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[graph cleaning] unit tests & cleanup

This commit is contained in:
Claudio Atzori 2023-03-23 15:57:47 +01:00
parent 90e61a8aba
commit c07857fa37
11 changed files with 944 additions and 2108 deletions
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122
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java
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@ -1,122 +0,0 @@
package eu.dnetlib.dhp.oa.graph.clean;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Result;
public class CleanContextSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
CleanContextSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/input_clean_context_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 workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
String contextId = parser.get("contextId");
log.info("contextId: {}", contextId);
String verifyParam = parser.get("verifyParam");
log.info("verifyParam: {}", verifyParam);
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 -> {
cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingDir);
});
}
private static <T extends Result> void cleanContext(SparkSession spark, String contextId, String verifyParam,
String inputPath, Class<T> entityClazz, String workingDir) {
Dataset<T> res = spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz));
res.map((MapFunction<T, T>) r -> {
if (!r
.getTitle()
.stream()
.filter(
t -> t
.getQualifier()
.getClassid()
.equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
.anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) {
return r;
}
r
.setContext(
r
.getContext()
.stream()
.filter(
c -> !c.getId().split("::")[0]
.equalsIgnoreCase(contextId))
.collect(Collectors.toList()));
return r;
}, Encoders.bean(entityClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir);
spark
.read()
.textFile(workingDir)
.map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath);
}
}

17
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java
View File

@ -4,10 +4,8 @@ package eu.dnetlib.dhp.oa.graph.clean;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.*; import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream; import java.util.stream.Stream;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
@ -29,8 +27,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.action.model.MasterDuplicate; import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; 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.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Oaf;
@ -38,6 +34,7 @@ import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import scala.Tuple2; import scala.Tuple2;
@ -76,7 +73,8 @@ public class CleanGraphSparkJob {
new CleanGraphSparkJob(parser).run(isSparkSessionManaged, isLookup); new CleanGraphSparkJob(parser).run(isSparkSessionManaged, isLookup);
} }
public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) throws ISLookUpException, ClassNotFoundException { public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService)
throws ISLookUpException, ClassNotFoundException {
String inputPath = parser.get("inputPath"); String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath); log.info("inputPath: {}", inputPath);
@ -99,7 +97,8 @@ public class CleanGraphSparkJob {
String country = parser.get("country"); String country = parser.get("country");
log.info("country: {}", country); log.info("country: {}", country);
String[] verifyCountryParam = Optional.ofNullable(parser.get("verifyCountryParam")) String[] verifyCountryParam = Optional
.ofNullable(parser.get("verifyCountryParam"))
.map(s -> s.split(";")) .map(s -> s.split(";"))
.orElse(new String[] {}); .orElse(new String[] {});
log.info("verifyCountryParam: {}", verifyCountryParam); log.info("verifyCountryParam: {}", verifyCountryParam);
@ -172,8 +171,8 @@ public class CleanGraphSparkJob {
.map(as(clazz), Encoders.bean(clazz)) .map(as(clazz), Encoders.bean(clazz))
.flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class)); .flatMap(flattenCfHbFn(), Encoders.bean(IdCfHbMapping.class));
// set the EMPTY master ID/NAME and save it // set the EMPTY master ID/NAME
resolved Dataset<IdCfHbMapping> resolvedDs = resolved
.joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId"))) .joinWith(md, resolved.col("cfhb").equalTo(md.col("duplicateId")))
.map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class)) .map(asIdCfHbMapping(), Encoders.bean(IdCfHbMapping.class))
.filter((FilterFunction<IdCfHbMapping>) m -> Objects.nonNull(m.getMasterId())); .filter((FilterFunction<IdCfHbMapping>) m -> Objects.nonNull(m.getMasterId()));
@ -198,7 +197,7 @@ public class CleanGraphSparkJob {
// Join the results with the resolved CF|HB mapping, apply the mapping and save it // Join the results with the resolved CF|HB mapping, apply the mapping and save it
cleaned_deep cleaned_deep
.joinWith(resolved, cleaned_deep.col("id").equalTo(resolved.col("resultId")), "left") .joinWith(resolvedDs, cleaned_deep.col("id").equalTo(resolvedDs.col("resultId")), "left")
.groupByKey( .groupByKey(
(MapFunction<Tuple2<T, IdCfHbMapping>, String>) t -> ((Result) t._1()).getId(), Encoders.STRING()) (MapFunction<Tuple2<T, IdCfHbMapping>, String>) t -> ((Result) t._1()).getId(), Encoders.STRING())
.mapGroups(getMapGroupsFunction(), Encoders.bean(clazz)) .mapGroups(getMapGroupsFunction(), Encoders.bean(clazz))

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/GetDatasourceFromCountry.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GetDatasourceFromCountry.java
View File

@ -1,10 +1,9 @@
package eu.dnetlib.dhp.oa.graph.clean.country; package eu.dnetlib.dhp.oa.graph.clean;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable; import java.io.Serializable;
import java.util.List;
import java.util.Optional; import java.util.Optional;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
@ -21,7 +20,6 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2; import scala.Tuple2;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/IdCfHbMapping.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/IdCfHbMapping.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.clean.cfhb; package eu.dnetlib.dhp.oa.graph.clean;
import java.io.Serializable; import java.io.Serializable;

227
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJob.java
View File

@ -1,227 +0,0 @@
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);
}
}

211
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java
View File

@ -1,211 +0,0 @@
package eu.dnetlib.dhp.oa.graph.clean.country;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.swing.text.html.Option;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
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;
/**
* @author miriam.baglioni
* @Date 20/07/22
*/
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
public class CleanCountrySparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.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_country_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 workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
String datasourcePath = parser.get("hostedBy");
log.info("datasourcePath: {}", datasourcePath);
String country = parser.get("country");
log.info("country: {}", country);
String[] verifyParam = parser.get("verifyParam").split(";");
log.info("verifyParam: {}", verifyParam);
String collectedfrom = parser.get("collectedfrom");
log.info("collectedfrom: {}", collectedfrom);
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 -> {
cleanCountry(
spark, country, verifyParam, inputPath, entityClazz, workingDir, collectedfrom, datasourcePath);
});
}
private static <T extends Result> void cleanCountry(SparkSession spark, String country, String[] verifyParam,
String inputPath, Class<T> entityClazz, String workingDir, String collectedfrom, String datasourcePath) {
List<String> hostedBy = spark
.read()
.textFile(datasourcePath)
.collectAsList();
Dataset<T> res = spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz));
res.map((MapFunction<T, T>) r -> {
if (r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) ||
!r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) {
return r;
}
List<StructuredProperty> ids = getPidsAndAltIds(r).collect(Collectors.toList());
if (ids
.stream()
.anyMatch(
p -> p
.getQualifier()
.getClassid()
.equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) {
r
.setCountry(
r
.getCountry()
.stream()
.filter(
c -> toTakeCountry(c, country))
.collect(Collectors.toList()));
}
return r;
}, Encoders.bean(entityClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir);
spark
.read()
.textFile(workingDir)
.map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath);
}
private static <T extends Result> Stream<StructuredProperty> getPidsAndAltIds(T r) {
final Stream<StructuredProperty> resultPids = Optional
.ofNullable(r.getPid())
.map(Collection::stream)
.orElse(Stream.empty());
final Stream<StructuredProperty> instancePids = Optional
.ofNullable(r.getInstance())
.map(
instance -> instance
.stream()
.flatMap(
i -> Optional
.ofNullable(i.getPid())
.map(Collection::stream)
.orElse(Stream.empty())))
.orElse(Stream.empty());
final Stream<StructuredProperty> instanceAltIds = Optional
.ofNullable(r.getInstance())
.map(
instance -> instance
.stream()
.flatMap(
i -> Optional
.ofNullable(i.getAlternateIdentifier())
.map(Collection::stream)
.orElse(Stream.empty())))
.orElse(Stream.empty());
return Stream
.concat(
Stream.concat(resultPids, instancePids),
instanceAltIds);
}
private static boolean pidInParam(String value, String[] verifyParam) {
for (String s : verifyParam)
if (value.startsWith(s))
return true;
return false;
}
private static boolean toTakeCountry(Country c, String country) {
// If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be
// inserted via propagation
if (!Optional.ofNullable(c.getDataInfo()).isPresent())
return true;
if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent())
return true;
return !(c
.getClassid()
.equalsIgnoreCase(country) &&
c.getDataInfo().getInferenceprovenance().equals("propagation"));
}
}

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
View File

@ -99,7 +99,7 @@
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Select datasource ID from country</name> <name>Select datasource ID from country</name>
<class>eu.dnetlib.dhp.oa.graph.clean.country.GetDatasourceFromCountry</class> <class>eu.dnetlib.dhp.oa.graph.clean.GetDatasourceFromCountry</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar> <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}

289
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java
View File

@ -1,289 +0,0 @@
package eu.dnetlib.dhp.oa.graph.clean;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class CleanContextTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(CleanContextTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(CleanContextTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(CleanContextTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void testResultClean() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json")
.getPath();
final String prefix = "gcube ";
spark
.read()
.textFile(sourcePath)
.map(
(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
Encoders.bean(Publication.class))
.write()
.json(workingDir.toString() + "/publication");
CleanContextSparkJob.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", workingDir.toString() + "/publication",
"--graphTableClassName", Publication.class.getCanonicalName(),
"--workingDir", workingDir.toString() + "/working",
"--contextId", "sobigdata",
"--verifyParam", "gCube "
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(7, tmp.count());
// original result with sobigdata context and gcube as starting string in the main title for the publication
Assertions
.assertEquals(
0,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
.collect()
.get(0)
.getContext()
.size());
// original result with sobigdata context without gcube as starting string in the main title for the publication
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"sobigdata::projects::2",
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
// original result with sobigdata context with gcube as starting string in the subtitle
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"sobigdata::projects::2",
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
List<StructuredProperty> titles = tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
.collect()
.get(0)
.getTitle();
Assertions.assertEquals(1, titles.size());
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid());
// original result with sobigdata context with gcube not as starting string in the main title
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"sobigdata::projects::1",
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
titles = tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
.collect()
.get(0)
.getTitle();
Assertions.assertEquals(1, titles.size());
Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix));
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()));
Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
// original result with sobigdata in context and also other contexts with gcube as starting string for the main
// title
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"dh-ch",
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
titles = tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
.collect()
.get(0)
.getTitle();
Assertions.assertEquals(1, titles.size());
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
// original result with multiple main title one of which whith gcube as starting string and with 2 contextes
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"dh-ch",
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
titles = tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
.collect()
.get(0)
.getTitle();
Assertions.assertEquals(2, titles.size());
Assertions
.assertTrue(
titles
.stream()
.anyMatch(
t -> t.getQualifier().getClassid().equals("main title")
&& t.getValue().toLowerCase().startsWith(prefix)));
// original result without sobigdata in context with gcube as starting string for the main title
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"dh-ch",
tmp
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
titles = tmp
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
.collect()
.get(0)
.getTitle();
Assertions.assertEquals(2, titles.size());
Assertions
.assertTrue(
titles
.stream()
.anyMatch(
t -> t.getQualifier().getClassid().equals("main title")
&& t.getValue().toLowerCase().startsWith(prefix)));
}
}

190
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java
View File

@ -1,190 +0,0 @@
package eu.dnetlib.dhp.oa.graph.clean;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* @author miriam.baglioni
* @Date 20/07/22
*/
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class CleanCountryTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(CleanCountryTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(CleanCountryTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(CleanCountryTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void testResultClean() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json")
.getPath();
spark
.read()
.textFile(sourcePath)
.map(
(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
Encoders.bean(Publication.class))
.write()
.json(workingDir.toString() + "/publication");
CleanCountrySparkJob.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", workingDir.toString() + "/publication",
"--graphTableClassName", Publication.class.getCanonicalName(),
"--workingDir", workingDir.toString() + "/working",
"--country", "NL",
"--verifyParam", "10.17632",
"--collectedfrom", "NARCIS",
"--hostedBy", getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")
.getPath()
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(8, tmp.count());
// original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
.collect()
.get(0)
.getCountry()
.size());
// original result with NL country and pid not starting with Mendely prefix
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
.collect()
.get(0)
.getCountry()
.size());
// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not
// inserted with propagation
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
.collect()
.get(0)
.getCountry()
.size());
// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with
// propagation
Assertions
.assertEquals(
0,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6ag"))
.collect()
.get(0)
.getCountry()
.size());
}
@Test
public void testDatasetClean() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json")
.getPath();
spark
.read()
.textFile(sourcePath)
.map(
(MapFunction<String, Dataset>) r -> OBJECT_MAPPER.readValue(r, Dataset.class),
Encoders.bean(Dataset.class))
.write()
.json(workingDir.toString() + "/dataset");
CleanCountrySparkJob.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", workingDir.toString() + "/dataset",
"-graphTableClassName", Dataset.class.getCanonicalName(),
"-workingDir", workingDir.toString() + "/working",
"-country", "NL",
"-verifyParam", "10.17632",
"-collectedfrom", "NARCIS",
"-hostedBy", getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")
.getPath()
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(1, tmp.count());
Assertions.assertEquals(0, tmp.first().getCountry().size());
}
}

369
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java
View File

@ -1,36 +1,8 @@
package eu.dnetlib.dhp.oa.graph.clean; package eu.dnetlib.dhp.oa.graph.clean;
import com.fasterxml.jackson.databind.DeserializationFeature; import static org.junit.jupiter.api.Assertions.*;
import com.fasterxml.jackson.databind.ObjectMapper; import static org.mockito.Mockito.lenient;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.clean.cfhb.CleanCfHbSparkJob;
import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.filefilter.*;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
@ -38,21 +10,46 @@ import java.net.URISyntaxException;
import java.nio.file.Files; import java.nio.file.Files;
import java.nio.file.Path; import java.nio.file.Path;
import java.nio.file.Paths; import java.nio.file.Paths;
import java.util.Collection; import java.util.*;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import java.util.stream.Stream;
import static org.junit.jupiter.api.Assertions.*; import org.apache.commons.cli.ParseException;
import static org.junit.jupiter.api.Assertions.assertEquals; import org.apache.commons.io.FileUtils;
import static org.mockito.Mockito.lenient; import org.apache.commons.io.IOUtils;
import org.apache.commons.io.filefilter.FalseFileFilter;
import org.apache.commons.io.filefilter.TrueFileFilter;
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.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class CleanGraphSparkJobTest { public class CleanGraphSparkJobTest {
private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); private static final Logger log = LoggerFactory.getLogger(CleanGraphSparkJobTest.class);
public static final ObjectMapper MAPPER = new ObjectMapper() public static final ObjectMapper MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@ -66,8 +63,6 @@ public class CleanGraphSparkJobTest {
private static SparkSession spark; private static SparkSession spark;
private static Path workingDir;
private static Path testBaseTmpPath; private static Path testBaseTmpPath;
private static String graphInputPath; private static String graphInputPath;
@ -82,10 +77,13 @@ public class CleanGraphSparkJobTest {
log.info("using test base path {}", testBaseTmpPath); log.info("using test base path {}", testBaseTmpPath);
File basePath = Paths File basePath = Paths
.get(CleanGraphSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/graph").toURI()) .get(
Objects
.requireNonNull(
CleanGraphSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/graph"))
.toURI())
.toFile(); .toFile();
List<File> paths = FileUtils List<File> paths = FileUtils
.listFilesAndDirs(basePath, FalseFileFilter.FALSE, TrueFileFilter.TRUE) .listFilesAndDirs(basePath, FalseFileFilter.FALSE, TrueFileFilter.TRUE)
.stream() .stream()
@ -114,11 +112,6 @@ public class CleanGraphSparkJobTest {
graphOutputPath = testBaseTmpPath.resolve("output").resolve("graph").toString(); graphOutputPath = testBaseTmpPath.resolve("output").resolve("graph").toString();
dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString(); dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString();
workingDir = Files.createTempDirectory(CleanGraphSparkJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.setAppName(CleanGraphSparkJobTest.class.getSimpleName()); conf.setAppName(CleanGraphSparkJobTest.class.getSimpleName());
@ -126,8 +119,8 @@ public class CleanGraphSparkJobTest {
conf.set("spark.driver.host", "localhost"); conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true"); conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false"); conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString()); conf.set("spark.sql.warehouse.dir", testBaseTmpPath.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); conf.set("hive.metastore.warehouse.dir", testBaseTmpPath.resolve("warehouse").toString());
spark = SparkSession spark = SparkSession
.builder() .builder()
@ -148,30 +141,35 @@ public class CleanGraphSparkJobTest {
@AfterAll @AfterAll
public static void afterAll() throws IOException { public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile()); FileUtils.deleteDirectory(testBaseTmpPath.toFile());
spark.stop(); spark.stop();
} }
@Test @Test
void testCleanRelations() throws Exception { void testCleanRelations() throws Exception {
spark.read() spark
.read()
.textFile(graphInputPath.toString() + "/relation") .textFile(graphInputPath.toString() + "/relation")
.map(as(Relation.class), Encoders.bean(Relation.class)) .map(as(Relation.class), Encoders.bean(Relation.class))
.collectAsList() .collectAsList()
.forEach(r -> assertFalse(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass()))); .forEach(
r -> assertFalse(
vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r.getRelClass())));
new CleanGraphSparkJob( new CleanGraphSparkJob(
args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", args(
"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
new String[] { new String[] {
"--inputPath", graphInputPath.toString() + "/relation", "--inputPath", graphInputPath + "/relation",
"--outputPath", graphOutputPath.toString() + "/relation", "--outputPath", graphOutputPath + "/relation",
"--isLookupUrl", "lookupurl", "--isLookupUrl", "lookupurl",
"--graphTableClassName", Relation.class.getCanonicalName(), "--graphTableClassName", Relation.class.getCanonicalName(),
"--deepClean", "false" "--deepClean", "false"
})).run(false, isLookUpService); })).run(false, isLookUpService);
spark.read() spark
.read()
.textFile(graphOutputPath.toString() + "/relation") .textFile(graphOutputPath.toString() + "/relation")
.map(as(Relation.class), Encoders.bean(Relation.class)) .map(as(Relation.class), Encoders.bean(Relation.class))
.collectAsList() .collectAsList()
@ -192,7 +190,10 @@ public class CleanGraphSparkJobTest {
assertNotNull(mapping); assertNotNull(mapping);
String json = IOUtils String json = IOUtils
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json")); .toString(
Objects
.requireNonNull(
getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json")));
Publication p_in = MAPPER.readValue(json, Publication.class); Publication p_in = MAPPER.readValue(json, Publication.class);
assertTrue(p_in instanceof Result); assertTrue(p_in instanceof Result);
@ -207,7 +208,11 @@ public class CleanGraphSparkJobTest {
assertNotNull(vocabularies); assertNotNull(vocabularies);
assertNotNull(mapping); assertNotNull(mapping);
String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json")); String json = IOUtils
.toString(
Objects
.requireNonNull(
getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json")));
Publication p_in = MAPPER.readValue(json, Publication.class); Publication p_in = MAPPER.readValue(json, Publication.class);
assertTrue(p_in instanceof Result); assertTrue(p_in instanceof Result);
@ -223,7 +228,11 @@ public class CleanGraphSparkJobTest {
assertNotNull(mapping); assertNotNull(mapping);
String json = IOUtils String json = IOUtils
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json")); .toString(
Objects
.requireNonNull(
getClass()
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json")));
Publication p_in = MAPPER.readValue(json, Publication.class); Publication p_in = MAPPER.readValue(json, Publication.class);
assertTrue(p_in instanceof Result); assertTrue(p_in instanceof Result);
@ -237,7 +246,7 @@ public class CleanGraphSparkJobTest {
final String id = "50|CSC_________::2250a70c903c6ac6e4c01438259e9375"; final String id = "50|CSC_________::2250a70c903c6ac6e4c01438259e9375";
Publication p_in = read(spark, graphInputPath.toString() + "/publication", Publication.class) Publication p_in = read(spark, graphInputPath + "/publication", Publication.class)
.filter(String.format("id = '%s'", id)) .filter(String.format("id = '%s'", id))
.first(); .first();
@ -246,16 +255,17 @@ public class CleanGraphSparkJobTest {
assertTrue(p_in instanceof Publication); assertTrue(p_in instanceof Publication);
new CleanGraphSparkJob( new CleanGraphSparkJob(
args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", args(
"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
new String[] { new String[] {
"--inputPath", graphInputPath.toString() + "/publication", "--inputPath", graphInputPath + "/publication",
"--outputPath", graphOutputPath.toString() + "/publication", "--outputPath", graphOutputPath + "/publication",
"--isLookupUrl", "lookupurl", "--isLookupUrl", "lookupurl",
"--graphTableClassName", Publication.class.getCanonicalName(), "--graphTableClassName", Publication.class.getCanonicalName(),
"--deepClean", "false" "--deepClean", "false"
})).run(false, isLookUpService); })).run(false, isLookUpService);
Publication p = read(spark, graphOutputPath.toString() + "/publication", Publication.class) Publication p = read(spark, graphOutputPath + "/publication", Publication.class)
.filter(String.format("id = '%s'", id)) .filter(String.format("id = '%s'", id))
.first(); .first();
@ -312,7 +322,6 @@ public class CleanGraphSparkJobTest {
assertEquals(3, p.getTitle().size()); assertEquals(3, p.getTitle().size());
List<String> titles = p List<String> titles = p
.getTitle() .getTitle()
.stream() .stream()
@ -385,41 +394,44 @@ public class CleanGraphSparkJobTest {
} }
@Test @Test
public void testCleanDoiBoost() throws IOException, ParseException, ISLookUpException, ClassNotFoundException { void testCleanDoiBoost() throws IOException, ParseException, ISLookUpException, ClassNotFoundException {
verifyFiltering(1, "50|doi_________::b0baa0eb88a5788f0b8815560d2a32f2"); verifyFiltering(1, "50|doi_________::b0baa0eb88a5788f0b8815560d2a32f2");
} }
@Test @Test
public void testCleanDoiBoost2() throws IOException, ParseException, ISLookUpException, ClassNotFoundException { void testCleanDoiBoost2() throws IOException, ParseException, ISLookUpException, ClassNotFoundException {
verifyFiltering(1, "50|doi_________::4972b0ca81b96b225aed8038bb965656"); verifyFiltering(1, "50|doi_________::4972b0ca81b96b225aed8038bb965656");
} }
private void verifyFiltering(int expectedCount, String id) throws ISLookUpException, ClassNotFoundException, IOException, ParseException { private void verifyFiltering(int expectedCount, String id)
throws ISLookUpException, ClassNotFoundException, IOException, ParseException {
new CleanGraphSparkJob( new CleanGraphSparkJob(
args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", args(
"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
new String[] { new String[] {
"--inputPath", graphInputPath.toString() + "/publication", "--inputPath", graphInputPath + "/publication",
"--outputPath", graphOutputPath.toString() + "/publication", "--outputPath", graphOutputPath + "/publication",
"--isLookupUrl", "lookupurl", "--isLookupUrl", "lookupurl",
"--graphTableClassName", Publication.class.getCanonicalName(), "--graphTableClassName", Publication.class.getCanonicalName(),
"--deepClean", "false" "--deepClean", "false"
})).run(false, isLookUpService); })).run(false, isLookUpService);
Dataset<Publication> p = read(spark, graphOutputPath.toString() + "/publication", Publication.class) Dataset<Publication> p = read(spark, graphOutputPath + "/publication", Publication.class)
.filter(String.format("id = '%s'", id)); .filter(String.format("id = '%s'", id));
assertEquals(expectedCount, p.count()); assertEquals(expectedCount, p.count());
} }
@Test @Test
public void testCleanContext() throws Exception { void testCleanContext() throws Exception {
final String prefix = "gcube "; final String prefix = "gcube ";
new CleanGraphSparkJob( new CleanGraphSparkJob(
args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", args(
"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
new String[] { new String[] {
"--inputPath", graphInputPath.toString() + "/publication", "--inputPath", graphInputPath + "/publication",
"--outputPath", graphOutputPath.toString() + "/publication", "--outputPath", graphOutputPath + "/publication",
"--isLookupUrl", "lookupurl", "--isLookupUrl", "lookupurl",
"--graphTableClassName", Publication.class.getCanonicalName(), "--graphTableClassName", Publication.class.getCanonicalName(),
"--deepClean", "true", "--deepClean", "true",
@ -429,12 +441,14 @@ public class CleanGraphSparkJobTest {
"--country", "NL", "--country", "NL",
"--verifyCountryParam", "10.17632", "--verifyCountryParam", "10.17632",
"--collectedfrom", "NARCIS", "--collectedfrom", "NARCIS",
"--hostedBy", getClass() "--hostedBy", Objects
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") .requireNonNull(
getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy"))
.getPath() .getPath()
})).run(false, isLookUpService); })).run(false, isLookUpService);
Dataset<Publication> pubs = read(spark, graphOutputPath.toString() + "/publication", Publication.class) Dataset<Publication> pubs = read(spark, graphOutputPath + "/publication", Publication.class)
.filter((FilterFunction<Publication>) p1 -> StringUtils.endsWith(p1.getId(), "_ctx")); .filter((FilterFunction<Publication>) p1 -> StringUtils.endsWith(p1.getId(), "_ctx"));
assertEquals(7, pubs.count()); assertEquals(7, pubs.count());
@ -443,7 +457,10 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
0, 0,
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439a_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::0224aae28af558f21768dbc6439a_ctx"))
.first() .first()
.getContext() .getContext()
.size()); .size());
@ -452,14 +469,20 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
1, 1,
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx"))
.first() .first()
.getContext() .getContext()
.size()); .size());
assertEquals( assertEquals(
"sobigdata::projects::2", "sobigdata::projects::2",
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67d_ctx"))
.first() .first()
.getContext() .getContext()
.get(0) .get(0)
@ -469,21 +492,30 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
1, 1,
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx"))
.first() .first()
.getContext() .getContext()
.size()); .size());
assertEquals( assertEquals(
"sobigdata::projects::2", "sobigdata::projects::2",
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx"))
.first() .first()
.getContext() .getContext()
.get(0) .get(0)
.getId()); .getId());
List<StructuredProperty> titles = pubs List<StructuredProperty> titles = pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6f_ctx"))
.first() .first()
.getTitle(); .getTitle();
@ -495,20 +527,29 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
1, 1,
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx"))
.first() .first()
.getContext() .getContext()
.size()); .size());
assertEquals( assertEquals(
"sobigdata::projects::1", "sobigdata::projects::1",
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx"))
.first() .first()
.getContext() .getContext()
.get(0) .get(0)
.getId()); .getId());
titles = pubs titles = pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9_ctx"))
.first() .first()
.getTitle(); .getTitle();
@ -522,20 +563,29 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
1, 1,
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx"))
.first() .first()
.getContext() .getContext()
.size()); .size());
assertEquals( assertEquals(
"dh-ch", "dh-ch",
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx"))
.first() .first()
.getContext() .getContext()
.get(0) .get(0)
.getId()); .getId());
titles = pubs titles = pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::4669a378a73661417182c208e6fd_ctx"))
.first() .first()
.getTitle(); .getTitle();
@ -547,20 +597,29 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
1, 1,
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx"))
.first() .first()
.getContext() .getContext()
.size()); .size());
assertEquals( assertEquals(
"dh-ch", "dh-ch",
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx"))
.first() .first()
.getContext() .getContext()
.get(0) .get(0)
.getId()); .getId());
titles = pubs titles = pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::4a9152e80f860eab99072e921d74_ctx"))
.first() .first()
.getTitle(); .getTitle();
@ -576,20 +635,29 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
1, 1,
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx"))
.first() .first()
.getContext() .getContext()
.size()); .size());
assertEquals( assertEquals(
"dh-ch", "dh-ch",
pubs pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx"))
.first() .first()
.getContext() .getContext()
.get(0) .get(0)
.getId()); .getId());
titles = pubs titles = pubs
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6_ctx"))
.first() .first()
.getTitle(); .getTitle();
@ -607,14 +675,15 @@ public class CleanGraphSparkJobTest {
@Test @Test
void testCleanCfHbSparkJob() throws Exception { void testCleanCfHbSparkJob() throws Exception {
final Dataset<Publication> pubs_in = read(spark, graphInputPath.toString() + "/publication", Publication.class); final Dataset<Publication> pubs_in = read(spark, graphInputPath + "/publication", Publication.class);
final Publication p1_in = pubs_in final Publication p1_in = pubs_in
.filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'") .filter("id = '50|doi_________::09821844208a5cd6300b2bfb13b_cfhb'")
.first(); .first();
assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", p1_in.getCollectedfrom().get(0).getKey()); assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", p1_in.getCollectedfrom().get(0).getKey());
assertEquals("Bacterial Protein Interaction Database - DUP", p1_in.getCollectedfrom().get(0).getValue()); assertEquals("Bacterial Protein Interaction Database - DUP", p1_in.getCollectedfrom().get(0).getValue());
assertEquals( assertEquals(
"10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", p1_in.getInstance().get(0).getCollectedfrom().getKey()); "10|re3data_____::4c4416659cb74c2e0e891a883a047cbc",
p1_in.getInstance().get(0).getCollectedfrom().getKey());
assertEquals( assertEquals(
"Bacterial Protein Interaction Database - DUP", p1_in.getInstance().get(0).getCollectedfrom().getValue()); "Bacterial Protein Interaction Database - DUP", p1_in.getInstance().get(0).getCollectedfrom().getValue());
@ -624,7 +693,8 @@ public class CleanGraphSparkJobTest {
assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", p2_in.getCollectedfrom().get(0).getKey()); assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", p2_in.getCollectedfrom().get(0).getKey());
assertEquals("FILUR DATA - DUP", p2_in.getCollectedfrom().get(0).getValue()); assertEquals("FILUR DATA - DUP", p2_in.getCollectedfrom().get(0).getValue());
assertEquals( assertEquals(
"10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", p2_in.getInstance().get(0).getCollectedfrom().getKey()); "10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35",
p2_in.getInstance().get(0).getCollectedfrom().getKey());
assertEquals("FILUR DATA - DUP", p2_in.getInstance().get(0).getCollectedfrom().getValue()); assertEquals("FILUR DATA - DUP", p2_in.getInstance().get(0).getCollectedfrom().getValue());
assertEquals( assertEquals(
"10|re3data_____::6ffd7bc058f762912dc494cd9c175341", p2_in.getInstance().get(0).getHostedby().getKey()); "10|re3data_____::6ffd7bc058f762912dc494cd9c175341", p2_in.getInstance().get(0).getHostedby().getKey());
@ -636,18 +706,21 @@ public class CleanGraphSparkJobTest {
assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getCollectedfrom().get(0).getKey()); assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getCollectedfrom().get(0).getKey());
assertEquals("DANS (Data Archiving and Networked Services)", p3_in.getCollectedfrom().get(0).getValue()); assertEquals("DANS (Data Archiving and Networked Services)", p3_in.getCollectedfrom().get(0).getValue());
assertEquals( assertEquals(
"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getInstance().get(0).getCollectedfrom().getKey()); "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f",
p3_in.getInstance().get(0).getCollectedfrom().getKey());
assertEquals( assertEquals(
"DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getCollectedfrom().getValue()); "DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getCollectedfrom().getValue());
assertEquals( assertEquals(
"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getInstance().get(0).getHostedby().getKey()); "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_in.getInstance().get(0).getHostedby().getKey());
assertEquals("DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getHostedby().getValue()); assertEquals(
"DANS (Data Archiving and Networked Services)", p3_in.getInstance().get(0).getHostedby().getValue());
new CleanGraphSparkJob( new CleanGraphSparkJob(
args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", args(
"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
new String[] { new String[] {
"--inputPath", graphInputPath.toString() + "/publication", "--inputPath", graphInputPath + "/publication",
"--outputPath", graphOutputPath.toString() + "/publication", "--outputPath", graphOutputPath + "/publication",
"--isLookupUrl", "lookupurl", "--isLookupUrl", "lookupurl",
"--graphTableClassName", Publication.class.getCanonicalName(), "--graphTableClassName", Publication.class.getCanonicalName(),
"--deepClean", "true", "--deepClean", "true",
@ -657,14 +730,16 @@ public class CleanGraphSparkJobTest {
"--country", "NL", "--country", "NL",
"--verifyCountryParam", "10.17632", "--verifyCountryParam", "10.17632",
"--collectedfrom", "NARCIS", "--collectedfrom", "NARCIS",
"--hostedBy", getClass() "--hostedBy", Objects
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") .requireNonNull(
getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy"))
.getPath() .getPath()
})).run(false, isLookUpService); })).run(false, isLookUpService);
assertTrue(Files.exists(Paths.get(graphOutputPath, "publication"))); assertTrue(Files.exists(Paths.get(graphOutputPath, "publication")));
final Dataset<Publication> pubs_out = read(spark, graphOutputPath.toString() + "/publication", Publication.class) final Dataset<Publication> pubs_out = read(spark, graphOutputPath + "/publication", Publication.class)
.filter((FilterFunction<Publication>) p -> StringUtils.endsWith(p.getId(), "_cfhb")); .filter((FilterFunction<Publication>) p -> StringUtils.endsWith(p.getId(), "_cfhb"));
assertEquals(3, pubs_out.count()); assertEquals(3, pubs_out.count());
@ -675,8 +750,10 @@ public class CleanGraphSparkJobTest {
assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", p1_out.getCollectedfrom().get(0).getKey()); assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", p1_out.getCollectedfrom().get(0).getKey());
assertEquals("Bacterial Protein Interaction Database", p1_out.getCollectedfrom().get(0).getValue()); assertEquals("Bacterial Protein Interaction Database", p1_out.getCollectedfrom().get(0).getValue());
assertEquals( assertEquals(
"10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", p1_out.getInstance().get(0).getCollectedfrom().getKey()); "10|fairsharing_::a29d1598024f9e87beab4b98411d48ce",
assertEquals("Bacterial Protein Interaction Database", p1_out.getInstance().get(0).getCollectedfrom().getValue()); p1_out.getInstance().get(0).getCollectedfrom().getKey());
assertEquals(
"Bacterial Protein Interaction Database", p1_out.getInstance().get(0).getCollectedfrom().getValue());
final Publication p2_out = pubs_out final Publication p2_out = pubs_out
.filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'") .filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3a_cfhb'")
@ -684,7 +761,8 @@ public class CleanGraphSparkJobTest {
assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", p2_out.getCollectedfrom().get(0).getKey()); assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", p2_out.getCollectedfrom().get(0).getKey());
assertEquals("FULIR Data", p2_out.getCollectedfrom().get(0).getValue()); assertEquals("FULIR Data", p2_out.getCollectedfrom().get(0).getValue());
assertEquals( assertEquals(
"10|re3data_____::fc1db64b3964826913b1e9eafe830490", p2_out.getInstance().get(0).getCollectedfrom().getKey()); "10|re3data_____::fc1db64b3964826913b1e9eafe830490",
p2_out.getInstance().get(0).getCollectedfrom().getKey());
assertEquals("FULIR Data", p2_out.getInstance().get(0).getCollectedfrom().getValue()); assertEquals("FULIR Data", p2_out.getInstance().get(0).getCollectedfrom().getValue());
assertEquals( assertEquals(
"10|fairsharing_::3f647cadf56541fb9513cb63ec370187", p2_out.getInstance().get(0).getHostedby().getKey()); "10|fairsharing_::3f647cadf56541fb9513cb63ec370187", p2_out.getInstance().get(0).getHostedby().getKey());
@ -696,22 +774,25 @@ public class CleanGraphSparkJobTest {
assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getCollectedfrom().get(0).getKey()); assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getCollectedfrom().get(0).getKey());
assertEquals("DANS (Data Archiving and Networked Services)", p3_out.getCollectedfrom().get(0).getValue()); assertEquals("DANS (Data Archiving and Networked Services)", p3_out.getCollectedfrom().get(0).getValue());
assertEquals( assertEquals(
"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getInstance().get(0).getCollectedfrom().getKey()); "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f",
p3_out.getInstance().get(0).getCollectedfrom().getKey());
assertEquals( assertEquals(
"DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getCollectedfrom().getValue()); "DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getCollectedfrom().getValue());
assertEquals( assertEquals(
"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getInstance().get(0).getHostedby().getKey()); "10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", p3_out.getInstance().get(0).getHostedby().getKey());
assertEquals("DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getHostedby().getValue()); assertEquals(
"DANS (Data Archiving and Networked Services)", p3_out.getInstance().get(0).getHostedby().getValue());
} }
@Test @Test
public void testCleanCountry() throws Exception { void testCleanCountry() throws Exception {
new CleanGraphSparkJob( new CleanGraphSparkJob(
args("/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json", args(
"/eu/dnetlib/dhp/oa/graph/input_clean_graph_parameters.json",
new String[] { new String[] {
"--inputPath", graphInputPath.toString() + "/publication", "--inputPath", graphInputPath + "/publication",
"--outputPath", graphOutputPath.toString() + "/publication", "--outputPath", graphOutputPath + "/publication",
"--isLookupUrl", "lookupurl", "--isLookupUrl", "lookupurl",
"--graphTableClassName", Publication.class.getCanonicalName(), "--graphTableClassName", Publication.class.getCanonicalName(),
"--deepClean", "true", "--deepClean", "true",
@ -721,13 +802,14 @@ public class CleanGraphSparkJobTest {
"--country", "NL", "--country", "NL",
"--verifyCountryParam", "10.17632", "--verifyCountryParam", "10.17632",
"--collectedfrom", "NARCIS", "--collectedfrom", "NARCIS",
"--hostedBy", getClass() "--hostedBy", Objects
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") .requireNonNull(
getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy"))
.getPath() .getPath()
})).run(false, isLookUpService); })).run(false, isLookUpService);
final Dataset<Publication> pubs_out = read(spark, graphOutputPath + "/publication", Publication.class)
final Dataset<Publication> pubs_out = read(spark, graphOutputPath.toString() + "/publication", Publication.class)
.filter((FilterFunction<Publication>) p -> StringUtils.endsWith(p.getId(), "_country")); .filter((FilterFunction<Publication>) p -> StringUtils.endsWith(p.getId(), "_country"));
assertEquals(8, pubs_out.count()); assertEquals(8, pubs_out.count());
@ -736,7 +818,10 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
1, 1,
pubs_out pubs_out
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6_country")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::0224aae28af558f21768dbc6_country"))
.first() .first()
.getCountry() .getCountry()
.size()); .size());
@ -745,7 +830,10 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
1, 1,
pubs_out pubs_out
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1_country")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1_country"))
.first() .first()
.getCountry() .getCountry()
.size()); .size());
@ -755,7 +843,10 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
1, 1,
pubs_out pubs_out
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817e_country")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::3c81248c335f0aa07e06817e_country"))
.first() .first()
.getCountry() .getCountry()
.size()); .size());
@ -765,7 +856,10 @@ public class CleanGraphSparkJobTest {
assertEquals( assertEquals(
0, 0,
pubs_out pubs_out
.filter((FilterFunction<Publication>) p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817d_country")) .filter(
(FilterFunction<Publication>) p -> p
.getId()
.equals("50|DansKnawCris::3c81248c335f0aa07e06817d_country"))
.first() .first()
.getCountry() .getCountry()
.size()); .size());
@ -774,13 +868,17 @@ public class CleanGraphSparkJobTest {
private List<String> vocs() throws IOException { private List<String> vocs() throws IOException {
return IOUtils return IOUtils
.readLines( .readLines(
GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); Objects
.requireNonNull(
getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")));
} }
private List<String> synonyms() throws IOException { private List<String> synonyms() throws IOException {
return IOUtils return IOUtils
.readLines( .readLines(
GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); Objects
.requireNonNull(
getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")));
} }
private <R> org.apache.spark.sql.Dataset<R> read(SparkSession spark, String path, Class<R> clazz) { private <R> org.apache.spark.sql.Dataset<R> read(SparkSession spark, String path, Class<R> clazz) {
@ -797,8 +895,9 @@ public class CleanGraphSparkJobTest {
private static String classPathResourceAsString(String path) throws IOException { private static String classPathResourceAsString(String path) throws IOException {
return IOUtils return IOUtils
.toString( .toString(
CleanGraphSparkJobTest.class Objects
.getResourceAsStream(path)); .requireNonNull(
CleanGraphSparkJobTest.class.getResourceAsStream(path)));
} }
private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException { private ArgumentApplicationParser args(String paramSpecs, String[] args) throws IOException, ParseException {
@ -819,12 +918,4 @@ public class CleanGraphSparkJobTest {
assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassname()); assertEquals(ModelConstants.DNET_SUBJECT_KEYWORD, s1.get().getQualifier().getClassname());
} }
private Stream<StructuredProperty> getAuthorPids(Result pub) {
return pub
.getAuthor()
.stream()
.map(Author::getPid)
.flatMap(Collection::stream);
}
} }

213
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/cfhb/CleanCfHbSparkJobTest.java
View File

@ -1,213 +0,0 @@
package eu.dnetlib.dhp.oa.graph.clean.cfhb;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.File;
import java.io.IOException;
import java.net.URISyntaxException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class CleanCfHbSparkJobTest {
private static final Logger log = LoggerFactory.getLogger(CleanCfHbSparkJobTest.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path testBaseTmpPath;
private static String resolvedPath;
private static String graphInputPath;
private static String graphOutputPath;
private static String dsMasterDuplicatePath;
@BeforeAll
public static void beforeAll() throws IOException, URISyntaxException {
testBaseTmpPath = Files.createTempDirectory(CleanCfHbSparkJobTest.class.getSimpleName());
log.info("using test base path {}", testBaseTmpPath);
final File entitiesSources = Paths
.get(CleanCfHbSparkJobTest.class.getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/entities").toURI())
.toFile();
FileUtils
.copyDirectory(
entitiesSources,
testBaseTmpPath.resolve("input").resolve("entities").toFile());
FileUtils
.copyFileToDirectory(
Paths
.get(
CleanCfHbSparkJobTest.class
.getResource("/eu/dnetlib/dhp/oa/graph/clean/cfhb/masterduplicate.json")
.toURI())
.toFile(),
testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toFile());
graphInputPath = testBaseTmpPath.resolve("input").resolve("entities").toString();
resolvedPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbResolved").toString();
graphOutputPath = testBaseTmpPath.resolve("workingDir").resolve("cfHbPatched").toString();
dsMasterDuplicatePath = testBaseTmpPath.resolve("workingDir").resolve("masterduplicate").toString();
SparkConf conf = new SparkConf();
conf.setAppName(CleanCfHbSparkJobTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("spark.ui.enabled", "false");
spark = SparkSession
.builder()
.appName(CleanCfHbSparkJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(testBaseTmpPath.toFile());
spark.stop();
}
@Test
void testCleanCfHbSparkJob() throws Exception {
final String outputPath = graphOutputPath + "/dataset";
final String inputPath = graphInputPath + "/dataset";
org.apache.spark.sql.Dataset<Dataset> records = read(spark, inputPath, Dataset.class);
Dataset d = records
.filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'")
.first();
assertEquals("10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getCollectedfrom().get(0).getKey());
assertEquals("Bacterial Protein Interaction Database - DUP", d.getCollectedfrom().get(0).getValue());
assertEquals(
"10|re3data_____::4c4416659cb74c2e0e891a883a047cbc", d.getInstance().get(0).getCollectedfrom().getKey());
assertEquals(
"Bacterial Protein Interaction Database - DUP", d.getInstance().get(0).getCollectedfrom().getValue());
d = records
.filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'")
.first();
assertEquals("10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getCollectedfrom().get(0).getKey());
assertEquals("FILUR DATA - DUP", d.getCollectedfrom().get(0).getValue());
assertEquals(
"10|opendoar____::788b4ac1e172d8e520c2b9461c0a3d35", d.getInstance().get(0).getCollectedfrom().getKey());
assertEquals("FILUR DATA - DUP", d.getInstance().get(0).getCollectedfrom().getValue());
assertEquals(
"10|re3data_____::6ffd7bc058f762912dc494cd9c175341", d.getInstance().get(0).getHostedby().getKey());
assertEquals("depositar - DUP", d.getInstance().get(0).getHostedby().getValue());
d = records
.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'")
.first();
assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey());
assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue());
assertEquals(
"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey());
assertEquals(
"DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue());
assertEquals(
"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey());
assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue());
CleanCfHbSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", inputPath,
"--outputPath", outputPath,
"--resolvedPath", resolvedPath + "/dataset",
"--graphTableClassName", Dataset.class.getCanonicalName(),
"--masterDuplicatePath", dsMasterDuplicatePath
});
assertTrue(Files.exists(Paths.get(graphOutputPath, "dataset")));
records = read(spark, outputPath, Dataset.class);
assertEquals(3, records.count());
d = records
.filter("id = '50|doi_________::09821844208a5cd6300b2bfb13bca1b9'")
.first();
assertEquals("10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getCollectedfrom().get(0).getKey());
assertEquals("Bacterial Protein Interaction Database", d.getCollectedfrom().get(0).getValue());
assertEquals(
"10|fairsharing_::a29d1598024f9e87beab4b98411d48ce", d.getInstance().get(0).getCollectedfrom().getKey());
assertEquals("Bacterial Protein Interaction Database", d.getInstance().get(0).getCollectedfrom().getValue());
d = records
.filter("id = '50|DansKnawCris::0dd644304b7116e8e58da3a5e3adc37a'")
.first();
assertEquals("10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getCollectedfrom().get(0).getKey());
assertEquals("FULIR Data", d.getCollectedfrom().get(0).getValue());
assertEquals(
"10|re3data_____::fc1db64b3964826913b1e9eafe830490", d.getInstance().get(0).getCollectedfrom().getKey());
assertEquals("FULIR Data", d.getInstance().get(0).getCollectedfrom().getValue());
assertEquals(
"10|fairsharing_::3f647cadf56541fb9513cb63ec370187", d.getInstance().get(0).getHostedby().getKey());
assertEquals("depositar", d.getInstance().get(0).getHostedby().getValue());
d = records
.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'")
.first();
assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey());
assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue());
assertEquals(
"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey());
assertEquals(
"DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue());
assertEquals(
"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey());
assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue());
d = records
.filter("id = '50|DansKnawCris::203a27996ddc0fd1948258e5b7dec61c'")
.first();
assertEquals("10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getCollectedfrom().get(0).getKey());
assertEquals("DANS (Data Archiving and Networked Services)", d.getCollectedfrom().get(0).getValue());
assertEquals(
"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getCollectedfrom().getKey());
assertEquals(
"DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getCollectedfrom().getValue());
assertEquals(
"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f", d.getInstance().get(0).getHostedby().getKey());
assertEquals("DANS (Data Archiving and Networked Services)", d.getInstance().get(0).getHostedby().getValue());
}
private <R> org.apache.spark.sql.Dataset<R> read(SparkSession spark, String path, Class<R> clazz) {
return spark
.read()
.textFile(path)
.map(as(clazz), Encoders.bean(clazz));
}
private static <R> MapFunction<String, R> as(Class<R> clazz) {
return s -> OBJECT_MAPPER.readValue(s, clazz);
}
}