forked from D-Net/dnet-hadoop
first tests for the pid graph dump
This commit is contained in:
parent
40c8d2de7b
commit
630a6a1fe7
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package eu.dnetlib.dhp.oa.graph.dump.pid;
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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 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.Dataset;
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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.dump.pidgraph.Entity;
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public class DumpAuthorTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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(DumpAuthorTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(DumpAuthorTest.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(DumpAuthorTest.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(DumpAuthorTest.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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public void testDumpAuthorPids() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/pid/result")
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.getPath();
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SparkDumpPidAuthor.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString(),
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"-sourcePath", sourcePath,
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"-allowedAuthorPids", "[\"orcid\", \"mag\"]"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Entity> tmp = sc
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.textFile(workingDir.toString() + "/author")
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.map(item -> OBJECT_MAPPER.readValue(item, Entity.class));
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org.apache.spark.sql.Dataset<Entity> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Entity.class));
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verificationDataset.show(false);
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Assertions.assertEquals(3, verificationDataset.count());
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Assertions.assertEquals(1, verificationDataset.filter("id = 'mag:fakemag'").count());
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Assertions.assertEquals(2, verificationDataset.filter("substr(id,1,5) = 'orcid'").count());
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}
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}
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package eu.dnetlib.dhp.oa.graph.dump.pid;
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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 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.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.dump.oaf.graph.Relation;
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import eu.dnetlib.dhp.schema.dump.pidgraph.Entity;
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public class DumpResultRelationTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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(DumpResultRelationTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(DumpResultRelationTest.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(DumpResultRelationTest.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(DumpAuthorTest.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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public void testDumpResultRelationPids() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/pid/preparedInfoDR")
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.getPath();
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SparkDumpResultRelation.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString(),
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"-preparedInfoPath", sourcePath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc
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.textFile(workingDir.toString() + "/relation")
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
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org.apache.spark.sql.Dataset<Relation> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
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verificationDataset.show(100, false);
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Assertions.assertEquals(32, verificationDataset.count());
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Assertions
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.assertEquals(
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1, verificationDataset
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.filter(
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"source.id = 'orcid:0000-0001-9317-9350' and " +
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"relType.name = 'sameAs' and target.id = 'mag:fakeMag'")
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.count());
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Assertions
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.assertEquals(
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4, verificationDataset
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.filter(
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"source.id = 'orcid:0000-0001-9317-9350' and " +
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"relType.name = 'isAuthorOf'")
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.count());
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Assertions
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.assertEquals(
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4, verificationDataset
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.filter(
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"target.id = 'orcid:0000-0001-9317-9350' and " +
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"relType.name = 'hasAuthor'")
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.count());
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Assertions
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.assertEquals(
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1, verificationDataset
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.filter(
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"source.id = 'orcid:0000-0001-9317-9350' and " +
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"relType.name = 'hasCoAuthor'")
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.count());
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Assertions
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.assertEquals(
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1, verificationDataset
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.filter(
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"source.id = 'orcid:0000-0001-9317-9350' and " +
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"relType.name = 'hasCoAuthor' and target.id = 'orcid:0000-0002-1114-4216'")
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.count());
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Assertions
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.assertEquals(
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2, verificationDataset
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.filter(
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"source.id = 'orcid:0000-0002-1114-4216' and " +
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"relType.name = 'hasCoAuthor'")
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.count());
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Assertions
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.assertEquals(
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1, verificationDataset
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.filter(
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"target.id = 'orcid:0000-0001-9317-9350' and " +
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"relType.name = 'hasCoAuthor' and source.id = 'orcid:0000-0002-1114-4216'")
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.count());
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Assertions
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.assertEquals(
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1, verificationDataset
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.filter(
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"target.id = 'mag:fakeMag' and " +
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"relType.name = 'hasCoAuthor' and source.id = 'orcid:0000-0002-1114-4216'")
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.count());
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Assertions.assertEquals(4, verificationDataset.filter("relType.name = 'hasOtherManifestation'").count());
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//
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// Assertions.assertEquals(1, verificationDataset.filter("id = 'mag:fakemag'").count());
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//
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// Assertions.assertEquals(2, verificationDataset.filter("substr(id,1,5) = 'orcid'").count());
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}
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}
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package eu.dnetlib.dhp.oa.graph.dump.pid;
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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 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.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.dump.pidgraph.Entity;
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public class DumpResultTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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(DumpResultTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(DumpResultTest.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(DumpAuthorTest.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(DumpResultTest.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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public void testDumpResultPids() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/pid/preparedInfo")
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.getPath();
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SparkDumpPidResult.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString(),
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"-preparedInfoPath", sourcePath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Entity> tmp = sc
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.textFile(workingDir.toString() + "/result")
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.map(item -> OBJECT_MAPPER.readValue(item, Entity.class));
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org.apache.spark.sql.Dataset<Entity> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Entity.class));
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Assertions.assertEquals(35, verificationDataset.count());
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Assertions.assertEquals(32, verificationDataset.filter("substr(id,1,3) = 'doi'").count());
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Assertions.assertEquals(1, verificationDataset.filter("substr(id,1,3) = 'pdb'").count());
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Assertions.assertEquals(1, verificationDataset.filter("substr(id,1,4) = 'pmid'").count());
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Assertions.assertEquals(1, verificationDataset.filter("substr(id,1,5) = 'arXiv'").count());
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}
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}
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package eu.dnetlib.dhp.oa.graph.dump.pid;
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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 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.Dataset;
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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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public class PreparedInfoCollectTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static SparkSession spark;
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private static Path workingDir;
|
||||||
|
|
||||||
|
private static final Logger log = LoggerFactory.getLogger(PreparedInfoCollectTest.class);
|
||||||
|
|
||||||
|
@BeforeAll
|
||||||
|
public static void beforeAll() throws IOException {
|
||||||
|
workingDir = Files.createTempDirectory(PreparedInfoCollectTest.class.getSimpleName());
|
||||||
|
log.info("using work dir {}", workingDir);
|
||||||
|
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
conf.setAppName(PreparedInfoCollectTest.class.getSimpleName());
|
||||||
|
|
||||||
|
conf.setMaster("local[*]");
|
||||||
|
conf.set("spark.driver.host", "localhost");
|
||||||
|
