402 lines
13 KiB
Java
402 lines
13 KiB
Java
|
|
package eu.dnetlib.dhp.countrypropagation;
|
|
|
|
import java.io.IOException;
|
|
import java.nio.file.Files;
|
|
import java.nio.file.Path;
|
|
import java.util.ArrayList;
|
|
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.FlatMapFunction;
|
|
import org.apache.spark.api.java.function.MapFunction;
|
|
import org.apache.spark.sql.*;
|
|
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.Country;
|
|
import eu.dnetlib.dhp.schema.oaf.Publication;
|
|
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
|
import eu.dnetlib.dhp.schema.oaf.Software;
|
|
import scala.Tuple2;
|
|
|
|
public class CountryPropagationJobTest {
|
|
|
|
private static final Logger log = LoggerFactory.getLogger(CountryPropagationJobTest.class);
|
|
|
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
|
|
|
private static SparkSession spark;
|
|
|
|
private static Path workingDir;
|
|
|
|
@BeforeAll
|
|
public static void beforeAll() throws IOException {
|
|
workingDir = Files.createTempDirectory(CountryPropagationJobTest.class.getSimpleName());
|
|
log.info("using work dir {}", workingDir);
|
|
|
|
SparkConf conf = new SparkConf();
|
|
conf.setAppName(CountryPropagationJobTest.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(CountryPropagationJobTest.class.getSimpleName())
|
|
.config(conf)
|
|
.getOrCreate();
|
|
}
|
|
|
|
@AfterAll
|
|
public static void afterAll() throws IOException {
|
|
FileUtils.deleteDirectory(workingDir.toFile());
|
|
spark.stop();
|
|
}
|
|
|
|
@Test
|
|
void testCountryPropagationSoftware() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/countrypropagation/graph/software")
|
|
.getPath();
|
|
final String preparedInfoPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/software")
|
|
.getPath();
|
|
SparkCountryPropagationJob
|
|
.main(
|
|
new String[] {
|
|
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"--sourcePath", sourcePath,
|
|
"-resultTableName", Software.class.getCanonicalName(),
|
|
"-outputPath", workingDir.toString() + "/software",
|
|
"-preparedInfoPath", preparedInfoPath
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<Software> tmp = sc
|
|
.textFile(workingDir.toString() + "/software")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
|
|
|
Assertions.assertEquals(10, tmp.count());
|
|
|
|
Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
|
|
|
|
Assertions.assertEquals(6, verificationDs.filter("size(country) > 0").count());
|
|
Assertions.assertEquals(3, verificationDs.filter("size(country) = 1").count());
|
|
Assertions.assertEquals(3, verificationDs.filter("size(country) = 2").count());
|
|
Assertions.assertEquals(0, verificationDs.filter("size(country) > 2").count());
|
|
|
|
Dataset<String> countryExploded = verificationDs
|
|
.flatMap(
|
|
(FlatMapFunction<Software, Country>) row -> row.getCountry().iterator(), Encoders.bean(Country.class))
|
|
.map((MapFunction<Country, String>) Qualifier::getClassid, Encoders.STRING());
|
|
|
|
Assertions.assertEquals(9, countryExploded.count());
|
|
|
|
Assertions.assertEquals(1, countryExploded.filter("value = 'FR'").count());
|
|
Assertions.assertEquals(1, countryExploded.filter("value = 'TR'").count());
|
|
Assertions.assertEquals(2, countryExploded.filter("value = 'IT'").count());
|
|
Assertions.assertEquals(1, countryExploded.filter("value = 'US'").count());
|
|
Assertions.assertEquals(1, countryExploded.filter("value = 'MX'").count());
|
|
Assertions.assertEquals(1, countryExploded.filter("value = 'CH'").count());
|
|
Assertions.assertEquals(2, countryExploded.filter("value = 'JP'").count());
|
|
|
|
Dataset<Tuple2<String, String>> countryExplodedWithCountryclassid = verificationDs
|
|
.flatMap((FlatMapFunction<Software, Tuple2<String, String>>) row -> {
|
|
List<Tuple2<String, String>> prova = new ArrayList<>();
|
|
List<Country> countryList = row.getCountry();
|
|
countryList
|
|
.forEach(
|
|
c -> prova
|
|
.add(
|
|
new Tuple2<>(
|
|
row.getId(), c.getClassid())));
|
|
return prova.iterator();
|
|
}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
|
|
|
Assertions.assertEquals(9, countryExplodedWithCountryclassid.count());
|
|
|
|
countryExplodedWithCountryclassid.show(false);
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'FR' ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'TR' ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'IT' or _2 = 'MX') ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'IT' or _2 = 'US') ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'JP'")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'CH' or _2 = 'JP') ")
|
|
.count());
|
|
|
|
Dataset<Tuple2<String, String>> countryExplodedWithCountryclassname = verificationDs
|
|
.flatMap(
|
|
(FlatMapFunction<Software, Tuple2<String, String>>) row -> {
|
|
List<Tuple2<String, String>> prova = new ArrayList<>();
|
|
List<Country> countryList = row.getCountry();
|
|
countryList
|
|
.forEach(
|
|
c -> prova
|
|
.add(
|
|
new Tuple2<>(
|
|
row.getId(),
|
|
c.getClassname())));
|
|
return prova.iterator();
|
|
},
|
|
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
|
|
|
countryExplodedWithCountryclassname.show(false);
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'France' ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'Turkey' ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'Italy' or _2 = 'Mexico') ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'Italy' or _2 = 'United States') ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'Japan' ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'Switzerland' or _2 = 'Japan') ")
|
|
.count());
|
|
|
|
Dataset<Tuple2<String, String>> countryExplodedWithCountryProvenance = verificationDs
|
|
.flatMap(
|
|
(FlatMapFunction<Software, Tuple2<String, String>>) row -> {
|
|
List<Tuple2<String, String>> prova = new ArrayList<>();
|
|
List<Country> countryList = row.getCountry();
|
|
countryList
|
|
.forEach(
|
|
c -> prova
|
|
.add(
|
|
new Tuple2<>(
|
|
row.getId(),
|
|
c
|
|
.getDataInfo()
|
|
.getInferenceprovenance())));
|
|
return prova.iterator();
|
|
},
|
|
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count());
|
|
}
|
|
|
|
@Test
|
|
void testCountryPropagationPublication() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication")
|
|
.getPath();
|
|
final String preparedInfoPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo/publication")
|
|
.getPath();
|
|
SparkCountryPropagationJob
|
|
.main(
|
|
new String[] {
|
|
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"--sourcePath", sourcePath,
|
|
"-resultTableName", Publication.class.getCanonicalName(),
|
|
"-outputPath", workingDir.toString() + "/publication",
|
|
"-preparedInfoPath", preparedInfoPath
|
|
});
|
|
|
|
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(12, tmp.count());
|
|
|
|
Assertions.assertEquals(5, tmp.filter(r -> r.getCountry().size() > 0).count());
|
|
|
|
tmp
|
|
.foreach(
|
|
r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemeid())));
|
|
tmp
|
|
.foreach(
|
|
r -> r
|
|
.getCountry()
|
|
.stream()
|
|
.forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemename())));
|
|
tmp
|
|
.foreach(
|
|
r -> r
|
|
.getCountry()
|
|
.stream()
|
|
.forEach(c -> Assertions.assertFalse(c.getDataInfo().getDeletedbyinference())));
|
|
tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertFalse(c.getDataInfo().getInvisible())));
|
|
tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertTrue(c.getDataInfo().getInferred())));
|
|
tmp
|
|
.foreach(
|
|
r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("0.85", c.getDataInfo().getTrust())));
|
|
tmp
|
|
.foreach(
|
|
r -> r
|
|
.getCountry()
|
|
.stream()
|
|
.forEach(c -> Assertions.assertEquals("propagation", c.getDataInfo().getInferenceprovenance())));
|
|
tmp
|
|
.foreach(
|
|
r -> r
|
|
.getCountry()
|
|
.stream()
|
|
.forEach(
|
|
c -> Assertions
|
|
.assertEquals("country:instrepos", c.getDataInfo().getProvenanceaction().getClassid())));
|
|
tmp
|
|
.foreach(
|
|
r -> r
|
|
.getCountry()
|
|
.stream()
|
|
.forEach(
|
|
c -> Assertions
|
|
.assertEquals(
|
|
"dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemeid())));
|
|
tmp
|
|
.foreach(
|
|
r -> r
|
|
.getCountry()
|
|
.stream()
|
|
.forEach(
|
|
c -> Assertions
|
|
.assertEquals(
|
|
"dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemename())));
|
|
|
|
List<Country> countries = tmp
|
|
.filter(r -> r.getId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072"))
|
|
.collect()
|
|
.get(0)
|
|
.getCountry();
|
|
Assertions.assertEquals(1, countries.size());
|
|
Assertions.assertEquals("NL", countries.get(0).getClassid());
|
|
Assertions.assertEquals("Netherlands", countries.get(0).getClassname());
|
|
|
|
countries = tmp
|
|
.filter(r -> r.getId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b"))
|
|
.collect()
|
|
.get(0)
|
|
.getCountry();
|
|
Assertions.assertEquals(1, countries.size());
|
|
Assertions.assertEquals("NL", countries.get(0).getClassid());
|
|
Assertions.assertEquals("Netherlands", countries.get(0).getClassname());
|
|
|
|
countries = tmp
|
|
.filter(r -> r.getId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6"))
|
|
.collect()
|
|
.get(0)
|
|
.getCountry();
|
|
Assertions.assertEquals(2, countries.size());
|
|
Assertions
|
|
.assertTrue(
|
|
countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
|
|
Assertions
|
|
.assertTrue(
|
|
countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
|
|
|
|
countries = tmp
|
|
.filter(r -> r.getId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df"))
|
|
.collect()
|
|
.get(0)
|
|
.getCountry();
|
|
Assertions.assertEquals(2, countries.size());
|
|
Assertions
|
|
.assertTrue(
|
|
countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
|
|
Assertions
|
|
.assertTrue(
|
|
countries
|
|
.stream()
|
|
.anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
|
|
|
|
countries = tmp
|
|
.filter(r -> r.getId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088"))
|
|
.collect()
|
|
.get(0)
|
|
.getCountry();
|
|
Assertions.assertEquals(2, countries.size());
|
|
Assertions
|
|
.assertTrue(
|
|
countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
|
|
Assertions
|
|
.assertTrue(
|
|
countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
|
|
}
|
|
|
|
}
|