forked from D-Net/dnet-hadoop
Merge branch 'master' into dhp_oaf_model
This commit is contained in:
commit
eeb2b7e4cd
|
|
@ -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>
|
||||
|
|
|
|||
|
|
@ -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) {
|
||||
|
||||
|
|
@ -13,6 +13,7 @@ public class ModelConstants {
|
|||
public static final String DNET_DATA_CITE_DATE = "dnet:dataCite_date";
|
||||
public static final String DNET_DATA_CITE_RESOURCE = "dnet:dataCite_resource";
|
||||
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
|
||||
public static final String DNET_COUNTRY_TYPE = "dnet:countries";
|
||||
|
||||
public static final String SYSIMPORT_CROSSWALK_REPOSITORY = "sysimport:crosswalk:repository";
|
||||
public static final String SYSIMPORT_CROSSWALK_ENTITYREGISTRY = "sysimport:crosswalk:entityregistry";
|
||||
|
|
@ -49,6 +50,13 @@ public class ModelConstants {
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|||
public static final String HAS_PARTICIPANT = "hasParticipant";
|
||||
public static final String IS_PARTICIPANT = "isParticipant";
|
||||
|
||||
public static final String RESULT_ORGANIZATION = "resultOrganization";
|
||||
public static final String AFFILIATION = "affiliation";
|
||||
public static final String IS_AUTHOR_INSTITUTION_OF = "isAuthorInstitutionOf";
|
||||
public static final String HAS_AUTHOR_INSTITUTION = "hasAuthorInstitution";
|
||||
|
||||
public static final String MERGES = "merges";
|
||||
|
||||
public static final String UNKNOWN = "UNKNOWN";
|
||||
public static final String NOT_AVAILABLE = "not available";
|
||||
|
||||
|
|
|
|||
|
|
@ -1,10 +1,15 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.common;
|
||||
|
||||
import static com.google.common.base.Preconditions.checkArgument;
|
||||
|
||||
import java.util.Map;
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
import java.util.function.Function;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
||||
import com.google.common.collect.Maps;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
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||||
|
|
@ -13,7 +18,7 @@ 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 +58,232 @@ 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() {
|
||||
|
|
@ -153,6 +384,21 @@ public class ModelSupport {
|
|||
entityMapping.get(EntityType.valueOf(targetType)).name());
|
||||
}
|
||||
|
||||
public static <T extends Oaf> String tableIdentifier(String dbName, String tableName) {
|
||||
|
||||
checkArgument(StringUtils.isNotBlank(dbName), "DB name cannot be empty");
|
||||
checkArgument(StringUtils.isNotBlank(tableName), "table name cannot be empty");
|
||||
|
||||
return String.format("%s.%s", dbName, tableName);
|
||||
}
|
||||
|
||||
public static <T extends Oaf> String tableIdentifier(String dbName, Class<T> clazz) {
|
||||
|
||||
checkArgument(Objects.nonNull(clazz), "clazz is needed to derive the table name, thus cannot be null");
|
||||
|
||||
return tableIdentifier(dbName, clazz.getSimpleName().toLowerCase());
|
||||
}
|
||||
|
||||
public static <T extends Oaf> Function<T, String> idFn() {
|
||||
return x -> {
|
||||
if (isSubClass(x, Relation.class)) {
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -523,7 +523,9 @@ public class ProtoConverter implements Serializable {
|
|||
}
|
||||
|
||||
private static Context mapContext(ResultProtos.Result.Context context) {
|
||||
|
||||
if (context == null || StringUtils.isBlank(context.getId())) {
|
||||
return null;
|
||||
}
|
||||
final Context entity = new Context();
|
||||
entity.setId(context.getId());
|
||||
entity
|
||||
|
|
@ -537,6 +539,10 @@ public class ProtoConverter implements Serializable {
|
|||
}
|
||||
|
||||
public static KeyValue mapKV(FieldTypeProtos.KeyValue kv) {
|
||||
if (kv == null || StringUtils.isBlank(kv.getKey()) & StringUtils.isBlank(kv.getValue())) {
|
||||
return null;
|
||||
}
|
||||
|
||||
final KeyValue keyValue = new KeyValue();
|
||||
keyValue.setKey(kv.getKey());
|
||||
keyValue.setValue(kv.getValue());
|
||||
|
|
@ -575,6 +581,10 @@ public class ProtoConverter implements Serializable {
|
|||
}
|
||||
|
||||
public static StructuredProperty mapStructuredProperty(FieldTypeProtos.StructuredProperty sp) {
|
||||
if (sp == null | StringUtils.isBlank(sp.getValue())) {
|
||||
return null;
|
||||
}
|
||||
|
||||
final StructuredProperty structuredProperty = new StructuredProperty();
|
||||
structuredProperty.setValue(sp.getValue());
|
||||
structuredProperty.setQualifier(mapQualifier(sp.getQualifier()));
|
||||
|
|
@ -611,6 +621,10 @@ public class ProtoConverter implements Serializable {
|
|||
}
|
||||
|
||||
public static Field<String> mapStringField(FieldTypeProtos.StringField s) {
|
||||
if (s == null || StringUtils.isBlank(s.getValue())) {
|
||||
return null;
|
||||
}
|
||||
|
||||
final Field<String> stringField = new Field<>();
|
||||
stringField.setValue(s.getValue());
|
||||
stringField.setDataInfo(mapDataInfo(s.getDataInfo()));
|
||||
|
|
@ -618,19 +632,16 @@ public class ProtoConverter implements Serializable {
|
|||
}
|
||||
|
||||
public static Field<Boolean> mapBoolField(FieldTypeProtos.BoolField b) {
|
||||
if (b == null) {
|
||||
return null;
|
||||
}
|
||||
|
||||
final Field<Boolean> booleanField = new Field<>();
|
||||
booleanField.setValue(b.getValue());
|
||||
booleanField.setDataInfo(mapDataInfo(b.getDataInfo()));
|
||||
return booleanField;
|
||||
}
|
||||
|
||||
public static Field<Integer> mapIntField(FieldTypeProtos.IntField b) {
|
||||
final Field<Integer> entity = new Field<>();
|
||||
entity.setValue(b.getValue());
|
||||
entity.setDataInfo(mapDataInfo(b.getDataInfo()));
|
||||
return entity;
|
||||
}
|
||||
|
||||
public static Journal mapJournal(FieldTypeProtos.Journal j) {
|
||||
final Journal journal = new Journal();
|
||||
journal.setConferencedate(j.getConferencedate());
|
||||
|
|
|
|||
|
|
@ -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>
|
||||
|
|
@ -0,0 +1,94 @@
|
|||
|
||||
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.common.HdfsSupport;
|
||||
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 -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
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);
|
||||
}
|
||||
|
||||
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));
|
||||
}
|
||||
|
||||
private static void removeOutputDir(SparkSession spark, String path) {
|
||||
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,141 @@
|
|||
|
||||
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);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,152 @@
|
|||
|
||||
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.common.HdfsSupport;
|
||||
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 -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
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((MapFunction<Tuple2<Relation, Relation>, Relation>) 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((MapFunction<Tuple2<Relation, Relation>, Relation>) 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((MapFunction<Tuple2<Relation, Relation>, Relation>) 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));
|
||||
}
|
||||
|
||||
private static void removeOutputDir(SparkSession spark, String path) {
|
||||
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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
|
||||
}
|
||||
]
|
||||
|
|
@ -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
|
||||
}
|
