refactoring

This commit is contained in:
Miriam Baglioni 2020-04-27 10:57:50 +02:00
parent d30e710165
commit 6135096ef1
3 changed files with 517 additions and 260 deletions

View File

@ -1,10 +1,13 @@
package eu.dnetlib.dhp.countrypropagation; package eu.dnetlib.dhp.countrypropagation;
import com.google.gson.Gson; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Country; import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Software; import eu.dnetlib.dhp.schema.oaf.Software;
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.commons.io.FileUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
@ -16,18 +19,8 @@ import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import scala.Array;
import scala.Tuple2; import scala.Tuple2;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
public class CountryPropagationJobTest { public class CountryPropagationJobTest {
private static final Logger log = LoggerFactory.getLogger(CountryPropagationJobTest.class); private static final Logger log = LoggerFactory.getLogger(CountryPropagationJobTest.class);
@ -54,13 +47,11 @@ public class CountryPropagationJobTest {
conf.set("spark.sql.warehouse.dir", workingDir.toString()); conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession spark =
.builder() SparkSession.builder()
.appName(CountryPropagationJobTest.class.getSimpleName()) .appName(CountryPropagationJobTest.class.getSimpleName())
.config(conf) .config(conf)
.getOrCreate(); .getOrCreate();
} }
@AfterAll @AfterAll
@ -69,95 +60,190 @@ public class CountryPropagationJobTest {
spark.stop(); spark.stop();
} }
@Test @Test
public void testCountryPropagationSoftware() throws Exception { public void testCountryPropagationSoftware() throws Exception {
SparkCountryPropagationJob2.main(new String[]{ SparkCountryPropagationJob2.main(
"-isSparkSessionManaged", Boolean.FALSE.toString(), new String[] {
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/countrypropagation/sample/software").getPath(), "-isSparkSessionManaged",
"-hive_metastore_uris", "", Boolean.FALSE.toString(),
"-writeUpdate","false", "-sourcePath",
"-saveGraph","true", getClass()
"-resultTableName","eu.dnetlib.dhp.schema.oaf.Software", .getResource("/eu/dnetlib/dhp/countrypropagation/sample/software")
"-outputPath",workingDir.toString() + "/software", .getPath(),
"-preparedInfoPath", getClass().getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo").getPath(), "-hive_metastore_uris",
}); "",
"-saveGraph",
"true",
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath",
workingDir.toString() + "/software",
"-preparedInfoPath",
getClass()
.getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo")
.getPath(),
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Software> tmp = sc.textFile(workingDir.toString()+"/software") JavaRDD<Software> tmp =
.map(item -> OBJECT_MAPPER.readValue(item, Software.class)); sc.textFile(workingDir.toString() + "/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
//tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); // tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s));
Assertions.assertEquals(10, tmp.count()); Assertions.assertEquals(10, tmp.count());
Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class)); Dataset<Software> verificationDs =
spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
Assertions.assertEquals(6, verificationDs.filter("size(country) > 0").count()); 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) = 1").count());
Assertions.assertEquals(3, verificationDs.filter("size(country) = 2").count()); Assertions.assertEquals(3, verificationDs.filter("size(country) = 2").count());
Assertions.assertEquals(0, verificationDs.filter("size(country) > 2").count()); Assertions.assertEquals(0, verificationDs.filter("size(country) > 2").count());
Dataset<String> countryExploded =
verificationDs
.flatMap(row -> row.getCountry().iterator(), Encoders.bean(Country.class))
.map(c -> c.getClassid(), Encoders.STRING());
Dataset<String> countryExploded = verificationDs Assertions.assertEquals(9, countryExploded.count());
.flatMap(row -> row.getCountry().iterator(), Encoders.bean(Country.class))
.map(c -> c.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());
Assertions.assertEquals(1, countryExploded.filter("value = 'FR'").count()); Dataset<Tuple2<String, String>> countryExplodedWithCountryclassid =
Assertions.assertEquals(1, countryExploded.filter("value = 'TR'").count()); verificationDs.flatMap(
Assertions.assertEquals(2, countryExploded.filter("value = 'IT'").count()); row -> {
Assertions.assertEquals(1, countryExploded.filter("value = 'US'").count()); List<Tuple2<String, String>> prova = new ArrayList();
Assertions.assertEquals(1, countryExploded.filter("value = 'MX'").count()); List<Country> country_list = row.getCountry();
Assertions.assertEquals(1, countryExploded.filter("value = 'CH'").count()); country_list.stream()
Assertions.assertEquals(2, countryExploded.filter("value = 'JP'").count()); .forEach(
c ->
prova.add(
new Tuple2<>(
row.getId(), c.getClassid())));
return prova.iterator();
},
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
Dataset<Tuple2<String, String>> countryExplodedWithCountryclassid = verificationDs Assertions.assertEquals(9, countryExplodedWithCountryclassid.count());
.flatMap(row -> {
List<Tuple2<String, String>> prova = new ArrayList();
List<Country> country_list = row.getCountry();
country_list.stream().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());
countryExplodedWithCountryclassid.show(false); Dataset<Tuple2<String, String>> countryExplodedWithCountryclassname =
Assertions.assertEquals(1, countryExplodedWithCountryclassid.filter("_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'FR' ").count()); verificationDs.flatMap(
Assertions.assertEquals(1, countryExplodedWithCountryclassid.filter("_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'TR' ").count()); row -> {
Assertions.assertEquals(2, countryExplodedWithCountryclassid.filter("_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'IT' or _2 = 'MX') ").count()); List<Tuple2<String, String>> prova = new ArrayList();
Assertions.assertEquals(2, countryExplodedWithCountryclassid.filter("_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'IT' or _2 = 'US') ").count()); List<Country> country_list = row.getCountry();
Assertions.assertEquals(1, countryExplodedWithCountryclassid.filter("_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'JP'").count()); country_list.stream()
Assertions.assertEquals(2, countryExplodedWithCountryclassid.filter("_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'CH' or _2 = 'JP') ").count()); .forEach(
c ->
prova.add(
new Tuple2<>(
row.getId(),
c.getClassname())));
return prova.iterator();
},
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
Dataset<Tuple2<String, String>> countryExplodedWithCountryclassname = verificationDs countryExplodedWithCountryclassname.show(false);
.flatMap(row -> { Assertions.assertEquals(
List<Tuple2<String, String>> prova = new ArrayList(); 1,
List<Country> country_list = row.getCountry(); countryExplodedWithCountryclassname
country_list.stream().forEach(c -> prova.add(new Tuple2<>(row.getId(), c.getClassname()))); .filter(
return prova.iterator(); "_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'France' ")
}, Encoders.tuple(Encoders.STRING(), Encoders.STRING())); .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());
countryExplodedWithCountryclassname.show(false); Dataset<Tuple2<String, String>> countryExplodedWithCountryProvenance =
Assertions.assertEquals(1, countryExplodedWithCountryclassname.filter("_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'France' ").count()); verificationDs.flatMap(
Assertions.assertEquals(1, countryExplodedWithCountryclassname.filter("_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'Turkey' ").count()); row -> {
Assertions.assertEquals(2, countryExplodedWithCountryclassname.filter("_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'Italy' or _2 = 'Mexico') ").count()); List<Tuple2<String, String>> prova = new ArrayList();
Assertions.assertEquals(2, countryExplodedWithCountryclassname.filter("_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'Italy' or _2 = 'United States') ").count()); List<Country> country_list = row.getCountry();
Assertions.assertEquals(1, countryExplodedWithCountryclassname.filter("_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'Japan' ").count()); country_list.stream()
Assertions.assertEquals(2, countryExplodedWithCountryclassname.filter("_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'Switzerland' or _2 = 'Japan') ").count()); .forEach(
c ->
Dataset<Tuple2<String, String>> countryExplodedWithCountryProvenance = verificationDs prova.add(
.flatMap(row -> { new Tuple2<>(
List<Tuple2<String, String>> prova = new ArrayList(); row.getId(),
List<Country> country_list = row.getCountry(); c.getDataInfo()
country_list.stream().forEach(c -> prova.add(new Tuple2<>(row.getId(), c.getDataInfo().getInferenceprovenance()))); .getInferenceprovenance())));
return prova.iterator(); return prova.iterator();
}, Encoders.tuple(Encoders.STRING(), Encoders.STRING())); },
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
Assertions.assertEquals(7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count());
}
Assertions.assertEquals(
7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count());
}
} }

View File

@ -1,8 +1,10 @@
package eu.dnetlib.dhp.orcidtoresultfromsemrel; package eu.dnetlib.dhp.orcidtoresultfromsemrel;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.resulttoorganizationfrominstrepo.Result2OrganizationJobTest;
import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.Dataset;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
@ -17,23 +19,18 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
public class OrcidPropagationJobTest { public class OrcidPropagationJobTest {
private static final Logger log = LoggerFactory.getLogger(Result2OrganizationJobTest.class); private static final Logger log = LoggerFactory.getLogger(OrcidPropagationJobTest.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ClassLoader cl = Result2OrganizationJobTest.class.getClassLoader(); private static final ClassLoader cl = OrcidPropagationJobTest.class.getClassLoader();
private static SparkSession spark; private static SparkSession spark;
private static Path workingDir; private static Path workingDir;
@BeforeAll @BeforeAll
public static void beforeAll() throws IOException { public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(OrcidPropagationJobTest.class.getSimpleName()); workingDir = Files.createTempDirectory(OrcidPropagationJobTest.class.getSimpleName());
@ -49,13 +46,11 @@ public class OrcidPropagationJobTest {
conf.set("spark.sql.warehouse.dir", workingDir.toString()); conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark =
spark = SparkSession SparkSession.builder()
.builder() .appName(OrcidPropagationJobTest.class.getSimpleName())
.appName(OrcidPropagationJobTest.class.getSimpleName()) .config(conf)
.config(conf) .getOrCreate();
.getOrCreate();
} }
@AfterAll @AfterAll
@ -64,132 +59,194 @@ public class OrcidPropagationJobTest {
spark.stop(); spark.stop();
} }
@Test @Test
public void noUpdateTest()throws Exception{ public void noUpdateTest() throws Exception {
SparkOrcidToResultFromSemRelJob3.main(new String[]{ SparkOrcidToResultFromSemRelJob3.main(
"-isTest", Boolean.TRUE.toString(), new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isTest",
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate").getPath(), Boolean.TRUE.toString(),
"-hive_metastore_uris", "", "-isSparkSessionManaged",
"-saveGraph","true", Boolean.FALSE.toString(),
"-resultTableName","eu.dnetlib.dhp.schema.oaf.Dataset", "-sourcePath",
"-outputPath",workingDir.toString() + "/dataset", getClass()
"-possibleUpdatesPath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc").getPath() .getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/noupdate")
}); .getPath(),
"-hive_metastore_uris",
"",
"-saveGraph",
"true",
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-possibleUpdatesPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc")
.getPath()
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc.textFile(workingDir.toString()+"/dataset") JavaRDD<Dataset> tmp =
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); sc.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
//tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); // tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s));
Assertions.assertEquals(10, tmp.count()); Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); org.apache.spark.sql.Dataset<Dataset> verificationDataset =
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset"); verificationDataset.createOrReplaceTempView("dataset");
String query = "select id " + String query =
"from dataset " + "select id "
"lateral view explode(author) a as MyT " + + "from dataset "
"lateral view explode(MyT.pid) p as MyP " + + "lateral view explode(author) a as MyT "
"where MyP.datainfo.inferenceprovenance = 'propagation'"; + "lateral view explode(MyT.pid) p as MyP "
+ "where MyP.datainfo.inferenceprovenance = 'propagation'";
Assertions.assertEquals(0, spark.sql(query).count()); Assertions.assertEquals(0, spark.sql(query).count());
} }
@Test @Test
public void oneUpdateTest() throws Exception{ public void oneUpdateTest() throws Exception {
