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claudio.atzori merged 275 commits from :master into enrichment_wfs 2020-05-11 15:14:56 +02:00
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dhp-workflows/dhp-propagation/src/test/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/OrcidPropagationJobTest.java
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@ -1,4 +1,195 @@
package eu.dnetlib.dhp.orcidtoresultfromsemrel;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.resulttoorganizationfrominstrepo.Result2OrganizationJobTest;
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 org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
public class OrcidPropagationJobTest {
private static final Logger log = LoggerFactory.getLogger(Result2OrganizationJobTest.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ClassLoader cl = Result2OrganizationJobTest.class.getClassLoader();
private static SparkSession spark;
private static Path workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(OrcidPropagationJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(OrcidPropagationJobTest.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(OrcidPropagationJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void noUpdateTest()throws Exception{
SparkOrcidToResultFromSemRelJob3.main(new String[]{
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().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());
JavaRDD<Dataset> tmp = 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));
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 " +
"from dataset " +
"lateral view explode(author) a as MyT " +
"lateral view explode(MyT.pid) p as MyP " +
"where MyP.datainfo.inferenceprovenance = 'propagation'";
Assertions.assertEquals(0, spark.sql(query).count());
}
@Test
public void oneUpdateTest() throws Exception{
SparkOrcidToResultFromSemRelJob3.main(new String[]{
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().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());
JavaRDD<Dataset> tmp = 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));
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.name name, MyT.surname surname, MyP.value pid, MyP.qualifier.classid pidType " +
"from dataset " +
"lateral view explode(author) a as MyT " +
"lateral view explode(MyT.pid) p as MyP " +
"where MyP.datainfo.inferenceprovenance = 'propagation'";
org.apache.spark.sql.Dataset<Row> propagatedAuthors = spark.sql(query);
Assertions.assertEquals(1, propagatedAuthors.count());
Assertions.assertEquals(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());
}
@Test
public void twoUpdatesTest() throws Exception{
SparkOrcidToResultFromSemRelJob3.main(new String[]{
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", getClass().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());
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.name name, MyT.surname surname, MyP.value pid, MyP.qualifier.classid pidType " +
"from dataset " +
"lateral view explode(author) a as MyT " +
"lateral view explode(MyT.pid) p as MyP " +
"where MyP.datainfo.inferenceprovenance = 'propagation'";
org.apache.spark.sql.Dataset<Row> propagatedAuthors = spark.sql(query);
Assertions.assertEquals(2, propagatedAuthors.count());
Assertions.assertEquals(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 " +
"from dataset " +
"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);
Assertions.assertEquals(2, authorsExplodedPids.filter("name = 'Marc' and surname = 'Schmidtmann'").count());
Assertions.assertEquals(1, authorsExplodedPids.filter("name = 'Marc' and surname = 'Schmidtmann' and pidType = 'MAG Identifier'").count());
}
}