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[EOSC context TAG] refactoring after compilation

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eosc_context_tagging
Miriam Baglioni 2 years ago
parent ffb0ce3fb9
commit 06a95daf60
2 changed files with 136 additions and 130 deletions
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6
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java
Unescape Escape View File

@ -93,13 +93,9 @@ public class SparkEoscBulkTag implements Serializable {
String datasourceMapPath,
Class<R> resultClazz) {
List<String> hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class)
.map((MapFunction<DatasourceMaster, String>) dm -> dm.getMaster(), Encoders.STRING())
.collectAsList();
.collectAsList();
readPath(spark, inputPath, resultClazz)
.map(patchResult(), Encoders.bean(resultClazz))

260
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java
Unescape Escape View File

@ -1,16 +1,11 @@
package eu.dnetlib.dhp.bulktag;
/**
* @author miriam.baglioni
* @Date 22/07/22
*/
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;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
@ -26,10 +21,17 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
/**
* @author miriam.baglioni
* @Date 22/07/22
*/
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::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc
@ -37,116 +39,124 @@ import java.util.List;
//"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag
public class EOSCContextTaggingTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(EOSCContextTaggingTest.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(EOSCTagJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void EoscContextTagTest() throws Exception {
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath())
.map(
(MapFunction<String, Dataset>) value -> OBJECT_MAPPER.readValue(value, Dataset.class),
Encoders.bean(Dataset.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/dataset");
SparkEoscBulkTag
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath",
workingDir.toString() + "/input/dataset",
"-workingPath", workingDir.toString() + "/working/dataset",
"-datasourceMapPath", getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster").getPath(),
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/input/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
Assertions
.assertEquals(
4,
tmp
.filter(
s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(1,
tmp
.filter(d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count()
);
Assertions
.assertEquals(1,
tmp
.filter(d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count()
);
Assertions
.assertEquals(1,
tmp
.filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count()
);
Assertions
.assertEquals(1,
tmp
.filter(d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))).count()
);
}
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(EOSCContextTaggingTest.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(EOSCTagJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void EoscContextTagTest() throws Exception {
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath())
.map(
(MapFunction<String, Dataset>) value -> OBJECT_MAPPER.readValue(value, Dataset.class),
Encoders.bean(Dataset.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/dataset");
SparkEoscBulkTag
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath",
workingDir.toString() + "/input/dataset",
"-workingPath", workingDir.toString() + "/working/dataset",
"-datasourceMapPath",
getClass()
.getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster")
.getPath(),
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/input/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
Assertions
.assertEquals(
4,
tmp
.filter(
s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
}
}

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