||||
]
|
||||
|
|
@ -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>
|
||||
|
|
@ -0,0 +1,200 @@
|
|||
<workflow-app name="blacklist_relations" 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>
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>the graph output path</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>mapreduce.job.queuename</name>
|
||||
<value>${queueName}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapred.job.queue.name</name>
|
||||
<value>${oozieLauncherQueueName}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="reset_outputpath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${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_publication"/>
|
||||
<path start="copy_dataset"/>
|
||||
<path start="copy_orp"/>
|
||||
<path start="copy_software"/>
|
||||
<path start="copy_datasource"/>
|
||||
<path start="copy_project"/>
|
||||
<path start="copy_organization"/>
|
||||
</fork>
|
||||
|
||||
<action name="copy_publication">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/publication</arg>
|
||||
<arg>${nameNode}/${outputPath}/publication</arg>
|
||||
</distcp>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_dataset">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/dataset</arg>
|
||||
<arg>${nameNode}/${outputPath}/dataset</arg>
|
||||
</distcp>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_orp">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/otherresearchproduct</arg>
|
||||
<arg>${nameNode}/${outputPath}/otherresearchproduct</arg>
|
||||
</distcp>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_software">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/software</arg>
|
||||
<arg>${nameNode}/${outputPath}/software</arg>
|
||||
</distcp>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_organization">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/organization</arg>
|
||||
<arg>${nameNode}/${outputPath}/organization</arg>
|
||||
</distcp>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_project">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/project</arg>
|
||||
<arg>${nameNode}/${outputPath}/project</arg>
|
||||
</distcp>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_datasource">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<arg>${nameNode}/${sourcePath}/datasource</arg>
|
||||
<arg>${nameNode}/${outputPath}/datasource</arg>
|
||||
</distcp>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="wait" to="read_blacklist"/>
|
||||
|
||||
<action name="read_blacklist">
|
||||
<java>
|
||||
<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}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</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}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/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>
|
||||
|
|
@ -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
|
||||
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,167 @@
|
|||
|
||||
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());
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -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"}
|
||||
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||||
|
|
@ -0,0 +1,13 @@
|
|||
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{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|doajarticles::15581a45537ceb854bbddee49b2942b4","subRelType":"provision","target":"20|doajarticles::0b25b0ce56da469cc8ad74c7d83c16a3"}
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|
|
@ -0,0 +1,13 @@
|
|||
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"hasParticipant","relType":"projectOrganization","source":"40|corda__h2020::5161f53ab205d803c36b4c888fe7deef","subRelType":"participation","target":"20|dedup_wf_001::157af406bc653aa4d9749318b644de43"}
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||||
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|
||||
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|doajarticles::0f4b6db6c02966acbfb60af527728c85","subRelType":"provision","target":"20|doajarticles::acd96b3bd87b176202b8ea494c318b21"}
|
||||
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|doajarticles::11f65dc66da7ef1b1f3a3e59199e4d70","subRelType":"provision","target":"20|dedup_wf_001::6132363e7458cbd7c22aa284c7df1307"}
|
||||
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|doajarticles::149fd06e8702d94aa648641fd1602284","subRelType":"provision","target":"20|dedup_wf_001::35ae35032078bc33bc92e2b0f2ecfa17"}
|
||||
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1588608946167,"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|doajarticles::15581a45537ceb854bbddee49b2942b4","subRelType":"provision","target":"20|doajarticles::0b25b0ce56da469cc8ad74c7d83c16a3"}
|
||||
|
|
@ -29,31 +29,32 @@ public class EventFactory {
|
|||
"yyyy-MM-dd"
|
||||
};
|
||||
|
||||
public static Event newBrokerEvent(final Result source, final Result target, final UpdateInfo<?> updateInfo) {
|
||||
public static Event newBrokerEvent(final UpdateInfo<?> updateInfo) {
|
||||
|
||||
final long now = new Date().getTime();
|
||||
|
||||
final Event res = new Event();
|
||||
|
||||
final Map<String, Object> map = createMapFromResult(target, source, updateInfo);
|
||||
final Map<String, Object> map = createMapFromResult(updateInfo);
|
||||
|
||||
final String payload = createPayload(target, updateInfo);
|
||||
final String payload = createPayload(updateInfo);
|
||||
|
||||
final String eventId = calculateEventId(
|
||||
updateInfo.getTopic(), target.getOriginalId().get(0), updateInfo.getHighlightValueAsString());
|
||||
updateInfo.getTopicPath(), updateInfo.getTarget().getOriginalId().get(0),
|
||||
updateInfo.getHighlightValueAsString());
|
||||
|
||||
res.setEventId(eventId);
|
||||
res.setProducerId(PRODUCER_ID);
|
||||
res.setPayload(payload);
|
||||
res.setMap(map);
|
||||
res.setTopic(updateInfo.getTopic());
|
||||
res.setTopic(updateInfo.getTopicPath());
|
||||
res.setCreationDate(now);
|
||||
res.setExpiryDate(calculateExpiryDate(now));
|
||||
res.setInstantMessage(false);
|
||||
return res;
|
||||
}
|
||||
|
||||
private static String createPayload(final Result result, final UpdateInfo<?> updateInfo) {
|
||||
private static String createPayload(final UpdateInfo<?> updateInfo) {
|
||||
final OpenAireEventPayload payload = new OpenAireEventPayload();
|
||||
// TODO
|
||||
|
||||
|
|
@ -62,32 +63,34 @@ public class EventFactory {
|
|||
return payload.toJSON();
|
||||
}
|
||||
|
||||
private static Map<String, Object> createMapFromResult(final Result oaf, final Result source,
|
||||
final UpdateInfo<?> updateInfo) {
|
||||
private static Map<String, Object> createMapFromResult(final UpdateInfo<?> updateInfo) {
|
||||
final Map<String, Object> map = new HashMap<>();
|
||||
|
||||
final List<KeyValue> collectedFrom = oaf.getCollectedfrom();
|
||||
final Result source = updateInfo.getSource();
|
||||
final Result target = updateInfo.getTarget();
|
||||
|
||||
final List<KeyValue> collectedFrom = target.getCollectedfrom();
|
||||
if (collectedFrom.size() == 1) {
|
||||
map.put("target_datasource_id", collectedFrom.get(0).getKey());
|
||||
map.put("target_datasource_name", collectedFrom.get(0).getValue());
|
||||
}
|
||||
|
||||
final List<String> ids = oaf.getOriginalId();
|
||||
final List<String> ids = target.getOriginalId();
|
||||
if (ids.size() > 0) {
|
||||
map.put("target_publication_id", ids.get(0));
|
||||
}
|
||||
|
||||
final List<StructuredProperty> titles = oaf.getTitle();
|
||||
final List<StructuredProperty> titles = target.getTitle();
|
||||
if (titles.size() > 0) {
|
||||
map.put("target_publication_title", titles.get(0));
|
||||
}
|
||||
|
||||
final long date = parseDateTolong(oaf.getDateofacceptance().getValue());
|
||||
final long date = parseDateTolong(target.getDateofacceptance().getValue());
|
||||
if (date > 0) {
|
||||
map.put("target_dateofacceptance", date);
|
||||
}
|
||||
|
||||
final List<StructuredProperty> subjects = oaf.getSubject();
|
||||
final List<StructuredProperty> subjects = target.getSubject();
|
||||
if (subjects.size() > 0) {
|
||||
map
|
||||
.put(
|
||||
|
|
@ -95,7 +98,7 @@ public class EventFactory {
|
|||
subjects.stream().map(StructuredProperty::getValue).collect(Collectors.toList()));
|
||||
}
|
||||
|
||||
final List<Author> authors = oaf.getAuthor();
|
||||
final List<Author> authors = target.getAuthor();
|
||||
if (authors.size() > 0) {
|
||||
map
|
||||
.put(
|
||||
|
|
|
|||
|
|
@ -0,0 +1,52 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.model;
|
||||
|
||||
public enum Topic {
|
||||
|
||||
// ENRICHMENT MISSING
|
||||
ENRICH_MISSING_OA_VERSION("ENRICH/MISSING/OPENACCESS_VERSION"), ENRICH_MISSING_ABSTRACT(
|
||||
"ENRICH/MISSING/ABSTRACT"), ENRICH_MISSING_PUBLICATION_DATE(
|
||||
"ENRICH/MISSING/PUBLICATION_DATE"), ENRICH_MISSING_PID(
|
||||
"ENRICH/MISSING/PID"), ENRICH_MISSING_PROJECT("ENRICH/MISSING/PROJECT"), ENRICH_MISSING_SOFTWARE(
|
||||
"ENRICH/MISSING/SOFTWARE"), ENRICH_MISSING_SUBJECT_MESHEUROPMC(
|
||||
"ENRICH/MISSING/SUBJECT/MESHEUROPMC"), ENRICH_MISSING_SUBJECT_ARXIV(
|
||||
"ENRICH/MISSING/SUBJECT/ARXIV"), ENRICH_MISSING_SUBJECT_JEL(
|
||||
"ENRICH/MISSING/SUBJECT/JEL"), ENRICH_MISSING_SUBJECT_DDC(
|
||||
"ENRICH/MISSING/SUBJECT/DDC"), ENRICH_MISSING_SUBJECT_ACM(
|
||||
"ENRICH/MISSING/SUBJECT/ACM"), ENRICH_MISSING_SUBJECT_RVK(
|
||||
"ENRICH/MISSING/SUBJECT/RVK"), ENRICH_MISSING_AUTHOR_ORCID(
|
||||
"ENRICH/MISSING/AUTHOR/ORCID"),
|
||||
|
||||
// ENRICHMENT MORE
|
||||
ENRICH_MORE_PID("ENRICH/MORE/PID"), ENRICH_MORE_OA_VERSION("ENRICH/MORE/OPENACCESS_VERSION"), ENRICH_MORE_ABSTRACT(
|
||||
"ENRICH/MORE/ABSTRACT"), ENRICH_MORE_PUBLICATION_DATE("ENRICH/MORE/PUBLICATION_DATE"), ENRICH_MORE_PROJECT(
|
||||
"ENRICH/MORE/PROJECT"), ENRICH_MORE_SUBJECT_MESHEUROPMC(
|
||||
"ENRICH/MORE/SUBJECT/MESHEUROPMC"), ENRICH_MORE_SUBJECT_ARXIV(
|
||||
"ENRICH/MORE/SUBJECT/ARXIV"), ENRICH_MORE_SUBJECT_JEL(
|
||||
"ENRICH/MORE/SUBJECT/JEL"), ENRICH_MORE_SUBJECT_DDC(
|
||||
"ENRICH/MORE/SUBJECT/DDC"), ENRICH_MORE_SUBJECT_ACM(
|
||||
"ENRICH/MORE/SUBJECT/ACM"), ENRICH_MORE_SUBJECT_RVK("ENRICH/MORE/SUBJECT/RVK"),
|
||||
|
||||
// ADDITION
|
||||
ADD_BY_PROJECT("ADD/BY_PROJECT");
|
||||
|
||||
Topic(final String path) {
|
||||
this.path = path;
|
||||
}
|
||||
|
||||
protected String path;
|
||||
|
||||
public String getPath() {
|
||||
return this.path;
|
||||
}
|
||||
|
||||
public static Topic fromPath(final String path) {
|
||||
for (final Topic t : Topic.values()) {
|
||||
if (t.getPath().equals(path)) {
|
||||
return t;
|
||||
}
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -14,21 +14,20 @@ 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.broker.model.Event;
|
||||
import eu.dnetlib.dhp.broker.model.EventFactory;
|
||||
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingAbstract;
|
||||
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingAuthorOrcid;
|
||||
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingOpenAccess;
|
||||
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingPid;
|
||||
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingProject;
|
||||
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingPublicationDate;
|
||||
import eu.dnetlib.dhp.broker.oa.util.EnrichMissingSubject;
|
||||
import eu.dnetlib.dhp.broker.oa.util.EnrichMoreOpenAccess;
|
||||
import eu.dnetlib.dhp.broker.oa.util.EnrichMorePid;
|
||||
import eu.dnetlib.dhp.broker.oa.util.EnrichMoreSubject;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAbstract;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingAuthorOrcid;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingOpenAccess;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPid;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingProject;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingPublicationDate;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.EnrichMissingSubject;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreOpenAccess;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.EnrichMorePid;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.EnrichMoreSubject;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
|
@ -37,7 +36,16 @@ public class GenerateEventsApplication {
|
|||
|
||||
private static final Logger log = LoggerFactory.getLogger(GenerateEventsApplication.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
private static final UpdateMatcher<?> enrichMissingAbstract = new EnrichMissingAbstract();
|
||||
private static final UpdateMatcher<?> enrichMissingAuthorOrcid = new EnrichMissingAuthorOrcid();
|
||||
private static final UpdateMatcher<?> enrichMissingOpenAccess = new EnrichMissingOpenAccess();
|
||||
private static final UpdateMatcher<?> enrichMissingPid = new EnrichMissingPid();
|
||||
private static final UpdateMatcher<?> enrichMissingProject = new EnrichMissingProject();
|
||||
private static final UpdateMatcher<?> enrichMissingPublicationDate = new EnrichMissingPublicationDate();
|
||||
private static final UpdateMatcher<?> enrichMissingSubject = new EnrichMissingSubject();
|
||||
private static final UpdateMatcher<?> enrichMoreOpenAccess = new EnrichMoreOpenAccess();
|
||||
private static final UpdateMatcher<?> enrichMorePid = new EnrichMorePid();
|
||||
private static final UpdateMatcher<?> enrichMoreSubject = new EnrichMoreSubject();
|
||||
|
||||
public static void main(final String[] args) throws Exception {
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
|
|
@ -76,37 +84,22 @@ public class GenerateEventsApplication {
|
|||
}
|
||||
|
||||
private List<Event> generateEvents(final Result... children) {
|
||||
final List<Event> list = new ArrayList<>();
|
||||
final List<UpdateInfo<?>> list = new ArrayList<>();
|
||||
|
||||
for (final Result source : children) {
|
||||
for (final Result target : children) {
|
||||
if (source != target) {
|
||||
list
|
||||
.addAll(
|
||||
findUpdates(source, target)
|
||||
.stream()
|
||||
.map(info -> EventFactory.newBrokerEvent(source, target, info))
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
}
|
||||
for (final Result target : children) {
|
||||
list.addAll(enrichMissingAbstract.searchUpdatesForRecord(target, children));
|
||||
list.addAll(enrichMissingAuthorOrcid.searchUpdatesForRecord(target, children));
|
||||
list.addAll(enrichMissingOpenAccess.searchUpdatesForRecord(target, children));
|
||||
list.addAll(enrichMissingPid.searchUpdatesForRecord(target, children));
|
||||
list.addAll(enrichMissingProject.searchUpdatesForRecord(target, children));
|
||||
list.addAll(enrichMissingPublicationDate.searchUpdatesForRecord(target, children));
|
||||
list.addAll(enrichMissingSubject.searchUpdatesForRecord(target, children));
|
||||
list.addAll(enrichMoreOpenAccess.searchUpdatesForRecord(target, children));
|
||||
list.addAll(enrichMorePid.searchUpdatesForRecord(target, children));
|
||||
list.addAll(enrichMoreSubject.searchUpdatesForRecord(target, children));
