Merge pull request 'master' (#11) from miriam.baglioni/dnet-hadoop:master into enrichment_wfs

This commit is contained in:
Claudio Atzori 2020-05-11 15:14:56 +02:00
commit c403971c2f
156 changed files with 13879 additions and 74 deletions

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@ -83,6 +83,10 @@
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
</dependencies>
</project>

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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
package eu.dnetlib.dhp.common;
import java.io.Closeable;
import java.io.IOException;
@ -14,7 +14,7 @@ public class DbClient implements Closeable {
private static final Log log = LogFactory.getLog(DbClient.class);
private final Connection connection;
private Connection connection;
public DbClient(final String address, final String login, final String password) {

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@ -1,4 +1,3 @@
package eu.dnetlib.dhp.schema.common;
import java.util.Map;
@ -13,7 +12,7 @@ import eu.dnetlib.dhp.schema.oaf.*;
public class ModelSupport {
/** Defines the mapping between the actual entity type and the main entity type */
private static final Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
private static Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
static {
entityMapping.put(EntityType.publication, MainEntityType.result);
@ -53,6 +52,232 @@ public class ModelSupport {
oafTypes.put("relation", Relation.class);
}
public static final Map<String, String> entityIdPrefix = Maps.newHashMap();
static {
entityIdPrefix.put("datasource", "10");
entityIdPrefix.put("organization", "20");
entityIdPrefix.put("project", "40");
entityIdPrefix.put("result", "50");
}
public static final Map<String, RelationInverse> relationInverseMap = Maps.newHashMap();
static {
relationInverseMap
.put(
"personResult_authorship_isAuthorOf", new RelationInverse()
.setRelation("isAuthorOf")
.setInverse("hasAuthor")
.setRelType("personResult")
.setSubReltype("authorship"));
relationInverseMap
.put(
"personResult_authorship_hasAuthor", new RelationInverse()
.setInverse("isAuthorOf")
.setRelation("hasAuthor")
.setRelType("personResult")
.setSubReltype("authorship"));
relationInverseMap
.put(
"projectOrganization_participation_isParticipant", new RelationInverse()
.setRelation("isParticipant")
.setInverse("hasParticipant")
.setRelType("projectOrganization")
.setSubReltype("participation"));
relationInverseMap
.put(
"projectOrganization_participation_hasParticipant", new RelationInverse()
.setInverse("isParticipant")
.setRelation("hasParticipant")
.setRelType("projectOrganization")
.setSubReltype("participation"));
relationInverseMap
.put(
"resultOrganization_affiliation_hasAuthorInstitution", new RelationInverse()
.setRelation("hasAuthorInstitution")
.setInverse("isAuthorInstitutionOf")
.setRelType("resultOrganization")
.setSubReltype("affiliation"));
relationInverseMap
.put(
"resultOrganization_affiliation_isAuthorInstitutionOf", new RelationInverse()
.setInverse("hasAuthorInstitution")
.setRelation("isAuthorInstitutionOf")
.setRelType("resultOrganization")
.setSubReltype("affiliation"));
relationInverseMap
.put(
"organizationOrganization_dedup_merges", new RelationInverse()
.setRelation("merges")
.setInverse("isMergedIn")
.setRelType("organizationOrganization")
.setSubReltype("dedup"));
relationInverseMap
.put(
"organizationOrganization_dedup_isMergedIn", new RelationInverse()
.setInverse("merges")
.setRelation("isMergedIn")
.setRelType("organizationOrganization")
.setSubReltype("dedup"));
relationInverseMap
.put(
"organizationOrganization_dedupSimilarity_isSimilarTo", new RelationInverse()
.setInverse("isSimilarTo")
.setRelation("isSimilarTo")
.setRelType("organizationOrganization")
.setSubReltype("dedupSimilarity"));
relationInverseMap
.put(
"resultProject_outcome_isProducedBy", new RelationInverse()
.setRelation("isProducedBy")
.setInverse("produces")
.setRelType("resultProject")
.setSubReltype("outcome"));
relationInverseMap
.put(
"resultProject_outcome_produces", new RelationInverse()
.setInverse("isProducedBy")
.setRelation("produces")
.setRelType("resultProject")
.setSubReltype("outcome"));
relationInverseMap
.put(
"projectPerson_contactPerson_isContact", new RelationInverse()
.setRelation("isContact")
.setInverse("hasContact")
.setRelType("projectPerson")
.setSubReltype("contactPerson"));
relationInverseMap
.put(
"projectPerson_contactPerson_hasContact", new RelationInverse()
.setInverse("isContact")
.setRelation("hasContact")
.setRelType("personPerson")
.setSubReltype("coAuthorship"));
relationInverseMap
.put(
"personPerson_coAuthorship_isCoauthorOf", new RelationInverse()
.setInverse("isCoAuthorOf")
.setRelation("isCoAuthorOf")
.setRelType("personPerson")
.setSubReltype("coAuthorship"));
relationInverseMap
.put(
"personPerson_dedup_merges", new RelationInverse()
.setInverse("isMergedIn")
.setRelation("merges")
.setRelType("personPerson")
.setSubReltype("dedup"));
relationInverseMap
.put(
"personPerson_dedup_isMergedIn", new RelationInverse()
.setInverse("merges")
.setRelation("isMergedIn")
.setRelType("personPerson")
.setSubReltype("dedup"));
relationInverseMap
.put(
"personPerson_dedupSimilarity_isSimilarTo", new RelationInverse()
.setInverse("isSimilarTo")
.setRelation("isSimilarTo")
.setRelType("personPerson")
.setSubReltype("dedupSimilarity"));
relationInverseMap
.put(
"datasourceOrganization_provision_isProvidedBy", new RelationInverse()
.setInverse("provides")
.setRelation("isProvidedBy")
.setRelType("datasourceOrganization")
.setSubReltype("provision"));
relationInverseMap
.put(
"datasourceOrganization_provision_provides", new RelationInverse()
.setInverse("isProvidedBy")
.setRelation("provides")
.setRelType("datasourceOrganization")
.setSubReltype("provision"));
relationInverseMap
.put(
"resultResult_similarity_hasAmongTopNSimilarDocuments", new RelationInverse()
.setInverse("isAmongTopNSimilarDocuments")
.setRelation("hasAmongTopNSimilarDocuments")
.setRelType("resultResult")
.setSubReltype("similarity"));
relationInverseMap
.put(
"resultResult_similarity_isAmongTopNSimilarDocuments", new RelationInverse()
.setInverse("hasAmongTopNSimilarDocuments")
.setRelation("isAmongTopNSimilarDocuments")
.setRelType("resultResult")
.setSubReltype("similarity"));
relationInverseMap
.put(
"resultResult_relationship_isRelatedTo", new RelationInverse()
.setInverse("isRelatedTo")
.setRelation("isRelatedTo")
.setRelType("resultResult")
.setSubReltype("relationship"));
relationInverseMap
.put(
"resultResult_similarity_isAmongTopNSimilarDocuments", new RelationInverse()
.setInverse("hasAmongTopNSimilarDocuments")
.setRelation("isAmongTopNSimilarDocuments")
.setRelType("resultResult")
.setSubReltype("similarity"));
relationInverseMap
.put(
"resultResult_supplement_isSupplementTo", new RelationInverse()
.setInverse("isSupplementedBy")
.setRelation("isSupplementTo")
.setRelType("resultResult")
.setSubReltype("supplement"));
relationInverseMap
.put(
"resultResult_supplement_isSupplementedBy", new RelationInverse()
.setInverse("isSupplementTo")
.setRelation("isSupplementedBy")
.setRelType("resultResult")
.setSubReltype("supplement"));
relationInverseMap
.put(
"resultResult_part_isPartOf", new RelationInverse()
.setInverse("hasPart")
.setRelation("isPartOf")
.setRelType("resultResult")
.setSubReltype("part"));
relationInverseMap
.put(
"resultResult_part_hasPart", new RelationInverse()
.setInverse("isPartOf")
.setRelation("hasPart")
.setRelType("resultResult")
.setSubReltype("part"));
relationInverseMap
.put(
"resultResult_dedup_merges", new RelationInverse()
.setInverse("isMergedIn")
.setRelation("merges")
.setRelType("resultResult")
.setSubReltype("dedup"));
relationInverseMap
.put(
"resultResult_dedup_isMergedIn", new RelationInverse()
.setInverse("merges")
.setRelation("isMergedIn")
.setRelType("resultResult")
.setSubReltype("dedup"));
relationInverseMap
.put(
"resultResult_dedupSimilarity_isSimilarTo", new RelationInverse()
.setInverse("isSimilarTo")
.setRelation("isSimilarTo")
.setRelType("resultResult")
.setSubReltype("dedupSimilarity"));
}
private static final String schemeTemplate = "dnet:%s_%s_relations";
private ModelSupport() {

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@ -0,0 +1,46 @@
package eu.dnetlib.dhp.schema.common;
public class RelationInverse {
private String relation;
private String inverse;
private String relType;
private String subReltype;
public String getRelType() {
return relType;
}
public RelationInverse setRelType(String relType) {
this.relType = relType;
return this;
}
public String getSubReltype() {
return subReltype;
}
public RelationInverse setSubReltype(String subReltype) {
this.subReltype = subReltype;
return this;
}
public String getRelation() {
return relation;
}
public RelationInverse setRelation(String relation) {
this.relation = relation;
return this;
}
public String getInverse() {
return inverse;
}
public RelationInverse setInverse(String inverse) {
this.inverse = inverse;
return this;
}
}

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@ -2,8 +2,7 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.List;
import java.util.Objects;
import java.util.*;
public class Author implements Serializable {
@ -86,4 +85,5 @@ public class Author implements Serializable {
public int hashCode() {
return Objects.hash(fullname, name, surname, rank, pid, affiliation);
}
}

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@ -0,0 +1,36 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-blacklist</artifactId>
<dependencies>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
</dependency>
</dependencies>
</project>

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@ -0,0 +1,100 @@
package eu.dnetlib.dhp.blacklist;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class PrepareMergedRelationJob {
private static final Logger log = LoggerFactory.getLogger(PrepareMergedRelationJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareMergedRelationJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/blacklist/input_preparerelation_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
String outputPath = parser.get("outputPath");
log.info("outputPath: {} ", outputPath);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
selectMergesRelations(
spark,
inputPath,
outputPath);
});
}
private static void selectMergesRelations(SparkSession spark, String inputPath, String outputPath) {
Dataset<Relation> relation = readRelations(spark, inputPath);
relation
.filter("relclass = 'merges' and datainfo.deletedbyinference=false")
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
// relation.createOrReplaceTempView("relation");
//
// spark
// .sql(
// "Select * from relation " +
// "where relclass = 'merges' " +
// "and datainfo.deletedbyinference = false")
// .as(Encoders.bean(Relation.class))
// .toJSON()
// .write()
// .mode(SaveMode.Overwrite)
// .option("compression", "gzip")
// .text(outputPath);
}
public static org.apache.spark.sql.Dataset<Relation> readRelations(
SparkSession spark, String inputPath) {
return spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
Encoders.bean(Relation.class));
}
}

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@ -0,0 +1,142 @@
package eu.dnetlib.dhp.blacklist;
import java.io.BufferedWriter;
import java.io.Closeable;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.nio.charset.StandardCharsets;
import java.sql.ResultSet;
import java.util.Arrays;
import java.util.List;
import java.util.function.Consumer;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.common.RelationInverse;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class ReadBlacklistFromDB implements Closeable {
private final DbClient dbClient;
private static final Log log = LogFactory.getLog(ReadBlacklistFromDB.class);
private final Configuration conf;
private final BufferedWriter writer;
private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private final static String query = "SELECT source_type, unnest(original_source_objects) as source, " +
"target_type, unnest(original_target_objects) as target, " +
"relationship FROM blacklist WHERE status = 'ACCEPTED'";
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
ReadBlacklistFromDB.class
.getResourceAsStream(
"/eu/dnetlib/dhp/blacklist/blacklist_parameters.json")));
parser.parseArgument(args);
final String dbUrl = parser.get("postgresUrl");
final String dbUser = parser.get("postgresUser");
final String dbPassword = parser.get("postgresPassword");
final String hdfsPath = parser.get("hdfsPath") + "/blacklist";
final String hdfsNameNode = parser.get("hdfsNameNode");
try (final ReadBlacklistFromDB rbl = new ReadBlacklistFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser,
dbPassword)) {
log.info("Processing blacklist...");
rbl.execute(query, rbl::processBlacklistEntry);
}
}
public void execute(final String sql, final Function<ResultSet, List<Relation>> producer)
throws Exception {
final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(r -> writeRelation(r));
dbClient.processResults(sql, consumer);
}
public List<Relation> processBlacklistEntry(ResultSet rs) {
try {
Relation direct = new Relation();
Relation inverse = new Relation();
String source_prefix = ModelSupport.entityIdPrefix.get(rs.getString("source_type"));
String target_prefix = ModelSupport.entityIdPrefix.get(rs.getString("target_type"));
String source_direct = source_prefix + "|" + rs.getString("source");
direct.setSource(source_direct);
inverse.setTarget(source_direct);
String target_direct = target_prefix + "|" + rs.getString("target");
direct.setTarget(target_direct);
inverse.setSource(target_direct);
String encoding = rs.getString("relationship");
RelationInverse ri = ModelSupport.relationInverseMap.get(encoding);
direct.setRelClass(ri.getRelation());
inverse.setRelClass(ri.getInverse());
direct.setRelType(ri.getRelType());
inverse.setRelType(ri.getRelType());
direct.setSubRelType(ri.getSubReltype());
inverse.setSubRelType(ri.getSubReltype());
return Arrays.asList(direct, inverse);
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
@Override
public void close() throws IOException {
dbClient.close();
writer.close();
}
public ReadBlacklistFromDB(
final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
throws Exception {
this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
this.conf = new Configuration();
this.conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(this.conf);
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fsDataOutputStream = fileSystem.append(hdfsWritePath);
} else {
fsDataOutputStream = fileSystem.create(hdfsWritePath);
}
this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
}
protected void writeRelation(final Relation r) {
try {
writer.write(OBJECT_MAPPER.writeValueAsString(r));
writer.newLine();
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
}

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@ -0,0 +1,151 @@
package eu.dnetlib.dhp.blacklist;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
public class SparkRemoveBlacklistedRelationJob {
private static final Logger log = LoggerFactory.getLogger(SparkRemoveBlacklistedRelationJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkRemoveBlacklistedRelationJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/blacklist/sparkblacklist_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
final String blacklistPath = parser.get("hdfsPath");
log.info("blacklistPath {}: ", blacklistPath);
final String mergesPath = parser.get("mergesPath");
log.info("mergesPath {}: ", mergesPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeBlacklistedRelations(
spark,
blacklistPath,
inputPath,
outputPath,
mergesPath);
});
}
private static void removeBlacklistedRelations(SparkSession spark, String blacklistPath, String inputPath,
String outputPath, String mergesPath) {
Dataset<Relation> blackListed = readRelations(spark, blacklistPath + "/blacklist");
Dataset<Relation> inputRelation = readRelations(spark, inputPath);
Dataset<Relation> mergesRelation = readRelations(spark, mergesPath);
log.info("InputRelationCount: {}", inputRelation.count());
Dataset<Relation> dedupSource = blackListed
.joinWith(
mergesRelation, blackListed.col("source").equalTo(mergesRelation.col("target")),
"left_outer")
.map(c -> {
Optional
.ofNullable(c._2())
.ifPresent(mr -> c._1().setSource(mr.getSource()));
return c._1();
}, Encoders.bean(Relation.class));
Dataset<Relation> dedupBL = dedupSource
.joinWith(
mergesRelation, dedupSource.col("target").equalTo(mergesRelation.col("target")),
"left_outer")
.map(c -> {
Optional
.ofNullable(c._2())
.ifPresent(mr -> c._1().setTarget(mr.getSource()));
return c._1();
}, Encoders.bean(Relation.class));
dedupBL
.write()
.mode(SaveMode.Overwrite)
.json(blacklistPath + "/deduped");
inputRelation
.joinWith(
dedupBL, (inputRelation
.col("source")
.equalTo(dedupBL.col("source"))
.and(
inputRelation
.col("target")
.equalTo(dedupBL.col("target")))),
"left_outer")
.map(c -> {
Relation ir = c._1();
Optional<Relation> obl = Optional.ofNullable(c._2());
if (obl.isPresent()) {
if (ir.equals(obl.get())) {
return null;
}
}
return ir;
}, Encoders.bean(Relation.class))
.filter(Objects::nonNull)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
public static org.apache.spark.sql.Dataset<Relation> readRelations(
SparkSession spark, String inputPath) {
return spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
Encoders.bean(Relation.class));
}
}

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@ -0,0 +1,32 @@
[
{
"paramName": "p",
"paramLongName": "hdfsPath",
"paramDescription": "the path where storing the sequential file",
"paramRequired": true
},
{
"paramName": "nn",
"paramLongName": "hdfsNameNode",
"paramDescription": "the name node on hdfs",
"paramRequired": true
},
{
"paramName": "pgurl",
"paramLongName": "postgresUrl",
"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb",
"paramRequired": true
},
{
"paramName": "pguser",
"paramLongName": "postgresUser",
"paramDescription": "postgres user",
"paramRequired": false
},
{
"paramName": "pgpasswd",
"paramLongName": "postgresPassword",
"paramDescription": "postgres password",
"paramRequired": false
}
]

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@ -0,0 +1,26 @@
[
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the path to the graph used to remove the relations ",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path where to store the temporary result ",
"paramRequired": true
},
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed",
"paramRequired": false
},
{
"paramName":"h",
"paramLongName":"hive_metastore_uris",
"paramDescription": "the hive metastore uris",
"paramRequired": true
}
]

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@ -0,0 +1,54 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
</property>
<property>
<name>sparkExecutorNumber</name>
<value>4</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>sparkDriverMemory</name>
<value>15G</value>
</property>
<property>
<name>sparkExecutorMemory</name>
<value>6G</value>
</property>
<property>
<name>sparkExecutorCores</name>
<value>1</value>
</property>
</configuration>

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@ -0,0 +1,98 @@
<workflow-app name="blacklisting" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>postgresURL</name>
<description>the url of the postgress server to query</description>
</property>
<property>
<name>postgresUser</name>
<description>the username to access the postgres db</description>
</property>
<property>
<name>postgresPassword</name>
<description>the postgres password</description>
</property>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
</parameters>
<start to="reset-outputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset-outputpath">
<fs>
<delete path='${workingDir}/blacklist'/>
</fs>
<ok to="read_blacklist"/>
<error to="Kill"/>
</action>
<action name="read_blacklist">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.blacklist.ReadBlacklistFromDB</main-class>
<arg>--hdfsPath</arg><arg>${workingDir}/blacklist</arg>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
</java>
<ok to="prepare_merged_relation"/>
<error to="Kill"/>
</action>
<action name="prepare_merged_relation">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>PrepareMergedRelation</name>
<class>eu.dnetlib.dhp.blacklist.PrepareMergedRelationJob</class>
<jar>dhp-blacklist-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
<arg>--outputPath</arg><arg>${workingDir}/mergesRelation</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
</spark>
<ok to="apply_blacklist"/>
<error to="Kill"/>
</action>
<action name="apply_blacklist">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ApplyBlacklist</name>
<class>eu.dnetlib.dhp.blacklist.SparkRemoveBlacklistedRelationJob</class>
<jar>dhp-blacklist-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
<arg>--outputPath</arg><arg>${workingDir}/relation</arg>
<arg>--hdfsPath</arg><arg>${workingDir}/blacklist</arg>
<arg>--mergesPath</arg><arg>${workingDir}/mergesRelation</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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@ -0,0 +1,33 @@
[
{
"paramName": "p",
"paramLongName": "hdfsPath",
"paramDescription": "the path where storing the sequential file",
"paramRequired": true
},
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the path to the graph used to remove the relations ",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path where to store the temporary result ",
"paramRequired": true
},
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed",
"paramRequired": false
},
{
"paramName": "m",
"paramLongName": "mergesPath",
"paramDescription": "true if the spark session is managed",
"paramRequired": true
}
]

View File

@ -0,0 +1,166 @@
package eu.dnetlib.dhp.blacklist;
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.Encoders;
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 org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class BlackListTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ClassLoader cl = eu.dnetlib.dhp.blacklist.BlackListTest.class.getClassLoader();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.blacklist.BlackListTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(eu.dnetlib.dhp.blacklist.BlackListTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(eu.dnetlib.dhp.blacklist.BlackListTest.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(BlackListTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
/*
* String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); final String outputPath =
* parser.get("outputPath"); log.info("outputPath {}: ", outputPath); final String blacklistPath =
* parser.get("hdfsPath"); log.info("blacklistPath {}: ", blacklistPath); final String mergesPath =
* parser.get("mergesPath"); log.info("mergesPath {}: ", mergesPath);
*/
@Test
public void noRemoveTest() throws Exception {
SparkRemoveBlacklistedRelationJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/blacklist/relationsNoRemoval").getPath(),
"-outputPath",
workingDir.toString() + "/relation",
"-hdfsPath",
getClass().getResource("/eu/dnetlib/dhp/blacklist/blacklist").getPath(),
"-mergesPath",
getClass().getResource("/eu/dnetlib/dhp/blacklist/mergesRel").getPath(),
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Assertions.assertEquals(13, tmp.count());
}
@Test
public void removeNoMergeMatchTest() throws Exception {
SparkRemoveBlacklistedRelationJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/blacklist/relationsOneRemoval").getPath(),
"-outputPath",
workingDir.toString() + "/relation",
"-hdfsPath",
getClass().getResource("/eu/dnetlib/dhp/blacklist/blacklist").getPath(),
"-mergesPath",
getClass().getResource("/eu/dnetlib/dhp/blacklist/mergesRel").getPath(),
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Assertions.assertEquals(12, tmp.count());
org.apache.spark.sql.Dataset<eu.dnetlib.dhp.schema.oaf.Relation> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.oaf.Relation.class));
Assertions
.assertEquals(
0, verificationDataset
.filter(
"source = '40|corda__h2020::5161f53ab205d803c36b4c888fe7deef' and " +
"target = '20|dedup_wf_001::157af406bc653aa4d9749318b644de43'")
.count());
Assertions.assertEquals(0, verificationDataset.filter("relClass = 'hasParticipant'").count());
}
@Test
public void removeMergeMatchTest() throws Exception {
SparkRemoveBlacklistedRelationJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/blacklist/relationOneRemovalWithMatch").getPath(),
"-outputPath",
workingDir.toString() + "/relation",
"-hdfsPath",
getClass().getResource("/eu/dnetlib/dhp/blacklist/blacklist").getPath(),
"-mergesPath",
getClass().getResource("/eu/dnetlib/dhp/blacklist/mergesRelOneMerge").getPath(),
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Assertions.assertEquals(12, tmp.count());
org.apache.spark.sql.Dataset<eu.dnetlib.dhp.schema.oaf.Relation> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.oaf.Relation.class));
Assertions.assertEquals(12, verificationDataset.filter("relClass = 'isProvidedBy'").count());
}
}

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@ -0,0 +1,20 @@
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"projectOrganization","subRelType":"participation","relClass":"hasParticipant","source":"40|corda__h2020::5161f53ab205d803c36b4c888fe7deef","target":"20|dedup_wf_001::157af406bc653aa4d9749318b644de43"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"projectOrganization","subRelType":"participation","relClass":"isParticipant","source":"20|dedup_wf_001::157af406bc653aa4d9749318b644de43","target":"40|corda__h2020::5161f53ab205d803c36b4c888fe7deef"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"isProducedBy","source":"50|od_______908::a47e1c3ede9a21ee5278a2e5c338d69b","target":"40|corda_______::189ff31d637eaaeaf4d3584dc490b1cf"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"produces","source":"40|corda_______::189ff31d637eaaeaf4d3584dc490b1cf","target":"50|od_______908::a47e1c3ede9a21ee5278a2e5c338d69b"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"isProducedBy","source":"50|od________18::a727cc288016db7132ef9a799aa83350","target":"40|corda_______::9826e8aba3e8f3a2a46545cf341838a8"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"produces","source":"40|corda_______::9826e8aba3e8f3a2a46545cf341838a8","target":"50|od________18::a727cc288016db7132ef9a799aa83350"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"isProducedBy","source":"50|od________18::062cf091d5c7a7d730001c34177042e3","target":"40|corda_______::9826e8aba3e8f3a2a46545cf341838a8"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"produces","source":"40|corda_______::9826e8aba3e8f3a2a46545cf341838a8","target":"50|od________18::062cf091d5c7a7d730001c34177042e3"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"isProducedBy","source":"50|webcrawl____::68c191d9b972b47a235d311804c7f6f5","target":"40|corda_______::c3d0b21615b129cd7395e24f9cf6bb64"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"produces","source":"40|corda_______::c3d0b21615b129cd7395e24f9cf6bb64","target":"50|webcrawl____::68c191d9b972b47a235d311804c7f6f5"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"isProducedBy","source":"50|od_______908::1b172ab34639e7935e2357119cf20830","target":"40|corda_______::c3d0b21615b129cd7395e24f9cf6bb64"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"produces","source":"40|corda_______::c3d0b21615b129cd7395e24f9cf6bb64","target":"50|od_______908::1b172ab34639e7935e2357119cf20830"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"isProducedBy","source":"50|doajarticles::cb234c66327d29ba5f13c0db7a4cf423","target":"40|corda_______::c3d0b21615b129cd7395e24f9cf6bb64"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"produces","source":"40|corda_______::c3d0b21615b129cd7395e24f9cf6bb64","target":"50|doajarticles::cb234c66327d29ba5f13c0db7a4cf423"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"isProducedBy","source":"50|od______1146::e2fafaba636a14e408f02c6ea26acb0e","target":"40|corda_______::35695c955c51f0bb39482ce5477047c7"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"produces","source":"40|corda_______::35695c955c51f0bb39482ce5477047c7","target":"50|od______1146::e2fafaba636a14e408f02c6ea26acb0e"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"isProducedBy","source":"50|od_______908::b8e86ed982ff331764456e1f0759ed9c","target":"40|corda_______::35695c955c51f0bb39482ce5477047c7"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"produces","source":"40|corda_______::35695c955c51f0bb39482ce5477047c7","target":"50|od_______908::b8e86ed982ff331764456e1f0759ed9c"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"isProducedBy","source":"50|webcrawl____::c472bf5944ce0495844d505d43d1c021","target":"40|corda_______::35695c955c51f0bb39482ce5477047c7"}
{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"relType":"resultProject","subRelType":"outcome","relClass":"produces","source":"40|corda_______::35695c955c51f0bb39482ce5477047c7","target":"50|webcrawl____::c472bf5944ce0495844d505d43d1c021"}

View File

@ -0,0 +1,14 @@
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::3668b9bd87532a085dc7a18ce2086715","subRelType":"dedup","target":"50|od_______177::67c1385662f2fa0bde310bec15427646"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::3668b9bd87532a085dc7a18ce2086715","subRelType":"dedup","target":"50|doiboost____::8ea1631fa01adcbafc3f384b6a2c5cc3"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::3668b9bd87532a085dc7a18ce2086715","subRelType":"dedup","target":"50|od_______166::67c1385662f2fa0bde310bec15427646"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::d2a45f0f42d8dd66c364219924c37c3f","subRelType":"dedup","target":"50|od_______935::0bf7d9c5d2e1115a31cd558f83ae8ee3"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::d2a45f0f42d8dd66c364219924c37c3f","subRelType":"dedup","target":"50|doajarticles::d695fee344cb367a38ce6622f5fe9430"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::325525b879b17d8059a4e58def2f7225","subRelType":"dedup","target":"50|od_______267::14e952745e4b602ff72919aa881b8945"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::325525b879b17d8059a4e58def2f7225","subRelType":"dedup","target":"50|doiboost____::43941031067842fac90604d37b2a4149"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::325525b879b17d8059a4e58def2f7225","subRelType":"dedup","target":"50|core________::5c62b3ad05a23de613636607a424899d"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::325525b879b17d8059a4e58def2f7225","subRelType":"dedup","target":"50|scholexplore::1c467aabe5108ee840a4500d58f19328"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::cd4fc0411683ee762d50bfd30436f95b","subRelType":"dedup","target":"50|doiboost____::0ff61beeb12c49ed8a826b2b1883c8f8"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::cd4fc0411683ee762d50bfd30436f95b","subRelType":"dedup","target":"50|doajarticles::fca1220426b10ccb8b46e4967b353f37"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::a87be24a4fcac13c9298f0cc3acfc6ea","subRelType":"dedup","target":"50|doiboost____::dd96d41ee05d4022065c9d3096e1023a"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::a87be24a4fcac13c9298f0cc3acfc6ea","subRelType":"dedup","target":"50|erc_________::7d9a29ff323c2fe0ecf037189bf71b8e"}
{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"decisiontree-dedup-test","inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:dedup","classname":"sysimport:dedup","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"relClass":"merges","source":"50|dedup_wf_001::a87be24a4fcac13c9298f0cc3acfc6ea","subRelType":"dedup","target":"50|webcrawl____::fdd999801fec35d4c6190bcabb850c52"}

View File

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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-bulktag</artifactId>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
</dependency>
<dependency>
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
</dependency>
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
<version>0.9.11</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>23.3-jre</version>
</dependency>
<dependency>
<groupId>io.github.classgraph</groupId>
<artifactId>classgraph</artifactId>
<version>4.8.71</version>
</dependency>
</dependencies>
</project>

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#sandboxName when not provided explicitly will be generated
sandboxName=${sandboxName}
sandboxDir=/user/${dhp.hadoop.frontend.user.name}/${sandboxName}
workingDir=${sandboxDir}/working_dir
oozie.wf.application.path = ${nameNode}${sandboxDir}/${oozieAppDir}
oozieTopWfApplicationPath = ${oozie.wf.application.path}

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@ -0,0 +1,120 @@
package eu.dnetlib.dhp.bulktag;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.community.*;
import eu.dnetlib.dhp.schema.oaf.*;
public class SparkBulkTagJob {
private static final Logger log = LoggerFactory.getLogger(SparkBulkTagJob.class);
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkBulkTagJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
Boolean isTest = Optional
.ofNullable(parser.get("isTest"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
log.info("isTest: {} ", isTest);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class);
log.info("pathMap: {}", new Gson().toJson(protoMappingParams));
final String resultClassName = parser.get("resultTableName");
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);
SparkConf conf = new SparkConf();
CommunityConfiguration cc;
String taggingConf = parser.get("taggingConf");
if (isTest) {
cc = CommunityConfigurationFactory.newInstance(taggingConf);
} else {
cc = QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl"));
}
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc);
});
}
private static <R extends Result> void execBulkTag(
SparkSession spark,
String inputPath,
String outputPath,
ProtoMap protoMappingParams,
Class<R> resultClazz,
CommunityConfiguration communityConfiguration) {
ResultTagger resultTagger = new ResultTagger();
readPath(spark, inputPath, resultClazz)
.map(
(MapFunction<R, R>) value -> resultTagger
.enrichContextCriteria(
value, communityConfiguration, protoMappingParams),
Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
}

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package eu.dnetlib.dhp.community;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.google.gson.Gson;
/** Created by miriam on 01/08/2018. */
public class Community implements Serializable {
private static final Log log = LogFactory.getLog(Community.class);
private String id;
private List<String> subjects = new ArrayList<>();
private List<Datasource> datasources = new ArrayList<>();
private List<ZenodoCommunity> zenodoCommunities = new ArrayList<>();
public String toJson() {
final Gson g = new Gson();
return g.toJson(this);
}
public boolean isValid() {
return !getSubjects().isEmpty()
|| !getDatasources().isEmpty()
|| !getZenodoCommunities().isEmpty();
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<String> getSubjects() {
return subjects;
}
public void setSubjects(List<String> subjects) {
this.subjects = subjects;
}
public List<Datasource> getDatasources() {
return datasources;
}
public void setDatasources(List<Datasource> datasources) {
this.datasources = datasources;
}
public List<ZenodoCommunity> getZenodoCommunities() {
return zenodoCommunities;
}
public void setZenodoCommunities(List<ZenodoCommunity> zenodoCommunities) {
this.zenodoCommunities = zenodoCommunities;
}
}

