master #11
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@ -1,13 +1,24 @@
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package eu.dnetlib.dhp;
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package eu.dnetlib.dhp;
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import static eu.dnetlib.dhp.community.TagginConstants.ZENODO_COMMUNITY_INDICATOR;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Software;
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import java.io.IOException;
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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.Files;
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import java.nio.file.Path;
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import java.nio.file.Path;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.FileUtils;
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import org.apache.spark.SparkConf;
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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.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.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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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.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.Test;
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import org.mortbay.util.IO;
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import org.mortbay.util.IO;
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@ -31,7 +42,7 @@ public class BulkTagJobTest {
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taggingConf =
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taggingConf =
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IO.toString(
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IO.toString(
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BulkTagJobTest.class.getResourceAsStream(
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BulkTagJobTest.class.getResourceAsStream(
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"/eu/dnetlib/dhp/communityconfiguration/tagging_conf.json"));
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"/eu/dnetlib/dhp/communityconfiguration/tagging_conf.xml"));
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} catch (IOException e) {
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} catch (IOException e) {
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e.printStackTrace();
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e.printStackTrace();
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}
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}
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@ -66,7 +77,7 @@ public class BulkTagJobTest {
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}
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}
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@Test
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@Test
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public void test1() throws Exception {
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public void noUpdatesTest() throws Exception {
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SparkBulkTagJob2.main(
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SparkBulkTagJob2.main(
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new String[] {
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new String[] {
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"-isTest",
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"-isTest",
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@ -74,7 +85,7 @@ public class BulkTagJobTest {
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"-isSparkSessionManaged",
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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Boolean.FALSE.toString(),
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"-sourcePath",
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"-sourcePath",
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getClass().getResource("/eu/dnetlib/dhp/sample/dataset").getPath(),
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getClass().getResource("/eu/dnetlib/dhp/sample/dataset/no_updates").getPath(),
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"-taggingConf",
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"-taggingConf",
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taggingConf,
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taggingConf,
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"-resultTableName",
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"-resultTableName",
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@ -92,142 +103,700 @@ public class BulkTagJobTest {
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// "-preparedInfoPath",
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// "-preparedInfoPath",
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// getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/preparedInfo").getPath()
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// getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/preparedInfo").getPath()
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});
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});
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}
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}
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/*
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import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest;
