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Merge branch 'beta' into datasource_pdf_consent

This commit is contained in:
Claudio Atzori 2022-03-28 09:20:48 +02:00
parent 3610f1749a 61319b2e83
commit 741bc99c47
29 changed files with 808 additions and 152 deletions
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2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
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@ -107,7 +107,7 @@ public class DedupRecordFactory {
entity.setId(id); entity.setId(id);
entity.setLastupdatetimestamp(ts); entity.setLastupdatetimestamp(ts);
entity.getDataInfo().setDeletedbyinference(false); entity.setDataInfo(dataInfo);
return entity; return entity;
} }

11
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
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@ -77,7 +77,16 @@ class EntityMergerTest implements Serializable {
// verify id // verify id
assertEquals(dedupId, pub_merged.getId()); assertEquals(dedupId, pub_merged.getId());
assertEquals(pub_top.getJournal(), pub_merged.getJournal()); assertEquals(pub_top.getJournal().getName(), pub_merged.getJournal().getName());
assertEquals(pub_top.getJournal().getIssnOnline(), pub_merged.getJournal().getIssnOnline());
assertEquals(pub_top.getJournal().getIssnLinking(), pub_merged.getJournal().getIssnLinking());
assertEquals(pub_top.getJournal().getIssnPrinted(), pub_merged.getJournal().getIssnPrinted());
assertEquals(pub_top.getJournal().getIss(), pub_merged.getJournal().getIss());
assertEquals(pub_top.getJournal().getEp(), pub_merged.getJournal().getEp());
assertEquals(pub_top.getJournal().getSp(), pub_merged.getJournal().getSp());
assertEquals(pub_top.getJournal().getVol(), pub_merged.getJournal().getVol());
assertEquals(pub_top.getJournal().getConferencedate(), pub_merged.getJournal().getConferencedate());
assertEquals(pub_top.getJournal().getConferenceplace(), pub_merged.getJournal().getConferenceplace());
assertEquals("OPEN", pub_merged.getBestaccessright().getClassid()); assertEquals("OPEN", pub_merged.getBestaccessright().getClassid());
assertEquals(pub_top.getResulttype(), pub_merged.getResulttype()); assertEquals(pub_top.getResulttype(), pub_merged.getResulttype());
assertEquals(pub_top.getLanguage(), pub_merged.getLanguage()); assertEquals(pub_top.getLanguage(), pub_merged.getLanguage());

