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implemented DedupRecord factory with the merge of publications

This commit is contained in:
Sandro La Bruzzo 2019-12-11 15:43:24 +01:00
parent 4b66b471a4
commit abd9034da0
30 changed files with 686 additions and 262 deletions
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3
.gitignore vendored
View File

@ -18,4 +18,5 @@
/*/build
/build
spark-warehouse
/dhp-workflows/dhp-graph-mapper/job-override.properties
/*/*/job-override.properties

10
dhp-common/pom.xml
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@ -17,6 +17,10 @@
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
@ -29,21 +33,15 @@
<groupId>javax.persistence</groupId>
<artifactId>javax.persistence-api</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/com.rabbitmq/amqp-client -->
<dependency>
<groupId>com.rabbitmq</groupId>
<artifactId>amqp-client</artifactId>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
</dependency>
</dependencies>
</project>

41
dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java
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@ -2,17 +2,25 @@ package eu.dnetlib.dhp.application;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.cli.*;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.Serializable;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
import java.io.StringWriter;
import java.util.*;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;
import java.util.zip.Inflater;
public class ArgumentApplicationParser implements Serializable {
private final Options options = new Options();
private final Map<String, String> objectMap = new HashMap<>();
private final List<String> compressedValues = new ArrayList<>();
public ArgumentApplicationParser(final String json_configuration) throws Exception {
final ObjectMapper mapper = new ObjectMapper();
final OptionsParameter[] configuration = mapper.readValue(json_configuration, OptionsParameter[].class);
@ -29,6 +37,9 @@ public class ArgumentApplicationParser implements Serializable {
final Option o = new Option(conf.getParamName(), true, conf.getParamDescription());
o.setLongOpt(conf.getParamLongName());
o.setRequired(conf.isParamRequired());
if (conf.isCompressed()) {
compressedValues.add(conf.getParamLongName());
}
return o;
}).forEach(options::addOption);
@ -38,10 +49,32 @@ public class ArgumentApplicationParser implements Serializable {
}
public static String decompressValue(final String abstractCompressed) {
try {
byte[] byteArray = Base64.decodeBase64(abstractCompressed.getBytes());
GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(byteArray));
final StringWriter stringWriter = new StringWriter();
IOUtils.copy(gis, stringWriter);
return stringWriter.toString();
} catch (Throwable e) {
System.out.println("Wrong value to decompress:" + abstractCompressed);
throw new RuntimeException(e);
}
}
public static String compressArgument(final String value) throws Exception{
ByteArrayOutputStream out = new ByteArrayOutputStream();
GZIPOutputStream gzip = new GZIPOutputStream(out);
gzip.write(value.getBytes());
gzip.close();
return java.util.Base64.getEncoder().encodeToString(out.toByteArray());
}
public void parseArgument(final String[] args) throws Exception {
CommandLineParser parser = new BasicParser();
CommandLine cmd = parser.parse(options, args);
Arrays.stream(cmd.getOptions()).forEach(it -> objectMap.put(it.getLongOpt(), it.getValue()));
Arrays.stream(cmd.getOptions()).forEach(it -> objectMap.put(it.getLongOpt(), compressedValues.contains(it.getLongOpt())? decompressValue(it.getValue()): it.getValue()));
}
public String get(final String key) {

9
dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java
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@ -7,6 +7,7 @@ public class OptionsParameter {
private String paramLongName;
private String paramDescription;
private boolean paramRequired;
private boolean compressed;
public OptionsParameter() {
}
@ -26,4 +27,12 @@ public class OptionsParameter {
public boolean isParamRequired() {
return paramRequired;
}
public boolean isCompressed() {
return compressed;
}
public void setCompressed(boolean compressed) {
this.compressed = compressed;
}
}

10
dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java
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@ -3,6 +3,10 @@ package eu.dnetlib.dhp.application;
import org.apache.commons.io.IOUtils;
import org.junit.Test;
import java.io.ByteArrayOutputStream;
import java.util.Base64;
import java.util.zip.GZIPOutputStream;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
@ -24,6 +28,7 @@ public class ArgumentApplicationParserTest {
"-ro", "value7",
"-rr", "value8",
"-w", "value9",
"-cc", ArgumentApplicationParser.compressArgument(jsonConfiguration)
});
assertNotNull(parser.get("hdfsPath"));
assertNotNull(parser.get("apidescriptor"));
@ -45,7 +50,12 @@ public class ArgumentApplicationParserTest {
assertEquals("value7", parser.get("rabbitOngoingQueue"));
assertEquals("value8", parser.get("rabbitReportQueue"));
assertEquals("value9", parser.get("workflowId"));
assertEquals(jsonConfiguration, parser.get("ccCoco"));
}
}

21
dhp-common/src/test/resources/eu/dnetlib/application/parameters.json
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@ -1,12 +1,13 @@
[
{"paramName":"p", "paramLongName":"hdfsPath", "paramDescription": "the path where storing the sequential file", "paramRequired": true},
{"paramName":"a", "paramLongName":"apidescriptor", "paramDescription": "the JSON encoding of the API Descriptor", "paramRequired": true},
{"paramName":"n", "paramLongName":"namenode", "paramDescription": "the Name Node URI", "paramRequired": true},
{"paramName":"u", "paramLongName":"userHDFS", "paramDescription": "the user wich create the hdfs seq file", "paramRequired": true},
{"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true},
{"paramName":"rp", "paramLongName":"rabbitPassWord", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true},
{"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true},
{"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true},
{"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true},
{"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true}
{"paramName":"p", "paramLongName":"hdfsPath", "paramDescription": "the path where storing the sequential file", "paramRequired": true},
{"paramName":"a", "paramLongName":"apidescriptor", "paramDescription": "the JSON encoding of the API Descriptor", "paramRequired": true},
{"paramName":"n", "paramLongName":"namenode", "paramDescription": "the Name Node URI", "paramRequired": true},
{"paramName":"u", "paramLongName":"userHDFS", "paramDescription": "the user wich create the hdfs seq file", "paramRequired": true},
{"paramName":"ru", "paramLongName":"rabbitUser", "paramDescription": "the user to connect with RabbitMq for messaging", "paramRequired": true},
{"paramName":"rp", "paramLongName":"rabbitPassWord", "paramDescription": "the password to connect with RabbitMq for messaging", "paramRequired": true},
{"paramName":"rh", "paramLongName":"rabbitHost", "paramDescription": "the host of the RabbitMq server", "paramRequired": true},
{"paramName":"ro", "paramLongName":"rabbitOngoingQueue", "paramDescription": "the name of the ongoing queue", "paramRequired": true},
{"paramName":"rr", "paramLongName":"rabbitReportQueue", "paramDescription": "the name of the report queue", "paramRequired": true},
{"paramName":"w", "paramLongName":"workflowId", "paramDescription": "the identifier of the dnet Workflow", "paramRequired": true},
{"paramName":"cc", "paramLongName":"ccCoco", "paramDescription": "the identifier of the dnet Workflow", "compressed":true,"paramRequired": true}
]

27
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java
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@ -84,4 +84,31 @@ public class Instance implements Serializable {
public void setDateofacceptance(Field<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public String toComparableString(){
return String.format("%s::%s::%s::%s",
hostedby != null && hostedby.getKey()!= null ? hostedby.getKey().toLowerCase() : "",
accessright!= null && accessright.getClassid()!= null ? accessright.getClassid() : "",
instancetype!= null && instancetype.getClassid()!= null ? instancetype.getClassid() : "",
url != null ? url:"");
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Instance other = (Instance) obj;
return toComparableString()
.equals(other.toComparableString());
}
}

84
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
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@ -6,6 +6,8 @@ import java.io.Serializable;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
public abstract class Result extends OafEntity implements Serializable {
@ -251,13 +253,12 @@ public abstract class Result extends OafEntity implements Serializable {
Result r = (Result) e;
mergeAuthors(r.getAuthor());
//TODO mergeFrom is used only for create Dedup Records since the creation of these two fields requires more complex functions (maybe they will be filled in an external function)
// if (author == null)
// author = r.getAuthor(); //authors will be replaced because they could be too much
// dateofacceptance = r.getDateofacceptance();
// instance = mergeLists(instance, r.getInstance());
instance = mergeLists(instance, r.getInstance());
if (r.getResulttype() != null)
resulttype = r.getResulttype();
@ -309,80 +310,5 @@ public abstract class Result extends OafEntity implements Serializable {
}
public void mergeAuthors(List<Author> authors){
int c1 = countAuthorsPids(author);
int c2 = countAuthorsPids(authors);
int s1 = authorsSize(author);
int s2 = authorsSize(authors);
//if both have no authors with pids and authors is bigger than author
if (c1 == 0 && c2 == 0 && author.size()<authors.size()) {
author = authors;
return;
}
//author is null and authors have 0 or more authors with pids
if (c1<c2 && c1<0) {
author = authors;
return;
}
//andiamo a mangiare
// if (author == null && authors == null)
// return;
//
// int c1 = countAuthorsPids(author);
// int c2 = countAuthorsPids(authors);
//
// if (c1<c2 && c1<1){
// author = authors;
// return;
// }
//
// if (c1<c2)
}
public int countAuthorsPids(List<Author> authors){
if (authors == null)
return -1;
return (int) authors.stream().map(this::extractAuthorPid).filter(Objects::nonNull).filter(StringUtils::isNotBlank).count();
}
public int authorsSize(List<Author> authors){
if (authors == null)
return 0;
return authors.size();
}
public String extractAuthorPid(Author a){
if(a == null || a.getPid() == null || a.getPid().size() == 0)
return null;
StringBuilder mainPid = new StringBuilder();
a.getPid().forEach(pid ->{
if (pid.getQualifier().getClassid().equalsIgnoreCase("orcid")) {
mainPid.setLength(0);
mainPid.append(pid.getValue());
}
else {
if(mainPid.length() == 0)
mainPid.append(pid.getValue());
}
});
return mainPid.toString();
}
}

2
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/ext_simple.xsl
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@ -9,7 +9,7 @@
<xsl:copy-of select="//oai:header"/>
<metadata>
<xsl:for-each select="//*[local-name()='subject']">
<subject><xsl:dedupId-of select="eg:clean(.,'dnet:languages')"/></subject>
<subject><xsl:value-of select="eg:clean(.,'dnet:languages')"/></subject>
</xsl:for-each>
</metadata>
<oaf:about>