|
||||
}
|
||||
|
||||
return list;
|
||||
}
|
||||
|
||||
private List<UpdateInfo<?>> findUpdates(final Result source, final Result target) {
|
||||
final List<UpdateInfo<?>> list = new ArrayList<>();
|
||||
list.addAll(EnrichMissingAbstract.findUpdates(source, target));
|
||||
list.addAll(EnrichMissingAuthorOrcid.findUpdates(source, target));
|
||||
list.addAll(EnrichMissingOpenAccess.findUpdates(source, target));
|
||||
list.addAll(EnrichMissingPid.findUpdates(source, target));
|
||||
list.addAll(EnrichMissingProject.findUpdates(source, target));
|
||||
list.addAll(EnrichMissingPublicationDate.findUpdates(source, target));
|
||||
list.addAll(EnrichMissingSubject.findUpdates(source, target));
|
||||
list.addAll(EnrichMoreOpenAccess.findUpdates(source, target));
|
||||
list.addAll(EnrichMorePid.findUpdates(source, target));
|
||||
list.addAll(EnrichMoreSubject.findUpdates(source, target));
|
||||
return list;
|
||||
return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,36 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingAbstract extends UpdateMatcher<String> {
|
||||
|
||||
public EnrichMissingAbstract() {
|
||||
super(false);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<UpdateInfo<String>> findUpdates(final Result source, final Result target) {
|
||||
if (isMissing(target.getDescription()) && !isMissing(source.getDescription())) {
|
||||
return Arrays.asList(generateUpdateInfo(source.getDescription().get(0).getValue(), source, target));
|
||||
}
|
||||
return new ArrayList<>();
|
||||
}
|
||||
|
||||
@Override
|
||||
public UpdateInfo<String> generateUpdateInfo(final String highlightValue, final Result source,
|
||||
final Result target) {
|
||||
return new UpdateInfo<>(
|
||||
Topic.ENRICH_MISSING_ABSTRACT,
|
||||
highlightValue, source, target,
|
||||
(p, s) -> p.getAbstracts().add(s),
|
||||
s -> s);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,34 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import org.apache.commons.lang3.tuple.Pair;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingAuthorOrcid extends UpdateMatcher<Pair<String, String>> {
|
||||
|
||||
public EnrichMissingAuthorOrcid() {
|
||||
super(true);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<UpdateInfo<Pair<String, String>>> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
@Override
|
||||
public UpdateInfo<Pair<String, String>> generateUpdateInfo(final Pair<String, String> highlightValue,
|
||||
final Result source, final Result target) {
|
||||
return new UpdateInfo<>(
|
||||
Topic.ENRICH_MISSING_AUTHOR_ORCID,
|
||||
highlightValue, source, target,
|
||||
(p, pair) -> p.getCreators().add(pair.getLeft() + " - ORCID: " + pair.getRight()),
|
||||
pair -> pair.getLeft() + "::" + pair.getRight());
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.broker.objects.Instance;
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
|
||||
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingOpenAccess extends UpdateMatcher<Instance> {
|
||||
|
||||
public EnrichMissingOpenAccess() {
|
||||
super(true);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<UpdateInfo<Instance>> findUpdates(final Result source, final Result target) {
|
||||
final long count = target
|
||||
.getInstance()
|
||||
.stream()
|
||||
.map(i -> i.getAccessright().getClassid())
|
||||
.filter(right -> right.equals(BrokerConstants.OPEN_ACCESS))
|
||||
.count();
|
||||
|
||||
if (count > 0) {
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
return source
|
||||
.getInstance()
|
||||
.stream()
|
||||
.filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS))
|
||||
.map(ConversionUtils::oafInstanceToBrokerInstances)
|
||||
.flatMap(s -> s)
|
||||
.map(i -> generateUpdateInfo(i, source, target))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
@Override
|
||||
public UpdateInfo<Instance> generateUpdateInfo(final Instance highlightValue,
|
||||
final Result source,
|
||||
final Result target) {
|
||||
return new UpdateInfo<>(
|
||||
Topic.ENRICH_MISSING_OA_VERSION,
|
||||
highlightValue, source, target,
|
||||
(p, i) -> p.getInstances().add(i),
|
||||
Instance::getUrl);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.broker.objects.Pid;
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingPid extends UpdateMatcher<Pid> {
|
||||
|
||||
public EnrichMissingPid() {
|
||||
super(true);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<UpdateInfo<Pid>> findUpdates(final Result source, final Result target) {
|
||||
final long count = target.getPid().size();
|
||||
|
||||
if (count > 0) {
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
return source
|
||||
.getPid()
|
||||
.stream()
|
||||
.map(ConversionUtils::oafPidToBrokerPid)
|
||||
.map(i -> generateUpdateInfo(i, source, target))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
@Override
|
||||
public UpdateInfo<Pid> generateUpdateInfo(final Pid highlightValue, final Result source, final Result target) {
|
||||
return new UpdateInfo<>(
|
||||
Topic.ENRICH_MISSING_PID,
|
||||
highlightValue, source, target,
|
||||
(p, pid) -> p.getPids().add(pid),
|
||||
pid -> pid.getType() + "::" + pid.getValue());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,35 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.Project;
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingProject extends UpdateMatcher<Project> {
|
||||
|
||||
public EnrichMissingProject() {
|
||||
super(true);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<UpdateInfo<Project>> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
@Override
|
||||
public UpdateInfo<Project> generateUpdateInfo(final Project highlightValue,
|
||||
final Result source,
|
||||
final Result target) {
|
||||
return new UpdateInfo<>(
|
||||
Topic.ENRICH_MISSING_PROJECT,
|
||||
highlightValue, source, target,
|
||||
(p, prj) -> p.getProjects().add(prj),
|
||||
prj -> prj.getFunder() + "::" + prj.getFundingProgram() + prj.getCode());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,33 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingPublicationDate extends UpdateMatcher<String> {
|
||||
|
||||
public EnrichMissingPublicationDate() {
|
||||
super(false);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<UpdateInfo<String>> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
@Override
|
||||
public UpdateInfo<String> generateUpdateInfo(final String highlightValue, final Result source,
|
||||
final Result target) {
|
||||
return new UpdateInfo<>(
|
||||
Topic.ENRICH_MISSING_PUBLICATION_DATE,
|
||||
highlightValue, source, target,
|
||||
(p, date) -> p.setPublicationdate(date),
|
||||
s -> s);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,53 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.lang3.tuple.Pair;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class EnrichMissingSubject extends UpdateMatcher<Pair<String, String>> {
|
||||
|
||||
public EnrichMissingSubject() {
|
||||
super(true);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<UpdateInfo<Pair<String, String>>> findUpdates(final Result source, final Result target) {
|
||||
final Set<String> existingTypes = target
|
||||
.getSubject()
|
||||
.stream()
|
||||
.map(StructuredProperty::getQualifier)
|
||||
.map(Qualifier::getClassid)
|
||||
.collect(Collectors.toSet());
|
||||
|
||||
return source
|
||||
.getPid()
|
||||
.stream()
|
||||
.filter(pid -> !existingTypes.contains(pid.getQualifier().getClassid()))
|
||||