62
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
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@ -206,11 +206,16 @@ public class SparkDedupTest implements Serializable {
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct")) .load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct"))
.count(); .count();
assertEquals(3082, orgs_simrel); assertEquals(3076, orgs_simrel);
assertEquals(7036, pubs_simrel); assertEquals(7040, pubs_simrel);
assertEquals(336, sw_simrel); assertEquals(336, sw_simrel);
assertEquals(442, ds_simrel); assertEquals(442, ds_simrel);
assertEquals(6750, orp_simrel); assertEquals(6784, orp_simrel);
// System.out.println("orgs_simrel = " + orgs_simrel);
// System.out.println("pubs_simrel = " + pubs_simrel);
// System.out.println("sw_simrel = " + sw_simrel);
// System.out.println("ds_simrel = " + ds_simrel);
// System.out.println("orp_simrel = " + orp_simrel);
} }
@Test @Test
@ -258,10 +263,14 @@ public class SparkDedupTest implements Serializable {
.count(); .count();
// entities simrels supposed to be equal to the number of previous step (no rels in whitelist) // entities simrels supposed to be equal to the number of previous step (no rels in whitelist)
assertEquals(3082, orgs_simrel); assertEquals(3076, orgs_simrel);
assertEquals(7036, pubs_simrel); assertEquals(7040, pubs_simrel);
assertEquals(442, ds_simrel); assertEquals(442, ds_simrel);
assertEquals(6750, orp_simrel); assertEquals(6784, orp_simrel);
// System.out.println("orgs_simrel = " + orgs_simrel);
// System.out.println("pubs_simrel = " + pubs_simrel);
// System.out.println("ds_simrel = " + ds_simrel);
// System.out.println("orp_simrel = " + orp_simrel);
// entities simrels to be different from the number of previous step (new simrels in the whitelist) // entities simrels to be different from the number of previous step (new simrels in the whitelist)
Dataset<Row> sw_simrel = spark Dataset<Row> sw_simrel = spark
@ -288,6 +297,7 @@ public class SparkDedupTest implements Serializable {
.count() > 0); .count() > 0);
assertEquals(338, sw_simrel.count()); assertEquals(338, sw_simrel.count());
// System.out.println("sw_simrel = " + sw_simrel.count());
} }
@ -435,11 +445,16 @@ public class SparkDedupTest implements Serializable {
.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel") .load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
.count(); .count();
assertEquals(1272, orgs_mergerel); assertEquals(1268, orgs_mergerel);
assertEquals(1438, pubs_mergerel); assertEquals(1444, pubs_mergerel);
assertEquals(286, sw_mergerel); assertEquals(286, sw_mergerel);
assertEquals(472, ds_mergerel); assertEquals(472, ds_mergerel);
assertEquals(718, orp_mergerel); assertEquals(738, orp_mergerel);
// System.out.println("orgs_mergerel = " + orgs_mergerel);
// System.out.println("pubs_mergerel = " + pubs_mergerel);
// System.out.println("sw_mergerel = " + sw_mergerel);
// System.out.println("ds_mergerel = " + ds_mergerel);
// System.out.println("orp_mergerel = " + orp_mergerel);
} }
@ -483,11 +498,17 @@ public class SparkDedupTest implements Serializable {
testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord") testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord")
.count(); .count();
assertEquals(85, orgs_deduprecord); assertEquals(86, orgs_deduprecord);
assertEquals(65, pubs_deduprecord); assertEquals(67, pubs_deduprecord);
assertEquals(49, sw_deduprecord); assertEquals(49, sw_deduprecord);
assertEquals(97, ds_deduprecord); assertEquals(97, ds_deduprecord);
assertEquals(89, orp_deduprecord); assertEquals(92, orp_deduprecord);
// System.out.println("orgs_deduprecord = " + orgs_deduprecord);
// System.out.println("pubs_deduprecord = " + pubs_deduprecord);
// System.out.println("sw_deduprecord = " + sw_deduprecord);
// System.out.println("ds_deduprecord = " + ds_deduprecord);
// System.out.println("orp_deduprecord = " + orp_deduprecord);
} }
@Test @Test
@ -566,13 +587,21 @@ public class SparkDedupTest implements Serializable {
.distinct() .distinct()
.count(); .count();
assertEquals(896, publications); assertEquals(898, publications);
assertEquals(838, organizations); assertEquals(839, organizations);
assertEquals(100, projects); assertEquals(100, projects);
assertEquals(100, datasource); assertEquals(100, datasource);
assertEquals(198, softwares); assertEquals(198, softwares);
assertEquals(389, dataset); assertEquals(389, dataset);
assertEquals(517, otherresearchproduct); assertEquals(520, otherresearchproduct);
// System.out.println("publications = " + publications);
// System.out.println("organizations = " + organizations);
// System.out.println("projects = " + projects);
// System.out.println("datasource = " + datasource);
// System.out.println("software = " + softwares);
// System.out.println("dataset = " + dataset);
// System.out.println("otherresearchproduct = " + otherresearchproduct);
long deletedOrgs = jsc long deletedOrgs = jsc
.textFile(testDedupGraphBasePath + "/organization") .textFile(testDedupGraphBasePath + "/organization")
@ -626,7 +655,8 @@ public class SparkDedupTest implements Serializable {
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
assertEquals(4860, relations); // assertEquals(4860, relations);
System.out.println("relations = " + relations);
// check deletedbyinference // check deletedbyinference
final Dataset<Relation> mergeRels = spark final Dataset<Relation> mergeRels = spark

7
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/CountrySbs.java
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@ -22,4 +22,11 @@ public class CountrySbs implements Serializable {
public void setClassname(String classname) { public void setClassname(String classname) {
this.classname = classname; this.classname = classname;
} }
public static CountrySbs newInstance(String classid, String classname) {
CountrySbs csbs = new CountrySbs();
csbs.classid = classid;
csbs.classname = classname;
return csbs;
}
} }

7
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountry.java
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@ -22,4 +22,11 @@ public class DatasourceCountry implements Serializable {
public void setCountry(CountrySbs country) { public void setCountry(CountrySbs country) {
this.country = country; this.country = country;
} }
public static DatasourceCountry newInstance(String dataSourceId, CountrySbs country) {
DatasourceCountry dsc = new DatasourceCountry();
dsc.dataSourceId = dataSourceId;
dsc.country = country;
return dsc;
}
} }

32
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/EntityEntityRel.java Normal file
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@ -0,0 +1,32 @@
package eu.dnetlib.dhp.countrypropagation;
import java.io.Serializable;
public class EntityEntityRel implements Serializable {
private String entity1Id;
private String entity2Id;
public static EntityEntityRel newInstance(String source, String target) {
EntityEntityRel dso = new EntityEntityRel();
dso.entity1Id = source;
dso.entity2Id = target;
return dso;
}
public String getEntity1Id() {
return entity1Id;
}
public void setEntity1Id(String entity1Id) {
this.entity1Id = entity1Id;
}
public String getEntity2Id() {
return entity2Id;
}
public void setEntity2Id(String entity2Id) {
this.entity2Id = entity2Id;
}
}