12
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/tr.xml
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@ -1,11 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<RESOURCE_PROFILE>
<HEADER>
<RESOURCE_IDENTIFIER dedupId="d6fa79f2-486e-482d-b37c-62129af2cd9a_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU="/>
<RESOURCE_TYPE dedupId="TransformationRuleDSResourceType"/>
<RESOURCE_KIND dedupId="TransformationRuleDSResources"/>
<RESOURCE_URI dedupId=""/>
<DATE_OF_CREATION dedupId="2019-04-11T11:15:30+00:00"/>
<RESOURCE_IDENTIFIER value="d6fa79f2-486e-482d-b37c-62129af2cd9a_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU="/>
<RESOURCE_TYPE value="TransformationRuleDSResourceType"/>
<RESOURCE_KIND value="TransformationRuleDSResources"/>
<RESOURCE_URI value=""/>
<DATE_OF_CREATION value="2019-04-11T11:15:30+00:00"/>
</HEADER>
<BODY>
<CONFIGURATION>
@ -24,7 +24,7 @@
<xsl:copy-of select="//oai:header"/>
<metadata>
<xsl:for-each select="//*[local-name()='subject']">
<subject><xsl:dedupId-of select="eg:clean(.,'dnet:languages')"/></subject>
<subject><xsl:value-of select="eg:clean(.,'dnet:languages')"/></subject>
</xsl:for-each>
</metadata>
<oaf:about>

119
dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DatePicker.java Normal file
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@ -0,0 +1,119 @@
package eu.dnetlib.dedup;
import eu.dnetlib.dhp.schema.oaf.Field;
import org.apache.commons.lang.StringUtils;
import java.time.Year;
import java.util.*;
import java.util.stream.Collectors;
import static java.util.Collections.reverseOrder;
import static java.util.Map.Entry.comparingByValue;
import static java.util.stream.Collectors.toMap;
import static org.apache.commons.lang.StringUtils.endsWith;
import static org.apache.commons.lang.StringUtils.substringBefore;
public class DatePicker {
private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}";
private static final String DATE_DEFAULT_SUFFIX = "01-01";
private static final int YEAR_LB = 1300;
private static final int YEAR_UB = Year.now().getValue() + 5;
public static Field<String> pick(final Collection<String> dateofacceptance) {
final Map<String, Integer> frequencies = dateofacceptance
.parallelStream()
.filter(StringUtils::isNotBlank)
.collect(
Collectors.toConcurrentMap(
w -> w, w -> 1, Integer::sum));
if (frequencies.isEmpty()) {
return new Field<>();
}
final Field<String> date = new Field<>();
date.setValue(frequencies.keySet().iterator().next());
// let's sort this map by values first, filtering out invalid dates
final Map<String, Integer> sorted = frequencies
.entrySet()
.stream()
.filter(d -> StringUtils.isNotBlank(d.getKey()))
.filter(d -> d.getKey().matches(DATE_PATTERN))
.filter(d -> inRange(d.getKey()))
.sorted(reverseOrder(comparingByValue()))
.collect(
toMap(
Map.Entry::getKey,
Map.Entry::getValue, (e1, e2) -> e2,
LinkedHashMap::new));
// shortcut
if (sorted.size() == 0) {
return date;
}
// voting method (1/3 + 1) wins
if (sorted.size() >= 3) {
final int acceptThreshold = (sorted.size() / 3) + 1;
final List<String> accepted = sorted.entrySet().stream()
.filter(e -> e.getValue() >= acceptThreshold)
.map(e -> e.getKey())
.collect(Collectors.toList());
// cannot find strong majority
if (accepted.isEmpty()) {
final int max = sorted.values().iterator().next();
Optional<String> first = sorted.entrySet().stream()
.filter(e -> e.getValue() == max && !endsWith(e.getKey(), DATE_DEFAULT_SUFFIX))
.map(Map.Entry::getKey)
.findFirst();
if (first.isPresent()) {
date.setValue(first.get());
return date;
}
date.setValue(sorted.keySet().iterator().next());
return date;
}
if (accepted.size() == 1) {
date.setValue(accepted.get(0));
return date;
} else {
final Optional<String> first = accepted.stream()
.filter(d -> !endsWith(d, DATE_DEFAULT_SUFFIX))
.findFirst();
if (first.isPresent()) {
date.setValue(first.get());
return date;
}
return date;
}
//1st non YYYY-01-01 is returned
} else {
if (sorted.size() == 2) {
for (Map.Entry<String, Integer> e : sorted.entrySet()) {
if (!endsWith(e.getKey(), DATE_DEFAULT_SUFFIX)) {
date.setValue(e.getKey());
return date;
}
}
}
// none of the dates seems good enough, return the 1st one
date.setValue(sorted.keySet().iterator().next());
return date;
}
}
private static boolean inRange(final String date) {
final int year = Integer.parseInt(substringBefore(date, "-"));
return year >= YEAR_LB && year <= YEAR_UB;
}
}

83
dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java
View File

@ -1,6 +1,5 @@
package eu.dnetlib.dedup;
import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.pace.config.DedupConfig;
@ -10,23 +9,20 @@ import org.apache.commons.lang.StringUtils;
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.Function;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.codehaus.jackson.map.ObjectMapper;
import scala.Tuple2;
import java.io.IOException;
import java.util.Collection;
import java.util.List;
import java.util.Random;
import static java.util.stream.Collectors.toMap;
public class DedupRecordFactory {
public JavaRDD<OafEntity> createDedupRecord(final JavaSparkContext sc, final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final OafEntityType entityType, final DedupConfig dedupConf){
public static JavaRDD<OafEntity> createDedupRecord(final JavaSparkContext sc, final SparkSession spark, final String mergeRelsInputPath, final String entitiesInputPath, final OafEntityType entityType, final DedupConfig dedupConf){
//<id, json_entity>
final JavaPairRDD<String, String> inputJsonEntities = sc.textFile(entitiesInputPath)
@ -51,7 +47,12 @@ public class DedupRecordFactory {
String idValue = json._1();
String trust = MapDocumentUtil.getJPathString("$.dataInfo.trust", json._2());
String trust ="";
try {
trust = MapDocumentUtil.getJPathString("$.dataInfo.trust", json._2());
} catch (Throwable e) {
}
//TODO remember to replace this with the actual trust retrieving
if (StringUtils.isBlank(trust)) {
@ -71,28 +72,32 @@ public class DedupRecordFactory {
.groupByKey();
switch(entityType){
case Publication:
return sortedJoinResult.map(this::publicationMerger);
case Dataset:
return sortedJoinResult.map(this::datasetMerger);
case Project:
return sortedJoinResult.map(this::projectMerger);
case Software:
return sortedJoinResult.map(this::softwareMerger);
case Datasource:
return sortedJoinResult.map(this::datasourceMerger);
case Organization:
return sortedJoinResult.map(this::organizationMerger);
case OtherResearchProduct:
return sortedJoinResult.map(this::otherresearchproductMerger);
case publication:
return sortedJoinResult.map(DedupRecordFactory::publicationMerger);
case dataset:
return sortedJoinResult.map(DedupRecordFactory::datasetMerger);
case project:
return sortedJoinResult.map(DedupRecordFactory::projectMerger);
case software:
return sortedJoinResult.map(DedupRecordFactory::softwareMerger);
case datasource:
return sortedJoinResult.map(DedupRecordFactory::datasourceMerger);
case organization:
return sortedJoinResult.map(DedupRecordFactory::organizationMerger);
case otherresearchproduct:
return sortedJoinResult.map(DedupRecordFactory::otherresearchproductMerger);
default:
return null;
}
}
private Publication publicationMerger(Tuple2<String, Iterable<String>> e){
private static Publication publicationMerger(Tuple2<String, Iterable<String>> e){
Publication p = new Publication(); //the result of the merge, to be returned at the end
@ -101,67 +106,59 @@ public class DedupRecordFactory {
final ObjectMapper mapper = new ObjectMapper();
final Collection<String> dateofacceptance = Lists.newArrayList();
final Collection<List<Author>> authors = Lists.newArrayList();
final Collection<List<Instance>> instances = Lists.newArrayList();
StringBuilder trust = new StringBuilder("0.0");
if (e._2() != null)
e._2().forEach(pub -> {
try {
Publication publication = mapper.readValue(pub, Publication.class);
final String currentTrust = publication.getDataInfo().getTrust();
if (!currentTrust.equals("1.0")) {
if (!"1.0".equals(currentTrust)) {
trust.setLength(0);
trust.append(currentTrust);
}
p.mergeFrom(publication);
p.setAuthor(DedupUtility.mergeAuthor(p.getAuthor(), publication.getAuthor()));
//add to the list if they are not null
if (publication.getDateofacceptance() != null)
dateofacceptance.add(publication.getDateofacceptance().getValue());
if (publication.getAuthor() != null)
authors.add(publication.getAuthor());
if (publication.getInstance() != null)
instances.add(publication.getInstance());
} catch (Exception exc){}
} catch (Exception exc){
throw new RuntimeException(exc);
}
});
p.setAuthor(null); //TODO create a single list of authors to put in the final publication
p.setDateofacceptance(DatePicker.pick(dateofacceptance));
return p;
}
private Dataset datasetMerger(Tuple2<String, Iterable<String>> e){
private static Dataset datasetMerger(Tuple2<String, Iterable<String>> e){
throw new NotImplementedException();
}
private Project projectMerger(Tuple2<String, Iterable<String>> e){
private static Project projectMerger(Tuple2<String, Iterable<String>> e){
throw new NotImplementedException();
}
private Software softwareMerger(Tuple2<String, Iterable<String>> e){
private static Software softwareMerger(Tuple2<String, Iterable<String>> e){
throw new NotImplementedException();
}
private Datasource datasourceMerger(Tuple2<String, Iterable<String>> e){
private static Datasource datasourceMerger(Tuple2<String, Iterable<String>> e){
throw new NotImplementedException();
}
private Organization organizationMerger(Tuple2<String, Iterable<String>> e){
private static Organization organizationMerger(Tuple2<String, Iterable<String>> e){
throw new NotImplementedException();
}
private OtherResearchProduct otherresearchproductMerger(Tuple2<String, Iterable<String>> e){
private static OtherResearchProduct otherresearchproductMerger(Tuple2<String, Iterable<String>> e){
throw new NotImplementedException();
}

196
dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/DedupUtility.java
View File