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package eu.dnetlib.dhp.community;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import eu.dnetlib.dhp.selectioncriteria.InterfaceAdapter;
import eu.dnetlib.dhp.selectioncriteria.Selection;
/** Created by miriam on 02/08/2018. */
public class CommunityConfiguration implements Serializable {
private static final Log log = LogFactory.getLog(CommunityConfiguration.class);
private Map<String, Community> communities;
// map subject -> communityid
private Map<String, List<Pair<String, SelectionConstraints>>> subjectMap = new HashMap<>();
// map datasourceid -> communityid
private Map<String, List<Pair<String, SelectionConstraints>>> datasourceMap = new HashMap<>();
// map zenodocommunityid -> communityid
private Map<String, List<Pair<String, SelectionConstraints>>> zenodocommunityMap = new HashMap<>();
public Map<String, List<Pair<String, SelectionConstraints>>> getSubjectMap() {
return subjectMap;
}
public void setSubjectMap(Map<String, List<Pair<String, SelectionConstraints>>> subjectMap) {
this.subjectMap = subjectMap;
}
public Map<String, List<Pair<String, SelectionConstraints>>> getDatasourceMap() {
return datasourceMap;
}
public void setDatasourceMap(
Map<String, List<Pair<String, SelectionConstraints>>> datasourceMap) {
this.datasourceMap = datasourceMap;
}
public Map<String, List<Pair<String, SelectionConstraints>>> getZenodocommunityMap() {
return zenodocommunityMap;
}
public void setZenodocommunityMap(
Map<String, List<Pair<String, SelectionConstraints>>> zenodocommunityMap) {
this.zenodocommunityMap = zenodocommunityMap;
}
CommunityConfiguration(final Map<String, Community> communities) {
this.communities = communities;
init();
}
void init() {
if (subjectMap == null) {
subjectMap = Maps.newHashMap();
}
if (datasourceMap == null) {
datasourceMap = Maps.newHashMap();
}
if (zenodocommunityMap == null) {
zenodocommunityMap = Maps.newHashMap();
}
for (Community c : getCommunities().values()) {
// get subjects
final String id = c.getId();
for (String sbj : c.getSubjects()) {
Pair<String, SelectionConstraints> p = new Pair<>(id, new SelectionConstraints());
add(sbj.toLowerCase().trim(), p, subjectMap);
}
// get datasources
for (Datasource d : c.getDatasources()) {
add(d.getOpenaireId(), new Pair<>(id, d.getSelectionConstraints()), datasourceMap);
}
// get zenodo communities
for (ZenodoCommunity zc : c.getZenodoCommunities()) {
add(
zc.getZenodoCommunityId(),
new Pair<>(id, zc.getSelCriteria()),
zenodocommunityMap);
}
}
}
private void add(
String key,
Pair<String, SelectionConstraints> value,
Map<String, List<Pair<String, SelectionConstraints>>> map) {
List<Pair<String, SelectionConstraints>> values = map.get(key);
if (values == null) {
values = new ArrayList<>();
map.put(key, values);
}
values.add(value);
}
public List<Pair<String, SelectionConstraints>> getCommunityForSubject(String sbj) {
return subjectMap.get(sbj);
}
public List<Pair<String, SelectionConstraints>> getCommunityForDatasource(String dts) {
return datasourceMap.get(dts);
}
public List<String> getCommunityForDatasource(
final String dts, final Map<String, List<String>> param) {
List<Pair<String, SelectionConstraints>> lp = datasourceMap.get(dts);
if (lp == null)
return Lists.newArrayList();
return lp
.stream()
.map(
p -> {
if (p.getSnd() == null)
return p.getFst();
if (((SelectionConstraints) p.getSnd()).verifyCriteria(param))
return p.getFst();
else
return null;
})
.filter(st -> (st != null))
.collect(Collectors.toList());
}
public List<Pair<String, SelectionConstraints>> getCommunityForZenodoCommunity(String zc) {
return zenodocommunityMap.get(zc);
}
public List<String> getCommunityForSubjectValue(String value) {
return getContextIds(subjectMap.get(value));
}
public List<String> getCommunityForDatasourceValue(String value) {
return getContextIds(datasourceMap.get(value.toLowerCase()));
}
public List<String> getCommunityForZenodoCommunityValue(String value) {
return getContextIds(zenodocommunityMap.get(value.toLowerCase()));
}
private List<String> getContextIds(List<Pair<String, SelectionConstraints>> list) {
if (list != null) {
return list.stream().map(p -> p.getFst()).collect(Collectors.toList());
}
return Lists.newArrayList();
}
public Map<String, Community> getCommunities() {
return communities;
}
public void setCommunities(Map<String, Community> communities) {
this.communities = communities;
}
public String toJson() {
GsonBuilder builder = new GsonBuilder();
builder.registerTypeAdapter(Selection.class, new InterfaceAdapter());
Gson gson = builder.create();
return gson.toJson(this);
}
public int size() {
return communities.keySet().size();
}
public Community getCommunityById(String id) {
return communities.get(id);
}
public List<Community> getCommunityList() {
return Lists.newLinkedList(communities.values());
}
}

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package eu.dnetlib.dhp.community;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import eu.dnetlib.dhp.selectioncriteria.InterfaceAdapter;
import eu.dnetlib.dhp.selectioncriteria.Selection;
import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
import eu.dnetlib.dhp.selectioncriteria.VerbResolverFactory;
/** Created by miriam on 03/08/2018. */
public class CommunityConfigurationFactory {
private static final Log log = LogFactory.getLog(CommunityConfigurationFactory.class);
private static VerbResolver resolver = VerbResolverFactory.newInstance();
public static CommunityConfiguration newInstance(final String xml) throws DocumentException {
log.debug(String.format("parsing community configuration from:\n%s", xml));
final Document doc = new SAXReader().read(new StringReader(xml));
final Map<String, Community> communities = Maps.newHashMap();
for (final Object o : doc.selectNodes("//community")) {
final Node node = (Node) o;
final Community community = parseCommunity(node);
if (community.isValid()) {
communities.put(community.getId(), community);
}
}
log.info(String.format("loaded %s community configuration profiles", communities.size()));
log.debug(String.format("loaded community configuration:\n%s", communities.toString()));
return new CommunityConfiguration(communities);
}
public static CommunityConfiguration fromJson(final String json) {
GsonBuilder builder = new GsonBuilder();
builder.registerTypeAdapter(Selection.class, new InterfaceAdapter());
Gson gson = builder.create();
final CommunityConfiguration conf = gson.fromJson(json, CommunityConfiguration.class);
log.info(String.format("loaded %s community configuration profiles", conf.size()));
conf.init();
log.info("created inverse maps");
return conf;
}
private static Community parseCommunity(final Node node) {
final Community c = new Community();
c.setId(node.valueOf("./@id"));
log.info(String.format("community id: %s", c.getId()));
c.setSubjects(parseSubjects(node));
c.setDatasources(parseDatasources(node));
c.setZenodoCommunities(parseZenodoCommunities(node));
return c;
}
private static List<String> parseSubjects(final Node node) {
final List<String> subjects = Lists.newArrayList();
final List<Node> list = node.selectNodes("./subjects/subject");
for (Node n : list) {
log.debug("text of the node " + n.getText());
subjects.add(StringUtils.trim(n.getText()));
}
log.info("size of the subject list " + subjects.size());
return subjects;
}
private static List<Datasource> parseDatasources(final Node node) {
final List<Node> list = node.selectNodes("./datasources/datasource");
final List<Datasource> datasourceList = new ArrayList<>();
for (Node n : list) {
Datasource d = new Datasource();
d.setOpenaireId(n.selectSingleNode("./openaireId").getText());
d.setSelCriteria(n.selectSingleNode("./selcriteria"), resolver);
datasourceList.add(d);
}
log.info("size of the datasource list " + datasourceList.size());
return datasourceList;
}
private static List<ZenodoCommunity> parseZenodoCommunities(final Node node) {
final Node oacommunitynode = node.selectSingleNode("./oacommunity");
String oacommunity = null;
if (oacommunitynode != null) {
String tmp = oacommunitynode.getText();
if (StringUtils.isNotBlank(tmp))
oacommunity = tmp;
}
final List<Node> list = node.selectNodes("./zenodocommunities/zenodocommunity");
final List<ZenodoCommunity> zenodoCommunityList = new ArrayList<>();
for (Node n : list) {
ZenodoCommunity zc = new ZenodoCommunity();
zc.setZenodoCommunityId(n.selectSingleNode("./zenodoid").getText());
zc.setSelCriteria(n.selectSingleNode("./selcriteria"));
zenodoCommunityList.add(zc);
}
if (oacommunity != null) {
ZenodoCommunity zc = new ZenodoCommunity();
zc.setZenodoCommunityId(oacommunity);
zenodoCommunityList.add(zc);
}
log.info("size of the zenodo community list " + zenodoCommunityList.size());
return zenodoCommunityList;
}
}

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package eu.dnetlib.dhp.community;
import java.io.Serializable;
import java.lang.reflect.InvocationTargetException;
import eu.dnetlib.dhp.selectioncriteria.Selection;
import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
public class Constraint implements Serializable {
private String verb;
private String field;
private String value;
private Selection selection;
public Constraint() {
}
public String getVerb() {
return verb;
}
public void setVerb(String verb) {
this.verb = verb;
}
public String getField() {
return field;
}
public void setField(String field) {
this.field = field;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
public void setSelection(Selection sel) {
selection = sel;
}
public void setSelection(VerbResolver resolver)
throws InvocationTargetException, NoSuchMethodException, InstantiationException,
IllegalAccessException {
selection = resolver.getSelectionCriteria(verb, value);
}
public boolean verifyCriteria(String metadata) {
return selection.apply(metadata);
}
}

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package eu.dnetlib.dhp.community;
import java.io.Serializable;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Type;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
/** Created by miriam on 02/08/2018. */
public class Constraints implements Serializable {
private static final Log log = LogFactory.getLog(Constraints.class);
// private ConstraintEncapsulator ce;
private List<Constraint> constraint;
public Constraints() {
}
public List<Constraint> getConstraint() {
return constraint;
}
public void setConstraint(List<Constraint> constraint) {
this.constraint = constraint;
}
public void setSc(String json) {
Type collectionType = new TypeToken<Collection<Constraint>>() {
}.getType();
constraint = new Gson().fromJson(json, collectionType);
}
void setSelection(VerbResolver resolver) {
for (Constraint st : constraint) {
try {
st.setSelection(resolver);
} catch (NoSuchMethodException e) {
log.error(e.getMessage());
} catch (IllegalAccessException e) {
log.error(e.getMessage());
} catch (InvocationTargetException e) {
log.error(e.getMessage());
} catch (InstantiationException e) {
log.error(e.getMessage());
}
}
}
// Constraint in and
public boolean verifyCriteria(final Map<String, List<String>> param) {
for (Constraint sc : constraint) {
boolean verified = false;
for (String value : param.get(sc.getField())) {
if (sc.verifyCriteria(value.trim())) {
verified = true;
}
}
if (!verified)
return verified;
}
return true;
}
}

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package eu.dnetlib.dhp.community;
import java.io.Serializable;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.dom4j.Node;
import com.google.gson.Gson;
import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
/** Created by miriam on 01/08/2018. */
public class Datasource implements Serializable {
private static final Log log = LogFactory.getLog(Datasource.class);
private String openaireId;
private SelectionConstraints selectionConstraints;
public SelectionConstraints getSelCriteria() {
return selectionConstraints;
}
public SelectionConstraints getSelectionConstraints() {
return selectionConstraints;
}
public void setSelectionConstraints(SelectionConstraints selectionConstraints) {
this.selectionConstraints = selectionConstraints;
}
public void setSelCriteria(SelectionConstraints selCriteria) {
this.selectionConstraints = selCriteria;
}
public String getOpenaireId() {
return openaireId;
}
public void setOpenaireId(String openaireId) {
this.openaireId = openaireId;
}
private void setSelCriteria(String json, VerbResolver resolver) {
log.info("Selection constraints for datasource = " + json);
selectionConstraints = new Gson().fromJson(json, SelectionConstraints.class);
selectionConstraints.setSelection(resolver);
}
public void setSelCriteria(Node n, VerbResolver resolver) {
try {
setSelCriteria(n.getText(), resolver);
} catch (Exception e) {
log.info("not set selection criteria... ");
selectionConstraints = null;
}
}
}

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package eu.dnetlib.dhp.community;
import java.io.Serializable;
import com.google.gson.Gson;
/** Created by miriam on 03/08/2018. */
public class Pair<A, B> implements Serializable {
private A fst;
private B snd;
public A getFst() {
return fst;
}
public Pair setFst(A fst) {
this.fst = fst;
return this;
}
public B getSnd() {
return snd;
}
public Pair setSnd(B snd) {
this.snd = snd;
return this;
}
public Pair(A a, B b) {
fst = a;
snd = b;
}
public String toJson() {
return new Gson().toJson(this);
}
}

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package eu.dnetlib.dhp.community;
import java.io.Serializable;
import java.util.HashMap;
public class ProtoMap extends HashMap<String, String> implements Serializable {
public ProtoMap() {
super();
}
}

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package eu.dnetlib.dhp.community;
import java.util.List;
import org.dom4j.DocumentException;
import com.google.common.base.Joiner;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class QueryInformationSystem {
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+ " let $subj := $x//CONFIGURATION/context/param[./@name='subject']/text() "
+ " let $datasources := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::contentproviders')]/concept "
+ " let $organizations := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::resultorganizations')]/concept "
+ " let $communities := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::zenodocommunities')]/concept "
+ " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] "
+ " return "
+ " <community> "
+ " { $x//CONFIGURATION/context/@id} "
+ " <subjects> "
+ " {for $y in tokenize($subj,',') "
+ " return "
+ " <subject>{$y}</subject>} "
+ " </subjects> "
+ " <datasources> "
+ " {for $d in $datasources "
+ " where $d/param[./@name='enabled']/text()='true' "
+ " return "
+ " <datasource> "
+ " <openaireId> "
+ " {$d//param[./@name='openaireId']/text()} "
+ " </openaireId> "
+ " <selcriteria> "
+ " {$d/param[./@name='selcriteria']/text()} "
+ " </selcriteria> "
+ " </datasource> } "
+ " </datasources> "
+ " <zenodocommunities> "
+ " {for $zc in $communities "
+ " return "
+ " <zenodocommunity> "
+ " <zenodoid> "
+ " {$zc/param[./@name='zenodoid']/text()} "
+ " </zenodoid> "
+ " <selcriteria> "
+ " {$zc/param[./@name='selcriteria']/text()} "
+ " </selcriteria> "
+ " </zenodocommunity>} "
+ " </zenodocommunities> "
+ " </community>";
public static CommunityConfiguration getCommunityConfiguration(final String isLookupUrl)
throws ISLookUpException, DocumentException {
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
final List<String> res = isLookUp.quickSearchProfile(XQUERY);
final String xmlConf = "<communities>" + Joiner.on(" ").join(res) + "</communities>";
return CommunityConfigurationFactory.newInstance(xmlConf);
}
}

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package eu.dnetlib.dhp.community;
import static eu.dnetlib.dhp.community.TagginConstants.*;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.schema.oaf.*;
/** Created by miriam on 02/08/2018. */
public class ResultTagger implements Serializable {
private String trust = "0.8";
private boolean clearContext(Result result) {
int tmp = result.getContext().size();
List<Context> clist = result
.getContext()
.stream()
.filter(c -> (!c.getId().contains(ZENODO_COMMUNITY_INDICATOR)))
.collect(Collectors.toList());
result.setContext(clist);
return (tmp != clist.size());
}
private Map<String, List<String>> getParamMap(final Result result, Map<String, String> params) {
Map<String, List<String>> param = new HashMap<>();
String json = new Gson().toJson(result, Result.class);
DocumentContext jsonContext = JsonPath.parse(json);
if (params == null) {
params = new HashMap<>();
}
for (String key : params.keySet()) {
try {
param.put(key, jsonContext.read(params.get(key)));
} catch (com.jayway.jsonpath.PathNotFoundException e) {
param.put(key, new ArrayList<>());
// throw e;
}
}
return param;
}
public <R extends Result> R enrichContextCriteria(
final R result, final CommunityConfiguration conf, final Map<String, String> criteria) {
// }
// public Result enrichContextCriteria(final Result result, final CommunityConfiguration
// conf, final Map<String,String> criteria) {
final Map<String, List<String>> param = getParamMap(result, criteria);
// Verify if the entity is deletedbyinference. In case verify if to clean the context list
// from all the zenodo communities
if (result.getDataInfo().getDeletedbyinference()) {
clearContext(result);
return result;
}
// communities contains all the communities to be added as context for the result
final Set<String> communities = new HashSet<>();
// tagging for Subject
final Set<String> subjects = new HashSet<>();
Optional<List<StructuredProperty>> oresultsubj = Optional.ofNullable(result.getSubject());
if (oresultsubj.isPresent()) {
oresultsubj
.get()
.stream()
.map(subject -> subject.getValue())
.filter(StringUtils::isNotBlank)
.map(String::toLowerCase)
.map(String::trim)
.collect(Collectors.toCollection(HashSet::new))
.forEach(s -> subjects.addAll(conf.getCommunityForSubjectValue(s)));
}
communities.addAll(subjects);
// Tagging for datasource
final Set<String> datasources = new HashSet<>();
final Set<String> tmp = new HashSet<>();
Optional<List<Instance>> oresultinstance = Optional.ofNullable(result.getInstance());
if (oresultinstance.isPresent()) {
for (Instance i : oresultinstance.get()) {
tmp.add(StringUtils.substringAfter(i.getCollectedfrom().getKey(), "|"));
tmp.add(StringUtils.substringAfter(i.getHostedby().getKey(), "|"));
}
oresultinstance
.get()
.stream()
.map(i -> new Pair<>(i.getCollectedfrom().getKey(), i.getHostedby().getKey()))
.flatMap(p -> Stream.of(p.getFst(), p.getSnd()))
.map(s -> StringUtils.substringAfter(s, "|"))
.collect(Collectors.toCollection(HashSet::new))
.forEach(
dsId -> datasources
.addAll(
conf.getCommunityForDatasource(dsId, param)));
}
communities.addAll(datasources);
/* Tagging for Zenodo Communities */
final Set<String> czenodo = new HashSet<>();
Optional<List<Context>> oresultcontext = Optional.ofNullable(result.getContext());
if (oresultcontext.isPresent()) {
oresultcontext
.get()
.stream()
.filter(c -> c.getId().contains(ZENODO_COMMUNITY_INDICATOR))
.collect(Collectors.toList())
.forEach(
c -> czenodo
.addAll(
conf
.getCommunityForZenodoCommunityValue(
c
.getId()
.substring(
c.getId().lastIndexOf("/") + 1)
.trim())));
}
communities.addAll(czenodo);
clearContext(result);
/* Verify if there is something to bulktag */
if (communities.isEmpty()) {
return result;
}
result
.getContext()
.stream()
.map(
c -> {
if (communities.contains(c.getId())) {
Optional<List<DataInfo>> opt_dataInfoList = Optional.ofNullable(c.getDataInfo());
List<DataInfo> dataInfoList;
if (opt_dataInfoList.isPresent())
dataInfoList = opt_dataInfoList.get();
else {
dataInfoList = new ArrayList<>();
c.setDataInfo(dataInfoList);
}
if (subjects.contains(c.getId()))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_SUBJECT,
CLASS_NAME_BULKTAG_SUBJECT));
if (datasources.contains(c.getId()))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_DATASOURCE,
CLASS_NAME_BULKTAG_DATASOURCE));
if (czenodo.contains(c.getId()))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_CZENODO,
CLASS_NAME_BULKTAG_ZENODO));
}
return c;
})
.collect(Collectors.toList());
communities
.removeAll(
result.getContext().stream().map(c -> c.getId()).collect(Collectors.toSet()));
if (communities.isEmpty())
return result;
List<Context> toaddcontext = communities
.stream()
.map(
c -> {
Context context = new Context();
context.setId(c);
List<DataInfo> dataInfoList = new ArrayList<>();
if (subjects.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_SUBJECT,
CLASS_NAME_BULKTAG_SUBJECT));
if (datasources.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_DATASOURCE,
CLASS_NAME_BULKTAG_DATASOURCE));
if (czenodo.contains(c))
dataInfoList
.add(
getDataInfo(
BULKTAG_DATA_INFO_TYPE,
CLASS_ID_CZENODO,
CLASS_NAME_BULKTAG_ZENODO));
context.setDataInfo(dataInfoList);
return context;
})
.collect(Collectors.toList());
result.getContext().addAll(toaddcontext);
return result;
}
public static DataInfo getDataInfo(
String inference_provenance, String inference_class_id, String inference_class_name) {
DataInfo di = new DataInfo();
di.setInferred(true);
di.setInferenceprovenance(inference_provenance);
di.setProvenanceaction(getQualifier(inference_class_id, inference_class_name));
return di;
}
public static Qualifier getQualifier(String inference_class_id, String inference_class_name) {
Qualifier pa = new Qualifier();
pa.setClassid(inference_class_id);
pa.setClassname(inference_class_name);
pa.setSchemeid(DNET_SCHEMA_ID);
pa.setSchemename(DNET_SCHEMA_NAME);
return pa;
}
}

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package eu.dnetlib.dhp.community;
import java.io.Serializable;
import java.lang.reflect.Type;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
public class SelectionConstraints implements Serializable {
private List<Constraints> criteria;
public SelectionConstraints() {
}
public List<Constraints> getCriteria() {
return criteria;
}
public void setCriteria(List<Constraints> criteria) {
this.criteria = criteria;
}
public void setSc(String json) {
Type collectionType = new TypeToken<Collection<Constraints>>() {
}.getType();
criteria = new Gson().fromJson(json, collectionType);
}
// Constraints in or
public boolean verifyCriteria(final Map<String, List<String>> param) {
for (Constraints selc : criteria) {
if (selc.verifyCriteria(param)) {
return true;
}
}
return false;
}
public void setSelection(VerbResolver resolver) {
for (Constraints cs : criteria) {
cs.setSelection(resolver);
}
}
}

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package eu.dnetlib.dhp.community;
public class TagginConstants {
public static final String BULKTAG_DATA_INFO_TYPE = "bulktagging";
public static final String DNET_SCHEMA_NAME = "dnet:provenanceActions";
public static final String DNET_SCHEMA_ID = "dnet:provenanceActions";
public static final String CLASS_ID_SUBJECT = "community:subject";
public static final String CLASS_ID_DATASOURCE = "community:datasource";
public static final String CLASS_ID_CZENODO = "community:zenodocommunity";
public static final String SCHEMA_ID = "dnet:provenanceActions";
public static final String COUNTER_GROUP = "Bulk Tagging";
public static final String ZENODO_COMMUNITY_INDICATOR = "zenodo.org/communities/";
public static final String CLASS_NAME_BULKTAG_SUBJECT = "Bulktagging for Community - Subject";
public static final String CLASS_NAME_BULKTAG_DATASOURCE = "Bulktagging for Community - Datasource";
public static final String CLASS_NAME_BULKTAG_ZENODO = "Bulktagging for Community - Zenodo";
}

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package eu.dnetlib.dhp.community;
import java.io.Serializable;
import org.dom4j.Node;
import com.google.gson.Gson;
/** Created by miriam on 01/08/2018. */
public class ZenodoCommunity implements Serializable {
private String zenodoCommunityId;
private SelectionConstraints selCriteria;
public String getZenodoCommunityId() {
return zenodoCommunityId;
}
public void setZenodoCommunityId(String zenodoCommunityId) {
this.zenodoCommunityId = zenodoCommunityId;
}
public SelectionConstraints getSelCriteria() {
return selCriteria;
}
public void setSelCriteria(SelectionConstraints selCriteria) {
this.selCriteria = selCriteria;
}
private void setSelCriteria(String json) {
// Type collectionType = new TypeToken<Collection<Constraints>>(){}.getType();
selCriteria = new Gson().fromJson(json, SelectionConstraints.class);
}
public void setSelCriteria(Node n) {
if (n == null) {
selCriteria = null;
} else {
setSelCriteria(n.getText());
}
}
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.io.Serializable;
@VerbClass("contains")
public class ContainsVerb implements Selection, Serializable {
private String param;
public ContainsVerb() {
}
public ContainsVerb(final String param) {
this.param = param;
}
@Override
public boolean apply(String value) {
return value.contains(param);
}
public String getParam() {
return param;
}
public void setParam(String param) {
this.param = param;
}
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.io.Serializable;
@VerbClass("contains_ignorecase")
public class ContainsVerbIgnoreCase implements Selection, Serializable {
private String param;
public ContainsVerbIgnoreCase() {
}
public ContainsVerbIgnoreCase(final String param) {
this.param = param;
}
@Override
public boolean apply(String value) {
return value.toLowerCase().contains(param.toLowerCase());
}
public String getParam() {
return param;
}
public void setParam(String param) {
this.param = param;
}
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.io.Serializable;
@VerbClass("equals")
public class EqualVerb implements Selection, Serializable {
private String param;
public EqualVerb() {
}
public EqualVerb(final String param) {
this.param = param;
}
@Override
public boolean apply(String value) {
return value.equals(param);
}
public String getParam() {
return param;
}
public void setParam(String param) {
this.param = param;
}
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.io.Serializable;
@VerbClass("equals_ignorecase")
public class EqualVerbIgnoreCase implements Selection, Serializable {
private String param;
public EqualVerbIgnoreCase() {
}
public EqualVerbIgnoreCase(final String param) {
this.param = param;
}
@Override
public boolean apply(String value) {
return value.equalsIgnoreCase(param);
}
public String getParam() {
return param;
}
public void setParam(String param) {
this.param = param;
}
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.lang.reflect.Type;
import com.google.gson.*;
public class InterfaceAdapter implements JsonSerializer, JsonDeserializer {
private static final String CLASSNAME = "CLASSNAME";
private static final String DATA = "DATA";
public Object deserialize(
JsonElement jsonElement,
Type type,
JsonDeserializationContext jsonDeserializationContext)
throws JsonParseException {
JsonObject jsonObject = jsonElement.getAsJsonObject();
JsonPrimitive prim = (JsonPrimitive) jsonObject.get(CLASSNAME);
String className = prim.getAsString();
Class klass = getObjectClass(className);
return jsonDeserializationContext.deserialize(jsonObject.get(DATA), klass);
}
public JsonElement serialize(
Object jsonElement, Type type, JsonSerializationContext jsonSerializationContext) {
JsonObject jsonObject = new JsonObject();
jsonObject.addProperty(CLASSNAME, jsonElement.getClass().getName());
jsonObject.add(DATA, jsonSerializationContext.serialize(jsonElement));
return jsonObject;
}
/** **** Helper method to get the className of the object to be deserialized **** */
public Class getObjectClass(String className) {
try {
return Class.forName(className);
} catch (ClassNotFoundException e) {
// e.printStackTrace();
throw new JsonParseException(e.getMessage());
}
}
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.io.Serializable;
@VerbClass("not_contains")
public class NotContainsVerb implements Selection, Serializable {
private String param;
public NotContainsVerb() {
}
public NotContainsVerb(final String param) {
this.param = param;
}
@Override
public boolean apply(String value) {
return !value.contains(param);
}
public String getParam() {
return param;
}
public void setParam(String param) {
this.param = param;
}
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.io.Serializable;
@VerbClass("not_contains_ignorecase")
public class NotContainsVerbIgnoreCase implements Selection, Serializable {
private String param;
public NotContainsVerbIgnoreCase() {
}
public NotContainsVerbIgnoreCase(final String param) {
this.param = param;
}
@Override
public boolean apply(String value) {
return !(value.toLowerCase().contains(param.toLowerCase()));
}
public String getParam() {
return param;
}
public void setParam(String param) {
this.param = param;
}
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.io.Serializable;
@VerbClass("not_equals")
public class NotEqualVerb implements Selection, Serializable {
private String param;
public NotEqualVerb(final String param) {
this.param = param;
}
public NotEqualVerb() {
}
public String getParam() {
return param;
}
public void setParam(String param) {
this.param = param;
}
@Override
public boolean apply(String value) {
return !value.equals(param);
}
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.io.Serializable;
@VerbClass("not_equals_ignorecase")
public class NotEqualVerbIgnoreCase implements Selection, Serializable {
private String param;
public NotEqualVerbIgnoreCase(final String param) {
this.param = param;
}
public NotEqualVerbIgnoreCase() {
}
public String getParam() {
return param;
}
public void setParam(String param) {
this.param = param;
}
@Override
public boolean apply(String value) {
return !value.equalsIgnoreCase(param);
}
}

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package eu.dnetlib.dhp.selectioncriteria;
public interface Selection {
boolean apply(String value);
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.TYPE)
@interface VerbClass {
String value();
}

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package eu.dnetlib.dhp.selectioncriteria;
import java.io.Serializable;
import java.lang.reflect.InvocationTargetException;
import java.util.Map;
import java.util.stream.Collectors;
import io.github.classgraph.ClassGraph;
import io.github.classgraph.ClassInfo;
import io.github.classgraph.ClassInfoList;
import io.github.classgraph.ScanResult;
public class VerbResolver implements Serializable {
private Map<String, Class<Selection>> map = null; // = new HashMap<>();
private final ClassGraph classgraph = new ClassGraph();
public VerbResolver() {
try (ScanResult scanResult = // Assign scanResult in try-with-resources
classgraph // Create a new ClassGraph instance
.verbose() // If you want to enable logging to stderr
.enableAllInfo() // Scan classes, methods, fields, annotations
.whitelistPackages(
"eu.dnetlib.dhp.selectioncriteria") // Scan com.xyz and subpackages
.scan()) { // Perform the scan and return a ScanResult
ClassInfoList routeClassInfoList = scanResult
.getClassesWithAnnotation(
"eu.dnetlib.dhp.selectioncriteria.VerbClass");
this.map = routeClassInfoList
.stream()
.collect(
Collectors
.toMap(
value -> (String) ((ClassInfo) value)
.getAnnotationInfo()
.get(0)
.getParameterValues()
.get(0)
.getValue(),
value -> (Class<Selection>) ((ClassInfo) value).loadClass()));
} catch (Exception e) {
e.printStackTrace();
}
}
public Selection getSelectionCriteria(String name, String param)
throws NoSuchMethodException, IllegalAccessException, InvocationTargetException,
InstantiationException {
// return Class.forName(tmp_map.get(name)).
return map.get(name).getDeclaredConstructor((String.class)).newInstance(param);
}
}

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package eu.dnetlib.dhp.selectioncriteria;
public class VerbResolverFactory {
public static VerbResolver newInstance() {
return new VerbResolver();
}
}

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[
{
"paramName":"is",
"paramLongName":"isLookUpUrl",
"paramDescription": "URL of the isLookUp Service",
"paramRequired": true
},
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "pm",
"paramLongName":"pathMap",
"paramDescription": "the json path associated to each selection field",
"paramRequired": true
},
{
"paramName":"tn",
"paramLongName":"resultTableName",
"paramDescription": "the name of the result table we are currently working on",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName": "test",
"paramLongName": "isTest",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName": "tg",
"paramLongName": "taggingConf",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
}
]

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<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
</property>
<property>
<name>sparkExecutorNumber</name>
<value>4</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>sparkDriverMemory</name>
<value>15G</value>
</property>
<property>
<name>sparkExecutorMemory</name>
<value>6G</value>
</property>
<property>
<name>sparkExecutorCores</name>
<value>1</value>
</property>
</configuration>

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<workflow-app name="bulk_tagging" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>isLookUpUrl</name>
<description>the isLookup service endpoint</description>
</property>
<property>
<name>pathMap</name>
<description>the json path associated to each selection field</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
</parameters>
<start to="reset_outputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset_outputpath">
<fs>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>
</action>
<fork name="copy_entities">
<path start="copy_relation"/>
<path start="copy_organization"/>
<path start="copy_projects"/>
<path start="copy_datasources"/>
</fork>
<action name="copy_relation">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<arg>${nameNode}/${sourcePath}/relation</arg>
<arg>${nameNode}/${outputPath}/relation</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_organization">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<arg>${nameNode}/${sourcePath}/organization</arg>
<arg>${nameNode}/${outputPath}/organization</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_projects">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<arg>${nameNode}/${sourcePath}/project</arg>
<arg>${nameNode}/${outputPath}/project</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_datasources">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<arg>${nameNode}/${sourcePath}/datasource</arg>
<arg>${nameNode}/${outputPath}/datasource</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<join name="copy_wait" to="fork_exec_bulktag"/>
<fork name="fork_exec_bulktag">
<path start="join_bulktag_publication"/>
<path start="join_bulktag_dataset"/>
<path start="join_bulktag_otherresearchproduct"/>
<path start="join_bulktag_software"/>
</fork>
<action name="join_bulktag_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-publication</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob</class>
<jar>dhp-bulktag-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_bulktag_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-dataset</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob</class>
<jar>dhp-bulktag-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_bulktag_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-orp</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob</class>
<jar>dhp-bulktag-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_bulktag_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-software</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob</class>
<jar>dhp-bulktag-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<join name="wait" to="End"/>
<end name="End"/>
</workflow-app>

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package eu.dnetlib.dhp;
import static eu.dnetlib.dhp.community.TagginConstants.ZENODO_COMMUNITY_INDICATOR;
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.Encoders;
import org.apache.spark.sql.Row;
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 org.mortbay.util.IO;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.bulktag.SparkBulkTagJob;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Software;
public class BulkTagJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ClassLoader cl = eu.dnetlib.dhp.BulkTagJobTest.class.getClassLoader();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.BulkTagJobTest.class);
private static String taggingConf = "";
static {
try {
taggingConf = IO
.toString(
BulkTagJobTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/communityconfiguration/tagging_conf.xml"));
} catch (IOException e) {
e.printStackTrace();
}
}
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(eu.dnetlib.dhp.BulkTagJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(eu.dnetlib.dhp.BulkTagJobTest.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(BulkTagJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void noUpdatesTest() throws Exception {
SparkBulkTagJob
.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/sample/dataset/no_updates").getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-isLookUpUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-pathMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
// "-preparedInfoPath",
// getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/preparedInfo").getPath()
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.id community "
+ "from dataset "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
Assertions.assertEquals(0, spark.sql(query).count());
}
@Test
public void bulktagBySubjectNoPreviousContextTest() throws Exception {
SparkBulkTagJob
.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource("/eu/dnetlib/dhp/sample/dataset/update_subject/nocontext")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-isLookUpUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-pathMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from dataset "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
Assertions.assertEquals(5, spark.sql(query).count());
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
Assertions
.assertEquals(
5, idExplodeCommunity.filter("provenance = 'community:subject'").count());
Assertions
.assertEquals(
5,
idExplodeCommunity.filter("name = 'Bulktagging for Community - Subject'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count());
Assertions
.assertEquals(
1,
idExplodeCommunity
.filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
.count());
Assertions
.assertEquals(
1,
idExplodeCommunity
.filter(
"community = 'covid-19' and id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
.count());
Assertions
.assertEquals(
2,
idExplodeCommunity
.filter("id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'")
.count());
Assertions
.assertEquals(
2,
idExplodeCommunity
.filter(
"(community = 'covid-19' or community = 'aginfra') and id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'")
.count());
Assertions
.assertEquals(
2,
idExplodeCommunity
.filter("id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'")
.count());
Assertions
.assertEquals(
2,
idExplodeCommunity
.filter(
"(community = 'mes' or community = 'fam') and id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'")
.count());
}
@Test
public void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception {
SparkBulkTagJob
.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource(
"/eu/dnetlib/dhp/sample/dataset/update_subject/contextnoprovenance")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-isLookUpUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-pathMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance "
+ "from dataset "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyT.id = 'covid-19' ";
Assertions.assertEquals(3, spark.sql(query).count());
org.apache.spark.sql.Dataset<Row> communityContext = spark.sql(query);
Assertions
.assertEquals(
2,
communityContext
.filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
.count());
Assertions
.assertEquals(
1,
communityContext
.filter(
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'community:subject'")
.count());
Assertions
.assertEquals(
1,
communityContext
.filter(
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'propagation:community:productsthroughsemrel'")
.count());
query = "select id, MyT.id community, size(MyT.datainfo) datainfosize "
+ "from dataset "
+ "lateral view explode (context) as MyT "
+ "where size(MyT.datainfo) > 0";
Assertions
.assertEquals(
2,
spark
.sql(query)
.select("datainfosize")
.where(
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' a"
+ "nd community = 'covid-19'")
.collectAsList()
.get(0)
.getInt(0));
}
@Test
public void bulktagByDatasourceTest() throws Exception {
SparkBulkTagJob
.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource("/eu/dnetlib/dhp/sample/publication/update_datasource")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/publication",
"-isLookUpUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-pathMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from publication "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
Assertions.assertEquals(5, idExplodeCommunity.count());
Assertions
.assertEquals(
5, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
Assertions
.assertEquals(
5,
idExplodeCommunity
.filter("name = 'Bulktagging for Community - Datasource'")
.count());
Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'fam'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count());
Assertions
.assertEquals(
3,
idExplodeCommunity
.filter(
"community = 'fam' and (id = '50|ec_fp7health::000085c89f4b96dc2269bd37edb35306' "
+ "or id = '50|ec_fp7health::000b9e61f83f5a4b0c35777b7bccdf38' "
+ "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')")
.count());
Assertions
.assertEquals(
2,
idExplodeCommunity
.filter(
"community = 'aginfra' and (id = '50|ec_fp7health::000c8195edd542e4e64ebb32172cbf89' "
+ "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')")
.count());
}
@Test
public void bulktagByZenodoCommunityTest() throws Exception {
SparkBulkTagJob
.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource(
"/eu/dnetlib/dhp/sample/otherresearchproduct/update_zenodocommunity")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
"-outputPath",
workingDir.toString() + "/orp",
"-isLookUpUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-pathMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<OtherResearchProduct> tmp = sc
.textFile(workingDir.toString() + "/orp")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<OtherResearchProduct> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(OtherResearchProduct.class));
verificationDataset.createOrReplaceTempView("orp");
String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from orp "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
Assertions.assertEquals(8, idExplodeCommunity.count());
Assertions
.assertEquals(
8, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count());
Assertions
.assertEquals(
8,
idExplodeCommunity.filter("name = 'Bulktagging for Community - Zenodo'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'covid-19'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'beopen'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'mes'").count());
Assertions
.assertEquals(
1,
idExplodeCommunity
.filter(
"id = '50|od______2017::0750a4d0782265873d669520f5e33c07' "
+ "and community = 'covid-19'")
.count());
Assertions
.assertEquals(
3,
idExplodeCommunity
.filter(
"id = '50|od______2017::1bd97baef19dbd2db3203b112bb83bc5' and "
+ "(community = 'aginfra' or community = 'mes' or community = 'fam')")
.count());
Assertions
.assertEquals(
1,
idExplodeCommunity
.filter(
"id = '50|od______2017::1e400f1747487fd15998735c41a55c72' "
+ "and community = 'beopen'")
.count());
Assertions
.assertEquals(
3,
idExplodeCommunity
.filter(
"id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' and "
+ "(community = 'beopen' or community = 'fam' or community = 'mes')")
.count());
query = "select id, MyT.id community, size(MyT.datainfo) datainfosize "
+ "from orp "
+ "lateral view explode (context) as MyT "
+ "where size(MyT.datainfo) > 0";
Assertions
.assertEquals(
2,
spark
.sql(query)
.select("datainfosize")
.where(
"id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' a"
+ "nd community = 'beopen'")
.collectAsList()
.get(0)
.getInt(0));
// verify the zenodo community context is not present anymore in the records
query = "select id, MyT.id community "
+ "from orp "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD ";
org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
Assertions
.assertEquals(
0,
tmp2
.select("community")
.where(tmp2.col("community").contains(ZENODO_COMMUNITY_INDICATOR))
.count());
}
@Test
public void bulktagBySubjectDatasourceTest() throws Exception {
SparkBulkTagJob
.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource("/eu/dnetlib/dhp/sample/dataset/update_subject_datasource")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-isLookUpUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-pathMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from dataset "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
Assertions.assertEquals(7, idExplodeCommunity.count());
Assertions
.assertEquals(
5, idExplodeCommunity.filter("provenance = 'community:subject'").count());
Assertions
.assertEquals(
2, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count());
query = "select id, MyT.id community, size(MyT.datainfo) datainfosize "
+ "from dataset "
+ "lateral view explode (context) as MyT "
+ "where size(MyT.datainfo) > 0";
org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
Assertions
.assertEquals(
2,
tmp2
.select("datainfosize")
.where(
"id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and "
+ "community = 'aginfra'")
.collectAsList()
.get(0)
.getInt(0));
Assertions
.assertEquals(
1,
tmp2
.select("datainfosize")
.where(
"id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and "
+ "community = 'covid-19'")
.collectAsList()
.get(0)
.getInt(0));
Assertions
.assertEquals(
2,
tmp2
.select("datainfosize")
.where(
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and "
+ "community = 'fam'")
.collectAsList()
.get(0)
.getInt(0));
Assertions
.assertEquals(
2,
tmp2
.select("datainfosize")
.where(
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and "
+ "community = 'covid-19'")
.collectAsList()
.get(0)
.getInt(0));
Assertions
.assertEquals(
1,
tmp2
.select("datainfosize")
.where(
"id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and "
+ "community = 'fam'")
.collectAsList()
.get(0)
.getInt(0));
Assertions
.assertEquals(
1,
tmp2
.select("datainfosize")
.where(
"id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and "
+ "community = 'mes'")
.collectAsList()
.get(0)
.getInt(0));
}
@Test
public void bulktagBySubjectDatasourceZenodoCommunityTest() throws Exception {
SparkBulkTagJob
.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/sample/software/").getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath",
workingDir.toString() + "/software",
"-isLookUpUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-pathMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Software> tmp = sc
.textFile(workingDir.toString() + "/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Software> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Software.class));
verificationDataset.createOrReplaceTempView("software");
String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from software "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
Assertions.assertEquals(10, idExplodeCommunity.count());
idExplodeCommunity.show(false);
Assertions
.assertEquals(
3, idExplodeCommunity.filter("provenance = 'community:subject'").count());
Assertions
.assertEquals(
3, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
Assertions
.assertEquals(
4, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count());
Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'covid-19'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dh-ch'").count());
Assertions.assertEquals(4, idExplodeCommunity.filter("community = 'aginfra'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dariah'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count());
Assertions
.assertEquals(
2,
idExplodeCommunity
.filter(
"provenance = 'community:zenodocommunity' and "
+ "id = '50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4' and ("
+ "community = 'dh-ch' or community = 'dariah')")
.count());
query = "select id, MyT.id community, size(MyT.datainfo) datainfosize "
+ "from software "
+ "lateral view explode (context) as MyT "
+ "where size(MyT.datainfo) > 0";
org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
Assertions
.assertEquals(
2,
tmp2
.select("datainfosize")
.where(
"id = '50|od______1582::501b25d420f808c8eddcd9b16e917f11' and "
+ "community = 'covid-19'")
.collectAsList()
.get(0)
.getInt(0));
Assertions
.assertEquals(
3,
tmp2
.select("datainfosize")
.where(
"id = '50|od______1582::581621232a561b7e8b4952b18b8b0e56' and "
+ "community = 'aginfra'")
.collectAsList()
.get(0)
.getInt(0));
}
@Test
public void bulktagDatasourcewithConstraintsTest() throws Exception {
SparkBulkTagJob
.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource(
"/eu/dnetlib/dhp/sample/dataset/update_datasourcewithconstraints")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-isLookUpUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-pathMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from dataset "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
idExplodeCommunity.show(false);
Assertions.assertEquals(3, idExplodeCommunity.count());
Assertions
.assertEquals(
3, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
}
}

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@ -0,0 +1,166 @@
package eu.dnetlib.dhp;
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.DocumentException;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import com.google.gson.Gson;
import eu.dnetlib.dhp.community.CommunityConfiguration;
import eu.dnetlib.dhp.community.CommunityConfigurationFactory;
import eu.dnetlib.dhp.community.Constraint;
import eu.dnetlib.dhp.community.SelectionConstraints;
import eu.dnetlib.dhp.selectioncriteria.VerbResolver;
/** Created by miriam on 03/08/2018. */
public class CommunityConfigurationFactoryTest {
private final VerbResolver resolver = new VerbResolver();
@Test
public void parseTest() throws DocumentException, IOException {
String xml = IOUtils
.toString(
getClass()
.getResourceAsStream(
"/eu/dnetlib/dhp/communityconfiguration/community_configuration.xml"));
final CommunityConfiguration cc = CommunityConfigurationFactory.newInstance(xml);
Assertions.assertEquals(5, cc.size());
cc
.getCommunityList()
.forEach(c -> Assertions.assertTrue(StringUtils.isNoneBlank(c.getId())));
}
@Test
public void applyVerb()
throws InvocationTargetException, IllegalAccessException, NoSuchMethodException,
InstantiationException {
Constraint sc = new Constraint();
sc.setVerb("not_contains");
sc.setField("contributor");
sc.setValue("DARIAH");
sc.setSelection(resolver.getSelectionCriteria(sc.getVerb(), sc.getValue()));
String metadata = "This work has been partially supported by DARIAH-EU infrastructure";
Assertions.assertFalse(sc.verifyCriteria(metadata));
}
@Test
public void loadSelCriteriaTest() throws DocumentException, IOException {
String xml = IOUtils
.toString(
getClass()
.getResourceAsStream(
"/eu/dnetlib/dhp/communityconfiguration/community_configuration_selcrit.xml"));
final CommunityConfiguration cc = CommunityConfigurationFactory.newInstance(xml);
Map<String, List<String>> param = new HashMap<>();
param.put("author", new ArrayList<>(Collections.singletonList("Pippo Pippi")));
param
.put(
"description",
new ArrayList<>(
Collections
.singletonList(
"This work has been partially supported by DARIAH-EU infrastructure")));
param
.put(
"contributor",
new ArrayList<>(
Collections
.singletonList(
"Pallino ha aiutato a scrivere il paper. Pallino lavora per DARIAH")));
List<String> comm = cc
.getCommunityForDatasource(
"openaire____::1cfdb2e14977f31a98e0118283401f32", param);
Assertions.assertEquals(1, comm.size());
Assertions.assertEquals("dariah", comm.get(0));
}
@Test
public void test4() throws DocumentException, IOException {
final CommunityConfiguration cc = CommunityConfigurationFactory
.fromJson(
IOUtils
.toString(
getClass()
.getResourceAsStream(
"/eu/dnetlib/dhp/communityconfiguration/community_configuration_selcrit.json")));
cc.toString();
}
@Test
public void test5() throws IOException, DocumentException {
// final CommunityConfiguration cc =
// CommunityConfigurationFactory.newInstance(IOUtils.toString(getClass().getResourceAsStream("test.xml")));
final CommunityConfiguration cc = CommunityConfigurationFactory
.fromJson(
IOUtils
.toString(
getClass()
.getResourceAsStream(
"/eu/dnetlib/dhp/communityconfiguration/community_configuration.json")));
System.out.println(cc.toJson());
}
@Test
public void test6() {
String json = "{\"criteria\":[{\"constraint\":[{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}]}]}";
String step1 = "{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}";
Constraint c = new Gson().fromJson(step1, Constraint.class);
//
// String step2 =
// "{\"constraint\":[{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}]}";
//
// ConstraintEncapsulator ce = new
// Gson().fromJson(step2,ConstraintEncapsulator.class);
//
//
// String step3 =
// "{\"ce\":{\"constraint\":[{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}]}}";
//
// Constraints cons = new Gson().fromJson(step3,Constraints.class);
//
// String step4 =
// "{\"criteria\":[{\"ce\":{\"constraint\":[{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}]}}]}";
//
// ConstraintsList cl = new Gson().fromJson(step4,ConstraintsList.class);
//
// String step5 =
// "{\"cl\":{\"criteria\":[{\"ce\":{\"constraint\":[{\"verb\":\"contains\",\"field\":\"contributor\",\"value\":\"DARIAH\"}]}}]}}";
SelectionConstraints sl = new Gson().fromJson(json, SelectionConstraints.class);
}
@Test
public void test7() throws IOException {
final CommunityConfiguration cc = CommunityConfigurationFactory
.fromJson(
IOUtils
.toString(
getClass()
.getResourceAsStream(
"/eu/dnetlib/dhp/communityconfiguration/tagging_conf.json")));
System.out.println(cc.toJson());
}
@Test
public void temporaneo() throws Exception {
String xml = IOUtils
.toString(
getClass()
.getResourceAsStream(
"/eu/dnetlib/dhp/communityconfiguration/tagging_conf.xml"));
final CommunityConfiguration cc = CommunityConfigurationFactory.newInstance(xml);
System.out.println(cc.toJson());
}
}

