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Merge pull request 'bipFinder: unresolved entities' (#174) from bipFinder into beta 

Reviewed-on: #174
This commit is contained in:
Miriam Baglioni 2021-12-22 16:42:30 +01:00
parent bf52a1847b 34ac56565d
commit b352fbe453
5 changed files with 24 additions and 14 deletions
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10
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java
View File

@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.actionmanager.bipmodel.Constants.UPDATE_CLASS_NAME;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
@ -28,6 +29,7 @@ import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Measure;
import eu.dnetlib.dhp.schema.oaf.Result;
@ -39,7 +41,7 @@ public class PrepareBipFinder implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static <I extends Result> void main(String[] args) throws Exception {
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
@ -75,7 +77,7 @@ public class PrepareBipFinder implements Serializable {
});
}
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath) {
private static void prepareResults(SparkSession spark, String inputPath, String outputPath) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -95,7 +97,9 @@ public class PrepareBipFinder implements Serializable {
Result r = new Result();
r.setId(DHPUtils.generateUnresolvedIdentifier(v.getId(), DOI));
r.setMeasures(getMeasure(v));
Instance inst = new Instance();
inst.setMeasures(getMeasure(v));
r.setInstance(Arrays.asList(inst));
return r;
}, Encoders.bean(Result.class))
.write()

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java
View File

@ -20,7 +20,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Result;
public class SparkSaveUnresolved implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class);
private static final Logger log = LoggerFactory.getLogger(SparkSaveUnresolved.class);
public static void main(String[] args) throws Exception {
@ -64,7 +64,7 @@ public class SparkSaveUnresolved implements Serializable {
.map(
(MapFunction<String, Result>) l -> OBJECT_MAPPER.readValue(l, Result.class),
Encoders.bean(Result.class))
.groupByKey((MapFunction<Result, String>) r -> r.getId(), Encoders.STRING())
.groupByKey((MapFunction<Result, String>) Result::getId, Encoders.STRING())
.mapGroups((MapGroupsFunction<String, Result, Result>) (k, it) -> {
Result ret = it.next();
it.forEachRemaining(r -> ret.mergeFrom(r));

6
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml
View File

@ -1,9 +1,5 @@
<workflow-app name="BipFinderScore" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>inputPath</name>
<description>the input path of the resources to be extended</description>
</property>
<property>
<name>bipScorePath</name>
@ -108,7 +104,5 @@
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

11
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java
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@ -96,13 +96,18 @@ public class PrepareTest {
String doi1 = "unresolved::10.0000/096020199389707::doi";
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count());
Assertions.assertEquals(3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getMeasures().size());
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().size());
Assertions
.assertEquals(
3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().get(0).getMeasures().size());
Assertions
.assertEquals(
"6.34596412687e-09", tmp
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.stream()
.filter(sl -> sl.getId().equals("influence"))
@ -117,6 +122,8 @@ public class PrepareTest {
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.stream()
.filter(sl -> sl.getId().equals("popularity_alt"))
@ -131,6 +138,8 @@ public class PrepareTest {
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.stream()
.filter(sl -> sl.getId().equals("popularity"))

7
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java
View File

@ -126,6 +126,8 @@ public class ProduceTest {
.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.size());
@ -179,7 +181,8 @@ public class ProduceTest {
List<Measure> measures = tmp
.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
.flatMap(row -> row.getMeasures().iterator())
.flatMap(row -> row.getInstance().iterator())
.flatMap(inst -> inst.getMeasures().iterator())
.collect();
Assertions
.assertEquals(
@ -226,7 +229,7 @@ public class ProduceTest {
85,
tmp
.filter(row -> !row.getId().equals("unresolved::10.3390/s18072310::doi"))
.filter(r -> r.getMeasures() != null)
.filter(r -> r.getInstance() != null)
.count());
}