@ -1,11 +1,17 @@
package eu.dnetlib.dedup;
import com.google.common.collect.Sets;
import com.wcohen.ss.JaroWinkler;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.clustering.BlacklistAwareClusteringCombiner;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.model.Person;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
@ -14,32 +20,35 @@ import org.apache.spark.SparkContext;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.util.LongAccumulator;
import scala.Tuple2;
import java.io.IOException;
import java.io.StringWriter;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.text.Normalizer;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
public class DedupUtility {
private static final Double THRESHOLD = 0.95;
public static Map<String, LongAccumulator> constructAccumulator(final DedupConfig dedupConf, final SparkContext context) {
Map<String, LongAccumulator> accumulators = new HashMap<>();
String acc1 = String.format("%s::%s",dedupConf.getWf().getEntityType(), "records per hash key = 1");
String acc1 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "records per hash key = 1");
accumulators.put(acc1, context.longAccumulator(acc1));
String acc2 = String.format("%s::%s",dedupConf.getWf().getEntityType(), "missing " + dedupConf.getWf().getOrderField());
String acc2 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "missing " + dedupConf.getWf().getOrderField());
accumulators.put(acc2, context.longAccumulator(acc2));
String acc3 = String.format("%s::%s",dedupConf.getWf().getEntityType(), String.format("Skipped records for count(%s) >= %s", dedupConf.getWf().getOrderField(), dedupConf.getWf().getGroupMaxSize()));
String acc3 = String.format("%s::%s", dedupConf.getWf().getEntityType(), String.format("Skipped records for count(%s) >= %s", dedupConf.getWf().getOrderField(), dedupConf.getWf().getGroupMaxSize()));
accumulators.put(acc3, context.longAccumulator(acc3));
String acc4 = String.format("%s::%s",dedupConf.getWf().getEntityType(), "skip list");
String acc4 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "skip list");
accumulators.put(acc4, context.longAccumulator(acc4));
String acc5 = String.format("%s::%s",dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)");
String acc5 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)");
accumulators.put(acc5, context.longAccumulator(acc5));
String acc6 = String.format("%s::%s",dedupConf.getWf().getEntityType(), "d < " + dedupConf.getWf().getThreshold());
String acc6 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "d < " + dedupConf.getWf().getThreshold());
accumulators.put(acc6, context.longAccumulator(acc6));
return accumulators;
@ -52,7 +61,7 @@ public class DedupUtility {
public static void deleteIfExists(String path) throws IOException {
Configuration conf = new Configuration();
FileSystem fileSystem = FileSystem.get(conf);
if (fileSystem.exists(new Path(path))){
if (fileSystem.exists(new Path(path))) {
fileSystem.delete(new Path(path), true);
}
}
@ -91,4 +100,171 @@ public class DedupUtility {
return null;
}
}
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
int pa = countAuthorsPids(a);
int pb = countAuthorsPids(b);
List<Author> base, enrich;
int sa = authorsSize(a);
int sb = authorsSize(b);
if(pa == pb){
base = sa>sb?a:b;
enrich = sa>sb?b:a;
} else {
base = pa>pb?a:b;
enrich = pa>pb?b:a;
}
enrichPidFromList(base, enrich);
return base;
// //if both have no authors with pids
// if (pa < 1 && pb < 1) {
// //B is bigger than A
// if (sa < sb)
// return b;
// //A is bigger than B
// else
// return a;
// }
// //If A has author with pids
// if (pa > 0) {
// //B has no author with pid
// if (pb < 1)
// return a;
// //B has author with pid
// else {
// enrichPidFromList(a, b);
// return a;
// }
// }
// //If B has author with pids
// //A has no author with pid
// if (pa < 1)
// return b;
// //A has author with pid
// else {
// enrichPidFromList(b, a);
// return b;
// }
}
private static void enrichPidFromList(List<Author> base, List<Author> enrich) {
if(base==null || enrich == null)
return;
final Map<String, Author> basePidAuthorMap = base.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
.flatMap(a -> a.getPid()
.stream()
.map(p -> new Tuple2<>(p.toComparableString(), a))
).collect(Collectors.toMap(Tuple2::_1, Tuple2::_2));
final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
.flatMap(a -> a.getPid().stream().filter(p -> !basePidAuthorMap.containsKey(p.toComparableString())).map(p -> new Tuple2<>(p, a)))
.collect(Collectors.toList());
pidToEnrich.forEach(a -> {
Optional<Tuple2<Double, Author>> simAuhtor = base.stream().map(ba -> new Tuple2<>(sim(ba, a._2()), ba)).max(Comparator.comparing(Tuple2::_1));
if (simAuhtor.isPresent() && simAuhtor.get()._1()> THRESHOLD) {
Author r = simAuhtor.get()._2();
r.getPid().add(a._1());
}
});
}
public static String createEntityPath(final String basePath, final String entityType) {
return String.format("%s/%s", basePath,entityType);
}
public static String createSimRelPath(final String basePath, final String entityType) {
return String.format("%s/%s_simRel", basePath,entityType);
}
public static String createMergeRelPath(final String basePath, final String entityType) {
return String.format("%s/%s_mergeRel", basePath,entityType);
}
private static Double sim(Author a, Author b) {
final Person pa = parse(a);
final Person pb = parse(b);
if (pa.isAccurate() & pb.isAccurate()) {
return new JaroWinkler().score(
normalize(pa.getSurnameString()),
normalize(pb.getSurnameString()));
} else {
return new JaroWinkler().score(
normalize(pa.getNormalisedFullname()),
normalize(pb.getNormalisedFullname()));
}
}
private static String normalize(final String s) {
return nfd(s).toLowerCase()
// do not compact the regexes in a single expression, would cause StackOverflowError in case of large input strings
.replaceAll("(\\W)+", " ")
.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
.replaceAll("(\\p{Punct})+", " ")
.replaceAll("(\\d)+", " ")
.replaceAll("(\\n)+", " ")
.trim();
}
private static String nfd(final String s) {
return Normalizer.normalize(s, Normalizer.Form.NFD);
}
private static Person parse(Author author) {
if (StringUtils.isNotBlank(author.getSurname())) {
return new Person(author.getSurname() + ", " + author.getName(), false);
} else {
return new Person(author.getFullname(), false);
}
}
private static int countAuthorsPids(List<Author> authors) {
if (authors == null)
return 0;
return (int) authors.stream().map(DedupUtility::extractAuthorPid).filter(Objects::nonNull).filter(StringUtils::isNotBlank).count();
}
private static int authorsSize(List<Author> authors) {
if (authors == null)
return 0;
return authors.size();
}
private static boolean isAccurate(final Author a) {
return StringUtils.isNotBlank(a.getName()) && StringUtils.isNotBlank(a.getSurname());
}
private static String extractAuthorPid(Author a) {
if (a == null || a.getPid() == null || a.getPid().size() == 0)
return null;
StringBuilder mainPid = new StringBuilder();
a.getPid().forEach(pid -> {
if (pid.getQualifier().getClassid().equalsIgnoreCase("orcid")) {
mainPid.setLength(0);
mainPid.append(pid.getValue());
} else {
if (mainPid.length() == 0)
mainPid.append(pid.getValue());
}
});
return mainPid.toString();
}
}

16
dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/OafEntityType.java
View File

@ -2,12 +2,14 @@ package eu.dnetlib.dedup;
public enum OafEntityType {
Datasource,
Organization,
Project,
Dataset,
OtherResearchProduct,
Software,
Publication
datasource,
organization,
project,
dataset,
otherresearchproduct,
software,
publication
}

4
dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java
View File

@ -46,7 +46,7 @@ public class SparkCreateConnectedComponent {
s -> new Tuple2<Object, String>((long) s.hashCode(), s)
);
final Dataset<Relation> similarityRelations = spark.read().load(targetPath + "/" + entity+"_simrel").as(Encoders.bean(Relation.class));
final Dataset<Relation> similarityRelations = spark.read().load(DedupUtility.createSimRelPath(targetPath,entity)).as(Encoders.bean(Relation.class));
final RDD<Edge<String>> edgeRdd = similarityRelations.javaRDD().map(it -> new Edge<>(it.getSource().hashCode(), it.getTarget().hashCode(), it.getRelClass())).rdd();
@ -73,7 +73,7 @@ public class SparkCreateConnectedComponent {
return tmp.stream();
}).iterator()).rdd(), Encoders.bean(Relation.class));
mergeRelation.write().mode("overwrite").save(targetPath+"/"+entity+"_mergeRels");
mergeRelation.write().mode("overwrite").save(DedupUtility.createMergeRelPath(targetPath,entity));
}

74
dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java
View File

@ -1,71 +1,39 @@
package eu.dnetlib.dedup;
import com.google.common.collect.ComparisonChain;
import com.google.common.collect.Lists;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.util.MapDocumentUtil;
import org.apache.commons.io.IOUtils;
import org.apache.spark.Partitioner;
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.Optional;
import org.apache.spark.api.java.function.Function;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.apache.spark.sql.types.StructType;
import scala.Tuple2;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
public class SparkCreateDedupRecord {
public static void main(String[] args) throws Exception {
// final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/dedup_parameters.json")));
// parser.parseArgument(args);
// final SparkSession spark = SparkSession
// .builder()
// .appName(SparkCreateDedupRecord.class.getSimpleName())
// .master(parser.get("master"))
// .getOrCreate();
//
// final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
// final String inputPath = parser.get("sourcePath");
// final String entity = parser.get("entity");
// final String targetPath = parser.get("targetPath");
//// final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json")));
// final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
//
// //<id, json_entity>
// final JavaPairRDD<String, String> inputJsonEntities = sc.textFile(inputPath + "/" + entity)
// .mapToPair((PairFunction<String,String,String>)it->
// new Tuple2<String,String>(MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), it),it)
// );
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/dedupRecord_parameters.json")));
parser.parseArgument(args);
final SparkSession spark = SparkSession
.builder()
.appName(SparkCreateDedupRecord.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
// //<source, target>: source is the dedup_id, target is the id of the mergedIn
// JavaPairRDD<String,String> mergeRels = spark
// .read().load(targetPath + "/" + entity+"_mergeRels").as(Encoders.bean(Relation.class))
// .where("relClass=='merges'")
// .javaRDD()
// .mapToPair(
// (PairFunction<Relation, String,String>)r->
// new Tuple2<String,String>(r.getTarget(), r.getSource())
// );
//
// //<dedup_id, json_entity_merged>
// final JavaPairRDD<String, String> p = mergeRels.join(inputJsonEntities).mapToPair((PairFunction<Tuple2<String, Tuple2<String, String>>, String, String>) Tuple2::_2);
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final String sourcePath = parser.get("sourcePath");
final String entity = parser.get("entity");
final String dedupPath = parser.get("dedupPath");
// final DedupConfig dedupConf = DedupConfig.load(IOUtils.toString(SparkCreateDedupRecord.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json")));
final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
final JavaRDD<OafEntity> dedupRecord = DedupRecordFactory.createDedupRecord(sc, spark, DedupUtility.createMergeRelPath(dedupPath,entity), DedupUtility.createEntityPath(sourcePath,entity), OafEntityType.valueOf(entity), dedupConf);
dedupRecord.map(r-> {
ObjectMapper mapper = new ObjectMapper();
return mapper.writeValueAsString(r);
}).saveAsTextFile(dedupPath+"/"+entity+"_dedup_record_json");
StructType schema = Encoders.bean(Publication.class).schema();
System.out.println(schema);
}
}

