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Read affiliation relations

This commit is contained in:
Serafeim Chatzopoulos 2023-07-06 00:51:01 +03:00
parent 7738372125
commit 347a889b20
7 changed files with 379 additions and 0 deletions
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5
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
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@ -3,6 +3,7 @@ package eu.dnetlib.dhp.actionmanager;
import java.util.Optional;
import eu.dnetlib.dhp.common.HdfsSupport;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
@ -93,4 +94,8 @@ public class Constants {
return s;
}
public static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
}

168
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java Normal file
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@ -0,0 +1,168 @@
package eu.dnetlib.dhp.actionmanager.bipaffiliations;
import static eu.dnetlib.dhp.actionmanager.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Iterator;
import java.util.List;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import eu.dnetlib.dhp.actionmanager.Constants;
import eu.dnetlib.dhp.actionmanager.bipaffiliations.model.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.apache.spark.sql.Dataset;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
/**
* created the Atomic Action for each tipe of results
*/
public class PrepareAffiliationRelations implements Serializable {
private static final String DOI = "doi";
private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static <I extends Result> void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareAffiliationRelations.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Constants.removeOutputDir(spark, outputPath);
prepareAffiliationRelations(spark, inputPath, outputPath);
});
}
private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath, String outputPath) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<AffiliationRelationDeserializer> bipDeserializeJavaRDD = sc
.textFile(inputPath)
.map(item -> OBJECT_MAPPER.readValue(item, AffiliationRelationDeserializer.class));
// for(AffiliationRelationDeserializer rel: bipDeserializeJavaRDD.collect()){
// System.out.println(rel);
// }
JavaRDD<AffiliationRelationModel> affiliationRelations =
bipDeserializeJavaRDD.flatMap(entry ->
entry.getMatchings().stream().flatMap(matching ->
matching.getRorId().stream().map( rorId -> new AffiliationRelationModel(
entry.getDoi(),
rorId,
matching.getConfidence()
))).collect(Collectors.toList()).iterator());
for(AffiliationRelationModel rel: affiliationRelations.collect()){
System.out.println(rel);
}
// Dataset<AffiliationRelationModel> relations = spark
// .createDataset(bipDeserializeJavaRDD.flatMap(entry -> {
//// entry.keySet().stream().map(key -> {
// AffiliationRelationModel rel = new AffiliationRelationModel(entry.getDoi())
// System.out.println(entry);
// return entry;
//// BipScore bs = new BipScore();
//// bs.setId(key);
//// bs.setScoreList(entry.get(key));
//// return bs;
// }).collect(Collectors.toList()).iterator()).rdd(), Encoßders.bean(AffiliationRelationModel.class));
// bipScores
//
// .map((MapFunction<BipScore, Result>) bs -> {
// Result ret = new Result();
//
// ret.setId(bs.getId());
//
// ret.setMeasures(getMeasure(bs));
//
// return ret;
// }, Encoders.bean(Result.class))
// .toJavaRDD()
// .map(p -> new AtomicAction(Result.class, p))
// .mapToPair(
// aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
// new Text(OBJECT_MAPPER.writeValueAsString(aa))))
// .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
// }
//
// private static List<Measure> getMeasure(BipScore value) {
// return value
// .getScoreList()
// .stream()
// .map(score -> {
// Measure m = new Measure();
// m.setId(score.getId());
// m
// .setUnit(
// score
// .getUnit()
// .stream()
// .map(unit -> {
// KeyValue kv = new KeyValue();
// kv.setValue(unit.getValue());
// kv.setKey(unit.getKey());
// kv
// .setDataInfo(
// OafMapperUtils
// .dataInfo(
// false,
// UPDATE_DATA_INFO_TYPE,
// true,
// false,
// OafMapperUtils
// .qualifier(
// UPDATE_MEASURE_BIP_CLASS_ID,
// UPDATE_CLASS_NAME,
// ModelConstants.DNET_PROVENANCE_ACTIONS,
// ModelConstants.DNET_PROVENANCE_ACTIONS),
// ""));
// return kv;
// })
// .collect(Collectors.toList()));
// return m;
// })
// .collect(Collectors.toList());
}
}

26
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/model/AffiliationRelationDeserializer.java Normal file
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@ -0,0 +1,26 @@
package eu.dnetlib.dhp.actionmanager.bipaffiliations.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import lombok.Data;
import java.io.Serializable;
import java.util.List;
@Data
public class AffiliationRelationDeserializer implements Serializable {
@JsonProperty("DOI")
private String doi;
@JsonProperty("Matchings")
private List<Matching> matchings;
@Data
public static class Matching implements Serializable {
@JsonProperty("RORid")
private List<String> rorId;
@JsonProperty("Confidence")
private double confidence;
}
}

15
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/model/AffiliationRelationModel.java Normal file
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@ -0,0 +1,15 @@
package eu.dnetlib.dhp.actionmanager.bipaffiliations.model;
import lombok.AllArgsConstructor;
import lombok.Data;
import lombok.NoArgsConstructor;
import java.io.Serializable;
@Data
@AllArgsConstructor
public class AffiliationRelationModel implements Serializable {
private String doi;
private String rorId;
private double confidence;
}

20
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json Normal file
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@ -0,0 +1,20 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

139
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java Normal file
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@ -0,0 +1,139 @@
package eu.dnetlib.dhp.actionmanager.bipaffiliations;
import static org.junit.jupiter.api.Assertions.*;
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.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.Result;
public class PrepareAffiliationRelationsTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(PrepareAffiliationRelationsTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(PrepareAffiliationRelationsTest.class.getSimpleName());
log.info("Using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(PrepareAffiliationRelationsTest.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(PrepareAffiliationRelationsTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testMatch() throws Exception {
String affiliationRelationsPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
.getPath();
PrepareAffiliationRelations
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
affiliationRelationsPath,
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
// JavaRDD<Result> tmp = sc
// .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
// .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
// .map(aa -> ((Result) aa.getPayload()));
//
// assertEquals(4, tmp.count());
//
// Dataset<Result> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Result.class));
// verificationDataset.createOrReplaceTempView("result");
//
// Dataset<Row> execVerification = spark
// .sql(
// "Select p.id oaid, mes.id, mUnit.value from result p " +
// "lateral view explode(measures) m as mes " +
// "lateral view explode(mes.unit) u as mUnit ");
//
// Assertions.assertEquals(12, execVerification.count());
// Assertions
// .assertEquals(
// "6.63451994567e-09", execVerification
// .filter(
// "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
// "and id = 'influence'")
// .select("value")
// .collectAsList()
// .get(0)
// .getString(0));
// Assertions
// .assertEquals(
// "0.348694533145", execVerification
// .filter(
// "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
// "and id = 'popularity_alt'")
// .select("value")
// .collectAsList()
// .get(0)
// .getString(0));
// Assertions
// .assertEquals(
// "2.16094680115e-09", execVerification
// .filter(
// "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
// "and id = 'popularity'")
// .select("value")
// .collectAsList()
// .get(0)
// .getString(0));
//
}
}

6
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json Normal file
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@ -0,0 +1,6 @@
{"DOI":"10.1061\/(asce)0733-9399(2002)128:7(759)","Matchings":[{"RORid":["https:\/\/ror.org\/01teme464"],"Confidence":0.73},{"RORid":["https:\/\/ror.org\/03yxnpp24"],"Confidence":0.7071067812}]}
{"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":["https:\/\/ror.org\/02k40bc56"],"Confidence":0.7071067812}]}
{"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":["https:\/\/ror.org\/00qjgza05"],"Confidence":1}]}
{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":["https:\/\/ror.org\/05apxxy63"],"Confidence":1},{"RORid":["https:\/\/ror.org\/035xkbk20"],"Confidence":1}]}
{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":["https:\/\/ror.org\/04j198w64"],"Confidence":0.58}]}
{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":["https:\/\/ror.org\/057xtrt18"],"Confidence":0.7071067812}]}