79
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java
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@ -2,14 +2,16 @@
package eu.dnetlib.dhp.countrypropagation; package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SaveMode;
@ -17,11 +19,15 @@ 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.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
/** /**
* For the association of the country to the datasource The association is computed only for datasource of specific type * For the association of the country to the datasource The association is computed only for datasource of specific type
@ -54,9 +60,8 @@ public class PrepareDatasourceCountryAssociation {
log.info("outputPath {}: ", outputPath); log.info("outputPath {}: ", outputPath);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
@ -77,40 +82,46 @@ public class PrepareDatasourceCountryAssociation {
String inputPath, String inputPath,
String outputPath) { String outputPath) {
final String whitelisted = whitelist // filtering of the datasource taking only the non deleted by inference and those with the allowed types or
.stream() // whose id is in whitelist
.map(id -> " d.id = '" + id + "'") Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class)
.collect(Collectors.joining(" OR ")); .filter(
(FilterFunction<Datasource>) ds -> !ds.getDataInfo().getDeletedbyinference() &&
(allowedtypes.contains(ds.getDatasourcetype().getClassid()) ||
whitelist.contains(ds.getId())));
final String allowed = allowedtypes // filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass
.stream() Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class)
.map(type -> " d.datasourcetype.classid = '" + type + "'") .filter(
.collect(Collectors.joining(" OR ")); (FilterFunction<Relation>) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) &&
!rel.getDataInfo().getDeletedbyinference());
Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class); // filtering of the organization taking only the non deleted by inference and those with information about the
Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class); // country
Dataset<Organization> organization = readPath(spark, inputPath + "/organization", Organization.class); Dataset<Organization> organization = readPath(spark, inputPath + "/organization", Organization.class)
.filter(
(FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference() &&
o.getCountry().getClassid().length() > 0 &&
!o.getCountry().getClassid().equals(ModelConstants.UNKNOWN));
datasource.createOrReplaceTempView("datasource"); // associated the datasource id with the id of the organization providing the datasource
relation.createOrReplaceTempView("relation"); Dataset<EntityEntityRel> dse = datasource
organization.createOrReplaceTempView("organization"); .joinWith(relation, datasource.col("id").equalTo(relation.col("source")))
.map(
(MapFunction<Tuple2<Datasource, Relation>, EntityEntityRel>) t2 -> EntityEntityRel
.newInstance(t2._2.getSource(), t2._2.getTarget()),
Encoders.bean(EntityEntityRel.class));
String query = "SELECT source dataSourceId, " + // joins with the information stored in the organization dataset to associate the country to the datasource id
"named_struct('classid', country.classid, 'classname', country.classname) country " + dse
"FROM datasource d " + .joinWith(organization, dse.col("entity2Id").equalTo(organization.col("id")))
"JOIN relation rel " + .map((MapFunction<Tuple2<EntityEntityRel, Organization>, DatasourceCountry>) t2 -> {
"ON d.id = rel.source " + Qualifier country = t2._2.getCountry();
"JOIN organization o " + return DatasourceCountry
"ON o.id = rel.target " + .newInstance(
"WHERE rel.datainfo.deletedbyinference = false " + t2._1.getEntity1Id(),
"and lower(rel.relclass) = '" + ModelConstants.IS_PROVIDED_BY.toLowerCase() + "'" + CountrySbs.newInstance(country.getClassid(), country.getClassname()));
"and o.datainfo.deletedbyinference = false " + }, Encoders.bean(DatasourceCountry.class))
"and length(o.country.classid) > 0 " +
"and (" + allowed + " or " + whitelisted + ")";
spark
.sql(query)
.as(Encoders.bean(DatasourceCountry.class))
.write() .write()
.option("compression", "gzip") .option("compression", "gzip")
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)

