[Cleaning] adding missing classes

This commit is contained in:
Miriam Baglioni 2022-12-21 12:49:08 +01:00
parent 11f2b470d3
commit b713132db7
4 changed files with 400 additions and 0 deletions

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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);
}
}
}

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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;
}
}

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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);
}
}

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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;
}
}