SparkOrcidToResultFromSemRelJob3.main(new String[]{ SparkOrcidToResultFromSemRelJob3.main(
"-isTest", Boolean.TRUE.toString(), new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isTest",
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/oneupdate").getPath(), Boolean.TRUE.toString(),
"-hive_metastore_uris", "", "-isSparkSessionManaged",
"-saveGraph","true", Boolean.FALSE.toString(),
"-resultTableName","eu.dnetlib.dhp.schema.oaf.Dataset", "-sourcePath",
"-outputPath",workingDir.toString() + "/dataset", getClass()
"-possibleUpdatesPath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc").getPath() .getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/oneupdate")
}); .getPath(),
"-hive_metastore_uris",
"",
"-saveGraph",
"true",
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-possibleUpdatesPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc")
.getPath()
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc.textFile(workingDir.toString()+"/dataset") JavaRDD<Dataset> tmp =
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); sc.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
//tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s)); // tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s));
Assertions.assertEquals(10, tmp.count()); Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); org.apache.spark.sql.Dataset<Dataset> verificationDataset =
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset"); verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.name name, MyT.surname surname, MyP.value pid, MyP.qualifier.classid pidType " + String query =
"from dataset " + "select id, MyT.name name, MyT.surname surname, MyP.value pid, MyP.qualifier.classid pidType "
"lateral view explode(author) a as MyT " + + "from dataset "
"lateral view explode(MyT.pid) p as MyP " + + "lateral view explode(author) a as MyT "
"where MyP.datainfo.inferenceprovenance = 'propagation'"; + "lateral view explode(MyT.pid) p as MyP "
+ "where MyP.datainfo.inferenceprovenance = 'propagation'";
org.apache.spark.sql.Dataset<Row> propagatedAuthors = spark.sql(query); org.apache.spark.sql.Dataset<Row> propagatedAuthors = spark.sql(query);
Assertions.assertEquals(1, propagatedAuthors.count()); Assertions.assertEquals(1, propagatedAuthors.count());
Assertions.assertEquals(1, propagatedAuthors.filter("id = '50|dedup_wf_001::95b033c0c3961f6a1cdcd41a99a9632e' " + Assertions.assertEquals(
"and name = 'Vajinder' and surname = 'Kumar' and pidType = 'ORCID'").count()); 1,
propagatedAuthors
.filter(
"id = '50|dedup_wf_001::95b033c0c3961f6a1cdcd41a99a9632e' "
+ "and name = 'Vajinder' and surname = 'Kumar' and pidType = 'ORCID'")
.count());
Assertions.assertEquals(1, propagatedAuthors.filter("pid = '0000-0002-8825-3517'").count()); Assertions.assertEquals(1, propagatedAuthors.filter("pid = '0000-0002-8825-3517'").count());
} }
@Test @Test
public void twoUpdatesTest() throws Exception{ public void twoUpdatesTest() throws Exception {
SparkOrcidToResultFromSemRelJob3.main(new String[]{ SparkOrcidToResultFromSemRelJob3.main(
"-isTest", Boolean.TRUE.toString(), new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isTest",
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/twoupdates").getPath(), Boolean.TRUE.toString(),
"-hive_metastore_uris", "", "-isSparkSessionManaged",
"-saveGraph","true", Boolean.FALSE.toString(),
"-resultTableName","eu.dnetlib.dhp.schema.oaf.Dataset", "-sourcePath",
"-outputPath",workingDir.toString() + "/dataset", getClass()
"-possibleUpdatesPath", getClass().getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc").getPath() .getResource(
}); "/eu/dnetlib/dhp/orcidtoresultfromsemrel/sample/twoupdates")
.getPath(),
"-hive_metastore_uris",
"",
"-saveGraph",
"true",
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-possibleUpdatesPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparedInfo/mergedOrcidAssoc")
.getPath()
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc.textFile(workingDir.toString()+"/dataset") JavaRDD<Dataset> tmp =
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); sc.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count()); Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class)); org.apache.spark.sql.Dataset<Dataset> verificationDataset =
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset"); verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.name name, MyT.surname surname, MyP.value pid, MyP.qualifier.classid pidType " + String query =
"from dataset " + "select id, MyT.name name, MyT.surname surname, MyP.value pid, MyP.qualifier.classid pidType "
"lateral view explode(author) a as MyT " + + "from dataset "
"lateral view explode(MyT.pid) p as MyP " + + "lateral view explode(author) a as MyT "
"where MyP.datainfo.inferenceprovenance = 'propagation'"; + "lateral view explode(MyT.pid) p as MyP "
+ "where MyP.datainfo.inferenceprovenance = 'propagation'";
org.apache.spark.sql.Dataset<Row> propagatedAuthors = spark.sql(query); org.apache.spark.sql.Dataset<Row> propagatedAuthors = spark.sql(query);
Assertions.assertEquals(2, propagatedAuthors.count()); Assertions.assertEquals(2, propagatedAuthors.count());
Assertions.assertEquals(1, propagatedAuthors.filter("name = 'Marc' and surname = 'Schmidtmann'").count()); Assertions.assertEquals(
Assertions.assertEquals(1, propagatedAuthors.filter("name = 'Ruediger' and surname = 'Beckhaus'").count()); 1, propagatedAuthors.filter("name = 'Marc' and surname = 'Schmidtmann'").count());
Assertions.assertEquals(
1, propagatedAuthors.filter("name = 'Ruediger' and surname = 'Beckhaus'").count());
query = "select id, MyT.name name, MyT.surname surname, MyP.value pid ,MyP.qualifier.classid pidType " + query =
"from dataset " + "select id, MyT.name name, MyT.surname surname, MyP.value pid ,MyP.qualifier.classid pidType "
"lateral view explode(author) a as MyT " + + "from dataset "
"lateral view explode(MyT.pid) p as MyP "; + "lateral view explode(author) a as MyT "
+ "lateral view explode(MyT.pid) p as MyP ";
org.apache.spark.sql.Dataset<Row> authorsExplodedPids = spark.sql(query); org.apache.spark.sql.Dataset<Row> authorsExplodedPids = spark.sql(query);
Assertions.assertEquals(2, authorsExplodedPids.filter("name = 'Marc' and surname = 'Schmidtmann'").count()); Assertions.assertEquals(
Assertions.assertEquals(1, authorsExplodedPids.filter("name = 'Marc' and surname = 'Schmidtmann' and pidType = 'MAG Identifier'").count()); 2, authorsExplodedPids.filter("name = 'Marc' and surname = 'Schmidtmann'").count());
Assertions.assertEquals(
1,
authorsExplodedPids
.filter(
"name = 'Marc' and surname = 'Schmidtmann' and pidType = 'MAG Identifier'")
.count());
} }
} }

View File

@ -2,6 +2,9 @@ package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
@ -16,10 +19,6 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
public class Result2OrganizationJobTest { public class Result2OrganizationJobTest {
private static final Logger log = LoggerFactory.getLogger(Result2OrganizationJobTest.class); private static final Logger log = LoggerFactory.getLogger(Result2OrganizationJobTest.class);
@ -32,10 +31,11 @@ public class Result2OrganizationJobTest {
private static Path workingDir; private static Path workingDir;
@BeforeAll @BeforeAll
public static void beforeAll() throws IOException { public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName()); workingDir =
Files.createTempDirectory(
SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName());
log.info("using work dir {}", workingDir); log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
@ -48,13 +48,11 @@ public class Result2OrganizationJobTest {
conf.set("spark.sql.warehouse.dir", workingDir.toString()); conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark =
spark = SparkSession SparkSession.builder()
.builder() .appName(SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName())
.appName(SparkResultToOrganizationFromIstRepoJob2.class.getSimpleName()) .config(conf)
.config(conf) .getOrCreate();
.getOrCreate();
} }
@AfterAll @AfterAll
@ -65,109 +63,225 @@ public class Result2OrganizationJobTest {
/** /**
* No modifications done to the sample sets, so that no possible updates are created * No modifications done to the sample sets, so that no possible updates are created
*
* @throws Exception * @throws Exception
*/ */
@Test @Test
public void NoUpdateTest() throws Exception { public void NoUpdateTest() throws Exception {
SparkResultToOrganizationFromIstRepoJob2.main(new String[]{ SparkResultToOrganizationFromIstRepoJob2.main(
"-isTest", Boolean.TRUE.toString(), new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isTest",
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix").getPath(), Boolean.TRUE.toString(),
"-hive_metastore_uris", "", "-isSparkSessionManaged",
"-resultTableName","eu.dnetlib.dhp.schema.oaf.Software", Boolean.FALSE.toString(),
"-writeUpdate", "false", "-sourcePath",
"-saveGraph", "true", getClass()
"-outputPath", workingDir.toString() + "/relation", .getResource(
"-datasourceOrganizationPath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/datasourceOrganization").getPath(), "/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix")
"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/alreadyLinked").getPath(), .getPath(),
}); "-hive_metastore_uris",
"",
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Software",
"-writeUpdate",
"false",
"-saveGraph",
"true",
"-outputPath",
workingDir.toString() + "/relation",
"-datasourceOrganizationPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/datasourceOrganization")
.getPath(),
"-alreadyLinkedPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/noupdate/preparedInfo/alreadyLinked")
.getPath(),
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc.textFile(workingDir.toString()+"/relation") JavaRDD<Relation> tmp =
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); sc.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Assertions.assertEquals(0, tmp.count()); Assertions.assertEquals(0, tmp.count());
} }
/** /**
* Testing set with modified association between datasource and organization. Copied some hostedby collectedfrom * Testing set with modified association between datasource and organization. Copied some
* from the software sample set. No intersection with the already linked (all the possible new relations, will became * hostedby collectedfrom from the software sample set. No intersection with the already linked
* new relations) * (all the possible new relations, will became new relations)
*
* @throws Exception * @throws Exception
*/ */
@Test @Test
public void UpdateNoMixTest() throws Exception { public void UpdateNoMixTest() throws Exception {
SparkResultToOrganizationFromIstRepoJob2.main(new String[]{ SparkResultToOrganizationFromIstRepoJob2.main(
"-isTest", Boolean.TRUE.toString(), new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isTest",
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix").getPath(), Boolean.TRUE.toString(),
"-hive_metastore_uris", "", "-isSparkSessionManaged",
"-resultTableName","eu.dnetlib.dhp.schema.oaf.Software", Boolean.FALSE.toString(),
"-writeUpdate", "false", "-sourcePath",
"-saveGraph", "true", getClass()
"-outputPath", workingDir.toString() + "/relation", .getResource(
"-datasourceOrganizationPath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/datasourceOrganization").getPath(), "/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/noupdate_updatenomix")
"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked").getPath(), .getPath(),
}); "-hive_metastore_uris",
"",
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Software",
"-writeUpdate",
"false",
"-saveGraph",
"true",
"-outputPath",
workingDir.toString() + "/relation",
"-datasourceOrganizationPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/datasourceOrganization")
.getPath(),
"-alreadyLinkedPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatenomix/preparedInfo/alreadyLinked")
.getPath(),
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc.textFile(workingDir.toString()+"/relation") JavaRDD<Relation> tmp =
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); sc.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Assertions.assertEquals(20, tmp.count()); Assertions.assertEquals(20, tmp.count());
Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class)); Dataset<Relation> verificationDs =
Assertions.assertEquals(8, verificationDs.filter("target = '20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2'").count()); spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
Assertions.assertEquals(1, verificationDs.filter("target = '20|opendoar____::124266ebc4ece2934eb80edfda3f2091'").count()); Assertions.assertEquals(
Assertions.assertEquals(1, verificationDs.filter("target = '20|opendoar____::4429502fa1936b0941f4647b69b844c8'").count()); 8,
verificationDs
.filter("target = '20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2'")
.count());
Assertions.assertEquals(
1,
verificationDs
.filter("target = '20|opendoar____::124266ebc4ece2934eb80edfda3f2091'")
.count());
Assertions.assertEquals(
1,
verificationDs
.filter("target = '20|opendoar____::4429502fa1936b0941f4647b69b844c8'")
.count());
Assertions.assertEquals(2, verificationDs.filter("source = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and " + Assertions.assertEquals(
"(target = '20|opendoar____::124266ebc4ece2934eb80edfda3f2091' " + 2,
"or target = '20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2')").count()); verificationDs
.filter(
"source = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and "
+ "(target = '20|opendoar____::124266ebc4ece2934eb80edfda3f2091' "
+ "or target = '20|dedup_wf_001::5168917a6aeeea55269daeac1af2ecd2')")
.count());
} }
@Test @Test
public void UpdateMixTest() throws Exception { public void UpdateMixTest() throws Exception {
SparkResultToOrganizationFromIstRepoJob2.main(new String[]{ SparkResultToOrganizationFromIstRepoJob2.main(
"-isTest", Boolean.TRUE.toString(), new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isTest",
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/updatemix").getPath(), Boolean.TRUE.toString(),
"-hive_metastore_uris", "", "-isSparkSessionManaged",
"-resultTableName","eu.dnetlib.dhp.schema.oaf.Software", Boolean.FALSE.toString(),
"-writeUpdate", "false", "-sourcePath",
"-saveGraph", "true", getClass()
"-outputPath", workingDir.toString() + "/relation", .getResource(
"-datasourceOrganizationPath", getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/datasourceOrganization").getPath(), "/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/sample/updatemix")
"-alreadyLinkedPath",getClass().getResource("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked").getPath(), .getPath(),
}); "-hive_metastore_uris",
"",
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Software",
"-writeUpdate",
"false",
"-saveGraph",
"true",
"-outputPath",
workingDir.toString() + "/relation",
"-datasourceOrganizationPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/datasourceOrganization")
.getPath(),
"-alreadyLinkedPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/updatemix/preparedInfo/alreadyLinked")
.getPath(),
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc.textFile(workingDir.toString()+"/relation") JavaRDD<Relation> tmp =
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); sc.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class)); Dataset<Relation> verificationDs =
spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
Assertions.assertEquals(8, verificationDs.count()); Assertions.assertEquals(8, verificationDs.count());
Assertions.assertEquals(2, verificationDs.filter("source = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6'").count()); Assertions.assertEquals(
Assertions.assertEquals(1, verificationDs.filter("source = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218'").count()); 2,
Assertions.assertEquals(1, verificationDs.filter("source = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523'").count()); verificationDs
.filter("source = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6'")
.count());
Assertions.assertEquals(
1,
verificationDs
.filter("source = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218'")
.count());
Assertions.assertEquals(
1,
verificationDs
.filter("source = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523'")
.count());
Assertions.assertEquals(1, verificationDs.filter("source = '20|wt__________::a72760363ca885e6bef165804770e00c'").count()); Assertions.assertEquals(
1,
verificationDs
.filter("source = '20|wt__________::a72760363ca885e6bef165804770e00c'")
.count());
Assertions.assertEquals(4, verificationDs.filter("relclass = 'hasAuthorInstitution' and substring(source, 1,2) = '50'").count()); Assertions.assertEquals(
Assertions.assertEquals(4, verificationDs.filter("relclass = 'isAuthorInstitutionOf' and substring(source, 1,2) = '20'").count()); 4,
verificationDs
.filter(
"relclass = 'hasAuthorInstitution' and substring(source, 1,2) = '50'")
.count());
Assertions.assertEquals(
4,
verificationDs
.filter(
"relclass = 'isAuthorInstitutionOf' and substring(source, 1,2) = '20'")
.count());
Assertions.assertEquals(4, verificationDs.filter("relclass = 'hasAuthorInstitution' and " + Assertions.assertEquals(
"substring(source, 1,2) = '50' and substring(target, 1, 2) = '20'").count()); 4,
Assertions.assertEquals(4, verificationDs.filter("relclass = 'isAuthorInstitutionOf' and " + verificationDs
"substring(source, 1,2) = '20' and substring(target, 1, 2) = '50'").count()); .filter(
"relclass = 'hasAuthorInstitution' and "
+ "substring(source, 1,2) = '50' and substring(target, 1, 2) = '20'")
.count());
Assertions.assertEquals(
4,
verificationDs
.filter(
"relclass = 'isAuthorInstitutionOf' and "
+ "substring(source, 1,2) = '20' and substring(target, 1, 2) = '50'")
.count());
} }
} }