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[EOSC BulkTag] refactoring

This commit is contained in:
Miriam Baglioni 2022-09-20 16:13:18 +02:00
parent 840465958b
commit 869e129288
2 changed files with 110 additions and 108 deletions
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10
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java
View File

@ -97,7 +97,8 @@ public class SparkEoscBulkTag implements Serializable {
}); });
} }
private static void selectCompliantDatasources(SparkSession spark, String inputPath, String workingPath, String datasourceMapPath) { private static void selectCompliantDatasources(SparkSession spark, String inputPath, String workingPath,
String datasourceMapPath) {
Dataset<Datasource> datasources = readPath(spark, inputPath + "datasource", Datasource.class) Dataset<Datasource> datasources = readPath(spark, inputPath + "datasource", Datasource.class)
.filter((FilterFunction<Datasource>) ds -> { .filter((FilterFunction<Datasource>) ds -> {
final String compatibility = ds.getOpenairecompatibility().getClassid(); final String compatibility = ds.getOpenairecompatibility().getClassid();
@ -109,8 +110,11 @@ public class SparkEoscBulkTag implements Serializable {
Dataset<DatasourceMaster> datasourceMaster = readPath(spark, datasourceMapPath, DatasourceMaster.class); Dataset<DatasourceMaster> datasourceMaster = readPath(spark, datasourceMapPath, DatasourceMaster.class);
datasources.joinWith(datasourceMaster, datasources.col("id").equalTo(datasourceMaster.col("master")), "left") datasources
.map((MapFunction<Tuple2<Datasource, DatasourceMaster>, DatasourceMaster>) t2 -> t2._2(), Encoders.bean(DatasourceMaster.class) ) .joinWith(datasourceMaster, datasources.col("id").equalTo(datasourceMaster.col("master")), "left")
.map(
(MapFunction<Tuple2<Datasource, DatasourceMaster>, DatasourceMaster>) t2 -> t2._2(),
Encoders.bean(DatasourceMaster.class))
.filter(Objects::nonNull) .filter(Objects::nonNull)
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)

18
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java
View File

@ -6,8 +6,6 @@ import java.nio.file.Files;
import java.nio.file.Path; import java.nio.file.Path;
import java.util.List; import java.util.List;
import eu.dnetlib.dhp.bulktag.eosc.DatasourceMaster;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
@ -29,7 +27,9 @@ import org.slf4j.LoggerFactory;
*/ */
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.bulktag.eosc.DatasourceMaster;
import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag;
import eu.dnetlib.dhp.schema.oaf.*;
//"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc (cris) //"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc (cris)
//"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc (zenodo) //"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc (zenodo)
@ -74,7 +74,7 @@ public class EOSCContextTaggingTest {
} }
@Test @Test
void EoscContextTagTest() throws Exception{ void EoscContextTagTest() throws Exception {
spark spark
.read() .read()
@ -114,10 +114,12 @@ public class EOSCContextTaggingTest {
}); });
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
Assertions.assertEquals(2, sc Assertions
.assertEquals(
2, sc
.textFile(workingDir.toString() + "/working/datasource") .textFile(workingDir.toString() + "/working/datasource")
.map(item -> OBJECT_MAPPER.readValue(item, DatasourceMaster.class)).count()); .map(item -> OBJECT_MAPPER.readValue(item, DatasourceMaster.class))
.count());
JavaRDD<Dataset> tmp = sc JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/input/dataset") .textFile(workingDir.toString() + "/input/dataset")
@ -187,7 +189,6 @@ public class EOSCContextTaggingTest {
.option("compression", "gzip") .option("compression", "gzip")
.json(workingDir.toString() + "/input/dataset"); .json(workingDir.toString() + "/input/dataset");
spark spark
.read() .read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasource/datasource").getPath()) .textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasource/datasource").getPath())
@ -216,8 +217,6 @@ public class EOSCContextTaggingTest {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/input/dataset") .textFile(workingDir.toString() + "/input/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
@ -232,7 +231,6 @@ public class EOSCContextTaggingTest {
s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count()); .count());
} }
} }