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Merge branch 'master' into dhp_oaf_model

This commit is contained in:
Miriam Baglioni 2020-05-20 10:57:30 +02:00
parent 3c0eb12d3e 76f3f73caa
commit 5e0e554000
9 changed files with 126 additions and 49 deletions
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7
dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/SparkRemoveBlacklistedRelationJob.java
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@ -79,8 +79,6 @@ public class SparkRemoveBlacklistedRelationJob {
Dataset<Relation> inputRelation = readRelations(spark, inputPath); Dataset<Relation> inputRelation = readRelations(spark, inputPath);
Dataset<Relation> mergesRelation = readRelations(spark, mergesPath); Dataset<Relation> mergesRelation = readRelations(spark, mergesPath);
log.info("InputRelationCount: {}", inputRelation.count());
Dataset<Relation> dedupSource = blackListed Dataset<Relation> dedupSource = blackListed
.joinWith( .joinWith(
mergesRelation, blackListed.col("source").equalTo(mergesRelation.col("target")), mergesRelation, blackListed.col("source").equalTo(mergesRelation.col("target")),
@ -103,11 +101,6 @@ public class SparkRemoveBlacklistedRelationJob {
return c._1(); return c._1();
}, Encoders.bean(Relation.class)); }, Encoders.bean(Relation.class));
dedupBL
.write()
.mode(SaveMode.Overwrite)
.json(blacklistPath + "/deduped");
inputRelation inputRelation
.joinWith( .joinWith(
dedupBL, (inputRelation dedupBL, (inputRelation

63
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Topic.java
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@ -4,31 +4,48 @@ package eu.dnetlib.dhp.broker.model;
public enum Topic { public enum Topic {
// ENRICHMENT MISSING // ENRICHMENT MISSING
ENRICH_MISSING_OA_VERSION("ENRICH/MISSING/OPENACCESS_VERSION"), ENRICH_MISSING_ABSTRACT( ENRICH_MISSING_OA_VERSION("ENRICH/MISSING/OPENACCESS_VERSION"),
"ENRICH/MISSING/ABSTRACT"), ENRICH_MISSING_PUBLICATION_DATE( ENRICH_MISSING_ABSTRACT("ENRICH/MISSING/ABSTRACT"),
"ENRICH/MISSING/PUBLICATION_DATE"), ENRICH_MISSING_PID( ENRICH_MISSING_PUBLICATION_DATE("ENRICH/MISSING/PUBLICATION_DATE"),
"ENRICH/MISSING/PID"), ENRICH_MISSING_PROJECT("ENRICH/MISSING/PROJECT"), ENRICH_MISSING_SOFTWARE( ENRICH_MISSING_PID("ENRICH/MISSING/PID"),
"ENRICH/MISSING/SOFTWARE"), ENRICH_MISSING_SUBJECT_MESHEUROPMC( ENRICH_MISSING_PROJECT("ENRICH/MISSING/PROJECT"),
"ENRICH/MISSING/SUBJECT/MESHEUROPMC"), ENRICH_MISSING_SUBJECT_ARXIV( ENRICH_MISSING_SOFTWARE("ENRICH/MISSING/SOFTWARE"),
"ENRICH/MISSING/SUBJECT/ARXIV"), ENRICH_MISSING_SUBJECT_JEL( ENRICH_MISSING_SUBJECT_MESHEUROPMC("ENRICH/MISSING/SUBJECT/MESHEUROPMC"),
"ENRICH/MISSING/SUBJECT/JEL"), ENRICH_MISSING_SUBJECT_DDC( ENRICH_MISSING_SUBJECT_ARXIV("ENRICH/MISSING/SUBJECT/ARXIV"),
"ENRICH/MISSING/SUBJECT/DDC"), ENRICH_MISSING_SUBJECT_ACM( ENRICH_MISSING_SUBJECT_JEL("ENRICH/MISSING/SUBJECT/JEL"),
"ENRICH/MISSING/SUBJECT/ACM"), ENRICH_MISSING_SUBJECT_RVK( ENRICH_MISSING_SUBJECT_DDC("ENRICH/MISSING/SUBJECT/DDC"),
"ENRICH/MISSING/SUBJECT/RVK"), ENRICH_MISSING_AUTHOR_ORCID( ENRICH_MISSING_SUBJECT_ACM("ENRICH/MISSING/SUBJECT/ACM"),
"ENRICH/MISSING/AUTHOR/ORCID"), ENRICH_MISSING_SUBJECT_RVK("ENRICH/MISSING/SUBJECT/RVK"),
ENRICH_MISSING_AUTHOR_ORCID("ENRICH/MISSING/AUTHOR/ORCID"),
// ENRICHMENT MORE // ENRICHMENT MORE
ENRICH_MORE_PID("ENRICH/MORE/PID"), ENRICH_MORE_OA_VERSION("ENRICH/MORE/OPENACCESS_VERSION"), ENRICH_MORE_ABSTRACT( ENRICH_MORE_PID("ENRICH/MORE/PID"),
"ENRICH/MORE/ABSTRACT"), ENRICH_MORE_PUBLICATION_DATE("ENRICH/MORE/PUBLICATION_DATE"), ENRICH_MORE_PROJECT( ENRICH_MORE_OA_VERSION("ENRICH/MORE/OPENACCESS_VERSION"),
"ENRICH/MORE/PROJECT"), ENRICH_MORE_SUBJECT_MESHEUROPMC( ENRICH_MORE_ABSTRACT("ENRICH/MORE/ABSTRACT"),
"ENRICH/MORE/SUBJECT/MESHEUROPMC"), ENRICH_MORE_SUBJECT_ARXIV( ENRICH_MORE_PUBLICATION_DATE("ENRICH/MORE/PUBLICATION_DATE"),
"ENRICH/MORE/SUBJECT/ARXIV"), ENRICH_MORE_SUBJECT_JEL( ENRICH_MORE_PROJECT("ENRICH/MORE/PROJECT"),
"ENRICH/MORE/SUBJECT/JEL"), ENRICH_MORE_SUBJECT_DDC( ENRICH_MORE_SUBJECT_MESHEUROPMC("ENRICH/MORE/SUBJECT/MESHEUROPMC"),
"ENRICH/MORE/SUBJECT/DDC"), ENRICH_MORE_SUBJECT_ACM( ENRICH_MORE_SUBJECT_ARXIV("ENRICH/MORE/SUBJECT/ARXIV"),
"ENRICH/MORE/SUBJECT/ACM"), ENRICH_MORE_SUBJECT_RVK("ENRICH/MORE/SUBJECT/RVK"), ENRICH_MORE_SUBJECT_JEL("ENRICH/MORE/SUBJECT/JEL"),
ENRICH_MORE_SUBJECT_DDC("ENRICH/MORE/SUBJECT/DDC"),
ENRICH_MORE_SUBJECT_ACM("ENRICH/MORE/SUBJECT/ACM"),
ENRICH_MORE_SUBJECT_RVK("ENRICH/MORE/SUBJECT/RVK"),
// ADDITION // ADDITION
ADD_BY_PROJECT("ADD/BY_PROJECT"); ADD_BY_PROJECT("ADD/BY_PROJECT"),
// OTHER RELS
ENRICH_MISSING_PUBLICATION_IS_RELATED_TO("ENRICH/MISSING/PUBLICATION/IS_RELATED_TO"),
ENRICH_MISSING_PUBLICATION_REFERENCES("ENRICH/MISSING/PUBLICATION/REFERENCES"),
ENRICH_MISSING_PUBLICATION_IS_REFERENCED_BY("ENRICH/MISSING/PUBLICATION/IS_REFERENCED_BY"),
ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_TO("ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_TO"),
ENRICH_MISSING_PUBLICATION_IS_SUPPLEMENTED_BY("ENRICH/MISSING/PUBLICATION/IS_SUPPLEMENTED_BY"),
ENRICH_MISSING_DATASET_IS_RELATED_TO("ENRICH/MISSING/DATASET/IS_RELATED_TO"),
ENRICH_MISSING_DATASET_REFERENCES("ENRICH/MISSING/DATASET/REFERENCES"),
ENRICH_MISSING_DATASET_IS_REFERENCED_BY("ENRICH/MISSING/DATASET/IS_REFERENCED_BY"),
ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_TO("ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_TO"),
ENRICH_MISSING_DATASET_IS_SUPPLEMENTED_BY("ENRICH/MISSING/DATASET/IS_SUPPLEMENTED_BY");
Topic(final String path) { Topic(final String path) {
this.path = path; this.path = path;
@ -42,9 +59,7 @@ public enum Topic {
public static Topic fromPath(final String path) { public static Topic fromPath(final String path) {
for (final Topic t : Topic.values()) { for (final Topic t : Topic.values()) {
if (t.getPath().equals(path)) { if (t.getPath().equals(path)) { return t; }
return t;
}
} }
return null; return null;
} }

74
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java
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@ -9,11 +9,21 @@ import java.util.Optional;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
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.sql.Column;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.model.Event;
import eu.dnetlib.dhp.broker.model.EventFactory; import eu.dnetlib.dhp.broker.model.EventFactory;
@ -30,7 +40,11 @@ import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSubject;
import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher; import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
public class GenerateEventsApplication { public class GenerateEventsApplication {
@ -47,12 +61,13 @@ public class GenerateEventsApplication {
private static final UpdateMatcher<?> enrichMorePid = new EnrichMorePid(); private static final UpdateMatcher<?> enrichMorePid = new EnrichMorePid();
private static final UpdateMatcher<?> enrichMoreSubject = new EnrichMoreSubject(); private static final UpdateMatcher<?> enrichMoreSubject = new EnrichMoreSubject();
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws Exception { public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser( final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils IOUtils
.toString( .toString(GenerateEventsApplication.class
GenerateEventsApplication.class .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json")));
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json")));
parser.parseArgument(args); parser.parseArgument(args);
final Boolean isSparkSessionManaged = Optional final Boolean isSparkSessionManaged = Optional
@ -67,10 +82,23 @@ public class GenerateEventsApplication {
final String eventsPath = parser.get("eventsPath"); final String eventsPath = parser.get("eventsPath");
log.info("eventsPath: {}", eventsPath); log.info("eventsPath: {}", eventsPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
runWithSparkSession(conf, isSparkSessionManaged, spark -> { runWithSparkSession(conf, isSparkSessionManaged, spark -> {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
removeOutputDir(spark, eventsPath); removeOutputDir(spark, eventsPath);
generateEvents(spark, graphPath, eventsPath);
final JavaRDD<Event> eventsRdd = sc.emptyRDD();
eventsRdd.union(generateSimpleEvents(spark, graphPath, Publication.class));
eventsRdd.union(generateSimpleEvents(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class));
eventsRdd.union(generateSimpleEvents(spark, graphPath, Software.class));
eventsRdd.union(generateSimpleEvents(spark, graphPath, OtherResearchProduct.class));
eventsRdd.saveAsTextFile(eventsPath, GzipCodec.class);
}); });
} }
@ -79,11 +107,34 @@ public class GenerateEventsApplication {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
} }
private static void generateEvents(final SparkSession spark, final String graphPath, final String eventsPath) { private static <R extends Result> JavaRDD<Event> generateSimpleEvents(final SparkSession spark,
// TODO final String graphPath,
final Class<R> resultClazz) {
final Dataset<R> results =
readPath(spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), resultClazz)
.filter(r -> r.getDataInfo().getDeletedbyinference());
final Dataset<Relation> rels =
readPath(spark, graphPath + "/relation", Relation.class)
.filter(r -> r.getRelClass().equals("TODO")); // TODO mergedIN
final Column c = null; // TODO
final Dataset<Row> aa = results.joinWith(rels, results.col("id").equalTo(rels.col("source")), "inner")
.groupBy(rels.col("target"))
.agg(c)
.filter(x -> x.size() > 1)
// generateSimpleEvents(...)
// flatMap()
// toRdd()
;
return null;
} }
private List<Event> generateEvents(final Result... children) { private List<Event> generateSimpleEvents(final Result... children) {
final List<UpdateInfo<?>> list = new ArrayList<>(); final List<UpdateInfo<?>> list = new ArrayList<>();
for (final Result target : children) { for (final Result target : children) {
@ -102,4 +153,13 @@ public class GenerateEventsApplication {
return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList()); return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
} }
public static <R> Dataset<R> readPath(
final SparkSession spark,
final String inputPath,
final Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
} }

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/EnrichMissingPublicationDate.java
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@ -1,6 +1,7 @@
package eu.dnetlib.dhp.broker.oa.matchers; package eu.dnetlib.dhp.broker.oa.matchers;
import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;
@ -16,12 +17,15 @@ public class EnrichMissingPublicationDate extends UpdateMatcher<String> {
@Override @Override
protected List<UpdateInfo<String>> findUpdates(final Result source, final Result target) { protected List<UpdateInfo<String>> findUpdates(final Result source, final Result target) {
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f)); if (isMissing(target.getDateofacceptance()) && !isMissing(source.getDateofacceptance())) {
return Arrays.asList(); return Arrays.asList(generateUpdateInfo(source.getDateofacceptance().getValue(), source, target));
}
return new ArrayList<>();
} }
@Override @Override
public UpdateInfo<String> generateUpdateInfo(final String highlightValue, final Result source, public UpdateInfo<String> generateUpdateInfo(final String highlightValue,
final Result source,
final Result target) { final Result target) {
return new UpdateInfo<>( return new UpdateInfo<>(
Topic.ENRICH_MISSING_PUBLICATION_DATE, Topic.ENRICH_MISSING_PUBLICATION_DATE,

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcher.java
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@ -30,8 +30,7 @@ public abstract class UpdateMatcher<T> {
if (source != res) { if (source != res) {
for (final UpdateInfo<T> info : findUpdates(source, res)) { for (final UpdateInfo<T> info : findUpdates(source, res)) {
final String s = DigestUtils.md5Hex(info.getHighlightValueAsString()); final String s = DigestUtils.md5Hex(info.getHighlightValueAsString());
if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) { if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) {} else {
} else {
infoMap.put(s, info); infoMap.put(s, info);
} }
} }
@ -54,11 +53,16 @@ public abstract class UpdateMatcher<T> {
protected abstract List<UpdateInfo<T>> findUpdates(Result source, Result target); protected abstract List<UpdateInfo<T>> findUpdates(Result source, Result target);
protected abstract UpdateInfo<T> generateUpdateInfo(final T highlightValue, final Result source, protected abstract UpdateInfo<T> generateUpdateInfo(final T highlightValue,
final Result source,
final Result target); final Result target);
protected static boolean isMissing(final List<Field<String>> list) { protected static boolean isMissing(final List<Field<String>> list) {
return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0).getValue()); return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0).getValue());
} }
protected boolean isMissing(final Field<String> field) {
return field == null || StringUtils.isBlank(field.getValue());
}
} }

3
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java
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@ -129,6 +129,9 @@ public class DedupUtility {
.max(Comparator.comparing(Tuple2::_1)); .max(Comparator.comparing(Tuple2::_1));
if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) { if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) {
Author r = simAuhtor.get()._2(); Author r = simAuhtor.get()._2();
if (r.getPid() == null) {
r.setPid(new ArrayList<>());
}
r.getPid().add(a._1()); r.getPid().add(a._1());
} }
}); });

4
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java
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@ -53,9 +53,7 @@ public class PrepareResultCommunitySetStep2 {
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
if (isTest(parser)) { removeOutputDir(spark, outputPath);
removeOutputDir(spark, outputPath);
}
mergeInfo(spark, inputPath, outputPath); mergeInfo(spark, inputPath, outputPath);
}); });
} }

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/SparkResultToOrganizationFromIstRepoJob.java
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@ -84,7 +84,7 @@ public class SparkResultToOrganizationFromIstRepoJob {
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
removeOutputDir(spark, outputPath); // removeOutputDir(spark, outputPath);
if (saveGraph) { if (saveGraph) {
execPropagation( execPropagation(
spark, spark,

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
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@ -42,8 +42,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
final String pid = e.attributeValue("nameIdentifier"); final String pid = e.attributeValue("nameIdentifier");
final String pidType = e.attributeValue("nameIdentifierScheme"); final String pidType = e.attributeValue("nameIdentifierScheme");
author.setPid(new ArrayList<>());
if (StringUtils.isNotBlank(pid) && StringUtils.isNotBlank(pidType)) { if (StringUtils.isNotBlank(pid) && StringUtils.isNotBlank(pidType)) {
author.setPid(new ArrayList<>());
author author
.getPid() .getPid()
.add(structuredProperty(pid, qualifier(pidType, pidType, DNET_PID_TYPES, DNET_PID_TYPES), info)); .add(structuredProperty(pid, qualifier(pidType, pidType, DNET_PID_TYPES, DNET_PID_TYPES), info));