99
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java
View File

@ -3,14 +3,21 @@ package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.*; import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set; import java.util.Set;
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.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.*; import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.slf4j.Logger; import org.slf4j.Logger;
@ -23,14 +30,6 @@ import scala.Tuple2;
public class PrepareResultCountrySet { public class PrepareResultCountrySet {
private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class); private static final Logger log = LoggerFactory.getLogger(PrepareResultCountrySet.class);
private static final String RESULT_COUNTRYSET_QUERY = "SELECT id resultId, collect_set(country) countrySet "
+ "FROM ( SELECT id, country "
+ "FROM datasource_country JOIN cfhb ON cf = dataSourceId "
+ "UNION ALL "
+ "SELECT id, country FROM datasource_country "
+ "JOIN cfhb ON hb = dataSourceId ) tmp "
+ "GROUP BY id";
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils String jsonConfiguration = IOUtils
.toString( .toString(
@ -45,6 +44,8 @@ public class PrepareResultCountrySet {
Boolean isSparkSessionManaged = isSparkSessionManaged(parser); Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String workingPath = parser.get("workingPath");
String inputPath = parser.get("sourcePath"); String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath); log.info("inputPath: {}", inputPath);
@ -60,9 +61,8 @@ public class PrepareResultCountrySet {
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName); Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
@ -72,6 +72,7 @@ public class PrepareResultCountrySet {
inputPath, inputPath,
outputPath, outputPath,
datasourcecountrypath, datasourcecountrypath,
workingPath,
resultClazz); resultClazz);
}); });
} }
@ -81,43 +82,63 @@ public class PrepareResultCountrySet {
String inputPath, String inputPath,
String outputPath, String outputPath,
String datasourcecountrypath, String datasourcecountrypath,
String workingPath,
Class<R> resultClazz) { Class<R> resultClazz) {
Dataset<R> result = readPath(spark, inputPath, resultClazz); // selects all the results non deleted by inference and non invisible
result.createOrReplaceTempView("result"); Dataset<R> result = readPath(spark, inputPath, resultClazz)
.filter(
(FilterFunction<R>) r -> !r.getDataInfo().getDeletedbyinference() &&
!r.getDataInfo().getInvisible());
createCfHbforResult(spark); // of the results collects the distinct keys for collected from (at the level of the result) and hosted by
// and produces pairs resultId, key for each distinct key associated to the result
result.flatMap((FlatMapFunction<R, EntityEntityRel>) r -> {
Set<String> cfhb = r.getCollectedfrom().stream().map(cf -> cf.getKey()).collect(Collectors.toSet());
cfhb.addAll(r.getInstance().stream().map(i -> i.getHostedby().getKey()).collect(Collectors.toSet()));
return cfhb
.stream()
.map(value -> EntityEntityRel.newInstance(r.getId(), value))
.collect(Collectors.toList())
.iterator();
}, Encoders.bean(EntityEntityRel.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath + "/resultCfHb");
Dataset<DatasourceCountry> datasource_country = readPath(spark, datasourcecountrypath, DatasourceCountry.class); Dataset<DatasourceCountry> datasource_country = readPath(spark, datasourcecountrypath, DatasourceCountry.class);
datasource_country.createOrReplaceTempView("datasource_country"); Dataset<EntityEntityRel> cfhb = readPath(spark, workingPath + "/resultCfHb", EntityEntityRel.class);
spark
.sql(RESULT_COUNTRYSET_QUERY)
.as(Encoders.bean(ResultCountrySet.class))
.toJavaRDD()
.mapToPair(value -> new Tuple2<>(value.getResultId(), value))
.reduceByKey((a, b) -> {
ArrayList<CountrySbs> countryList = a.getCountrySet();
Set<String> countryCodes = countryList
.stream()
.map(CountrySbs::getClassid)
.collect(Collectors.toSet());
b
.getCountrySet()
.stream()
.forEach(c -> {
if (!countryCodes.contains(c.getClassid())) {
countryList.add(c);
countryCodes.add(c.getClassid());
}
datasource_country
.joinWith(
cfhb, cfhb
.col("entity2Id")
.equalTo(datasource_country.col("datasourceId")))
.groupByKey(
(MapFunction<Tuple2<DatasourceCountry, EntityEntityRel>, String>) t2 -> t2._2().getEntity1Id(),
Encoders.STRING())
.mapGroups(
(MapGroupsFunction<String, Tuple2<DatasourceCountry, EntityEntityRel>, ResultCountrySet>) (k, it) -> {
ResultCountrySet rcs = new ResultCountrySet();
rcs.setResultId(k);
Set<CountrySbs> set = new HashSet<>();
Set<String> countryCodes = new HashSet<>();
DatasourceCountry first = it.next()._1();
countryCodes.add(first.getCountry().getClassid());
set.add(first.getCountry());
it.forEachRemaining(t2 -> {
if (!countryCodes.contains(t2._1().getCountry().getClassid()))
set.add(t2._1().getCountry());
}); });
a.setCountrySet(countryList); rcs.setCountrySet(new ArrayList<>(set));
return a; return rcs;
}) }, Encoders.bean(ResultCountrySet.class))
.map(couple -> OBJECT_MAPPER.writeValueAsString(couple._2())) .write()
.saveAsTextFile(outputPath, GzipCodec.class); .mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
} }
} }

15
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java
View File

@ -56,12 +56,6 @@ public class SparkCountryPropagationJob {
final String resultClassName = parser.get("resultTableName"); final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName); log.info("resultTableName: {}", resultClassName);
final Boolean saveGraph = Optional
.ofNullable(parser.get("saveGraph"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("saveGraph: {}", saveGraph);
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName); Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
@ -75,8 +69,7 @@ public class SparkCountryPropagationJob {
sourcePath, sourcePath,
preparedInfoPath, preparedInfoPath,
outputPath, outputPath,
resultClazz, resultClazz);
saveGraph);
}); });
} }
@ -85,10 +78,8 @@ public class SparkCountryPropagationJob {
String sourcePath, String sourcePath,
String preparedInfoPath, String preparedInfoPath,
String outputPath, String outputPath,
Class<R> resultClazz, Class<R> resultClazz) {
boolean saveGraph) {
if (saveGraph) {
log.info("Reading Graph table from: {}", sourcePath); log.info("Reading Graph table from: {}", sourcePath);
Dataset<R> res = readPath(spark, sourcePath, resultClazz); Dataset<R> res = readPath(spark, sourcePath, resultClazz);
@ -105,7 +96,7 @@ public class SparkCountryPropagationJob {
.option("compression", "gzip") .option("compression", "gzip")
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.json(outputPath); .json(outputPath);
}
} }
private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() { private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() {

12
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json
View File

@ -5,18 +5,6 @@
"paramDescription": "the path of the sequencial file to read", "paramDescription": "the path of the sequencial file to read",
"paramRequired": true "paramRequired": true
}, },
{
"paramName":"h",
"paramLongName":"hive_metastore_uris",
"paramDescription": "the hive metastore uris",
"paramRequired": false
},
{
"paramName":"sg",
"paramLongName":"saveGraph",
"paramDescription": "true if the new version of the graph must be saved",
"paramRequired": false
},
{ {
"paramName":"tn", "paramName":"tn",
"paramLongName":"resultTableName", "paramLongName":"resultTableName",

6
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json
View File

@ -5,12 +5,6 @@
"paramDescription": "the path of the sequencial file to read", "paramDescription": "the path of the sequencial file to read",
"paramRequired": true "paramRequired": true
}, },
{
"paramName":"h",
"paramLongName":"hive_metastore_uris",
"paramDescription": "the hive metastore uris",
"paramRequired": true
},
{ {
"paramName": "out", "paramName": "out",
"paramLongName": "outputPath", "paramLongName": "outputPath",

6
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json
View File

@ -12,9 +12,9 @@
"paramRequired": true "paramRequired": true
}, },
{ {
"paramName":"h", "paramName":"w",
"paramLongName":"hive_metastore_uris", "paramLongName":"workingPath",
"paramDescription": "the hive metastore uris", "paramDescription": "the working path",
"paramRequired": true "paramRequired": true
}, },
{ {

9
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml
View File

@ -110,7 +110,6 @@
<arg>--sourcePath</arg><arg>${sourcePath}</arg> <arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--whitelist</arg><arg>${whitelist}</arg> <arg>--whitelist</arg><arg>${whitelist}</arg>
<arg>--allowedtypes</arg><arg>${allowedtypes}</arg> <arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg> <arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark> </spark>
<ok to="fork_join_prepare_result_country"/> <ok to="fork_join_prepare_result_country"/>
@ -146,7 +145,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg> <arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/publication</arg> <arg>--outputPath</arg><arg>${workingDir}/publication</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--workingPath</arg><arg>${workingDir}/workingP</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark> </spark>
@ -176,7 +175,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg> <arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/dataset</arg> <arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--workingPath</arg><arg>${workingDir}/workingD</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark> </spark>
@ -206,7 +205,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg> <arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg> <arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--workingPath</arg><arg>${workingDir}/workingO</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark> </spark>
@ -236,7 +235,7 @@
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg> <arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--outputPath</arg><arg>${workingDir}/software</arg> <arg>--outputPath</arg><arg>${workingDir}/software</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--workingPath</arg><arg>${workingDir}/workingS</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark> </spark>

1
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml
View File

@ -173,6 +173,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors} --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
--conf spark.sql.shuffle.partitions=3840
</spark-opts> </spark-opts>
<arg>--relationPath</arg><arg>${workingDir}/preparedInfo/relation</arg> <arg>--relationPath</arg><arg>${workingDir}/preparedInfo/relation</arg>
<arg>--outputPath</arg><arg>${outputPath}/relation</arg> <arg>--outputPath</arg><arg>${outputPath}/relation</arg>

149
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java
View File

@ -24,6 +24,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Country; import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.Software;
import scala.Tuple2; import scala.Tuple2;
@ -69,17 +70,16 @@ public class CountryPropagationJobTest {
@Test @Test
void testCountryPropagationSoftware() throws Exception { void testCountryPropagationSoftware() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/sample/software") .getResource("/eu/dnetlib/dhp/countrypropagation/graph/software")
.getPath(); .getPath();
final String preparedInfoPath = getClass() final String preparedInfoPath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo") .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/software")
.getPath(); .getPath();
SparkCountryPropagationJob SparkCountryPropagationJob
.main( .main(
new String[] { new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(), "--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath, "--sourcePath", sourcePath,
"-saveGraph", "true",
"-resultTableName", Software.class.getCanonicalName(), "-resultTableName", Software.class.getCanonicalName(),
"-outputPath", workingDir.toString() + "/software", "-outputPath", workingDir.toString() + "/software",
"-preparedInfoPath", preparedInfoPath "-preparedInfoPath", preparedInfoPath
@ -91,8 +91,6 @@ public class CountryPropagationJobTest {
.textFile(workingDir.toString() + "/software") .textFile(workingDir.toString() + "/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class)); .map(item -> OBJECT_MAPPER.readValue(item, Software.class));
// tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s));
Assertions.assertEquals(10, tmp.count()); Assertions.assertEquals(10, tmp.count());
Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class)); Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
@ -259,4 +257,145 @@ public class CountryPropagationJobTest {
7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count()); 7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count());
} }
@Test
void testCountryPropagationPublication() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication")
.getPath();
final String preparedInfoPath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication")
.getPath();
SparkCountryPropagationJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"-resultTableName", Publication.class.getCanonicalName(),
"-outputPath", workingDir.toString() + "/publication",
"-preparedInfoPath", preparedInfoPath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(12, tmp.count());
Assertions.assertEquals(5, tmp.filter(r -> r.getCountry().size() > 0).count());
tmp
.foreach(
r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemeid())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemename())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(c -> Assertions.assertFalse(c.getDataInfo().getDeletedbyinference())));
tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertFalse(c.getDataInfo().getInvisible())));
tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertTrue(c.getDataInfo().getInferred())));
tmp
.foreach(
r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("0.85", c.getDataInfo().getTrust())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(c -> Assertions.assertEquals("propagation", c.getDataInfo().getInferenceprovenance())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(
c -> Assertions
.assertEquals("country:instrepos", c.getDataInfo().getProvenanceaction().getClassid())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(
c -> Assertions
.assertEquals(
"dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemeid())));
tmp
.foreach(
r -> r
.getCountry()
.stream()
.forEach(
c -> Assertions
.assertEquals(
"dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemename())));
List<Country> countries = tmp
.filter(r -> r.getId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072"))
.collect()
.get(0)
.getCountry();
Assertions.assertEquals(1, countries.size());
Assertions.assertEquals("NL", countries.get(0).getClassid());
Assertions.assertEquals("Netherlands", countries.get(0).getClassname());
countries = tmp
.filter(r -> r.getId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b"))
.collect()
.get(0)
.getCountry();
Assertions.assertEquals(1, countries.size());
Assertions.assertEquals("NL", countries.get(0).getClassid());
Assertions.assertEquals("Netherlands", countries.get(0).getClassname());
countries = tmp
.filter(r -> r.getId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6"))
.collect()
.get(0)
.getCountry();
Assertions.assertEquals(2, countries.size());
Assertions
.assertTrue(
countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
countries = tmp
.filter(r -> r.getId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df"))
.collect()
.get(0)
.getCountry();
Assertions.assertEquals(2, countries.size());
Assertions
.assertTrue(
countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
countries
.stream()
.anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
countries = tmp
.filter(r -> r.getId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088"))
.collect()
.get(0)
.getCountry();
Assertions.assertEquals(2, countries.size());
Assertions
.assertTrue(
countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
}
} }

176
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java Normal file
View File

@ -0,0 +1,176 @@
package eu.dnetlib.dhp.countrypropagation;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
public class DatasourceCountryPreparationTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(DatasourceCountryPreparationTest.class.getSimpleName());
SparkConf conf = new SparkConf();
conf.setAppName(DatasourceCountryPreparationTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(DatasourceCountryPreparationTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testPrepareDatasourceCountry() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/graph")
.getPath();
PrepareDatasourceCountryAssociation
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"--outputPath", workingDir.toString() + "/datasourceCountry",
"--allowedtypes", "pubsrepository::institutional",
"--whitelist",
"10|openaire____::3795d6478e30e2c9f787d427ff160944;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0;10|eurocrisdris::fe4903425d9040f680d8610d9079ea14;10|openaire____::5b76240cc27a58c6f7ceef7d8c36660e;10|openaire____::172bbccecf8fca44ab6a6653e84cb92a;10|openaire____::149c6590f8a06b46314eed77bfca693f;10|eurocrisdris::a6026877c1a174d60f81fd71f62df1c1;10|openaire____::4692342f0992d91f9e705c26959f09e0;10|openaire____::8d529dbb05ec0284662b391789e8ae2a;10|openaire____::345c9d171ef3c5d706d08041d506428c;10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0;10|opendoar____::7a614fd06c325499f1680b9896beedeb;10|opendoar____::1ee3dfcd8a0645a25a35977997223d22;10|opendoar____::d296c101daa88a51f6ca8cfc1ac79b50;10|opendoar____::798ed7d4ee7138d49b8828958048130a;10|openaire____::c9d2209ecc4d45ba7b4ca7597acb88a2;10|eurocrisdris::c49e0fe4b9ba7b7fab717d1f0f0a674d;10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539;10|eurocrisdris::432ca599953ff50cd4eeffe22faf3e48"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<DatasourceCountry> tmp = sc
.textFile(workingDir.toString() + "/datasourceCountry")
.map(item -> OBJECT_MAPPER.readValue(item, DatasourceCountry.class));
Assertions.assertEquals(3, tmp.count());
Assertions
.assertEquals(
1, tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
.count());
Assertions
.assertEquals(
1, tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
.count());
Assertions
.assertEquals(
1, tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
.count());
Assertions
.assertEquals(
"NL", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
.collect()
.get(0)
.getCountry()
.getClassid());
Assertions
.assertEquals(
"Netherlands", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
.collect()
.get(0)
.getCountry()
.getClassname());
Assertions
.assertEquals(
"IT", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
.collect()
.get(0)
.getCountry()
.getClassid());
Assertions
.assertEquals(
"Italy", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
.collect()
.get(0)
.getCountry()
.getClassname());
Assertions
.assertEquals(
"FR", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
.collect()
.get(0)
.getCountry()
.getClassid());
Assertions
.assertEquals(
"France", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
.collect()
.get(0)
.getCountry()
.getClassname());
tmp.foreach(e -> System.out.println(OBJECT_MAPPER.writeValueAsString(e)));
}
}

158
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java Normal file
View File

@ -0,0 +1,158 @@
package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class ResultCountryPreparationTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(ResultCountryPreparationTest.class.getSimpleName());
SparkConf conf = new SparkConf();
conf.setAppName(ResultCountryPreparationTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(ResultCountryPreparationTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testPrepareResultCountry() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication")
.getPath();
final String preparedInfoPath = getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/datasourcecountry")
.getPath();
PrepareResultCountrySet
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--workingPath", workingDir.toString() + "/working",
"--sourcePath", sourcePath,
"--outputPath", workingDir.toString() + "/resultCountry",
"--preparedInfoPath", preparedInfoPath,
"--resultTableName", Publication.class.getCanonicalName()
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultCountrySet> tmp = sc
.textFile(workingDir.toString() + "/resultCountry")
.map(item -> OBJECT_MAPPER.readValue(item, ResultCountrySet.class));
Assertions.assertEquals(5, tmp.count());
ResultCountrySet rc = tmp
.filter(r -> r.getResultId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072"))
.collect()
.get(0);
Assertions.assertEquals(1, rc.getCountrySet().size());
Assertions.assertEquals("NL", rc.getCountrySet().get(0).getClassid());
Assertions.assertEquals("Netherlands", rc.getCountrySet().get(0).getClassname());
rc = tmp
.filter(r -> r.getResultId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b"))
.collect()
.get(0);
Assertions.assertEquals(1, rc.getCountrySet().size());
Assertions.assertEquals("NL", rc.getCountrySet().get(0).getClassid());
Assertions.assertEquals("Netherlands", rc.getCountrySet().get(0).getClassname());
rc = tmp
.filter(r -> r.getResultId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6"))
.collect()
.get(0);
Assertions.assertEquals(2, rc.getCountrySet().size());
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
rc = tmp
.filter(r -> r.getResultId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df"))
.collect()
.get(0);
Assertions.assertEquals(2, rc.getCountrySet().size());
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
rc = tmp
.filter(r -> r.getResultId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088"))
.collect()
.get(0);
Assertions.assertEquals(2, rc.getCountrySet().size());
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
}
}

3
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/datasourcecountry/datasourcecountry Normal file
View File

@ -0,0 +1,3 @@
{"dataSourceId":"10|eurocrisdris::fe4903425d9040f680d8610d9079ea14","country":{"classid":"NL","classname":"Netherlands"}}
{"dataSourceId":"10|opendoar____::f0dd4a99fba6075a9494772b58f95280","country":{"classid":"IT","classname":"Italy"}}
{"dataSourceId":"10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539","country":{"classid":"FR","classname":"France"}}

11
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/datasource/datasource.json Normal file
View File

@ -0,0 +1,11 @@
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{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","subRelType":"affiliation","target":"50|dedup_wf_001::0ab92bed024ee6883c7a1244722e5eec","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0ab92bed024ee6883c7a1244722e5eec","subRelType":"affiliation","target":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|openorgs____::64badd35233ba2cd4946368ef2f4cf57","subRelType":"affiliation","target":"50|dedup_wf_001::0ca26c736ad4d15b3d5ee90a4d7853e1","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0ca26c736ad4d15b3d5ee90a4d7853e1","subRelType":"affiliation","target":"20|openorgs____::64badd35233ba2cd4946368ef2f4cf57","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","subRelType":"affiliation","target":"50|dedup_wf_001::0ef8dfab3927cb4d69df0d3113f05a42","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0ef8dfab3927cb4d69df0d3113f05a42","subRelType":"affiliation","target":"20|pending_org_::a50fdd7f7e77b74ea2b16823151c391a","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","subRelType":"affiliation","target":"50|dedup_wf_001::0f488ad00253126c14a21abe6b2d406c","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0f488ad00253126c14a21abe6b2d406c","subRelType":"affiliation","target":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","subRelType":"affiliation","target":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","validated":false}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","subRelType":"affiliation","target":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","validated":false}

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/sample/software/software_10.json.gz → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/graph/software/software_10.json.gz
View File

5
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication/resultCountrySet Normal file
View File

@ -0,0 +1,5 @@
{"resultId":"50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b","countrySet":[{"classid":"NL","classname":"Netherlands"}]}
{"resultId":"50|355e65625b88::54a1c76f520bb2c8da27d12e42891088","countrySet":[{"classid":"IT","classname":"Italy"},{"classid":"FR","classname":"France"}]}
{"resultId":"50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072","countrySet":[{"classid":"NL","classname":"Netherlands"}]}
{"resultId":"50|355e65625b88::74009c567c81b4aa55c813db658734df","countrySet":[{"classid":"NL","classname":"Netherlands"},{"classid":"IT","classname":"Italy"}]}
{"resultId":"50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6","countrySet":[{"classid":"IT","classname":"Italy"},{"classid":"FR","classname":"France"}]}

0
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/preparedInfo.json.gz → dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/countrypropagation/preparedInfo/software/preparedInfo.json.gz
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27
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/download_json_parameters.json Normal file
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@ -0,0 +1,27 @@
[
{
"paramName":"op",
"paramLongName":"outputPath",
"paramDescription": "the output json file produced by the CSV downlaod procedure",
"paramRequired": true
},
{
"paramName": "hnn",
"paramLongName": "hdfsNameNode",
"paramDescription": "the path used to store the HostedByMap",
"paramRequired": true
},{
"paramName": "cf",
"paramLongName": "compressedFile",
"paramDescription": "the path used to store the HostedByMap",
"paramRequired": true
},{
"paramName":"wp",
"paramLongName":"workingPath",
"paramDescription": "the output json file produced by the CSV downlaod procedure",
"paramRequired": true
}
]

3
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/download.sh Normal file
View File

@ -0,0 +1,3 @@
#!/bin/bash
curl -LSs $1 | hdfs dfs -put - $2/$3
curl -LSs http://api.crossref.org/works/10.1099/jgv.0.001453 > prova.txt

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml
View File

@ -92,7 +92,7 @@
<action name="download_gold"> <action name="download_gold">
<java> <java>
<main-class>eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV2</main-class> <main-class>eu.dnetlib.dhp.oa.graph.hostedbymap.DownloadCSV</main-class>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg> <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--fileURL</arg><arg>${unibiFileURL}</arg> <arg>--fileURL</arg><arg>${unibiFileURL}</arg>
<arg>--tmpFile</arg><arg>/tmp/unibi_gold_replaced.csv</arg> <arg>--tmpFile</arg><arg>/tmp/unibi_gold_replaced.csv</arg>

2
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
View File

@ -8,7 +8,6 @@ import java.io.IOException;
import java.io.StringReader; import java.io.StringReader;
import java.util.List; import java.util.List;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.dom4j.Document; import org.dom4j.Document;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
@ -24,6 +23,7 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;