.map(ConversionUtils::oafSubjectToPair)
|
||||
.map(i -> generateUpdateInfo(i, source, target))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
@Override
|
||||
public UpdateInfo<Pair<String, String>> generateUpdateInfo(final Pair<String, String> highlightValue,
|
||||
final Result source,
|
||||
final Result target) {
|
||||
|
||||
return new UpdateInfo<>(
|
||||
Topic.fromPath("ENRICH/MISSING/SUBJECT/" + highlightValue.getLeft()),
|
||||
highlightValue, source, target,
|
||||
(p, pair) -> p.getSubjects().add(pair.getRight()),
|
||||
pair -> pair.getLeft() + "::" + pair.getRight());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,53 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.broker.objects.Instance;
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
|
||||
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMoreOpenAccess extends UpdateMatcher<Instance> {
|
||||
|
||||
public EnrichMoreOpenAccess() {
|
||||
super(true);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<UpdateInfo<Instance>> findUpdates(final Result source, final Result target) {
|
||||
final Set<String> urls = target
|
||||
.getInstance()
|
||||
.stream()
|
||||
.filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS))
|
||||
.map(i -> i.getUrl())
|
||||
.flatMap(List::stream)
|
||||
.collect(Collectors.toSet());
|
||||
|
||||
return source
|
||||
.getInstance()
|
||||
.stream()
|
||||
.filter(i -> i.getAccessright().getClassid().equals(BrokerConstants.OPEN_ACCESS))
|
||||
.map(ConversionUtils::oafInstanceToBrokerInstances)
|
||||
.flatMap(s -> s)
|
||||
.filter(i -> !urls.contains(i.getUrl()))
|
||||
.map(i -> generateUpdateInfo(i, source, target))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
@Override
|
||||
public UpdateInfo<Instance> generateUpdateInfo(final Instance highlightValue,
|
||||
final Result source,
|
||||
final Result target) {
|
||||
return new UpdateInfo<>(
|
||||
Topic.ENRICH_MORE_OA_VERSION,
|
||||
highlightValue, source, target,
|
||||
(p, i) -> p.getInstances().add(i),
|
||||
Instance::getUrl);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.broker.objects.Pid;
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMorePid extends UpdateMatcher<Pid> {
|
||||
|
||||
public EnrichMorePid() {
|
||||
super(true);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<UpdateInfo<Pid>> findUpdates(final Result source, final Result target) {
|
||||
final Set<String> existingPids = target
|
||||
.getPid()
|
||||
.stream()
|
||||
.map(pid -> pid.getQualifier().getClassid() + "::" + pid.getValue())
|
||||
.collect(Collectors.toSet());
|
||||
|
||||
return source
|
||||
.getPid()
|
||||
.stream()
|
||||
.filter(pid -> !existingPids.contains(pid.getQualifier().getClassid() + "::" + pid.getValue()))
|
||||
.map(ConversionUtils::oafPidToBrokerPid)
|
||||
.map(i -> generateUpdateInfo(i, source, target))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
@Override
|
||||
public UpdateInfo<Pid> generateUpdateInfo(final Pid highlightValue, final Result source, final Result target) {
|
||||
return new UpdateInfo<>(
|
||||
Topic.ENRICH_MORE_PID,
|
||||
highlightValue, source, target,
|
||||
(p, pid) -> p.getPids().add(pid),
|
||||
pid -> pid.getType() + "::" + pid.getValue());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.lang3.tuple.Pair;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMoreSubject extends UpdateMatcher<Pair<String, String>> {
|
||||
|
||||
public EnrichMoreSubject() {
|
||||
super(true);
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<UpdateInfo<Pair<String, String>>> findUpdates(final Result source, final Result target) {
|
||||
final Set<String> existingSubjects = target
|
||||
.getSubject()
|
||||
.stream()
|
||||
.map(pid -> pid.getQualifier().getClassid() + "::" + pid.getValue())
|
||||
.collect(Collectors.toSet());
|
||||
|
||||
return source
|
||||
.getPid()
|
||||
.stream()
|
||||
.filter(pid -> !existingSubjects.contains(pid.getQualifier().getClassid() + "::" + pid.getValue()))
|
||||
.map(ConversionUtils::oafSubjectToPair)
|
||||
.map(i -> generateUpdateInfo(i, source, target))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
@Override
|
||||
public UpdateInfo<Pair<String, String>> generateUpdateInfo(final Pair<String, String> highlightValue,
|
||||
final Result source,
|
||||
final Result target) {
|
||||
|
||||
return new UpdateInfo<>(
|
||||
Topic.fromPath("ENRICH/MORE/SUBJECT/" + highlightValue.getLeft()),
|
||||
highlightValue, source, target,
|
||||
(p, pair) -> p.getSubjects().add(pair.getRight()),
|
||||
pair -> pair.getLeft() + "::" + pair.getRight());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,64 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.matchers;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Collection;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import org.apache.commons.codec.digest.DigestUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Field;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public abstract class UpdateMatcher<T> {
|
||||
|
||||
private final boolean multipleUpdate;
|
||||
|
||||
public UpdateMatcher(final boolean multipleUpdate) {
|
||||
this.multipleUpdate = multipleUpdate;
|
||||
}
|
||||
|
||||
public Collection<UpdateInfo<T>> searchUpdatesForRecord(final Result res, final Result... others) {
|
||||
|
||||
final Map<String, UpdateInfo<T>> infoMap = new HashMap<>();
|
||||
|
||||
for (final Result source : others) {
|
||||
if (source != res) {
|
||||
for (final UpdateInfo<T> info : findUpdates(source, res)) {
|
||||
final String s = DigestUtils.md5Hex(info.getHighlightValueAsString());
|
||||
if (!infoMap.containsKey(s) || infoMap.get(s).getTrust() < info.getTrust()) {
|
||||
} else {
|
||||
infoMap.put(s, info);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
final Collection<UpdateInfo<T>> values = infoMap.values();
|
||||
|
||||
if (values.isEmpty() || multipleUpdate) {
|
||||
return values;
|
||||
} else {
|
||||
final UpdateInfo<T> v = values
|
||||
.stream()
|
||||
.sorted((o1, o2) -> Float.compare(o1.getTrust(), o2.getTrust()))
|
||||
.findFirst()
|
||||
.get();
|
||||
return Arrays.asList(v);
|
||||
}
|
||||
}
|
||||
|
||||
protected abstract List<UpdateInfo<T>> findUpdates(Result source, Result target);
|
||||
|
||||
protected abstract UpdateInfo<T> generateUpdateInfo(final T highlightValue, final Result source,
|
||||
final Result target);
|
||||
|
||||
protected static boolean isMissing(final List<Field<String>> list) {
|
||||
return list == null || list.isEmpty() || StringUtils.isBlank(list.get(0).getValue());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
public class BrokerConstants {
|
||||
|
||||
public final static String OPEN_ACCESS = "OPEN";
|
||||
}
|
||||
|
|
@ -0,0 +1,36 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.stream.Stream;
|
||||
|
||||
import org.apache.commons.lang3.tuple.Pair;
|
||||
|
||||
import eu.dnetlib.broker.objects.Instance;
|
||||
import eu.dnetlib.broker.objects.Pid;
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class ConversionUtils {
|
||||
|
||||
public static Stream<Instance> oafInstanceToBrokerInstances(final eu.dnetlib.dhp.schema.oaf.Instance i) {
|
||||
return i.getUrl().stream().map(url -> {
|
||||
final Instance r = new Instance();
|
||||
r.setUrl(url);
|
||||
r.setInstancetype(i.getInstancetype().getClassid());
|
||||
r.setLicense(BrokerConstants.OPEN_ACCESS);
|
||||
r.setHostedby(i.getHostedby().getValue());
|
||||
return r;
|
||||
});
|
||||
}
|
||||
|
||||
public static Pid oafPidToBrokerPid(final StructuredProperty sp) {
|
||||
final Pid pid = new Pid();
|
||||
pid.setValue(sp.getValue());
|
||||
pid.setType(sp.getQualifier().getClassid());
|
||||
return pid;
|
||||
}
|
||||
|
||||
public static final Pair<String, String> oafSubjectToPair(final StructuredProperty sp) {
|
||||
return Pair.of(sp.getQualifier().getClassid(), sp.getValue());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,31 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingAbstract extends UpdateInfo<String> {
|
||||
|
||||
public static List<EnrichMissingAbstract> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
private EnrichMissingAbstract(final String highlightValue, final float trust) {
|
||||
super("ENRICH/MISSING/ABSTRACT", highlightValue, trust);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
payload.getHighlight().getAbstracts().add(getHighlightValue());
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getHighlightValueAsString() {
|
||||
return getHighlightValue();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,31 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingAuthorOrcid extends UpdateInfo<String> {
|
||||
|
||||
public static List<EnrichMissingAuthorOrcid> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
private EnrichMissingAuthorOrcid(final String highlightValue, final float trust) {
|
||||
super("ENRICH/MISSING/AUTHOR/ORCID", highlightValue, trust);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
// TODO
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getHighlightValueAsString() {
|
||||
return getHighlightValue();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,32 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.Instance;
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingOpenAccess extends UpdateInfo<Instance> {
|
||||
|
||||
public static List<EnrichMissingOpenAccess> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
private EnrichMissingOpenAccess(final Instance highlightValue, final float trust) {
|
||||
super("ENRICH/MISSING/OPENACCESS_VERSION", highlightValue, trust);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
payload.getHighlight().getInstances().add(getHighlightValue());
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getHighlightValueAsString() {
|
||||
return getHighlightValue().getUrl();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,32 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.broker.objects.Pid;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingPid extends UpdateInfo<Pid> {
|
||||
|
||||
public static List<EnrichMissingPid> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
private EnrichMissingPid(final Pid highlightValue, final float trust) {
|
||||
super("ENRICH/MISSING/PID", highlightValue, trust);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
payload.getHighlight().getPids().add(getHighlightValue());
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getHighlightValueAsString() {
|
||||
return getHighlightValue().getType() + "::" + getHighlightValue().getValue();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,33 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.broker.objects.Project;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingProject extends UpdateInfo<Project> {
|
||||
|
||||
public static List<EnrichMissingProject> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
private EnrichMissingProject(final Project highlightValue, final float trust) {
|
||||
super("ENRICH/MISSING/PROJECT", highlightValue, trust);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
payload.getHighlight().getProjects().add(getHighlightValue());
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getHighlightValueAsString() {
|
||||
return getHighlightValue().getFunder() + "::" + getHighlightValue().getFundingProgram()
|
||||
+ getHighlightValue().getCode();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,31 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingPublicationDate extends UpdateInfo<String> {
|
||||
|
||||
public static List<EnrichMissingPublicationDate> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
private EnrichMissingPublicationDate(final String highlightValue, final float trust) {
|
||||
super("ENRICH/MISSING/PUBLICATION_DATE", highlightValue, trust);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
payload.getHighlight().setPublicationdate(getHighlightValue());
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getHighlightValueAsString() {
|
||||
return getHighlightValue();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,36 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMissingSubject extends UpdateInfo<String> {
|
||||
|
||||
public static List<EnrichMissingSubject> findUpdates(final Result source, final Result target) {
|
||||
// MESHEUROPMC
|
||||
// ARXIV
|
||||
// JEL
|
||||
// DDC
|
||||
// ACM
|
||||
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
private EnrichMissingSubject(final String subjectClassification, final String highlightValue, final float trust) {
|
||||
super("ENRICH/MISSING/SUBJECT/" + subjectClassification, highlightValue, trust);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
payload.getHighlight().getSubjects().add(getHighlightValue());
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getHighlightValueAsString() {
|
||||
return getHighlightValue();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,32 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.Instance;
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMoreOpenAccess extends UpdateInfo<Instance> {
|
||||
|
||||
public static List<EnrichMoreOpenAccess> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
private EnrichMoreOpenAccess(final Instance highlightValue, final float trust) {
|
||||
super("ENRICH/MORE/OPENACCESS_VERSION", highlightValue, trust);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
payload.getHighlight().getInstances().add(getHighlightValue());
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getHighlightValueAsString() {
|
||||
return getHighlightValue().getUrl();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,32 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.broker.objects.Pid;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMorePid extends UpdateInfo<Pid> {
|
||||
|
||||
public static List<EnrichMorePid> findUpdates(final Result source, final Result target) {
|
||||
// return Arrays.asList(new EnrichMissingAbstract("xxxxxxx", 0.9f));
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
private EnrichMorePid(final Pid highlightValue, final float trust) {
|
||||
super("ENRICH/MORE/PID", highlightValue, trust);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
payload.getHighlight().getPids().add(getHighlightValue());
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getHighlightValueAsString() {
|
||||
return getHighlightValue().getType() + "::" + getHighlightValue().getValue();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,36 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class EnrichMoreSubject extends UpdateInfo<String> {
|
||||
|
||||
public static List<EnrichMoreSubject> findUpdates(final Result source, final Result target) {
|
||||
// MESHEUROPMC
|
||||
// ARXIV
|
||||
// JEL
|
||||
// DDC
|
||||
// ACM
|
||||
|
||||
return Arrays.asList();
|
||||
}
|
||||
|
||||
private EnrichMoreSubject(final String subjectClassification, final String highlightValue, final float trust) {
