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dnet-hadoop
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merge upstream

This commit is contained in:
Miriam Baglioni 2020-08-03 18:13:42 +02:00
parent 9e997e63a2 8cc067fe76
commit b34177d8ef
34 changed files with 1165 additions and 203 deletions
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1
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
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@ -7,6 +7,7 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class ModelConstants {
public static final String DNET_SUBJECT_TYPOLOGIES = "dnet:subject_classification_typologies";
public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies";
public static final String DNET_PUBLICATION_RESOURCE = "dnet:publication_resource";
public static final String DNET_ACCESS_MODES = "dnet:access_modes";

8
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java
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@ -289,4 +289,12 @@ public class JsonPathTest {
System.out.println("d = " + d);
}
@Test
public void testNull() throws Exception {
final Object p = null;
System.out.println((String) p);
}
}

23
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java
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@ -6,6 +6,7 @@ import java.util.Collection;
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.PairFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
@ -15,6 +16,8 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset;
import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
@ -30,10 +33,16 @@ public class DedupRecordFactory {
final DedupConfig dedupConf) {
long ts = System.currentTimeMillis();
// <id, json_entity>
final JavaPairRDD<String, String> inputJsonEntities = sc
.textFile(entitiesInputPath)
final JavaPairRDD<String, String> inputJsonEntities = spark
.read()
.load(entitiesInputPath)
.as(Encoders.kryo(Oaf.class))
.map(
(MapFunction<Oaf, String>) p -> new org.codehaus.jackson.map.ObjectMapper().writeValueAsString(p),
Encoders.STRING())
.javaRDD()
.mapToPair(
(PairFunction<String, String, String>) it -> new Tuple2<String, String>(
(PairFunction<String, String, String>) it -> new Tuple2<>(
MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), it), it));
// <source, target>: source is the dedup_id, target is the id of the mergedIn
@ -74,9 +83,9 @@ public class DedupRecordFactory {
}
}
private static Publication publicationMerger(Tuple2<String, Iterable<String>> e, final long ts) {
private static DLIPublication publicationMerger(Tuple2<String, Iterable<String>> e, final long ts) {
Publication p = new Publication(); // the result of the merge, to be returned at the end
DLIPublication p = new DLIPublication(); // the result of the merge, to be returned at the end
p.setId(e._1());
@ -110,9 +119,9 @@ public class DedupRecordFactory {
return p;
}
private static Dataset datasetMerger(Tuple2<String, Iterable<String>> e, final long ts) {
private static DLIDataset datasetMerger(Tuple2<String, Iterable<String>> e, final long ts) {
Dataset d = new Dataset(); // the result of the merge, to be returned at the end
DLIDataset d = new DLIDataset(); // the result of the merge, to be returned at the end
d.setId(e._1());

12
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java
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@ -9,18 +9,21 @@ 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.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.graphx.Edge;
import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.codehaus.jackson.map.ObjectMapper;
import com.google.common.hash.Hashing;
import eu.dnetlib.dedup.graph.ConnectedComponent;
import eu.dnetlib.dedup.graph.GraphProcessor;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.util.MapDocumentUtil;
@ -42,7 +45,6 @@ public class SparkCreateConnectedComponent {
.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");
@ -50,8 +52,12 @@ public class SparkCreateConnectedComponent {
// DedupConfig.load(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json")));
final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
final JavaPairRDD<Object, String> vertexes = sc
.textFile(inputPath + "/" + entity)
final JavaPairRDD<Object, String> vertexes = spark
.read()
.load(inputPath + "/" + entity)
.as(Encoders.kryo(Oaf.class))
.map((MapFunction<Oaf, String>) p -> new ObjectMapper().writeValueAsString(p), Encoders.STRING())
.javaRDD()
.map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s))
.mapToPair(
(PairFunction<String, Object, String>) s -> new Tuple2<Object, String>(getHashcode(s), s));

25
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java
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@ -4,10 +4,10 @@ package eu.dnetlib.dedup;
import org.apache.commons.io.IOUtils;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.pace.config.DedupConfig;
@ -41,12 +41,19 @@ public class SparkCreateDedupRecord {
DedupUtility.createEntityPath(sourcePath, entity),
OafEntityType.valueOf(entity),
dedupConf);
dedupRecord
.map(
r -> {
ObjectMapper mapper = new ObjectMapper();
return mapper.writeValueAsString(r);
})
.saveAsTextFile(dedupPath + "/" + entity + "/dedup_records");
spark
.createDataset(dedupRecord.rdd(), Encoders.kryo(OafEntity.class))
.write()
.mode(SaveMode.Overwrite)
.save(dedupPath + "/" + entity + "/dedup_records");
//
//
// dedupRecord
// .map(
// r -> {
// ObjectMapper mapper = new ObjectMapper();
// return mapper.writeValueAsString(r);
// })
// .saveAsTextFile(dedupPath + "/" + entity + "/dedup_records");
}
}

11
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java
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@ -7,10 +7,13 @@ import org.apache.commons.io.IOUtils;
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.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.codehaus.jackson.map.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
@ -46,8 +49,12 @@ public class SparkCreateSimRels {
// DedupConfig.load(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
JavaPairRDD<String, MapDocument> mapDocument = sc
.textFile(inputPath + "/" + entity)
JavaPairRDD<String, MapDocument> mapDocument = spark
.read()
.load(inputPath + "/" + entity)
.as(Encoders.kryo(Oaf.class))
.map((MapFunction<Oaf, String>) p -> new ObjectMapper().writeValueAsString(p), Encoders.STRING())
.javaRDD()
.mapToPair(
s -> {
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);

63
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java
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@ -14,16 +14,11 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation;
import eu.dnetlib.dhp.utils.DHPUtils;
import scala.Tuple2;
public class SparkPropagateRelationsJob {
enum FieldType {
SOURCE, TARGET
}
static final String SOURCEJSONPATH = "$.source";
static final String TARGETJSONPATH = "$.target";
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -39,7 +34,6 @@ public class SparkPropagateRelationsJob {
.master(parser.get("master"))
.getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final String relationPath = parser.get("relationPath");
final String mergeRelPath = parser.get("mergeRelPath");
final String targetRelPath = parser.get("targetRelPath");
@ -50,63 +44,38 @@ public class SparkPropagateRelationsJob {
.as(Encoders.bean(Relation.class))
.where("relClass == 'merges'");
final Dataset<Relation> rels = spark.read().load(relationPath).as(Encoders.bean(Relation.class));
final Dataset<DLIRelation> rels = spark
.read()
.load(relationPath)
.as(Encoders.kryo(DLIRelation.class))
.map(
(MapFunction<DLIRelation, DLIRelation>) r -> r,
Encoders.bean(DLIRelation.class));
final Dataset<Relation> firstJoin = rels
final Dataset<DLIRelation> firstJoin = rels
.joinWith(merge, merge.col("target").equalTo(rels.col("source")), "left_outer")
.map(
(MapFunction<Tuple2<Relation, Relation>, Relation>) r -> {
(MapFunction<Tuple2<DLIRelation, Relation>, DLIRelation>) r -> {
final Relation mergeRelation = r._2();
final Relation relation = r._1();
final DLIRelation relation = r._1();
if (mergeRelation != null)
relation.setSource(mergeRelation.getSource());
return relation;
},
Encoders.bean(Relation.class));
Encoders.bean(DLIRelation.class));
final Dataset<Relation> secondJoin = firstJoin
final Dataset<DLIRelation> secondJoin = firstJoin
.joinWith(merge, merge.col("target").equalTo(firstJoin.col("target")), "left_outer")
.map(
(MapFunction<Tuple2<Relation, Relation>, Relation>) r -> {
(MapFunction<Tuple2<DLIRelation, Relation>, DLIRelation>) r -> {
final Relation mergeRelation = r._2();
final Relation relation = r._1();
final DLIRelation relation = r._1();
if (mergeRelation != null)
relation.setTarget(mergeRelation.getSource());
return relation;
},
Encoders.bean(Relation.class));
Encoders.kryo(DLIRelation.class));
secondJoin.write().mode(SaveMode.Overwrite).save(targetRelPath);
}
private static boolean containsDedup(final String json) {
final String source = DHPUtils.getJPathString(SOURCEJSONPATH, json);
final String target = DHPUtils.getJPathString(TARGETJSONPATH, json);
return source.toLowerCase().contains("dedup") || target.toLowerCase().contains("dedup");
}
private static String replaceField(final String json, final String id, final FieldType type) {
ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
try {
Relation relation = mapper.readValue(json, Relation.class);
if (relation.getDataInfo() == null)
relation.setDataInfo(new DataInfo());
relation.getDataInfo().setDeletedbyinference(false);
switch (type) {
case SOURCE:
relation.setSource(id);
return mapper.writeValueAsString(relation);
case TARGET:
relation.setTarget(id);
return mapper.writeValueAsString(relation);
default:
throw new IllegalArgumentException("");
}
} catch (IOException e) {
throw new RuntimeException("unable to deserialize json relation: " + json, e);
}
}
}

75
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityWithDedupInfo.scala Normal file
View File

@ -0,0 +1,75 @@
package eu.dnetlib.dedup.sx
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation, DLIUnknown, OafUtils}
import org.apache.commons.io.IOUtils
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.LoggerFactory
import org.apache.spark.sql.functions.col
object SparkUpdateEntityWithDedupInfo {
def main(args: Array[String]): Unit = {
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkUpdateEntityWithDedupInfo.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json")))
val logger = LoggerFactory.getLogger(SparkUpdateEntityWithDedupInfo.getClass)
parser.parseArgument(args)
val workingPath: String = parser.get("workingPath")
logger.info(s"Working dir path = $workingPath")
implicit val oafEncoder: Encoder[OafEntity] = Encoders.kryo[OafEntity]
implicit val relEncoder: Encoder[Relation] = Encoders.bean(classOf[Relation])
implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication]
implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset]
implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown]
implicit val dlirelEncoder: Encoder[DLIRelation] = Encoders.kryo[DLIRelation]
val spark: SparkSession = SparkSession
.builder()
.appName(SparkUpdateEntityWithDedupInfo.getClass.getSimpleName)
.master(parser.get("master"))
.getOrCreate()
val entityPath = parser.get("entityPath")
val mergeRelPath = parser.get("mergeRelPath")
val dedupRecordPath = parser.get("dedupRecordPath")
val entity = parser.get("entity")
val destination = parser.get("targetPath")
val mergedIds = spark.read.load(mergeRelPath).as[Relation]
.where("relClass == 'merges'")
.select(col("target"))
val entities: Dataset[(String, OafEntity)] = spark
.read
.load(entityPath).as[OafEntity]
.map(o => (o.getId, o))(Encoders.tuple(Encoders.STRING, oafEncoder))
val finalDataset:Dataset[OafEntity] = entities.joinWith(mergedIds, entities("_1").equalTo(mergedIds("target")), "left")
.map(k => {
val e: OafEntity = k._1._2
val t = k._2
if (t != null && t.getString(0).nonEmpty) {
if (e.getDataInfo == null) {
e.setDataInfo(OafUtils.generateDataInfo())
}
e.getDataInfo.setDeletedbyinference(true)
}
e
})
val dedupRecords :Dataset[OafEntity] = spark.read.load(dedupRecordPath).as[OafEntity]
finalDataset.union(dedupRecords)
.repartition(1200).write
.mode(SaveMode.Overwrite).save(destination)
}
}

2
dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/oozie_app/workflow.xml
View File

@ -144,7 +144,7 @@
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Update ${entity} and add DedupRecord</name>
<class>eu.dnetlib.dedup.sx.SparkUpdateEntityJob</class>
<class>eu.dnetlib.dedup.sx.SparkUpdateEntityWithDedupInfo</class>
<jar>dhp-dedup-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}

63
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java
View File

@ -90,6 +90,7 @@ public class CleanGraphSparkJob {
final CleaningRuleMap mapping = CleaningRuleMap.create(vocs);
readTableFromPath(spark, inputPath, clazz)
.map((MapFunction<T, T>) value -> fixVocabularyNames(value), Encoders.bean(clazz))
.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
.map((MapFunction<T, T>) value -> fixDefaults(value), Encoders.bean(clazz))
.write()
@ -98,6 +99,65 @@ public class CleanGraphSparkJob {
.json(outputPath);
}
protected static <T extends Oaf> T fixVocabularyNames(T value) {
if (value instanceof Datasource) {
// nothing to clean here
} else if (value instanceof Project) {
// nothing to clean here
} else if (value instanceof Organization) {
Organization o = (Organization) value;
if (Objects.nonNull(o.getCountry())) {
fixVocabName(o.getCountry(), ModelConstants.DNET_COUNTRY_TYPE);
}
} else if (value instanceof Relation) {
// nothing to clean here
} else if (value instanceof Result) {
Result r = (Result) value;
fixVocabName(r.getLanguage(), ModelConstants.DNET_LANGUAGES);
fixVocabName(r.getResourcetype(), ModelConstants.DNET_DATA_CITE_RESOURCE);
fixVocabName(r.getBestaccessright(), ModelConstants.DNET_ACCESS_MODES);
if (Objects.nonNull(r.getSubject())) {
r.getSubject().forEach(s -> fixVocabName(s.getQualifier(), ModelConstants.DNET_SUBJECT_TYPOLOGIES));
}
if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) {
fixVocabName(i.getAccessright(), ModelConstants.DNET_ACCESS_MODES);
fixVocabName(i.getRefereed(), ModelConstants.DNET_REVIEW_LEVELS);
}
}
if (Objects.nonNull(r.getAuthor())) {
r.getAuthor().forEach(a -> {
if (Objects.nonNull(a.getPid())) {
a.getPid().forEach(p -> {
fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES);
});
}
});
}
if (value instanceof Publication) {
} else if (value instanceof eu.dnetlib.dhp.schema.oaf.Dataset) {
} else if (value instanceof OtherResearchProduct) {
} else if (value instanceof Software) {
}
}
return value;
}
private static void fixVocabName(Qualifier q, String vocabularyName) {
if (Objects.nonNull(q) && StringUtils.isBlank(q.getSchemeid())) {
q.setSchemeid(vocabularyName);
q.setSchemename(vocabularyName);
}
}
protected static <T extends Oaf> T fixDefaults(T value) {
if (value instanceof Datasource) {
// nothing to clean here
@ -113,6 +173,9 @@ public class CleanGraphSparkJob {
} else if (value instanceof Result) {
Result r = (Result) value;
if (Objects.nonNull(r.getPublisher()) && StringUtils.isBlank(r.getPublisher().getValue())) {
r.setPublisher(null);
}
if (Objects.isNull(r.getLanguage()) || StringUtils.isBlank(r.getLanguage().getClassid())) {
r
.setLanguage(

33
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -44,6 +44,7 @@ import java.util.Date;
import java.util.List;
import java.util.function.Consumer;
import java.util.function.Function;
import java.util.function.Predicate;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
@ -53,6 +54,7 @@ import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.oa.graph.raw.common.VerifyNsPrefixPredicate;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
@ -113,6 +115,11 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final String hdfsPath = parser.get("hdfsPath");
log.info("hdfsPath: {}", hdfsPath);
final String nsPrefixBlacklist = parser.get("nsPrefixBlacklist");
log.info("nsPrefixBlacklist: {}", nsPrefixBlacklist);
final Predicate<Oaf> verifyNamespacePrefix = new VerifyNsPrefixPredicate(nsPrefixBlacklist);
final boolean processClaims = parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims");
log.info("processClaims: {}", processClaims);
@ -123,23 +130,25 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
smdbe.execute("queryClaims.sql", smdbe::processClaims);
} else {
log.info("Processing datasources...");
smdbe.execute("queryDatasources.sql", smdbe::processDatasource);
smdbe.execute("queryDatasources.sql", smdbe::processDatasource, verifyNamespacePrefix);
log.info("Processing projects...");
if (dbSchema.equalsIgnoreCase("beta")) {
smdbe.execute("queryProjects.sql", smdbe::processProject);
smdbe.execute("queryProjects.sql", smdbe::processProject, verifyNamespacePrefix);
} else {
smdbe.execute("queryProjects_production.sql", smdbe::processProject);
smdbe.execute("queryProjects_production.sql", smdbe::processProject, verifyNamespacePrefix);
}
log.info("Processing orgs...");
smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
smdbe.execute("queryOrganizations.sql", smdbe::processOrganization, verifyNamespacePrefix);
log.info("Processing relationsNoRemoval ds <-> orgs ...");
smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
smdbe
.execute(
"queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization, verifyNamespacePrefix);
log.info("Processing projects <-> orgs ...");
smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization);
smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization, verifyNamespacePrefix);
}
log.info("All done.");
}
@ -163,10 +172,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
}
public void execute(final String sqlFile, final Function<ResultSet, List<Oaf>> producer)
throws Exception {
execute(sqlFile, producer, oaf -> true);
}
public void execute(final String sqlFile, final Function<ResultSet, List<Oaf>> producer,
final Predicate<Oaf> predicate)
throws Exception {
final String sql = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile));
final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf));
final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(oaf -> {
if (predicate.test(oaf)) {
emitOaf(oaf);
}
});
dbClient.processResults(sql, consumer);
}

62
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VerifyNsPrefixPredicate.java Normal file
View File

@ -0,0 +1,62 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
import java.util.HashSet;
import java.util.Set;
import java.util.function.Predicate;
import java.util.regex.Pattern;
import org.apache.commons.lang3.StringUtils;
import com.google.common.base.Splitter;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation;
/**
* This predicate should be used to skip oaf objects using a blacklist of nsprefixes.
*
* @author michele
*/
public class VerifyNsPrefixPredicate implements Predicate<Oaf> {
final Set<String> invalids = new HashSet<>();
public VerifyNsPrefixPredicate(final String blacklist) {
if (StringUtils.isNotBlank(blacklist)) {
Splitter
.on(",")
.trimResults()
.omitEmptyStrings()
.split(blacklist)
.forEach(invalids::add);
}
}
@Override
public boolean test(final Oaf oaf) {
if (oaf instanceof Datasource) {
return testValue(((Datasource) oaf).getNamespaceprefix().getValue());
} else if (oaf instanceof OafEntity) {
return testValue(((OafEntity) oaf).getId());
} else if (oaf instanceof Relation) {
return testValue(((Relation) oaf).getSource()) && testValue(((Relation) oaf).getTarget());
} else {
return true;
}
}
protected boolean testValue(final String s) {
if (StringUtils.isNotBlank(s)) {
for (final String invalid : invalids) {
if (Pattern.matches("^(\\d\\d\\|)?" + invalid + ".*$", s)) {
return false;
}
}
}
return true;
}
}

105
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/EBIAggregator.scala
View File

@ -1,5 +1,6 @@
package eu.dnetlib.dhp.sx.ebi
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation, DLIUnknown}
import org.apache.spark.sql.{Encoder, Encoders}
import org.apache.spark.sql.expressions.Aggregator
@ -35,6 +36,88 @@ object EBIAggregator {
}
def getDLIUnknownAggregator(): Aggregator[(String, DLIUnknown), DLIUnknown, DLIUnknown] = new Aggregator[(String, DLIUnknown), DLIUnknown, DLIUnknown]{
override def zero: DLIUnknown = new DLIUnknown()
override def reduce(b: DLIUnknown, a: (String, DLIUnknown)): DLIUnknown = {
b.mergeFrom(a._2)
if (b.getId == null)
b.setId(a._2.getId)
b
}
override def merge(wx: DLIUnknown, wy: DLIUnknown): DLIUnknown = {
wx.mergeFrom(wy)
if(wx.getId == null && wy.getId.nonEmpty)
wx.setId(wy.getId)
wx
}
override def finish(reduction: DLIUnknown): DLIUnknown = reduction
override def bufferEncoder: Encoder[DLIUnknown] =
Encoders.kryo(classOf[DLIUnknown])
override def outputEncoder: Encoder[DLIUnknown] =
Encoders.kryo(classOf[DLIUnknown])
}
def getDLIDatasetAggregator(): Aggregator[(String, DLIDataset), DLIDataset, DLIDataset] = new Aggregator[(String, DLIDataset), DLIDataset, DLIDataset]{
override def zero: DLIDataset = new DLIDataset()
override def reduce(b: DLIDataset, a: (String, DLIDataset)): DLIDataset = {
b.mergeFrom(a._2)
if (b.getId == null)
b.setId(a._2.getId)
b
}
override def merge(wx: DLIDataset, wy: DLIDataset): DLIDataset = {
wx.mergeFrom(wy)
if(wx.getId == null && wy.getId.nonEmpty)
wx.setId(wy.getId)
wx
}
override def finish(reduction: DLIDataset): DLIDataset = reduction
override def bufferEncoder: Encoder[DLIDataset] =
Encoders.kryo(classOf[DLIDataset])
override def outputEncoder: Encoder[DLIDataset] =
Encoders.kryo(classOf[DLIDataset])
}
def getDLIPublicationAggregator(): Aggregator[(String, DLIPublication), DLIPublication, DLIPublication] = new Aggregator[(String, DLIPublication), DLIPublication, DLIPublication]{
override def zero: DLIPublication = new DLIPublication()
override def reduce(b: DLIPublication, a: (String, DLIPublication)): DLIPublication = {
b.mergeFrom(a._2)
if (b.getId == null)
b.setId(a._2.getId)
b
}
override def merge(wx: DLIPublication, wy: DLIPublication): DLIPublication = {
wx.mergeFrom(wy)
if(wx.getId == null && wy.getId.nonEmpty)
wx.setId(wy.getId)
wx
}
override def finish(reduction: DLIPublication): DLIPublication = reduction
override def bufferEncoder: Encoder[DLIPublication] =
Encoders.kryo(classOf[DLIPublication])
override def outputEncoder: Encoder[DLIPublication] =
Encoders.kryo(classOf[DLIPublication])
}
def getPublicationAggregator(): Aggregator[(String, Publication), Publication, Publication] = new Aggregator[(String, Publication), Publication, Publication]{
override def zero: Publication = new Publication()
@ -85,5 +168,27 @@ object EBIAggregator {
}
def getDLIRelationAggregator(): Aggregator[(String, DLIRelation), DLIRelation, DLIRelation] = new Aggregator[(String, DLIRelation), DLIRelation, DLIRelation]{
override def zero: DLIRelation = new DLIRelation()
override def reduce(b: DLIRelation, a: (String, DLIRelation)): DLIRelation = {
a._2
}
override def merge(a: DLIRelation, b: DLIRelation): DLIRelation = {
if(b!= null) b else a
}
override def finish(reduction: DLIRelation): DLIRelation = reduction
override def bufferEncoder: Encoder[DLIRelation] =
Encoders.kryo(classOf[DLIRelation])
override def outputEncoder: Encoder[DLIRelation] =
Encoders.kryo(classOf[DLIRelation])
}
}

112
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala
View File

@ -1,8 +1,9 @@
package eu.dnetlib.dhp.sx.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Instance, KeyValue, Oaf}
import eu.dnetlib.dhp.schema.oaf.{Author, Instance, Journal, KeyValue, Oaf, Publication, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils.createQualifier
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIRelation, OafUtils, ProvenaceInfo}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation, OafUtils, ProvenaceInfo}
import eu.dnetlib.dhp.sx.ebi.model.{PMArticle, PMAuthor, PMJournal}
import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.scholexplorer.relation.RelationMapper
import org.apache.commons.io.IOUtils
@ -12,6 +13,7 @@ import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import org.apache.spark.sql.functions._
import scala.collection.JavaConverters._
@ -28,6 +30,64 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin
}
def journalToOAF(pj:PMJournal): Journal = {
val j = new Journal
j.setIssnPrinted(pj.getIssn)
j.setVol(pj.getVolume)
j.setName(pj.getTitle)
j.setIss(pj.getIssue)
j.setDataInfo(OafUtils.generateDataInfo())
j
}
def pubmedTOPublication(input:PMArticle):DLIPublication = {
val dnetPublicationId = s"50|${DHPUtils.md5(s"${input.getPmid}::pmid")}"
val p = new DLIPublication
p.setId(dnetPublicationId)
p.setDataInfo(OafUtils.generateDataInfo())
p.setPid(List(OafUtils.createSP(input.getPmid.toLowerCase.trim, "pmid", "dnet:pid_types")).asJava)
p.setCompletionStatus("complete")
val pi = new ProvenaceInfo
pi.setId("dli_________::europe_pmc__")
pi.setName( "Europe PMC")
pi.setCompletionStatus("complete")
pi.setCollectionMode("collected")
p.setDlicollectedfrom(List(pi).asJava)
p.setCollectedfrom(List(generatePubmedDLICollectedFrom()).asJava)
if (input.getAuthors != null && input.getAuthors.size() >0) {
var aths: List[Author] = List()
input.getAuthors.asScala.filter(a=> a!= null).foreach(a => {
val c = new Author
c.setFullname(a.getFullName)
c.setName(a.getForeName)
c.setSurname(a.getLastName)
aths = aths ::: List(c)
})
if (aths.nonEmpty)
p.setAuthor(aths.asJava)
}
if (input.getJournal != null)
p.setJournal(journalToOAF(input.getJournal))
p.setTitle(List(OafUtils.createSP(input.getTitle, "main title", "dnet:dataCite_title")).asJava)
p.setDateofacceptance(OafUtils.asField(input.getDate))
val i = new Instance
i.setCollectedfrom(generatePubmedDLICollectedFrom())
i.setDateofacceptance(p.getDateofacceptance)
i.setUrl(List(s"https://pubmed.ncbi.nlm.nih.gov/${input.getPmid}").asJava)
i.setInstancetype(createQualifier("0001", "Article", "dnet:publication_resource", "dnet:publication_resource"))
p.setInstance(List(i).asJava)
p
}
def ebiLinksToOaf(input:(String, String)):List[Oaf] = {
val pmid :String = input._1
val input_json :String = input._2
@ -116,8 +176,16 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin
val workingPath = parser.get("workingPath")
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
implicit val oafpubEncoder: Encoder[Publication] = Encoders.kryo[Publication]
implicit val relEncoder: Encoder[DLIRelation] = Encoders.kryo(classOf[DLIRelation])
implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo(classOf[DLIDataset])
implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo(classOf[DLIPublication])
implicit val atEncoder: Encoder[Author] = Encoders.kryo(classOf[Author])
implicit val strEncoder:Encoder[String] = Encoders.STRING
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
val ds:Dataset[(String,String)] = spark.read.load(s"$workingPath/baseline_links_updates").as[(String,String)](Encoders.tuple(Encoders.STRING, Encoders.STRING))
@ -133,6 +201,46 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin
oDataset.filter(p =>p.isInstanceOf[DLIDataset]).map(p => p.asInstanceOf[DLIDataset]).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_links_updates_dataset")
val idPublicationSolved:Dataset[String] = spark.read.load(s"$workingPath/baseline_links_updates").where(col("links").isNotNull).select("pmid").as[String]
val baseline:Dataset[(String, PMArticle)]= spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle].map(p=> (p.getPmid, p))(Encoders.tuple(strEncoder,PMEncoder))
idPublicationSolved.joinWith(baseline, idPublicationSolved("pmid").equalTo(baseline("_1"))).map(k => pubmedTOPublication(k._2._2)).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_links_updates_publication")
val pmaDatasets = spark.read.load("/user/sandro.labruzzo/scholix/EBI/ebi_garr/baseline_dataset").as[PMArticle]
pmaDatasets.map(p => pubmedTOPublication(p)).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_publication_all")
val pubs: Dataset[(String,Publication)] = spark.read.load("/user/sandro.labruzzo/scholix/EBI/publication").as[Publication].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING,oafpubEncoder))
val pubdate:Dataset[(String,DLIPublication)] = spark.read.load(s"$workingPath/baseline_publication_all").as[DLIPublication].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING,pubEncoder))
pubs.joinWith(pubdate, pubs("_1").equalTo(pubdate("_1"))).map(k => k._2._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_publication_ebi")
val dt : Dataset[DLIDataset] = spark.read.load(s"$workingPath/dataset").as[DLIDataset]
val update : Dataset[DLIDataset] = spark.read.load(s"$workingPath/ebi_garr/baseline_links_updates_dataset").as[DLIDataset]
dt.union(update).map(d => (d.getId,d))(Encoders.tuple(Encoders.STRING, datEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getDLIDatasetAggregator().toColumn)
.map(p => p._2)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset_ebi")
val rel: Dataset[DLIRelation] = spark.read.load(s"$workingPath/relation").as[DLIRelation]
val relupdate : Dataset[DLIRelation] = spark.read.load(s"$workingPath/ebi_garr/baseline_links_updates_relation").as[DLIRelation]
rel.union(relupdate)
.map(d => (s"${d.getSource}::${d.getRelType}::${d.getTarget}", d))(Encoders.tuple(Encoders.STRING, relEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getDLIRelationAggregator().toColumn)
.map(p => p._2)
.write.mode(SaveMode.Overwrite)
.save(s"$workingPath/baseline_relation_ebi")
}
}

63
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateEBIDataFrame.scala
View File

@ -2,6 +2,7 @@ package eu.dnetlib.dhp.sx.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation}
import eu.dnetlib.dhp.sx.graph.parser.{DatasetScholexplorerParser, PublicationScholexplorerParser}
import eu.dnetlib.scholexplorer.relation.RelationMapper
import org.apache.commons.io.IOUtils
@ -10,6 +11,7 @@ import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
object SparkCreateEBIDataFrame {
@ -34,54 +36,51 @@ object SparkCreateEBIDataFrame {
val relationMapper = RelationMapper.load
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
implicit val pubEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
implicit val datasetEncoder: Encoder[DLIDataset] = Encoders.kryo(classOf[DLIDataset])
implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo(classOf[DLIPublication])
implicit val relEncoder: Encoder[DLIRelation] = Encoders.kryo(classOf[DLIRelation])
logger.info("Extract Publication and relation from publication_xml")
val oafPubsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/publication_xml").map(s =>
{
new ObjectMapper().readValue(s, classOf[String])
}).flatMap(s => {
val d = new PublicationScholexplorerParser
d.parseObject(s, relationMapper).asScala.iterator})
// logger.info("Extract Publication and relation from publication_xml")
// val oafPubsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/publication_xml").map(s =>
// {
// new ObjectMapper().readValue(s, classOf[String])
// }).flatMap(s => {
// val d = new PublicationScholexplorerParser
// d.parseObject(s, relationMapper).asScala.iterator})
//
// val mapper = new ObjectMapper()
// mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
// spark.createDataset(oafPubsRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/oaf")
//
// logger.info("Extract Publication and relation from dataset_xml")
// val oafDatsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/dataset_xml").map(s =>
// {
// new ObjectMapper().readValue(s, classOf[String])
// }).flatMap(s => {
// val d = new DatasetScholexplorerParser
// d.parseObject(s, relationMapper).asScala.iterator})
val mapper = new ObjectMapper()
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
spark.createDataset(oafPubsRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/oaf")
logger.info("Extract Publication and relation from dataset_xml")
val oafDatsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/dataset_xml").map(s =>
{
new ObjectMapper().readValue(s, classOf[String])
}).flatMap(s => {
val d = new DatasetScholexplorerParser
d.parseObject(s, relationMapper).asScala.iterator})
spark.createDataset(oafDatsRDD).write.mode(SaveMode.Append).save(s"$workingPath/oaf")
val dataset: Dataset[OafDataset] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[OafDataset]).map(d => d.asInstanceOf[OafDataset])
val publication: Dataset[Publication] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[Publication]).map(d => d.asInstanceOf[Publication])
val relations: Dataset[Relation] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[Relation]).map(d => d.asInstanceOf[Relation])
// spark.createDataset(oafDatsRDD).write.mode(SaveMode.Append).save(s"$workingPath/oaf")
val dataset: Dataset[DLIDataset] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[DLIDataset]).map(d => d.asInstanceOf[DLIDataset])
val publication: Dataset[DLIPublication] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[DLIPublication]).map(d => d.asInstanceOf[DLIPublication])
val relations: Dataset[DLIRelation] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[DLIRelation]).map(d => d.asInstanceOf[DLIRelation])
publication.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, pubEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getPublicationAggregator().toColumn)
.agg(EBIAggregator.getDLIPublicationAggregator().toColumn)
.map(p => p._2)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/publication")
dataset.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datasetEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getDatasetAggregator().toColumn)
.agg(EBIAggregator.getDLIDatasetAggregator().toColumn)
.map(p => p._2)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/dataset")
relations.map(d => (s"${d.getSource}::${d.getRelType}::${d.getTarget}", d))(Encoders.tuple(Encoders.STRING, relEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getRelationAggregator().toColumn)
.agg(EBIAggregator.getDLIRelationAggregator().toColumn)
.map(p => p._2)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/relation")
relations.map(r => (r.getSource, r.getTarget))(Encoders.tuple(Encoders.STRING,Encoders.STRING))
}
}

3
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMAuthor.java
View File

@ -25,7 +25,8 @@ public class PMAuthor implements Serializable {
}
public String getFullName() {
return String.format("%s, %s", this.foreName, this.lastName);
return String
.format("%s, %s", this.foreName != null ? this.foreName : "", this.lastName != null ? this.lastName : "");
}
}

106
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSplitOafTODLIEntities.scala Normal file
View File

@ -0,0 +1,106 @@
package eu.dnetlib.dhp.sx.graph
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation, DLIUnknown}
import eu.dnetlib.dhp.sx.ebi.EBIAggregator
import eu.dnetlib.dhp.sx.ebi.model.{PMArticle, PMAuthor, PMJournal}
import org.apache.commons.io.IOUtils
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.LoggerFactory
object SparkSplitOafTODLIEntities {
def getKeyRelation(rel:DLIRelation):String = {
s"${rel.getSource}::${rel.getRelType}::${rel.getTarget}"
}
def main(args: Array[String]): Unit = {
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkSplitOafTODLIEntities.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json")))
val logger = LoggerFactory.getLogger(SparkSplitOafTODLIEntities.getClass)
parser.parseArgument(args)
val workingPath: String = parser.get("workingPath")
logger.info(s"Working dir path = $workingPath")
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication]
implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset]
implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown]
implicit val relEncoder: Encoder[DLIRelation] = Encoders.kryo[DLIRelation]
val spark:SparkSession = SparkSession
.builder()
.appName(SparkSplitOafTODLIEntities.getClass.getSimpleName)
.master(parser.get("master"))
.getOrCreate()
val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf]
val ebi_dataset:Dataset[DLIDataset] = spark.read.load(s"$workingPath/ebi/baseline_dataset_ebi").as[DLIDataset]
val ebi_publication:Dataset[DLIPublication] = spark.read.load(s"$workingPath/ebi/baseline_publication_ebi").as[DLIPublication]
val ebi_relation:Dataset[DLIRelation] = spark.read.load(s"$workingPath/ebi/baseline_relation_ebi").as[DLIRelation]
OAFDataset
.filter(s => s != null && s.isInstanceOf[DLIPublication])
.map(s =>s.asInstanceOf[DLIPublication])
.union(ebi_publication)
.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, pubEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getDLIPublicationAggregator().toColumn)
.map(p => p._2)
.repartition(1000)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/publication")
OAFDataset
.filter(s => s != null && s.isInstanceOf[DLIDataset])
.map(s =>s.asInstanceOf[DLIDataset])
.union(ebi_dataset)
.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getDLIDatasetAggregator().toColumn)
.map(p => p._2)
.repartition(1000)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/dataset")
OAFDataset
.filter(s => s != null && s.isInstanceOf[DLIUnknown])
.map(s =>s.asInstanceOf[DLIUnknown])
.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, unkEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getDLIUnknownAggregator().toColumn)
.map(p => p._2)
.repartition(1000)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/unknown")
OAFDataset
.filter(s => s != null && s.isInstanceOf[DLIRelation])
.map(s =>s.asInstanceOf[DLIRelation])
.union(ebi_relation)
.map(d => (getKeyRelation(d), d))(Encoders.tuple(Encoders.STRING, relEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(EBIAggregator.getDLIRelationAggregator().toColumn)
.map(p => p._2)
.repartition(1000)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/relation")
}
}

73
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkXMLToOAFDataset.scala Normal file
View File

@ -0,0 +1,73 @@
package eu.dnetlib.dhp.sx.graph
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation}
import eu.dnetlib.dhp.sx.graph.parser.{DatasetScholexplorerParser, PublicationScholexplorerParser}
import eu.dnetlib.scholexplorer.relation.RelationMapper
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.{IntWritable, Text}
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.LoggerFactory
import scala.collection.JavaConverters._
/**
* This new version of the Job read a sequential File containing XML stored in the aggregator and generates a Dataset OAF of heterogeneous
* entities like Dataset, Relation, Publication and Unknown
*/
object SparkXMLToOAFDataset {
def main(args: Array[String]): Unit = {
val logger = LoggerFactory.getLogger(SparkXMLToOAFDataset.getClass)
val conf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkXMLToOAFDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_graph_scholix_parameters.json")))
parser.parseArgument(args)
val spark =
SparkSession
.builder()
.config(conf)
.appName(SparkXMLToOAFDataset.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sc = spark.sparkContext
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val datasetEncoder:Encoder[DLIDataset] = Encoders.kryo[DLIDataset]
implicit val publicationEncoder:Encoder[DLIPublication] = Encoders.kryo[DLIPublication]
implicit val relationEncoder:Encoder[DLIRelation] = Encoders.kryo[DLIRelation]
val relationMapper = RelationMapper.load
val inputPath: String = parser.get("sourcePath")
val entity: String = parser.get("entity")
val targetPath = parser.get("targetPath")
logger.info(s"Input path is $inputPath")
logger.info(s"Entity path is $entity")
logger.info(s"Target Path is $targetPath")
val scholixRdd:RDD[Oaf] = sc.sequenceFile(inputPath, classOf[IntWritable], classOf[Text])
.map(s => s._2.toString)
.flatMap(s => {
entity match {
case "publication" =>
val p = new PublicationScholexplorerParser
val l =p.parseObject(s, relationMapper)
if (l != null) l.asScala else List()
case "dataset" =>
val d = new DatasetScholexplorerParser
val l =d.parseObject(s, relationMapper)
if (l != null) l.asScala else List()
}
}).filter(s => s!= null)
spark.createDataset(scholixRdd).write.mode(SaveMode.Append).save(targetPath)
}
}

9
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java
View File

@ -317,6 +317,15 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser {
.collect(Collectors.toList()));
}
// TERRIBLE HACK TO AVOID EMPTY COLLECTED FROM
if (parsedObject.getDlicollectedfrom() == null) {
final KeyValue cf = new KeyValue();
cf.setKey("dli_________::europe_pmc__");
cf.setValue("Europe PMC");
parsedObject.setCollectedfrom(Collections.singletonList(cf));
}
if (StringUtils.isNotBlank(resolvedURL)) {
Instance i = new Instance();
i.setCollectedfrom(parsedObject.getCollectedfrom().get(0));

6
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json
View File

@ -40,5 +40,11 @@
"paramLongName": "dbschema",
"paramDescription": "the database schema according to the D-Net infrastructure (beta or production)",
"paramRequired": true
},
{
"paramName": "nsbl",
"paramLongName": "nsPrefixBlacklist",
"paramDescription": "a blacklist of nsprefixes (comma separeted)",
"paramRequired": false
}
]

8
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
View File

@ -43,7 +43,11 @@
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>nsPrefixBlacklist</name>
<value></value>
<description>a blacklist of nsprefixes (comma separeted)</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -131,6 +135,7 @@
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--action</arg><arg>claims</arg>
<arg>--dbschema</arg><arg>${dbSchema}</arg>
<arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg>
</java>
<ok to="ImportODF_claims"/>
<error to="Kill"/>
@ -182,6 +187,7 @@
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--dbschema</arg><arg>${dbSchema}</arg>
<arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg>
</java>
<ok to="ImportODF"/>
<error to="Kill"/>

7
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/oozie_app/workflow.xml
View File

@ -38,7 +38,11 @@
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>nsPrefixBlacklist</name>
<value></value>
<description>a blacklist of nsprefixes (comma separeted)</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -113,6 +117,7 @@
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--action</arg><arg>claims</arg>
<arg>--dbschema</arg><arg>${dbSchema}</arg>
<arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg>
</java>
<ok to="ImportODF_claims"/>
<error to="Kill"/>

8
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml
View File

@ -25,7 +25,11 @@
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>nsPrefixBlacklist</name>
<value></value>
<description>a blacklist of nsprefixes (comma separeted)</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -99,6 +103,7 @@
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--dbschema</arg><arg>${dbSchema}</arg>
<arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg>
</java>
<ok to="ImportDB_claims"/>
<error to="Kill"/>
@ -117,6 +122,7 @@
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--dbschema</arg><arg>${dbSchema}</arg>
<arg>--action</arg><arg>claims</arg>
<arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>

6
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml
View File

@ -28,6 +28,11 @@
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>nsPrefixBlacklist</name>
<value></value>
<description>a blacklist of nsprefixes (comma separeted)</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -67,6 +72,7 @@
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
<arg>-islookup</arg><arg>${isLookupUrl}</arg>
<arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg>
</java>
<ok to="ImportODF"/>
<error to="Kill"/>

36
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/config-default.xml
View File

@ -1,7 +1,7 @@
<configuration>
<!-- OCEAN -->
<!--
<property>
<name>jobTracker</name>
<value>yarnRM</value>
@ -18,26 +18,26 @@
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
-->
<!-- GARR -->
<property>
<name>jobTracker</name>
<value>yarn</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://hadoop-rm1.garr-pa1.d4science.org:8020</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://hadoop-edge3.garr-pa1.d4science.org:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://hadoop-rm2.garr-pa1.d4science.org:19888</value>
</property>
<!-- <property>-->
<!-- <name>jobTracker</name>-->
<!-- <value>yarn</value>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>nameNode</name>-->
<!-- <value>hdfs://hadoop-rm1.garr-pa1.d4science.org:8020</value>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>hive_metastore_uris</name>-->
<!-- <value>thrift://hadoop-edge3.garr-pa1.d4science.org:9083</value>-->
<!-- </property>-->
<!-- <property>-->
<!-- <name>spark2YarnHistoryServerAddress</name>-->
<!-- <value>http://hadoop-rm2.garr-pa1.d4science.org:19888</value>-->
<!-- </property>-->
<property>

44
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/workflow.xml
View File

@ -18,7 +18,7 @@
</property>
</parameters>
<start to="GenerateUpdates"/>
<start to="CreateEBIDataSet"/>
<kill name="Kill">
@ -48,6 +48,28 @@
<error to="Kill"/>
</action>
<action name="CreateEBIDataSet">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create EBI DataSet</name>
<class>eu.dnetlib.dhp.sx.ebi.SparkCreateEBIDataFrame</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=1000
${sparkExtraOPT}
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn</arg>
</spark>
<ok to="GenerateUpdates"/>
<error to="Kill"/>
</action>
<action name="GenerateUpdates">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
@ -71,27 +93,7 @@
</action>
<action name="CreateEBIDataSet">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create EBI DataSet</name>
<class>eu.dnetlib.dhp.sx.ebi.SparkCreateEBIDataFrame</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=1000
${sparkExtraOPT}
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--master</arg><arg>yarn</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

7
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json
View File

@ -1,7 +1,4 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the result data", "paramRequired": true},
{"paramName":"td", "paramLongName":"targetDir", "paramDescription": "the name of the result data", "paramRequired": true},
{"paramName":"e", "paramLongName":"entities", "paramDescription": "the entity type to be filtered", "paramRequired": true}
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the work dir path", "paramRequired": true}
]

13
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml
View File

@ -101,12 +101,17 @@
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Import ${entity} and related entities</name>
<class>eu.dnetlib.dhp.sx.graph.SparkScholexplorerGraphImporter</class>
<class>eu.dnetlib.dhp.sx.graph.SparkXMLToOAFDataset</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg> <arg>yarn</arg>
<arg>--sourcePath</arg><arg>${targetXMLPath}</arg>
<arg>--targetPath</arg><arg>${targetEntityPath}</arg>
<arg>--targetPath</arg><arg>${workingPath}/input/OAFDataset</arg>
<arg>--entity</arg><arg>${entity}</arg>
</spark>
<ok to="End"/>

44
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml
View File

@ -1,16 +1,8 @@
<workflow-app name="Create Raw Graph Step 2: Map XML to OAF Entities" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>targetPath</name>
<description>the source path</description>
</property>
<property>
<name>targetDir</name>
<description>the name of the path</description>
<name>workingPath</name>
<description>the working path</description>
</property>
<property>
<name>sparkDriverMemory</name>
@ -20,32 +12,13 @@
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>entities</name>
<description>the entities to be extracted</description>
</property>
</parameters>
<start to="DeleteTargetPath"/>
<start to="ExtractDLIEntities"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DeleteTargetPath">
<fs>
<mkdir path="${targetPath}"/>
<mkdir path="${targetPath}/dataset"/>
<mkdir path="${targetPath}/publication"/>
<mkdir path="${targetPath}/unknown"/>
<mkdir path="${targetPath}/relation"/>
<delete path='${targetPath}/dataset/${targetDir}'/>
<delete path='${targetPath}/publication/${targetDir}'/>
<delete path='${targetPath}/unknown/${targetDir}'/>
<delete path='${targetPath}/relation/${targetDir}'/>
</fs>
<ok to="ExtractDLIEntities"/>
<error to="Kill"/>
</action>
<action name="ExtractDLIEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
@ -53,19 +26,18 @@
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Extract ${entities}</name>
<class>eu.dnetlib.dhp.sx.graph.SparkExtractEntitiesJob</class>
<name>Extract DLI Entities</name>
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--targetDir</arg><arg>${targetDir}</arg>
<arg>--entities</arg><arg>${entities}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

30
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java
View File

@ -7,6 +7,8 @@ import static org.mockito.Mockito.lenient;
import java.io.IOException;
import java.util.List;
import java.util.Set;
import java.util.function.Predicate;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.io.IOUtils;
@ -19,9 +21,7 @@ import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -62,10 +62,12 @@ public class CleaningFunctionTest {
assertTrue(p_in instanceof Result);
assertTrue(p_in instanceof Publication);
Publication p_out = OafCleaner.apply(p_in, mapping);
Publication p_out = OafCleaner.apply(CleanGraphSparkJob.fixVocabularyNames(p_in), mapping);
assertNotNull(p_out);
assertNotNull(p_out.getPublisher());
assertNull(p_out.getPublisher().getValue());
assertEquals("und", p_out.getLanguage().getClassid());
assertEquals("Undetermined", p_out.getLanguage().getClassname());
@ -88,6 +90,16 @@ public class CleaningFunctionTest {
Publication p_defaults = CleanGraphSparkJob.fixDefaults(p_out);
assertEquals("CLOSED", p_defaults.getBestaccessright().getClassid());
assertNull(p_out.getPublisher());
getAuthorPids(p_defaults).forEach(pid -> {
System.out
.println(
String
.format(
"%s [%s - %s]", pid.getValue(), pid.getQualifier().getClassid(),
pid.getQualifier().getClassname()));
});
// TODO add more assertions to verity the cleaned values
System.out.println(MAPPER.writeValueAsString(p_out));
@ -97,7 +109,7 @@ public class CleaningFunctionTest {
*/
}
private Stream<Qualifier> getAuthorPidTypes(Publication pub) {
private Stream<Qualifier> getAuthorPidTypes(Result pub) {
return pub
.getAuthor()
.stream()
@ -106,6 +118,14 @@ public class CleaningFunctionTest {
.map(s -> s.getQualifier());
}
private Stream<StructuredProperty> getAuthorPids(Result pub) {
return pub
.getAuthor()
.stream()
.map(a -> a.getPid())
.flatMap(p -> p.stream());
}
private List<String> vocs() throws IOException {
return IOUtils
.readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"));

11
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -276,6 +276,17 @@ public class MappersTest {
System.out.println("***************");
}
@Test
void testClaimDedup() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_dedup.xml"));
final List<Oaf> list = new OafToOafMapper(vocs, false).processMdRecord(xml);
System.out.println("***************");
System.out.println(new ObjectMapper().writeValueAsString(list));
System.out.println("***************");
}
private void assertValidId(final String id) {
assertEquals(49, id.length());
assertEquals('|', id.charAt(2));

92
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/common/VerifyNsPrefixPredicateTest.java Normal file
View File

@ -0,0 +1,92 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Relation;
class VerifyNsPrefixPredicateTest {
private VerifyNsPrefixPredicate predicate;
@BeforeEach
void setUp() throws Exception {
predicate = new VerifyNsPrefixPredicate("corda,nsf,wt");
}
@Test
void testTestValue() {
assertFalse(predicate.testValue("corda__2020"));
assertFalse(predicate.testValue("nsf________"));
assertFalse(predicate.testValue("nsf"));
assertFalse(predicate.testValue("corda"));
assertFalse(predicate.testValue("10|corda_______::fjkdsfjksdhfksj"));
assertFalse(predicate.testValue("20|corda_______::fjkdsfjksdhfksj"));
assertTrue(predicate.testValue("xxxxxx_____"));
assertTrue(predicate.testValue("10|xxxxxx_____::sdasdasaddasad"));
assertTrue(predicate.testValue(null));
assertTrue(predicate.testValue(""));
}
@Test
void testTest_ds_true() {
final Field<String> prefix = new Field<>();
prefix.setValue("xxxxxx______");
final Datasource ds = new Datasource();
ds.setNamespaceprefix(prefix);
assertTrue(predicate.test(ds));
}
@Test
void testTest_ds_false() {
final Field<String> prefix = new Field<>();
prefix.setValue("corda__2020");
final Datasource ds = new Datasource();
ds.setNamespaceprefix(prefix);
assertFalse(predicate.test(ds));
}
@Test
void testTest_rel_true() {
final Relation rel = new Relation();
rel.setSource("10|yyyyyy______:sdfsfsffsdfs");
rel.setTarget("10|xxxxxx______:sdfsfsffsdfs");
assertTrue(predicate.test(rel));
}
@Test
void testTest_rel_false() {
final Relation rel = new Relation();
rel.setSource("10|corda_______:sdfsfsffsdfs");
rel.setTarget("10|xxxxxx______:sdfsfsffsdfs");
assertFalse(predicate.test(rel));
}
@Test
void testTest_proj_true() {
final Project p = new Project();
p.setId("10|xxxxxx______:sdfsfsffsdfs");
assertTrue(predicate.test(p));
}
@Test
void testTest_proj_false() {
final Project p = new Project();
p.setId("10|corda_____:sdfsfsffsdfs");
assertFalse(predicate.test(p));
}
}

25
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
View File

@ -59,6 +59,28 @@
"schemename": "dnet:pid_types"
},
"value": "qwerty"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
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Morocco; FOM and NWO, Netherlands; RCN, Norway; MNiSW, Poland; GRICES and FCT, Portugal;
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SRC and Wallenberg Foundation, Sweden; SER, SNSF and Cantons of Bern and Geneva,
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