314 lines
10 KiB
Java
314 lines
10 KiB
Java
|
|
package eu.dnetlib.dhp.oa.graph.clean;
|
|
|
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
|
|
|
import java.util.*;
|
|
import java.util.stream.Collectors;
|
|
import java.util.stream.Stream;
|
|
|
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
|
import org.apache.commons.io.IOUtils;
|
|
import org.apache.commons.lang3.StringUtils;
|
|
import org.apache.spark.SparkConf;
|
|
import org.apache.spark.api.java.function.FilterFunction;
|
|
import org.apache.spark.api.java.function.FlatMapFunction;
|
|
import org.apache.spark.api.java.function.MapFunction;
|
|
import org.apache.spark.api.java.function.MapGroupsFunction;
|
|
import org.apache.spark.sql.Dataset;
|
|
import org.apache.spark.sql.Encoders;
|
|
import org.apache.spark.sql.SaveMode;
|
|
import org.apache.spark.sql.SparkSession;
|
|
import org.slf4j.Logger;
|
|
import org.slf4j.LoggerFactory;
|
|
|
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
import com.google.common.collect.Sets;
|
|
|
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
import eu.dnetlib.dhp.common.HdfsSupport;
|
|
import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
|
|
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
|
|
import eu.dnetlib.dhp.oa.graph.clean.cfhb.IdCfHbMapping;
|
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
|
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
|
import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
|
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
|
import scala.Tuple2;
|
|
|
|
public class CleanGraphSparkJob {
|
|
|
|
private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJob.class);
|
|
|
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
|
|
|
private ArgumentApplicationParser parser;
|
|
|
|
public CleanGraphSparkJob(ArgumentApplicationParser parser) {
|
|
this.parser = parser;
|
|
}
|
|
|
|
public static void main(String[] args) throws Exception {
|
|
String jsonConfiguration = IOUtils
|
|
.toString(
|
|
CleanGraphSparkJob.class
|
|
.getResourceAsStream(
|
|
"/eu/dnetlib/dhp/oa/graph/input_clean_graph_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 isLookupUrl = parser.get("isLookupUrl");
|
|
log.info("isLookupUrl: {}", isLookupUrl);
|
|
|
|
ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
|
|
|
|
new CleanGraphSparkJob(parser).run(isSparkSessionManaged, isLookup);
|
|
}
|
|
|
|
public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) throws ISLookUpException, ClassNotFoundException {
|
|
|
|
String inputPath = parser.get("inputPath");
|
|
log.info("inputPath: {}", inputPath);
|
|
|
|
String outputPath = parser.get("outputPath");
|
|
log.info("outputPath: {}", outputPath);
|
|
|
|
String graphTableClassName = parser.get("graphTableClassName");
|
|
log.info("graphTableClassName: {}", graphTableClassName);
|
|
|
|
String contextId = parser.get("contextId");
|
|
log.info("contextId: {}", contextId);
|
|
|
|
String verifyParam = parser.get("verifyParam");
|
|
log.info("verifyParam: {}", verifyParam);
|
|
|
|
String datasourcePath = parser.get("hostedBy");
|
|
log.info("datasourcePath: {}", datasourcePath);
|
|
|
|
String country = parser.get("country");
|
|
log.info("country: {}", country);
|
|
|
|
String[] verifyCountryParam = Optional.ofNullable(parser.get("verifyCountryParam"))
|
|
.map(s -> s.split(";"))
|
|
.orElse(new String[]{});
|
|
log.info("verifyCountryParam: {}", verifyCountryParam);
|
|
|
|
String collectedfrom = parser.get("collectedfrom");
|
|
log.info("collectedfrom: {}", collectedfrom);
|
|
|
|
String dsMasterDuplicatePath = parser.get("masterDuplicatePath");
|
|
log.info("masterDuplicatePath: {}", dsMasterDuplicatePath);
|
|
|
|
Boolean deepClean = Optional
|
|
.ofNullable(parser.get("deepClean"))
|
|
.map(Boolean::valueOf)
|
|
.orElse(Boolean.FALSE);
|
|
log.info("deepClean: {}", deepClean);
|
|
|
|
Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
|
|
|
|
final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService);
|
|
|
|
SparkConf conf = new SparkConf();
|
|
conf.setAppName(CleanGraphSparkJob.class.getSimpleName() + "#" + entityClazz.getSimpleName());
|
|
runWithSparkSession(
|
|
conf,
|
|
isSparkSessionManaged,
|
|
spark -> {
|
|
HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
|
|
cleanGraphTable(
|
|
spark, vocs, inputPath, entityClazz, outputPath, contextId, verifyParam, datasourcePath, country,
|
|
verifyCountryParam, collectedfrom, dsMasterDuplicatePath, deepClean);
|
|
});
|
|
}
|
|
|
|
private static <T extends Oaf> void cleanGraphTable(
|
|
SparkSession spark,
|
|
VocabularyGroup vocs,
|
|
String inputPath,
|
|
Class<T> clazz,
|
|
String outputPath, String contextId, String verifyParam, String datasourcePath, String country,
|
|
String[] verifyCountryParam, String collectedfrom, String dsMasterDuplicatePath,
|
|
Boolean deepClean) {
|
|
|
|
final CleaningRuleMap mapping = CleaningRuleMap.create(vocs);
|
|
|
|
final Dataset<T> cleaned_basic = readTableFromPath(spark, inputPath, clazz)
|
|
.map((MapFunction<T, T>) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz))
|
|
.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
|
|
.map((MapFunction<T, T>) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz))
|
|
.filter((FilterFunction<T>) GraphCleaningFunctions::filter);
|
|
|
|
if (Boolean.FALSE.equals(deepClean)) {
|
|
cleaned_basic
|
|
.write()
|
|
.mode(SaveMode.Overwrite)
|
|
.option("compression", "gzip")
|
|
.json(outputPath);
|
|
|
|
} else if (Boolean.TRUE.equals(ModelSupport.isSubClass(clazz, Result.class))) {
|
|
|
|
// read the master-duplicate tuples
|
|
Dataset<MasterDuplicate> md = spark
|
|
.read()
|
|
.textFile(dsMasterDuplicatePath)
|
|
.map(as(MasterDuplicate.class), Encoders.bean(MasterDuplicate.class));
|
|
|
|
// prepare the resolved CF|HB references with the corresponding EMPTY master ID
|
|
Dataset<IdCfHbMapping> resolved = spark
|
|
.read()
|
|
.textFile(inputPath)
|
|
.map(as(clazz), Encoders.bean(clazz))
|
|
.flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class));
|
|
|
|
// set the EMPTY master ID/NAME and save it
|
|
resolved
|
|
.joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId")))
|
|
.map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class))
|
|
.filter((FilterFunction<IdCfHbMapping>) m -> Objects.nonNull(m.getMasterId()));
|
|
|
|
// load the hostedby mapping
|
|
Set<String> hostedBy = Sets
|
|
.newHashSet(
|
|
spark
|
|
.read()
|
|
.textFile(datasourcePath)
|
|
.collectAsList());
|
|
|
|
// perform the deep cleaning steps
|
|
final Dataset<T> cleaned_deep = cleaned_basic
|
|
.map(
|
|
(MapFunction<T, T>) value -> GraphCleaningFunctions.cleanContext(value, contextId, verifyParam),
|
|
Encoders.bean(clazz))
|
|
.map(
|
|
(MapFunction<T, T>) value -> GraphCleaningFunctions
|
|
.cleanCountry(value, verifyCountryParam, hostedBy, collectedfrom, country),
|
|
Encoders.bean(clazz));
|
|
|
|
// Join the results with the resolved CF|HB mapping, apply the mapping and save it
|
|
cleaned_deep
|
|
.joinWith(resolved, cleaned_deep.col("id").equalTo(resolved.col("resultId")), "left")
|
|
.groupByKey(
|
|
(MapFunction<Tuple2<T, IdCfHbMapping>, String>) t -> ((Result) t._1()).getId(), Encoders.STRING())
|
|
.mapGroups(getMapGroupsFunction(), Encoders.bean(clazz))
|
|
.write()
|
|
.mode(SaveMode.Overwrite)
|
|
.option("compression", "gzip")
|
|
.json(outputPath);
|
|
}
|
|
}
|
|
|
|
private static <T extends Oaf> Dataset<T> readTableFromPath(
|
|
SparkSession spark, String inputEntityPath, Class<T> clazz) {
|
|
|
|
log.info("Reading Graph table from: {}", inputEntityPath);
|
|
return spark
|
|
.read()
|
|
.textFile(inputEntityPath)
|
|
.map(as(clazz), Encoders.bean(clazz));
|
|
}
|
|
|
|
private static <R> MapFunction<String, R> as(Class<R> clazz) {
|
|
return s -> OBJECT_MAPPER.readValue(s, clazz);
|
|
}
|
|
|
|
private static <T extends Oaf> FlatMapFunction<T, IdCfHbMapping> flattenCfHbFn() {
|
|
return r -> Stream
|
|
.concat(
|
|
Optional
|
|
.ofNullable(r.getCollectedfrom())
|
|
.map(cf -> cf.stream().map(KeyValue::getKey))
|
|
.orElse(Stream.empty()),
|
|
Stream
|
|
.concat(
|
|
Optional
|
|
.ofNullable(((Result) r).getInstance())
|
|
.map(
|
|
instances -> instances
|
|
.stream()
|
|
.map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse("")))
|
|
.orElse(Stream.empty())
|
|
.filter(StringUtils::isNotBlank),
|
|
Optional
|
|
.ofNullable(((Result) r).getInstance())
|
|
.map(
|
|
instances -> instances
|
|
.stream()
|
|
.map(
|
|
i -> Optional
|
|
.ofNullable(i.getCollectedfrom())
|
|
.map(KeyValue::getKey)
|
|
.orElse("")))
|
|
.orElse(Stream.empty())
|
|
.filter(StringUtils::isNotBlank)))
|
|
.distinct()
|
|
.filter(StringUtils::isNotBlank)
|
|
.map(cfHb -> asIdCfHbMapping(((Result) r).getId(), cfHb))
|
|
.iterator();
|
|
}
|
|
|
|
private static MapFunction<Tuple2<IdCfHbMapping, MasterDuplicate>, IdCfHbMapping> asIdCfHbMapping() {
|
|
return t -> {
|
|
final IdCfHbMapping mapping = t._1();
|
|
Optional
|
|
.ofNullable(t._2())
|
|
.ifPresent(t2 -> {
|
|
mapping.setMasterId(t2.getMasterId());
|
|
mapping.setMasterName(t2.getMasterName());
|
|
|
|
});
|
|
return mapping;
|
|
};
|
|
}
|
|
|
|
private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) {
|
|
IdCfHbMapping m = new IdCfHbMapping(resultId);
|
|
m.setCfhb(cfHb);
|
|
return m;
|
|
}
|
|
|
|
private static <T extends Oaf> MapGroupsFunction<String, Tuple2<T, IdCfHbMapping>, T> getMapGroupsFunction() {
|
|
return new MapGroupsFunction<String, Tuple2<T, IdCfHbMapping>, T>() {
|
|
@Override
|
|
public T call(String key, Iterator<Tuple2<T, IdCfHbMapping>> values) {
|
|
final Tuple2<T, IdCfHbMapping> first = values.next();
|
|
final T res = first._1();
|
|
|
|
updateResult(res, first._2());
|
|
values.forEachRemaining(t -> updateResult(res, t._2()));
|
|
return res;
|
|
}
|
|
|
|
private void updateResult(T res, IdCfHbMapping m) {
|
|
if (Objects.nonNull(m)) {
|
|
res.getCollectedfrom().forEach(kv -> updateKeyValue(kv, m));
|
|
((Result) res).getInstance().forEach(i -> {
|
|
updateKeyValue(i.getHostedby(), m);
|
|
updateKeyValue(i.getCollectedfrom(), m);
|
|
});
|
|
}
|
|
}
|
|
|
|
private void updateKeyValue(final KeyValue kv, final IdCfHbMapping a) {
|
|
if (kv.getKey().equals(a.getCfhb())) {
|
|
kv.setKey(a.getMasterId());
|
|
kv.setValue(a.getMasterName());
|
|
}
|
|
}
|
|
|
|
};
|
|
}
|
|
|
|
}
|