final class UpdateInfo<T> {
 		return target;
 	}
 
-	private float calculateTrust(final DedupConfig dedupConfig,
-		final OaBrokerMainEntity r1,
-		final OaBrokerMainEntity r2) {
-
-		if (dedupConfig == null) {
-			return BrokerConstants.MIN_TRUST;
-		}
-
-		try {
-			final ObjectMapper objectMapper = new ObjectMapper();
-			final MapDocument doc1 = MapDocumentUtil
-				.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r1));
-			final MapDocument doc2 = MapDocumentUtil
-				.asMapDocumentWithJPath(dedupConfig, objectMapper.writeValueAsString(r2));
-
-			final double score = new TreeProcessor(dedupConfig).computeScore(doc1, doc2);
-			final double threshold = dedupConfig.getWf().getThreshold();
-
-			return TrustUtils.rescale(score, threshold);
-		} catch (final Exception e) {
-			log.error("Error computing score between results", e);
-			return BrokerConstants.MIN_TRUST;
-		}
-	}
-
 	protected Topic getTopic() {
 		return topic;
 	}

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/dedupConfig/dedupConfig.json

@@ -0,0 +1,122 @@
+{
+	"wf": {
+		
+	},
+	"pace": {
+		"clustering": [
+			{
+				"name": "wordssuffixprefix",
+				"fields": [
+					"title"
+				],
+				"params": {
+					"max": "2",
+					"len": "3"
+				}
+			},
+			{
+				"name": "lowercase",
+				"fields": [
+					"doi"
+				],
+				"params": {
+					
+				}
+			}
+		],
+		"decisionTree": {
+			"start": {
+				"fields": [
+					{
+						"field": "doi",
+						"comparator": "exactMatch",
+						"weight": 1.0,
+						"countIfUndefined": "false",
+						"params": {
+							
+						}
+					}
+				],
+				"threshold": 0.5,
+				"aggregation": "AVG",
+				"positive": "MATCH",
+				"negative": "layer1",
+				"undefined": "layer1",
+				"ignoreUndefined": "true"
+			},
+			"layer1": {
+				"fields": [
+					{
+						"field": "title",
+						"comparator": "titleVersionMatch",
+						"weight": 0.9,
+						"countIfUndefined": "false",
+						"params": {
+							
+						}
+					},
+					{
+						"field": "authors",
+						"comparator": "sizeMatch",
+						"weight": 0.9,
+						"countIfUndefined": "false",
+						"params": {
+							
+						}
+					}
+				],
+				"threshold": 0.5,
+				"aggregation": "AVG",
+				"positive": "MATCH",
+				"negative": "layer2",
+				"undefined": "layer2",
+				"ignoreUndefined": "true"
+			},
+			"layer2": {
+				"fields": [
+					{
+						"field": "title",
+						"comparator": "levensteinTitle",
+						"weight": 1.0,
+						"countIfUndefined": "true",
+						"params": {
+							
+						}
+					}
+				],
+				"threshold": 0.99,
+				"aggregation": "AVG",
+				"positive": "MATCH",
+				"negative": "NO_MATCH",
+				"undefined": "NO_MATCH",
+				"ignoreUndefined": "true"
+			}
+		},
+		"model": [
+			{
+				"name": "doi",
+				"type": "String",
+				"path": "$.pids[?(@.type == 'doi')].value"
+			},
+			{
+				"name": "title",
+				"type": "String",
+				"path": "$.titles",
+				"length": 250,
+				"size": 5
+			},
+			{
+				"name": "authors",
+				"type": "List",
+				"path": "$.creators[*].fullname",
+				"size": 200
+			}
+		],
+		"blacklists": {
+			
+		},
+		"synonyms": {
+			
+		}
+	}
+}

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml

@@ -8,14 +8,6 @@
         <property>
             <name>workingPath</name>
             <description>the path where the the generated data will be stored</description>
-        </property>
-        <property>
-            <name>isLookupUrl</name>
-            <description>the address of the lookUp service</description>
-        </property>
-        <property>
-            <name>dedupConfProfId</name>
-            <description>the id of a valid Dedup Configuration Profile</description>
         </property>
 		<property>
             <name>datasourceIdWhitelist</name>
@@ -427,8 +419,6 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--workingPath</arg><arg>${workingPath}</arg>
-            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
-            <arg>--dedupConfProfile</arg><arg>${dedupConfProfId}</arg>
 			<arg>--datasourceIdWhitelist</arg><arg>${datasourceIdWhitelist}</arg>
 			<arg>--datasourceTypeWhitelist</arg><arg>${datasourceTypeWhitelist}</arg>
 			<arg>--datasourceIdBlacklist</arg><arg>${datasourceIdBlacklist}</arg>

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json

@@ -5,18 +5,6 @@
 		"paramDescription": "the path where the generated events will be stored",
 		"paramRequired": true
 	},
-	{
-		"paramName": "lu",
-		"paramLongName": "isLookupUrl",
-		"paramDescription": "the address of the ISLookUpService",
-		"paramRequired": true
-	},
-	{
-		"paramName": "d",
-		"paramLongName": "dedupConfProfile",
-		"paramDescription": "the id of a valid Dedup Configuration Profile",
-		"paramRequired": true
-	},
 	{
 		"paramName": "datasourceIdWhitelist",
 		"paramLongName": "datasourceIdWhitelist",

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml

@@ -9,15 +9,6 @@
             <name>workingPath</name>
             <description>the path where the the generated data will be stored</description>
         </property>
-        <property>
-            <name>isLookupUrl</name>
-            <description>the address of the lookUp service</description>
-        </property>
-        <property>
-            <name>dedupConfProfId</name>
-            <description>the id of a valid Dedup Configuration Profile</description>
-        </property>
-
         <property>
             <name>sparkDriverMemory</name>
             <description>memory for driver process</description>

dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java

@@ -30,7 +30,7 @@ class UpdateMatcherTest {
 		final OaBrokerMainEntity p4 = new OaBrokerMainEntity();
 
 		final Collection<UpdateInfo<String>> list = matcher
-			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
+			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
 
 		assertTrue(list.isEmpty());
 	}
@@ -46,7 +46,7 @@ class UpdateMatcherTest {
 		res.setPublicationdate("2018");
 
 		final Collection<UpdateInfo<String>> list = matcher
-			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
+			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
 
 		assertTrue(list.isEmpty());
 	}
@@ -62,7 +62,7 @@ class UpdateMatcherTest {
 		p2.setPublicationdate("2018");
 
 		final Collection<UpdateInfo<String>> list = matcher
-			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
+			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
 
 		assertTrue(list.size() == 1);
 	}
@@ -79,7 +79,7 @@ class UpdateMatcherTest {
 		p2.setPublicationdate("2018");
 
 		final Collection<UpdateInfo<String>> list = matcher
-			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
+			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
 
 		assertTrue(list.isEmpty());
 	}
@@ -98,7 +98,7 @@ class UpdateMatcherTest {
 		p4.setPublicationdate("2018");
 
 		final Collection<UpdateInfo<String>> list = matcher
-			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
+			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
 
 		assertTrue(list.isEmpty());
 	}
@@ -117,7 +117,7 @@ class UpdateMatcherTest {
 		p4.setPublicationdate("2018");
 
 		final Collection<UpdateInfo<String>> list = matcher
-			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null, null);
+			.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
 
 		assertTrue(list.size() == 1);
 	}

dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java

@@ -5,6 +5,10 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
 
 import org.junit.jupiter.api.Test;
 
+import eu.dnetlib.broker.objects.OaBrokerAuthor;
+import eu.dnetlib.broker.objects.OaBrokerMainEntity;
+import eu.dnetlib.broker.objects.OaBrokerTypedValue;
+
 public class TrustUtilsTest {
 
 	private static final double THRESHOLD = 0.95;
@@ -64,6 +68,23 @@ public class TrustUtilsTest {
 		verifyValue(2.00, BrokerConstants.MAX_TRUST);
 	}
 
+	@Test
+	public void test() throws Exception {
+		final OaBrokerMainEntity r1 = new OaBrokerMainEntity();
+		r1.getTitles().add("D-NET Service Package: Data Import");
+		r1.getPids().add(new OaBrokerTypedValue("doi", "123"));
+		r1.getCreators().add(new OaBrokerAuthor("Michele Artini", null));
+		r1.getCreators().add(new OaBrokerAuthor("Claudio Atzori", null));
+
+		final OaBrokerMainEntity r2 = new OaBrokerMainEntity();
+		r2.getTitles().add("D-NET Service Package: Data Import");
+		// r2.getPids().add(new OaBrokerTypedValue("doi", "123"));
+		r2.getCreators().add(new OaBrokerAuthor("Michele Artini", null));
+		// r2.getCreators().add(new OaBrokerAuthor("Claudio Atzori", null));
+
+		System.out.println("TRUST: " + TrustUtils.calculateTrust(r1, r2));
+	}
+
 	private void verifyValue(final double originalScore, final float expectedTrust) {
 		final float trust = TrustUtils.rescale(originalScore, THRESHOLD);
 		System.out.println(trust);