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dedup test implementation & graph drawing tools

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optimized-clustering
miconis 3 years ago
parent 30aeed3803
commit 5a52aed8e1
24 changed files with 2094 additions and 197 deletions
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2
dhp-build/dhp-build-properties-maven-plugin/test.properties
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@ -1,2 +1,2 @@
# Mon May 03 16:05:14 CEST 2021
# Mon Sep 13 14:51:29 CEST 2021
projectPropertyKey=projectPropertyValue

7
dnet-dedup-test/job-override.properties
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@ -1,5 +1,6 @@
entitiesPath = /tmp/prod_provision/graph/01_graph_raw/publication
workingPath = /user/michele.debonis/erf_test/workingdir
#entitiesPath = /tmp/prod_provision/graph/01_graph_raw/publication
entitiesPath = /tmp/publications_test_dump
workingPath = /user/michele.debonis/erf_test/workingdirtree
dedupConfPath = /user/michele.debonis/erf_test/pubs.tree.conf.json
numPartitions = 20
useTree = true
useTree = false

11
dnet-dedup-test/pom.xml
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@ -132,6 +132,17 @@
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

156
dnet-dedup-test/src/main/java/eu/dnetlib/Deduper.java
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@ -1,34 +1,22 @@
package eu.dnetlib;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.hash.Hashing;
import eu.dnetlib.graph.GraphProcessor;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.config.WfConfig;
import eu.dnetlib.pace.model.Field;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.model.MapDocumentComparator;
import eu.dnetlib.pace.tree.JsonListMatch;
import eu.dnetlib.pace.tree.LevensteinTitle;
import eu.dnetlib.pace.tree.SizeMatch;
import eu.dnetlib.pace.tree.TitleVersionMatch;
import eu.dnetlib.pace.tree.support.TreeProcessor;
import eu.dnetlib.pace.util.BlockProcessor;
import eu.dnetlib.pace.util.BlockProcessorForTesting;
import eu.dnetlib.pace.util.MapDocumentUtil;
import eu.dnetlib.pace.util.Reporter;
import eu.dnetlib.pace.utils.Utility;
import eu.dnetlib.reporter.SparkReporter;
import eu.dnetlib.support.Block;
import eu.dnetlib.support.ConnectedComponent;
import eu.dnetlib.support.Relation;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.PairFlatMapFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.graphx.Edge;
import org.apache.spark.rdd.RDD;
@ -39,7 +27,6 @@ import org.apache.spark.sql.SparkSession;
import org.apache.spark.util.LongAccumulator;
import scala.Serializable;
import scala.Tuple2;
import scala.math.Ordering;
import java.nio.charset.Charset;
import java.util.*;
@ -98,15 +85,15 @@ public class Deduper implements Serializable {
}
public static JavaRDD<Relation> computeRelations(
JavaSparkContext context, JavaPairRDD<String, Block> blocks, DedupConfig config) {
JavaSparkContext context, JavaPairRDD<String, Block> blocks, DedupConfig config, boolean useTree) {
Map<String, LongAccumulator> accumulators = Utility.constructAccumulator(config, context.sc());
return blocks
.flatMapToPair(
it -> {
final SparkReporter reporter = new SparkReporter(accumulators);
new BlockProcessor(config)
.processSortedBlock(it._1(), it._2().getDocuments(), reporter);
new BlockProcessorForTesting(config)
.processSortedBlock(it._1(), it._2().getDocuments(), reporter, useTree);
return reporter.getRelations().iterator();
})
.mapToPair(it -> new Tuple2<>(it._1() + it._2(), new Relation(it._1(), it._2(), "simRel")))
@ -114,138 +101,7 @@ public class Deduper implements Serializable {
.map(Tuple2::_2);
}
public static Queue<MapDocument> prepareQueue(final Iterable<MapDocument> documents, DedupConfig config) {
final Queue<MapDocument> queue = new PriorityQueue<>(100, new MapDocumentComparator(config.getWf().getOrderField()));
final Set<String> seen = new HashSet<String>();
final int queueMaxSize = config.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;
}
public static JavaRDD<Relation> computePublicationRelations(
JavaSparkContext context, JavaPairRDD<String, Block> blocks, DedupConfig config) {
return blocks.
flatMapToPair((PairFlatMapFunction<Tuple2<String, Block>, String, String>)
it -> {
List<Tuple2<String,String>> relations = new ArrayList<>();
if (it._2().getDocuments().size()>1) {
Queue<MapDocument> queue = prepareQueue(it._2().getDocuments(), config);
while (!queue.isEmpty()) {
final MapDocument pivot = queue.remove();
final String idPivot = pivot.getIdentifier();
WfConfig wf = config.getWf();
final Field fieldsPivot = pivot.values(wf.getOrderField());
final String fieldPivot = (fieldsPivot == null) || fieldsPivot.isEmpty() ? "" : fieldsPivot.stringValue();
if (fieldPivot != null) {
int i = 0;
for (final MapDocument curr : queue) {
final String idCurr = curr.getIdentifier();
if (config.getWf().getSkipList().contains(StringUtils.substringBetween(idCurr, "|", "::"))) {
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)) {
double score = 0.0;
Map<String, String> params = new HashMap<>();
params.put("jpath_value", "$.value");
params.put("jpath_classid", "$.qualifier.classid");
JsonListMatch jsonListMatch = new JsonListMatch(params);
double result = jsonListMatch.compare(pivot.getFieldMap().get("pid"), curr.getFieldMap().get("pid"), config);
if (result > 0.5) //if the result of the comparison is greater than the threshold
score += 10.0; //high score because it should match when the first condition is satisfied
else
score += 0.0;
TitleVersionMatch titleVersionMatch = new TitleVersionMatch(params);
double result1 = titleVersionMatch.compare(pivot.getFieldMap().get("title"), curr.getFieldMap().get("title"), config);
SizeMatch sizeMatch = new SizeMatch(params);
double result2 = sizeMatch.compare(pivot.getFieldMap().get("authors"), curr.getFieldMap().get("authors"), config);
if ((result1 == 1.0 && result2 == 1.0) || (result1 == -1.0 && result2 == 1.0) || (result1 == 1.0 && result2 == -1.0) || (result1 == -1.0 && result2 == -1.0))
score += 0.0;
else
score -= 1.0;
LevensteinTitle levensteinTitle = new LevensteinTitle(params);
double result3 = levensteinTitle.compare(pivot.getFieldMap().get("title"), curr.getFieldMap().get("title"), config);
score += result3;
if (score >= 0.99) {
relations.add(new Tuple2<>(idPivot, idCurr));
relations.add(new Tuple2<>(idCurr, idPivot));
}
}
}
}
}
}
return relations.iterator();
})
.mapToPair(it -> new Tuple2<>(it._1() + it._2(), new Relation(it._1(), it._2(), "simRel")))
.reduceByKey((a,b) -> a)
.map(Tuple2::_2);
}
public static boolean comparePublications(MapDocument a, MapDocument b, DedupConfig config){
double score = 0.0;
Map<String, String> params = new HashMap<>();
params.put("jpath_value", "$.value");
params.put("jpath_classid", "$.qualifier.classid");
JsonListMatch jsonListMatch = new JsonListMatch(params);
double result = jsonListMatch.compare(a.getFieldMap().get("pid"), b.getFieldMap().get("pid"), config);
if (result > 0.5) //if the result of the comparison is greater than the threshold
score += 1.0;
else
score += 0.0;
TitleVersionMatch titleVersionMatch = new TitleVersionMatch(params);
double result1 = titleVersionMatch.compare(a.getFieldMap().get("title"), b.getFieldMap().get("title"), config);
SizeMatch sizeMatch = new SizeMatch(params);
double result2 = sizeMatch.compare(a.getFieldMap().get("authors"), b.getFieldMap().get("authors"), config);
if ((result1 == 1.0 && result2 == 1.0) || (result1 == -1.0 && result2 == 1.0) || (result1 == 1.0 && result2 == -1.0) || (result1 == -1.0 && result2 == -1.0))
score += 0.0;
else
score -= 1.0;
LevensteinTitle levensteinTitle = new LevensteinTitle(params);
double result3 = levensteinTitle.compare(a.getFieldMap().get("title"), b.getFieldMap().get("title"), config);
score += result3;
return score >= 0.99;
}
public static void createSimRels(DedupConfig dedupConf, SparkSession spark, String entitiesPath, String simRelsPath){
public static void createSimRels(DedupConfig dedupConf, SparkSession spark, String entitiesPath, String simRelsPath, boolean useTree){
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -261,7 +117,7 @@ public class Deduper implements Serializable {
JavaPairRDD<String, Block> blocks = Deduper.createSortedBlocks(mapDocuments, dedupConf);
// create relations by comparing only elements in the same group
JavaRDD<Relation> relations = Deduper.computeRelations(sc, blocks, dedupConf);
JavaRDD<Relation> relations = Deduper.computeRelations(sc, blocks, dedupConf, useTree);
// save the simrel in the workingdir
spark

2
dnet-dedup-test/src/main/java/eu/dnetlib/jobs/SparkCreateDedupEntity.java
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@ -61,7 +61,7 @@ public class SparkCreateDedupEntity extends AbstractSparkJob {
log.info("dedupConfPath: '{}'", dedupConfPath);
log.info("numPartitions: '{}'", numPartitions);
DedupConfig dedupConf = DedupConfig.load(readResource("/jobs/parameters/createDedupEntity_parameters.json", SparkCreateDedupEntity.class));
DedupConfig dedupConf = DedupConfig.load(readFileFromHDFS(dedupConfPath));
JavaPairRDD<String, String> entities = spark
.read()

7
dnet-dedup-test/src/main/java/eu/dnetlib/jobs/SparkCreateSimRels.java
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@ -82,12 +82,7 @@ public class SparkCreateSimRels extends AbstractSparkJob {
JavaPairRDD<String, Block> blocks = Deduper.createSortedBlocks(mapDocuments, dedupConfig);
// create relations by comparing only elements in the same group
JavaRDD<Relation> relations;
if (useTree)
relations = Deduper.computeRelations(sc, blocks, dedupConfig);
else
relations = Deduper.computePublicationRelations(sc, blocks, dedupConfig);
JavaRDD<Relation> relations = Deduper.computeRelations(sc, blocks, dedupConfig, useTree);
// save the simrel in the workingdir
spark

2
dnet-dedup-test/src/main/resources/dedup/oozie_app/workflow.xml
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@ -131,7 +131,7 @@
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
--conf spark.dynamicAllocation.enabled=false
--conf spark.dynamicAllocation.enabled=true
</spark-opts>
<arg>--entitiesPath</arg><arg>${entitiesPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>

235
dnet-dedup-test/src/test/java/eu/dnetlib/pace/DedupLocalTest.java
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dnet-dedup-test/src/test/java/eu/dnetlib/pace/GraphDraw.java
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package eu.dnetlib.pace;
import java.util.*;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
public class GraphDraw extends JFrame {
int width;
int height;
ArrayList<Node> nodes;
ArrayList<edge> edges;
public GraphDraw() { //Constructor
this.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
nodes = new ArrayList<Node>();
edges = new ArrayList<edge>();
width = 15;
height = 15;
}
public GraphDraw(String name) { //Construct with label
this.setTitle(name);
this.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
nodes = new ArrayList<Node>();
edges = new ArrayList<edge>();
width = 15;
height = 15;
}
class Node {
int x, y;
String name;
Color color;
public Node(String myName, int myX, int myY) {
x = myX;
y = myY;
name = myName;
color = Color.white;
}
public Node(String myName, int myX, int myY, Color myColor) {
x = myX;
y = myY;
name = myName;
color = myColor;
}
}
class edge {
int i,j;
public edge(int ii, int jj) {
i = ii;
j = jj;
}
}
public void addNode(String name, int x, int y) {
//add a node at pixel (x,y)
nodes.add(new Node(name,x,y));
this.repaint();
}
public void addEdge(int i, int j) {
//add an edge between nodes i and j
edges.add(new edge(i,j));
this.repaint();
}
public void paint(Graphics g) { // draw the nodes and edges
FontMetrics f = g.getFontMetrics();
int nodeHeight = Math.max(height, f.getHeight());
g.setColor(Color.black);
for (edge e : edges) {
g.drawLine(nodes.get(e.i).x, nodes.get(e.i).y,
nodes.get(e.j).x, nodes.get(e.j).y);
}
for (Node n : nodes) {
n.name = n.name.substring(0, 20);
int nodeWidth = Math.max(width, f.stringWidth(n.name)+width/2);
g.setColor(n.color);
g.fillRoundRect(n.x-nodeWidth/2, n.y-nodeHeight/2,
nodeWidth, nodeHeight, 2, 2);
g.setColor(Color.black);
g.drawRoundRect(n.x-nodeWidth/2, n.y-nodeHeight/2, nodeWidth, nodeHeight, 2, 2);
g.drawString(n.name, n.x-f.stringWidth(n.name)/2,
n.y+f.getHeight()/5);
}
}
}
class testGraphDraw {
//Here is some example syntax for the GraphDraw class
public static void main(String[] args) {
GraphDraw frame = new GraphDraw("Test Window");
frame.setSize(400,300);
frame.setVisible(true);
frame.addNode("a", 50,50);
frame.addNode("b", 100,100);
frame.addNode("longNode", 200,200);
frame.addEdge(0,1);
frame.addEdge(0,2);
}
}

67
dnet-dedup-test/src/test/resources/eu/dnetlib/pace/config/ds.tree.conf.json
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@ -0,0 +1,67 @@
{
"wf" : {
"threshold" : "0.99",
"dedupRun" : "001",
"entityType" : "datasource",
"orderField" : "name",
"queueMaxSize" : "2000",
"groupMaxSize" : "50",
"slidingWindowSize" : "200",
"idPath":"$.id",
"rootBuilder" : [ "organization", "projectOrganization_participation_isParticipant", "datasourceOrganization_provision_isProvidedBy" ],
"includeChildren" : "true",
"maxIterations": "20"
},
"pace" : {
"clustering" : [
{ "name" : "sortedngrampairs", "fields" : [ "name" ], "params" : { "max" : 2, "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "name" ], "params" : { "max" : 1, "len" : "3" } },
{ "name" : "urlclustering", "fields" : [ "websiteurl" ], "params" : { } }
],
"decisionTree" : {
"start": {
"fields": [
{
"field": "websiteurl",
"comparator": "domainExactMatch",
"weight": 1,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1,
"aggregation": "AVG",
"positive": "layer2",
"negative": "NO_MATCH",
"undefined": "layer2",
"ignoreUndefined": "true"
},
"layer2": {
"fields": [
{
"field": "name",
"comparator": "jaroWinkler",
"weight": 1.0,
"countIfUndefined": "true",
"params": {
}
}
],
"threshold": 0.9,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
}
},
"model" : [
{ "name" : "name", "type" : "String", "path" : "$.name" },
{ "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl" }
],
"blacklists" : {
"legalname" : []
},
"synonyms": {}
}
}

401
dnet-dedup-test/src/test/resources/eu/dnetlib/pace/config/pub.prod.tree.conf.json
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@ -0,0 +1,401 @@
{
"wf": {
"threshold": "0.99",
"dedupRun": "001",
"entityType": "result",
"subEntityType": "resulttype",
"subEntityValue": "publication",
"orderField": "title",
"queueMaxSize": "200",
"groupMaxSize": "100",
"maxChildren": "100",
"slidingWindowSize": "50",
"rootBuilder": [
"result",
"resultProject_outcome_isProducedBy",
"resultResult_publicationDataset_isRelatedTo",
"resultResult_similarity_isAmongTopNSimilarDocuments",
"resultResult_similarity_hasAmongTopNSimilarDocuments",
"resultOrganization_affiliation_isAffiliatedWith",
"resultResult_part_hasPart",
"resultResult_part_isPartOf",
"resultResult_supplement_isSupplementTo",
"resultResult_supplement_isSupplementedBy",
"resultResult_version_isVersionOf"
],
"includeChildren": "true",
"maxIterations": 20,
"idPath": "$.id"
},
"pace": {
"clustering" : [
{ "name" : "wordsStatsSuffixPrefixChain", "fields" : [ "title" ], "params" : { "mod" : "10" } },
{ "name" : "lowercase", "fields" : [ "doi", "altdoi" ], "params" : { "collapseOn:pid": "0"} }
],
"decisionTree": {
"start": {
"fields": [
{
"field": "pid",
"comparator": "jsonListMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {
"jpath_value": "$.value",
"jpath_classid": "$.qualifier.classid"
}
},
{
"field": "pid",
"comparator": "jsonListMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {
"jpath_value": "$.value",
"jpath_classid": "$.qualifier.classid",
"crossCompare": "alternateid"
}
}
],
"threshold": 0.5,
"aggregation": "MAX",
"positive": "layer1",
"negative": "layer2",
"undefined": "layer2",
"ignoreUndefined": "true"
},
"layer1": {
"fields": [
{
"field": "title",
"comparator": "levensteinTitle",
"weight": 1.0,
"countIfUndefined": "true",
"params": {}
}
],
"threshold": 0.9,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
},
"layer2": {
"fields": [
{
"field": "title",
"comparator": "titleVersionMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
},
{
"field": "authors",
"comparator": "sizeMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1.0,
"aggregation": "AND",
"positive": "layer3",
"negative": "NO_MATCH",
"undefined": "layer3",
"ignoreUndefined": "false"
},
"layer3": {
"fields": [
{
"field": "title",
"comparator": "levensteinTitle",
"weight": 1.0,
"countIfUndefined": "true",
"params": {}
}
],
"threshold": 0.99,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
}
},
"model": [
{
"name": "doi",
"type": "String",
"path": "$.instance[*].pid[?(@.qualifier.classid == 'doi')].value"
},
{
"name": "altdoi",
"type": "String",
"path": "$.instance[*].alternateIdentifier[?(@.qualifier.classid == 'doi')].value"
},
{
"name": "pid",
"type": "JSON",
"path": "$.instance[*].pid[*]",
"overrideMatch": "true"
},
{
"name": "alternateid",
"type": "JSON",
"path": "$.instance[*].alternateIdentifier[*]",
"overrideMatch": "true"
},
{
"name": "title",
"type": "String",
"path": "$.title[?(@.qualifier.classid == 'main title')].value",
"length": 250,
"size": 5
},
{
"name": "authors",
"type": "List",
"path": "$.author[*].fullname",
"size": 200
},
{
"name": "resulttype",
"type": "String",
"path": "$.resulttype.classid"
}
],
"blacklists": {
"title": [
"(?i)^Data Management Plan",
"^Inside Front Cover$",
"(?i)^Poster presentations$",
"^THE ASSOCIATION AND THE GENERAL MEDICAL COUNCIL$",
"^Problems with perinatal pathology\\.?$",
"(?i)^Cases? of Puerperal Convulsions$",
"(?i)^Operative Gyna?ecology$",
"(?i)^Mind the gap\\!?\\:?$",
"^Chronic fatigue syndrome\\.?$",
"^Cartas? ao editor Letters? to the Editor$",
"^Note from the Editor$",
"^Anesthesia Abstract$",
"^Annual report$",
"(?i)^“?THE RADICAL PREVENTION OF VENEREAL DISEASE\\.?”?$",
"(?i)^Graph and Table of Infectious Diseases?$",
"^Presentation$",
"(?i)^Reviews and Information on Publications$",
"(?i)^PUBLIC HEALTH SERVICES?$",
"(?i)^COMBINED TEXT-?BOOK OF OBSTETRICS AND GYN(Æ|ae)COLOGY$",
"(?i)^Adrese autora$",
"(?i)^Systematic Part .*\\. Catalogus Fossilium Austriae, Band 2: Echinoidea neogenica$",
"(?i)^Acknowledgement to Referees$",
"(?i)^Behçet's disease\\.?$",
"(?i)^Isolation and identification of restriction endonuclease.*$",
"(?i)^CEREBROVASCULAR DISEASES?.?$",
"(?i)^Screening for abdominal aortic aneurysms?\\.?$",
"^Event management$",
"(?i)^Breakfast and Crohn's disease.*\\.?$",
"^Cálculo de concentraciones en disoluciones acuosas. Ejercicio interactivo\\..*\\.$",
"(?i)^Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of Autism spectrum disorders?\\.?$",
"^Gushi hakubutsugaku$",
"^Starobosanski nadpisi u Bosni i Hercegovini \\(.*\\)$",
"^Intestinal spirocha?etosis$",
"^Treatment of Rodent Ulcer$",
"(?i)^\\W*Cloud Computing\\W*$",
"^Compendio mathematico : en que se contienen todas las materias mas principales de las Ciencias que tratan de la cantidad$",
"^Free Communications, Poster Presentations: Session [A-F]$",
"^“The Historical Aspects? of Quackery\\.?”$",
"^A designated centre for people with disabilities operated by St John of God Community Services (Limited|Ltd), Louth$",
"^P(er|re)-Mile Premiums for Auto Insurance\\.?$",
"(?i)^Case Report$",
"^Boletín Informativo$",
"(?i)^Glioblastoma Multiforme$",
"(?i)^Nuevos táxones animales descritos en la península Ibérica y Macaronesia desde 1994 \\(.*\\)$",
"^Zaměstnanecké výhody$",
"(?i)^The Economics of Terrorism and Counter-Terrorism: A Survey \\(Part .*\\)$",
"(?i)^Carotid body tumours?\\.?$",
"(?i)^\\[Españoles en Francia : La condición Emigrante.*\\]$",
"^Avant-propos$",
"(?i)^St\\. Patrick's Cathedral, Dublin, County Dublin - Head(s)? and Capital(s)?$",
"(?i)^St\\. Patrick's Cathedral, Dublin, County Dublin - Bases?$",
"(?i)^PUBLIC HEALTH VERSUS THE STATE$",
"^Viñetas de Cortázar$",
"(?i)^Search for heavy neutrinos and W(\\[|_|\\(|_\\{|-)?R(\\]|\\)|\\})? bosons with right-handed couplings in a left-right symmetric model in pp collisions at.*TeV(\\.)?$",
"(?i)^Measurement of the pseudorapidity and centrality dependence of the transverse energy density in Pb(-?)Pb collisions at.*tev(\\.?)$",
"(?i)^Search for resonances decaying into top-quark pairs using fully hadronic decays in pp collisions with ATLAS at.*TeV$",
"(?i)^Search for neutral minimal supersymmetric standard model Higgs bosons decaying to tau pairs in pp collisions at.*tev$",
"(?i)^Relatório de Estágio (de|em) Angiologia e Cirurgia Vascular$",
"^Aus der AGMB$",
"^Znanstveno-stručni prilozi$",
"(?i)^Zhodnocení finanční situace podniku a návrhy na zlepšení$",
"(?i)^Evaluation of the Financial Situation in the Firm and Proposals to its Improvement$",
"(?i)^Hodnocení finanční situace podniku a návrhy na její zlepšení$",
"^Finanční analýza podniku$",
"^Financial analysis( of business)?$",
"(?i)^Textbook of Gyn(a)?(Æ)?(e)?cology$",
"^Jikken nihon shūshinsho$",
"(?i)^CORONER('|s)(s|') INQUESTS$",
"(?i)^(Μελέτη παραγόντων )?risk management( για ανάπτυξη και εφαρμογή ενός πληροφοριακού συστήματος| και ανάπτυξη συστήματος)?$",
"(?i)^Consultants' contract(s)?$",
"(?i)^Upute autorima$",
"(?i)^Bijdrage tot de Kennis van den Godsdienst der Dajaks van Lan(d|f)ak en Tajan$",
"^Joshi shin kokubun$",
"^Kōtō shōgaku dokuhon nōson'yō$",
"^Jinjō shōgaku shōka$",
"^Shōgaku shūjichō$",
"^Nihon joshi dokuhon$",
"^Joshi shin dokuhon$",
"^Chūtō kanbun dokuhon$",
"^Wabun dokuhon$",
"(?i)^(Analysis of economy selected village or town|Rozbor hospodaření vybrané obce či města)$",
"(?i)^cardiac rehabilitation$",
"(?i)^Analytical summary$",
"^Thesaurus resolutionum Sacrae Congregationis Concilii$",
"(?i)^Sumario analítico(\\s{1})?(Analitic summary)?$",
"^Prikazi i osvrti$",
"^Rodinný dům s provozovnou$",
"^Family house with an establishment$",
"^Shinsei chūtō shin kokugun$",
"^Pulmonary alveolar proteinosis(\\.?)$",
"^Shinshū kanbun$",
"^Viñeta(s?) de Rodríguez$",
"(?i)^RUBRIKA UREDNIKA$",
"^A Matching Model of the Academic Publication Market$",
"^Yōgaku kōyō$",
"^Internetový marketing$",
"^Internet marketing$",
"^Chūtō kokugo dokuhon$",
"^Kokugo dokuhon$",
"^Antibiotic Cover for Dental Extraction(s?)$",
"^Strategie podniku$",
"^Strategy of an Enterprise$",
"(?i)^respiratory disease(s?)(\\.?)$",
"^Award(s?) for Gallantry in Civil Defence$",
"^Podniková kultura$",
"^Corporate Culture$",
"^Severe hyponatraemia in hospital inpatient(s?)(\\.?)$",
"^Pracovní motivace$",
"^Work Motivation$",
"^Kaitei kōtō jogaku dokuhon$",
"^Konsolidovaná účetní závěrka$",
"^Consolidated Financial Statements$",
"(?i)^intracranial tumour(s?)$",
"^Climate Change Mitigation Options and Directed Technical Change: A Decentralized Equilibrium Analysis$",
"^\\[CERVECERIAS MAHOU(\\.|\\:) INTERIOR\\] \\[Material gráfico\\]$",
"^Housing Market Dynamics(\\:|\\.) On the Contribution of Income Shocks and Credit Constraint(s?)$",
"^\\[Funciones auxiliares de la música en Radio París,.*\\]$",
"^Úroveň motivačního procesu jako způsobu vedení lidí$",
"^The level of motivation process as a leadership$",
"^Pay-beds in N(\\.?)H(\\.?)S(\\.?) Hospitals$",
"(?i)^news and events$",
"(?i)^NOVOSTI I DOGAĐAJI$",
"^Sansū no gakushū$",
"^Posouzení informačního systému firmy a návrh změn$",
"^Information System Assessment and Proposal for ICT Modification$",
"^Stresové zatížení pracovníků ve vybrané profesi$",
"^Stress load in a specific job$",
"^Sunday: Poster Sessions, Pt.*$",
"^Monday: Poster Sessions, Pt.*$",
"^Wednesday: Poster Sessions, Pt.*",
"^Tuesday: Poster Sessions, Pt.*$",
"^Analýza reklamy$",
"^Analysis of advertising$",
"^Shōgaku shūshinsho$",
"^Shōgaku sansū$",
"^Shintei joshi kokubun$",
"^Taishō joshi kokubun dokuhon$",
"^Joshi kokubun$",
"^Účetní uzávěrka a účetní závěrka v ČR$",
"(?i)^The \"?Causes\"? of Cancer$",
"^Normas para la publicación de artículos$",
"^Editor('|s)(s|') [Rr]eply$",
"^Editor(’|s)(s|’) letter$",
"^Redaktoriaus žodis$",
"^DISCUSSION ON THE PRECEDING PAPER$",
"^Kōtō shōgaku shūshinsho jidōyō$",
"^Shōgaku nihon rekishi$",
"^(Theory of the flow of action currents in isolated myelinated nerve fibers).*$",
"^Préface$",
"^Occupational [Hh]ealth [Ss]ervices.$",
"^In Memoriam Professor Toshiyuki TAKESHIMA$",
"^Účetní závěrka ve vybraném podniku.*$",
"^Financial statements in selected company$",
"^Abdominal [Aa]ortic [Aa]neurysms.*$",
"^Pseudomyxoma peritonei$",
"^Kazalo autora$",
"(?i)^uvodna riječ$",
"^Motivace jako způsob vedení lidí$",
"^Motivation as a leadership$",
"^Polyfunkční dům$",
"^Multi\\-funkcional building$",
"^Podnikatelský plán$",
"(?i)^Podnikatelský záměr$",
"(?i)^Business Plan$",
"^Oceňování nemovitostí$",
"^Marketingová komunikace$",
"^Marketing communication$",
"^Sumario Analítico$",
"^Riječ uredništva$",
"^Savjetovanja i priredbe$",
"^Índice$",
"^(Starobosanski nadpisi).*$",
"^Vzdělávání pracovníků v organizaci$",
"^Staff training in organization$",
"^(Life Histories of North American Geometridae).*$",
"^Strategická analýza podniku$",
"^Strategic Analysis of an Enterprise$",
"^Sadržaj$",
"^Upute suradnicima$",
"^Rodinný dům$",
"(?i)^Fami(l)?ly house$",
"^Upute autorima$",
"^Strategic Analysis$",
"^Finanční analýza vybraného podniku$",
"^Finanční analýza$",
"^Riječ urednika$",
"(?i)^Content(s?)$",
"(?i)^Inhalt$",
"^Jinjō shōgaku shūshinsho jidōyō$",
"(?i)^Index$",
"^Chūgaku kokubun kyōkasho$",
"^Retrato de una mujer$",
"^Retrato de un hombre$",
"^Kōtō shōgaku dokuhon$",
"^Shotōka kokugo$",
"^Shōgaku dokuhon$",
"^Jinjō shōgaku kokugo dokuhon$",
"^Shinsei kokugo dokuhon$",
"^Teikoku dokuhon$",
"^Instructions to Authors$",
"^KİTAP TAHLİLİ$",
"^PRZEGLĄD PIŚMIENNICTWA$",
"(?i)^Presentación$",
"^İçindekiler$",
"(?i)^Tabl?e of contents$",
"^(CODICE DEL BEATO DE LOS REYES FERNANDO I Y SANCHA).*$",
"^(\\[MADRID\\. BIBL\\. NAC\\. N.*KING FERDINAND I.*FROM SAN ISIDORO DE LEON\\. FACUNDUS SCRIPSIT DATED.*\\]).*",
"^Editorial( Board)?$",
"(?i)^Editorial \\(English\\)$",
"^Editörden$",
"^(Corpus Oral Dialectal \\(COD\\)\\.).*$",
"^(Kiri Karl Morgensternile).*$",
"^(\\[Eksliibris Aleksandr).*\\]$",
"^(\\[Eksliibris Aleksandr).*$",
"^(Eksliibris Aleksandr).*$",
"^(Kiri A\\. de Vignolles).*$",
"^(2 kirja Karl Morgensternile).*$",
"^(Pirita kloostri idaosa arheoloogilised).*$",
"^(Kiri tundmatule).*$",
"^(Kiri Jenaer Allgemeine Literaturzeitung toimetusele).*$",
"^(Eksliibris Nikolai Birukovile).*$",
"^(Eksliibris Nikolai Issakovile).*$",
"^(WHP Cruise Summary Information of section).*$",
"^(Measurement of the top quark\\-pair production cross section with ATLAS in pp collisions at).*$",
"^(Measurement of the spin\\-dependent structure function).*",
"(?i)^.*authors['’′]? reply\\.?$",
"(?i)^.*authors['’′]? response\\.?$"
]
},
"synonyms": {}
}
}

12
dnet-dedup-test/src/test/resources/eu/dnetlib/pace/config/publication.current.conf.json
Unescape Escape View File

@ -6,10 +6,10 @@
"subEntityType": "resulttype",
"subEntityValue": "publication",
"orderField": "title",
"queueMaxSize": "2000",
"groupMaxSize": "100",
"maxChildren": "100",
"slidingWindowSize": "200",
"queueMaxSize": "5000",
"groupMaxSize": "2000",
"maxChildren": "1000",
"slidingWindowSize": "50",
"rootBuilder": [
"result",
"resultProject_outcome_isProducedBy",
@ -29,8 +29,7 @@
},
"pace": {
"clustering" : [
{ "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
{ "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
{ "name" : "wordsStatsSuffixPrefixChain", "fields" : [ "title" ], "params" : { "mod" : "10" } },
{ "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
],
"decisionTree": {
@ -129,6 +128,7 @@
],
"blacklists": {
"title": [
"(?i)^Data Management Plan",
"^Inside Front Cover$",
"(?i)^Poster presentations$",
"^THE ASSOCIATION AND THE GENERAL MEDICAL COUNCIL$",

4
dnet-dedup-test/src/test/resources/eu/dnetlib/pace/examples/publications.to.fix.json
View File

File diff suppressed because one or more lines are too long

6
dnet-dedup-test/src/test/resources/eu/dnetlib/pace/parameters/createSimRels_parameters.json
Unescape Escape View File

@ -22,5 +22,11 @@
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"paramDescription": "path of the dedup configuration",
"paramRequired": true
},
{
"paramName": "ut",
"paramLongName": "useTree",
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"paramRequired": true
}
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113
dnet-dedup.ipr
Unescape Escape View File

@ -0,0 +1,113 @@
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Licensed to the Apache Software Foundation (ASF) under one
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to you under the Apache License, Version 2.0 (the
"License"); you may not use this file except in compliance
with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing,
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Unescape Escape View File

@ -0,0 +1,418 @@
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Licensed to the Apache Software Foundation (ASF) under one
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to you under the Apache License, Version 2.0 (the
"License"); you may not use this file except in compliance
with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing,
software distributed under the License is distributed on an
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<option name="PATTERN" value="sun.*"/>
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<option name="PATTERN" value="junit.*"/>
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<activeType name="Application"/>
<configuration selected="false" default="true" type="Applet" factoryName="Applet">
<module name=""/>
<option name="MAIN_CLASS_NAME"/>
<option name="HTML_FILE_NAME"/>
<option name="HTML_USED" value="false"/>
<option name="WIDTH" value="400"/>
<option name="HEIGHT" value="300"/>
<option name="POLICY_FILE" value="$APPLICATION_HOME_DIR$/bin/appletviewer.policy"/>
<option name="VM_PARAMETERS"/>
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<configuration selected="false" default="true" type="Remote" factoryName="Remote">
<option name="USE_SOCKET_TRANSPORT" value="true"/>
<option name="SERVER_MODE" value="false"/>
<option name="SHMEM_ADDRESS" value="javadebug"/>
<option name="HOST" value="localhost"/>
<option name="PORT" value="5005"/>
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<configuration selected="false" default="true" type="Application" factoryName="Application">
<option name="MAIN_CLASS_NAME"/>
<option name="VM_PARAMETERS"/>
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<module name=""/>
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<configuration selected="false" default="true" type="JUnit" factoryName="JUnit">
<module name=""/>
<option name="PACKAGE_NAME"/>
<option name="MAIN_CLASS_NAME"/>
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<option name="TEST_OBJECT" value="class"/>
<option name="VM_PARAMETERS"/>
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<option name="WORKING_DIRECTORY" value="$PROJECT_DIR$"/>
<option name="ADDITIONAL_CLASS_PATH"/>
<option name="TEST_SEARCH_SCOPE">
<value defaultName="wholeProject"/>
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<component name="VcsManagerConfiguration">
<option name="ACTIVE_VCS_NAME" value="git"/>
<option name="STATE" value="0"/>
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<component name="VssConfiguration">
<CheckoutOptions>
<option name="COMMENT" value=""/>
<option name="DO_NOT_GET_LATEST_VERSION" value="false"/>
<option name="REPLACE_WRITABLE" value="false"/>
<option name="RECURSIVE" value="false"/>
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<CheckinOptions>
<option name="COMMENT" value=""/>
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<option name="RECURSIVE" value="false"/>
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<AddOptions>
<option name="COMMENT" value=""/>
<option name="STORE_ONLY_LATEST_VERSION" value="false"/>
<option name="CHECK_OUT_IMMEDIATELY" value="false"/>
<option name="FILE_TYPE" value="0"/>
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<UndocheckoutOptions>
<option name="MAKE_WRITABLE" value="false"/>
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<option name="CLIENT_PATH" value=""/>
<option name="SRCSAFEINI_PATH" value=""/>
<option name="USER_NAME" value=""/>
<option name="PWD" value=""/>
<option name="SHOW_CHECKOUT_OPTIONS" value="true"/>
<option name="SHOW_ADD_OPTIONS" value="true"/>
<option name="SHOW_UNDOCHECKOUT_OPTIONS" value="true"/>
<option name="SHOW_DIFF_OPTIONS" value="true"/>
<option name="SHOW_GET_OPTIONS" value="true"/>
<option name="USE_EXTERNAL_DIFF" value="false"/>
<option name="EXTERNAL_DIFF_PATH" value=""/>
<option name="REUSE_LAST_COMMENT" value="false"/>
<option name="PUT_FOCUS_INTO_COMMENT" value="false"/>
<option name="SHOW_CHECKIN_OPTIONS" value="true"/>
<option name="LAST_COMMIT_MESSAGE" value=""/>
<option name="CHECKIN_DIALOG_SPLITTER_PROPORTION" value="0.8"/>
</component>
<component name="CheckinPanelState"/>
<component name="WebViewSettings">
<webview flattenPackages="false" showMembers="false" autoscrollToSource="false"/>
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<component name="AppServerRunManager"/>
<component name="StarteamConfiguration">
<option name="SERVER" value=""/>
<option name="PORT" value="49201"/>
<option name="USER" value=""/>
<option name="PASSWORD" value=""/>
<option name="PROJECT" value=""/>
<option name="VIEW" value=""/>
<option name="ALTERNATIVE_WORKING_PATH" value=""/>
<option name="PUT_FOCUS_INTO_COMMENT" value="false"/>
<option name="SHOW_CHECKIN_OPTIONS" value="true"/>
<option name="LAST_COMMIT_MESSAGE" value=""/>
<option name="CHECKIN_DIALOG_SPLITTER_PROPORTION" value="0.8"/>
</component>
<component name="Cvs2Configuration">
<option name="ON_FILE_ADDING" value="0"/>
<option name="ON_FILE_REMOVING" value="0"/>
<option name="PRUNE_EMPTY_DIRECTORIES" value="true"/>
<option name="SHOW_UPDATE_OPTIONS" value="true"/>
<option name="SHOW_ADD_OPTIONS" value="true"/>
<option name="SHOW_REMOVE_OPTIONS" value="true"/>
<option name="MERGING_MODE" value="0"/>
<option name="MERGE_WITH_BRANCH1_NAME" value="HEAD"/>
<option name="MERGE_WITH_BRANCH2_NAME" value="HEAD"/>
<option name="RESET_STICKY" value="false"/>
<option name="CREATE_NEW_DIRECTORIES" value="true"/>
<option name="DEFAULT_TEXT_FILE_SUBSTITUTION" value="kv"/>
<option name="PROCESS_UNKNOWN_FILES" value="false"/>
<option name="PROCESS_DELETED_FILES" value="false"/>
<option name="SHOW_EDIT_DIALOG" value="true"/>
<option name="RESERVED_EDIT" value="false"/>
<option name="FILE_HISTORY_SPLITTER_PROPORTION" value="0.6"/>
<option name="SHOW_CHECKOUT_OPTIONS" value="true"/>
<option name="CHECKOUT_DATE_OR_REVISION_SETTINGS">
<value>
<option name="BRANCH" value=""/>
<option name="DATE" value=""/>
<option name="USE_BRANCH" value="false"/>
<option name="USE_DATE" value="false"/>
</value>
</option>
<option name="UPDATE_DATE_OR_REVISION_SETTINGS">
<value>
<option name="BRANCH" value=""/>
<option name="DATE" value=""/>
<option name="USE_BRANCH" value="false"/>
<option name="USE_DATE" value="false"/>
</value>
</option>
<option name="SHOW_CHANGES_REVISION_SETTINGS">
<value>
<option name="BRANCH" value=""/>
<option name="DATE" value=""/>
<option name="USE_BRANCH" value="false"/>
<option name="USE_DATE" value="false"/>
</value>
</option>
<option name="SHOW_OUTPUT" value="false"/>
<option name="SHOW_FILE_HISTORY_AS_TREE" value="false"/>
<option name="UPDATE_GROUP_BY_PACKAGES" value="false"/>
<option name="ADD_WATCH_INDEX" value="0"/>
<option name="REMOVE_WATCH_INDEX" value="0"/>
<option name="UPDATE_KEYWORD_SUBSTITUTION"/>
<option name="MAKE_NEW_FILES_READONLY" value="false"/>
<option name="SHOW_CORRUPTED_PROJECT_FILES" value="0"/>
<option name="TAG_AFTER_FILE_COMMIT" value="false"/>
<option name="TAG_AFTER_FILE_COMMIT_NAME" value=""/>
<option name="TAG_AFTER_PROJECT_COMMIT" value="false"/>
<option name="TAG_AFTER_PROJECT_COMMIT_NAME" value=""/>
<option name="PUT_FOCUS_INTO_COMMENT" value="false"/>
<option name="SHOW_CHECKIN_OPTIONS" value="true"/>
<option name="FORCE_NON_EMPTY_COMMENT" value="false"/>
<option name="LAST_COMMIT_MESSAGE" value=""/>
<option name="SAVE_LAST_COMMIT_MESSAGE" value="true"/>
<option name="CHECKIN_DIALOG_SPLITTER_PROPORTION" value="0.8"/>
<option name="OPTIMIZE_IMPORTS_BEFORE_PROJECT_COMMIT" value="false"/>
<option name="OPTIMIZE_IMPORTS_BEFORE_FILE_COMMIT" value="false"/>
<option name="REFORMAT_BEFORE_PROJECT_COMMIT" value="false"/>
<option name="REFORMAT_BEFORE_FILE_COMMIT" value="false"/>
<option name="FILE_HISTORY_DIALOG_COMMENTS_SPLITTER_PROPORTION" value="0.8"/>
<option name="FILE_HISTORY_DIALOG_SPLITTER_PROPORTION" value="0.5"/>
</component>
<component name="CvsTabbedWindow"/>
<component name="SvnConfiguration">
<option name="USER" value=""/>
<option name="PASSWORD" value=""/>
<option name="AUTO_ADD_FILES" value="0"/>
<option name="AUTO_DEL_FILES" value="0"/>
</component>
<component name="PerforceConfiguration">
<option name="PORT" value="magic:1666"/>
<option name="USER" value=""/>
<option name="PASSWORD" value=""/>
<option name="CLIENT" value=""/>
<option name="TRACE" value="false"/>
<option name="PERFORCE_STATUS" value="true"/>
<option name="CHANGELIST_OPTION" value="false"/>
<option name="SYSTEMROOT" value=""/>
<option name="P4_EXECUTABLE" value="p4"/>
<option name="SHOW_BRANCH_HISTORY" value="false"/>
<option name="GENERATE_COMMENT" value="false"/>
<option name="SYNC_OPTION" value="Sync"/>
<option name="PUT_FOCUS_INTO_COMMENT" value="false"/>
<option name="SHOW_CHECKIN_OPTIONS" value="true"/>
<option name="FORCE_NON_EMPTY_COMMENT" value="true"/>
<option name="LAST_COMMIT_MESSAGE" value=""/>
<option name="SAVE_LAST_COMMIT_MESSAGE" value="true"/>
<option name="CHECKIN_DIALOG_SPLITTER_PROPORTION" value="0.8"/>
<option name="OPTIMIZE_IMPORTS_BEFORE_PROJECT_COMMIT" value="false"/>
<option name="OPTIMIZE_IMPORTS_BEFORE_FILE_COMMIT" value="false"/>
<option name="REFORMAT_BEFORE_PROJECT_COMMIT" value="false"/>
<option name="REFORMAT_BEFORE_FILE_COMMIT" value="false"/>
<option name="FILE_HISTORY_DIALOG_COMMENTS_SPLITTER_PROPORTION" value="0.8"/>
<option name="FILE_HISTORY_DIALOG_SPLITTER_PROPORTION" value="0.5"/>
</component>
</project>