|
||||
super("ENRICH/MORE/SUBJECT/" + subjectClassification, highlightValue, trust);
|
||||
}
|
||||
|
||||
@Override
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
payload.getHighlight().getSubjects().add(getHighlightValue());
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getHighlightValueAsString() {
|
||||
return getHighlightValue();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,36 +1,77 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.util.function.BiConsumer;
|
||||
import java.util.function.Function;
|
||||
|
||||
import eu.dnetlib.broker.objects.OpenAireEventPayload;
|
||||
import eu.dnetlib.broker.objects.Publication;
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public abstract class UpdateInfo<T> {
|
||||
public final class UpdateInfo<T> {
|
||||
|
||||
private final String topic;
|
||||
private final Topic topic;
|
||||
|
||||
private final T highlightValue;
|
||||
|
||||
private final Result source;
|
||||
|
||||
private final Result target;
|
||||
|
||||
private final BiConsumer<Publication, T> compileHighlight;
|
||||
|
||||
private final Function<T, String> highlightToString;
|
||||
|
||||
private final float trust;
|
||||
|
||||
protected UpdateInfo(final String topic, final T highlightValue, final float trust) {
|
||||
public UpdateInfo(final Topic topic, final T highlightValue, final Result source, final Result target,
|
||||
final BiConsumer<Publication, T> compileHighlight,
|
||||
final Function<T, String> highlightToString) {
|
||||
this.topic = topic;
|
||||
this.highlightValue = highlightValue;
|
||||
this.trust = trust;
|
||||
this.source = source;
|
||||
this.target = target;
|
||||
this.compileHighlight = compileHighlight;
|
||||
this.highlightToString = highlightToString;
|
||||
this.trust = calculateTrust(source, target);
|
||||
}
|
||||
|
||||
public T getHighlightValue() {
|
||||
return highlightValue;
|
||||
}
|
||||
|
||||
public Result getSource() {
|
||||
return source;
|
||||
}
|
||||
|
||||
public Result getTarget() {
|
||||
return target;
|
||||
}
|
||||
|
||||
private float calculateTrust(final Result source, final Result target) {
|
||||
// TODO
|
||||
return 0.9f;
|
||||
}
|
||||
|
||||
protected Topic getTopic() {
|
||||
return topic;
|
||||
}
|
||||
|
||||
public String getTopicPath() {
|
||||
return topic.getPath();
|
||||
}
|
||||
|
||||
public float getTrust() {
|
||||
return trust;
|
||||
}
|
||||
|
||||
public String getTopic() {
|
||||
return topic;
|
||||
public void compileHighlight(final OpenAireEventPayload payload) {
|
||||
compileHighlight.accept(payload.getHighlight(), getHighlightValue());
|
||||
}
|
||||
|
||||
abstract public void compileHighlight(OpenAireEventPayload payload);
|
||||
|
||||
abstract public String getHighlightValueAsString();
|
||||
public String getHighlightValueAsString() {
|
||||
return highlightToString.apply(getHighlightValue());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,64 @@
|
|||
<?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-enrichment</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>
|
||||
|
||||
<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>io.github.classgraph</groupId>
|
||||
<artifactId>classgraph</artifactId>
|
||||
<version>4.8.71</version>
|
||||
</dependency>
|
||||
|
||||
|
||||
</dependencies>
|
||||
|
||||
|
||||
|
||||
</project>
|
||||
|
|
@ -0,0 +1,151 @@
|
|||
|
||||
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.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
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 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 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(ModelConstants.DNET_COUNTRY_TYPE);
|
||||
nc.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE);
|
||||
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(ModelConstants.DNET_PID_TYPES);
|
||||
pa.setSchemename(ModelConstants.DNET_PID_TYPES);
|
||||
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));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,122 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag;
|
||||
|
||||
import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
|
||||
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.bulktag.community.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
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 -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
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));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,65 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.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<Provider> providers = 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()
|
||||
|| !getProviders().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<Provider> getProviders() {
|
||||
return providers;
|
||||
}
|
||||
|
||||
public void setProviders(List<Provider> providers) {
|
||||
this.providers = providers;
|
||||
}
|
||||
|
||||
public List<ZenodoCommunity> getZenodoCommunities() {
|
||||
return zenodoCommunities;
|
||||
}
|
||||
|
||||
public void setZenodoCommunities(List<ZenodoCommunity> zenodoCommunities) {
|
||||
this.zenodoCommunities = zenodoCommunities;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,196 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.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.bulktag.criteria.InterfaceAdapter;
|
||||
import eu.dnetlib.dhp.bulktag.criteria.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 (Provider d : c.getProviders()) {
|
||||
|
||||
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());
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,138 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.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.bulktag.criteria.InterfaceAdapter;
|
||||
import eu.dnetlib.dhp.bulktag.criteria.Selection;
|
||||
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
|
||||
import eu.dnetlib.dhp.bulktag.criteria.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.setProviders(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<Provider> parseDatasources(final Node node) {
|
||||
final List<Node> list = node.selectNodes("./datasources/datasource");
|
||||
final List<Provider> providerList = new ArrayList<>();
|
||||
for (Node n : list) {
|
||||
Provider d = new Provider();
|
||||
d.setOpenaireId(n.selectSingleNode("./openaireId").getText());
|
||||
d.setSelCriteria(n.selectSingleNode("./selcriteria"), resolver);
|
||||
providerList.add(d);
|
||||
}
|
||||
log.info("size of the datasource list " + providerList.size());
|
||||
return providerList;
|
||||
}
|
||||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,56 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.community;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.lang.reflect.InvocationTargetException;
|
||||
|
||||
import eu.dnetlib.dhp.bulktag.criteria.Selection;
|
||||
import eu.dnetlib.dhp.bulktag.criteria.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);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,74 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.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.bulktag.criteria.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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,39 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.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);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.community;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.HashMap;
