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[EOSC context TAG] refactoring after compilation

This commit is contained in:
Miriam Baglioni 2022-07-22 14:57:06 +02:00
parent ffb0ce3fb9
commit 06a95daf60
2 changed files with 118 additions and 112 deletions
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4
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java
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@ -93,14 +93,10 @@ public class SparkEoscBulkTag implements Serializable {
String datasourceMapPath, String datasourceMapPath,
Class<R> resultClazz) { Class<R> resultClazz) {
List<String> hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class) List<String> hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class)
.map((MapFunction<DatasourceMaster, String>) dm -> dm.getMaster(), Encoders.STRING()) .map((MapFunction<DatasourceMaster, String>) dm -> dm.getMaster(), Encoders.STRING())
.collectAsList(); .collectAsList();
readPath(spark, inputPath, resultClazz) readPath(spark, inputPath, resultClazz)
.map(patchResult(), Encoders.bean(resultClazz)) .map(patchResult(), Encoders.bean(resultClazz))
.filter(Objects::nonNull) .filter(Objects::nonNull)

78
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java
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@ -1,16 +1,11 @@
package eu.dnetlib.dhp.bulktag; package eu.dnetlib.dhp.bulktag;
/**
* @author miriam.baglioni
* @Date 22/07/22
*/
import com.fasterxml.jackson.databind.ObjectMapper; import java.io.IOException;
import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag; import java.nio.file.Files;
import eu.dnetlib.dhp.schema.oaf.Dataset; import java.nio.file.Path;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; import java.util.List;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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;
@ -26,10 +21,17 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.io.IOException; /**
import java.nio.file.Files; * @author miriam.baglioni
import java.nio.file.Path; * @Date 22/07/22
import java.util.List; */
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
//"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc //"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc
//"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc //"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc
@ -87,7 +89,6 @@ public class EOSCContextTaggingTest {
.option("compression", "gzip") .option("compression", "gzip")
.json(workingDir.toString() + "/input/dataset"); .json(workingDir.toString() + "/input/dataset");
SparkEoscBulkTag SparkEoscBulkTag
.main( .main(
new String[] { new String[] {
@ -95,7 +96,10 @@ public class EOSCContextTaggingTest {
"-sourcePath", "-sourcePath",
workingDir.toString() + "/input/dataset", workingDir.toString() + "/input/dataset",
"-workingPath", workingDir.toString() + "/working/dataset", "-workingPath", workingDir.toString() + "/working/dataset",
"-datasourceMapPath", getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster").getPath(), "-datasourceMapPath",
getClass()
.getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster")
.getPath(),
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset" "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset"
}); });
@ -116,37 +120,43 @@ public class EOSCContextTaggingTest {
.count()); .count());
Assertions Assertions
.assertEquals(1, .assertEquals(
1,
tmp tmp
.filter(d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea") .filter(
d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea")
&& &&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
); .count());
Assertions Assertions
.assertEquals(1, .assertEquals(
1,
tmp tmp
.filter(d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1") .filter(
d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1")
&& &&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
); .count());
Assertions Assertions
.assertEquals(1, .assertEquals(
1,
tmp tmp
.filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") .filter(
d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&& &&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
); .count());
Assertions Assertions
.assertEquals(1, .assertEquals(
1,
tmp tmp
.filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb") .filter(
d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&& &&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count() d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
); .count());
} }
} }