forked from D-Net/dnet-hadoop
[Cleaning] adding missing classes
This commit is contained in:
parent
11f2b470d3
commit
b713132db7
|
|
@ -0,0 +1,81 @@
|
|||
|
||||
package eu.dnetlib.dhp.common.action;
|
||||
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.IOException;
|
||||
import java.io.OutputStreamWriter;
|
||||
import java.nio.charset.StandardCharsets;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FSDataOutputStream;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.common.DbClient;
|
||||
import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
|
||||
|
||||
public class ReadDatasourceMasterDuplicateFromDB {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(ReadDatasourceMasterDuplicateFromDB.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static final String QUERY = "SELECT distinct dd.id as masterId, d.officialname as masterName, dd.duplicate as duplicateId "
|
||||
+
|
||||
"FROM dsm_dedup_services dd join dsm_services d on (dd.id = d.id);";
|
||||
|
||||
public static int execute(String dbUrl, String dbUser, String dbPassword, String hdfsPath, String hdfsNameNode)
|
||||
throws IOException {
|
||||
int count = 0;
|
||||
try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
|
||||
Configuration conf = new Configuration();
|
||||
conf.set("fs.defaultFS", hdfsNameNode);
|
||||
FileSystem fileSystem = FileSystem.get(conf);
|
||||
FSDataOutputStream fos = fileSystem.create(new Path(hdfsPath));
|
||||
|
||||
log.info("running query: {}", QUERY);
|
||||
log.info("storing results in: {}", hdfsPath);
|
||||
|
||||
try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) {
|
||||
dbClient.processResults(QUERY, rs -> writeMap(datasourceMasterMap(rs), writer));
|
||||
count++;
|
||||
}
|
||||
}
|
||||
return count;
|
||||
}
|
||||
|
||||
private static MasterDuplicate datasourceMasterMap(ResultSet rs) {
|
||||
try {
|
||||
final MasterDuplicate md = new MasterDuplicate();
|
||||
|
||||
final String duplicateId = rs.getString("duplicateId");
|
||||
final String masterId = rs.getString("masterId");
|
||||
final String masterName = rs.getString("masterName");
|
||||
|
||||
md.setDuplicateId(OafMapperUtils.createOpenaireId(10, duplicateId, true));
|
||||
md.setMasterId(OafMapperUtils.createOpenaireId(10, masterId, true));
|
||||
md.setMasterName(masterName);
|
||||
|
||||
return md;
|
||||
} catch (final SQLException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
private static void writeMap(final MasterDuplicate dm, final BufferedWriter writer) {
|
||||
try {
|
||||
writer.write(OBJECT_MAPPER.writeValueAsString(dm));
|
||||
writer.newLine();
|
||||
} catch (final IOException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,38 @@
|
|||
|
||||
package eu.dnetlib.dhp.common.action.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 21/07/22
|
||||
*/
|
||||
public class MasterDuplicate implements Serializable {
|
||||
private String duplicateId;
|
||||
private String masterId;
|
||||
private String masterName;
|
||||
|
||||
public String getDuplicateId() {
|
||||
return duplicateId;
|
||||
}
|
||||
|
||||
public void setDuplicateId(String duplicateId) {
|
||||
this.duplicateId = duplicateId;
|
||||
}
|
||||
|
||||
public String getMasterId() {
|
||||
return masterId;
|
||||
}
|
||||
|
||||
public void setMasterId(String masterId) {
|
||||
this.masterId = masterId;
|
||||
}
|
||||
|
||||
public String getMasterName() {
|
||||
return masterName;
|
||||
}
|
||||
|
||||
public void setMasterName(String masterName) {
|
||||
this.masterName = masterName;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,227 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.clean.cfhb;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
import java.util.stream.Stream;
|
||||
|
||||
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.*;
|
||||
import org.apache.spark.sql.expressions.Aggregator;
|
||||
import org.jetbrains.annotations.NotNull;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
|
||||
import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
|
||||
import eu.dnetlib.dhp.schema.oaf.Instance;
|
||||
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class CleanCfHbSparkJob {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJob.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
CleanCountrySparkJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/input_clean_cfhb_parameters.json"));
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
String inputPath = parser.get("inputPath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
String resolvedPath = parser.get("resolvedPath");
|
||||
log.info("resolvedPath: {}", resolvedPath);
|
||||
|
||||
String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
String dsMasterDuplicatePath = parser.get("masterDuplicatePath");
|
||||
log.info("masterDuplicatePath: {}", dsMasterDuplicatePath);
|
||||
|
||||
String graphTableClassName = parser.get("graphTableClassName");
|
||||
log.info("graphTableClassName: {}", graphTableClassName);
|
||||
|
||||
Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
|
||||
HdfsSupport.remove(resolvedPath, spark.sparkContext().hadoopConfiguration());
|
||||
cleanCfHb(
|
||||
spark, inputPath, entityClazz, resolvedPath, dsMasterDuplicatePath, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static <T extends Result> void cleanCfHb(SparkSession spark, String inputPath, Class<T> entityClazz,
|
||||
String resolvedPath, String masterDuplicatePath, String outputPath) {
|
||||
|
||||
// read the master-duplicate tuples
|
||||
Dataset<MasterDuplicate> md = spark
|
||||
.read()
|
||||
.textFile(masterDuplicatePath)
|
||||
.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(entityClazz), Encoders.bean(entityClazz))
|
||||
.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()))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.json(resolvedPath);
|
||||
|
||||
// read again the resolved CF|HB mapping
|
||||
Dataset<IdCfHbMapping> resolvedDS = spark
|
||||
.read()
|
||||
.textFile(resolvedPath)
|
||||
.map(as(IdCfHbMapping.class), Encoders.bean(IdCfHbMapping.class));
|
||||
|
||||
// read the result table
|
||||
Dataset<T> res = spark
|
||||
.read()
|
||||
.textFile(inputPath)
|
||||
.map(as(entityClazz), Encoders.bean(entityClazz));
|
||||
|
||||
// Join the results with the resolved CF|HB mapping, apply the mapping and save it
|
||||
res
|
||||
.joinWith(resolvedDS, res.col("id").equalTo(resolvedDS.col("resultId")), "left")
|
||||
.groupByKey((MapFunction<Tuple2<T, IdCfHbMapping>, String>) t -> t._1().getId(), Encoders.STRING())
|
||||
.mapGroups(getMapGroupsFunction(), Encoders.bean(entityClazz))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
||||
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 <T extends Result> 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(r.getInstance())
|
||||
.map(
|
||||
instances -> instances
|
||||
.stream()
|
||||
.map(i -> Optional.ofNullable(i.getHostedby()).map(KeyValue::getKey).orElse("")))
|
||||
.orElse(Stream.empty())
|
||||
.filter(StringUtils::isNotBlank),
|
||||
Optional
|
||||
.ofNullable(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(r.getId(), cfHb))
|
||||
.iterator();
|
||||
}
|
||||
|
||||
private static <T extends Result> 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));
|
||||
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());
|
||||
}
|
||||
}
|
||||
|
||||
};
|
||||
}
|
||||
|
||||
private static IdCfHbMapping asIdCfHbMapping(String resultId, String cfHb) {
|
||||
IdCfHbMapping m = new IdCfHbMapping(resultId);
|
||||
m.setCfhb(cfHb);
|
||||
return m;
|
||||
}
|
||||
|
||||
private static <R> MapFunction<String, R> as(Class<R> clazz) {
|
||||
return s -> OBJECT_MAPPER.readValue(s, clazz);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.graph.clean.cfhb;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class IdCfHbMapping implements Serializable {
|
||||
|
||||
private String resultId;
|
||||
|
||||
private String cfhb;
|
||||
|
||||
private String masterId;
|
||||
|
||||
private String masterName;
|
||||
|
||||
public IdCfHbMapping() {
|
||||
}
|
||||
|
||||
public IdCfHbMapping(String id) {
|
||||
this.resultId = id;
|
||||
}
|
||||
|
||||
public String getResultId() {
|
||||
return resultId;
|
||||
}
|
||||
|
||||
public void setResultId(String resultId) {
|
||||
this.resultId = resultId;
|
||||
}
|
||||
|
||||
public String getCfhb() {
|
||||
return cfhb;
|
||||
}
|
||||
|
||||
public void setCfhb(String cfhb) {
|
||||
this.cfhb = cfhb;
|
||||
}
|
||||
|
||||
public String getMasterId() {
|
||||
return masterId;
|
||||
}
|
||||
|
||||
public void setMasterId(String masterId) {
|
||||
this.masterId = masterId;
|
||||
}
|
||||
|
||||
public String getMasterName() {
|
||||
return masterName;
|
||||
}
|
||||
|
||||
public void setMasterName(String masterName) {
|
||||
this.masterName = masterName;
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue