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dnet-hadoop
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This commit is contained in:
Miriam Baglioni 2021-11-10 17:00:37 +01:00
parent 9e214ce0eb
commit c371b23077
23 changed files with 1319 additions and 847 deletions
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9
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java
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@ -30,11 +30,11 @@ public class PropagationConstant {
public static final String UPDATE_DATA_INFO_TYPE = "update";
public static final String UPDATE_SUBJECT_FOS_CLASS_ID = "subject:fos";
public static final String UPDATE_SUBJECT_FOS_CLASS_NAME = "Update of results with FOS subjects";
public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE";
public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip";
public static final String UPDATE_MEASURE_BIP_CLASS_NAME = "Update of results with BipFinder! measures";
public static final String FOS_CLASS_ID = "FOS";
public static final String FOS_CLASS_NAME = "Subject from fos classification";
public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification";
public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
@ -100,7 +100,8 @@ public class PropagationConstant {
public static DataInfo getDataInfo(
String inference_provenance, String inference_class_id, String inference_class_name, String qualifierSchema,
String trust) {
return getDataInfo(inference_provenance, inference_class_id, inference_class_name, qualifierSchema, trust, true);
return getDataInfo(
inference_provenance, inference_class_id, inference_class_name, qualifierSchema, trust, true);
}

4
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/Utils.java
View File

@ -1,8 +1,10 @@
package eu.dnetlib.dhp.bypassactionset;
import org.jetbrains.annotations.NotNull;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import org.jetbrains.annotations.NotNull;
public class Utils {
private static final String ID_PREFIX = "50|doi_________";

31
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/bipfinder/PrepareBipFinder.java
View File

@ -1,10 +1,13 @@
package eu.dnetlib.dhp.bypassactionset.bipfinder;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bypassactionset.model.BipDeserialize;
import eu.dnetlib.dhp.bypassactionset.model.BipScore;
import eu.dnetlib.dhp.schema.oaf.Result;
import static eu.dnetlib.dhp.bypassactionset.Utils.getIdentifier;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
@ -15,15 +18,15 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.Serializable;
import java.util.Optional;
import java.util.stream.Collectors;
import com.fasterxml.jackson.databind.ObjectMapper;
import static eu.dnetlib.dhp.bypassactionset.Utils.getIdentifier;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bypassactionset.model.BipDeserialize;
import eu.dnetlib.dhp.bypassactionset.model.BipScore;
import eu.dnetlib.dhp.schema.oaf.Result;
public class PrepareBipFinder implements Serializable {
private static final String DOI = "doi";
private static final Logger log = LoggerFactory.getLogger(SparkUpdateBip.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@ -33,7 +36,7 @@ public class PrepareBipFinder implements Serializable {
.toString(
SparkUpdateBip.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json"));
"/eu/dnetlib/dhp/bypassactionset/bip_prepare_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
@ -52,7 +55,6 @@ public class PrepareBipFinder implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
@ -66,7 +68,6 @@ public class PrepareBipFinder implements Serializable {
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
@ -82,7 +83,7 @@ public class PrepareBipFinder implements Serializable {
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.option("compression", "gzip")
.json(outputPath);
}
}

62
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/bipfinder/SparkUpdateBip.java
View File

@ -1,36 +1,35 @@
package eu.dnetlib.dhp.bypassactionset.bipfinder;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bypassactionset.model.BipScore;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bypassactionset.model.BipScore;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;
/**
* created the Atomic Action for each tipe of results
*/
public class SparkUpdateBip implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkUpdateBip.class);
public static <I extends Result> void main(String[] args) throws Exception {
@ -39,7 +38,7 @@ public class SparkUpdateBip implements Serializable {
.toString(
SparkUpdateBip.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json"));
"/eu/dnetlib/dhp/bypassactionset/bip_update_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
@ -71,8 +70,7 @@ public class SparkUpdateBip implements Serializable {
runWithSparkSession(
conf,
isSparkSessionManaged,
spark ->
updateBipFinder(spark, inputPath, outputPath, bipScorePath, inputClazz)
spark -> updateBipFinder(spark, inputPath, outputPath, bipScorePath, inputClazz)
);
}
@ -83,9 +81,10 @@ public class SparkUpdateBip implements Serializable {
Dataset<I> results = readPath(spark, inputPath, inputClazz);
Dataset<BipScore> bipScores = readPath(spark, bipScorePath, BipScore.class);
results.joinWith(bipScores, results.col("id").equalTo(bipScores.col("id")), "left")
.map((MapFunction<Tuple2<I,BipScore>, I>) value -> {
if (!Optional.ofNullable(value._2()).isPresent()){
results
.joinWith(bipScores, results.col("id").equalTo(bipScores.col("id")), "left")
.map((MapFunction<Tuple2<I, BipScore>, I>) value -> {
if (!Optional.ofNullable(value._2()).isPresent()) {
return value._1();
}
value._1().setMeasures(getMeasure(value._2()));
@ -93,7 +92,7 @@ public class SparkUpdateBip implements Serializable {
}, Encoders.bean(inputClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.option("compression", "gzip")
.json(outputPath + "/bip");
}
@ -114,9 +113,12 @@ public class SparkUpdateBip implements Serializable {
KeyValue kv = new KeyValue();
kv.setValue(unit.getValue());
kv.setKey(unit.getKey());
kv.setDataInfo(getDataInfo(UPDATE_DATA_INFO_TYPE,
kv
.setDataInfo(
getDataInfo(
UPDATE_DATA_INFO_TYPE,
UPDATE_MEASURE_BIP_CLASS_ID,
UPDATE_MEASURE_BIP_CLASS_NAME,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS, ""));
return kv;
})
@ -126,10 +128,4 @@ public class SparkUpdateBip implements Serializable {
.collect(Collectors.toList());
}
}

26
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/fos/GetFOSData.java
View File

@ -1,8 +1,10 @@
package eu.dnetlib.dhp.bypassactionset.fos;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import java.io.*;
import java.util.Objects;
import java.util.Optional;
import eu.dnetlib.dhp.common.collection.GetCSV;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
@ -10,10 +12,8 @@ import org.apache.hadoop.fs.Path;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.*;
import java.util.Objects;
import java.util.Optional;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.collection.GetCSV;
public class GetFOSData implements Serializable {
@ -33,11 +33,11 @@ public class GetFOSData implements Serializable {
parser.parseArgument(args);
//the path where the original fos csv file is stored
// the path where the original fos csv file is stored
final String inputPath = parser.get("inputPath");
log.info("inputPath {}", inputPath);
//the path where to put the file as json
// the path where to put the file as json
final String outputFile = parser.get("outputFile");
log.info("outputFile {}", outputFile);
@ -63,17 +63,13 @@ public class GetFOSData implements Serializable {
}
public void doRewrite(String inputPath, String outputFile, String classForName, char delimiter, FileSystem fs)
throws IOException, ClassNotFoundException{
throws IOException, ClassNotFoundException {
//reads the csv and writes it as its json equivalent
try (InputStreamReader reader = new InputStreamReader(fs.open(new Path (inputPath)))) {
// reads the csv and writes it as its json equivalent
try (InputStreamReader reader = new InputStreamReader(fs.open(new Path(inputPath)))) {
GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter);
}
}
}

44
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/fos/PrepareFOSSparkJob.java
View File

@ -1,9 +1,15 @@
package eu.dnetlib.dhp.bypassactionset.fos;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.bypassactionset.Utils.getIdentifier;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FlatMapFunction;
@ -15,19 +21,14 @@ import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.bypassactionset.Utils.getIdentifier;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class PrepareFOSSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
@ -46,13 +47,9 @@ public class PrepareFOSSparkJob implements Serializable {
String sourcePath = parser.get("sourcePath");
log.info("sourcePath: {}", sourcePath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
@ -63,8 +60,7 @@ public class PrepareFOSSparkJob implements Serializable {
spark,
sourcePath,
outputPath
);
outputPath);
});
}
@ -76,17 +72,15 @@ public class PrepareFOSSparkJob implements Serializable {
final String level1 = v.getLevel1();
final String level2 = v.getLevel2();
final String level3 = v.getLevel3();
Arrays.stream(v.getDoi().split("\u0002")).forEach(d ->
fosList.add(FOSDataModel.newInstance(getIdentifier(d), level1, level2, level3)));
Arrays
.stream(v.getDoi().split("\u0002"))
.forEach(d -> fosList.add(FOSDataModel.newInstance(getIdentifier(d), level1, level2, level3)));
return fosList.iterator();
}, Encoders.bean(FOSDataModel.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.option("compression", "gzip")
.json(outputPath);
}
}

55
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/fos/SparkUpdateFOS.java
View File

@ -1,11 +1,13 @@
package eu.dnetlib.dhp.bypassactionset.fos;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
@ -15,26 +17,24 @@ import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import scala.Tuple2;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
public class SparkUpdateFOS implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkUpdateFOS.class);
public static <I extends Result> void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkUpdateFOS.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json"));
"/eu/dnetlib/dhp/bypassactionset/fos_update_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
@ -66,21 +66,21 @@ public class SparkUpdateFOS implements Serializable {
runWithSparkSession(
conf,
isSparkSessionManaged,
spark ->
updateFos(spark, inputPath, outputPath, fosPath, inputClazz)
spark -> updateFos(spark, inputPath, outputPath, fosPath, inputClazz)
);
}
private static <I extends Result> void updateFos(SparkSession spark, String inputPath, String outputPath,
String bipScorePath, Class<I> inputClazz) {
String fosPath, Class<I> inputClazz) {
Dataset<I> results = readPath(spark, inputPath, inputClazz);
Dataset<FOSDataModel> bipScores = readPath(spark, bipScorePath, FOSDataModel.class);
Dataset<FOSDataModel> fosDataModelDataset = readPath(spark, fosPath, FOSDataModel.class);
results.joinWith(bipScores, results.col("id").equalTo(bipScores.col("id")), "left")
.map((MapFunction<Tuple2<I,FOSDataModel>, I>) value -> {
if (!Optional.ofNullable(value._2()).isPresent()){
results
.joinWith(fosDataModelDataset, results.col("id").equalTo(fosDataModelDataset.col("doi")), "left")
.map((MapFunction<Tuple2<I, FOSDataModel>, I>) value -> {
if (!Optional.ofNullable(value._2()).isPresent()) {
return value._1();
}
value._1().getSubject().addAll(getSubjects(value._2()));
@ -88,13 +88,14 @@ public class SparkUpdateFOS implements Serializable {
}, Encoders.bean(inputClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.option("compression", "gzip")
.json(outputPath);
}
private static List<StructuredProperty> getSubjects(FOSDataModel fos) {
return Arrays.asList(getSubject(fos.getLevel1()), getSubject(fos.getLevel2()), getSubject(fos.getLevel3()))
return Arrays
.asList(getSubject(fos.getLevel1()), getSubject(fos.getLevel2()), getSubject(fos.getLevel3()))
.stream()
.filter(Objects::nonNull)
.collect(Collectors.toList());
@ -106,13 +107,15 @@ public class SparkUpdateFOS implements Serializable {
StructuredProperty sp = new StructuredProperty();
sp.setValue(sbj);
sp.setQualifier(getQualifier(FOS_CLASS_ID, FOS_CLASS_NAME, ModelConstants.DNET_SUBJECT_TYPOLOGIES));
sp.setDataInfo(getDataInfo(UPDATE_DATA_INFO_TYPE,
sp
.setDataInfo(
getDataInfo(
UPDATE_DATA_INFO_TYPE,
UPDATE_SUBJECT_FOS_CLASS_ID,
UPDATE_SUBJECT_FOS_CLASS_NAME,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS, ""));
return sp;
}
}

6
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/model/FOSDataModel.java
View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.bypassactionset.model;
import com.opencsv.bean.CsvBindByPosition;
import java.io.Serializable;
import com.opencsv.bean.CsvBindByPosition;
public class FOSDataModel implements Serializable {
@CsvBindByPosition(position = 1)
// @CsvBindByName(column = "doi")
@ -21,7 +22,6 @@ public class FOSDataModel implements Serializable {
// @CsvBindByName(column = "level3")
private String level3;
public FOSDataModel() {
}

1
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/opencitations/GetOpenCitationsRefs.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.bypassactionset.opencitations;
import java.io.*;

20
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/opencitations/SparkUpdateOCRels.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.bypassactionset.opencitations;
package eu.dnetlib.dhp.bypassactionset.opencitations;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
@ -10,7 +10,6 @@ import java.util.*;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
@ -23,15 +22,11 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
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.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class SparkUpdateOCRels implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkUpdateOCRels.class);
@ -63,8 +58,8 @@ public class SparkUpdateOCRels implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final boolean shouldDuplicateRels =
Optional.ofNullable(parser.get("shouldDuplicateRels"))
final boolean shouldDuplicateRels = Optional
.ofNullable(parser.get("shouldDuplicateRels"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
@ -72,9 +67,7 @@ public class SparkUpdateOCRels implements Serializable {
runWithSparkSession(
conf,
isSparkSessionManaged,
spark ->
addOCRelations(spark, inputPath, outputPath, shouldDuplicateRels)
);
spark -> addOCRelations(spark, inputPath, outputPath, shouldDuplicateRels));
}
@ -140,7 +133,8 @@ public class SparkUpdateOCRels implements Serializable {
r.setSubRelType(ModelConstants.CITATION);
r
.setDataInfo(
getDataInfo(UPDATE_DATA_INFO_TYPE, OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME,
getDataInfo(
UPDATE_DATA_INFO_TYPE, OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME,
ModelConstants.DNET_PROVENANCE_ACTIONS, OC_TRUST, false));
return r;
}
@ -153,6 +147,4 @@ public class SparkUpdateOCRels implements Serializable {
return Arrays.asList(kv);
}
}

20
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bypassactionset/bip_prepare_parameters.json Normal file
View File

@ -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
}
]

32
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bypassactionset/bip_update_parameters.json Normal file
View File

@ -0,0 +1,32 @@
[
{
"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
},
{
"paramName": "rtn",
"paramLongName": "resultTableName",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "bsp",
"paramLongName": "bipScorePath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

32
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bypassactionset/fos_update_parameters.json Normal file
View File

@ -0,0 +1,32 @@
[
{
"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
},
{
"paramName": "rtn",
"paramLongName": "resultTableName",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "fp",
"paramLongName": "fosPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

250
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bypassactionset/BipTest.java Normal file
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package eu.dnetlib.dhp.bypassactionset;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.oaf.Author;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocalFileSystem;
import org.apache.neethi.Assertion;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
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.bypassactionset.bipfinder.PrepareBipFinder;
import eu.dnetlib.dhp.bypassactionset.bipfinder.SparkUpdateBip;
import eu.dnetlib.dhp.bypassactionset.model.BipScore;
import eu.dnetlib.dhp.countrypropagation.CountryPropagationJobTest;
import eu.dnetlib.dhp.schema.oaf.Measure;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class BipTest {
private static final Logger log = LoggerFactory.getLogger(FOSTest.class);
private static Path workingDir;
private static SparkSession spark;
private static LocalFileSystem fs;
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String ID_PREFIX = "50|doi_________";
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(BipTest.class.getSimpleName());
fs = FileSystem.getLocal(new Configuration());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(FOSTest.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(CountryPropagationJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void prepareBipTest() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/bip/bip.json")
.getPath();
PrepareBipFinder
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", sourcePath,
"--outputPath", workingDir.toString() + "/remapDoi"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<BipScore> tmp = sc
.textFile(workingDir.toString() + "/remapDoi")
.map(item -> OBJECT_MAPPER.readValue(item, BipScore.class));
Assertions.assertEquals(86, tmp.count());
// tmp.foreach(v -> System.out.println(OBJECT_MAPPER.writeValueAsString(v)));
String doi1 = ID_PREFIX +
IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.0000/096020199389707"));
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count());
Assertions.assertEquals(3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getScoreList().size());
Assertions
.assertEquals(
"6.34596412687e-09", tmp
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getScoreList()
.stream()
.filter(sl -> sl.getId().equals("influence"))
.collect(Collectors.toList())
.get(0)
.getUnit()
.get(0)
.getValue());
Assertions
.assertEquals(
"0.641151896994", tmp
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getScoreList()
.stream()
.filter(sl -> sl.getId().equals("popularity_alt"))
.collect(Collectors.toList())
.get(0)
.getUnit()
.get(0)
.getValue());
Assertions
.assertEquals(
"2.33375102921e-09", tmp
.filter(r -> r.getId().equals(doi1))
.collect()
.get(0)
.getScoreList()
.stream()
.filter(sl -> sl.getId().equals("popularity"))
.collect(Collectors.toList())
.get(0)
.getUnit()
.get(0)
.getValue());
}
@Test
void updateResult() throws Exception {
final String bipScorePath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/bip/preparedbip.json")
.getPath();
final String inputPath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/bip/publicationnomatch.json")
.getPath();
SparkUpdateBip
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--bipScorePath", bipScorePath,
"--inputPath", inputPath,
"--outputPath", workingDir.toString() + "/publication",
"--resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication/bip")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(6, tmp.count());
Assertions.assertEquals(0, tmp.filter(r -> r.getMeasures() != null).count());
tmp.foreach(r -> Assertions.assertEquals("publication", r.getResulttype().getClassid()));
}
@Test
void updateResultMatchCheckMeasures() throws Exception {
final String bipScorePath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/bip/preparedbip.json")
.getPath();
final String inputPath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/bip/publicationmatch.json")
.getPath();
SparkUpdateBip
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--bipScorePath", bipScorePath,
"--inputPath", inputPath,
"--outputPath", workingDir.toString() + "/publication",
"--resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication/bip")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(6, tmp.count());
Assertions.assertEquals(1, tmp.filter(r -> r.getMeasures() != null).count());
Assertions
.assertEquals(
1, tmp.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f")).count());
Assertions
.assertEquals(
1,
tmp
.filter(
r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f")
&& r.getMeasures() != null)
.count());
Assertions.assertEquals(3, tmp
.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f"))
.collect()
.get(0)
.getMeasures().size());
Assertions.assertEquals("5.91019644836e-09",
tmp.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f"))
.collect()
.get(0).getMeasures().stream().filter(m -> m.getId().equals("influence")).collect(Collectors.toList()).get(0).getUnit().get(0).getValue());
Assertions.assertEquals("0.0",
tmp.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f"))
.collect()
.get(0).getMeasures().stream().filter(m -> m.getId().equals("popularity_alt")).collect(Collectors.toList()).get(0).getUnit().get(0).getValue());
Assertions.assertEquals("9.88840807598e-09",
tmp.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f"))
.collect()
.get(0).getMeasures().stream().filter(m -> m.getId().equals("popularity")).collect(Collectors.toList()).get(0).getUnit().get(0).getValue());
tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
}
}

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package eu.dnetlib.dhp.bypassactionset;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import eu.dnetlib.dhp.PropagationConstant;
import eu.dnetlib.dhp.bypassactionset.fos.SparkUpdateFOS;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocalFileSystem;
import org.apache.neethi.Assertion;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
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.bypassactionset.fos.GetFOSData;
import eu.dnetlib.dhp.bypassactionset.fos.PrepareFOSSparkJob;
import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.countrypropagation.CountryPropagationJobTest;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class FOSTest {
private static final Logger log = LoggerFactory.getLogger(FOSTest.class);
private static Path workingDir;
private static SparkSession spark;
private static LocalFileSystem fs;
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String ID_PREFIX = "50|doi_________";
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(CountryPropagationJobTest.class.getSimpleName());
fs = FileSystem.getLocal(new Configuration());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(FOSTest.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(CountryPropagationJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void getFOSFileTest() throws CollectorException, IOException, ClassNotFoundException {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/fos/h2020_fos_sbs.csv")
.getPath();
final String outputPath = workingDir.toString() + "/fos.json";
new GetFOSData()
.doRewrite(sourcePath, outputPath, "eu.dnetlib.dhp.bypassactionset.FOSDataModel", '\t', fs);
BufferedReader in = new BufferedReader(
new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
String line;
int count = 0;
while ((line = in.readLine()) != null) {
FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class);
System.out.println(new ObjectMapper().writeValueAsString(fos));
count += 1;
}
assertEquals(38, count);
}
@Test
void distributeDoiTest() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/fos/fos.json")
.getPath();
PrepareFOSSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"-outputPath", workingDir.toString() + "/distribute"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<FOSDataModel> tmp = sc
.textFile(workingDir.toString() + "/distribute")
.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
String doi1 = ID_PREFIX +
IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.3390/s18072310"));
assertEquals(50, tmp.count());
assertEquals(1, tmp.filter(row -> row.getDoi().equals(doi1)).count());
assertEquals(
"engineering and technology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel1());
assertEquals("nano-technology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel2());
assertEquals(
"nanoscience & nanotechnology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel3());
String doi = ID_PREFIX +
IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/1365-2656.12831"));
assertEquals(1, tmp.filter(row -> row.getDoi().equals(doi)).count());
assertEquals("social sciences", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel1());
assertEquals(
"psychology and cognitive sciences", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel2());
assertEquals("NULL", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel3());
}
@Test
void updateResult() throws Exception{
final String fosPath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/fos/fos_prepared.json")
.getPath();
final String inputPath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/bip/publicationnomatch.json")
.getPath();
SparkUpdateFOS
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--fosPath", fosPath,
"--inputPath", inputPath,
"--outputPath", workingDir.toString() + "/publication",
"--resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(6, tmp.count());
tmp.filter(r -> r.getSubject() != null).map(p -> p.getSubject())
.foreach(s -> s.stream().forEach(sbj -> Assertions.assertFalse("FOS".equals(sbj.getQualifier().getClassid()))));
}
@Test
void updateResultMatch() throws Exception{
final String fosPath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/fos/fos_prepared.json")
.getPath();
final String inputPath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/fos/publicationmatch.json")
.getPath();
SparkUpdateFOS
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--fosPath", fosPath,
"--inputPath", inputPath,
"--outputPath", workingDir.toString() + "/publication",
"--resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(6, tmp.count());
Assertions.assertEquals(3, tmp.filter(r -> r.getSubject() != null).map(p -> p.getSubject()).flatMap(v -> v.iterator())
.filter(sbj -> sbj.getQualifier().getClassid().equals("FOS")).collect().size());
List<StructuredProperty> sbjs = tmp.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f"))
.map(p -> p.getSubject()).collect().get(0);
Assertions.assertEquals(12, sbjs.size());
Stream<StructuredProperty> fosSubjs = sbjs.stream().filter(sbj -> sbj.getQualifier().getClassid().equals("FOS"));
Assertions.assertTrue(fosSubjs
.map(sbj -> sbj.getValue()).collect(Collectors.toList()).contains("engineering and technology"));
Assertions.assertTrue(fosSubjs
.map(sbj -> sbj.getValue()).collect(Collectors.toList()).contains("nano-technology"));
Assertions.assertTrue(fosSubjs
.map(sbj -> sbj.getValue()).collect(Collectors.toList()).contains("nanoscience & nanotechnology"));
fosSubjs.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance()) );
fosSubjs.forEach(sbj -> Assertions.assertEquals("subject:fos", sbj.getDataInfo().getProvenanceaction().getClassid()) );
fosSubjs.forEach(sbj -> Assertions.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname() ));
fosSubjs.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust() ));
fosSubjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference() ));
fosSubjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getInvisible() ));
fosSubjs.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred() ));
}
}

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dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bypassactionset/GetFOSTest.java
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package eu.dnetlib.dhp.bypassactionset;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.bypassactionset.fos.PrepareFOSSparkJob;
import eu.dnetlib.dhp.bypassactionset.fos.GetFOSData;
import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.countrypropagation.CountryPropagationJobTest;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocalFileSystem;
import java.nio.file.Path;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.nio.file.Files;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class GetFOSTest {
private static final Logger log = LoggerFactory.getLogger(GetFOSTest.class);
private static Path workingDir;
private static SparkSession spark;
private static LocalFileSystem fs;
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String ID_PREFIX = "50|doi_________";
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(CountryPropagationJobTest.class.getSimpleName());
fs = FileSystem.getLocal(new Configuration());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(GetFOSTest.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(CountryPropagationJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void getFOSFileTest() throws CollectorException, IOException, ClassNotFoundException {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/fos/h2020_fos_sbs.csv")
.getPath();
final String outputPath = workingDir.toString() + "/fos.json";
new GetFOSData()
.doRewrite(sourcePath, outputPath, "eu.dnetlib.dhp.bypassactionset.FOSDataModel", '\t',fs );
BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
String line;
int count = 0;
while ((line = in.readLine()) != null) {
FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class);
System.out.println(new ObjectMapper().writeValueAsString(fos));
count += 1;
}
assertEquals(38, count);
}
@Test
void distributeDoiTest() throws Exception{
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/bypassactionset/fos/fos.json")
.getPath();
PrepareFOSSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"-outputPath", workingDir.toString() + "/distribute"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<FOSDataModel> tmp = sc
.textFile(workingDir.toString() + "/distribute")
.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
String doi1 = ID_PREFIX +
IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.3390/s18072310"));
assertEquals(50, tmp.count());
assertEquals(1, tmp.filter(row -> row.getDoi().equals(doi1)).count());
assertEquals("engineering and technology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel1());
assertEquals("nano-technology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel2());
assertEquals("nanoscience & nanotechnology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel3());
String doi = ID_PREFIX +
IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/1365-2656.12831"));
assertEquals(1, tmp.filter(row -> row.getDoi().equals(doi)).count());
assertEquals("social sciences", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel1());
assertEquals("psychology and cognitive sciences", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel2());
assertEquals("NULL", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel3());
// {"doi":"10.1111/1365-2656.12831\u000210.17863/cam.24369","level1":"social sciences","level2":"psychology and cognitive sciences","level3":"NULL"}
}
/**
* @Test
* void testCountryPropagationSoftware() throws Exception {
* final String sourcePath = getClass()
* .getResource("/eu/dnetlib/dhp/countrypropagation/sample/software")
* .getPath();
* final String preparedInfoPath = getClass()
* .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo")
* .getPath();
* SparkCountryPropagationJob
* .main(
* new String[] {
* "--isSparkSessionManaged", Boolean.FALSE.toString(),
* "--sourcePath", sourcePath,
* "-saveGraph", "true",
* "-resultTableName", Software.class.getCanonicalName(),
* "-outputPath", workingDir.toString() + "/software",
* "-preparedInfoPath", preparedInfoPath
* });
*
* final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
*
* JavaRDD<Software> tmp = sc
* .textFile(workingDir.toString() + "/software")
* .map(item -> OBJECT_MAPPER.readValue(item, Software.class));
*
* // tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s));
*
* Assertions.assertEquals(10, tmp.count());
*
* Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
*
* Assertions.assertEquals(6, verificationDs.filter("size(country) > 0").count());
* Assertions.assertEquals(3, verificationDs.filter("size(country) = 1").count());
* Assertions.assertEquals(3, verificationDs.filter("size(country) = 2").count());
* Assertions.assertEquals(0, verificationDs.filter("size(country) > 2").count());
*
* Dataset<String> countryExploded = verificationDs
* .flatMap(
* (FlatMapFunction<Software, Country>) row -> row.getCountry().iterator(), Encoders.bean(Country.class))
* .map((MapFunction<Country, String>) Qualifier::getClassid, Encoders.STRING());
*
* Assertions.assertEquals(9, countryExploded.count());
*
* Assertions.assertEquals(1, countryExploded.filter("value = 'FR'").count());
* Assertions.assertEquals(1, countryExploded.filter("value = 'TR'").count());
* Assertions.assertEquals(2, countryExploded.filter("value = 'IT'").count());
* Assertions.assertEquals(1, countryExploded.filter("value = 'US'").count());
* Assertions.assertEquals(1, countryExploded.filter("value = 'MX'").count());
* Assertions.assertEquals(1, countryExploded.filter("value = 'CH'").count());
* Assertions.assertEquals(2, countryExploded.filter("value = 'JP'").count());
*
* Dataset<Tuple2<String, String>> countryExplodedWithCountryclassid = verificationDs
* .flatMap((FlatMapFunction<Software, Tuple2<String, String>>) row -> {
* List<Tuple2<String, String>> prova = new ArrayList<>();
* List<Country> countryList = row.getCountry();
* countryList
* .forEach(
* c -> prova
* .add(
* new Tuple2<>(
* row.getId(), c.getClassid())));
* return prova.iterator();
* }, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
*
* Assertions.assertEquals(9, countryExplodedWithCountryclassid.count());
*
* countryExplodedWithCountryclassid.show(false);
* Assertions
* .assertEquals(
* 1,
* countryExplodedWithCountryclassid
* .filter(
* "_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'FR' ")
* .count());
* Assertions
* .assertEquals(
* 1,
* countryExplodedWithCountryclassid
* .filter(
* "_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'TR' ")
* .count());
* Assertions
* .assertEquals(
* 2,
* countryExplodedWithCountryclassid
* .filter(
* "_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'IT' or _2 = 'MX') ")
* .count());
* Assertions
* .assertEquals(
* 2,
* countryExplodedWithCountryclassid
* .filter(
* "_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'IT' or _2 = 'US') ")
* .count());
* Assertions
* .assertEquals(
* 1,
* countryExplodedWithCountryclassid
* .filter(
* "_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'JP'")
* .count());
* Assertions
* .assertEquals(
* 2,
* countryExplodedWithCountryclassid
* .filter(
* "_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'CH' or _2 = 'JP') ")
* .count());
*
* Dataset<Tuple2<String, String>> countryExplodedWithCountryclassname = verificationDs
* .flatMap(
* (FlatMapFunction<Software, Tuple2<String, String>>) row -> {
* List<Tuple2<String, String>> prova = new ArrayList<>();
* List<Country> countryList = row.getCountry();
* countryList
* .forEach(
* c -> prova
* .add(
* new Tuple2<>(
* row.getId(),
* c.getClassname())));
* return prova.iterator();
* },
* Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
*
* countryExplodedWithCountryclassname.show(false);
* Assertions
* .assertEquals(
* 1,
* countryExplodedWithCountryclassname
* .filter(
* "_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'France' ")
* .count());
* Assertions
* .assertEquals(
* 1,
* countryExplodedWithCountryclassname
* .filter(
* "_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'Turkey' ")
* .count());
* Assertions
* .assertEquals(
* 2,
* countryExplodedWithCountryclassname
* .filter(
* "_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'Italy' or _2 = 'Mexico') ")
* .count());
* Assertions
* .assertEquals(
* 2,
* countryExplodedWithCountryclassname
* .filter(
* "_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'Italy' or _2 = 'United States') ")
* .count());
* Assertions
* .assertEquals(
* 1,
* countryExplodedWithCountryclassname
* .filter(
* "_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'Japan' ")
* .count());
* Assertions
* .assertEquals(
* 2,
* countryExplodedWithCountryclassname
* .filter(
* "_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'Switzerland' or _2 = 'Japan') ")
* .count());
*
* Dataset<Tuple2<String, String>> countryExplodedWithCountryProvenance = verificationDs
* .flatMap(
* (FlatMapFunction<Software, Tuple2<String, String>>) row -> {
* List<Tuple2<String, String>> prova = new ArrayList<>();
* List<Country> countryList = row.getCountry();
* countryList
* .forEach(
* c -> prova
* .add(
* new Tuple2<>(
* row.getId(),
* c
* .getDataInfo()
* .getInferenceprovenance())));
* return prova.iterator();
* },
* Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
*
* Assertions
* .assertEquals(
* 7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count());
* }
*/
}

86
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bypassactionset/bip/bip.json Normal file
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@ -0,0 +1,86 @@
{"10.0000/000000": [{"id": "influence", "unit": [{"value": "7.5597134689e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "4.903880192", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "1.17977512835e-08", "key": "score"}]}]}
{"10.0000/096020199389707": [{"id": "influence", "unit": [{"value": "6.34596412687e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.641151896994", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "2.33375102921e-09", "key": "score"}]}]}
{"10.00000/jpmc.2017.106": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "5.39172290649e-09", "key": "score"}]}]}
{"10.0000/9781845416881": [{"id": "influence", "unit": [{"value": "5.96492048955e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "1.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "1.12641925838e-08", "key": "score"}]}]}
{"10.0000/anziamj.v0i0.266": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "3.76260934675e-10", "key": "score"}]}]}
{"10.0000/anziamj.v48i0.79": [{"id": "influence", "unit": [{"value": "6.93311506443e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.002176782336", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "1.7668105708e-09", "key": "score"}]}]}
{"10.0000/anziamj.v50i0.1472": [{"id": "influence", "unit": [{"value": "6.26777280882e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.406656", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "3.39745193285e-09", "key": "score"}]}]}
{"10.0000/cja5553": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]}
{"10.0000/czastest.16": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "4.01810569717e-09", "key": "score"}]}]}
{"10.0000/czastest.17": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "3.47956715615e-09", "key": "score"}]}]}
{"10.0000/czastest.18": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "3.47956715615e-09", "key": "score"}]}]}
{"10.0000/czastest.20": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "4.01810569717e-09", "key": "score"}]}]}
{"10.0000/czastest.21": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "3.47956715615e-09", "key": "score"}]}]}
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{"10.0000/geoekonomi.v4i02.37": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "4.01810569717e-09", "key": "score"}]}]}
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{"10.0000/geoekonomi.v6i01.27": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "4.01810569717e-09", "key": "score"}]}]}
{"10.0000/geoekonomi.v6i02.41": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "4.01810569717e-09", "key": "score"}]}]}
{"10.0000/geoekonomi.v6i02.44": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "4.01810569717e-09", "key": "score"}]}]}
{"10.0000/geoekonomi.v7i01.40": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "4.01810569717e-09", "key": "score"}]}]}
{"10.0000/geoekonomi.v7i01.42": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "4.65008652949e-09", "key": "score"}]}]}
{"10.0000/geoekonomi.v7i01.47": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "4.65008652949e-09", "key": "score"}]}]}
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{"10.0000/geoekonomi.v8i01.180": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "5.39172290649e-09", "key": "score"}]}]}
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{"10.0000/hbv2004w010": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.48190886761e-09", "key": "score"}]}]}
{"10.0000/hbv2101w001": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "9.88840807598e-09", "key": "score"}]}]}
{"10.0000/hbv2101w002": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "9.88840807598e-09", "key": "score"}]}]}
{"10.0000/hbv2101w003": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "9.88840807598e-09", "key": "score"}]}]}
{"10.0000/hbv2101w004": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "9.88840807598e-09", "key": "score"}]}]}
{"10.0000/hbv2101w005": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "9.88840807598e-09", "key": "score"}]}]}
{"10.0000/hbv2101w006": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "9.88840807598e-09", "key": "score"}]}]}
{"10.0000/hbv2101w007": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "9.88840807598e-09", "key": "score"}]}]}
{"10.0000/hbv2102w001": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "9.88840807598e-09", "key": "score"}]}]}
{"10.0000/hbv2102w010": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "9.88840807598e-09", "key": "score"}]}]}
{"10.0000/hoplos.v1i1.13207": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "6.26204125721e-09", "key": "score"}]}]}
{"10.0000/hoplos.v1i1.13208": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "5.39172290649e-09", "key": "score"}]}]}
{"10.0000/hoplos.v1i1.13209": [{"id": "influence", "unit": [{"value": "6.32078461509e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "1.6", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "8.3168486939e-09", "key": "score"}]}]}
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6
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@ -753,7 +753,7 @@
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