2
dhp-workflows/dhp-dedup/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java
View File

@ -77,7 +77,7 @@ public class SparkCreateSimRels {
return r;
});
spark.createDataset(isSimilarToRDD.rdd(), Encoders.bean(Relation.class)).write().mode("overwrite").save(targetPath+"/"+entity+"_simrel");
spark.createDataset(isSimilarToRDD.rdd(), Encoders.bean(Relation.class)).write().mode("overwrite").save( DedupUtility.createSimRelPath(targetPath,entity));

33
dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/dedupRecord_parameters.json Normal file
View File

@ -0,0 +1,33 @@
[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the path of the sequential file to read",
"paramRequired": true
},
{
"paramName": "e",
"paramLongName": "entity",
"paramDescription": "the type of entity to be deduped",
"paramRequired": true
},
{
"paramName": "c",
"paramLongName": "dedupConf",
"paramDescription": "dedup configuration to be used",
"compressed": true,
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "dedupPath",
"paramDescription": "dedup path to load mergeRelation",
"paramRequired": true
}
]

36
dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/dedup_parameters.json
View File

@ -1,7 +1,33 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequential file to read", "paramRequired": true},
{"paramName":"e", "paramLongName":"entity", "paramDescription": "the type of entity to be deduped", "paramRequired": true},
{"paramName":"c", "paramLongName":"dedupConf", "paramDescription": "dedup configuration to be used", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "target path to save dedup result", "paramRequired": true}
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the path of the sequential file to read",
"paramRequired": true
},
{
"paramName": "e",
"paramLongName": "entity",
"paramDescription": "the type of entity to be deduped",
"paramRequired": true
},
{
"paramName": "c",
"paramLongName": "dedupConf",
"paramDescription": "dedup configuration to be used",
"compressed": true,
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "target path to save dedup result",
"paramRequired": true
}
]

17
dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/oozie_app/config-default.xml
View File

File diff suppressed because one or more lines are too long

25
dhp-workflows/dhp-dedup/src/main/resources/eu/dnetlib/dhp/dedup/oozie_app/workflow.xml
View File

@ -93,6 +93,31 @@
<arg>--entity</arg><arg>${entity}</arg>
<arg>--dedupConf</arg><arg>${dedupConf}</arg>
</spark>
<ok to="CreateDedupRecord"/>
<error to="Kill"/>
</action>
<action name="CreateDedupRecord">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create Connected Components</name>
<class>eu.dnetlib.dedup.SparkCreateDedupRecord</class>
<jar>dhp-dedup-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores ${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --conf
spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" --conf
spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" --conf
spark.sql.warehouse.dir="/user/hive/warehouse"
</spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--dedupPath</arg><arg>${dedupPath}</arg>
<arg>--entity</arg><arg>${entity}</arg>
<arg>--dedupConf</arg><arg>${dedupConf}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>

61
dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/MergeAuthorTest.java Normal file
View File

@ -0,0 +1,61 @@
package eu.dnetlib.dedup;
import eu.dnetlib.dhp.schema.oaf.Publication;
import org.apache.commons.io.IOUtils;
import org.codehaus.jackson.map.ObjectMapper;
import org.junit.Before;
import org.junit.Test;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
public class MergeAuthorTest {
List<Publication> publicationsToMerge;
final ObjectMapper mapper = new ObjectMapper();
@Before
public void setUp() throws Exception {
final String json = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/dedup/json/authors_merge.json"));
publicationsToMerge = Arrays.asList(json.split("\n")).stream().map(s-> {
try {
return mapper.readValue(s, Publication.class);
} catch (IOException e) {
throw new RuntimeException(e);
}
}).collect(Collectors.toList());
}
@Test
public void test() throws Exception {
Publication dedup = new Publication();
publicationsToMerge.forEach(p-> {
dedup.mergeFrom(p);
dedup.setAuthor(DedupUtility.mergeAuthor(dedup.getAuthor(),p.getAuthor()));
});
System.out.println(mapper.writeValueAsString(dedup));
}
}

23
dhp-workflows/dhp-dedup/src/test/java/eu/dnetlib/dedup/SparkCreateDedupTest.java
View File

@ -1,6 +1,7 @@
package eu.dnetlib.dedup;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Publication;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
@ -27,9 +28,9 @@ public class SparkCreateDedupTest {
public void createSimRelsTest() throws Exception {
SparkCreateSimRels.main(new String[] {
"-mt", "local[*]",
"-s", "/Users/miconis/dumps",
"-s", "/home/sandro/betadump",
"-e", "publication",
"-c", configuration,
"-c", ArgumentApplicationParser.compressArgument(configuration),
"-t", "/tmp/dedup",
});
}
@ -40,9 +41,9 @@ public class SparkCreateDedupTest {
SparkCreateConnectedComponent.main(new String[] {
"-mt", "local[*]",
"-s", "/Users/miconis/dumps",
"-s", "/home/sandro/betadump",
"-e", "publication",
"-c", configuration,
"-c", ArgumentApplicationParser.compressArgument(configuration),
"-t", "/tmp/dedup",
});
}
@ -52,10 +53,18 @@ public class SparkCreateDedupTest {
public void dedupRecordTest() throws Exception {
SparkCreateDedupRecord.main(new String[] {
"-mt", "local[*]",
"-s", "/Users/miconis/dumps",
"-s", "/home/sandro/betadump",
"-e", "publication",
"-c", configuration,
"-t", "/tmp/dedup",
"-c", ArgumentApplicationParser.compressArgument(configuration),
"-d", "/tmp/dedup",
});
}
@Test
public void printCC() throws Exception {
System.out.println(ArgumentApplicationParser.compressArgument(configuration));
}
}

3
dhp-workflows/dhp-dedup/src/test/resources/eu/dnetlib/dedup/json/authors_merge.json Normal file
View File

File diff suppressed because one or more lines are too long

8
dhp-workflows/dhp-distcp/src/main/resources/eu/dnetlib/dhp/distcp/oozie_app/config-default.xml
View File

@ -1,18 +1,18 @@
<configuration>
<property>
<name>jobTracker</name>
<dedupId>yarnRM</dedupId>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<dedupId>hdfs://nameservice1</dedupId>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>sourceNN</name>
<dedupId>webhdfs://namenode2.hadoop.dm.openaire.eu:50071</dedupId>
<value>webhdfs://namenode2.hadoop.dm.openaire.eu:50071</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<dedupId>true</dedupId>
<value>true</value>
</property>
</configuration>

4
dhp-workflows/dhp-distcp/src/main/resources/eu/dnetlib/dhp/distcp/oozie_app/workflow.xml
View File

@ -14,12 +14,12 @@
</property>
<property>
<name>hbase_dump_distcp_memory_mb</name>
<dedupId>6144</dedupId>
<value>6144</value>
<description>memory for distcp action copying InfoSpace dump from remote cluster</description>
</property>
<property>
<name>hbase_dump_distcp_num_maps</name>
<dedupId>1</dedupId>
<value>1</value>
<description>maximum number of simultaneous copies of InfoSpace dump from remote location</description>
</property>
</parameters>

12
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/graph/oozie_app/config-default.xml
View File

@ -1,26 +1,26 @@
<configuration>
<property>
<name>jobTracker</name>
<dedupId>yarnRM</dedupId>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<dedupId>hdfs://nameservice1</dedupId>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<dedupId>true</dedupId>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<dedupId>spark2</dedupId>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<dedupId>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</dedupId>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hive_db_name</name>
<dedupId>openaire</dedupId>
<value>openaire</value>
</property>
</configuration>

4
dhp-workflows/docs/oozie-installer.markdown
View File

@ -54,7 +54,7 @@ Properties overriding order is the following:
2. `~/.dhp/application.properties` defined properties
3. `${workflow.source.dir}/job.properties`
4. `job-override.properties` (located in the project root dir)
5. `maven -Dparam=dedupId`
5. `maven -Dparam=value`
where the maven `-Dparam` property is overriding all the other ones.
@ -73,7 +73,7 @@ Workflow definition requirements
This property can be set using maven `-D` switch.
`[oozie_app]` is the default directory name however it can be set to any dedupId as soon as `oozieAppDir` property is provided with directory name as dedupId.
`[oozie_app]` is the default directory name however it can be set to any value as soon as `oozieAppDir` property is provided with directory name as value.
Subworkflows are supported as well and subworkflow directories should be nested within `[oozie_app]` directory.

4
dhp-workflows/pom.xml
View File

@ -73,7 +73,7 @@
<!-- This profile sets properties that are required for test oozie workflows To be used only with 'oozie-package' profile -->
<id>attach-test-resources</id>
<properties>
<!--overriding default scope (set to 'runtime') with the 'test' dedupId. Test resources attached to oozie package requires all test dependencies. -->
<!--overriding default scope (set to 'runtime') with the 'test' value. Test resources attached to oozie package requires all test dependencies. -->
<oozie.package.dependencies.include.scope />
<oozie.package.dependencies.exclude.scope>provided</oozie.package.dependencies.exclude.scope>
<!-- Do not skip creation of test jar for priming (in oozie-package profile) -->
@ -326,7 +326,7 @@
</goals>
<configuration>
<tasks>
<property name="assembly-resources.loc" dedupId="${maven.dependency.eu.dnetlib.dhp.dhp-build-assembly-resources.jar.path}" />
<property name="assembly-resources.loc" value="${maven.dependency.eu.dnetlib.dhp.dhp-build-assembly-resources.jar.path}" />
<unjar src="${assembly-resources.loc}" dest="${project.build.directory}/assembly-resources" />
</tasks>
</configuration>

5
pom.xml
View File

@ -236,6 +236,11 @@
<artifactId>java-jq</artifactId>
<version>0.10.1</version>
</dependency>
<dependency>
<groupId>edu.cmu</groupId>
<artifactId>secondstring</artifactId>
<version>1.0.0</version>
</dependency>
<dependency>
<groupId>org.apache.oozie</groupId>