master #59
|
|
@ -232,9 +232,9 @@ public class PropagationConstant {
|
|||
|
||||
if (HdfsSupport.exists(inputPath, spark.sparkContext().hadoopConfiguration())) {
|
||||
return spark
|
||||
.read()
|
||||
.textFile(inputPath)
|
||||
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
|
||||
.read()
|
||||
.textFile(inputPath)
|
||||
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
|
||||
} else {
|
||||
return spark.emptyDataset(Encoders.bean(clazz));
|
||||
}
|
||||
|
|
|
|||
|
|
@ -95,7 +95,6 @@ public class ResultTagger implements Serializable {
|
|||
|
||||
}
|
||||
|
||||
|
||||
tmp
|
||||
.forEach(
|
||||
dsId -> datasources
|
||||
|
|
|
|||
|
|
@ -774,47 +774,47 @@ public class BulkTagJobTest {
|
|||
void bulktagPublicationwithConstraintsTest() throws Exception {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/bulktag/sample/publication/orcidbulktagfordatasource")
|
||||
.getPath();
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/bulktag/sample/publication/orcidbulktagfordatasource")
|
||||
.getPath();
|
||||
SparkBulkTagJob
|
||||
.main(
|
||||
new String[] {
|
||||
"-isTest", Boolean.TRUE.toString(),
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-sourcePath", sourcePath,
|
||||
"-taggingConf", IOUtils
|
||||
.toString(
|
||||
BulkTagJobTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_neanias.xml")),
|
||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
|
||||
"-outputPath", workingDir.toString() + "/publication",
|
||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
||||
"-pathMap", pathMap
|
||||
});
|
||||
.main(
|
||||
new String[] {
|
||||
"-isTest", Boolean.TRUE.toString(),
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-sourcePath", sourcePath,
|
||||
"-taggingConf", IOUtils
|
||||
.toString(
|
||||
BulkTagJobTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_neanias.xml")),
|
||||
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
|
||||
"-outputPath", workingDir.toString() + "/publication",
|
||||
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
||||
"-pathMap", pathMap
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Publication> tmp = sc
|
||||
.textFile(workingDir.toString() + "/publication")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
|
||||
.textFile(workingDir.toString() + "/publication")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
|
||||
|
||||
Assertions.assertEquals(2, tmp.count());
|
||||
org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
|
||||
.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
|
||||
.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
|
||||
|
||||
verificationDataset.createOrReplaceTempView("dataset");
|
||||
String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||
+ "from dataset "
|
||||
+ "lateral view explode(context) c as MyT "
|
||||
+ "lateral view explode(MyT.datainfo) d as MyD "
|
||||
+ "where MyD.inferenceprovenance = 'bulktagging'";
|
||||
+ "from dataset "
|
||||
+ "lateral view explode(context) c as MyT "
|
||||
+ "lateral view explode(MyT.datainfo) d as MyD "
|
||||
+ "where MyD.inferenceprovenance = 'bulktagging'";
|
||||
|
||||
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||
|
||||
idExplodeCommunity.show(false);
|
||||
Assertions.assertEquals(0, idExplodeCommunity.count());
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -39,173 +39,173 @@ 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 Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
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);
|
||||
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);
|
||||
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 inputPath = parser.get("inputPath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
String workingDir = parser.get("workingDir");
|
||||
log.info("workingDir: {}", workingDir);
|
||||
String workingDir = parser.get("workingDir");
|
||||
log.info("workingDir: {}", workingDir);
|
||||
|
||||
String datasourcePath = parser.get("hostedBy");
|
||||
log.info("datasourcePath: {}", datasourcePath);
|
||||
String datasourcePath = parser.get("hostedBy");
|
||||
log.info("datasourcePath: {}", datasourcePath);
|
||||
|
||||
String country = parser.get("country");
|
||||
log.info("country: {}", country);
|
||||
String country = parser.get("country");
|
||||
log.info("country: {}", country);
|
||||
|
||||
String[] verifyParam = parser.get("verifyParam").split(";");
|
||||
log.info("verifyParam: {}", verifyParam);
|
||||
String[] verifyParam = parser.get("verifyParam").split(";");
|
||||
log.info("verifyParam: {}", verifyParam);
|
||||
|
||||
String collectedfrom = parser.get("collectedfrom");
|
||||
log.info("collectedfrom: {}", collectedfrom);
|
||||
String collectedfrom = parser.get("collectedfrom");
|
||||
log.info("collectedfrom: {}", collectedfrom);
|
||||
|
||||
String graphTableClassName = parser.get("graphTableClassName");
|
||||
log.info("graphTableClassName: {}", graphTableClassName);
|
||||
String graphTableClassName = parser.get("graphTableClassName");
|
||||
log.info("graphTableClassName: {}", graphTableClassName);
|
||||
|
||||
Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
|
||||
Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
|
||||
cleanCountry(
|
||||
spark, country, verifyParam, inputPath, entityClazz, workingDir, collectedfrom, datasourcePath);
|
||||
});
|
||||
}
|
||||
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) {
|
||||
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();
|
||||
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));
|
||||
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;
|
||||
}
|
||||
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()));
|
||||
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);
|
||||
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);
|
||||
}
|
||||
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());
|
||||
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> 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());
|
||||
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);
|
||||
}
|
||||
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 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"));
|
||||
}
|
||||
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"));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -31,76 +31,76 @@ import scala.Tuple2;
|
|||
* @Date 22/07/22
|
||||
*/
|
||||
public class GetDatasourceFromCountry implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class);
|
||||
private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
GetDatasourceFromCountry.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json"));
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
GetDatasourceFromCountry.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/graph/input_datasource_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);
|
||||
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 inputPath = parser.get("inputPath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
String workingPath = parser.get("workingDir");
|
||||
log.info("workingDir: {}", workingPath);
|
||||
String workingPath = parser.get("workingDir");
|
||||
log.info("workingDir: {}", workingPath);
|
||||
|
||||
String country = parser.get("country");
|
||||
log.info("country: {}", country);
|
||||
String country = parser.get("country");
|
||||
log.info("country: {}", country);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
getDatasourceFromCountry(spark, country, inputPath, workingPath);
|
||||
});
|
||||
}
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
getDatasourceFromCountry(spark, country, inputPath, workingPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath,
|
||||
String workingDir) {
|
||||
private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath,
|
||||
String workingDir) {
|
||||
|
||||
Dataset<Organization> organization = spark
|
||||
.read()
|
||||
.textFile(inputPath + "/organization")
|
||||
.map(
|
||||
(MapFunction<String, Organization>) value -> OBJECT_MAPPER.readValue(value, Organization.class),
|
||||
Encoders.bean(Organization.class))
|
||||
.filter(
|
||||
(FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference() &&
|
||||
o.getCountry().getClassid().length() > 0 &&
|
||||
o.getCountry().getClassid().equals(country));
|
||||
Dataset<Organization> organization = spark
|
||||
.read()
|
||||
.textFile(inputPath + "/organization")
|
||||
.map(
|
||||
(MapFunction<String, Organization>) value -> OBJECT_MAPPER.readValue(value, Organization.class),
|
||||
Encoders.bean(Organization.class))
|
||||
.filter(
|
||||
(FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference() &&
|
||||
o.getCountry().getClassid().length() > 0 &&
|
||||
o.getCountry().getClassid().equals(country));
|
||||
|
||||
// filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass
|
||||
Dataset<Relation> relation = spark
|
||||
.read()
|
||||
.textFile(inputPath + "/relation")
|
||||
.map(
|
||||
(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
|
||||
Encoders.bean(Relation.class))
|
||||
.filter(
|
||||
(FilterFunction<Relation>) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) &&
|
||||
!rel.getDataInfo().getDeletedbyinference());
|
||||
// filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass
|
||||
Dataset<Relation> relation = spark
|
||||
.read()
|
||||
.textFile(inputPath + "/relation")
|
||||
.map(
|
||||
(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
|
||||
Encoders.bean(Relation.class))
|
||||
.filter(
|
||||
(FilterFunction<Relation>) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) &&
|
||||
!rel.getDataInfo().getDeletedbyinference());
|
||||
|
||||
organization
|
||||
.joinWith(relation, organization.col("id").equalTo(relation.col("target")))
|
||||
.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getSource(), Encoders.STRING())
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(workingDir);
|
||||
organization
|
||||
.joinWith(relation, organization.col("id").equalTo(relation.col("target")))
|
||||
.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getSource(), Encoders.STRING())
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(workingDir);
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,7 +5,6 @@ import java.io.IOException;
|
|||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
|
|
@ -27,165 +26,165 @@ import org.slf4j.LoggerFactory;
|
|||
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 final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static SparkSession spark;
|
||||
private static SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
private static Path workingDir;
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
|
||||
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);
|
||||
@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());
|
||||
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());
|
||||
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();
|
||||
}
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(CleanCountryTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
@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();
|
||||
@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");
|
||||
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()
|
||||
});
|
||||
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));
|
||||
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());
|
||||
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 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 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 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());
|
||||
}
|
||||
// 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();
|
||||
@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");
|
||||
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()
|
||||
});
|
||||
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));
|
||||
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(1, tmp.count());
|
||||
|
||||
Assertions.assertEquals(0, tmp.first().getCountry().size());
|
||||
Assertions.assertEquals(0, tmp.first().getCountry().size());
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -12,7 +12,6 @@ import java.util.Objects;
|
|||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.dom4j.DocumentException;
|
||||
|
|
@ -22,6 +21,7 @@ import org.junit.jupiter.api.extension.ExtendWith;
|
|||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
|
||||
|
|
@ -995,7 +995,7 @@ class MappersTest {
|
|||
@Test
|
||||
void testEoscFutureHackZenodo() throws IOException {
|
||||
final String xml = IOUtils
|
||||
.toString(Objects.requireNonNull(getClass().getResourceAsStream("zenodo7351221.xml")));
|
||||
.toString(Objects.requireNonNull(getClass().getResourceAsStream("zenodo7351221.xml")));
|
||||
|
||||
final List<Oaf> actual = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
||||
actual.forEach(a -> {
|
||||
|
|
|
|||
Loading…
Reference in New Issue