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@ -0,0 +1,694 @@
{"communities": {
"clarin": {
"id": "clarin",
"subjects": [],
"datasources": [
{
"openaireId": "re3data_____::a507cdacc5bbcc08761c92185dee5cab"
}
],
"zenodoCommunities": [
]
},
"ee": {
"id": "ee",
"subjects": [
"SDG13 - Climate action",
"SDG8 - Decent work and economic\n\t\t\t\t\tgrowth",
"SDG15 - Life on land",
"SDG2 - Zero hunger",
"SDG17 - Partnerships for the\n\t\t\t\t\tgoals",
"SDG10 - Reduced inequalities",
"SDG5 - Gender equality",
"SDG12 - Responsible\n\t\t\t\t\tconsumption and production",
"SDG14 - Life below water",
"SDG6 - Clean water and\n\t\t\t\t\tsanitation",
"SDG11 - Sustainable cities and communities",
"SDG1 - No poverty",
"SDG3 -\n\t\t\t\t\tGood health and well being",
"SDG7 - Affordable and clean energy",
"SDG4 - Quality\n\t\t\t\t\teducation",
"SDG9 - Industry innovation and infrastructure",
"SDG16 - Peace justice\n\t\t\t\t\tand strong institutions"
],
"datasources": [
],
"zenodoCommunities": [
]
},
"aginfra": {
"id": "aginfra",
"subjects": [
"animal production and health",
"fisheries and aquaculture",
"food safety and human nutrition",
"information management",
"food technology",
"agri-food education and extension",
"natural resources and environment",
"food system",
"engineering technology and Research",
"agriculture",
"food safety risk assessment",
"food security",
"farming practices and systems",
"plant production and protection",
"agri-food economics and policy",
"food distribution",
"forestry"
],
"datasources": [
{
"openaireId": "opendoar____::1a551829d50f1400b0dab21fdd969c04"
},
{
"openaireId": "opendoar____::49af6c4e558a7569d80eee2e035e2bd7"
},
{
"openaireId": "opendoar____::0266e33d3f546cb5436a10798e657d97"
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<subject>farming practices and systems</subject>
<subject>plant production and protection</subject>
<subject>agri-food economics and policy</subject>
<subject>food distribution</subject>
<subject>forestry</subject>
</subjects>
<datasources>
<datasource>
<openaireId>opendoar____::1a551829d50f1400b0dab21fdd969c04</openaireId>
<selcriteria/>
</datasource>
<datasource>
<openaireId>opendoar____::49af6c4e558a7569d80eee2e035e2bd7</openaireId>
<selcriteria/>
</datasource>
<datasource>
<openaireId>opendoar____::0266e33d3f546cb5436a10798e657d97</openaireId>
<selcriteria/>
</datasource>
<datasource>
<openaireId>opendoar____::fd4c2dc64ccb8496e6f1f94c85f30d06</openaireId>
<selcriteria/>
</datasource>
<datasource>
<openaireId>opendoar____::41bfd20a38bb1b0bec75acf0845530a7</openaireId>
<selcriteria/>
</datasource>
<datasource>
<openaireId>opendoar____::87ae6fb631f7c8a627e8e28785d9992d</openaireId>
<selcriteria/>
</datasource>
</datasources>
<zenodocommunities/>
</community>
<community id="clarin">
<oacommunity>oac_clarin</oacommunity>
<subjects/>
<datasources>
<datasource>
<openaireId>re3data_____::a507cdacc5bbcc08761c92185dee5cab</openaireId>
<selcriteria/>
</datasource>
</datasources>
<zenodocommunities/>
</community>
<community id="dariah">
<oacommunity>oaa_dariah</oacommunity>
<subjects/>
<datasources>
<datasource>
<openaireId>openaire____::1cfdb2e14977f31a98e0118283401f32</openaireId>
<selcriteria>{"criteria":[{"constraint":[{"verb":"contains","field":"contributor","value":"DARIAH"}]}]}
</selcriteria>
</datasource>
</datasources>
<zenodocommunities>
<zenodocommunity>
<zenodoid>dimpo</zenodoid>
<selcriteria/>
</zenodocommunity>
</zenodocommunities>
</community>
</communities>

File diff suppressed because one or more lines are too long

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@ -24,8 +24,8 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.raw.common.DbClient;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;

View File

@ -30,8 +30,8 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
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.DbClient;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset;
@ -94,7 +94,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
log.info("Processing orgs...");
smdbe.execute("queryOrganizations.sql", smdbe::processOrganization);
log.info("Processing relations ds <-> orgs ...");
log.info("Processing relationsNoRemoval ds <-> orgs ...");
smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization);
log.info("Processing projects <-> orgs ...");
@ -370,6 +370,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
final DataInfo info = dataInfo(
false, null, false, false,
qualifier(USER_CLAIM, USER_CLAIM, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), "0.9");
final List<KeyValue> collectedFrom = listKeyValues(
@ -460,7 +461,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
final Boolean inferred = rs.getBoolean("inferred");
final String trust = rs.getString("trust");
return dataInfo(
deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust);
}
private Qualifier prepareQualifierSplitting(final String s) {
@ -516,6 +519,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
if (arr.length == 3) {
final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0].trim() : null;
final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1].trim() : null;
final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2].trim() : null;
if (issn != null || eissn != null || lissn != null) {

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@ -0,0 +1,43 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.1-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-propagation</artifactId>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-hive_2.11</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
</project>

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@ -0,0 +1,169 @@
package eu.dnetlib.dhp;
import java.util.List;
import java.util.Optional;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
import eu.dnetlib.dhp.schema.oaf.*;
public class PropagationConstant {
public static final String INSTITUTIONAL_REPO_TYPE = "pubsrepository::institutional";
public static final String PROPAGATION_DATA_INFO_TYPE = "propagation";
public static final String TRUE = "true";
public static final String DNET_COUNTRY_SCHEMA = "dnet:countries";
public static final String DNET_SCHEMA_NAME = "dnet:provenanceActions";
public static final String DNET_SCHEMA_ID = "dnet:provenanceActions";
public static final String PROPAGATION_COUNTRY_INSTREPO_CLASS_ID = "country:instrepos";
public static final String PROPAGATION_COUNTRY_INSTREPO_CLASS_NAME = "Propagation of country to result collected from datasources of type institutional repositories";
public static final String PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID = "result:organization:instrepo";
public static final String PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME = "Propagation of affiliation to result collected from datasources of type institutional repository";
public static final String PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID = "result:project:semrel";
public static final String PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME = "Propagation of result to project through semantic relation";
public static final String PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID = "result:community:semrel";
public static final String PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME = " Propagation of result belonging to community through semantic relation";
public static final String PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID = "result:community:organization";
public static final String PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME = " Propagation of result belonging to community through organization";
public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID = "authorpid:result";
public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME = "Propagation of authors pid to result through semantic relations";
public static final String RELATION_DATASOURCE_ORGANIZATION_REL_CLASS = "isProvidedBy";
public static final String RELATION_RESULTORGANIZATION_REL_TYPE = "resultOrganization";
public static final String RELATION_RESULTORGANIZATION_SUBREL_TYPE = "affiliation";
public static final String RELATION_ORGANIZATION_RESULT_REL_CLASS = "isAuthorInstitutionOf";
public static final String RELATION_RESULT_ORGANIZATION_REL_CLASS = "hasAuthorInstitution";
public static final String RELATION_RESULTRESULT_REL_TYPE = "resultResult";
public static final String RELATION_RESULTPROJECT_REL_TYPE = "resultProject";
public static final String RELATION_RESULTPROJECT_SUBREL_TYPE = "outcome";
public static final String RELATION_RESULT_PROJECT_REL_CLASS = "isProducedBy";
public static final String RELATION_PROJECT_RESULT_REL_CLASS = "produces";
public static final String RELATION_REPRESENTATIVERESULT_RESULT_CLASS = "merges";
public static final String PROPAGATION_AUTHOR_PID = "ORCID";
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String cfHbforResultQuery = "select distinct r.id, inst.collectedfrom.key cf, inst.hostedby.key hb "
+
"from result r " +
"lateral view explode(instance) i as inst " +
"where r.datainfo.deletedbyinference=false";
public static Country getCountry(String classid, String classname) {
Country nc = new Country();
nc.setClassid(classid);
nc.setClassname(classname);
nc.setSchemename(DNET_COUNTRY_SCHEMA);
nc.setSchemeid(DNET_COUNTRY_SCHEMA);
nc
.setDataInfo(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_COUNTRY_INSTREPO_CLASS_ID,
PROPAGATION_COUNTRY_INSTREPO_CLASS_NAME));
return nc;
}
public static DataInfo getDataInfo(
String inference_provenance, String inference_class_id, String inference_class_name) {
DataInfo di = new DataInfo();
di.setInferred(true);
di.setDeletedbyinference(false);
di.setTrust("0.85");
di.setInferenceprovenance(inference_provenance);
di.setProvenanceaction(getQualifier(inference_class_id, inference_class_name));
return di;
}
public static Qualifier getQualifier(String inference_class_id, String inference_class_name) {
Qualifier pa = new Qualifier();
pa.setClassid(inference_class_id);
pa.setClassname(inference_class_name);
pa.setSchemeid(DNET_SCHEMA_ID);
pa.setSchemename(DNET_SCHEMA_NAME);
return pa;
}
public static Relation getRelation(
String source,
String target,
String rel_class,
String rel_type,
String subrel_type,
String inference_provenance,
String inference_class_id,
String inference_class_name) {
Relation r = new Relation();
r.setSource(source);
r.setTarget(target);
r.setRelClass(rel_class);
r.setRelType(rel_type);
r.setSubRelType(subrel_type);
r.setDataInfo(getDataInfo(inference_provenance, inference_class_id, inference_class_name));
return r;
}
public static String getConstraintList(String text, List<String> constraints) {
String ret = " and (" + text + constraints.get(0) + "'";
for (int i = 1; i < constraints.size(); i++) {
ret += " OR " + text + constraints.get(i) + "'";
}
ret += ")";
return ret;
}
public static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
public static Boolean isSparkSessionManaged(ArgumentApplicationParser parser) {
return Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
}
public static Boolean isTest(ArgumentApplicationParser parser) {
return Optional
.ofNullable(parser.get("isTest"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
}
public static void createCfHbforResult(SparkSession spark) {
org.apache.spark.sql.Dataset<Row> cfhb = spark.sql(cfHbforResultQuery);
cfhb.createOrReplaceTempView("cfhb");
}
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
}

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@ -0,0 +1,25 @@
package eu.dnetlib.dhp.countrypropagation;
import java.io.Serializable;
public class CountrySbs implements Serializable {
private String classid;
private String classname;
public String getClassid() {
return classid;
}
public void setClassid(String classid) {
this.classid = classid;
}
public String getClassname() {
return classname;
}
public void setClassname(String classname) {
this.classname = classname;
}
}

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@ -0,0 +1,25 @@
package eu.dnetlib.dhp.countrypropagation;
import java.io.Serializable;
public class DatasourceCountry implements Serializable {
private String dataSourceId;
private CountrySbs country;
public String getDataSourceId() {
return dataSourceId;
}
public void setDataSourceId(String dataSourceId) {
this.dataSourceId = dataSourceId;
}
public CountrySbs getCountry() {
return country;
}
public void setCountry(CountrySbs country) {
this.country = country;
}
}

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@ -0,0 +1,121 @@
package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.*;
/**
* For the association of the country to the datasource The association is computed only for datasource of specific type
* or having whitelisted ids The country is registered in the Organization associated to the Datasource, so the relation
* provides between Datasource and Organization is exploited to get the country for the datasource
*/
public class PrepareDatasourceCountryAssociation {
private static final Logger log = LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareDatasourceCountryAssociation.class
.getResourceAsStream(
"/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
prepareDatasourceCountryAssociation(
spark,
Arrays.asList(parser.get("whitelist").split(";")),
Arrays.asList(parser.get("allowedtypes").split(";")),
inputPath,
outputPath);
});
}
private static void prepareDatasourceCountryAssociation(
SparkSession spark,
List<String> whitelist,
List<String> allowedtypes,
String inputPath,
String outputPath) {
String whitelisted = "";
for (String i : whitelist) {
whitelisted += " OR id = '" + i + "'";
}
Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class);
Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class);
Dataset<Organization> organization = readPath(spark, inputPath + "/organization", Organization.class);
datasource.createOrReplaceTempView("datasource");
relation.createOrReplaceTempView("relation");
organization.createOrReplaceTempView("organization");
String query = "SELECT source dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) country "
+ "FROM ( SELECT id "
+ " FROM datasource "
+ " WHERE (datainfo.deletedbyinference = false "
+ whitelisted
+ ") "
+ getConstraintList("datasourcetype.classid = '", allowedtypes)
+ ") d "
+ "JOIN ( SELECT source, target "
+ " FROM relation "
+ " WHERE relclass = '"
+ RELATION_DATASOURCE_ORGANIZATION_REL_CLASS
+ "' "
+ " AND datainfo.deletedbyinference = false ) rel "
+ "ON d.id = rel.source "
+ "JOIN (SELECT id, country "
+ " FROM organization "
+ " WHERE datainfo.deletedbyinference = false "
+ " AND length(country.classid) > 0) o "
+ "ON o.id = rel.target";
spark
.sql(query)
.as(Encoders.bean(DatasourceCountry.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}

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@ -0,0 +1,98 @@
package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.*;
public class PrepareResultCountrySet {
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 {
String jsonConfiguration = IOUtils
.toString(
PrepareResultCountrySet.class
.getResourceAsStream(
"/eu/dnetlib/dhp/countrypropagation/input_prepareresultcountry_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String datasourcecountrypath = parser.get("preparedInfoPath");
log.info("preparedInfoPath: {}", datasourcecountrypath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
getPotentialResultToUpdate(
spark,
inputPath,
outputPath,
datasourcecountrypath,
resultClazz);
});
}
private static <R extends Result> void getPotentialResultToUpdate(
SparkSession spark,
String inputPath,
String outputPath,
String datasourcecountrypath,
Class<R> resultClazz) {
Dataset<R> result = readPath(spark, inputPath, resultClazz);
result.createOrReplaceTempView("result");
// log.info("number of results: {}", result.count());
createCfHbforResult(spark);
Dataset<DatasourceCountry> datasource_country = readPath(spark, datasourcecountrypath, DatasourceCountry.class);
datasource_country.createOrReplaceTempView("datasource_country");
// log.info("datasource_country number : {}", datasource_country.count());
spark
.sql(RESULT_COUNTRYSET_QUERY)
.as(Encoders.bean(ResultCountrySet.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Append)
.json(outputPath);
}
}

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@ -0,0 +1,26 @@
package eu.dnetlib.dhp.countrypropagation;
import java.io.Serializable;
import java.util.ArrayList;
public class ResultCountrySet implements Serializable {
private String resultId;
private ArrayList<CountrySbs> countrySet;
public String getResultId() {
return resultId;
}
public void setResultId(String resultId) {
this.resultId = resultId;
}
public ArrayList<CountrySbs> getCountrySet() {
return countrySet;
}
public void setCountrySet(ArrayList<CountrySbs> countrySet) {
this.countrySet = countrySet;
}
}

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@ -0,0 +1,132 @@
package eu.dnetlib.dhp.countrypropagation;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Result;
import scala.Tuple2;
public class SparkCountryPropagationJob {
private static final Logger log = LoggerFactory.getLogger(SparkCountryPropagationJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkCountryPropagationJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String sourcePath = parser.get("sourcePath");
log.info("sourcePath: {}", sourcePath);
String preparedInfoPath = parser.get("preparedInfoPath");
log.info("preparedInfoPath: {}", preparedInfoPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String resultClassName = parser.get("resultTableName");
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);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> execPropagation(
spark,
sourcePath,
preparedInfoPath,
outputPath,
resultClazz,
saveGraph));
}
private static <R extends Result> void execPropagation(
SparkSession spark,
String sourcePath,
String preparedInfoPath,
String outputPath,
Class<R> resultClazz,
boolean saveGraph) {
if (saveGraph) {
// updateResultTable(spark, potentialUpdates, inputPath, resultClazz, outputPath);
log.info("Reading Graph table from: {}", sourcePath);
Dataset<R> res = readPath(spark, sourcePath, resultClazz);
log.info("Reading prepared info: {}", preparedInfoPath);
Dataset<ResultCountrySet> prepared = spark
.read()
.json(preparedInfoPath)
.as(Encoders.bean(ResultCountrySet.class));
res
.joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer")
.map(getCountryMergeFn(), Encoders.bean(resultClazz))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}
private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() {
return (MapFunction<Tuple2<R, ResultCountrySet>, R>) t -> {
Optional.ofNullable(t._2()).ifPresent(r -> {
t._1().getCountry().addAll(merge(t._1().getCountry(), r.getCountrySet()));
});
return t._1();
};
}
private static List<Country> merge(List<Country> c1, List<CountrySbs> c2) {
HashSet<String> countries = c1
.stream()
.map(c -> c.getClassid())
.collect(Collectors.toCollection(HashSet::new));
return c2
.stream()
.filter(c -> !countries.contains(c.getClassid()))
.map(c -> getCountry(c.getClassid(), c.getClassname()))
.collect(Collectors.toList());
}
}

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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
public class AutoritativeAuthor {
private String name;
private String surname;
private String fullname;
private String orcid;
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getSurname() {
return surname;
}
public void setSurname(String surname) {
this.surname = surname;
}
public String getFullname() {
return fullname;
}
public void setFullname(String fullname) {
this.fullname = fullname;
}
public String getOrcid() {
return orcid;
}
public void setOrcid(String orcid) {
this.orcid = orcid;
}
}

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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
public class PrepareResultOrcidAssociationStep1 {
private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep1.class);
public static void main(String[] args) throws Exception {
String jsonConf = IOUtils
.toString(
PrepareResultOrcidAssociationStep1.class
.getResourceAsStream(
"/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConf);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
log.info("resultType: {}", resultType);
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
String inputRelationPath = inputPath + "/relation";
log.info("inputRelationPath: {}", inputRelationPath);
String inputResultPath = inputPath + "/" + resultType;
log.info("inputResultPath: {}", inputResultPath);
String outputResultPath = outputPath + "/" + resultType;
log.info("outputResultPath: {}", outputResultPath);
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
prepareInfo(
spark, inputRelationPath, inputResultPath, outputResultPath, resultClazz, allowedsemrel);
});
}
private static <R extends Result> void prepareInfo(
SparkSession spark,
String inputRelationPath,
String inputResultPath,
String outputResultPath,
Class<R> resultClazz,
List<String> allowedsemrel) {
Dataset<Relation> relation = readPath(spark, inputRelationPath, Relation.class);
relation.createOrReplaceTempView("relation");
log.info("Reading Graph table from: {}", inputResultPath);
Dataset<R> result = readPath(spark, inputResultPath, resultClazz);
result.createOrReplaceTempView("result");
String query = " select target resultId, author authorList"
+ " from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author "
+ " from ( "
+ " select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid "
+ " from result "
+ " lateral view explode (author) a as MyT "
+ " lateral view explode (MyT.pid) p as MyP "
+ " where MyP.qualifier.classid = 'ORCID') tmp "
+ " group by id) r_t "
+ " join ("
+ " select source, target "
+ " from relation "
+ " where datainfo.deletedbyinference = false "
+ getConstraintList(" relclass = '", allowedsemrel)
+ ") rel_rel "
+ " on source = id";
spark
.sql(query)
.as(Encoders.bean(ResultOrcidList.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputResultPath);
}
}

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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.HashSet;
import java.util.Set;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import scala.Tuple2;
public class PrepareResultOrcidAssociationStep2 {
private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep2.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareResultOrcidAssociationStep2.class
.getResourceAsStream(
"/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters2.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
mergeInfo(spark, inputPath, outputPath);
});
}
private static void mergeInfo(SparkSession spark, String inputPath, String outputPath) {
Dataset<ResultOrcidList> resultOrcidAssoc = readPath(spark, inputPath + "/publication", ResultOrcidList.class)
.union(readPath(spark, inputPath + "/dataset", ResultOrcidList.class))
.union(readPath(spark, inputPath + "/otherresearchproduct", ResultOrcidList.class))
.union(readPath(spark, inputPath + "/software", ResultOrcidList.class));
resultOrcidAssoc
.toJavaRDD()
.mapToPair(r -> new Tuple2<>(r.getResultId(), r))
.reduceByKey(
(a, b) -> {
if (a == null) {
return b;
}
if (b == null) {
return a;
}
Set<String> orcid_set = new HashSet<>();
a.getAuthorList().stream().forEach(aa -> orcid_set.add(aa.getOrcid()));
b
.getAuthorList()
.stream()
.forEach(
aa -> {
if (!orcid_set.contains(aa.getOrcid())) {
a.getAuthorList().add(aa);
orcid_set.add(aa.getOrcid());
}
});
return a;
})
.map(c -> c._2())
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
.saveAsTextFile(outputPath, GzipCodec.class);
}
}

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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
public class ResultOrcidList implements Serializable {
String resultId;
List<AutoritativeAuthor> authorList = new ArrayList<>();
public String getResultId() {
return resultId;
}
public void setResultId(String resultId) {
this.resultId = resultId;
}
public List<AutoritativeAuthor> getAuthorList() {
return authorList;
}
public void setAuthorList(List<AutoritativeAuthor> authorList) {
this.authorList = authorList;
}
}

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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import scala.Tuple2;
public class SparkOrcidToResultFromSemRelJob {
private static final Logger log = LoggerFactory.getLogger(SparkOrcidToResultFromSemRelJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkOrcidToResultFromSemRelJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_orcidtoresult_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String possibleUpdates = parser.get("possibleUpdatesPath");
log.info("possibleUpdatesPath: {}", possibleUpdates);
final String resultClassName = parser.get("resultTableName");
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);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
if (saveGraph)
execPropagation(spark, possibleUpdates, inputPath, outputPath, resultClazz);
});
}
private static <R extends Result> void execPropagation(
SparkSession spark,
String possibleUpdatesPath,
String inputPath,
String outputPath,
Class<R> resultClazz) {
// read possible updates (resultId and list of possible orcid to add
Dataset<ResultOrcidList> possible_updates = readPath(spark, possibleUpdatesPath, ResultOrcidList.class);
// read the result we have been considering
Dataset<R> result = readPath(spark, inputPath, resultClazz);
// make join result left_outer with possible updates
result
.joinWith(
possible_updates,
result.col("id").equalTo(possible_updates.col("resultId")),
"left_outer")
.map(authorEnrichFn(), Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static <R extends Result> MapFunction<Tuple2<R, ResultOrcidList>, R> authorEnrichFn() {
return (MapFunction<Tuple2<R, ResultOrcidList>, R>) value -> {
R ret = value._1();
Optional<ResultOrcidList> rol = Optional.ofNullable(value._2());
if (rol.isPresent()) {
List<Author> toenrich_author = ret.getAuthor();
List<AutoritativeAuthor> autoritativeAuthors = rol.get().getAuthorList();
for (Author author : toenrich_author) {
if (!containsAllowedPid(author)) {
enrichAuthor(author, autoritativeAuthors);
}
}
}
return ret;
};
}
private static void enrichAuthor(Author a, List<AutoritativeAuthor> au) {
for (AutoritativeAuthor aa : au) {
if (enrichAuthor(aa, a)) {
return;
}
}
}
private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author) {
boolean toaddpid = false;
if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
if (StringUtils.isNoneEmpty(author.getSurname())) {
if (autoritative_author
.getSurname()
.trim()
.equalsIgnoreCase(author.getSurname().trim())) {
// have the same surname. Check the name
if (StringUtils.isNoneEmpty(autoritative_author.getName())) {
if (StringUtils.isNoneEmpty(author.getName())) {
if (autoritative_author
.getName()
.trim()
.equalsIgnoreCase(author.getName().trim())) {
toaddpid = true;
}
// they could be differently written (i.e. only the initials of the name
// in one of the two
if (autoritative_author
.getName()
.trim()
.substring(0, 0)
.equalsIgnoreCase(author.getName().trim().substring(0, 0))) {
toaddpid = true;
}
}
}
}
}
}
if (toaddpid) {
StructuredProperty p = new StructuredProperty();
p.setValue(autoritative_author.getOrcid());
p.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID));
p
.setDataInfo(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID,
PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME));
Optional<List<StructuredProperty>> authorPid = Optional.ofNullable(author.getPid());
if (authorPid.isPresent()) {
authorPid.get().add(p);
} else {
author.setPid(Lists.newArrayList(p));
}
}
return toaddpid;
}
private static boolean containsAllowedPid(Author a) {
Optional<List<StructuredProperty>> pids = Optional.ofNullable(a.getPid());
if (!pids.isPresent()) {
return false;
}
for (StructuredProperty pid : pids.get()) {
if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
return true;
}
}
return false;
}
}

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package eu.dnetlib.dhp.projecttoresult;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.PropagationConstant.getConstraintList;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class PrepareProjectResultsAssociation {
private static final Logger log = LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareProjectResultsAssociation.class
.getResourceAsStream(
"/eu/dnetlib/dhp/projecttoresult/input_prepareprojecttoresult_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String potentialUpdatePath = parser.get("potentialUpdatePath");
log.info("potentialUpdatePath {}: ", potentialUpdatePath);
String alreadyLinkedPath = parser.get("alreadyLinkedPath");
log.info("alreadyLinkedPath: {} ", alreadyLinkedPath);
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
prepareResultProjProjectResults(
spark,
inputPath,
potentialUpdatePath,
alreadyLinkedPath,
allowedsemrel);
});
}
private static void prepareResultProjProjectResults(
SparkSession spark,
String inputPath,
String potentialUpdatePath,
String alreadyLinkedPath,
List<String> allowedsemrel) {
Dataset<Relation> relation = readPath(spark, inputPath, Relation.class);
relation.createOrReplaceTempView("relation");
String resproj_relation_query = "SELECT source, target "
+ " FROM relation "
+ " WHERE datainfo.deletedbyinference = false "
+ " AND relClass = '"
+ RELATION_RESULT_PROJECT_REL_CLASS
+ "'";
Dataset<Row> resproj_relation = spark.sql(resproj_relation_query);
resproj_relation.createOrReplaceTempView("resproj_relation");
String potential_update_query = "SELECT resultId, collect_set(projectId) projectSet "
+ "FROM ( "
+ "SELECT r1.target resultId, r2.target projectId "
+ " FROM (SELECT source, target "
+ " FROM relation "
+ " WHERE datainfo.deletedbyinference = false "
+ getConstraintList(" relClass = '", allowedsemrel)
+ " ) r1"
+ " JOIN resproj_relation r2 "
+ " ON r1.source = r2.source "
+ " ) tmp "
+ "GROUP BY resultId ";
spark
.sql(potential_update_query)
.as(Encoders.bean(ResultProjectSet.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(potentialUpdatePath);
String result_projectset_query = "SELECT source resultId, collect_set(target) projectSet "
+ "FROM resproj_relation "
+ "GROUP BY source";
spark
.sql(result_projectset_query)
.as(Encoders.bean(ResultProjectSet.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(alreadyLinkedPath);
}
}

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package eu.dnetlib.dhp.projecttoresult;
import java.io.Serializable;
import java.util.ArrayList;
public class ResultProjectSet implements Serializable {
private String resultId;
private ArrayList<String> projectSet;
public String getResultId() {
return resultId;
}
public void setResultId(String resultId) {
this.resultId = resultId;
}
public ArrayList<String> getProjectSet() {
return projectSet;
}
public void setProjectSet(ArrayList<String> project) {
this.projectSet = project;
}
}

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package eu.dnetlib.dhp.projecttoresult;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation;
import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
public class SparkResultToProjectThroughSemRelJob {
private static final Logger log = LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkResultToProjectThroughSemRelJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/projecttoresult/input_projecttoresult_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
final String potentialUpdatePath = parser.get("potentialUpdatePath");
log.info("potentialUpdatePath {}: ", potentialUpdatePath);
final String alreadyLinkedPath = parser.get("alreadyLinkedPath");
log.info("alreadyLinkedPath {}: ", alreadyLinkedPath);
final Boolean saveGraph = Boolean.valueOf(parser.get("saveGraph"));
log.info("saveGraph: {}", saveGraph);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
execPropagation(
spark, outputPath, alreadyLinkedPath, potentialUpdatePath, saveGraph);
});
}
private static void execPropagation(
SparkSession spark,
String outputPath,
String alreadyLinkedPath,
String potentialUpdatePath,
Boolean saveGraph) {
Dataset<ResultProjectSet> toaddrelations = readPath(spark, potentialUpdatePath, ResultProjectSet.class);
Dataset<ResultProjectSet> alreadyLinked = readPath(spark, alreadyLinkedPath, ResultProjectSet.class);
if (saveGraph) {
toaddrelations
.joinWith(
alreadyLinked,
toaddrelations.col("resultId").equalTo(alreadyLinked.col("resultId")),
"left_outer")
.flatMap(mapRelationRn(), Encoders.bean(Relation.class))
.write()
.mode(SaveMode.Append)
.option("compression", "gzip")
.json(outputPath);
}
}
private static FlatMapFunction<Tuple2<ResultProjectSet, ResultProjectSet>, Relation> mapRelationRn() {
return (FlatMapFunction<Tuple2<ResultProjectSet, ResultProjectSet>, Relation>) value -> {
List<Relation> new_relations = new ArrayList<>();
ResultProjectSet potential_update = value._1();
Optional<ResultProjectSet> already_linked = Optional.ofNullable(value._2());
if (already_linked.isPresent()) {
already_linked
.get()
.getProjectSet()
.stream()
.forEach(
(p -> {
if (potential_update
.getProjectSet()
.contains(p)) {
potential_update.getProjectSet().remove(p);
}
}));
}
String resId = potential_update.getResultId();
potential_update
.getProjectSet()
.stream()
.forEach(
projectId -> {
new_relations
.add(
getRelation(
resId,
projectId,
RELATION_RESULT_PROJECT_REL_CLASS,
RELATION_RESULTPROJECT_REL_TYPE,
RELATION_RESULTPROJECT_SUBREL_TYPE,
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
new_relations
.add(
getRelation(
projectId,
resId,
RELATION_PROJECT_RESULT_REL_CLASS,
RELATION_RESULTPROJECT_REL_TYPE,
RELATION_RESULTPROJECT_SUBREL_TYPE,
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
});
return new_relations.iterator();
};
}
}

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package eu.dnetlib.dhp.resulttocommunityfromorganization;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
public class OrganizationMap extends HashMap<String, List<String>> {
public OrganizationMap() {
super();
}
public List<String> get(String key) {
if (super.get(key) == null) {
return new ArrayList<>();
}
return super.get(key);
}
}

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package eu.dnetlib.dhp.resulttocommunityfromorganization;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class PrepareResultCommunitySet {
private static final Logger log = LoggerFactory.getLogger(PrepareResultCommunitySet.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareResultCommunitySet.class
.getResourceAsStream(
"/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final OrganizationMap organizationMap = new Gson()
.fromJson(
parser.get("organizationtoresultcommunitymap"),
OrganizationMap.class);
log.info("organizationMap: {}", new Gson().toJson(organizationMap));
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
prepareInfo(spark, inputPath, outputPath, organizationMap);
});
}
private static void prepareInfo(
SparkSession spark,
String inputPath,
String outputPath,
OrganizationMap organizationMap) {
Dataset<Relation> relation = readPath(spark, inputPath, Relation.class);
relation.createOrReplaceTempView("relation");
String query = "SELECT result_organization.source resultId, result_organization.target orgId, org_set merges "
+ "FROM (SELECT source, target "
+ " FROM relation "
+ " WHERE datainfo.deletedbyinference = false "
+ " AND relClass = '"
+ RELATION_RESULT_ORGANIZATION_REL_CLASS
+ "') result_organization "
+ "LEFT JOIN (SELECT source, collect_set(target) org_set "
+ " FROM relation "
+ " WHERE datainfo.deletedbyinference = false "
+ " AND relClass = '"
+ RELATION_REPRESENTATIVERESULT_RESULT_CLASS
+ "' "
+ " GROUP BY source) organization_organization "
+ "ON result_organization.target = organization_organization.source ";
Dataset<ResultOrganizations> result_organizationset = spark
.sql(query)
.as(Encoders.bean(ResultOrganizations.class));
result_organizationset
.map(mapResultCommunityFn(organizationMap), Encoders.bean(ResultCommunityList.class))
.filter(Objects::nonNull)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static MapFunction<ResultOrganizations, ResultCommunityList> mapResultCommunityFn(
OrganizationMap organizationMap) {
return (MapFunction<ResultOrganizations, ResultCommunityList>) value -> {
String rId = value.getResultId();
Optional<List<String>> orgs = Optional.ofNullable(value.getMerges());
String oTarget = value.getOrgId();
Set<String> communitySet = new HashSet<>();
if (organizationMap.containsKey(oTarget)) {
communitySet.addAll(organizationMap.get(oTarget));
}
if (orgs.isPresent())
for (String oId : orgs.get()) {
if (organizationMap.containsKey(oId)) {
communitySet.addAll(organizationMap.get(oId));
}
}
if (communitySet.size() > 0) {
ResultCommunityList rcl = new ResultCommunityList();
rcl.setResultId(rId);
ArrayList<String> communityList = new ArrayList<>();
communityList.addAll(communitySet);
rcl.setCommunityList(communityList);
return rcl;
}
return null;
};
}
}

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package eu.dnetlib.dhp.resulttocommunityfromorganization;
import java.io.Serializable;
import java.util.ArrayList;
public class ResultCommunityList implements Serializable {
private String resultId;
private ArrayList<String> communityList;
public String getResultId() {
return resultId;
}
public void setResultId(String resultId) {
this.resultId = resultId;
}
public ArrayList<String> getCommunityList() {
return communityList;
}
public void setCommunityList(ArrayList<String> communityList) {
this.communityList = communityList;
}
}

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package eu.dnetlib.dhp.resulttocommunityfromorganization;
import java.io.Serializable;
import java.util.ArrayList;
public class ResultOrganizations implements Serializable {
private String resultId;
private String orgId;
private ArrayList<String> merges;
public String getResultId() {
return resultId;
}
public void setResultId(String resultId) {
this.resultId = resultId;
}
public String getOrgId() {
return orgId;
}
public void setOrgId(String orgId) {
this.orgId = orgId;
}
public ArrayList<String> getMerges() {
return merges;
}
public void setMerges(ArrayList<String> merges) {
this.merges = merges;
}
}

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package eu.dnetlib.dhp.resulttocommunityfromorganization;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;
public class SparkResultToCommunityFromOrganizationJob {
private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityFromOrganizationJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkResultToCommunityFromOrganizationJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String possibleupdatespath = parser.get("preparedInfoPath");
log.info("preparedInfoPath: {}", possibleupdatespath);
final String resultClassName = parser.get("resultTableName");
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);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
if (saveGraph)
execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath);
});
}
private static <R extends Result> void execPropagation(
SparkSession spark,
String inputPath,
String outputPath,
Class<R> resultClazz,
String possibleUpdatesPath) {
Dataset<ResultCommunityList> possibleUpdates = readPath(spark, possibleUpdatesPath, ResultCommunityList.class);
Dataset<R> result = readPath(spark, inputPath, resultClazz);
result
.joinWith(
possibleUpdates,
result.col("id").equalTo(possibleUpdates.col("resultId")),
"left_outer")
.map(resultCommunityFn(), Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static <R extends Result> MapFunction<Tuple2<R, ResultCommunityList>, R> resultCommunityFn() {
return (MapFunction<Tuple2<R, ResultCommunityList>, R>) value -> {
R ret = value._1();
Optional<ResultCommunityList> rcl = Optional.ofNullable(value._2());
if (rcl.isPresent()) {
ArrayList<String> communitySet = rcl.get().getCommunityList();
List<String> contextList = ret
.getContext()
.stream()
.map(con -> con.getId())
.collect(Collectors.toList());
Result res = new Result();
res.setId(ret.getId());
List<Context> propagatedContexts = new ArrayList<>();
for (String cId : communitySet) {
if (!contextList.contains(cId)) {
Context newContext = new Context();
newContext.setId(cId);
newContext
.setDataInfo(
Arrays
.asList(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME)));
propagatedContexts.add(newContext);
}
}
res.setContext(propagatedContexts);
ret.mergeFrom(res);
}
return ret;
};
}
}

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package eu.dnetlib.dhp.resulttocommunityfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class PrepareResultCommunitySetStep1 {
private static final Logger log = LoggerFactory.getLogger(PrepareResultCommunitySetStep1.class);
private static final String COMMUNITY_LIST_XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType')"
+ " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri']"
+ " and $x//CONFIGURATION/context/param[./@name='status']/text() != 'hidden'"
+ " return $x//CONFIGURATION/context/@id/string()";
/**
* associates to each result the set of community contexts they are associated to; associates to each target of a
* relation with allowed semantics the set of community context it could possibly inherit from the source of the
* relation
*/
// TODO
private static final String RESULT_CONTEXT_QUERY_TEMPLATE = "select target resultId, community_context "
+ "from (select id, collect_set(co.id) community_context "
+ " from result "
+ " lateral view explode (context) c as co "
+ " where datainfo.deletedbyinference = false %s group by id) p "
+ " JOIN "
+ " (select source, target from relation "
+ " where datainfo.deletedbyinference = false %s ) r ON p.id = r.source";
/**
* a dataset for example could be linked to more than one publication. For each publication linked to that dataset
* the previous query will produce a row: targetId set of community context the target could possibly inherit with
* the following query there will be a single row for each result linked to more than one result of the result type
* currently being used
*/
// TODO
private static final String RESULT_COMMUNITY_LIST_QUERY = "select resultId , collect_set(co) communityList "
+ "from result_context "
+ "lateral view explode (community_context) c as co "
+ "where length(co) > 0 "
+ "group by resultId";
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareResultCommunitySetStep1.class
.getResourceAsStream(
"/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_preparecommunitytoresult_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
final String isLookupUrl = parser.get("isLookUpUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final List<String> communityIdList = getCommunityList(isLookupUrl);
log.info("communityIdList: {}", new Gson().toJson(communityIdList));
final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
log.info("resultType: {}", resultType);
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
prepareInfo(
spark,
inputPath,
outputPath,
allowedsemrel,
resultClazz,
resultType,
communityIdList);
});
}
private static <R extends Result> void prepareInfo(
SparkSession spark,
String inputPath,
String outputPath,
List<String> allowedsemrel,
Class<R> resultClazz,
String resultType,
List<String> communityIdList) {
final String inputResultPath = inputPath + "/" + resultType;
log.info("Reading Graph table from: {}", inputResultPath);
final String inputRelationPath = inputPath + "/relation";
log.info("Reading relation table from: {}", inputResultPath);
Dataset<Relation> relation = readPath(spark, inputRelationPath, Relation.class);
relation.createOrReplaceTempView("relation");
Dataset<R> result = readPath(spark, inputResultPath, resultClazz);
result.createOrReplaceTempView("result");
final String outputResultPath = outputPath + "/" + resultType;
log.info("writing output results to: {}", outputResultPath);
String resultContextQuery = String
.format(
RESULT_CONTEXT_QUERY_TEMPLATE,
getConstraintList(" co.id = '", communityIdList),
getConstraintList(" relClass = '", allowedsemrel));
Dataset<Row> result_context = spark.sql(resultContextQuery);
result_context.createOrReplaceTempView("result_context");
spark
.sql(RESULT_COMMUNITY_LIST_QUERY)
.as(Encoders.bean(ResultCommunityList.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputResultPath);
}
public static List<String> getCommunityList(final String isLookupUrl) throws ISLookUpException {
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
return isLookUp.quickSearchProfile(COMMUNITY_LIST_XQUERY);
}
}

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package eu.dnetlib.dhp.resulttocommunityfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.HashSet;
import java.util.Set;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
import scala.Tuple2;
public class PrepareResultCommunitySetStep2 {
private static final Logger log = LoggerFactory.getLogger(PrepareResultCommunitySetStep2.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareResultCommunitySetStep2.class
.getResourceAsStream(
"/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_preparecommunitytoresult2_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
mergeInfo(spark, inputPath, outputPath);
});
}
private static void mergeInfo(SparkSession spark, String inputPath, String outputPath) {
Dataset<ResultCommunityList> resultOrcidAssocCommunityList = readPath(
spark, inputPath + "/publication", ResultCommunityList.class)
.union(readPath(spark, inputPath + "/dataset", ResultCommunityList.class))
.union(readPath(spark, inputPath + "/otherresearchproduct", ResultCommunityList.class))
.union(readPath(spark, inputPath + "/software", ResultCommunityList.class));
resultOrcidAssocCommunityList
.toJavaRDD()
.mapToPair(r -> new Tuple2<>(r.getResultId(), r))
.reduceByKey(
(a, b) -> {
if (a == null) {
return b;
}
if (b == null) {
return a;
}
Set<String> community_set = new HashSet<>();
a.getCommunityList().stream().forEach(aa -> community_set.add(aa));
b
.getCommunityList()
.stream()
.forEach(
aa -> {
if (!community_set.contains(aa)) {
a.getCommunityList().add(aa);
community_set.add(aa);
}
});
return a;
})
.map(c -> c._2())
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
.saveAsTextFile(outputPath, GzipCodec.class);
}
}

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package eu.dnetlib.dhp.resulttocommunityfromsemrel;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;
public class SparkResultToCommunityThroughSemRelJob {
private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityThroughSemRelJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkResultToCommunityThroughSemRelJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_communitytoresult_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String preparedInfoPath = parser.get("preparedInfoPath");
log.info("preparedInfoPath: {}", preparedInfoPath);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
final String resultClassName = parser.get("resultTableName");
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);
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
if (saveGraph) {
execPropagation(
spark, inputPath, outputPath, preparedInfoPath, resultClazz);
}
});
}
private static <R extends Result> void execPropagation(
SparkSession spark,
String inputPath,
String outputPath,
String preparedInfoPath,
Class<R> resultClazz) {
Dataset<ResultCommunityList> possibleUpdates = readPath(spark, preparedInfoPath, ResultCommunityList.class);
Dataset<R> result = readPath(spark, inputPath, resultClazz);
result
.joinWith(
possibleUpdates,
result.col("id").equalTo(possibleUpdates.col("resultId")),
"left_outer")
.map(contextUpdaterFn(), Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static <R extends Result> MapFunction<Tuple2<R, ResultCommunityList>, R> contextUpdaterFn() {
return (MapFunction<Tuple2<R, ResultCommunityList>, R>) value -> {
R ret = value._1();
Optional<ResultCommunityList> rcl = Optional.ofNullable(value._2());
if (rcl.isPresent()) {
Set<String> context_set = new HashSet<>();
ret.getContext().stream().forEach(c -> context_set.add(c.getId()));
List<Context> contextList = rcl
.get()
.getCommunityList()
.stream()
.map(
c -> {
if (!context_set.contains(c)) {
Context newContext = new Context();
newContext.setId(c);
newContext
.setDataInfo(
Arrays
.asList(
getDataInfo(
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_ID,
PROPAGATION_RESULT_COMMUNITY_SEMREL_CLASS_NAME)));
return newContext;
}
return null;
})
.filter(Objects::nonNull)
.collect(Collectors.toList());
Result r = new Result();
r.setId(ret.getId());
r.setContext(contextList);
ret.mergeFrom(r);
}
return ret;
};
}
}

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package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
import java.io.Serializable;
public class DatasourceOrganization implements Serializable {
private String datasourceId;
private String organizationId;
public String getDatasourceId() {
return datasourceId;
}
public void setDatasourceId(String datasourceId) {
this.datasourceId = datasourceId;
}
public String getOrganizationId() {
return organizationId;
}
public void setOrganizationId(String organizationId) {
this.organizationId = organizationId;
}
}

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package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class PrepareResultInstRepoAssociation {
private static final Logger log = LoggerFactory.getLogger(PrepareResultInstRepoAssociation.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareResultInstRepoAssociation.class
.getResourceAsStream(
"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_prepareresultorg_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String datasourceOrganizationPath = parser.get("datasourceOrganizationPath");
log.info("datasourceOrganizationPath {}: ", datasourceOrganizationPath);
final String alreadyLinkedPath = parser.get("alreadyLinkedPath");
log.info("alreadyLinkedPath {}: ", alreadyLinkedPath);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
readNeededResources(spark, inputPath);
prepareDatasourceOrganization(spark, datasourceOrganizationPath);
prepareAlreadyLinkedAssociation(spark, alreadyLinkedPath);
});
}
private static void prepareAlreadyLinkedAssociation(
SparkSession spark, String alreadyLinkedPath) {
String query = "Select source resultId, collect_set(target) organizationSet "
+ "from relation "
+ "where datainfo.deletedbyinference = false "
+ "and relClass = '"
+ RELATION_RESULT_ORGANIZATION_REL_CLASS
+ "' "
+ "group by source";
spark
.sql(query)
.as(Encoders.bean(ResultOrganizationSet.class))
// TODO retry to stick with datasets
.toJavaRDD()
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
.saveAsTextFile(alreadyLinkedPath, GzipCodec.class);
}
private static void readNeededResources(SparkSession spark, String inputPath) {
Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class);
datasource.createOrReplaceTempView("datasource");
Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class);
relation.createOrReplaceTempView("relation");
Dataset<Organization> organization = readPath(spark, inputPath + "/organization", Organization.class);
organization.createOrReplaceTempView("organization");
}
private static void prepareDatasourceOrganization(
SparkSession spark, String datasourceOrganizationPath) {
String query = "SELECT source datasourceId, target organizationId "
+ "FROM ( SELECT id "
+ "FROM datasource "
+ "WHERE datasourcetype.classid = '"
+ INSTITUTIONAL_REPO_TYPE
+ "' "
+ "AND datainfo.deletedbyinference = false ) d "
+ "JOIN ( SELECT source, target "
+ "FROM relation "
+ "WHERE relclass = '"
+ RELATION_DATASOURCE_ORGANIZATION_REL_CLASS
+ "' "
+ "AND datainfo.deletedbyinference = false ) rel "
+ "ON d.id = rel.source ";
spark
.sql(query)
.as(Encoders.bean(DatasourceOrganization.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(datasourceOrganizationPath);
}
}

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@ -0,0 +1,26 @@
package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
import java.io.Serializable;
import java.util.ArrayList;
public class ResultOrganizationSet implements Serializable {
private String resultId;
private ArrayList<String> organizationSet;
public String getResultId() {
return resultId;
}
public void setResultId(String resultId) {
this.resultId = resultId;
}
public ArrayList<String> getOrganizationSet() {
return organizationSet;
}
public void setOrganizationSet(ArrayList<String> organizationSet) {
this.organizationSet = organizationSet;
}
}

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@ -0,0 +1,193 @@
package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.broadcast.Broadcast;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;
public class SparkResultToOrganizationFromIstRepoJob {
private static final Logger log = LoggerFactory.getLogger(SparkResultToOrganizationFromIstRepoJob.class);
private static final String RESULT_ORGANIZATIONSET_QUERY = "SELECT id resultId, collect_set(organizationId) organizationSet "
+ "FROM ( SELECT id, organizationId "
+ "FROM rels "
+ "JOIN cfhb "
+ " ON cf = datasourceId "
+ "UNION ALL "
+ "SELECT id , organizationId "
+ "FROM rels "
+ "JOIN cfhb "
+ " ON hb = datasourceId ) tmp "
+ "GROUP BY id";
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkResultToOrganizationFromIstRepoJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_propagationresulaffiliationfrominstrepo_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String datasourceorganization = parser.get("datasourceOrganizationPath");
log.info("datasourceOrganizationPath: {}", datasourceorganization);
final String alreadylinked = parser.get("alreadyLinkedPath");
log.info("alreadyLinkedPath: {}", alreadylinked);
final String resultClassName = parser.get("resultTableName");
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);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
if (saveGraph)
execPropagation(
spark,
datasourceorganization,
alreadylinked,
inputPath,
outputPath,
resultClazz);
});
}
private static void execPropagation(
SparkSession spark,
String datasourceorganization,
String alreadyLinkedPath,
String inputPath,
String outputPath,
Class<? extends Result> clazz) {
Dataset<DatasourceOrganization> ds_org = readPath(spark, datasourceorganization, DatasourceOrganization.class);
Dataset<ResultOrganizationSet> potentialUpdates = getPotentialRelations(spark, inputPath, clazz, ds_org);
Dataset<ResultOrganizationSet> alreadyLinked = readPath(spark, alreadyLinkedPath, ResultOrganizationSet.class);
potentialUpdates
.joinWith(
alreadyLinked,
potentialUpdates.col("resultId").equalTo(alreadyLinked.col("resultId")),
"left_outer")
.flatMap(createRelationFn(), Encoders.bean(Relation.class))
.write()
.mode(SaveMode.Append)
.option("compression", "gzip")
.json(outputPath);
}
private static FlatMapFunction<Tuple2<ResultOrganizationSet, ResultOrganizationSet>, Relation> createRelationFn() {
return (FlatMapFunction<Tuple2<ResultOrganizationSet, ResultOrganizationSet>, Relation>) value -> {
List<Relation> new_relations = new ArrayList<>();
ResultOrganizationSet potential_update = value._1();
Optional<ResultOrganizationSet> already_linked = Optional.ofNullable(value._2());
List<String> organization_list = potential_update.getOrganizationSet();
if (already_linked.isPresent()) {
already_linked
.get()
.getOrganizationSet()
.stream()
.forEach(
rId -> {
if (organization_list.contains(rId)) {
organization_list.remove(rId);
}
});
}
String resultId = potential_update.getResultId();
organization_list
.stream()
.forEach(
orgId -> {
new_relations
.add(
getRelation(
orgId,
resultId,
RELATION_ORGANIZATION_RESULT_REL_CLASS,
RELATION_RESULTORGANIZATION_REL_TYPE,
RELATION_RESULTORGANIZATION_SUBREL_TYPE,
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
new_relations
.add(
getRelation(
resultId,
orgId,
RELATION_RESULT_ORGANIZATION_REL_CLASS,
RELATION_RESULTORGANIZATION_REL_TYPE,
RELATION_RESULTORGANIZATION_SUBREL_TYPE,
PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
});
return new_relations.iterator();
};
}
private static <R extends Result> Dataset<ResultOrganizationSet> getPotentialRelations(
SparkSession spark,
String inputPath,
Class<R> resultClazz,
Dataset<DatasourceOrganization> ds_org) {
Dataset<R> result = readPath(spark, inputPath, resultClazz);
result.createOrReplaceTempView("result");
createCfHbforResult(spark);
ds_org.createOrReplaceTempView("rels");
return spark
.sql(RESULT_ORGANIZATIONSET_QUERY)
.as(Encoders.bean(ResultOrganizationSet.class));
}
}

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