1703 lines
48 KiB
Java
1703 lines
48 KiB
Java
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package eu.dnetlib.dhp.bulktag;
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import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.List;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.Row;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.*;
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public class BulkTagJobTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static final String pathMap = "{\"author\":{\"path\":\"$['author'][*]['fullname']\"}," +
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" \"title\":{\"path\":\"$['title'][*]['value']\"}, " +
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" \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " +
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" \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ,"
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+
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"\"contributor\" : {\"path\":\"$['contributor'][*]['value']\"}," +
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" \"description\" : {\"path\":\"$['description'][*]['value']\"}," +
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" \"subject\" :{\"path\":\"$['subject'][*]['value']\"}, " +
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" \"fos\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"} , " +
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"\"sdg\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"}," +
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"\"journal\":{\"path\":\"$['journal'].name\"}," +
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"\"hostedby\":{\"path\":\"$['instance'][*]['hostedby']['key']\"}," +
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"\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"}," +
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"\"publisher\":{\"path\":\"$['publisher'].value\"}," +
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"\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\", " +
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" \"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\"," +
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"\"method\":\"execSubstring\"," +
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"\"params\":[" +
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"{\"paramName\":\"From\", \"paramValue\":0}, " +
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"{\"paramName\":\"To\",\"paramValue\":4}]}}}";
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private static SparkSession spark;
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private static Path workingDir;
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private static final Logger log = LoggerFactory.getLogger(BulkTagJobTest.class);
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private static String taggingConf = "";
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static {
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try {
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taggingConf = IOUtils
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.toString(
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BulkTagJobTest.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_remove.xml"));
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(BulkTagJobTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(BulkTagJobTest.class.getSimpleName());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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spark = SparkSession
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.builder()
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.appName(BulkTagJobTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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@Test
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void noUpdatesTest() throws Exception {
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final String pathMap = BulkTagJobTest.pathMap;
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SparkBulkTagJob
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath",
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getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/").getPath(),
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"-taggingConf", taggingConf,
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"-outputPath", workingDir.toString() + "/",
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"-pathMap", pathMap
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Dataset> tmp = sc
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.textFile(workingDir.toString() + "/dataset")
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.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
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Assertions.assertEquals(10, tmp.count());
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org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
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verificationDataset.createOrReplaceTempView("dataset");
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String query = "select id, MyT.id community "
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+ "from dataset "
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+ "lateral view explode(context) c as MyT "
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+ "lateral view explode(MyT.datainfo) d as MyD "
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+ "where MyD.inferenceprovenance = 'bulktagging'";
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Assertions.assertEquals(0, spark.sql(query).count());
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}
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@Test
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void bulktagBySubjectNoPreviousContextTest() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext/")
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.getPath();
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final String pathMap = BulkTagJobTest.pathMap;
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SparkBulkTagJob
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", sourcePath,
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"-taggingConf", taggingConf,
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"-outputPath", workingDir.toString() + "/",
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"-pathMap", pathMap
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Dataset> tmp = sc
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.textFile(workingDir.toString() + "/dataset")
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.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
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Assertions.assertEquals(10, tmp.count());
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org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
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verificationDataset.createOrReplaceTempView("dataset");
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String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
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+ "from dataset "
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+ "lateral view explode(context) c as MyT "
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+ "lateral view explode(MyT.datainfo) d as MyD "
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+ "where MyD.inferenceprovenance = 'bulktagging'";
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Assertions.assertEquals(5, spark.sql(query).count());
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org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
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Assertions
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.assertEquals(
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5, idExplodeCommunity.filter("provenance = 'community:subject'").count());
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Assertions
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.assertEquals(
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5,
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idExplodeCommunity.filter("name = 'Bulktagging for Community - Subject'").count());
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Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count());
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Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count());
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Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count());
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Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count());
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Assertions
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.assertEquals(
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1,
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idExplodeCommunity
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.filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
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.count());
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Assertions
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.assertEquals(
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1,
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idExplodeCommunity
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.filter(
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"community = 'covid-19' and id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
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.count());
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Assertions
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.assertEquals(
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2,
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idExplodeCommunity
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.filter("id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'")
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.count());
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Assertions
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.assertEquals(
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2,
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idExplodeCommunity
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.filter(
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"(community = 'covid-19' or community = 'aginfra') and id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'")
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.count());
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Assertions
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.assertEquals(
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2,
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idExplodeCommunity
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.filter("id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'")
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.count());
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Assertions
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.assertEquals(
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2,
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idExplodeCommunity
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.filter(
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"(community = 'mes' or community = 'fam') and id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'")
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.count());
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}
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@Test
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void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception {
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final String sourcePath = getClass()
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.getResource(
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"/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/")
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.getPath();
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final String pathMap = BulkTagJobTest.pathMap;
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SparkBulkTagJob
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", sourcePath,
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"-taggingConf", taggingConf,
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"-outputPath", workingDir.toString() + "/",
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"-pathMap", pathMap
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Dataset> tmp = sc
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.textFile(workingDir.toString() + "/dataset")
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.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
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Assertions.assertEquals(10, tmp.count());
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org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
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verificationDataset.createOrReplaceTempView("dataset");
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String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance "
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+ "from dataset "
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+ "lateral view explode(context) c as MyT "
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+ "lateral view explode(MyT.datainfo) d as MyD "
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+ "where MyT.id = 'covid-19' ";
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Assertions.assertEquals(3, spark.sql(query).count());
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org.apache.spark.sql.Dataset<Row> communityContext = spark.sql(query);
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Assertions
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.assertEquals(
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2,
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communityContext
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.filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
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.count());
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Assertions
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.assertEquals(
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1,
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communityContext
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.filter(
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"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'community:subject'")
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.count());
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Assertions
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.assertEquals(
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1,
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communityContext
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.filter(
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"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'propagation:community:productsthroughsemrel'")
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.count());
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query = "select id, MyT.id community, size(MyT.datainfo) datainfosize "
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+ "from dataset "
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+ "lateral view explode (context) as MyT "
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+ "where size(MyT.datainfo) > 0";
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Assertions
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.assertEquals(
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2,
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spark
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.sql(query)
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.select("datainfosize")
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.where(
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"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' a"
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+ "nd community = 'covid-19'")
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.collectAsList()
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.get(0)
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.getInt(0));
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}
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@Test
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void bulktagByDatasourceTest() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/")
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.getPath();
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SparkBulkTagJob
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", sourcePath,
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"-taggingConf", taggingConf,
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"-outputPath", workingDir.toString() + "/",
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"-pathMap", pathMap
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Publication> tmp = sc
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.textFile(workingDir.toString() + "/publication")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
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Assertions.assertEquals(10, tmp.count());
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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verificationDataset.createOrReplaceTempView("publication");
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String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
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+ "from publication "
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+ "lateral view explode(context) c as MyT "
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+ "lateral view explode(MyT.datainfo) d as MyD "
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+ "where MyD.inferenceprovenance = 'bulktagging'";
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org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
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Assertions.assertEquals(5, idExplodeCommunity.count());
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Assertions
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.assertEquals(
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5, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
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Assertions
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.assertEquals(
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5,
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idExplodeCommunity
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.filter("name = 'Bulktagging for Community - Datasource'")
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.count());
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Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'fam'").count());
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Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count());
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Assertions
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.assertEquals(
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3,
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idExplodeCommunity
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.filter(
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"community = 'fam' and (id = '50|ec_fp7health::000085c89f4b96dc2269bd37edb35306' "
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+ "or id = '50|ec_fp7health::000b9e61f83f5a4b0c35777b7bccdf38' "
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+ "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')")
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.count());
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Assertions
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.assertEquals(
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2,
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idExplodeCommunity
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.filter(
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"community = 'aginfra' and (id = '50|ec_fp7health::000c8195edd542e4e64ebb32172cbf89' "
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+ "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')")
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.count());
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}
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@Test
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void bulktagByZenodoCommunityTest() throws Exception {
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final String sourcePath = getClass()
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.getResource(
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"/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity/")
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.getPath();
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SparkBulkTagJob
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", sourcePath,
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"-taggingConf", taggingConf,
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"-outputPath", workingDir.toString() + "/",
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"-pathMap", pathMap
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<OtherResearchProduct> tmp = sc
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.textFile(workingDir.toString() + "/otherresearchproduct")
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.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
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Assertions.assertEquals(10, tmp.count());
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org.apache.spark.sql.Dataset<OtherResearchProduct> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(OtherResearchProduct.class));
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verificationDataset.createOrReplaceTempView("orp");
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String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
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+ "from orp "
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+ "lateral view explode(context) c as MyT "
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+ "lateral view explode(MyT.datainfo) d as MyD "
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+ "where MyD.inferenceprovenance = 'bulktagging'";
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org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
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Assertions.assertEquals(8, idExplodeCommunity.count());
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Assertions
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.assertEquals(
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8, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count());
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Assertions
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.assertEquals(
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8,
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idExplodeCommunity.filter("name = 'Bulktagging for Community - Zenodo'").count());
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Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'covid-19'").count());
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Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count());
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Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'beopen'").count());
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Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count());
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Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'mes'").count());
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Assertions
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.assertEquals(
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1,
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idExplodeCommunity
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.filter(
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"id = '50|od______2017::0750a4d0782265873d669520f5e33c07' "
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+ "and community = 'covid-19'")
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.count());
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Assertions
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.assertEquals(
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3,
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idExplodeCommunity
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.filter(
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"id = '50|od______2017::1bd97baef19dbd2db3203b112bb83bc5' and "
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+ "(community = 'aginfra' or community = 'mes' or community = 'fam')")
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.count());
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Assertions
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.assertEquals(
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1,
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idExplodeCommunity
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.filter(
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"id = '50|od______2017::1e400f1747487fd15998735c41a55c72' "
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+ "and community = 'beopen'")
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.count());
|
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Assertions
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|
.assertEquals(
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3,
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idExplodeCommunity
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.filter(
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"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
|
|
void bulktagBySubjectDatasourceTest() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/")
|
|
.getPath();
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(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
|
|
void bulktagBySubjectDatasourceZenodoCommunityTest() throws Exception {
|
|
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath",
|
|
getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(),
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(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 = 'dth'").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 = 'dth')")
|
|
.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
|
|
void bulktagDatasourcewithConstraintsTest() throws Exception {
|
|
|
|
final String sourcePath = getClass()
|
|
.getResource(
|
|
"/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/")
|
|
.getPath();
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<Dataset> tmp = sc
|
|
.textFile(workingDir.toString() + "/dataset")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
|
|
|
Assertions.assertEquals(12, 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);
|
|
|
|
}
|
|
|
|
@Test
|
|
void bulkTagOtherJupyter() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource(
|
|
"/eu/dnetlib/dhp/eosctag/jupyter/")
|
|
.getPath();
|
|
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
10, sc
|
|
.textFile(workingDir.toString() + "/otherresearchproduct")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
|
|
.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
0, sc
|
|
.textFile(workingDir.toString() + "/otherresearchproduct")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
|
|
.filter(
|
|
orp -> orp
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook")))
|
|
.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
0, sc
|
|
.textFile(workingDir.toString() + "/otherresearchproduct")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
|
|
.filter(
|
|
orp -> orp
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook")))
|
|
.count());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void bulkTagDatasetJupyter() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource(
|
|
"/eu/dnetlib/dhp/eosctag/jupyter/")
|
|
.getPath();
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
Assertions
|
|
.assertEquals(
|
|
10, sc
|
|
.textFile(workingDir.toString() + "/dataset")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
|
|
.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
0, sc
|
|
.textFile(workingDir.toString() + "/dataset")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
|
|
.filter(
|
|
ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook")))
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
0, sc
|
|
.textFile(workingDir.toString() + "/dataset")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
|
|
.filter(
|
|
ds -> ds
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook")))
|
|
.count());
|
|
}
|
|
|
|
@Test
|
|
public void bulkTagSoftwareJupyter() throws Exception {
|
|
|
|
final String sourcePath = getClass()
|
|
.getResource(
|
|
"/eu/dnetlib/dhp/eosctag/jupyter/")
|
|
.getPath();
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<Software> tmp = sc
|
|
.textFile(workingDir.toString() + "/software")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
|
|
|
Assertions.assertEquals(10, tmp.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
4,
|
|
tmp
|
|
.filter(s -> s.getEoscifguidelines() != null)
|
|
.filter(
|
|
s -> s
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook")))
|
|
.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
1, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.size());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
1, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
Assertions
|
|
.assertTrue(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
|
|
|
|
Assertions
|
|
.assertFalse(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
5, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
Assertions
|
|
.assertFalse(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
0,
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.size());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
8, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
Assertions
|
|
.assertFalse(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
|
|
Assertions
|
|
.assertEquals(
|
|
1, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.size());
|
|
Assertions
|
|
.assertTrue(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
5, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
Assertions
|
|
.assertFalse(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
|
|
Assertions
|
|
.assertEquals(
|
|
0,
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.size());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
8, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
Assertions
|
|
.assertFalse(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.size());
|
|
Assertions
|
|
.assertTrue(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
|
|
|
|
List<Subject> subjects = tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject();
|
|
Assertions.assertEquals(7, subjects.size());
|
|
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter")));
|
|
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation")));
|
|
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire")));
|
|
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("algorithme")));
|
|
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("simulation numérique")));
|
|
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de gaz")));
|
|
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de liquide")));
|
|
|
|
}
|
|
|
|
@Test
|
|
void galaxyOtherTest() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource(
|
|
"/eu/dnetlib/dhp/eosctag/galaxy/")
|
|
.getPath();
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
JavaRDD<OtherResearchProduct> orp = sc
|
|
.textFile(workingDir.toString() + "/otherresearchproduct")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
|
|
|
|
Assertions.assertEquals(10, orp.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
0,
|
|
orp
|
|
.filter(
|
|
s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow")))
|
|
.count());
|
|
orp.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o)));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
1, orp
|
|
.filter(o -> o.getEoscifguidelines() != null)
|
|
.filter(
|
|
o -> o
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")))
|
|
.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
2, orp
|
|
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
Assertions
|
|
.assertFalse(
|
|
orp
|
|
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
|
|
Assertions
|
|
.assertEquals(
|
|
1, orp
|
|
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.size());
|
|
Assertions
|
|
.assertTrue(
|
|
orp
|
|
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow")));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
2, orp
|
|
.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
Assertions
|
|
.assertFalse(
|
|
orp
|
|
.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
2, orp
|
|
.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
Assertions
|
|
.assertFalse(
|
|
orp
|
|
.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
|
|
}
|
|
|
|
@Test
|
|
void galaxySoftwareTest() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource(
|
|
"/eu/dnetlib/dhp/eosctag/galaxy/")
|
|
.getPath();
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<Software> tmp = sc
|
|
.textFile(workingDir.toString() + "/software")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
|
|
|
Assertions.assertEquals(11, tmp.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
0,
|
|
tmp
|
|
.filter(
|
|
s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow")))
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
tmp
|
|
.filter(
|
|
s -> s.getEoscifguidelines().size() > 0)
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
tmp
|
|
.filter(
|
|
s -> s.getEoscifguidelines().size() > 0)
|
|
.filter(
|
|
s -> s
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")))
|
|
.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
1, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
Assertions
|
|
.assertFalse(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
1, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.size());
|
|
Assertions
|
|
.assertTrue(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
|
|
.collect()
|
|
.get(0)
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
5, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
8, tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.size());
|
|
Assertions
|
|
.assertFalse(
|
|
tmp
|
|
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
|
|
.collect()
|
|
.get(0)
|
|
.getSubject()
|
|
.stream()
|
|
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
|
|
|
|
}
|
|
|
|
@Test
|
|
void twitterDatasetTest() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource(
|
|
"/eu/dnetlib/dhp/eosctag/twitter/")
|
|
.getPath();
|
|
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
JavaRDD<Dataset> dats = sc
|
|
.textFile(workingDir.toString() + "/dataset")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
|
|
|
Assertions.assertEquals(11, dats.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
3,
|
|
dats
|
|
.filter(
|
|
s -> s
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data")))
|
|
.count());
|
|
|
|
}
|
|
|
|
@Test
|
|
void twitterOtherTest() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource(
|
|
"/eu/dnetlib/dhp/eosctag/twitter/")
|
|
.getPath();
|
|
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
JavaRDD<OtherResearchProduct> orp = sc
|
|
.textFile(workingDir.toString() + "/otherresearchproduct")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
|
|
|
|
Assertions.assertEquals(10, orp.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
0,
|
|
orp
|
|
.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data")))
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
3,
|
|
orp
|
|
.filter(
|
|
s -> s
|
|
.getEoscifguidelines()
|
|
.stream()
|
|
.anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data")))
|
|
.count());
|
|
}
|
|
|
|
@Test
|
|
void twitterSoftwareTest() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource(
|
|
"/eu/dnetlib/dhp/eosctag/twitter/")
|
|
.getPath();
|
|
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<Software> tmp = sc
|
|
.textFile(workingDir.toString() + "/software")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
|
|
|
Assertions.assertEquals(10, tmp.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
0,
|
|
tmp
|
|
.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data")))
|
|
.count());
|
|
|
|
}
|
|
|
|
@Test
|
|
void EoscContextTagTest() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource(
|
|
"/eu/dnetlib/dhp/bulktag/eosc/dataset/")
|
|
.getPath();
|
|
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath", sourcePath,
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<Dataset> tmp = sc
|
|
.textFile(workingDir.toString() + "/dataset")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
|
|
|
Assertions.assertEquals(8, tmp.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
4,
|
|
tmp
|
|
.filter(
|
|
s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
|
|
.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
tmp
|
|
.filter(
|
|
d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea")
|
|
&&
|
|
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
tmp
|
|
.filter(
|
|
d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1")
|
|
&&
|
|
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
|
|
.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
tmp
|
|
.filter(
|
|
d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
|
|
&&
|
|
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
|
|
.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
tmp
|
|
.filter(
|
|
d -> d.getId().equals("50|475c1990cbb2::449f28eefccf9f70c04ad70d61e041c7")
|
|
&&
|
|
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
|
|
.count());
|
|
}
|
|
|
|
@Test
|
|
void removeTest() throws Exception {
|
|
final String pathMap = BulkTagJobTest.pathMap;
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath",
|
|
getClass()
|
|
.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/")
|
|
.getPath(),
|
|
"-taggingConf", taggingConf,
|
|
|
|
"-outputPath", workingDir.toString() + "/",
|
|
|
|
"-pathMap", pathMap
|
|
});
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<Dataset> tmp = sc
|
|
.textFile(workingDir.toString() + "/dataset")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
|
|
|
Assertions.assertEquals(12, 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(3, idExplodeCommunity.filter("community = 'dth'").count());
|
|
|
|
}
|
|
|
|
@Test
|
|
void newConfTest() throws Exception {
|
|
final String pathMap = BulkTagJobTest.pathMap;
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath",
|
|
getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/").getPath(),
|
|
"-outputPath", workingDir.toString() + "/",
|
|
// "-baseURL", "https://services.openaire.eu/openaire/community/",
|
|
"-pathMap", pathMap,
|
|
"-taggingConf", taggingConf
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(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());
|
|
}
|
|
|
|
@Test
|
|
void pubdateTest() throws Exception {
|
|
|
|
final String pathMap = BulkTagJobTest.pathMap;
|
|
SparkBulkTagJob
|
|
.main(
|
|
new String[] {
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath",
|
|
getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/").getPath(),
|
|
"-taggingConf",
|
|
IOUtils
|
|
.toString(
|
|
BulkTagJobTest.class
|
|
.getResourceAsStream(
|
|
"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml")),
|
|
"-outputPath", workingDir.toString() + "/",
|
|
"-pathMap", pathMap
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(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 "
|
|
+ "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> queryResult = spark.sql(query);
|
|
queryResult.show(false);
|
|
Assertions.assertEquals(5, queryResult.count());
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
queryResult
|
|
.filter(
|
|
(FilterFunction<Row>) r -> r
|
|
.getAs("id")
|
|
.equals("50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529"))
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
queryResult
|
|
.filter(
|
|
(FilterFunction<Row>) r -> r
|
|
.getAs("id")
|
|
.equals("50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf"))
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
queryResult
|
|
.filter(
|
|
(FilterFunction<Row>) r -> r
|
|
.getAs("id")
|
|
.equals("50|od______3989::7fcbe3a03280663cddebfd3cb9203177"))
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
queryResult
|
|
.filter(
|
|
(FilterFunction<Row>) r -> r
|
|
.getAs("id")
|
|
.equals("50|od______3989::d791339867bec6d3eb2104deeb4e4961"))
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
queryResult
|
|
.filter(
|
|
(FilterFunction<Row>) r -> r
|
|
.getAs("id")
|
|
.equals("50|od______3989::d90d3a1f64ad264b5ebed8a35b280343"))
|
|
.count());
|
|
|
|
}
|
|
|
|
}
|