261 lines
8.2 KiB
Java
261 lines
8.2 KiB
Java
|
|
||
|
package eu.dnetlib.dhp.oa.graph.dump.pid;
|
||
|
|
||
|
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.Dataset;
|
||
|
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 com.fasterxml.jackson.databind.ObjectMapper;
|
||
|
|
||
|
public class PreparedInfoPidTest {
|
||
|
|
||
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||
|
|
||
|
private static SparkSession spark;
|
||
|
|
||
|
private static Path workingDir;
|
||
|
|
||
|
private static final Logger log = LoggerFactory.getLogger(PreparedInfoPidTest.class);
|
||
|
|
||
|
@BeforeAll
|
||
|
public static void beforeAll() throws IOException {
|
||
|
workingDir = Files.createTempDirectory(PreparedInfoPidTest.class.getSimpleName());
|
||
|
log.info("using work dir {}", workingDir);
|
||
|
|
||
|
SparkConf conf = new SparkConf();
|
||
|
conf.setAppName(PreparedInfoPidTest.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(PreparedInfoPidTest.class.getSimpleName())
|
||
|
.config(conf)
|
||
|
.getOrCreate();
|
||
|
}
|
||
|
|
||
|
@AfterAll
|
||
|
public static void afterAll() throws IOException {
|
||
|
FileUtils.deleteDirectory(workingDir.toFile());
|
||
|
spark.stop();
|
||
|
}
|
||
|
|
||
|
@Test
|
||
|
public void testPublication() throws Exception {
|
||
|
|
||
|
final String sourcePath = getClass()
|
||
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/pid/result/publication")
|
||
|
.getPath();
|
||
|
|
||
|
SparkPrepareResultPids.main(new String[] {
|
||
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||
|
"-outputPath", workingDir.toString() + "/preparedInfo",
|
||
|
"-sourcePath", sourcePath,
|
||
|
"-allowedResultPids", "[\"doi\",\"arxiv\",\"pmc\",\"pmid\",\"pdb\"]",
|
||
|
"-allowedAuthorPids", "[\"orcid\"]",
|
||
|
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication"
|
||
|
});
|
||
|
|
||
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||
|
|
||
|
JavaRDD<ResultPidsList> tmp = sc
|
||
|
.textFile(workingDir.toString() + "/preparedInfo/publication")
|
||
|
.map(item -> OBJECT_MAPPER.readValue(item, ResultPidsList.class));
|
||
|
|
||
|
org.apache.spark.sql.Dataset<ResultPidsList> verificationDataset = spark
|
||
|
.createDataset(tmp.rdd(), Encoders.bean(ResultPidsList.class));
|
||
|
|
||
|
Assertions.assertEquals(31, verificationDataset.count());
|
||
|
|
||
|
verificationDataset.createOrReplaceTempView("check");
|
||
|
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
31, spark
|
||
|
.sql(
|
||
|
"Select resultId " +
|
||
|
"from check " +
|
||
|
"lateral view explode (resultAllowedPids) r as resallowed " +
|
||
|
" where resallowed.key = 'doi'")
|
||
|
.count());
|
||
|
|
||
|
Dataset<Row> check = spark
|
||
|
.sql(
|
||
|
"Select resultId, pids.value orcid, resallowed.key pid_type, resallowed.value pid " +
|
||
|
"from check" +
|
||
|
" lateral view explode(authorAllowedPids) a as authallowed " +
|
||
|
" lateral view explode(authallowed) p as pids " +
|
||
|
" lateral view explode (resultAllowedPids) r as resallowed " +
|
||
|
"where pids.key = 'orcid'");
|
||
|
|
||
|
Assertions.assertEquals(2, check.count());
|
||
|
|
||
|
Assertions
|
||
|
.assertEquals(1, check.filter("resultId = '50|base_oa_____::1a700385222228181f20835bae60a71e'").count());
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
1, check
|
||
|
.filter(
|
||
|
"resultId = '50|base_oa_____::1a700385222228181f20835bae60a71e' " +
|
||
|
"and orcid = '0000-0002-1114-4216'")
|
||
|
.count());
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
1, check
|
||
|
.filter(
|
||
|
"resultId = '50|base_oa_____::1a700385222228181f20835bae60a71e' " +
|
||
|
"and pid = '10.1016/j.jrmge.2016.11.005'")
|
||
|
.count());
|
||
|
|
||
|
Assertions
|
||
|
.assertEquals(1, check.filter("resultId = '50|base_oa_____::06546a1ad6b1c71e5e366ef15b9ade1f'").count());
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
1, check
|
||
|
.filter(
|
||
|
"resultId = '50|base_oa_____::06546a1ad6b1c71e5e366ef15b9ade1f' " +
|
||
|
"and orcid = '0000-0001-9317-9350'")
|
||
|
.count());
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
1, check
|
||
|
.filter(
|
||
|
"resultId = '50|base_oa_____::06546a1ad6b1c71e5e366ef15b9ade1f' " +
|
||
|
"and pid = '10.1016/j.jotr.2014.10.003'")
|
||
|
.count());
|
||
|
|
||
|
}
|
||
|
|
||
|
@Test
|
||
|
public void testDataset() throws Exception {
|
||
|
final String sourcePath = getClass()
|
||
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/pid/result/dataset")
|
||
|
.getPath();
|
||
|
|
||
|
SparkPrepareResultPids.main(new String[] {
|
||
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||
|
"-outputPath", workingDir.toString() + "/preparedInfo",
|
||
|
"-sourcePath", sourcePath,
|
||
|
"-allowedResultPids", "[\"doi\",\"arxiv\",\"pmc\",\"pmid\",\"pdb\"]",
|
||
|
"-allowedAuthorPids", "[\"orcid\"]",
|
||
|
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset"
|
||
|
});
|
||
|
|
||
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||
|
|
||
|
JavaRDD<ResultPidsList> tmp = sc
|
||
|
.textFile(workingDir.toString() + "/preparedInfo/dataset")
|
||
|
.map(item -> OBJECT_MAPPER.readValue(item, ResultPidsList.class));
|
||
|
|
||
|
org.apache.spark.sql.Dataset<ResultPidsList> verificationDataset = spark
|
||
|
.createDataset(tmp.rdd(), Encoders.bean(ResultPidsList.class));
|
||
|
|
||
|
Assertions.assertEquals(3, verificationDataset.count());
|
||
|
|
||
|
verificationDataset.createOrReplaceTempView("check");
|
||
|
|
||
|
Dataset<Row> check = spark
|
||
|
.sql(
|
||
|
"Select resultId, pids.value orcid, resallowed.key pid_type, resallowed.value pid " +
|
||
|
"from check" +
|
||
|
" lateral view explode(authorAllowedPids) a as authallowed " +
|
||
|
" lateral view explode(authallowed) p as pids " +
|
||
|
" lateral view explode (resultAllowedPids) r as resallowed ");
|
||
|
|
||
|
Assertions.assertEquals(4, check.count());
|
||
|
|
||
|
Assertions
|
||
|
.assertEquals(4, check.filter("resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02'").count());
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
2, check
|
||
|
.filter(
|
||
|
"resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02' " +
|
||
|
"and (orcid = '0000-0001-9317-9350' or orcid = '0000-0002-1114-4216') and " +
|
||
|
"pid = '10.1016/fake' and pid_type = 'doi' ")
|
||
|
.count());
|
||
|
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
2, check
|
||
|
.filter(
|
||
|
"resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02' " +
|
||
|
"and (orcid = '0000-0001-9317-9350' or orcid = '0000-0002-1114-4216') and " +
|
||
|
"pid = '10443fake' and pid_type = 'pmid' ")
|
||
|
.count());
|
||
|
|
||
|
check = spark
|
||
|
.sql(
|
||
|
"Select resultId, authorAllowedPids, resallowed.key pid_type, resallowed.value pid " +
|
||
|
"from check" +
|
||
|
" lateral view explode (resultAllowedPids) r as resallowed ");
|
||
|
|
||
|
Assertions.assertEquals(5, check.count());
|
||
|
|
||
|
Assertions
|
||
|
.assertEquals(2, check.filter("resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02'").count());
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
1, check
|
||
|
.filter(
|
||
|
"resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02' " +
|
||
|
" and pid = '10.1016/fake' and pid_type = 'doi' ")
|
||
|
.count());
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
1, check
|
||
|
.filter(
|
||
|
"resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02' " +
|
||
|
" and pid = '10443fake' and pid_type = 'pmid' ")
|
||
|
.count());
|
||
|
|
||
|
Assertions
|
||
|
.assertEquals(1, check.filter("resultId = '50|_____OmicsDI::023fd1fcbb64f0f7df0671798a62f379'").count());
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
1, check
|
||
|
.filter(
|
||
|
"resultId = '50|_____OmicsDI::023fd1fcbb64f0f7df0671798a62f379' " +
|
||
|
" and pid = 'fakepdb' and pid_type = 'pdb' ")
|
||
|
.count());
|
||
|
|
||
|
Assertions
|
||
|
.assertEquals(2, check.filter("resultId = '50|_____OmicsDI::036d65211a6ac14237c6e2d7cc223386'").count());
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
1, check
|
||
|
.filter(
|
||
|
"resultId = '50|_____OmicsDI::036d65211a6ac14237c6e2d7cc223386' " +
|
||
|
" and pid = '10.1016/j.tcs.2012.06.029' and pid_type = 'doi' ")
|
||
|
.count());
|
||
|
Assertions
|
||
|
.assertEquals(
|
||
|
1, check
|
||
|
.filter(
|
||
|
"resultId = '50|_____OmicsDI::036d65211a6ac14237c6e2d7cc223386' " +
|
||
|
" and pid = 'fake_arxiv' and pid_type = 'arXiv' ")
|
||
|
.count());
|
||
|
|
||
|
}
|
||
|
}
|