Merge remote-tracking branch 'origin/master' into doiboost
This commit is contained in:
commit
8c95b50f26
|
@ -13,6 +13,7 @@ public class ModelConstants {
|
|||
public static final String DNET_DATA_CITE_DATE = "dnet:dataCite_date";
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||||
public static final String DNET_DATA_CITE_RESOURCE = "dnet:dataCite_resource";
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public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
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||||
public static final String DNET_COUNTRY_TYPE = "dnet:countries";
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||||
|
||||
public static final String SYSIMPORT_CROSSWALK_REPOSITORY = "sysimport:crosswalk:repository";
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||||
public static final String SYSIMPORT_CROSSWALK_ENTITYREGISTRY = "sysimport:crosswalk:entityregistry";
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||||
|
@ -49,6 +50,13 @@ public class ModelConstants {
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public static final String HAS_PARTICIPANT = "hasParticipant";
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public static final String IS_PARTICIPANT = "isParticipant";
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||||
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||||
public static final String RESULT_ORGANIZATION = "resultOrganization";
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||||
public static final String AFFILIATION = "affiliation";
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||||
public static final String IS_AUTHOR_INSTITUTION_OF = "isAuthorInstitutionOf";
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||||
public static final String HAS_AUTHOR_INSTITUTION = "hasAuthorInstitution";
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||||
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||||
public static final String MERGES = "merges";
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||||
public static final String UNKNOWN = "UNKNOWN";
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public static final String NOT_AVAILABLE = "not available";
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||||
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|
|
|
@ -1,10 +1,15 @@
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|||
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package eu.dnetlib.dhp.schema.common;
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import static com.google.common.base.Preconditions.checkArgument;
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import java.util.Map;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.function.Function;
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||||
import org.apache.commons.lang3.StringUtils;
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import com.google.common.collect.Maps;
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import eu.dnetlib.dhp.schema.oaf.*;
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|
@ -379,6 +384,21 @@ public class ModelSupport {
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entityMapping.get(EntityType.valueOf(targetType)).name());
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}
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public static <T extends Oaf> String tableIdentifier(String dbName, String tableName) {
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checkArgument(StringUtils.isNotBlank(dbName), "DB name cannot be empty");
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checkArgument(StringUtils.isNotBlank(tableName), "table name cannot be empty");
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||||
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return String.format("%s.%s", dbName, tableName);
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}
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public static <T extends Oaf> String tableIdentifier(String dbName, Class<T> clazz) {
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checkArgument(Objects.nonNull(clazz), "clazz is needed to derive the table name, thus cannot be null");
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return tableIdentifier(dbName, clazz.getSimpleName().toLowerCase());
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||||
}
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public static <T extends Oaf> Function<T, String> idFn() {
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return x -> {
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if (isSubClass(x, Relation.class)) {
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|
|
|
@ -523,7 +523,9 @@ public class ProtoConverter implements Serializable {
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}
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private static Context mapContext(ResultProtos.Result.Context context) {
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|
||||
if (context == null || StringUtils.isBlank(context.getId())) {
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return null;
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||||
}
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final Context entity = new Context();
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entity.setId(context.getId());
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entity
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|
@ -537,6 +539,10 @@ public class ProtoConverter implements Serializable {
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}
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|
||||
public static KeyValue mapKV(FieldTypeProtos.KeyValue kv) {
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||||
if (kv == null || StringUtils.isBlank(kv.getKey()) & StringUtils.isBlank(kv.getValue())) {
|
||||
return null;
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||||
}
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||||
|
||||
final KeyValue keyValue = new KeyValue();
|
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keyValue.setKey(kv.getKey());
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||||
keyValue.setValue(kv.getValue());
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||||
|
@ -575,6 +581,10 @@ public class ProtoConverter implements Serializable {
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|||
}
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||||
|
||||
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());
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||||
structuredProperty.setQualifier(mapQualifier(sp.getQualifier()));
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||||
|
@ -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());
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||||
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()));
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||||
return entity;
|
||||
}
|
||||
|
||||
public static Journal mapJournal(FieldTypeProtos.Journal j) {
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||||
final Journal journal = new Journal();
|
||||
journal.setConferencedate(j.getConferencedate());
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||||
|
|
|
@ -18,6 +18,7 @@ import org.slf4j.LoggerFactory;
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|||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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||||
import eu.dnetlib.dhp.common.HdfsSupport;
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||||
import eu.dnetlib.dhp.schema.oaf.Relation;
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||||
|
||||
public class PrepareMergedRelationJob {
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||||
|
@ -56,6 +57,7 @@ public class PrepareMergedRelationJob {
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conf,
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||||
isSparkSessionManaged,
|
||||
spark -> {
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||||
removeOutputDir(spark, outputPath);
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selectMergesRelations(
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||||
spark,
|
||||
inputPath,
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||||
|
@ -84,4 +86,9 @@ public class PrepareMergedRelationJob {
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|||
(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
|
||||
Encoders.bean(Relation.class));
|
||||
}
|
||||
|
||||
private static void removeOutputDir(SparkSession spark, String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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||||
}
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||||
|
||||
}
|
||||
|
|
|
@ -18,6 +18,7 @@ import org.slf4j.LoggerFactory;
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|||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
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||||
import eu.dnetlib.dhp.schema.oaf.Relation;
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||||
import scala.Tuple2;
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||||
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||||
|
@ -62,6 +63,7 @@ public class SparkRemoveBlacklistedRelationJob {
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|||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
removeOutputDir(spark, outputPath);
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||||
removeBlacklistedRelations(
|
||||
spark,
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||||
blacklistPath,
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||||
|
@ -69,7 +71,6 @@ public class SparkRemoveBlacklistedRelationJob {
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|||
outputPath,
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||||
mergesPath);
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||||
});
|
||||
|
||||
}
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||||
|
||||
private static void removeBlacklistedRelations(SparkSession spark, String blacklistPath, String inputPath,
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||||
|
@ -78,8 +79,6 @@ public class SparkRemoveBlacklistedRelationJob {
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|||
Dataset<Relation> inputRelation = readRelations(spark, inputPath);
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||||
Dataset<Relation> mergesRelation = readRelations(spark, mergesPath);
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||||
|
||||
log.info("InputRelationCount: {}", inputRelation.count());
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||||
|
||||
Dataset<Relation> dedupSource = blackListed
|
||||
.joinWith(
|
||||
mergesRelation, blackListed.col("source").equalTo(mergesRelation.col("target")),
|
||||
|
@ -102,11 +101,6 @@ public class SparkRemoveBlacklistedRelationJob {
|
|||
return c._1();
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||||
}, Encoders.bean(Relation.class));
|
||||
|
||||
dedupBL
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.json(blacklistPath + "/deduped");
|
||||
|
||||
inputRelation
|
||||
.joinWith(
|
||||
dedupBL, (inputRelation
|
||||
|
@ -144,4 +138,8 @@ public class SparkRemoveBlacklistedRelationJob {
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|||
Encoders.bean(Relation.class));
|
||||
}
|
||||
|
||||
private static void removeOutputDir(SparkSession spark, String path) {
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||||
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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||||
}
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||||
|
||||
}
|
||||
|
|
|
@ -22,6 +22,25 @@
|
|||
</property>
|
||||
</parameters>
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||||
|
||||
<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>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="reset_outputpath"/>
|
||||
|
||||
<kill name="Kill">
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||||
|
@ -49,8 +68,6 @@
|
|||
|
||||
<action name="copy_publication">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/publication</arg>
|
||||
<arg>${nameNode}/${outputPath}/publication</arg>
|
||||
</distcp>
|
||||
|
@ -60,8 +77,6 @@
|
|||
|
||||
<action name="copy_dataset">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/dataset</arg>
|
||||
<arg>${nameNode}/${outputPath}/dataset</arg>
|
||||
</distcp>
|
||||
|
@ -71,8 +86,6 @@
|
|||
|
||||
<action name="copy_orp">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/otherresearchproduct</arg>
|
||||
<arg>${nameNode}/${outputPath}/otherresearchproduct</arg>
|
||||
</distcp>
|
||||
|
@ -82,8 +95,6 @@
|
|||
|
||||
<action name="copy_software">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/software</arg>
|
||||
<arg>${nameNode}/${outputPath}/software</arg>
|
||||
</distcp>
|
||||
|
@ -93,8 +104,6 @@
|
|||
|
||||
<action name="copy_organization">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/organization</arg>
|
||||
<arg>${nameNode}/${outputPath}/organization</arg>
|
||||
</distcp>
|
||||
|
@ -104,8 +113,6 @@
|
|||
|
||||
<action name="copy_project">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/project</arg>
|
||||
<arg>${nameNode}/${outputPath}/project</arg>
|
||||
</distcp>
|
||||
|
@ -115,8 +122,6 @@
|
|||
|
||||
<action name="copy_datasource">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/datasource</arg>
|
||||
<arg>${nameNode}/${outputPath}/datasource</arg>
|
||||
</distcp>
|
||||
|
@ -128,8 +133,6 @@
|
|||
|
||||
<action name="read_blacklist">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.dhp.blacklist.ReadBlacklistFromDB</main-class>
|
||||
<arg>--hdfsPath</arg><arg>${workingDir}/blacklist</arg>
|
||||
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
|
||||
|
@ -156,6 +159,7 @@
|
|||
--conf spark.sql.queryExecutionListeners=${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>${workingDir}/mergesRelation</arg>
|
||||
|
@ -180,6 +184,7 @@
|
|||
--conf spark.sql.queryExecutionListeners=${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>
|
||||
|
|
|
@ -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());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -129,6 +129,9 @@ public class DedupUtility {
|
|||
.max(Comparator.comparing(Tuple2::_1));
|
||||
if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) {
|
||||
Author r = simAuhtor.get()._2();
|
||||
if (r.getPid() == null) {
|
||||
r.setPid(new ArrayList<>());
|
||||
}
|
||||
r.getPid().add(a._1());
|
||||
}
|
||||
});
|
||||
|
|
|
@ -15,6 +15,8 @@ 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 {
|
||||
|
@ -24,10 +26,6 @@ public class PropagationConstant {
|
|||
|
||||
public static final String TRUE = "true";
|
||||
|
||||
public static final String DNET_COUNTRY_SCHEMA = "dnet:countries";
|
||||
public static final String DNET_SCHEMA_NAME = "dnet:provenanceActions";
|
||||
public static final String DNET_SCHEMA_ID = "dnet:provenanceActions";
|
||||
|
||||
public static final String PROPAGATION_COUNTRY_INSTREPO_CLASS_ID = "country:instrepos";
|
||||
public static final String PROPAGATION_COUNTRY_INSTREPO_CLASS_NAME = "Propagation of country to result collected from datasources of type institutional repositories";
|
||||
|
||||
|
@ -46,22 +44,6 @@ public class PropagationConstant {
|
|||
public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID = "authorpid:result";
|
||||
public static final String PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME = "Propagation of authors pid to result through semantic relations";
|
||||
|
||||
public static final String RELATION_DATASOURCE_ORGANIZATION_REL_CLASS = "isProvidedBy";
|
||||
|
||||
public static final String RELATION_RESULTORGANIZATION_REL_TYPE = "resultOrganization";
|
||||
public static final String RELATION_RESULTORGANIZATION_SUBREL_TYPE = "affiliation";
|
||||
public static final String RELATION_ORGANIZATION_RESULT_REL_CLASS = "isAuthorInstitutionOf";
|
||||
public static final String RELATION_RESULT_ORGANIZATION_REL_CLASS = "hasAuthorInstitution";
|
||||
|
||||
public static final String RELATION_RESULTRESULT_REL_TYPE = "resultResult";
|
||||
|
||||
public static final String RELATION_RESULTPROJECT_REL_TYPE = "resultProject";
|
||||
public static final String RELATION_RESULTPROJECT_SUBREL_TYPE = "outcome";
|
||||
public static final String RELATION_RESULT_PROJECT_REL_CLASS = "isProducedBy";
|
||||
public static final String RELATION_PROJECT_RESULT_REL_CLASS = "produces";
|
||||
|
||||
public static final String RELATION_REPRESENTATIVERESULT_RESULT_CLASS = "merges";
|
||||
|
||||
public static final String PROPAGATION_AUTHOR_PID = "ORCID";
|
||||
|
||||
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
@ -76,8 +58,8 @@ public class PropagationConstant {
|
|||
Country nc = new Country();
|
||||
nc.setClassid(classid);
|
||||
nc.setClassname(classname);
|
||||
nc.setSchemename(DNET_COUNTRY_SCHEMA);
|
||||
nc.setSchemeid(DNET_COUNTRY_SCHEMA);
|
||||
nc.setSchemename(ModelConstants.DNET_COUNTRY_TYPE);
|
||||
nc.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE);
|
||||
nc
|
||||
.setDataInfo(
|
||||
getDataInfo(
|
||||
|
@ -102,8 +84,8 @@ public class PropagationConstant {
|
|||
Qualifier pa = new Qualifier();
|
||||
pa.setClassid(inference_class_id);
|
||||
pa.setClassname(inference_class_name);
|
||||
pa.setSchemeid(DNET_SCHEMA_ID);
|
||||
pa.setSchemename(DNET_SCHEMA_NAME);
|
||||
pa.setSchemeid(ModelConstants.DNET_PID_TYPES);
|
||||
pa.setSchemename(ModelConstants.DNET_PID_TYPES);
|
||||
return pa;
|
||||
}
|
||||
|
||||
|
|
|
@ -1,6 +1,7 @@
|
|||
|
||||
package eu.dnetlib.dhp.bulktag;
|
||||
|
||||
import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.util.Optional;
|
||||
|
@ -84,6 +85,7 @@ public class SparkBulkTagJob {
|
|||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc);
|
||||
});
|
||||
}
|
||||
|
|
|
@ -21,6 +21,7 @@ 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.*;
|
||||
|
||||
/**
|
||||
|
@ -100,7 +101,7 @@ public class PrepareDatasourceCountryAssociation {
|
|||
+ "JOIN ( SELECT source, target "
|
||||
+ " FROM relation "
|
||||
+ " WHERE relclass = '"
|
||||
+ RELATION_DATASOURCE_ORGANIZATION_REL_CLASS
|
||||
+ ModelConstants.IS_PROVIDED_BY
|
||||
+ "' "
|
||||
+ " AND datainfo.deletedbyinference = false ) rel "
|
||||
+ "ON d.id = rel.source "
|
||||
|
|
|
@ -69,13 +69,16 @@ public class SparkCountryPropagationJob {
|
|||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> execPropagation(
|
||||
spark,
|
||||
sourcePath,
|
||||
preparedInfoPath,
|
||||
outputPath,
|
||||
resultClazz,
|
||||
saveGraph));
|
||||
spark -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
execPropagation(
|
||||
spark,
|
||||
sourcePath,
|
||||
preparedInfoPath,
|
||||
outputPath,
|
||||
resultClazz,
|
||||
saveGraph);
|
||||
});
|
||||
}
|
||||
|
||||
private static <R extends Result> void execPropagation(
|
||||
|
|
|
@ -74,9 +74,7 @@ public class PrepareResultOrcidAssociationStep1 {
|
|||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
if (isTest(parser)) {
|
||||
removeOutputDir(spark, outputPath);
|
||||
}
|
||||
removeOutputDir(spark, outputPath);
|
||||
prepareInfo(
|
||||
spark, inputRelationPath, inputResultPath, outputResultPath, resultClazz, allowedsemrel);
|
||||
});
|
||||
|
@ -97,22 +95,22 @@ public class PrepareResultOrcidAssociationStep1 {
|
|||
Dataset<R> result = readPath(spark, inputResultPath, resultClazz);
|
||||
result.createOrReplaceTempView("result");
|
||||
|
||||
String query = " select target resultId, author authorList"
|
||||
+ " from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author "
|
||||
+ " from ( "
|
||||
+ " select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid "
|
||||
+ " from result "
|
||||
+ " lateral view explode (author) a as MyT "
|
||||
+ " lateral view explode (MyT.pid) p as MyP "
|
||||
+ " where MyP.qualifier.classid = 'ORCID') tmp "
|
||||
+ " group by id) r_t "
|
||||
+ " join ("
|
||||
+ " select source, target "
|
||||
+ " from relation "
|
||||
+ " where datainfo.deletedbyinference = false "
|
||||
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";
|
||||
+ " ) rel_rel "
|
||||
+ " ON source = id";
|
||||
spark
|
||||
.sql(query)
|
||||
.as(Encoders.bean(ResultOrcidList.class))
|
||||
|
|
|
@ -50,9 +50,7 @@ public class PrepareResultOrcidAssociationStep2 {
|
|||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
if (isTest(parser)) {
|
||||
removeOutputDir(spark, outputPath);
|
||||
}
|
||||
removeOutputDir(spark, outputPath);
|
||||
mergeInfo(spark, inputPath, outputPath);
|
||||
});
|
||||
}
|
||||
|
|
|
@ -70,11 +70,10 @@ public class SparkOrcidToResultFromSemRelJob {
|
|||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
if (isTest(parser)) {
|
||||
removeOutputDir(spark, outputPath);
|
||||
}
|
||||
if (saveGraph)
|
||||
removeOutputDir(spark, outputPath);
|
||||
if (saveGraph) {
|
||||
execPropagation(spark, possibleUpdates, inputPath, outputPath, resultClazz);
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
|
@ -132,16 +131,16 @@ public class SparkOrcidToResultFromSemRelJob {
|
|||
private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, Author author) {
|
||||
boolean toaddpid = false;
|
||||
|
||||
if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
|
||||
if (StringUtils.isNoneEmpty(author.getSurname())) {
|
||||
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.isNoneEmpty(autoritative_author.getName())) {
|
||||
if (StringUtils.isNoneEmpty(author.getName())) {
|
||||
if (StringUtils.isNotEmpty(autoritative_author.getName())) {
|
||||
if (StringUtils.isNotEmpty(author.getName())) {
|
||||
if (autoritative_author
|
||||
.getName()
|
||||
.trim()
|
||||
|
@ -150,12 +149,14 @@ public class SparkOrcidToResultFromSemRelJob {
|
|||
}
|
||||
// they could be differently written (i.e. only the initials of the name
|
||||
// in one of the two
|
||||
if (autoritative_author
|
||||
.getName()
|
||||
.trim()
|
||||
.substring(0, 0)
|
||||
.equalsIgnoreCase(author.getName().trim().substring(0, 0))) {
|
||||
toaddpid = true;
|
||||
else {
|
||||
if (autoritative_author
|
||||
.getName()
|
||||
.trim()
|
||||
.substring(0, 0)
|
||||
.equalsIgnoreCase(author.getName().trim().substring(0, 0))) {
|
||||
toaddpid = true;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
@ -21,6 +21,7 @@ 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 {
|
||||
|
@ -60,6 +61,8 @@ public class PrepareProjectResultsAssociation {
|
|||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
removeOutputDir(spark, potentialUpdatePath);
|
||||
removeOutputDir(spark, alreadyLinkedPath);
|
||||
prepareResultProjProjectResults(
|
||||
spark,
|
||||
inputPath,
|
||||
|
@ -83,7 +86,7 @@ public class PrepareProjectResultsAssociation {
|
|||
+ " FROM relation "
|
||||
+ " WHERE datainfo.deletedbyinference = false "
|
||||
+ " AND relClass = '"
|
||||
+ RELATION_RESULT_PROJECT_REL_CLASS
|
||||
+ ModelConstants.IS_PRODUCED_BY
|
||||
+ "'";
|
||||
|
||||
Dataset<Row> resproj_relation = spark.sql(resproj_relation_query);
|
||||
|
|
|
@ -20,6 +20,7 @@ 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;
|
||||
|
||||
|
@ -122,9 +123,9 @@ public class SparkResultToProjectThroughSemRelJob {
|
|||
getRelation(
|
||||
resId,
|
||||
projectId,
|
||||
RELATION_RESULT_PROJECT_REL_CLASS,
|
||||
RELATION_RESULTPROJECT_REL_TYPE,
|
||||
RELATION_RESULTPROJECT_SUBREL_TYPE,
|
||||
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));
|
||||
|
@ -133,9 +134,9 @@ public class SparkResultToProjectThroughSemRelJob {
|
|||
getRelation(
|
||||
projectId,
|
||||
resId,
|
||||
RELATION_PROJECT_RESULT_REL_CLASS,
|
||||
RELATION_RESULTPROJECT_REL_TYPE,
|
||||
RELATION_RESULTPROJECT_SUBREL_TYPE,
|
||||
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));
|
||||
|
|
|
@ -17,6 +17,7 @@ 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 {
|
||||
|
@ -55,9 +56,7 @@ public class PrepareResultCommunitySet {
|
|||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
if (isTest(parser)) {
|
||||
removeOutputDir(spark, outputPath);
|
||||
}
|
||||
removeOutputDir(spark, outputPath);
|
||||
prepareInfo(spark, inputPath, outputPath, organizationMap);
|
||||
});
|
||||
}
|
||||
|
@ -76,13 +75,13 @@ public class PrepareResultCommunitySet {
|
|||
+ " FROM relation "
|
||||
+ " WHERE datainfo.deletedbyinference = false "
|
||||
+ " AND relClass = '"
|
||||
+ RELATION_RESULT_ORGANIZATION_REL_CLASS
|
||||
+ ModelConstants.HAS_AUTHOR_INSTITUTION
|
||||
+ "') result_organization "
|
||||
+ "LEFT JOIN (SELECT source, collect_set(target) org_set "
|
||||
+ " FROM relation "
|
||||
+ " WHERE datainfo.deletedbyinference = false "
|
||||
+ " AND relClass = '"
|
||||
+ RELATION_REPRESENTATIVERESULT_RESULT_CLASS
|
||||
+ ModelConstants.MERGES
|
||||
+ "' "
|
||||
+ " GROUP BY source) organization_organization "
|
||||
+ "ON result_organization.target = organization_organization.source ";
|
||||
|
|
|
@ -68,11 +68,10 @@ public class SparkResultToCommunityFromOrganizationJob {
|
|||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
if (isTest(parser)) {
|
||||
removeOutputDir(spark, outputPath);
|
||||
}
|
||||
if (saveGraph)
|
||||
removeOutputDir(spark, outputPath);
|
||||
if (saveGraph) {
|
||||
execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath);
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
|
|
|
@ -53,9 +53,7 @@ public class PrepareResultCommunitySetStep2 {
|
|||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
if (isTest(parser)) {
|
||||
removeOutputDir(spark, outputPath);
|
||||
}
|
||||
removeOutputDir(spark, outputPath);
|
||||
mergeInfo(spark, inputPath, outputPath);
|
||||
});
|
||||
}
|
||||
|
|
|
@ -17,6 +17,7 @@ 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.Datasource;
|
||||
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
|
@ -58,30 +59,15 @@ public class PrepareResultInstRepoAssociation {
|
|||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
readNeededResources(spark, inputPath);
|
||||
|
||||
removeOutputDir(spark, datasourceOrganizationPath);
|
||||
prepareDatasourceOrganization(spark, datasourceOrganizationPath);
|
||||
|
||||
removeOutputDir(spark, alreadyLinkedPath);
|
||||
prepareAlreadyLinkedAssociation(spark, alreadyLinkedPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void prepareAlreadyLinkedAssociation(
|
||||
SparkSession spark, String alreadyLinkedPath) {
|
||||
String query = "Select source resultId, collect_set(target) organizationSet "
|
||||
+ "from relation "
|
||||
+ "where datainfo.deletedbyinference = false "
|
||||
+ "and relClass = '"
|
||||
+ RELATION_RESULT_ORGANIZATION_REL_CLASS
|
||||
+ "' "
|
||||
+ "group by source";
|
||||
|
||||
spark
|
||||
.sql(query)
|
||||
.as(Encoders.bean(ResultOrganizationSet.class))
|
||||
// TODO retry to stick with datasets
|
||||
.toJavaRDD()
|
||||
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
|
||||
.saveAsTextFile(alreadyLinkedPath, GzipCodec.class);
|
||||
}
|
||||
|
||||
private static void readNeededResources(SparkSession spark, String inputPath) {
|
||||
Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class);
|
||||
datasource.createOrReplaceTempView("datasource");
|
||||
|
@ -106,7 +92,7 @@ public class PrepareResultInstRepoAssociation {
|
|||
+ "JOIN ( SELECT source, target "
|
||||
+ "FROM relation "
|
||||
+ "WHERE relclass = '"
|
||||
+ RELATION_DATASOURCE_ORGANIZATION_REL_CLASS
|
||||
+ ModelConstants.IS_PROVIDED_BY
|
||||
+ "' "
|
||||
+ "AND datainfo.deletedbyinference = false ) rel "
|
||||
+ "ON d.id = rel.source ";
|
||||
|
@ -119,4 +105,24 @@ public class PrepareResultInstRepoAssociation {
|
|||
.option("compression", "gzip")
|
||||
.json(datasourceOrganizationPath);
|
||||
}
|
||||
|
||||
private static void prepareAlreadyLinkedAssociation(
|
||||
SparkSession spark, String alreadyLinkedPath) {
|
||||
String query = "Select source resultId, collect_set(target) organizationSet "
|
||||
+ "from relation "
|
||||
+ "where datainfo.deletedbyinference = false "
|
||||
+ "and relClass = '"
|
||||
+ ModelConstants.HAS_AUTHOR_INSTITUTION
|
||||
+ "' "
|
||||
+ "group by source";
|
||||
|
||||
spark
|
||||
.sql(query)
|
||||
.as(Encoders.bean(ResultOrganizationSet.class))
|
||||
// TODO retry to stick with datasets
|
||||
.toJavaRDD()
|
||||
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
|
||||
.saveAsTextFile(alreadyLinkedPath, GzipCodec.class);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -19,6 +19,7 @@ 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.*;
|
||||
import scala.Tuple2;
|
||||
|
||||
|
@ -83,10 +84,8 @@ public class SparkResultToOrganizationFromIstRepoJob {
|
|||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
if (isTest(parser)) {
|
||||
removeOutputDir(spark, outputPath);
|
||||
}
|
||||
if (saveGraph)
|
||||
// removeOutputDir(spark, outputPath);
|
||||
if (saveGraph) {
|
||||
execPropagation(
|
||||
spark,
|
||||
datasourceorganization,
|
||||
|
@ -94,6 +93,7 @@ public class SparkResultToOrganizationFromIstRepoJob {
|
|||
inputPath,
|
||||
outputPath,
|
||||
resultClazz);
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
|
@ -151,9 +151,9 @@ public class SparkResultToOrganizationFromIstRepoJob {
|
|||
getRelation(
|
||||
orgId,
|
||||
resultId,
|
||||
RELATION_ORGANIZATION_RESULT_REL_CLASS,
|
||||
RELATION_RESULTORGANIZATION_REL_TYPE,
|
||||
RELATION_RESULTORGANIZATION_SUBREL_TYPE,
|
||||
ModelConstants.IS_AUTHOR_INSTITUTION_OF,
|
||||
ModelConstants.RESULT_ORGANIZATION,
|
||||
ModelConstants.AFFILIATION,
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID,
|
||||
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
|
||||
|
@ -162,9 +162,9 @@ public class SparkResultToOrganizationFromIstRepoJob {
|
|||
getRelation(
|
||||
resultId,
|
||||
orgId,
|
||||
RELATION_RESULT_ORGANIZATION_REL_CLASS,
|
||||
RELATION_RESULTORGANIZATION_REL_TYPE,
|
||||
RELATION_RESULTORGANIZATION_SUBREL_TYPE,
|
||||
ModelConstants.HAS_AUTHOR_INSTITUTION,
|
||||
ModelConstants.RESULT_ORGANIZATION,
|
||||
ModelConstants.AFFILIATION,
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID,
|
||||
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
|
||||
|
|
|
@ -18,6 +18,17 @@
|
|||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="reset_outputpath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
|
@ -42,8 +53,6 @@
|
|||
|
||||
<action name="copy_relation">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/relation</arg>
|
||||
<arg>${nameNode}/${outputPath}/relation</arg>
|
||||
</distcp>
|
||||
|
@ -53,8 +62,6 @@
|
|||
|
||||
<action name="copy_organization">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/organization</arg>
|
||||
<arg>${nameNode}/${outputPath}/organization</arg>
|
||||
</distcp>
|
||||
|
@ -64,8 +71,6 @@
|
|||
|
||||
<action name="copy_projects">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/project</arg>
|
||||
<arg>${nameNode}/${outputPath}/project</arg>
|
||||
</distcp>
|
||||
|
@ -75,8 +80,6 @@
|
|||
|
||||
<action name="copy_datasources">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/datasource</arg>
|
||||
<arg>${nameNode}/${outputPath}/datasource</arg>
|
||||
</distcp>
|
||||
|
@ -95,8 +98,6 @@
|
|||
|
||||
<action name="join_bulktag_publication">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>bulkTagging-publication</name>
|
||||
|
@ -124,8 +125,6 @@
|
|||
|
||||
<action name="join_bulktag_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>bulkTagging-dataset</name>
|
||||
|
@ -153,8 +152,6 @@
|
|||
|
||||
<action name="join_bulktag_otherresearchproduct">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>bulkTagging-orp</name>
|
||||
|
@ -182,8 +179,6 @@
|
|||
|
||||
<action name="join_bulktag_software">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>bulkTagging-software</name>
|
||||
|
|
|
@ -19,6 +19,17 @@
|
|||
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="reset_outputpath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
|
@ -43,8 +54,6 @@
|
|||
|
||||
<action name="copy_relation">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/relation</arg>
|
||||
<arg>${nameNode}/${outputPath}/relation</arg>
|
||||
</distcp>
|
||||
|
@ -54,18 +63,15 @@
|
|||
|
||||
<action name="copy_organization">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/organization</arg>
|
||||
<arg>${nameNode}/${outputPath}/organization</arg>
|
||||
</distcp>
|
||||
<ok to="copy_wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_projects">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/project</arg>
|
||||
<arg>${nameNode}/${outputPath}/project</arg>
|
||||
</distcp>
|
||||
|
@ -75,8 +81,6 @@
|
|||
|
||||
<action name="copy_datasources">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/datasource</arg>
|
||||
<arg>${nameNode}/${outputPath}/datasource</arg>
|
||||
</distcp>
|
||||
|
|
|
@ -57,6 +57,7 @@
|
|||
<ok to="copy_wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_projects">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
|
@ -81,7 +82,6 @@
|
|||
|
||||
<join name="copy_wait" to="fork_prepare_assoc_step1"/>
|
||||
|
||||
|
||||
<fork name="fork_prepare_assoc_step1">
|
||||
<path start="join_prepare_publication"/>
|
||||
<path start="join_prepare_dataset"/>
|
||||
|
@ -230,8 +230,8 @@
|
|||
</spark>
|
||||
<ok to="fork-join-exec-propagation"/>
|
||||
<error to="Kill"/>
|
||||
|
||||
</action>
|
||||
|
||||
<fork name="fork-join-exec-propagation">
|
||||
<path start="join_propagate_publication"/>
|
||||
<path start="join_propagate_dataset"/>
|
||||
|
@ -271,6 +271,7 @@
|
|||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="join_propagate_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
@ -302,6 +303,7 @@
|
|||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="join_propagate_otherresearchproduct">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
@ -333,6 +335,7 @@
|
|||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="join_propagate_software">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
|
|
@ -14,6 +14,17 @@
|
|||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="reset_outputpath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
|
@ -42,8 +53,6 @@
|
|||
|
||||
<action name="copy_relation">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/relation</arg>
|
||||
<arg>${nameNode}/${outputPath}/relation</arg>
|
||||
</distcp>
|
||||
|
@ -53,8 +62,6 @@
|
|||
|
||||
<action name="copy_publication">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/publication</arg>
|
||||
<arg>${nameNode}/${outputPath}/publication</arg>
|
||||
</distcp>
|
||||
|
@ -64,8 +71,6 @@
|
|||
|
||||
<action name="copy_dataset">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/dataset</arg>
|
||||
<arg>${nameNode}/${outputPath}/dataset</arg>
|
||||
</distcp>
|
||||
|
@ -75,8 +80,6 @@
|
|||
|
||||
<action name="copy_orp">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/otherresearchproduct</arg>
|
||||
<arg>${nameNode}/${outputPath}/otherresearchproduct</arg>
|
||||
</distcp>
|
||||
|
@ -86,28 +89,24 @@
|
|||
|
||||
<action name="copy_software">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/software</arg>
|
||||
<arg>${nameNode}/${outputPath}/software</arg>
|
||||
</distcp>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_organization">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/organization</arg>
|
||||
<arg>${nameNode}/${outputPath}/organization</arg>
|
||||
</distcp>
|
||||
<ok to="wait"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="copy_projects">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/project</arg>
|
||||
<arg>${nameNode}/${outputPath}/project</arg>
|
||||
</distcp>
|
||||
|
@ -117,8 +116,6 @@
|
|||
|
||||
<action name="copy_datasources">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/datasource</arg>
|
||||
<arg>${nameNode}/${outputPath}/datasource</arg>
|
||||
</distcp>
|
||||
|
|
|
@ -14,6 +14,17 @@
|
|||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="reset_outputpath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
|
@ -38,8 +49,6 @@
|
|||
|
||||
<action name="copy_relation">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/relation</arg>
|
||||
<arg>${nameNode}/${outputPath}/relation</arg>
|
||||
</distcp>
|
||||
|
@ -49,8 +58,6 @@
|
|||
|
||||
<action name="copy_organization">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/organization</arg>
|
||||
<arg>${nameNode}/${outputPath}/organization</arg>
|
||||
</distcp>
|
||||
|
@ -60,8 +67,6 @@
|
|||
|
||||
<action name="copy_projects">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/project</arg>
|
||||
<arg>${nameNode}/${outputPath}/project</arg>
|
||||
</distcp>
|
||||
|
@ -71,8 +76,6 @@
|
|||
|
||||
<action name="copy_datasources">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/datasource</arg>
|
||||
<arg>${nameNode}/${outputPath}/datasource</arg>
|
||||
</distcp>
|
||||
|
@ -101,8 +104,8 @@
|
|||
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--organizationtoresultcommunitymap</arg><arg>${organizationtoresultcommunitymap}</arg>
|
||||
</spark>
|
||||
<ok to="fork-join-exec-propagation"/>
|
||||
|
@ -136,9 +139,9 @@
|
|||
</spark-opts>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
|
@ -165,9 +168,9 @@
|
|||
</spark-opts>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
|
@ -194,9 +197,9 @@
|
|||
</spark-opts>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
|
@ -223,9 +226,9 @@
|
|||
</spark-opts>
|
||||
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
|
|
|
@ -10,6 +10,17 @@
|
|||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="reset_outputpath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
|
@ -38,8 +49,6 @@
|
|||
|
||||
<action name="copy_relation">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/relation</arg>
|
||||
<arg>${nameNode}/${outputPath}/relation</arg>
|
||||
</distcp>
|
||||
|
@ -49,8 +58,6 @@
|
|||
|
||||
<action name="copy_publication">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/publication</arg>
|
||||
<arg>${nameNode}/${outputPath}/publication</arg>
|
||||
</distcp>
|
||||
|
@ -60,8 +67,6 @@
|
|||
|
||||
<action name="copy_dataset">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/dataset</arg>
|
||||
<arg>${nameNode}/${outputPath}/dataset</arg>
|
||||
</distcp>
|
||||
|
@ -71,8 +76,6 @@
|
|||
|
||||
<action name="copy_orp">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/otherresearchproduct</arg>
|
||||
<arg>${nameNode}/${outputPath}/otherresearchproduct</arg>
|
||||
</distcp>
|
||||
|
@ -82,8 +85,6 @@
|
|||
|
||||
<action name="copy_software">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/software</arg>
|
||||
<arg>${nameNode}/${outputPath}/software</arg>
|
||||
</distcp>
|
||||
|
@ -93,8 +94,6 @@
|
|||
|
||||
<action name="copy_organization">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/organization</arg>
|
||||
<arg>${nameNode}/${outputPath}/organization</arg>
|
||||
</distcp>
|
||||
|
@ -104,8 +103,6 @@
|
|||
|
||||
<action name="copy_projects">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/project</arg>
|
||||
<arg>${nameNode}/${outputPath}/project</arg>
|
||||
</distcp>
|
||||
|
@ -115,8 +112,6 @@
|
|||
|
||||
<action name="copy_datasources">
|
||||
<distcp xmlns="uri:oozie:distcp-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<arg>${nameNode}/${sourcePath}/datasource</arg>
|
||||
<arg>${nameNode}/${outputPath}/datasource</arg>
|
||||
</distcp>
|
||||
|
@ -125,6 +120,7 @@
|
|||
</action>
|
||||
|
||||
<join name="wait" to="prepare_result_organization_association"/>
|
||||
|
||||
<action name="prepare_result_organization_association">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
@ -176,12 +172,12 @@
|
|||
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
|
||||
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
|
||||
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -206,12 +202,12 @@
|
|||
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
|
||||
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
|
||||
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -236,12 +232,12 @@
|
|||
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
|
||||
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
|
||||
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
|
@ -266,12 +262,12 @@
|
|||
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}/relation</arg>
|
||||
<arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
|
||||
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
|
||||
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
|
||||
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
</spark>
|
||||
<ok to="wait2"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
@ -0,0 +1,79 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.hive;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelSupport.tableIdentifier;
|
||||
|
||||
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.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.Oaf;
|
||||
|
||||
public class GraphHiveTableImporterJob {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(GraphHiveTableImporterJob.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
GraphHiveTableImporterJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/hive_table_importer_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
String inputPath = parser.get("inputPath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
String hiveDbName = parser.get("hiveDbName");
|
||||
log.info("hiveDbName: {}", hiveDbName);
|
||||
|
||||
final String className = parser.get("className");
|
||||
log.info("className: {}", className);
|
||||
|
||||
Class<? extends Oaf> clazz = (Class<? extends Oaf>) Class.forName(className);
|
||||
|
||||
String hiveMetastoreUris = parser.get("hiveMetastoreUris");
|
||||
log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("hive.metastore.uris", hiveMetastoreUris);
|
||||
|
||||
runWithSparkHiveSession(
|
||||
conf, isSparkSessionManaged, spark -> loadGraphTable(spark, inputPath, hiveDbName, clazz));
|
||||
}
|
||||
|
||||
// protected for testing
|
||||
private static <T extends Oaf> void loadGraphTable(SparkSession spark, String inputPath, String hiveDbName,
|
||||
Class<T> clazz) {
|
||||
|
||||
spark
|
||||
.read()
|
||||
.textFile(inputPath)
|
||||
.map((MapFunction<String, T>) s -> OBJECT_MAPPER.readValue(s, clazz), Encoders.bean(clazz))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.saveAsTable(tableIdentifier(hiveDbName, clazz));
|
||||
}
|
||||
|
||||
}
|
|
@ -127,7 +127,6 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
final List<Oaf> oafs = new ArrayList<>();
|
||||
|
||||
switch (type.toLowerCase()) {
|
||||
case "":
|
||||
case "publication":
|
||||
final Publication p = new Publication();
|
||||
populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
|
@ -138,7 +137,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
case "dataset":
|
||||
final Dataset d = new Dataset();
|
||||
populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
|
||||
d.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE);
|
||||
d.setResulttype(DATASET_DEFAULT_RESULTTYPE);
|
||||
d.setStoragedate(prepareDatasetStorageDate(doc, info));
|
||||
d.setDevice(prepareDatasetDevice(doc, info));
|
||||
d.setSize(prepareDatasetSize(doc, info));
|
||||
|
@ -158,6 +157,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
|
||||
oafs.add(s);
|
||||
break;
|
||||
case "":
|
||||
case "otherresearchproducts":
|
||||
default:
|
||||
final OtherResearchProduct o = new OtherResearchProduct();
|
||||
|
|
|
@ -50,8 +50,7 @@ import eu.dnetlib.dhp.schema.oaf.Result;
|
|||
import eu.dnetlib.dhp.schema.oaf.Software;
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
|
||||
implements Closeable {
|
||||
public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable {
|
||||
|
||||
private static final Log log = LogFactory.getLog(MigrateDbEntitiesApplication.class);
|
||||
|
||||
|
@ -128,9 +127,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
|
|||
}
|
||||
|
||||
public List<Oaf> processDatasource(final ResultSet rs) {
|
||||
|
||||
try {
|
||||
|
||||
final DataInfo info = prepareDataInfo(rs);
|
||||
|
||||
final Datasource ds = new Datasource();
|
||||
|
@ -194,7 +191,6 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
|
|||
|
||||
public List<Oaf> processProject(final ResultSet rs) {
|
||||
try {
|
||||
|
||||
final DataInfo info = prepareDataInfo(rs);
|
||||
|
||||
final Project p = new Project();
|
||||
|
@ -249,9 +245,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
|
|||
}
|
||||
|
||||
public List<Oaf> processOrganization(final ResultSet rs) {
|
||||
|
||||
try {
|
||||
|
||||
final DataInfo info = prepareDataInfo(rs);
|
||||
|
||||
final Organization o = new Organization();
|
||||
|
@ -370,14 +364,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
|
|||
|
||||
final DataInfo info = dataInfo(
|
||||
false, null, false, false,
|
||||
|
||||
qualifier(USER_CLAIM, USER_CLAIM, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), "0.9");
|
||||
|
||||
final List<KeyValue> collectedFrom = listKeyValues(
|
||||
createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE");
|
||||
|
||||
try {
|
||||
|
||||
if (rs.getString(SOURCE_TYPE).equals("context")) {
|
||||
final Result r;
|
||||
|
||||
|
@ -461,9 +453,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
|
|||
final Boolean inferred = rs.getBoolean("inferred");
|
||||
final String trust = rs.getString("trust");
|
||||
return dataInfo(
|
||||
|
||||
deletedbyinference, inferenceprovenance, inferred, false, ENTITYREGISTRY_PROVENANCE_ACTION, trust);
|
||||
|
||||
deletedbyinference,
|
||||
inferenceprovenance,
|
||||
inferred,
|
||||
false,
|
||||
ENTITYREGISTRY_PROVENANCE_ACTION,
|
||||
trust);
|
||||
}
|
||||
|
||||
private Qualifier prepareQualifierSplitting(final String s) {
|
||||
|
@ -535,4 +530,5 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
|
|||
super.close();
|
||||
dbClient.close();
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -1,8 +1,7 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.raw;
|
||||
|
||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
|
||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
|
||||
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*;
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
|
||||
|
||||
import java.util.*;
|
||||
|
@ -10,11 +9,13 @@ import java.util.stream.Collectors;
|
|||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.Element;
|
||||
import org.dom4j.Node;
|
||||
|
||||
import com.google.common.collect.Lists;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
|
||||
public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
||||
|
@ -28,15 +29,26 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
final List<Author> res = new ArrayList<>();
|
||||
int pos = 1;
|
||||
for (final Object o : doc.selectNodes("//dc:creator")) {
|
||||
final Node n = (Node) o;
|
||||
final Element e = (Element) o;
|
||||
final Author author = new Author();
|
||||
author.setFullname(n.getText());
|
||||
author.setFullname(e.getText());
|
||||
author.setRank(pos++);
|
||||
final PacePerson p = new PacePerson(n.getText(), false);
|
||||
final PacePerson p = new PacePerson(e.getText(), false);
|
||||
if (p.isAccurate()) {
|
||||
author.setName(p.getNormalisedFirstName());
|
||||
author.setSurname(p.getNormalisedSurname());
|
||||
}
|
||||
|
||||
final String pid = e.attributeValue("nameIdentifier");
|
||||
final String pidType = e.attributeValue("nameIdentifierScheme");
|
||||
|
||||
author.setPid(new ArrayList<>());
|
||||
if (StringUtils.isNotBlank(pid) && StringUtils.isNotBlank(pidType)) {
|
||||
author
|
||||
.getPid()
|
||||
.add(structuredProperty(pid, qualifier(pidType, pidType, DNET_PID_TYPES, DNET_PID_TYPES), info));
|
||||
}
|
||||
|
||||
res.add(author);
|
||||
}
|
||||
return res;
|
||||
|
|
|
@ -12,6 +12,7 @@ import org.apache.commons.lang3.StringUtils;
|
|||
import org.dom4j.Document;
|
||||
import org.dom4j.Node;
|
||||
|
||||
import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Author;
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
|
@ -44,20 +45,35 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
for (final Object o : doc.selectNodes("//datacite:creator")) {
|
||||
final Node n = (Node) o;
|
||||
final Author author = new Author();
|
||||
author.setFullname(n.valueOf("./datacite:creatorName"));
|
||||
author.setName(n.valueOf("./datacite:givenName"));
|
||||
author.setSurname(n.valueOf("./datacite:familyName"));
|
||||
author.setAffiliation(prepareListFields(doc, "./datacite:affiliation", info));
|
||||
author.setPid(preparePids(doc, info));
|
||||
final String fullname = n.valueOf("./datacite:creatorName");
|
||||
author.setFullname(fullname);
|
||||
|
||||
PacePerson pp = new PacePerson(fullname, false);
|
||||
final String name = n.valueOf("./datacite:givenName");
|
||||
if (StringUtils.isBlank(name) & pp.isAccurate()) {
|
||||
author.setName(pp.getNormalisedFirstName());
|
||||
} else {
|
||||
author.setName(name);
|
||||
}
|
||||
|
||||
final String surname = n.valueOf("./datacite:familyName");
|
||||
if (StringUtils.isBlank(surname) & pp.isAccurate()) {
|
||||
author.setSurname(pp.getNormalisedSurname());
|
||||
} else {
|
||||
author.setSurname(surname);
|
||||
}
|
||||
|
||||
author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info));
|
||||
author.setPid(preparePids(n, info));
|
||||
author.setRank(pos++);
|
||||
res.add(author);
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
private List<StructuredProperty> preparePids(final Document doc, final DataInfo info) {
|
||||
private List<StructuredProperty> preparePids(final Node n, final DataInfo info) {
|
||||
final List<StructuredProperty> res = new ArrayList<>();
|
||||
for (final Object o : doc.selectNodes("./datacite:nameIdentifier")) {
|
||||
for (final Object o : n.selectNodes("./datacite:nameIdentifier")) {
|
||||
res
|
||||
.add(
|
||||
structuredProperty(
|
||||
|
@ -77,8 +93,6 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
final KeyValue hostedby) {
|
||||
|
||||
final Instance instance = new Instance();
|
||||
final Set<String> url = new HashSet<>();
|
||||
instance.setUrl(new ArrayList<>());
|
||||
instance
|
||||
.setInstancetype(
|
||||
prepareQualifier(
|
||||
|
@ -97,6 +111,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
.setProcessingchargecurrency(
|
||||
field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
|
||||
|
||||
final Set<String> url = new HashSet<>();
|
||||
for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
|
||||
url.add(((Node) o).getText().trim());
|
||||
}
|
||||
|
@ -109,7 +124,10 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
for (final Object o : doc.selectNodes("//datacite:identifier[@identifierType='DOI']")) {
|
||||
url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim());
|
||||
}
|
||||
instance.getUrl().addAll(url);
|
||||
if (!url.isEmpty()) {
|
||||
instance.setUrl(new ArrayList<>());
|
||||
instance.getUrl().addAll(url);
|
||||
}
|
||||
return Arrays.asList(instance);
|
||||
}
|
||||
|
||||
|
|
|
@ -1,7 +1,6 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.raw.common;
|
||||
|
||||
import java.nio.charset.Charset;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.text.Normalizer;
|
||||
import java.util.HashSet;
|
||||
|
|
|
@ -0,0 +1,2 @@
|
|||
DROP DATABASE IF EXISTS ${hiveDbName} CASCADE;
|
||||
CREATE DATABASE ${hiveDbName};
|
|
@ -72,18 +72,45 @@
|
|||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="MapGraphAsHiveDB"/>
|
||||
<start to="reset_DB"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="MapGraphAsHiveDB">
|
||||
<action name="reset_DB">
|
||||
<hive2 xmlns="uri:oozie:hive2-action:0.1">
|
||||
<configuration>
|
||||
<property>
|
||||
<name>hive.metastore.uris</name>
|
||||
<value>${hiveMetastoreUris}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<jdbc-url>${hiveJdbcUrl}/${hiveDbName}</jdbc-url>
|
||||
<script>lib/scripts/reset_db.sql</script>
|
||||
<param>hiveDbName=${hiveDbName}</param>
|
||||
</hive2>
|
||||
<ok to="fork_import"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="fork_import">
|
||||
<path start="import_publication"/>
|
||||
<path start="import_dataset"/>
|
||||
<path start="import_orp"/>
|
||||
<path start="import_software"/>
|
||||
<path start="import_datasource"/>
|
||||
<path start="import_organization"/>
|
||||
<path start="import_project"/>
|
||||
<path start="import_relation"/>
|
||||
</fork>
|
||||
|
||||
<action name="import_publication">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>MapGraphAsHiveDB</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveImporterJob</class>
|
||||
<name>Import table publication</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
|
@ -95,18 +122,201 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${inputPath}</arg>
|
||||
<arg>--inputPath</arg><arg>${inputPath}/publication</arg>
|
||||
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
|
||||
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
</spark>
|
||||
<ok to="PostProcessing"/>
|
||||
<ok to="join_import"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="import_dataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Import table dataset</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
|
||||
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
|
||||
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
</spark>
|
||||
<ok to="join_import"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="import_orp">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Import table otherresearchproduct</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
|
||||
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
|
||||
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
</spark>
|
||||
<ok to="join_import"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="import_software">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Import table software</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${inputPath}/software</arg>
|
||||
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
|
||||
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
</spark>
|
||||
<ok to="join_import"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="import_datasource">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Import table datasource</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${inputPath}/datasource</arg>
|
||||
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
|
||||
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
</spark>
|
||||
<ok to="join_import"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="import_organization">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Import table organization</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${inputPath}/organization</arg>
|
||||
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
|
||||
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
</spark>
|
||||
<ok to="join_import"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="import_project">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Import table project</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${inputPath}/project</arg>
|
||||
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
|
||||
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
</spark>
|
||||
<ok to="join_import"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="import_relation">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Import table project</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${inputPath}/relation</arg>
