Add basic tests for affiliation relations
This commit is contained in:
Serafeim Chatzopoulos
parent
bc7b00bcd1
commit
c2998a14e8
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@ -5,8 +5,11 @@ import static org.junit.jupiter.api.Assertions.*;
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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 eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import org.apache.commons.io.FileUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.SparkConf;
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@ -26,7 +29,6 @@ import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class PrepareAffiliationRelationsTest {
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@ -35,6 +37,7 @@ public class PrepareAffiliationRelationsTest {
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private static SparkSession spark;
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private static Path workingDir;
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private static final String ID_PREFIX = "50|doi_________::";
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private static final Logger log = LoggerFactory
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.getLogger(PrepareAffiliationRelationsTest.class);
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@ -69,71 +72,64 @@ public class PrepareAffiliationRelationsTest {
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@Test
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void testMatch() throws Exception {
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String affiliationRelationsPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
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.getPath();
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String outputPath = workingDir.toString() + "/actionSet";
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PrepareAffiliationRelations
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-inputPath",
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affiliationRelationsPath,
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"-outputPath",
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workingDir.toString() + "/actionSet"
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath", affiliationRelationsPath,
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"-outputPath", outputPath
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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// JavaRDD<Result> tmp = sc
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// .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
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// .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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// .map(aa -> ((Result) aa.getPayload()));
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//
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// assertEquals(4, tmp.count());
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//
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// Dataset<Result> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Result.class));
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// verificationDataset.createOrReplaceTempView("result");
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//
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// Dataset<Row> execVerification = spark
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// .sql(
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// "Select p.id oaid, mes.id, mUnit.value from result p " +
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// "lateral view explode(measures) m as mes " +
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// "lateral view explode(mes.unit) u as mUnit ");
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//
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// Assertions.assertEquals(12, execVerification.count());
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// Assertions
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// .assertEquals(
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// "6.63451994567e-09", execVerification
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// .filter(
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// "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
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// "and id = 'influence'")
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// .select("value")
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// .collectAsList()
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// .get(0)
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// .getString(0));
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// Assertions
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// .assertEquals(
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// "0.348694533145", execVerification
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// .filter(
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// "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
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// "and id = 'popularity_alt'")
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// .select("value")
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// .collectAsList()
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// .get(0)
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// .getString(0));
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// Assertions
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// .assertEquals(
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// "2.16094680115e-09", execVerification
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// .filter(
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// "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
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// "and id = 'popularity'")
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// .select("value")
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// .collectAsList()
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// .get(0)
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// .getString(0));
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//
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JavaRDD<Relation> tmp = sc
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.sequenceFile(outputPath, Text.class, Text.class)
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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for (Relation r : tmp.collect()) {
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System.out.println(
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r.getSource() + "\t" + r.getTarget() + "\t" + r.getRelType() + "\t" + r.getRelClass() + "\t" + r.getSubRelType() + "\t" + r.getValidationDate() + "\t" + r.getDataInfo().getTrust() + "\t" + r.getDataInfo().getInferred()
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);
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}
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// count the number of relations
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assertEquals(16, tmp.count());
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Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
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dataset.createOrReplaceTempView("result");
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Dataset<Row> execVerification = spark.sql("select r.relType, r.relClass, r.source, r.target, r.dataInfo.trust from result r");
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// verify that we have equal number of bi-directional relations
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Assertions.assertEquals(8, execVerification
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.filter(
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"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION +"'")
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.collectAsList()
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.size());
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Assertions.assertEquals(8, execVerification
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.filter(
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"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF +"'")
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.collectAsList()
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.size());
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// check confidence value of a specific relation
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String sourceDOI = "10.1105/tpc.8.3.343";
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final String sourceOpenaireId = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI));
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Assertions.assertEquals("0.7071067812", execVerification
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.filter(
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"source='" + sourceOpenaireId +"'")
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.collectAsList().get(0).getString(4));
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}
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}
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