reverted behaviour of the cleaning workflow: grouping entities by ID will be managed differently
This commit is contained in:
parent
e43ab07af6
commit
33bae02451
|
|
@ -1,206 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.clean;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.List;
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.*;
|
||||
import org.apache.spark.sql.expressions.Aggregator;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import com.jayway.jsonpath.Configuration;
|
||||
import com.jayway.jsonpath.DocumentContext;
|
||||
import com.jayway.jsonpath.JsonPath;
|
||||
import com.jayway.jsonpath.Option;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import scala.Tuple2;
|
||||
|
||||
/**
|
||||
* Groups the graph content by entity identifier to ensure ID uniqueness
|
||||
*/
|
||||
public class GroupEntitiesAndRelationsSparkJob {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(GroupEntitiesAndRelationsSparkJob.class);
|
||||
|
||||
private final static String ID_JPATH = "$.id";
|
||||
|
||||
private final static String SOURCE_JPATH = "$.source";
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
GroupEntitiesAndRelationsSparkJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/group_graph_entities_parameters.json"));
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
String graphInputPath = parser.get("graphInputPath");
|
||||
log.info("graphInputPath: {}", graphInputPath);
|
||||
|
||||
String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
|
||||
groupEntitiesAndRelations(spark, graphInputPath, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void groupEntitiesAndRelations(
|
||||
SparkSession spark,
|
||||
String inputPath,
|
||||
String outputPath) {
|
||||
|
||||
TypedColumn<Oaf, Oaf> aggregator = new GroupingAggregator().toColumn();
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
spark
|
||||
.read()
|
||||
.textFile(toSeq(listPaths(inputPath, sc)))
|
||||
.map((MapFunction<String, Oaf>) s -> parseOaf(s), Encoders.kryo(Oaf.class))
|
||||
.filter((FilterFunction<Oaf>) oaf -> StringUtils.isNotBlank(ModelSupport.idFn().apply(oaf)))
|
||||
.groupByKey((MapFunction<Oaf, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
|
||||
.agg(aggregator)
|
||||
.map(
|
||||
(MapFunction<Tuple2<String, Oaf>, String>) t -> t._2().getClass().getName() +
|
||||
"|" + OBJECT_MAPPER.writeValueAsString(t._2()),
|
||||
Encoders.STRING())
|
||||
.write()
|
||||
.option("compression", "gzip")
|
||||
.mode(SaveMode.Overwrite)
|
||||
.text(outputPath);
|
||||
}
|
||||
|
||||
public static class GroupingAggregator extends Aggregator<Oaf, Oaf, Oaf> {
|
||||
|
||||
@Override
|
||||
public Oaf zero() {
|
||||
return null;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Oaf reduce(Oaf b, Oaf a) {
|
||||
return mergeAndGet(b, a);
|
||||
}
|
||||
|
||||
private Oaf mergeAndGet(Oaf b, Oaf a) {
|
||||
if (Objects.nonNull(a) && Objects.nonNull(b)) {
|
||||
return OafMapperUtils.merge(b, a);
|
||||
}
|
||||
return Objects.isNull(a) ? b : a;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Oaf merge(Oaf b, Oaf a) {
|
||||
return mergeAndGet(b, a);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Oaf finish(Oaf j) {
|
||||
return j;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Encoder<Oaf> bufferEncoder() {
|
||||
return Encoders.kryo(Oaf.class);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Encoder<Oaf> outputEncoder() {
|
||||
return Encoders.kryo(Oaf.class);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static Oaf parseOaf(String s) {
|
||||
|
||||
DocumentContext dc = JsonPath
|
||||
.parse(s, Configuration.defaultConfiguration().addOptions(Option.SUPPRESS_EXCEPTIONS));
|
||||
final String id = dc.read(ID_JPATH);
|
||||
if (StringUtils.isNotBlank(id)) {
|
||||
|
||||
String prefix = StringUtils.substringBefore(id, "|");
|
||||
switch (prefix) {
|
||||
case "10":
|
||||
return parse(s, Datasource.class);
|
||||
case "20":
|
||||
return parse(s, Organization.class);
|
||||
case "40":
|
||||
return parse(s, Project.class);
|
||||
case "50":
|
||||
String resultType = dc.read("$.resulttype.classid");
|
||||
switch (resultType) {
|
||||
case "publication":
|
||||
return parse(s, Publication.class);
|
||||
case "dataset":
|
||||
return parse(s, eu.dnetlib.dhp.schema.oaf.Dataset.class);
|
||||
case "software":
|
||||
return parse(s, Software.class);
|
||||
case "other":
|
||||
return parse(s, OtherResearchProduct.class);
|
||||
default:
|
||||
throw new IllegalArgumentException(String.format("invalid resultType: '%s'", resultType));
|
||||
}
|
||||
default:
|
||||
throw new IllegalArgumentException(String.format("invalid id prefix: '%s'", prefix));
|
||||
}
|
||||
} else {
|
||||
String source = dc.read(SOURCE_JPATH);
|
||||
if (StringUtils.isNotBlank(source)) {
|
||||
return parse(s, Relation.class);
|
||||
} else {
|
||||
throw new IllegalArgumentException(String.format("invalid oaf: '%s'", s));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private static <T extends Oaf> Oaf parse(String s, Class<T> clazz) {
|
||||
try {
|
||||
return OBJECT_MAPPER.readValue(s, clazz);
|
||||
} catch (IOException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
private static List<String> listPaths(String inputPath, JavaSparkContext sc) {
|
||||
return HdfsSupport
|
||||
.listFiles(inputPath, sc.hadoopConfiguration())
|
||||
.stream()
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -50,36 +50,12 @@
|
|||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="group_entities"/>
|
||||
<start to="fork_clean_graph"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="group_entities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>group graph entities and relations</name>
|
||||
<class>eu.dnetlib.dhp.oa.graph.clean.GroupEntitiesAndRelationsSparkJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--graphInputPath</arg><arg>${graphInputPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
</spark>
|
||||
<ok to="fork_clean_graph"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<fork name="fork_clean_graph">
|
||||
<path start="clean_publication"/>
|
||||
<path start="clean_dataset"/>
|
||||
|
|
@ -108,7 +84,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--inputPath</arg><arg>${graphInputPath}/publication</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/publication</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
|
|
@ -134,7 +110,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--inputPath</arg><arg>${graphInputPath}/dataset</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/dataset</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
|
|
@ -160,7 +136,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--inputPath</arg><arg>${graphInputPath}/otherresearchproduct</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
|
|
@ -186,7 +162,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--inputPath</arg><arg>${graphInputPath}/software</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/software</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
|
|
@ -212,7 +188,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--inputPath</arg><arg>${graphInputPath}/datasource</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/datasource</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
|
|
@ -238,7 +214,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--inputPath</arg><arg>${graphInputPath}/organization</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/organization</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
|
|
@ -264,7 +240,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--inputPath</arg><arg>${graphInputPath}/project</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/project</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
|
|
@ -290,7 +266,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=7680
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingDir}/grouped_entities</arg>
|
||||
<arg>--inputPath</arg><arg>${graphInputPath}/relation</arg>
|
||||
<arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
|
||||
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
|
|
|
|||
Loading…
Reference in New Issue