|
||||
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
|
||||
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
|
||||
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
|
||||
</spark>
|
||||
<ok to="join_import"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<join name="join_import" to="PostProcessing"/>
|
||||
|
||||
<action name="PostProcessing">
|
||||
<hive2 xmlns="uri:oozie:hive2-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>hive.metastore.uris</name>
|
||||
|
@ -122,4 +332,5 @@
|
|||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
|
||||
</workflow-app>
|
|
@ -0,0 +1,26 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "in",
|
||||
"paramLongName": "inputPath",
|
||||
"paramDescription": "the path to the graph data dump to read",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "hmu",
|
||||
"paramLongName": "hiveMetastoreUris",
|
||||
"paramDescription": "the hive metastore uris",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "db",
|
||||
"paramLongName": "hiveDbName",
|
||||
"paramDescription": "the target hive database name",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
|
@ -0,0 +1,32 @@
|
|||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "in",
|
||||
"paramLongName": "inputPath",
|
||||
"paramDescription": "the path to the graph data dump to read",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "hmu",
|
||||
"paramLongName": "hiveMetastoreUris",
|
||||
"paramDescription": "the hive metastore uris",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "db",
|
||||
"paramLongName": "hiveDbName",
|
||||
"paramDescription": "the target hive database name",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "tn",
|
||||
"paramLongName": "className",
|
||||
"paramDescription": "the class modelling the target table",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
|
@ -1,10 +0,0 @@
|
|||
[
|
||||
{"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true},
|
||||
{"paramName":"sn", "paramLongName":"sourceNameNode", "paramDescription": "nameNode of the source cluster", "paramRequired": true},
|
||||
{"paramName":"tn", "paramLongName":"targetNameNode", "paramDescription": "namoNode of the target cluster", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingDirectory", "paramDescription": "working directory", "paramRequired": true},
|
||||
{"paramName":"nm", "paramLongName":"distcp_num_maps", "paramDescription": "maximum number of map tasks used in the distcp process", "paramRequired": true},
|
||||
{"paramName":"mm", "paramLongName":"distcp_memory_mb", "paramDescription": "memory for distcp action copying actionsets from remote cluster", "paramRequired": true},
|
||||
{"paramName":"tt", "paramLongName":"distcp_task_timeout", "paramDescription": "timeout for distcp copying actions from remote cluster", "paramRequired": true},
|
||||
{"paramName":"tr", "paramLongName":"transform_only", "paramDescription": "activate tranform-only mode. Only apply transformation step", "paramRequired": true}
|
||||
]
|
|
@ -1,20 +0,0 @@
|
|||
[
|
||||
{
|
||||
"paramName": "mt",
|
||||
"paramLongName": "master",
|
||||
"paramDescription": "should be local or yarn",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "is",
|
||||
"paramLongName": "isLookupUrl",
|
||||
"paramDescription": "URL of the isLookUp Service",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "i",
|
||||
"paramLongName": "inputPaths",
|
||||
"paramDescription": "URL of the isLookUp Service",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
|
@ -10,6 +10,7 @@ import static org.mockito.Mockito.when;
|
|||
import java.io.IOException;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Optional;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
@ -19,11 +20,8 @@ import org.junit.jupiter.api.extension.ExtendWith;
|
|||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.Software;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
public class MappersTest {
|
||||
|
@ -54,7 +52,29 @@ public class MappersTest {
|
|||
assertValidId(p.getId());
|
||||
assertValidId(p.getCollectedfrom().get(0).getKey());
|
||||
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
|
||||
|
||||
assertTrue(p.getAuthor().size() > 0);
|
||||
Optional<Author> author = p
|
||||
.getAuthor()
|
||||
.stream()
|
||||
.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
|
||||
.findFirst();
|
||||
assertTrue(author.isPresent());
|
||||
StructuredProperty pid = author
|
||||
.get()
|
||||
.getPid()
|
||||
.stream()
|
||||
.findFirst()
|
||||
.get();
|
||||
assertEquals("0000-0001-6651-1178", pid.getValue());
|
||||
assertEquals("ORCID", pid.getQualifier().getClassid());
|
||||
assertEquals("ORCID", pid.getQualifier().getClassname());
|
||||
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
|
||||
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
|
||||
assertEquals("Votsi,Nefta", author.get().getFullname());
|
||||
assertEquals("Votsi", author.get().getSurname());
|
||||
assertEquals("Nefta", author.get().getName());
|
||||
|
||||
assertTrue(p.getSubject().size() > 0);
|
||||
assertTrue(StringUtils.isNotBlank(p.getJournal().getIssnOnline()));
|
||||
assertTrue(StringUtils.isNotBlank(p.getJournal().getName()));
|
||||
|
@ -100,6 +120,38 @@ public class MappersTest {
|
|||
assertValidId(d.getCollectedfrom().get(0).getKey());
|
||||
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
|
||||
assertTrue(d.getAuthor().size() > 0);
|
||||
|
||||
Optional<Author> author = d
|
||||
.getAuthor()
|
||||
.stream()
|
||||
.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
|
||||
.findFirst();
|
||||
assertTrue(author.isPresent());
|
||||
StructuredProperty pid = author
|
||||
.get()
|
||||
.getPid()
|
||||
.stream()
|
||||
.findFirst()
|
||||
.get();
|
||||
assertEquals("0000-0001-9074-1619", pid.getValue());
|
||||
assertEquals("ORCID", pid.getQualifier().getClassid());
|
||||
assertEquals("ORCID", pid.getQualifier().getClassname());
|
||||
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
|
||||
assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
|
||||
assertEquals("Baracchini, Theo", author.get().getFullname());
|
||||
assertEquals("Baracchini", author.get().getSurname());
|
||||
assertEquals("Theo", author.get().getName());
|
||||
|
||||
assertEquals(1, author.get().getAffiliation().size());
|
||||
Optional<Field<String>> opAff = author
|
||||
.get()
|
||||
.getAffiliation()
|
||||
.stream()
|
||||
.findFirst();
|
||||
assertTrue(opAff.isPresent());
|
||||
Field<String> affiliation = opAff.get();
|
||||
assertEquals("ISTI-CNR", affiliation.getValue());
|
||||
|
||||
assertTrue(d.getSubject().size() > 0);
|
||||
assertTrue(d.getInstance().size() > 0);
|
||||
assertTrue(d.getContext().size() > 0);
|
||||
|
|
|
@ -19,7 +19,7 @@
|
|||
<metadata xmlns="http://namespace.openaire.eu/">
|
||||
<dc:title>Ecosystem Service capacity is higher in areas of multiple designation types</dc:title>
|
||||
<dc:creator>Nikolaidou,Charitini</dc:creator>
|
||||
<dc:creator>Votsi,Nefta</dc:creator>
|
||||
<dc:creator nameIdentifier="0000-0001-6651-1178" nameIdentifierScheme="ORCID">Votsi,Nefta</dc:creator>
|
||||
<dc:creator>Sgardelis,Steanos</dc:creator>
|
||||
<dc:creator>Halley,John</dc:creator>
|
||||
<dc:creator>Pantis,John</dc:creator>
|
||||
|
|
|
@ -35,9 +35,10 @@
|
|||
</creator>
|
||||
<creator>
|
||||
<creatorName>Baracchini, Theo</creatorName>
|
||||
<nameIdentifier nameIdentifierScheme="ORCID">0000-0001-9074-1619</nameIdentifier>
|
||||
<givenName>Theo</givenName>
|
||||
<familyName>Baracchini</familyName>
|
||||
<affiliation>Physics of Aquatic Systems Laboratory (APHYS) – Margaretha Kamprad Chair, ENAC, EPFL, Lausanne, 1015, Switzerland</affiliation>
|
||||
<affiliation>ISTI-CNR</affiliation>
|
||||
</creator>
|
||||
<creator>
|
||||
<creatorName>Wüest, Alfred</creatorName>
|
||||
|
|
Loading…
Reference in New Issue