conf.set("hive.metastore.local", "true");
|
||||||
|
conf.set("spark.ui.enabled", "false");
|
||||||
|
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
||||||
|
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
||||||
|
|
||||||
|
spark = SparkSession
|
||||||
|
.builder()
|
||||||
|
.appName(PreparedInfoCollectTest.class.getSimpleName())
|
||||||
|
.config(conf)
|
||||||
|
.getOrCreate();
|
||||||
|
}
|
||||||
|
|
||||||
|
@AfterAll
|
||||||
|
public static void afterAll() throws IOException {
|
||||||
|
FileUtils.deleteDirectory(workingDir.toFile());
|
||||||
|
spark.stop();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testCollectAndSave() throws Exception {
|
||||||
|
//software and otherresearchproduct associated preparedInfo files intended to be empty
|
||||||
|
final String sourcePath = getClass()
|
||||||
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/pid/preparedInfoSplit")
|
||||||
|
.getPath();
|
||||||
|
|
||||||
|
SparkCollectPreparedInfo.main(new String[] {
|
||||||
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
"-outputPath", workingDir.toString() + "/preparedInfo",
|
||||||
|
"-preparedInfoPath", sourcePath
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<ResultPidsList> tmp = sc
|
||||||
|
.textFile(workingDir.toString() + "/preparedInfo")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, ResultPidsList.class));
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<ResultPidsList> verificationDataset = spark
|
||||||
|
.createDataset(tmp.rdd(), Encoders.bean(ResultPidsList.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(34, verificationDataset.count());
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("check");
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
33, spark
|
||||||
|
.sql(
|
||||||
|
"Select resultId " +
|
||||||
|
"from check " +
|
||||||
|
"lateral view explode (resultAllowedPids) r as resallowed " +
|
||||||
|
" where resallowed.key = 'doi'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
4, spark
|
||||||
|
.sql(
|
||||||
|
"SELECT pids.value " +
|
||||||
|
"FROM check " +
|
||||||
|
"LATERAL VIEW EXPLODE (authorAllowedPids) a as authallowed " +
|
||||||
|
"LATERAL VIEW EXPLODE (authallowed) a as pids " +
|
||||||
|
"WHERE pids.key = 'orcid'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, spark
|
||||||
|
.sql(
|
||||||
|
"SELECT pids.value " +
|
||||||
|
"FROM check " +
|
||||||
|
"LATERAL VIEW EXPLODE (authorAllowedPids) a as authallowed " +
|
||||||
|
"LATERAL VIEW EXPLODE (authallowed) a as pids " +
|
||||||
|
"WHERE pids.key = 'mag'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Dataset<Row> check = spark
|
||||||
|
.sql(
|
||||||
|
"Select resultId, pids.value orcid, resallowed.key pid_type, resallowed.value pid " +
|
||||||
|
"from check" +
|
||||||
|
" lateral view explode(authorAllowedPids) a as authallowed " +
|
||||||
|
" lateral view explode(authallowed) p as pids " +
|
||||||
|
" lateral view explode (resultAllowedPids) r as resallowed " +
|
||||||
|
"where pids.key = 'orcid'");
|
||||||
|
|
||||||
|
Assertions.assertEquals(6, check.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(1, check.filter("resultId = '50|base_oa_____::1a700385222228181f20835bae60a71e'").count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|base_oa_____::1a700385222228181f20835bae60a71e' " +
|
||||||
|
"and orcid = '0000-0002-1114-4216'")
|
||||||
|
.count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|base_oa_____::1a700385222228181f20835bae60a71e' " +
|
||||||
|
"and pid = '10.1016/j.jrmge.2016.11.005'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(1, check.filter("resultId = '50|base_oa_____::06546a1ad6b1c71e5e366ef15b9ade1f'").count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|base_oa_____::06546a1ad6b1c71e5e366ef15b9ade1f' " +
|
||||||
|
"and orcid = '0000-0001-9317-9350'")
|
||||||
|
.count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|base_oa_____::06546a1ad6b1c71e5e366ef15b9ade1f' " +
|
||||||
|
"and pid = '10.1016/j.jotr.2014.10.003'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,260 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.oa.graph.dump.pid;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.nio.file.Files;
|
||||||
|
import java.nio.file.Path;
|
||||||
|
|
||||||
|
import org.apache.commons.io.FileUtils;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
|
import org.apache.spark.sql.Dataset;
|
||||||
|
import org.apache.spark.sql.Encoders;
|
||||||
|
import org.apache.spark.sql.Row;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import org.junit.jupiter.api.AfterAll;
|
||||||
|
import org.junit.jupiter.api.Assertions;
|
||||||
|
import org.junit.jupiter.api.BeforeAll;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
|
public class PreparedInfoPidTest {
|
||||||
|
|
||||||
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||||
|
|
||||||
|
private static SparkSession spark;
|
||||||
|
|
||||||
|
private static Path workingDir;
|
||||||
|
|
||||||
|
private static final Logger log = LoggerFactory.getLogger(PreparedInfoPidTest.class);
|
||||||
|
|
||||||
|
@BeforeAll
|
||||||
|
public static void beforeAll() throws IOException {
|
||||||
|
workingDir = Files.createTempDirectory(PreparedInfoPidTest.class.getSimpleName());
|
||||||
|
log.info("using work dir {}", workingDir);
|
||||||
|
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
conf.setAppName(PreparedInfoPidTest.class.getSimpleName());
|
||||||
|
|
||||||
|
conf.setMaster("local[*]");
|
||||||
|
conf.set("spark.driver.host", "localhost");
|
||||||
|
conf.set("hive.metastore.local", "true");
|
||||||
|
conf.set("spark.ui.enabled", "false");
|
||||||
|
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
||||||
|
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
||||||
|
|
||||||
|
spark = SparkSession
|
||||||
|
.builder()
|
||||||
|
.appName(PreparedInfoPidTest.class.getSimpleName())
|
||||||
|
.config(conf)
|
||||||
|
.getOrCreate();
|
||||||
|
}
|
||||||
|
|
||||||
|
@AfterAll
|
||||||
|
public static void afterAll() throws IOException {
|
||||||
|
FileUtils.deleteDirectory(workingDir.toFile());
|
||||||
|
spark.stop();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testPublication() throws Exception {
|
||||||
|
|
||||||
|
final String sourcePath = getClass()
|
||||||
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/pid/result/publication")
|
||||||
|
.getPath();
|
||||||
|
|
||||||
|
SparkPrepareResultPids.main(new String[] {
|
||||||
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
"-outputPath", workingDir.toString() + "/preparedInfo",
|
||||||
|
"-sourcePath", sourcePath,
|
||||||
|
"-allowedResultPids", "[\"doi\",\"arxiv\",\"pmc\",\"pmid\",\"pdb\"]",
|
||||||
|
"-allowedAuthorPids", "[\"orcid\"]",
|
||||||
|
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication"
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<ResultPidsList> tmp = sc
|
||||||
|
.textFile(workingDir.toString() + "/preparedInfo/publication")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, ResultPidsList.class));
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<ResultPidsList> verificationDataset = spark
|
||||||
|
.createDataset(tmp.rdd(), Encoders.bean(ResultPidsList.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(31, verificationDataset.count());
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("check");
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
31, spark
|
||||||
|
.sql(
|
||||||
|
"Select resultId " +
|
||||||
|
"from check " +
|
||||||
|
"lateral view explode (resultAllowedPids) r as resallowed " +
|
||||||
|
" where resallowed.key = 'doi'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Dataset<Row> check = spark
|
||||||
|
.sql(
|
||||||
|
"Select resultId, pids.value orcid, resallowed.key pid_type, resallowed.value pid " +
|
||||||
|
"from check" +
|
||||||
|
" lateral view explode(authorAllowedPids) a as authallowed " +
|
||||||
|
" lateral view explode(authallowed) p as pids " +
|
||||||
|
" lateral view explode (resultAllowedPids) r as resallowed " +
|
||||||
|
"where pids.key = 'orcid'");
|
||||||
|
|
||||||
|
Assertions.assertEquals(2, check.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(1, check.filter("resultId = '50|base_oa_____::1a700385222228181f20835bae60a71e'").count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|base_oa_____::1a700385222228181f20835bae60a71e' " +
|
||||||
|
"and orcid = '0000-0002-1114-4216'")
|
||||||
|
.count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|base_oa_____::1a700385222228181f20835bae60a71e' " +
|
||||||
|
"and pid = '10.1016/j.jrmge.2016.11.005'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(1, check.filter("resultId = '50|base_oa_____::06546a1ad6b1c71e5e366ef15b9ade1f'").count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|base_oa_____::06546a1ad6b1c71e5e366ef15b9ade1f' " +
|
||||||
|
"and orcid = '0000-0001-9317-9350'")
|
||||||
|
.count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|base_oa_____::06546a1ad6b1c71e5e366ef15b9ade1f' " +
|
||||||
|
"and pid = '10.1016/j.jotr.2014.10.003'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testDataset() throws Exception {
|
||||||
|
final String sourcePath = getClass()
|
||||||
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/pid/result/dataset")
|
||||||
|
.getPath();
|
||||||
|
|
||||||
|
SparkPrepareResultPids.main(new String[] {
|
||||||
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
"-outputPath", workingDir.toString() + "/preparedInfo",
|
||||||
|
"-sourcePath", sourcePath,
|
||||||
|
"-allowedResultPids", "[\"doi\",\"arxiv\",\"pmc\",\"pmid\",\"pdb\"]",
|
||||||
|
"-allowedAuthorPids", "[\"orcid\"]",
|
||||||
|
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset"
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<ResultPidsList> tmp = sc
|
||||||
|
.textFile(workingDir.toString() + "/preparedInfo/dataset")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, ResultPidsList.class));
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<ResultPidsList> verificationDataset = spark
|
||||||
|
.createDataset(tmp.rdd(), Encoders.bean(ResultPidsList.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(3, verificationDataset.count());
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("check");
|
||||||
|
|
||||||
|
Dataset<Row> check = spark
|
||||||
|
.sql(
|
||||||
|
"Select resultId, pids.value orcid, resallowed.key pid_type, resallowed.value pid " +
|
||||||
|
"from check" +
|
||||||
|
" lateral view explode(authorAllowedPids) a as authallowed " +
|
||||||
|
" lateral view explode(authallowed) p as pids " +
|
||||||
|
" lateral view explode (resultAllowedPids) r as resallowed ");
|
||||||
|
|
||||||
|
Assertions.assertEquals(4, check.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(4, check.filter("resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02'").count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
2, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02' " +
|
||||||
|
"and (orcid = '0000-0001-9317-9350' or orcid = '0000-0002-1114-4216') and " +
|
||||||
|
"pid = '10.1016/fake' and pid_type = 'doi' ")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
2, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02' " +
|
||||||
|
"and (orcid = '0000-0001-9317-9350' or orcid = '0000-0002-1114-4216') and " +
|
||||||
|
"pid = '10443fake' and pid_type = 'pmid' ")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
check = spark
|
||||||
|
.sql(
|
||||||
|
"Select resultId, authorAllowedPids, resallowed.key pid_type, resallowed.value pid " +
|
||||||
|
"from check" +
|
||||||
|
" lateral view explode (resultAllowedPids) r as resallowed ");
|
||||||
|
|
||||||
|
Assertions.assertEquals(5, check.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(2, check.filter("resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02'").count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02' " +
|
||||||
|
" and pid = '10.1016/fake' and pid_type = 'doi' ")
|
||||||
|
.count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|_____OmicsDI::00899d9cb1163754943a3277365adc02' " +
|
||||||
|
" and pid = '10443fake' and pid_type = 'pmid' ")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(1, check.filter("resultId = '50|_____OmicsDI::023fd1fcbb64f0f7df0671798a62f379'").count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|_____OmicsDI::023fd1fcbb64f0f7df0671798a62f379' " +
|
||||||
|
" and pid = 'fakepdb' and pid_type = 'pdb' ")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Assertions
|
||||||
|
.assertEquals(2, check.filter("resultId = '50|_____OmicsDI::036d65211a6ac14237c6e2d7cc223386'").count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|_____OmicsDI::036d65211a6ac14237c6e2d7cc223386' " +
|
||||||
|
" and pid = '10.1016/j.tcs.2012.06.029' and pid_type = 'doi' ")
|
||||||
|
.count());
|
||||||
|
Assertions
|
||||||
|
.assertEquals(
|
||||||
|
1, check
|
||||||
|
.filter(
|
||||||
|
"resultId = '50|_____OmicsDI::036d65211a6ac14237c6e2d7cc223386' " +
|
||||||
|
" and pid = 'fake_arxiv' and pid_type = 'arXiv' ")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue