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[Create Unresolved Entities] Moving Measure at the level of the Instance #160

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miriam.baglioni wants to merge 4 commits from bypass_acstionset into beta
pull from: bypass_acstionset
merge into: D-Net:beta
Conversation 1 Commits 4 Files Changed 8 +32 -46
8 changed files with 32 additions and 46 deletions
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13
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java
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@ -6,12 +6,13 @@ import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.UP
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;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.hdfs.client.HdfsUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
@ -29,6 +30,7 @@ import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.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;
@ -40,7 +42,7 @@ 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(
@ -76,7 +78,7 @@ 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());
@ -93,9 +95,10 @@ public class PrepareBipFinder implements Serializable {
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class))
.map((MapFunction<BipScore, Result>) v -> {
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()

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java
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@ -55,13 +55,13 @@ public class PrepareFOSSparkJob implements Serializable {
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
spark ->
distributeFOSdois(
spark,
sourcePath,
outputPath);
});
outputPath)
);
}
private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {

12
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java
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@ -20,13 +20,13 @@ 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 {
String jsonConfiguration = IOUtils
.toString(
PrepareFOSSparkJob.class
SparkSaveUnresolved.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/produce_unresolved_parameters.json"));
@ -47,13 +47,13 @@ public class SparkSaveUnresolved implements Serializable {
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
spark ->
saveUnresolved(
spark,
sourcePath,
outputPath);
});
outputPath)
);
}
private static void saveUnresolved(SparkSession spark, String sourcePath, String outputPath) {
@ -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));

9
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java
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@ -96,13 +96,16 @@ 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 +120,8 @@ 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 +136,8 @@ public class PrepareTest {
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getInstance()
.get(0)
.getMeasures()
.stream()
.filter(sl -> sl.getId().equals("popularity"))

9
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java
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@ -27,7 +27,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
public class ProduceTest {
class ProduceTest {
private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
private static Path workingDir;
@ -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());
}

9
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java
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@ -43,15 +43,6 @@ public class ResultMapper implements Serializable {
try {
addTypeSpecificInformation(out, input, ort);
Optional<List<Measure>> mes = Optional.ofNullable(input.getMeasures());
if (mes.isPresent()) {
List<KeyValue> measure = new ArrayList<>();
mes
.get()
.forEach(
m -> m.getUnit().forEach(u -> measure.add(KeyValue.newInstance(m.getId(), u.getValue()))));
out.setMeasures(measure);
}
Optional
.ofNullable(input.getAuthor())

18
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java
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@ -171,24 +171,6 @@ public class DumpJobTest {
GraphResult gr = verificationDataset.first();
Assertions.assertEquals(2, gr.getMeasures().size());
Assertions
.assertTrue(
gr
.getMeasures()
.stream()
.anyMatch(
m -> m.getKey().equals("influence")
&& m.getValue().equals("1.62759106106e-08")));
Assertions
.assertTrue(
gr
.getMeasures()
.stream()
.anyMatch(
m -> m.getKey().equals("popularity")
&& m.getValue().equals("0.22519296")));
Assertions.assertEquals(6, gr.getAuthor().size());
Assertions
.assertTrue(

2
pom.xml
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@ -753,7 +753,7 @@
<mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version>
<dhp-schemas.version>[2.8.22]</dhp-schemas.version>
<dhp-schemas.version>[2.9.23]</dhp-schemas.version>
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>