232
dnet-pace-core/src/main/java/eu/dnetlib/pace/util/BlockProcessorForTesting.java
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@ -0,0 +1,232 @@
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.model.Field;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.model.MapDocumentComparator;
import eu.dnetlib.pace.tree.JsonListMatch;
import eu.dnetlib.pace.tree.LevensteinTitle;
import eu.dnetlib.pace.tree.SizeMatch;
import eu.dnetlib.pace.tree.TitleVersionMatch;
import eu.dnetlib.pace.tree.support.FieldStats;
import eu.dnetlib.pace.tree.support.TreeProcessor;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import java.util.*;
public class BlockProcessorForTesting {
public static final List<String> accumulators= new ArrayList<>();
private static final Log log = LogFactory.getLog(eu.dnetlib.pace.util.BlockProcessorForTesting.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 BlockProcessorForTesting(DedupConfig dedupConf) {
this.dedupConf = dedupConf;
}
public void processSortedBlock(final String key, final List<MapDocument> documents, final Reporter context, boolean useTree) {
if (documents.size() > 1) {
// log.info("reducing key: '" + key + "' records: " + q.size());
process(prepare(documents), context, useTree);
} else {
context.incrementCounter(dedupConf.getWf().getEntityType(), "records per hash key = 1", 1);
}
}
public void process(final String key, final Iterable<MapDocument> documents, final Reporter context, boolean useTree) {
final Queue<MapDocument> q = prepare(documents);
if (q.size() > 1) {
// log.info("reducing key: '" + key + "' records: " + q.size());
process(simplifyQueue(q, key, context), context, useTree);
} 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, boolean useTree) {
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() ? "" : fieldsPivot.stringValue();
if (fieldPivot != null) {
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)) {
// if (new TreeProcessor(dedupConf).compare(pivot, curr) == true && publicationCompare(pivot, curr, dedupConf) == false)
// emitOutput(true, idPivot, idCurr, context);
//
if(useTree)
emitOutput(new TreeProcessor(dedupConf).compare(pivot, curr), idPivot, idCurr, context);
else
emitOutput(publicationCompare(pivot, curr, dedupConf), idPivot, idCurr, context);
}
}
}
}
}
private boolean publicationCompare(MapDocument a, MapDocument b, DedupConfig config) {
double score = 0.0;
//LAYER 1 - comparison of the PIDs json lists
Map<String, String> params = new HashMap<>();
params.put("jpath_value", "$.value");
params.put("jpath_classid", "$.qualifier.classid");
JsonListMatch jsonListMatch = new JsonListMatch(params);
double result = jsonListMatch.compare(a.getFieldMap().get("pid"), b.getFieldMap().get("pid"), config);
if (result >= 0.5) //if the result of the comparison is greater than the threshold
score += 10.0; //high score because it should match when the first condition is satisfied
else
score += 0.0;
//LAYER 2 - comparison of the title version and the size of the authors lists
TitleVersionMatch titleVersionMatch = new TitleVersionMatch(params);
double result1 = titleVersionMatch.compare(a.getFieldMap().get("title"), b.getFieldMap().get("title"), config);
SizeMatch sizeMatch = new SizeMatch(params);
double result2 = sizeMatch.compare(a.getFieldMap().get("authors"), b.getFieldMap().get("authors"), config);
if (Math.min(result1, result2) != 0)
score+=0;
else
score-=2;
//LAYER 3 - computation of levenshtein on titles
LevensteinTitle levensteinTitle = new LevensteinTitle(params);
double result3 = levensteinTitle.compare(a.getFieldMap().get("title"), b.getFieldMap().get("title"), config);
score += Double.isNaN(result3)?0.0:result3;
return score >= 0.99;
}
private void emitOutput(final boolean result, final String idPivot, final String idCurr, final Reporter context) {
if (result) {
writeSimilarity(context, idPivot, idCurr);
context.incrementCounter(dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)", 1);
} else {
context.incrementCounter(dedupConf.getWf().getEntityType(), "d < " + dedupConf.getWf().getThreshold(), 1);
}
}
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);
}
}

17
dnet-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java
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@ -47,7 +47,7 @@ public class ClusteringFunctionTest extends AbstractPaceTest {
@Test
public void testNgramPairs() {
params.put("ngramLen", 3);
params.put("max", 1);
params.put("max", 2);
final ClusteringFunction np = new NgramPairs(params);
@ -59,7 +59,7 @@ public class ClusteringFunctionTest extends AbstractPaceTest {
@Test
public void testSortedNgramPairs() {
params.put("ngramLen", 3);
params.put("max", 1);
params.put("max", 2);
final ClusteringFunction np = new SortedNgramPairs(params);
@ -70,6 +70,11 @@ public class ClusteringFunctionTest extends AbstractPaceTest {
final String s2 = "Pisa University";
System.out.println(s2);
System.out.println(np.apply(conf, Lists.newArrayList(title(s2))));
final String s3 = "Parco Tecnologico Agroalimentare Umbria";
System.out.println(s3);
System.out.println(np.apply(conf, Lists.newArrayList(title(s3))));
}
@Test
@ -132,6 +137,14 @@ public class ClusteringFunctionTest extends AbstractPaceTest {
System.out.println(s);
System.out.println(sp.apply(conf, Lists.newArrayList(title(s))));
s = "JRC Open Power Plants Database (JRC-PPDB-OPEN)";
System.out.println(s);
System.out.println(sp.apply(conf, Lists.newArrayList(title(s))));
s = "JRC Open Power Plants Database";
System.out.println(s);
System.out.println(sp.apply(conf, Lists.newArrayList(title(s))));
}
@Test

38
dnet-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
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@ -14,7 +14,7 @@ import eu.dnetlib.pace.common.AbstractPaceFunctions;
import java.util.HashMap;
import java.util.Map;
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
public class ComparatorTest extends AbstractPaceFunctions {
private Map<String, String> params;
@ -119,6 +119,42 @@ public class ComparatorTest extends AbstractPaceFunctions {
}
@Test
public void jaroWinklerTest() {
final JaroWinkler jaroWinkler = new JaroWinkler(params);
double result = jaroWinkler.distance("Sofia", "Sofìa", conf);
System.out.println("result = " + result);
result = jaroWinkler.distance("University of Victoria Dataverse", "University of Windsor Dataverse", conf);
System.out.println("result = " + result);
result = jaroWinkler.distance("Victoria Dataverse", "Windsor Dataverse", conf);
System.out.println("result = " + result);
final Levenstein levenstein = new Levenstein(params);
result = levenstein.distance("Victoria", "Windsor", conf);
System.out.println("result = " + result);
//University of Victoria Dataverse
//University of British Columbia Dataverse
//University of Windsor Dataverse
//University of Waterloo Dataverse
//University of Toronto Dataverse
//University of Ottawa Dataverse
}
@Test
public void levensteinTitleTest() {
final LevensteinTitle levensteinTitle = new LevensteinTitle(params);
double result = levensteinTitle.distance("JRC: Open Power Plants Database", "JRC Open Power Plants Database (JRC-PPDB-OPEN)", conf);
System.out.println("result = " + result);
}
@Test
public void jsonListMatchTest(){

18
dnet-pace-core/src/test/java/eu/dnetlib/pace/config/ConfigTest.java
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@ -2,6 +2,7 @@ package eu.dnetlib.pace.config;
import eu.dnetlib.pace.AbstractPaceTest;
import eu.dnetlib.pace.clustering.BlacklistAwareClusteringCombiner;
import eu.dnetlib.pace.clustering.ClusteringClass;
import eu.dnetlib.pace.clustering.ClusteringCombiner;
import eu.dnetlib.pace.model.Field;
@ -128,6 +129,23 @@ public class ConfigTest extends AbstractPaceTest {
assertEquals("doi", combine[2].split(":")[1]);
}
@Test
public void filterAndCombineTest() {
DedupConfig dedupConf = DedupConfig.load(readFromClasspath("pub.prod.conf.json"));
final String json = readFromClasspath("publication.example.json");
final MapDocument mapDocument = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, json);
Collection<String> strings = BlacklistAwareClusteringCombiner.filterAndCombine(mapDocument, dedupConf);
for (String s: strings) {
System.out.println("s = " + s);
}
}
@Test
public void crossCompareTest() {

402
dnet-pace-core/src/test/resources/eu/dnetlib/pace/config/pub.prod.conf.json
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@ -0,0 +1,402 @@
{
"wf": {
"threshold": "0.99",
"dedupRun": "001",
"entityType": "result",
"subEntityType": "resulttype",
"subEntityValue": "publication",
"orderField": "title",
"queueMaxSize": "200",
"groupMaxSize": "100",
"maxChildren": "100",
"slidingWindowSize": "50",
"rootBuilder": [
"result",
"resultProject_outcome_isProducedBy",
"resultResult_publicationDataset_isRelatedTo",
"resultResult_similarity_isAmongTopNSimilarDocuments",
"resultResult_similarity_hasAmongTopNSimilarDocuments",
"resultOrganization_affiliation_isAffiliatedWith",
"resultResult_part_hasPart",
"resultResult_part_isPartOf",
"resultResult_supplement_isSupplementTo",
"resultResult_supplement_isSupplementedBy",
"resultResult_version_isVersionOf"
],
"includeChildren": "true",
"maxIterations": 20,
"idPath": "$.id"
},
"pace": {
"clustering" : [
{ "name" : "wordsStatsSuffixPrefixChain", "fields" : [ "title" ], "params" : { "mod" : "10" } },
{ "name" : "lowercase", "fields" : [ "doi", "altdoi" ], "params" : { "collapseOn:pid": "0"} }
],
"decisionTree": {
"start": {
"fields": [
{
"field": "pid",
"comparator": "jsonListMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {
"jpath_value": "$.value",
"jpath_classid": "$.qualifier.classid"
}
},
{
"field": "pid",
"comparator": "jsonListMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {
"jpath_value": "$.value",
"jpath_classid": "$.qualifier.classid",
"crossCompare": "alternateid"
}
}
],
"threshold": 0.5,
"aggregation": "MAX",
"positive": "layer1",
"negative": "layer2",
"undefined": "layer2",
"ignoreUndefined": "true"
},
"layer1": {
"fields": [
{
"field": "title",
"comparator": "levensteinTitle",
"weight": 1.0,
"countIfUndefined": "true",
"params": {}
}
],
"threshold": 0.9,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
},
"layer2": {
"fields": [
{
"field": "title",
"comparator": "titleVersionMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
},
{
"field": "authors",
"comparator": "sizeMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1.0,
"aggregation": "AND",
"positive": "layer3",
"negative": "NO_MATCH",
"undefined": "layer3",
"ignoreUndefined": "false"
},
"layer3": {
"fields": [
{
"field": "title",
"comparator": "levensteinTitle",
"weight": 1.0,
"countIfUndefined": "true",
"params": {}
}
],
"threshold": 0.99,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
}
},
"model": [
{
"name": "doi",
"type": "String",
"path": "$.instance.pid[?(@.qualifier.classid == 'doi')].value"
},
{
"name": "altdoi",
"type": "String",
"path": "$.instance.alternateIdentifier[?(@.qualifier.classid == 'doi')].value"
},
{
"name": "pid",
"type": "JSON",
"path": "$.instance.pid",
"overrideMatch": "true"
},
{
"name": "alternateid",
"type": "JSON",
"path": "$.instance.alternateIdentifier",
"overrideMatch": "true"
},
{
"name": "title",
"type": "String",
"path": "$.title[?(@.qualifier.classid == 'main title')].value",
"length": 250,
"size": 5
},
{
"name": "authors",
"type": "List",
"path": "$.author[*].fullname",
"size": 200
},
{
"name": "resulttype",
"type": "String",
"path": "$.resulttype.classid"
}
],
"blacklists": {
"title": [
"(?i)^Data Management Plan",
"^Inside Front Cover$",
"(?i)^Poster presentations$",
"^THE ASSOCIATION AND THE GENERAL MEDICAL COUNCIL$",
"^Problems with perinatal pathology\\.?$",
"(?i)^Cases? of Puerperal Convulsions$",
"(?i)^Operative Gyna?ecology$",
"(?i)^Mind the gap\\!?\\:?$",
"^Chronic fatigue syndrome\\.?$",
"^Cartas? ao editor Letters? to the Editor$",
"^Note from the Editor$",
"^Anesthesia Abstract$",
"^Annual report$",
"(?i)^“?THE RADICAL PREVENTION OF VENEREAL DISEASE\\.?”?$",
"(?i)^Graph and Table of Infectious Diseases?$",
"^Presentation$",
"(?i)^Reviews and Information on Publications$",
"(?i)^PUBLIC HEALTH SERVICES?$",
"(?i)^COMBINED TEXT-?BOOK OF OBSTETRICS AND GYN(Æ|ae)COLOGY$",
"(?i)^Adrese autora$",
"(?i)^Systematic Part .*\\. Catalogus Fossilium Austriae, Band 2: Echinoidea neogenica$",
"(?i)^Acknowledgement to Referees$",
"(?i)^Behçet's disease\\.?$",
"(?i)^Isolation and identification of restriction endonuclease.*$",
"(?i)^CEREBROVASCULAR DISEASES?.?$",
"(?i)^Screening for abdominal aortic aneurysms?\\.?$",
"^Event management$",
"(?i)^Breakfast and Crohn's disease.*\\.?$",
"^Cálculo de concentraciones en disoluciones acuosas. Ejercicio interactivo\\..*\\.$",
"(?i)^Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of Autism spectrum disorders?\\.?$",
"^Gushi hakubutsugaku$",
"^Starobosanski nadpisi u Bosni i Hercegovini \\(.*\\)$",
"^Intestinal spirocha?etosis$",
"^Treatment of Rodent Ulcer$",
"(?i)^\\W*Cloud Computing\\W*$",
"^Compendio mathematico : en que se contienen todas las materias mas principales de las Ciencias que tratan de la cantidad$",
"^Free Communications, Poster Presentations: Session [A-F]$",
"^“The Historical Aspects? of Quackery\\.?”$",
"^A designated centre for people with disabilities operated by St John of God Community Services (Limited|Ltd), Louth$",
"^P(er|re)-Mile Premiums for Auto Insurance\\.?$",
"(?i)^Case Report$",
"^Boletín Informativo$",
"(?i)^Glioblastoma Multiforme$",
"(?i)^Nuevos táxones animales descritos en la península Ibérica y Macaronesia desde 1994 \\(.*\\)$",
"^Zaměstnanecké výhody$",
"(?i)^The Economics of Terrorism and Counter-Terrorism: A Survey \\(Part .*\\)$",
"(?i)^Carotid body tumours?\\.?$",
"(?i)^\\[Españoles en Francia : La condición Emigrante.*\\]$",
"^Avant-propos$",
"(?i)^St\\. Patrick's Cathedral, Dublin, County Dublin - Head(s)? and Capital(s)?$",
"(?i)^St\\. Patrick's Cathedral, Dublin, County Dublin - Bases?$",
"(?i)^PUBLIC HEALTH VERSUS THE STATE$",
"^Viñetas de Cortázar$",
"(?i)^Search for heavy neutrinos and W(\\[|_|\\(|_\\{|-)?R(\\]|\\)|\\})? bosons with right-handed couplings in a left-right symmetric model in pp collisions at.*TeV(\\.)?$",
"(?i)^Measurement of the pseudorapidity and centrality dependence of the transverse energy density in Pb(-?)Pb collisions at.*tev(\\.?)$",
"(?i)^Search for resonances decaying into top-quark pairs using fully hadronic decays in pp collisions with ATLAS at.*TeV$",
"(?i)^Search for neutral minimal supersymmetric standard model Higgs bosons decaying to tau pairs in pp collisions at.*tev$",
"(?i)^Relatório de Estágio (de|em) Angiologia e Cirurgia Vascular$",
"^Aus der AGMB$",
"^Znanstveno-stručni prilozi$",
"(?i)^Zhodnocení finanční situace podniku a návrhy na zlepšení$",
"(?i)^Evaluation of the Financial Situation in the Firm and Proposals to its Improvement$",
"(?i)^Hodnocení finanční situace podniku a návrhy na její zlepšení$",
"^Finanční analýza podniku$",
"^Financial analysis( of business)?$",
"(?i)^Textbook of Gyn(a)?(Æ)?(e)?cology$",
"^Jikken nihon shūshinsho$",
"(?i)^CORONER('|s)(s|') INQUESTS$",
"(?i)^(Μελέτη παραγόντων )?risk management( για ανάπτυξη και εφαρμογή ενός πληροφοριακού συστήματος| και ανάπτυξη συστήματος)?$",
"(?i)^Consultants' contract(s)?$",
"(?i)^Upute autorima$",
"(?i)^Bijdrage tot de Kennis van den Godsdienst der Dajaks van Lan(d|f)ak en Tajan$",
"^Joshi shin kokubun$",
"^Kōtō shōgaku dokuhon nōson'yō$",
"^Jinjō shōgaku shōka$",
"^Shōgaku shūjichō$",
"^Nihon joshi dokuhon$",
"^Joshi shin dokuhon$",
"^Chūtō kanbun dokuhon$",
"^Wabun dokuhon$",
"(?i)^(Analysis of economy selected village or town|Rozbor hospodaření vybrané obce či města)$",
"(?i)^cardiac rehabilitation$",
"(?i)^Analytical summary$",
"^Thesaurus resolutionum Sacrae Congregationis Concilii$",
"(?i)^Sumario analítico(\\s{1})?(Analitic summary)?$",
"^Prikazi i osvrti$",
"^Rodinný dům s provozovnou$",
"^Family house with an establishment$",
"^Shinsei chūtō shin kokugun$",
"^Pulmonary alveolar proteinosis(\\.?)$",
"^Shinshū kanbun$",
"^Viñeta(s?) de Rodríguez$",
"(?i)^RUBRIKA UREDNIKA$",
"^A Matching Model of the Academic Publication Market$",
"^Yōgaku kōyō$",
"^Internetový marketing$",
"^Internet marketing$",
"^Chūtō kokugo dokuhon$",
"^Kokugo dokuhon$",
"^Antibiotic Cover for Dental Extraction(s?)$",
"^Strategie podniku$",
"^Strategy of an Enterprise$",
"(?i)^respiratory disease(s?)(\\.?)$",
"^Award(s?) for Gallantry in Civil Defence$",
"^Podniková kultura$",
"^Corporate Culture$",
"^Severe hyponatraemia in hospital inpatient(s?)(\\.?)$",
"^Pracovní motivace$",
"^Work Motivation$",
"^Kaitei kōtō jogaku dokuhon$",
"^Konsolidovaná účetní závěrka$",
"^Consolidated Financial Statements$",
"(?i)^intracranial tumour(s?)$",
"^Climate Change Mitigation Options and Directed Technical Change: A Decentralized Equilibrium Analysis$",
"^\\[CERVECERIAS MAHOU(\\.|\\:) INTERIOR\\] \\[Material gráfico\\]$",
"^Housing Market Dynamics(\\:|\\.) On the Contribution of Income Shocks and Credit Constraint(s?)$",
"^\\[Funciones auxiliares de la música en Radio París,.*\\]$",
"^Úroveň motivačního procesu jako způsobu vedení lidí$",
"^The level of motivation process as a leadership$",
"^Pay-beds in N(\\.?)H(\\.?)S(\\.?) Hospitals$",
"(?i)^news and events$",
"(?i)^NOVOSTI I DOGAĐAJI$",
"^Sansū no gakushū$",
"^Posouzení informačního systému firmy a návrh změn$",
"^Information System Assessment and Proposal for ICT Modification$",
"^Stresové zatížení pracovníků ve vybrané profesi$",
"^Stress load in a specific job$",
"^Sunday: Poster Sessions, Pt.*$",
"^Monday: Poster Sessions, Pt.*$",
"^Wednesday: Poster Sessions, Pt.*",
"^Tuesday: Poster Sessions, Pt.*$",
"^Analýza reklamy$",
"^Analysis of advertising$",
"^Shōgaku shūshinsho$",
"^Shōgaku sansū$",
"^Shintei joshi kokubun$",
"^Taishō joshi kokubun dokuhon$",
"^Joshi kokubun$",
"^Účetní uzávěrka a účetní závěrka v ČR$",
"(?i)^The \"?Causes\"? of Cancer$",
"^Normas para la publicación de artículos$",
"^Editor('|s)(s|') [Rr]eply$",
"^Editor(’|s)(s|’) letter$",
"^Redaktoriaus žodis$",
"^DISCUSSION ON THE PRECEDING PAPER$",
"^Kōtō shōgaku shūshinsho jidōyō$",
"^Shōgaku nihon rekishi$",
"^(Theory of the flow of action currents in isolated myelinated nerve fibers).*$",
"^Préface$",
"^Occupational [Hh]ealth [Ss]ervices.$",
"^In Memoriam Professor Toshiyuki TAKESHIMA$",
"^Účetní závěrka ve vybraném podniku.*$",
"^Financial statements in selected company$",
"^Abdominal [Aa]ortic [Aa]neurysms.*$",
"^Pseudomyxoma peritonei$",
"^Kazalo autora$",
"(?i)^uvodna riječ$",
"^Motivace jako způsob vedení lidí$",
"^Motivation as a leadership$",
"^Polyfunkční dům$",
"^Multi\\-funkcional building$",
"^Podnikatelský plán$",
"(?i)^Podnikatelský záměr$",
"(?i)^Business Plan$",
"^Oceňování nemovitostí$",
"^Marketingová komunikace$",
"^Marketing communication$",
"^Sumario Analítico$",
"^Riječ uredništva$",
"^Savjetovanja i priredbe$",
"^Índice$",
"^(Starobosanski nadpisi).*$",
"^Vzdělávání pracovníků v organizaci$",
"^Staff training in organization$",
"^(Life Histories of North American Geometridae).*$",
"^Strategická analýza podniku$",
"^Strategic Analysis of an Enterprise$",
"^Sadržaj$",
"^Upute suradnicima$",
"^Rodinný dům$",
"(?i)^Fami(l)?ly house$",
"^Upute autorima$",
"^Strategic Analysis$",
"^Finanční analýza vybraného podniku$",
"^Finanční analýza$",
"^Riječ urednika$",
"(?i)^Content(s?)$",
"(?i)^Inhalt$",
"^Jinjō shōgaku shūshinsho jidōyō$",
"(?i)^Index$",
"^Chūgaku kokubun kyōkasho$",
"^Retrato de una mujer$",
"^Retrato de un hombre$",
"^Kōtō shōgaku dokuhon$",
"^Shotōka kokugo$",
"^Shōgaku dokuhon$",
"^Jinjō shōgaku kokugo dokuhon$",
"^Shinsei kokugo dokuhon$",
"^Teikoku dokuhon$",
"^Instructions to Authors$",
"^KİTAP TAHLİLİ$",
"^PRZEGLĄD PIŚMIENNICTWA$",
"(?i)^Presentación$",
"^İçindekiler$",
"(?i)^Tabl?e of contents$",
"^(CODICE DEL BEATO DE LOS REYES FERNANDO I Y SANCHA).*$",
"^(\\[MADRID\\. BIBL\\. NAC\\. N.*KING FERDINAND I.*FROM SAN ISIDORO DE LEON\\. FACUNDUS SCRIPSIT DATED.*\\]).*",
"^Editorial( Board)?$",
"(?i)^Editorial \\(English\\)$",
"^Editörden$",
"^(Corpus Oral Dialectal \\(COD\\)\\.).*$",
"^(Kiri Karl Morgensternile).*$",
"^(\\[Eksliibris Aleksandr).*\\]$",
"^(\\[Eksliibris Aleksandr).*$",
"^(Eksliibris Aleksandr).*$",
"^(Kiri A\\. de Vignolles).*$",
"^(2 kirja Karl Morgensternile).*$",
"^(Pirita kloostri idaosa arheoloogilised).*$",
"^(Kiri tundmatule).*$",
"^(Kiri Jenaer Allgemeine Literaturzeitung toimetusele).*$",
"^(Eksliibris Nikolai Birukovile).*$",
"^(Eksliibris Nikolai Issakovile).*$",
"^(WHP Cruise Summary Information of section).*$",
"^(Measurement of the top quark\\-pair production cross section with ATLAS in pp collisions at).*$",
"^(Measurement of the spin\\-dependent structure function).*",
"(?i)^.*authors['’′]? reply\\.?$",
"(?i)^.*authors['’′]? response\\.?$"
]
},
"synonyms": {}
}
}

1
dnet-pace-core/src/test/resources/eu/dnetlib/pace/config/publication.example.json
Unescape Escape View File

@ -0,0 +1 @@
{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "pid": [], "oaiprovenance": {"originDescription": {"metadataNamespace": "", "harvestDate": "2021-06-10T10:03:36.091Z", "baseURL": "file%3A%2F%2F%2Fvar%2Flib%2Fdnet%2Fdata%2Fsygma%2Fnew_ingestion%2Fcrossref", "datestamp": "", "altered": true, "identifier": ""}}, "relevantdate": [], "contributor": [], "id": "50|sygma_______::3bbb03e6ec8df0d219b2d2165ea1d446", "subject": [], "lastupdatetimestamp": 1628684944004, "author": [{"surname": "Pan", "fullname": "Pan, Mengwu", "pid": [], "name": "Mengwu", "rank": 1}, {"surname": "Blattner", "fullname": "Blattner, Christine", "pid": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "qualifier": {"classid": "orcid_pending", "classname": "Open Researcher and Contributor ID", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "0000-0002-7250-5273"}], "name": "Christine", "rank": 2}], "collectedfrom": [{"value": "Sygma", "key": "10|openaire____::a8db6f6b2ce4fe72e8b2314a9a93e7d9"}], "instance": [{"refereed": {"classid": "UNKNOWN", "classname": "Unknown", "schemename": "dnet:review_levels", "schemeid": "dnet:review_levels"}, "hostedby": {"value": "Cancers", "key": "10|issn__online::69ba871b903253074dcf4054e619afff"}, "license": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "https://creativecommons.org/licenses/by/4.0/"}, "url": ["http://dx.doi.org/10.3390/cancers13040745"], "pid": [], "distributionlocation": "", "alternateIdentifier": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.3390/cancers13040745"}], "collectedfrom": {"value": "Sygma", "key": "10|openaire____::a8db6f6b2ce4fe72e8b2314a9a93e7d9"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "instancetype": {"classid": "0001", "classname": "Article", "schemename": "dnet:publication_resource", "schemeid": "dnet:publication_resource"}}], "resulttype": {"classid": "publication", "classname": "publication", "schemename": "dnet:result_typologies", "schemeid": "dnet:result_typologies"}, "dateofcollection": "2021-06-10T10:03:36.091Z", "fulltext": [], "dateoftransformation": "2021-07-20T16:59:21.682Z", "description": [], "format": [], "journal": {"issnPrinted": "", "vol": "13", "dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "name": "Cancers", "iss": "4", "sp": "745", "edition": "", "issnOnline": "2072-6694", "ep": "", "issnLinking": ""}, "coverage": [], "externalReference": [], "language": {"classid": "eng", "classname": "English", "schemename": "dnet:languages", "schemeid": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": ["10.3390/cancers13040745", "50|sygma_______::3bbb03e6ec8df0d219b2d2165ea1d446"], "source": [], "context": [], "title": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "Regulation of p53 by E3s"}]}

18
pom.xml
Unescape Escape View File

@ -228,7 +228,8 @@
<google.guava.version>15.0</google.guava.version>
<spark.version>2.2.0</spark.version>
<jackson.version>2.9.6</jackson.version>
<!--<jackson.version>2.9.6</jackson.version>-->
<jackson.version>2.6.5</jackson.version>
<mockito-core.version>3.3.3</mockito-core.version>
<commons.lang.version>3.5</commons.lang.version>
@ -260,7 +261,7 @@
<oozie.use.system.libpath>true</oozie.use.system.libpath>
<properties.maven.plugin.version>2.0.1</properties.maven.plugin.version>
<junit-jupiter.version>5.6.1</junit-jupiter.version>
<maven.dependency.eu.dnetlib.dhp.dhp-build-assembly-resources.jar.path>../dhp-build/dhp-build-assembly-resources/target/dhp-build-assembly-resources-4.0.6-SNAPSHOT.jar</maven.dependency.eu.dnetlib.dhp.dhp-build-assembly-resources.jar.path>
<maven.dependency.eu.dnetlib.dhp.dhp-build-assembly-resources.jar.path>../dhp-build/dhp-build-assembly-resources/target/dhp-build-assembly-resources-4.1.8-SNAPSHOT.jar</maven.dependency.eu.dnetlib.dhp.dhp-build-assembly-resources.jar.path>
</properties>
@ -409,6 +410,19 @@
<version>2.4.0</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>3.3.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>3.3.3</version>
<scope>test</scope>
</dependency>
</dependencies>

11
release.properties
Unescape Escape View File

@ -1,11 +0,0 @@
#release configuration
#Tue Sep 29 12:04:49 CEST 2020
scm.tagNameFormat=@{project.artifactId}-@{project.version}
pushChanges=true
scm.url=scm\:git\:https\://code-repo.d4science.org/D-Net/dnet-dedup.git
preparationGoals=clean verify
projectVersionPolicyId=default
remoteTagging=true
scm.commentPrefix=[maven-release-plugin]
exec.snapshotReleasePluginAllowed=false
completedPhase=check-poms
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