|
||||
|
||||
public class ProtoMap extends HashMap<String, String> implements Serializable {
|
||||
|
||||
public ProtoMap() {
|
||||
super();
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,61 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.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.bulktag.criteria.VerbResolver;
|
||||
|
||||
/** Created by miriam on 01/08/2018. */
|
||||
public class Provider implements Serializable {
|
||||
private static final Log log = LogFactory.getLog(Provider.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;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,65 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.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);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,247 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.community;
|
||||
|
||||
import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
|
||||
|
||||
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_PROVENANCE_ACTIONS);
|
||||
pa.setSchemename(DNET_PROVENANCE_ACTIONS);
|
||||
return pa;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,51 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.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.bulktag.criteria.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);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,17 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.community;
|
||||
|
||||
public class TaggingConstants {
|
||||
|
||||
public static final String BULKTAG_DATA_INFO_TYPE = "bulktagging";
|
||||
|
||||
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 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";
|
||||
}
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.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());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
public interface Selection {
|
||||
|
||||
boolean apply(String value);
|
||||
}
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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();
|
||||
}
|
||||
|
|
@ -0,0 +1,56 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
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.bulktag.criteria") // Scan com.xyz and subpackages
|
||||
.scan()) { // Perform the scan and return a ScanResult
|
||||
|
||||
ClassInfoList routeClassInfoList = scanResult
|
||||
.getClassesWithAnnotation(
|
||||
"eu.dnetlib.dhp.bulktag.criteria.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);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag.criteria;
|
||||
|
||||
public class VerbResolverFactory {
|
||||
|
||||
public static VerbResolver newInstance() {
|
||||
|
||||
return new VerbResolver();
|
||||
}
|
||||
}
|
||||
|
|
@ -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;
|
||||
}
|
||||
}
|
||||
|
|
@ -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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,122 @@
|
|||
|
||||
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.common.ModelConstants;
|
||||
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 = '"
|
||||
+ ModelConstants.IS_PROVIDED_BY
|
||||
+ "' "
|
||||
+ " 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);
|
||||
}
|
||||
}
|
||||
|
|
@ -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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,135 @@
|
|||
|
||||
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 -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
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());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
|
||||
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;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,123 @@
|
|||
|
||||
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 -> {
|
||||
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 DISTINCT 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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,95 @@
|
|||
|
||||
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 -> {
|
||||
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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,27 @@
|
|||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,200 @@
|
|||
|
||||
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 -> {
|
||||
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.isNotEmpty(autoritative_author.getSurname())) {
|
||||
if (StringUtils.isNotEmpty(author.getSurname())) {
|
||||
if (autoritative_author
|
||||
.getSurname()
|
||||
.trim()
|
||||
.equalsIgnoreCase(author.getSurname().trim())) {
|
||||
|
||||
// have the same surname. Check the name
|
||||
if (StringUtils.isNotEmpty(autoritative_author.getName())) {
|
||||
if (StringUtils.isNotEmpty(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
|
||||
else {
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,129 @@
|
|||
|
||||
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.common.ModelConstants;
|
||||
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 -> {
|
||||
removeOutputDir(spark, potentialUpdatePath);
|
||||
removeOutputDir(spark, alreadyLinkedPath);
|
||||
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 = '"
|
||||
+ ModelConstants.IS_PRODUCED_BY
|
||||
+ "'";
|
||||
|
||||
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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,148 @@
|
|||
|
||||
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.common.ModelConstants;
|
||||
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,
|
||||
ModelConstants.IS_PRODUCED_BY,
|
||||
ModelConstants.RESULT_PROJECT,
|
||||
ModelConstants.OUTCOME,
|
||||
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,
|
||||
ModelConstants.PRODUCES,
|
||||
ModelConstants.RESULT_PROJECT,
|
||||
ModelConstants.OUTCOME,
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
|
||||
PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
|
||||
});
|
||||
return new_relations.iterator();
|
||||
};
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
|
||||
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);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,129 @@
|
|||
|
||||
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.common.ModelConstants;
|
||||
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 -> {
|
||||
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 = '"
|
||||
+ ModelConstants.HAS_AUTHOR_INSTITUTION
|
||||
+ "') result_organization "
|
||||
+ "LEFT JOIN (SELECT source, collect_set(target) org_set "
|
||||
+ " FROM relation "
|
||||
+ " WHERE datainfo.deletedbyinference = false "
|
||||
+ " AND relClass = '"
|
||||
+ ModelConstants.MERGES
|
||||
+ "' "
|
||||
+ " 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;
|
||||
};
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,35 @@
|
|||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,136 @@
|
|||
|
||||
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 -> {
|
||||
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;
|
||||
};
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,167 @@
|
|||
|
||||
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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,101 @@
|
|||
|
||||
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);
|
||||
}
|
||||
|
||||
}
|
||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue