test for bulktag

This commit is contained in:
Miriam Baglioni 2020-04-23 10:00:10 +02:00
parent 259525cb93
commit 3b2e4ab670
13 changed files with 1957 additions and 135 deletions

View File

@ -1,13 +1,24 @@
package eu.dnetlib.dhp;
import static eu.dnetlib.dhp.community.TagginConstants.ZENODO_COMMUNITY_INDICATOR;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Software;
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.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.mortbay.util.IO;
@ -31,7 +42,7 @@ public class BulkTagJobTest {
taggingConf =
IO.toString(
BulkTagJobTest.class.getResourceAsStream(
"/eu/dnetlib/dhp/communityconfiguration/tagging_conf.json"));
"/eu/dnetlib/dhp/communityconfiguration/tagging_conf.xml"));
} catch (IOException e) {
e.printStackTrace();
}
@ -66,7 +77,7 @@ public class BulkTagJobTest {
}
@Test
public void test1() throws Exception {
public void noUpdatesTest() throws Exception {
SparkBulkTagJob2.main(
new String[] {
"-isTest",
@ -74,7 +85,7 @@ public class BulkTagJobTest {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/sample/dataset").getPath(),
getClass().getResource("/eu/dnetlib/dhp/sample/dataset/no_updates").getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
@ -92,142 +103,700 @@ public class BulkTagJobTest {
// "-preparedInfoPath",
// getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/preparedInfo").getPath()
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp =
sc.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset =
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset");
String query =
"select id, MyT.id community "
+ "from dataset "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
Assertions.assertEquals(0, spark.sql(query).count());
}
}
/*
import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest;
import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob2;
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;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
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 java.util.List;
import static org.apache.spark.sql.functions.desc;
@Test
public void test1() throws Exception {
SparkResultToCommunityThroughSemRelJob4.main(new String[]{
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/sample").getPath(),
"-hive_metastore_uris", "",
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset",
"-preparedInfoPath", getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/preparedInfo").getPath()
public void bulktagBySubjectNoPreviousContextTest() throws Exception {
SparkBulkTagJob2.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource("/eu/dnetlib/dhp/sample/dataset/update_subject/nocontext")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-isLookupUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-protoMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc.textFile(workingDir.toString() + "/dataset")
JavaRDD<Dataset> tmp =
sc.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
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");
String query = "select id, MyT.id community " +
"from dataset " +
"lateral view explode(context) c as MyT " +
"lateral view explode(MyT.datainfo) d as MyD " +
"where MyD.inferenceprovenance = 'propagation'";
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'";
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
Assertions.assertEquals(5, resultExplodedProvenance.count());
Assertions.assertEquals(5, spark.sql(query).count());
Assertions.assertEquals(0, resultExplodedProvenance.filter("id = '50|dedup_wf_001::2305908abeca9da37eaf3bddcaf81b7b'").count());
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
Assertions.assertEquals(
5, idExplodeCommunity.filter("provenance = 'community:subject'").count());
Assertions.assertEquals(
5,
idExplodeCommunity.filter("name = 'Bulktagging for Community - Subject'").count());
Assertions.assertEquals(1, resultExplodedProvenance.filter("id = '50|dedup_wf_001::0489ae524201eedaa775da282dce35e7'").count());
Assertions.assertEquals("dh-ch",resultExplodedProvenance.select("community")
.where(resultExplodedProvenance.col("id").equalTo("50|dedup_wf_001::0489ae524201eedaa775da282dce35e7"))
.collectAsList().get(0).getString(0));
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count());
Assertions.assertEquals(3, resultExplodedProvenance.filter("id = '50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28'").count());
List<Row> rowList = resultExplodedProvenance.select("community")
.where(resultExplodedProvenance.col("id")
.equalTo("50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28"))
.sort(desc("community")).collectAsList();
Assertions.assertEquals("mes", rowList.get(0).getString(0));
Assertions.assertEquals("fam", rowList.get(1).getString(0));
Assertions.assertEquals("ee", rowList.get(2).getString(0));
Assertions.assertEquals(1, resultExplodedProvenance.filter("id = '50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc'").count());
Assertions.assertEquals("aginfra", resultExplodedProvenance.select("community")
.where(resultExplodedProvenance.col("id")
.equalTo("50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc"))
.collectAsList().get(0).getString(0));
query = "select id, MyT.id community " +
"from dataset " +
"lateral view explode(context) c as MyT " +
"lateral view explode(MyT.datainfo) d as MyD ";
org.apache.spark.sql.Dataset<Row> resultCommunityId = spark.sql(query);
Assertions.assertEquals(10, resultCommunityId.count());
Assertions.assertEquals(2, resultCommunityId.filter("id = '50|dedup_wf_001::0489ae524201eedaa775da282dce35e7'").count());
rowList = resultCommunityId.select("community")
.where(resultCommunityId.col("id").equalTo("50|dedup_wf_001::0489ae524201eedaa775da282dce35e7"))
.sort(desc("community"))
.collectAsList();
Assertions.assertEquals("dh-ch", rowList.get(0).getString(0));
Assertions.assertEquals("beopen", rowList.get(1).getString(0));
Assertions.assertEquals(3, resultCommunityId.filter("id = '50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28'").count());
rowList = resultCommunityId.select("community")
.where(resultCommunityId.col("id").equalTo("50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28"))
.sort(desc("community"))
.collectAsList();
Assertions.assertEquals("mes", rowList.get(0).getString(0));
Assertions.assertEquals("fam", rowList.get(1).getString(0));
Assertions.assertEquals("ee", rowList.get(2).getString(0));
Assertions.assertEquals(2, resultCommunityId.filter("id = '50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc'").count());
rowList = resultCommunityId.select("community")
.where(resultCommunityId.col("id").equalTo("50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc"))
.sort(desc("community"))
.collectAsList();
Assertions.assertEquals("beopen", rowList.get(0).getString(0));
Assertions.assertEquals("aginfra", rowList.get(1).getString(0));
Assertions.assertEquals(2, resultCommunityId.filter("id = '50|dedup_wf_001::2305908abeca9da37eaf3bddcaf81b7b'").count());
rowList = resultCommunityId.select("community")
.where(resultCommunityId.col("id").equalTo("50|dedup_wf_001::2305908abeca9da37eaf3bddcaf81b7b"))
.sort(desc("community"))
.collectAsList();
Assertions.assertEquals("euromarine", rowList.get(1).getString(0));
Assertions.assertEquals("ni", rowList.get(0).getString(0));
Assertions.assertEquals(1, resultCommunityId.filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'").count());
Assertions.assertEquals("euromarine", resultCommunityId.select("community")
.where(resultCommunityId.col("id")
.equalTo("50|doajarticles::8d817039a63710fcf97e30f14662c6c8"))
.collectAsList().get(0).getString(0));
Assertions.assertEquals(
1,
idExplodeCommunity
.filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
.count());
Assertions.assertEquals(
1,
idExplodeCommunity
.filter(
"community = 'covid-19' and id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
.count());
Assertions.assertEquals(
2,
idExplodeCommunity
.filter("id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'")
.count());
Assertions.assertEquals(
2,
idExplodeCommunity
.filter(
"(community = 'covid-19' or community = 'aginfra') and id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'")
.count());
Assertions.assertEquals(
2,
idExplodeCommunity
.filter("id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'")
.count());
Assertions.assertEquals(
2,
idExplodeCommunity
.filter(
"(community = 'mes' or community = 'fam') and id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'")
.count());
}
*/
@Test
public void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception {
SparkBulkTagJob2.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource(
"/eu/dnetlib/dhp/sample/dataset/update_subject/contextnoprovenance")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-isLookupUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-protoMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp =
sc.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset =
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset");
String query =
"select id, MyT.id community, MyD.provenanceaction.classid provenance "
+ "from dataset "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyT.id = 'covid-19' ";
Assertions.assertEquals(3, spark.sql(query).count());
org.apache.spark.sql.Dataset<Row> communityContext = spark.sql(query);
Assertions.assertEquals(
2,
communityContext
.filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
.count());
Assertions.assertEquals(
1,
communityContext
.filter(
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'community:subject'")
.count());
Assertions.assertEquals(
1,
communityContext
.filter(
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'propagation:community:productsthroughsemrel'")
.count());
query =
"select id, MyT.id community, size(MyT.datainfo) datainfosize "
+ "from dataset "
+ "lateral view explode (context) as MyT "
+ "where size(MyT.datainfo) > 0";
Assertions.assertEquals(
2,
spark.sql(query)
.select("datainfosize")
.where(
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' a"
+ "nd community = 'covid-19'")
.collectAsList()
.get(0)
.getInt(0));
}
@Test
public void bulktagByDatasourceTest() throws Exception {
SparkBulkTagJob2.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource("/eu/dnetlib/dhp/sample/publication/update_datasource")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/publication",
"-isLookupUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-protoMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp =
sc.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Publication> verificationDataset =
spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
String query =
"select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from publication "
+ "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);
Assertions.assertEquals(5, idExplodeCommunity.count());
Assertions.assertEquals(
5, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
Assertions.assertEquals(
5,
idExplodeCommunity
.filter("name = 'Bulktagging for Community - Datasource'")
.count());
Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'fam'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count());
Assertions.assertEquals(
3,
idExplodeCommunity
.filter(
"community = 'fam' and (id = '50|ec_fp7health::000085c89f4b96dc2269bd37edb35306' "
+ "or id = '50|ec_fp7health::000b9e61f83f5a4b0c35777b7bccdf38' "
+ "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')")
.count());
Assertions.assertEquals(
2,
idExplodeCommunity
.filter(
"community = 'aginfra' and (id = '50|ec_fp7health::000c8195edd542e4e64ebb32172cbf89' "
+ "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')")
.count());
}
@Test
public void bulktagByZenodoCommunityTest() throws Exception {
SparkBulkTagJob2.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource(
"/eu/dnetlib/dhp/sample/otherresearchproduct/update_zenodocommunity")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
"-outputPath",
workingDir.toString() + "/orp",
"-isLookupUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-protoMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<OtherResearchProduct> tmp =
sc.textFile(workingDir.toString() + "/orp")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<OtherResearchProduct> verificationDataset =
spark.createDataset(tmp.rdd(), Encoders.bean(OtherResearchProduct.class));
verificationDataset.createOrReplaceTempView("orp");
String query =
"select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from orp "
+ "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);
Assertions.assertEquals(8, idExplodeCommunity.count());
Assertions.assertEquals(
8, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count());
Assertions.assertEquals(
8,
idExplodeCommunity.filter("name = 'Bulktagging for Community - Zenodo'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'covid-19'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'beopen'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'mes'").count());
Assertions.assertEquals(
1,
idExplodeCommunity
.filter(
"id = '50|od______2017::0750a4d0782265873d669520f5e33c07' "
+ "and community = 'covid-19'")
.count());
Assertions.assertEquals(
3,
idExplodeCommunity
.filter(
"id = '50|od______2017::1bd97baef19dbd2db3203b112bb83bc5' and "
+ "(community = 'aginfra' or community = 'mes' or community = 'fam')")
.count());
Assertions.assertEquals(
1,
idExplodeCommunity
.filter(
"id = '50|od______2017::1e400f1747487fd15998735c41a55c72' "
+ "and community = 'beopen'")
.count());
Assertions.assertEquals(
3,
idExplodeCommunity
.filter(
"id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' and "
+ "(community = 'beopen' or community = 'fam' or community = 'mes')")
.count());
query =
"select id, MyT.id community, size(MyT.datainfo) datainfosize "
+ "from orp "
+ "lateral view explode (context) as MyT "
+ "where size(MyT.datainfo) > 0";
Assertions.assertEquals(
2,
spark.sql(query)
.select("datainfosize")
.where(
"id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' a"
+ "nd community = 'beopen'")
.collectAsList()
.get(0)
.getInt(0));
// verify the zenodo community context is not present anymore in the records
query =
"select id, MyT.id community "
+ "from orp "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD ";
org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
Assertions.assertEquals(
0,
tmp2.select("community")
.where(tmp2.col("community").contains(ZENODO_COMMUNITY_INDICATOR))
.count());
}
@Test
public void bulktagBySubjectDatasourceTest() throws Exception {
SparkBulkTagJob2.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource("/eu/dnetlib/dhp/sample/dataset/update_subject_datasource")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-isLookupUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-protoMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp =
sc.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset =
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.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'";
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
Assertions.assertEquals(7, idExplodeCommunity.count());
Assertions.assertEquals(
5, idExplodeCommunity.filter("provenance = 'community:subject'").count());
Assertions.assertEquals(
2, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count());
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count());
query =
"select id, MyT.id community, size(MyT.datainfo) datainfosize "
+ "from dataset "
+ "lateral view explode (context) as MyT "
+ "where size(MyT.datainfo) > 0";
org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
Assertions.assertEquals(
2,
tmp2.select("datainfosize")
.where(
"id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and "
+ "community = 'aginfra'")
.collectAsList()
.get(0)
.getInt(0));
Assertions.assertEquals(
1,
tmp2.select("datainfosize")
.where(
"id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and "
+ "community = 'covid-19'")
.collectAsList()
.get(0)
.getInt(0));
Assertions.assertEquals(
2,
tmp2.select("datainfosize")
.where(
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and "
+ "community = 'fam'")
.collectAsList()
.get(0)
.getInt(0));
Assertions.assertEquals(
2,
tmp2.select("datainfosize")
.where(
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and "
+ "community = 'covid-19'")
.collectAsList()
.get(0)
.getInt(0));
Assertions.assertEquals(
1,
tmp2.select("datainfosize")
.where(
"id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and "
+ "community = 'fam'")
.collectAsList()
.get(0)
.getInt(0));
Assertions.assertEquals(
1,
tmp2.select("datainfosize")
.where(
"id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and "
+ "community = 'mes'")
.collectAsList()
.get(0)
.getInt(0));
}
@Test
public void bulktagBySubjectDatasourceZenodoCommunityTest() throws Exception {
SparkBulkTagJob2.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/sample/software/").getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath",
workingDir.toString() + "/software",
"-isLookupUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-protoMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Software> tmp =
sc.textFile(workingDir.toString() + "/software")
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Software> verificationDataset =
spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
verificationDataset.createOrReplaceTempView("software");
String query =
"select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+ "from software "
+ "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);
Assertions.assertEquals(10, idExplodeCommunity.count());
idExplodeCommunity.show(false);
Assertions.assertEquals(
3, idExplodeCommunity.filter("provenance = 'community:subject'").count());
Assertions.assertEquals(
3, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
Assertions.assertEquals(
4, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count());
Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'covid-19'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dh-ch'").count());
Assertions.assertEquals(4, idExplodeCommunity.filter("community = 'aginfra'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dariah'").count());
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count());
Assertions.assertEquals(
2,
idExplodeCommunity
.filter(
"provenance = 'community:zenodocommunity' and "
+ "id = '50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4' and ("
+ "community = 'dh-ch' or community = 'dariah')")
.count());
query =
"select id, MyT.id community, size(MyT.datainfo) datainfosize "
+ "from software "
+ "lateral view explode (context) as MyT "
+ "where size(MyT.datainfo) > 0";
org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
Assertions.assertEquals(
2,
tmp2.select("datainfosize")
.where(
"id = '50|od______1582::501b25d420f808c8eddcd9b16e917f11' and "
+ "community = 'covid-19'")
.collectAsList()
.get(0)
.getInt(0));
Assertions.assertEquals(
3,
tmp2.select("datainfosize")
.where(
"id = '50|od______1582::581621232a561b7e8b4952b18b8b0e56' and "
+ "community = 'aginfra'")
.collectAsList()
.get(0)
.getInt(0));
}
@Test
public void bulktagDatasourcewithConstraintsTest() throws Exception {
SparkBulkTagJob2.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource(
"/eu/dnetlib/dhp/sample/dataset/update_datasourcewithconstraints")
.getPath(),
"-taggingConf",
taggingConf,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-isLookupUrl",
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
"-protoMap",
"{ \"author\" : \"$['author'][*]['fullname']\","
+ " \"title\" : \"$['title'][*]['value']\","
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
+ " \"contributor\" : \"$['contributor'][*]['value']\","
+ " \"description\" : \"$['description'][*]['value']\"}"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp =
sc.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset =
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.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'";
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
idExplodeCommunity.show(false);
Assertions.assertEquals(2, idExplodeCommunity.count());
Assertions.assertEquals(
2, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
}
}

View File

@ -18,9 +18,6 @@ import org.junit.jupiter.api.Test;
/** Created by miriam on 03/08/2018. */
public class CommunityConfigurationFactoryTest {
private static String xml;
private static String xml1;
private final VerbResolver resolver = new VerbResolver();
@Test