[UnresolvedEntities] Changed the way to merge the unresolved because the new merge removed the dataInfo from the merged result. Added also data info for subjects
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dce7f5fea8
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73eba34d42
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@ -21,8 +21,10 @@ import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.utils.DHPUtils;
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public class PrepareFOSSparkJob implements Serializable {
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@ -71,6 +73,7 @@ public class PrepareFOSSparkJob implements Serializable {
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Result r = new Result();
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FOSDataModel first = it.next();
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r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
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HashSet<String> level1 = new HashSet<>();
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HashSet<String> level2 = new HashSet<>();
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HashSet<String> level3 = new HashSet<>();
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@ -81,6 +84,19 @@ public class PrepareFOSSparkJob implements Serializable {
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level2.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
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level3.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
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r.setSubject(sbjs);
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r
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.setDataInfo(
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OafMapperUtils
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.dataInfo(
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false, null, true,
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false,
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OafMapperUtils
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.qualifier(
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ModelConstants.PROVENANCE_ENRICH,
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null,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS),
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null));
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return r;
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}, Encoders.bean(Result.class))
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.write()
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@ -21,8 +21,10 @@ import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.utils.DHPUtils;
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public class PrepareSDGSparkJob implements Serializable {
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@ -78,6 +80,19 @@ public class PrepareSDGSparkJob implements Serializable {
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s -> sbjs
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.add(getSubject(s.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
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r.setSubject(sbjs);
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r
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.setDataInfo(
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OafMapperUtils
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.dataInfo(
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false, null, true,
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false,
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OafMapperUtils
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.qualifier(
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ModelConstants.PROVENANCE_ENRICH,
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null,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS),
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null));
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return r;
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}, Encoders.bean(Result.class))
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.write()
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@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.actionmanager.Constants.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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@ -67,7 +68,19 @@ public class SparkSaveUnresolved implements Serializable {
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.groupByKey((MapFunction<Result, String>) Result::getId, Encoders.STRING())
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.mapGroups((MapGroupsFunction<String, Result, Result>) (k, it) -> {
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Result ret = it.next();
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it.forEachRemaining(r -> ret.mergeFrom(r));
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it.forEachRemaining(r -> {
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if (r.getInstance() != null) {
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ret.setInstance(r.getInstance());
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}
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if (r.getSubject() != null) {
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if (ret.getSubject() != null)
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ret.getSubject().addAll(r.getSubject());
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else
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ret.setSubject(r.getSubject());
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}
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// ret.mergeFrom(r)
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});
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return ret;
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}, Encoders.bean(Result.class))
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.write()
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@ -146,6 +146,11 @@ public class PrepareTest {
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.get(0)
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.getValue());
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final String doi2 = "unresolved::10.3390/s18072310::doi";
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Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).count());
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Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).collect().get(0).getInstance().size());
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}
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@Test
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@ -259,59 +264,61 @@ public class PrepareTest {
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.collect()
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.contains("8. Economic growth"));
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}
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@Test
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void test3() throws Exception {
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final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_fos_results_20_12_2021.csv.gz";
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final String outputPath = workingDir.toString() + "/fos.json";
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GetFOSSparkJob
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--sourcePath", sourcePath,
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"-outputPath", outputPath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<FOSDataModel> tmp = sc
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.textFile(outputPath)
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.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
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tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
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tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
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tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
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tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
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Assertions.assertEquals(32, tmp.filter(row -> row.getDataInfo() != null).count());
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}
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@Test
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void test4() throws Exception {
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final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_sdg_results_20_12_21.csv.gz";
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final String outputPath = workingDir.toString() + "/sdg.json";
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GetSDGSparkJob
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--sourcePath", sourcePath,
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"-outputPath", outputPath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<SDGDataModel> tmp = sc
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.textFile(outputPath)
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.map(item -> OBJECT_MAPPER.readValue(item, SDGDataModel.class));
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tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
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tmp.foreach(t -> Assertions.assertTrue(t.getSbj() != null));
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}
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// @Test
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// void test3() throws Exception {
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// final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_fos_results_20_12_2021.csv.gz";
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//
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// final String outputPath = workingDir.toString() + "/fos.json";
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// GetFOSSparkJob
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// .main(
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// new String[] {
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// "--isSparkSessionManaged", Boolean.FALSE.toString(),
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// "--sourcePath", sourcePath,
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//
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// "-outputPath", outputPath
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//
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// });
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//
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// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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//
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// JavaRDD<FOSDataModel> tmp = sc
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// .textFile(outputPath)
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// .map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
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//
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// tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
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// tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
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// tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
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// tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
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//
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// }
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//
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// @Test
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// void test4() throws Exception {
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// final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_sdg_results_20_12_21.csv.gz";
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//
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// final String outputPath = workingDir.toString() + "/sdg.json";
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// GetSDGSparkJob
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// .main(
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// new String[] {
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// "--isSparkSessionManaged", Boolean.FALSE.toString(),
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// "--sourcePath", sourcePath,
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//
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// "-outputPath", outputPath
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//
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// });
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//
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// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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//
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// JavaRDD<SDGDataModel> tmp = sc
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// .textFile(outputPath)
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// .map(item -> OBJECT_MAPPER.readValue(item, SDGDataModel.class));
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//
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// tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
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// tmp.foreach(t -> Assertions.assertTrue(t.getSbj() != null));
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//
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// }
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}
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@ -196,6 +196,9 @@ public class ProduceTest {
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final String doi = "unresolved::10.3390/s18072310::doi";
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JavaRDD<Result> tmp = getResultJavaRDD();
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tmp
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.filter(row -> row.getId().equals(doi))
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.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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Assertions
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.assertEquals(
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3, tmp
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