test for propagation of result to community from organization and result to community from semrel

This commit is contained in:
Miriam Baglioni 2020-04-27 10:59:53 +02:00
parent ec7f166690
commit c925e2be16
2 changed files with 588 additions and 0 deletions

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@ -1,4 +1,316 @@
package eu.dnetlib.dhp.resulttocommunityfromorganization;
import static org.apache.spark.sql.functions.*;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest;
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.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;
public class ResultToCommunityJobTest {
private static final Logger log = LoggerFactory.getLogger(ResultToCommunityJobTest.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ClassLoader cl = ResultToCommunityJobTest.class.getClassLoader();
private static SparkSession spark;
private static Path workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(ResultToCommunityJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(ResultToCommunityJobTest.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 test1() throws Exception {
SparkResultToCommunityFromOrganizationJob2.main(
new String[] {
"-isTest",
Boolean.TRUE.toString(),
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
getClass()
.getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/sample")
.getPath(),
"-hive_metastore_uris",
"",
"-saveGraph",
"true",
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath",
workingDir.toString() + "/dataset",
"-preparedInfoPath",
getClass()
.getResource(
"/eu/dnetlib/dhp/resulttocommunityfromorganization/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 = 'propagation'";
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
Assertions.assertEquals(5, resultExplodedProvenance.count());
Assertions.assertEquals(
0,
resultExplodedProvenance
.filter("id = '50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe'")
.count());
Assertions.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b'")
.count());
Assertions.assertEquals(
"beopen",
resultExplodedProvenance
.select("community")
.where(
resultExplodedProvenance
.col("id")
.equalTo(
"50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b"))
.collectAsList()
.get(0)
.getString(0));
Assertions.assertEquals(
2,
resultExplodedProvenance
.filter("id = '50|od________18::8887b1df8b563c4ea851eb9c882c9d7b'")
.count());
Assertions.assertEquals(
"mes",
resultExplodedProvenance
.select("community")
.where(
resultExplodedProvenance
.col("id")
.equalTo(
"50|od________18::8887b1df8b563c4ea851eb9c882c9d7b"))
.sort(desc("community"))
.collectAsList()
.get(0)
.getString(0));
Assertions.assertEquals(
"euromarine",
resultExplodedProvenance
.select("community")
.where(
resultExplodedProvenance
.col("id")
.equalTo(
"50|od________18::8887b1df8b563c4ea851eb9c882c9d7b"))
.sort(desc("community"))
.collectAsList()
.get(1)
.getString(0));
Assertions.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'")
.count());
Assertions.assertEquals(
"mes",
resultExplodedProvenance
.select("community")
.where(
resultExplodedProvenance
.col("id")
.equalTo(
"50|doajarticles::8d817039a63710fcf97e30f14662c6c8"))
.sort(desc("community"))
.collectAsList()
.get(0)
.getString(0));
Assertions.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6'")
.count());
Assertions.assertEquals(
"mes",
resultExplodedProvenance
.select("community")
.where(
resultExplodedProvenance
.col("id")
.equalTo(
"50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6"))
.sort(desc("community"))
.collectAsList()
.get(0)
.getString(0));
/*
{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::8d817039a63710fcf97e30f14662c6c8"} "context" ["id": euromarine] updates = 1
{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6"} context = [ni, euromarine] updates = 1
*/
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(
1,
resultCommunityId
.filter("id = '50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe'")
.count());
Assertions.assertEquals(
"beopen",
resultCommunityId
.select("community")
.where(
resultCommunityId
.col("id")
.equalTo(
"50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe"))
.collectAsList()
.get(0)
.getString(0));
Assertions.assertEquals(
1,
resultCommunityId
.filter("id = '50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b'")
.count());
Assertions.assertEquals(
3,
resultCommunityId
.filter("id = '50|od________18::8887b1df8b563c4ea851eb9c882c9d7b'")
.count());
Assertions.assertEquals(
"beopen",
resultCommunityId
.select("community")
.where(
resultCommunityId
.col("id")
.equalTo(
"50|od________18::8887b1df8b563c4ea851eb9c882c9d7b"))
.sort(desc("community"))
.collectAsList()
.get(2)
.getString(0));
Assertions.assertEquals(
2,
resultCommunityId
.filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'")
.count());
Assertions.assertEquals(
"euromarine",
resultCommunityId
.select("community")
.where(
resultCommunityId
.col("id")
.equalTo(
"50|doajarticles::8d817039a63710fcf97e30f14662c6c8"))
.sort(desc("community"))
.collectAsList()
.get(1)
.getString(0));
Assertions.assertEquals(
3,
resultCommunityId
.filter("id = '50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6'")
.count());
Assertions.assertEquals(
"euromarine",
resultCommunityId
.select("community")
.where(
resultCommunityId
.col("id")
.equalTo(
"50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6"))
.sort(desc("community"))
.collectAsList()
.get(2)
.getString(0));
Assertions.assertEquals(
"ni",
resultCommunityId
.select("community")
.where(
resultCommunityId
.col("id")
.equalTo(
"50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6"))
.sort(desc("community"))
.collectAsList()
.get(0)
.getString(0));
}
}

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package eu.dnetlib.dhp.resulttocommunityfromsemrel;
import static org.apache.spark.sql.functions.desc;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.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;
public class ResultToCommunityJobTest {
private static final Logger log =
LoggerFactory.getLogger(
eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ClassLoader cl =
eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class
.getClassLoader();
private static SparkSession spark;
private static Path workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir =
Files.createTempDirectory(
eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class
.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(
eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.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 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()
});
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 = 'propagation'";
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
Assertions.assertEquals(5, resultExplodedProvenance.count());
Assertions.assertEquals(
0,
resultExplodedProvenance
.filter("id = '50|dedup_wf_001::2305908abeca9da37eaf3bddcaf81b7b'")
.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(
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));
}
}