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[Country Propagation] left out from previous commit

This commit is contained in:
Miriam Baglioni 2022-03-11 14:17:02 +01:00
parent 2fbb35ade5
commit 12de9acb0d
6 changed files with 383 additions and 199 deletions
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3
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java
View File

@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Arrays;
import java.util.List;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -20,6 +19,8 @@ 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.Datasource;

1
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java
View File

@ -80,7 +80,6 @@ public class SparkCountryPropagationJob {
String outputPath,
Class<R> resultClazz) {
log.info("Reading Graph table from: {}", sourcePath);
Dataset<R> res = readPath(spark, sourcePath, resultClazz);

116
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/CountryPropagationJobTest.java
View File

@ -7,7 +7,6 @@ import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
import eu.dnetlib.dhp.schema.oaf.Publication;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
@ -25,6 +24,7 @@ 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;
@ -285,41 +285,117 @@ public class CountryPropagationJobTest {
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.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())));
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();
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();
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();
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")));
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();
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")));
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();
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")));
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")));
}
}

129
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java
View File

@ -1,23 +1,21 @@
package eu.dnetlib.dhp.countrypropagation;
import com.fasterxml.jackson.databind.ObjectMapper;
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.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 java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import com.fasterxml.jackson.databind.ObjectMapper;
public class DatasourceCountryPreparationTest {
@ -67,7 +65,8 @@ public class DatasourceCountryPreparationTest {
"--sourcePath", sourcePath,
"--outputPath", workingDir.toString() + "/datasourceCountry",
"--allowedtypes", "pubsrepository::institutional",
"--whitelist","10|openaire____::3795d6478e30e2c9f787d427ff160944;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0;10|eurocrisdris::fe4903425d9040f680d8610d9079ea14;10|openaire____::5b76240cc27a58c6f7ceef7d8c36660e;10|openaire____::172bbccecf8fca44ab6a6653e84cb92a;10|openaire____::149c6590f8a06b46314eed77bfca693f;10|eurocrisdris::a6026877c1a174d60f81fd71f62df1c1;10|openaire____::4692342f0992d91f9e705c26959f09e0;10|openaire____::8d529dbb05ec0284662b391789e8ae2a;10|openaire____::345c9d171ef3c5d706d08041d506428c;10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0;10|opendoar____::7a614fd06c325499f1680b9896beedeb;10|opendoar____::1ee3dfcd8a0645a25a35977997223d22;10|opendoar____::d296c101daa88a51f6ca8cfc1ac79b50;10|opendoar____::798ed7d4ee7138d49b8828958048130a;10|openaire____::c9d2209ecc4d45ba7b4ca7597acb88a2;10|eurocrisdris::c49e0fe4b9ba7b7fab717d1f0f0a674d;10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539;10|eurocrisdris::432ca599953ff50cd4eeffe22faf3e48"
"--whitelist",
"10|openaire____::3795d6478e30e2c9f787d427ff160944;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0;10|eurocrisdris::fe4903425d9040f680d8610d9079ea14;10|openaire____::5b76240cc27a58c6f7ceef7d8c36660e;10|openaire____::172bbccecf8fca44ab6a6653e84cb92a;10|openaire____::149c6590f8a06b46314eed77bfca693f;10|eurocrisdris::a6026877c1a174d60f81fd71f62df1c1;10|openaire____::4692342f0992d91f9e705c26959f09e0;10|openaire____::8d529dbb05ec0284662b391789e8ae2a;10|openaire____::345c9d171ef3c5d706d08041d506428c;10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0;10|opendoar____::7a614fd06c325499f1680b9896beedeb;10|opendoar____::1ee3dfcd8a0645a25a35977997223d22;10|opendoar____::d296c101daa88a51f6ca8cfc1ac79b50;10|opendoar____::798ed7d4ee7138d49b8828958048130a;10|openaire____::c9d2209ecc4d45ba7b4ca7597acb88a2;10|eurocrisdris::c49e0fe4b9ba7b7fab717d1f0f0a674d;10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539;10|eurocrisdris::432ca599953ff50cd4eeffe22faf3e48"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -77,33 +76,99 @@ public class DatasourceCountryPreparationTest {
.map(item -> OBJECT_MAPPER.readValue(item, DatasourceCountry.class));
Assertions.assertEquals(3, tmp.count());
Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).count());
Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).count());
Assertions.assertEquals(1, tmp.filter(dsc -> dsc.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).count());
Assertions
.assertEquals(
1, tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
.count());
Assertions
.assertEquals(
1, tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
.count());
Assertions
.assertEquals(
1, tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
.count());
Assertions.assertEquals("NL", tmp.filter(dsc -> dsc.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).collect()
.get(0).getCountry().getClassid());
Assertions.assertEquals("Netherlands", tmp.filter(dsc -> dsc.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14")).collect()
.get(0).getCountry().getClassname());
Assertions
.assertEquals(
"NL", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
.collect()
.get(0)
.getCountry()
.getClassid());
Assertions
.assertEquals(
"Netherlands", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
.collect()
.get(0)
.getCountry()
.getClassname());
Assertions.assertEquals("IT", tmp.filter(dsc -> dsc.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).collect()
.get(0).getCountry().getClassid());
Assertions.assertEquals("Italy", tmp.filter(dsc -> dsc.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280")).collect()
.get(0).getCountry().getClassname());
Assertions
.assertEquals(
"IT", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
.collect()
.get(0)
.getCountry()
.getClassid());
Assertions
.assertEquals(
"Italy", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
.collect()
.get(0)
.getCountry()
.getClassname());
Assertions.assertEquals("FR", tmp.filter(dsc -> dsc.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).collect()
.get(0).getCountry().getClassid());
Assertions.assertEquals("France", tmp.filter(dsc -> dsc.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539")).collect()
.get(0).getCountry().getClassname());
Assertions
.assertEquals(
"FR", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
.collect()
.get(0)
.getCountry()
.getClassid());
Assertions
.assertEquals(
"France", tmp
.filter(
dsc -> dsc
.getDataSourceId()
.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
.collect()
.get(0)
.getCountry()
.getClassname());
tmp.foreach(e -> System.out.println(OBJECT_MAPPER.writeValueAsString(e)));

85
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java
View File

@ -1,8 +1,12 @@
package eu.dnetlib.dhp.countrypropagation;
import com.fasterxml.jackson.databind.ObjectMapper;
import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import eu.dnetlib.dhp.schema.oaf.Publication;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
@ -13,11 +17,9 @@ import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import com.fasterxml.jackson.databind.ObjectMapper;
import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class ResultCountryPreparationTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@ -63,7 +65,6 @@ public class ResultCountryPreparationTest {
.getResource("/eu/dnetlib/dhp/countrypropagation/datasourcecountry")
.getPath();
PrepareResultCountrySet
.main(
new String[] {
@ -81,35 +82,77 @@ public class ResultCountryPreparationTest {
.textFile(workingDir.toString() + "/resultCountry")
.map(item -> OBJECT_MAPPER.readValue(item, ResultCountrySet.class));
Assertions.assertEquals(5, tmp.count());
ResultCountrySet rc = tmp.filter(r -> r.getResultId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072")).collect().get(0);
ResultCountrySet rc = tmp
.filter(r -> r.getResultId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072"))
.collect()
.get(0);
Assertions.assertEquals(1, rc.getCountrySet().size());
Assertions.assertEquals("NL", rc.getCountrySet().get(0).getClassid());
Assertions.assertEquals("Netherlands", rc.getCountrySet().get(0).getClassname());
rc = tmp.filter(r -> r.getResultId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b")).collect().get(0);
rc = tmp
.filter(r -> r.getResultId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b"))
.collect()
.get(0);
Assertions.assertEquals(1, rc.getCountrySet().size());
Assertions.assertEquals("NL", rc.getCountrySet().get(0).getClassid());
Assertions.assertEquals("Netherlands", rc.getCountrySet().get(0).getClassname());
rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6")).collect().get(0);
rc = tmp
.filter(r -> r.getResultId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6"))
.collect()
.get(0);
Assertions.assertEquals(2, rc.getCountrySet().size());
Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df")).collect().get(0);
rc = tmp
.filter(r -> r.getResultId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df"))
.collect()
.get(0);
Assertions.assertEquals(2, rc.getCountrySet().size());
Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
rc = tmp.filter(r -> r.getResultId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088")).collect().get(0);
rc = tmp
.filter(r -> r.getResultId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088"))
.collect()
.get(0);
Assertions.assertEquals(2, rc.getCountrySet().size());
Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions.assertTrue(rc.getCountrySet().stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
Assertions
.assertTrue(
rc
.getCountrySet()
.stream()
.anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
}
}