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import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob2;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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import org.apache.commons.io.FileUtils;
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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.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 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 static org.apache.spark.sql.functions.desc;
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@Test
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public void test1() throws Exception {
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SparkResultToCommunityThroughSemRelJob4.main(new String[]{
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"-isTest", Boolean.TRUE.toString(),
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/sample").getPath(),
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"-hive_metastore_uris", "",
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
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"-outputPath", workingDir.toString() + "/dataset",
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"-preparedInfoPath", getClass().getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/preparedInfo").getPath()
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Dataset> tmp = sc.textFile(workingDir.toString() + "/dataset")
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JavaRDD<Dataset> tmp =
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.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
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sc.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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Assertions.assertEquals(10, tmp.count());
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org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
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org.apache.spark.sql.Dataset<Dataset> verificationDataset =
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spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
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verificationDataset.createOrReplaceTempView("dataset");
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verificationDataset.createOrReplaceTempView("dataset");
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String query = "select id, MyT.id community " +
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String query =
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"from dataset " +
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"select id, MyT.id community "
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"lateral view explode(context) c as MyT " +
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+ "from dataset "
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"lateral view explode(MyT.datainfo) d as MyD " +
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+ "lateral view explode(context) c as MyT "
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"where MyD.inferenceprovenance = 'propagation'";
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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> resultExplodedProvenance = spark.sql(query);
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Assertions.assertEquals(5, resultExplodedProvenance.count());
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Assertions.assertEquals(0, resultExplodedProvenance.filter("id = '50|dedup_wf_001::2305908abeca9da37eaf3bddcaf81b7b'").count());
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Assertions.assertEquals(1, resultExplodedProvenance.filter("id = '50|dedup_wf_001::0489ae524201eedaa775da282dce35e7'").count());
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Assertions.assertEquals("dh-ch",resultExplodedProvenance.select("community")
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.where(resultExplodedProvenance.col("id").equalTo("50|dedup_wf_001::0489ae524201eedaa775da282dce35e7"))
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.collectAsList().get(0).getString(0));
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Assertions.assertEquals(3, resultExplodedProvenance.filter("id = '50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28'").count());
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List<Row> rowList = resultExplodedProvenance.select("community")
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.where(resultExplodedProvenance.col("id")
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.equalTo("50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28"))
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.sort(desc("community")).collectAsList();
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Assertions.assertEquals("mes", rowList.get(0).getString(0));
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Assertions.assertEquals("fam", rowList.get(1).getString(0));
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Assertions.assertEquals("ee", rowList.get(2).getString(0));
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Assertions.assertEquals(1, resultExplodedProvenance.filter("id = '50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc'").count());
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Assertions.assertEquals("aginfra", resultExplodedProvenance.select("community")
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.where(resultExplodedProvenance.col("id")
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.equalTo("50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc"))
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.collectAsList().get(0).getString(0));
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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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org.apache.spark.sql.Dataset<Row> resultCommunityId = spark.sql(query);
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Assertions.assertEquals(10, resultCommunityId.count());
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Assertions.assertEquals(2, resultCommunityId.filter("id = '50|dedup_wf_001::0489ae524201eedaa775da282dce35e7'").count());
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rowList = resultCommunityId.select("community")
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.where(resultCommunityId.col("id").equalTo("50|dedup_wf_001::0489ae524201eedaa775da282dce35e7"))
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.sort(desc("community"))
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.collectAsList();
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Assertions.assertEquals("dh-ch", rowList.get(0).getString(0));
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Assertions.assertEquals("beopen", rowList.get(1).getString(0));
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Assertions.assertEquals(3, resultCommunityId.filter("id = '50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28'").count());
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rowList = resultCommunityId.select("community")
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.where(resultCommunityId.col("id").equalTo("50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28"))
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.sort(desc("community"))
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.collectAsList();
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Assertions.assertEquals("mes", rowList.get(0).getString(0));
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Assertions.assertEquals("fam", rowList.get(1).getString(0));
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Assertions.assertEquals("ee", rowList.get(2).getString(0));
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Assertions.assertEquals(2, resultCommunityId.filter("id = '50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc'").count());
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rowList = resultCommunityId.select("community")
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.where(resultCommunityId.col("id").equalTo("50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc"))
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.sort(desc("community"))
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.collectAsList();
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Assertions.assertEquals("beopen", rowList.get(0).getString(0));
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Assertions.assertEquals("aginfra", rowList.get(1).getString(0));
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Assertions.assertEquals(2, resultCommunityId.filter("id = '50|dedup_wf_001::2305908abeca9da37eaf3bddcaf81b7b'").count());
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rowList = resultCommunityId.select("community")
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.where(resultCommunityId.col("id").equalTo("50|dedup_wf_001::2305908abeca9da37eaf3bddcaf81b7b"))
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.sort(desc("community"))
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.collectAsList();
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Assertions.assertEquals("euromarine", rowList.get(1).getString(0));
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Assertions.assertEquals("ni", rowList.get(0).getString(0));
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Assertions.assertEquals(1, resultCommunityId.filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'").count());
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Assertions.assertEquals("euromarine", resultCommunityId.select("community")
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.where(resultCommunityId.col("id")
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.equalTo("50|doajarticles::8d817039a63710fcf97e30f14662c6c8"))
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.collectAsList().get(0).getString(0));
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Assertions.assertEquals(0, spark.sql(query).count());
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}
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}
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*/
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@Test
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public void bulktagBySubjectNoPreviousContextTest() throws Exception {
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SparkBulkTagJob2.main(
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new String[] {
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"-isTest",
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Boolean.TRUE.toString(),
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-sourcePath",
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getClass()
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.getResource("/eu/dnetlib/dhp/sample/dataset/update_subject/nocontext")
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.getPath(),
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"-taggingConf",
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taggingConf,
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"-resultTableName",
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"eu.dnetlib.dhp.schema.oaf.Dataset",
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"-outputPath",
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workingDir.toString() + "/dataset",
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"-isLookupUrl",
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"http://beta.services.openaire.eu:8280/is/services/isLookUp",
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"-protoMap",
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"{ \"author\" : \"$['author'][*]['fullname']\","
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+ " \"title\" : \"$['title'][*]['value']\","
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+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
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+ " \"contributor\" : \"$['contributor'][*]['value']\","
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+ " \"description\" : \"$['description'][*]['value']\"}"
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Dataset> tmp =
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sc.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 =
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spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
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verificationDataset.createOrReplaceTempView("dataset");
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String query =
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"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.assertEquals(
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5, idExplodeCommunity.filter("provenance = 'community:subject'").count());
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Assertions.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.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.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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|
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|
Assertions.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.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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|
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|
Assertions.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.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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|
|
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|
@Test
|
||||||
|
public void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception {
|
||||||
|
SparkBulkTagJob2.main(
|
||||||
|
new String[] {
|
||||||
|
"-isTest",
|
||||||
|
Boolean.TRUE.toString(),
|
||||||
|
"-isSparkSessionManaged",
|
||||||
|
Boolean.FALSE.toString(),
|
||||||
|
"-sourcePath",
|
||||||
|
getClass()
|
||||||
|
.getResource(
|
||||||
|
"/eu/dnetlib/dhp/sample/dataset/update_subject/contextnoprovenance")
|
||||||
|
.getPath(),
|
||||||
|
"-taggingConf",
|
||||||
|
taggingConf,
|
||||||
|
"-resultTableName",
|
||||||
|
"eu.dnetlib.dhp.schema.oaf.Dataset",
|
||||||
|
"-outputPath",
|
||||||
|
workingDir.toString() + "/dataset",
|
||||||
|
"-isLookupUrl",
|
||||||
|
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
|
||||||
|
"-protoMap",
|
||||||
|
"{ \"author\" : \"$['author'][*]['fullname']\","
|
||||||
|
+ " \"title\" : \"$['title'][*]['value']\","
|
||||||
|
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
|
||||||
|
+ " \"contributor\" : \"$['contributor'][*]['value']\","
|
||||||
|
+ " \"description\" : \"$['description'][*]['value']\"}"
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<Dataset> tmp =
|
||||||
|
sc.textFile(workingDir.toString() + "/dataset")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(10, tmp.count());
|
||||||
|
org.apache.spark.sql.Dataset<Dataset> verificationDataset =
|
||||||
|
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("dataset");
|
||||||
|
|
||||||
|
String query =
|
||||||
|
"select id, MyT.id community, MyD.provenanceaction.classid provenance "
|
||||||
|
+ "from dataset "
|
||||||
|
+ "lateral view explode(context) c as MyT "
|
||||||
|
+ "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
+ "where MyT.id = 'covid-19' ";
|
||||||
|
|
||||||
|
Assertions.assertEquals(3, spark.sql(query).count());
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> communityContext = spark.sql(query);
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
communityContext
|
||||||
|
.filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
|
||||||
|
.count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
1,
|
||||||
|
communityContext
|
||||||
|
.filter(
|
||||||
|
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'community:subject'")
|
||||||
|
.count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
1,
|
||||||
|
communityContext
|
||||||
|
.filter(
|
||||||
|
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'propagation:community:productsthroughsemrel'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
query =
|
||||||
|
"select id, MyT.id community, size(MyT.datainfo) datainfosize "
|
||||||
|
+ "from dataset "
|
||||||
|
+ "lateral view explode (context) as MyT "
|
||||||
|
+ "where size(MyT.datainfo) > 0";
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
spark.sql(query)
|
||||||
|
.select("datainfosize")
|
||||||
|
.where(
|
||||||
|
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' a"
|
||||||
|
+ "nd community = 'covid-19'")
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getInt(0));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void bulktagByDatasourceTest() throws Exception {
|
||||||
|
SparkBulkTagJob2.main(
|
||||||
|
new String[] {
|
||||||
|
"-isTest",
|
||||||
|
Boolean.TRUE.toString(),
|
||||||
|
"-isSparkSessionManaged",
|
||||||
|
Boolean.FALSE.toString(),
|
||||||
|
"-sourcePath",
|
||||||
|
getClass()
|
||||||
|
.getResource("/eu/dnetlib/dhp/sample/publication/update_datasource")
|
||||||
|
.getPath(),
|
||||||
|
"-taggingConf",
|
||||||
|
taggingConf,
|
||||||
|
"-resultTableName",
|
||||||
|
"eu.dnetlib.dhp.schema.oaf.Publication",
|
||||||
|
"-outputPath",
|
||||||
|
workingDir.toString() + "/publication",
|
||||||
|
"-isLookupUrl",
|
||||||
|
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
|
||||||
|
"-protoMap",
|
||||||
|
"{ \"author\" : \"$['author'][*]['fullname']\","
|
||||||
|
+ " \"title\" : \"$['title'][*]['value']\","
|
||||||
|
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
|
||||||
|
+ " \"contributor\" : \"$['contributor'][*]['value']\","
|
||||||
|
+ " \"description\" : \"$['description'][*]['value']\"}"
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<Publication> tmp =
|
||||||
|
sc.textFile(workingDir.toString() + "/publication")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(10, tmp.count());
|
||||||
|
org.apache.spark.sql.Dataset<Publication> verificationDataset =
|
||||||
|
spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("publication");
|
||||||
|
|
||||||
|
String query =
|
||||||
|
"select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||||
|
+ "from publication "
|
||||||
|
+ "lateral view explode(context) c as MyT "
|
||||||
|
+ "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
+ "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||||
|
|
||||||
|
Assertions.assertEquals(5, idExplodeCommunity.count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
5, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
5,
|
||||||
|
idExplodeCommunity
|
||||||
|
.filter("name = 'Bulktagging for Community - Datasource'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'fam'").count());
|
||||||
|
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
3,
|
||||||
|
idExplodeCommunity
|
||||||
|
.filter(
|
||||||
|
"community = 'fam' and (id = '50|ec_fp7health::000085c89f4b96dc2269bd37edb35306' "
|
||||||
|
+ "or id = '50|ec_fp7health::000b9e61f83f5a4b0c35777b7bccdf38' "
|
||||||
|
+ "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
idExplodeCommunity
|
||||||
|
.filter(
|
||||||
|
"community = 'aginfra' and (id = '50|ec_fp7health::000c8195edd542e4e64ebb32172cbf89' "
|
||||||
|
+ "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')")
|
||||||
|
.count());
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void bulktagByZenodoCommunityTest() throws Exception {
|
||||||
|
SparkBulkTagJob2.main(
|
||||||
|
new String[] {
|
||||||
|
"-isTest",
|
||||||
|
Boolean.TRUE.toString(),
|
||||||
|
"-isSparkSessionManaged",
|
||||||
|
Boolean.FALSE.toString(),
|
||||||
|
"-sourcePath",
|
||||||
|
getClass()
|
||||||
|
.getResource(
|
||||||
|
"/eu/dnetlib/dhp/sample/otherresearchproduct/update_zenodocommunity")
|
||||||
|
.getPath(),
|
||||||
|
"-taggingConf",
|
||||||
|
taggingConf,
|
||||||
|
"-resultTableName",
|
||||||
|
"eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
|
||||||
|
"-outputPath",
|
||||||
|
workingDir.toString() + "/orp",
|
||||||
|
"-isLookupUrl",
|
||||||
|
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
|
||||||
|
"-protoMap",
|
||||||
|
"{ \"author\" : \"$['author'][*]['fullname']\","
|
||||||
|
+ " \"title\" : \"$['title'][*]['value']\","
|
||||||
|
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
|
||||||
|
+ " \"contributor\" : \"$['contributor'][*]['value']\","
|
||||||
|
+ " \"description\" : \"$['description'][*]['value']\"}"
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<OtherResearchProduct> tmp =
|
||||||
|
sc.textFile(workingDir.toString() + "/orp")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(10, tmp.count());
|
||||||
|
org.apache.spark.sql.Dataset<OtherResearchProduct> verificationDataset =
|
||||||
|
spark.createDataset(tmp.rdd(), Encoders.bean(OtherResearchProduct.class));
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("orp");
|
||||||
|
|
||||||
|
String query =
|
||||||
|
"select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||||
|
+ "from orp "
|
||||||
|
+ "lateral view explode(context) c as MyT "
|
||||||
|
+ "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
+ "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||||
|
Assertions.assertEquals(8, idExplodeCommunity.count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
8, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
8,
|
||||||
|
idExplodeCommunity.filter("name = 'Bulktagging for Community - Zenodo'").count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'covid-19'").count());
|
||||||
|
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count());
|
||||||
|
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'beopen'").count());
|
||||||
|
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count());
|
||||||
|
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'mes'").count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
1,
|
||||||
|
idExplodeCommunity
|
||||||
|
.filter(
|
||||||
|
"id = '50|od______2017::0750a4d0782265873d669520f5e33c07' "
|
||||||
|
+ "and community = 'covid-19'")
|
||||||
|
.count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
3,
|
||||||
|
idExplodeCommunity
|
||||||
|
.filter(
|
||||||
|
"id = '50|od______2017::1bd97baef19dbd2db3203b112bb83bc5' and "
|
||||||
|
+ "(community = 'aginfra' or community = 'mes' or community = 'fam')")
|
||||||
|
.count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
1,
|
||||||
|
idExplodeCommunity
|
||||||
|
.filter(
|
||||||
|
"id = '50|od______2017::1e400f1747487fd15998735c41a55c72' "
|
||||||
|
+ "and community = 'beopen'")
|
||||||
|
.count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
3,
|
||||||
|
idExplodeCommunity
|
||||||
|
.filter(
|
||||||
|
"id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' and "
|
||||||
|
+ "(community = 'beopen' or community = 'fam' or community = 'mes')")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
query =
|
||||||
|
"select id, MyT.id community, size(MyT.datainfo) datainfosize "
|
||||||
|
+ "from orp "
|
||||||
|
+ "lateral view explode (context) as MyT "
|
||||||
|
+ "where size(MyT.datainfo) > 0";
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
spark.sql(query)
|
||||||
|
.select("datainfosize")
|
||||||
|
.where(
|
||||||
|
"id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' a"
|
||||||
|
+ "nd community = 'beopen'")
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getInt(0));
|
||||||
|
|
||||||
|
// verify the zenodo community context is not present anymore in the records
|
||||||
|
query =
|
||||||
|
"select id, MyT.id community "
|
||||||
|
+ "from orp "
|
||||||
|
+ "lateral view explode(context) c as MyT "
|
||||||
|
+ "lateral view explode(MyT.datainfo) d as MyD ";
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
0,
|
||||||
|
tmp2.select("community")
|
||||||
|
.where(tmp2.col("community").contains(ZENODO_COMMUNITY_INDICATOR))
|
||||||
|
.count());
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void bulktagBySubjectDatasourceTest() throws Exception {
|
||||||
|
SparkBulkTagJob2.main(
|
||||||
|
new String[] {
|
||||||
|
"-isTest",
|
||||||
|
Boolean.TRUE.toString(),
|
||||||
|
"-isSparkSessionManaged",
|
||||||
|
Boolean.FALSE.toString(),
|
||||||
|
"-sourcePath",
|
||||||
|
getClass()
|
||||||
|
.getResource("/eu/dnetlib/dhp/sample/dataset/update_subject_datasource")
|
||||||
|
.getPath(),
|
||||||
|
"-taggingConf",
|
||||||
|
taggingConf,
|
||||||
|
"-resultTableName",
|
||||||
|
"eu.dnetlib.dhp.schema.oaf.Dataset",
|
||||||
|
"-outputPath",
|
||||||
|
workingDir.toString() + "/dataset",
|
||||||
|
"-isLookupUrl",
|
||||||
|
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
|
||||||
|
"-protoMap",
|
||||||
|
"{ \"author\" : \"$['author'][*]['fullname']\","
|
||||||
|
+ " \"title\" : \"$['title'][*]['value']\","
|
||||||
|
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
|
||||||
|
+ " \"contributor\" : \"$['contributor'][*]['value']\","
|
||||||
|
+ " \"description\" : \"$['description'][*]['value']\"}"
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<Dataset> tmp =
|
||||||
|
sc.textFile(workingDir.toString() + "/dataset")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(10, tmp.count());
|
||||||
|
org.apache.spark.sql.Dataset<Dataset> verificationDataset =
|
||||||
|
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("dataset");
|
||||||
|
|
||||||
|
String query =
|
||||||
|
"select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||||
|
+ "from dataset "
|
||||||
|
+ "lateral view explode(context) c as MyT "
|
||||||
|
+ "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
+ "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||||
|
Assertions.assertEquals(7, idExplodeCommunity.count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
5, idExplodeCommunity.filter("provenance = 'community:subject'").count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
|
||||||
|
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count());
|
||||||
|
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count());
|
||||||
|
Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count());
|
||||||
|
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count());
|
||||||
|
|
||||||
|
query =
|
||||||
|
"select id, MyT.id community, size(MyT.datainfo) datainfosize "
|
||||||
|
+ "from dataset "
|
||||||
|
+ "lateral view explode (context) as MyT "
|
||||||
|
+ "where size(MyT.datainfo) > 0";
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
tmp2.select("datainfosize")
|
||||||
|
.where(
|
||||||
|
"id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and "
|
||||||
|
+ "community = 'aginfra'")
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getInt(0));
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
1,
|
||||||
|
tmp2.select("datainfosize")
|
||||||
|
.where(
|
||||||
|
"id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and "
|
||||||
|
+ "community = 'covid-19'")
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getInt(0));
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
tmp2.select("datainfosize")
|
||||||
|
.where(
|
||||||
|
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and "
|
||||||
|
+ "community = 'fam'")
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getInt(0));
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
tmp2.select("datainfosize")
|
||||||
|
.where(
|
||||||
|
"id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and "
|
||||||
|
+ "community = 'covid-19'")
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getInt(0));
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
1,
|
||||||
|
tmp2.select("datainfosize")
|
||||||
|
.where(
|
||||||
|
"id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and "
|
||||||
|
+ "community = 'fam'")
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getInt(0));
|
||||||
|
Assertions.assertEquals(
|
||||||
|
1,
|
||||||
|
tmp2.select("datainfosize")
|
||||||
|
.where(
|
||||||
|
"id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and "
|
||||||
|
+ "community = 'mes'")
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getInt(0));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void bulktagBySubjectDatasourceZenodoCommunityTest() throws Exception {
|
||||||
|
|
||||||
|
SparkBulkTagJob2.main(
|
||||||
|
new String[] {
|
||||||
|
"-isTest",
|
||||||
|
Boolean.TRUE.toString(),
|
||||||
|
"-isSparkSessionManaged",
|
||||||
|
Boolean.FALSE.toString(),
|
||||||
|
"-sourcePath",
|
||||||
|
getClass().getResource("/eu/dnetlib/dhp/sample/software/").getPath(),
|
||||||
|
"-taggingConf",
|
||||||
|
taggingConf,
|
||||||
|
"-resultTableName",
|
||||||
|
"eu.dnetlib.dhp.schema.oaf.Software",
|
||||||
|
"-outputPath",
|
||||||
|
workingDir.toString() + "/software",
|
||||||
|
"-isLookupUrl",
|
||||||
|
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
|
||||||
|
"-protoMap",
|
||||||
|
"{ \"author\" : \"$['author'][*]['fullname']\","
|
||||||
|
+ " \"title\" : \"$['title'][*]['value']\","
|
||||||
|
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
|
||||||
|
+ " \"contributor\" : \"$['contributor'][*]['value']\","
|
||||||
|
+ " \"description\" : \"$['description'][*]['value']\"}"
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<Software> tmp =
|
||||||
|
sc.textFile(workingDir.toString() + "/software")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(10, tmp.count());
|
||||||
|
org.apache.spark.sql.Dataset<Software> verificationDataset =
|
||||||
|
spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("software");
|
||||||
|
|
||||||
|
String query =
|
||||||
|
"select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||||
|
+ "from software "
|
||||||
|
+ "lateral view explode(context) c as MyT "
|
||||||
|
+ "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
+ "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||||
|
Assertions.assertEquals(10, idExplodeCommunity.count());
|
||||||
|
|
||||||
|
idExplodeCommunity.show(false);
|
||||||
|
Assertions.assertEquals(
|
||||||
|
3, idExplodeCommunity.filter("provenance = 'community:subject'").count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
3, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
4, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'covid-19'").count());
|
||||||
|
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dh-ch'").count());
|
||||||
|
Assertions.assertEquals(4, idExplodeCommunity.filter("community = 'aginfra'").count());
|
||||||
|
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dariah'").count());
|
||||||
|
Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
idExplodeCommunity
|
||||||
|
.filter(
|
||||||
|
"provenance = 'community:zenodocommunity' and "
|
||||||
|
+ "id = '50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4' and ("
|
||||||
|
+ "community = 'dh-ch' or community = 'dariah')")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
query =
|
||||||
|
"select id, MyT.id community, size(MyT.datainfo) datainfosize "
|
||||||
|
+ "from software "
|
||||||
|
+ "lateral view explode (context) as MyT "
|
||||||
|
+ "where size(MyT.datainfo) > 0";
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
tmp2.select("datainfosize")
|
||||||
|
.where(
|
||||||
|
"id = '50|od______1582::501b25d420f808c8eddcd9b16e917f11' and "
|
||||||
|
+ "community = 'covid-19'")
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getInt(0));
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
3,
|
||||||
|
tmp2.select("datainfosize")
|
||||||
|
.where(
|
||||||
|
"id = '50|od______1582::581621232a561b7e8b4952b18b8b0e56' and "
|
||||||
|
+ "community = 'aginfra'")
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getInt(0));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void bulktagDatasourcewithConstraintsTest() throws Exception {
|
||||||
|
|
||||||
|
SparkBulkTagJob2.main(
|
||||||
|
new String[] {
|
||||||
|
"-isTest",
|
||||||
|
Boolean.TRUE.toString(),
|
||||||
|
"-isSparkSessionManaged",
|
||||||
|
Boolean.FALSE.toString(),
|
||||||
|
"-sourcePath",
|
||||||
|
getClass()
|
||||||
|
.getResource(
|
||||||
|
"/eu/dnetlib/dhp/sample/dataset/update_datasourcewithconstraints")
|
||||||
|
.getPath(),
|
||||||
|
"-taggingConf",
|
||||||
|
taggingConf,
|
||||||
|
"-resultTableName",
|
||||||
|
"eu.dnetlib.dhp.schema.oaf.Dataset",
|
||||||
|
"-outputPath",
|
||||||
|
workingDir.toString() + "/dataset",
|
||||||
|
"-isLookupUrl",
|
||||||
|
"http://beta.services.openaire.eu:8280/is/services/isLookUp",
|
||||||
|
"-protoMap",
|
||||||
|
"{ \"author\" : \"$['author'][*]['fullname']\","
|
||||||
|
+ " \"title\" : \"$['title'][*]['value']\","
|
||||||
|
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
|
||||||
|
+ " \"contributor\" : \"$['contributor'][*]['value']\","
|
||||||
|
+ " \"description\" : \"$['description'][*]['value']\"}"
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<Dataset> tmp =
|
||||||
|
sc.textFile(workingDir.toString() + "/dataset")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(10, tmp.count());
|
||||||
|
org.apache.spark.sql.Dataset<Dataset> verificationDataset =
|
||||||
|
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("dataset");
|
||||||
|
String query =
|
||||||
|
"select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||||
|
+ "from dataset "
|
||||||
|
+ "lateral view explode(context) c as MyT "
|
||||||
|
+ "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
+ "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||||
|
|
||||||
|
idExplodeCommunity.show(false);
|
||||||
|
Assertions.assertEquals(2, idExplodeCommunity.count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
|
||||||
|
|
@ -18,9 +18,6 @@ import org.junit.jupiter.api.Test;
|
||||||
/** Created by miriam on 03/08/2018. */
|
/** Created by miriam on 03/08/2018. */
|
||||||
public class CommunityConfigurationFactoryTest {
|
public class CommunityConfigurationFactoryTest {
|
||||||
|
|
||||||
private static String xml;
|
|
||||||
private static String xml1;
|
|
||||||
|
|
||||||
private final VerbResolver resolver = new VerbResolver();
|
private final VerbResolver resolver = new VerbResolver();
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
|
|
|
||||||
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Loading…
Reference in New Issue