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dnet-hadoop
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pull/157/head
Miriam Baglioni 2 years ago
parent 9e214ce0eb
commit c371b23077
23 changed files with 1369 additions and 897 deletions
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17
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";
@ -98,15 +98,16 @@ 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);
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);
}
public static DataInfo getDataInfo(
String inference_provenance, String inference_class_id, String inference_class_name, String qualifierSchema,
String trust, boolean inferred) {
String inference_provenance, String inference_class_id, String inference_class_name, String qualifierSchema,
String trust, boolean inferred) {
DataInfo di = new DataInfo();
di.setInferred(inferred);
di.setDeletedbyinference(false);

16
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/Utils.java
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@ -1,15 +1,17 @@
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_________";
private static final String ID_PREFIX = "50|doi_________";
@NotNull
public static String getIdentifier(String d) {
return ID_PREFIX +
IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", d));
}
@NotNull
public static String getIdentifier(String d) {
return ID_PREFIX +
IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", d));
}
}

113
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/bipfinder/PrepareBipFinder.java
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@ -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;
@ -15,74 +18,72 @@ 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();
public static <I extends Result> void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkUpdateBip.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json"));
private static final Logger log = LoggerFactory.getLogger(SparkUpdateBip.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
public static <I extends Result> void main(String[] args) throws Exception {
parser.parseArgument(args);
String jsonConfiguration = IOUtils
.toString(
SparkUpdateBip.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bypassactionset/bip_prepare_parameters.json"));
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
parser.parseArgument(args);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
SparkConf conf = new SparkConf();
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
SparkConf conf = new SparkConf();
prepareResults(spark, inputPath, outputPath);
});
}
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath) {
prepareResults(spark, inputPath, outputPath);
});
}
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
.textFile(inputPath)
.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
.textFile(inputPath)
.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
spark
.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
BipScore bs = new BipScore();
bs.setId(getIdentifier(key));
bs.setScoreList(entry.get(key));
return bs;
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(outputPath);
}
spark
.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
BipScore bs = new BipScore();
bs.setId(getIdentifier(key));
bs.setScoreList(entry.get(key));
return bs;
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
}

76
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/bipfinder/SparkUpdateBip.java
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@ -1,45 +1,44 @@
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 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 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 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 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 {
String jsonConfiguration = IOUtils
.toString(
SparkUpdateBip.class
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);
@ -71,10 +70,9 @@ public class SparkUpdateBip implements Serializable {
runWithSparkSession(
conf,
isSparkSessionManaged,
spark ->
updateBipFinder(spark, inputPath, outputPath, bipScorePath, inputClazz)
spark -> updateBipFinder(spark, inputPath, outputPath, bipScorePath, inputClazz)
);
);
}
private static <I extends Result> void updateBipFinder(SparkSession spark, String inputPath, String outputPath,
@ -83,18 +81,19 @@ 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()){
return value._1();
}
value._1().setMeasures(getMeasure(value._2()));
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();
}, Encoders.bean(inputClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(outputPath + "/bip");
}
value._1().setMeasures(getMeasure(value._2()));
return value._1();
}, Encoders.bean(inputClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + "/bip");
}
@ -114,10 +113,13 @@ public class SparkUpdateBip implements Serializable {
KeyValue kv = new KeyValue();
kv.setValue(unit.getValue());
kv.setKey(unit.getKey());
kv.setDataInfo(getDataInfo(UPDATE_DATA_INFO_TYPE,
UPDATE_MEASURE_BIP_CLASS_ID,
UPDATE_MEASURE_BIP_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS, ""));
kv
.setDataInfo(
getDataInfo(
UPDATE_DATA_INFO_TYPE,
UPDATE_MEASURE_BIP_CLASS_ID,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS, ""));
return kv;
})
.collect(Collectors.toList()));
@ -126,10 +128,4 @@ public class SparkUpdateBip implements Serializable {
.collect(Collectors.toList());
}
}

94
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/fos/GetFOSData.java
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@ -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;
@ -10,70 +12,64 @@ 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 {
private static final Logger log = LoggerFactory.getLogger(GetFOSData.class);
public static final char DEFAULT_DELIMITER = '\t';
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
GetFOSData.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bypassactionset/get_fos_parameters.json"))));
parser.parseArgument(args);
//the path where the original fos csv file is stored
final String inputPath = parser.get("inputPath");
log.info("inputPath {}", inputPath);
private static final Logger log = LoggerFactory.getLogger(GetFOSData.class);
//the path where to put the file as json
final String outputFile = parser.get("outputFile");
log.info("outputFile {}", outputFile);
public static final char DEFAULT_DELIMITER = '\t';
final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode);
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
GetFOSData.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bypassactionset/get_fos_parameters.json"))));
final String classForName = parser.get("classForName");
log.info("classForName {}", classForName);
parser.parseArgument(args);
final char delimiter = Optional
.ofNullable(parser.get("delimiter"))
.map(s -> s.charAt(0))
.orElse(DEFAULT_DELIMITER);
log.info("delimiter {}", delimiter);
// the path where the original fos csv file is stored
final String inputPath = parser.get("inputPath");
log.info("inputPath {}", inputPath);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
// the path where to put the file as json
final String outputFile = parser.get("outputFile");
log.info("outputFile {}", outputFile);
FileSystem fileSystem = FileSystem.get(conf);
final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode);
new GetFOSData().doRewrite(inputPath, outputFile, classForName, delimiter, fileSystem);
final String classForName = parser.get("classForName");
log.info("classForName {}", classForName);
}
final char delimiter = Optional
.ofNullable(parser.get("delimiter"))
.map(s -> s.charAt(0))
.orElse(DEFAULT_DELIMITER);
log.info("delimiter {}", delimiter);
public void doRewrite(String inputPath, String outputFile, String classForName, char delimiter, FileSystem fs)
throws IOException, ClassNotFoundException{
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
//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);
}
FileSystem fileSystem = FileSystem.get(conf);
new GetFOSData().doRewrite(inputPath, outputFile, classForName, delimiter, fileSystem);
}
}
public void doRewrite(String inputPath, String outputFile, String classForName, char delimiter, FileSystem fs)
throws IOException, ClassNotFoundException {
// 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);
}
}
}

144
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/fos/PrepareFOSSparkJob.java
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@ -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;
@ -15,78 +21,66 @@ 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
.toString(
PrepareFOSSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bypassactionset/distribute_fos_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
distributeFOSdois(
spark,
sourcePath,
outputPath
);
});
}
private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {
Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
fosDataset.flatMap((FlatMapFunction<FOSDataModel, FOSDataModel>) v -> {
List<FOSDataModel> fosList = new ArrayList<>();
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)));
return fosList.iterator();
}, Encoders.bean(FOSDataModel.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(outputPath);
}
private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
PrepareFOSSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bypassactionset/distribute_fos_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
distributeFOSdois(
spark,
sourcePath,
outputPath);
});
}
private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {
Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
fosDataset.flatMap((FlatMapFunction<FOSDataModel, FOSDataModel>) v -> {
List<FOSDataModel> fosList = new ArrayList<>();
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)));
return fosList.iterator();
}, Encoders.bean(FOSDataModel.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
}

205
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/fos/SparkUpdateFOS.java
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@ -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;
@ -15,104 +17,105 @@ import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
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;
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;
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"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
final String fosPath = parser.get("fosPath");
log.info("fosPath: {}", fosPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
Class<I> inputClazz = (Class<I>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
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) {
Dataset<I> results = readPath(spark, inputPath, inputClazz);
Dataset<FOSDataModel> bipScores = readPath(spark, bipScorePath, 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()){
return value._1();
}
value._1().getSubject().addAll(getSubjects(value._2()));
return value._1();
}, Encoders.bean(inputClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(outputPath);
}
private static List<StructuredProperty> getSubjects(FOSDataModel fos) {
return Arrays.asList(getSubject(fos.getLevel1()), getSubject(fos.getLevel2()), getSubject(fos.getLevel3()))
.stream()
.filter(Objects::nonNull)
.collect(Collectors.toList());
}
private static StructuredProperty getSubject(String sbj) {
if (sbj.equals(NULL))
return null;
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,
UPDATE_SUBJECT_FOS_CLASS_ID,
UPDATE_SUBJECT_FOS_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS, ""));
return sp;
}
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/bypassactionset/fos_update_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
final String fosPath = parser.get("fosPath");
log.info("fosPath: {}", fosPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
Class<I> inputClazz = (Class<I>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> updateFos(spark, inputPath, outputPath, fosPath, inputClazz)
);
}
private static <I extends Result> void updateFos(SparkSession spark, String inputPath, String outputPath,
String fosPath, Class<I> inputClazz) {
Dataset<I> results = readPath(spark, inputPath, inputClazz);
Dataset<FOSDataModel> fosDataModelDataset = readPath(spark, fosPath, FOSDataModel.class);
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()));
return value._1();
}, Encoders.bean(inputClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static List<StructuredProperty> getSubjects(FOSDataModel fos) {
return Arrays
.asList(getSubject(fos.getLevel1()), getSubject(fos.getLevel2()), getSubject(fos.getLevel3()))
.stream()
.filter(Objects::nonNull)
.collect(Collectors.toList());
}
private static StructuredProperty getSubject(String sbj) {
if (sbj.equals(NULL))
return null;
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,
UPDATE_SUBJECT_FOS_CLASS_ID,
UPDATE_CLASS_NAME,
ModelConstants.DNET_PROVENANCE_ACTIONS, ""));
return sp;
}
}

92
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/model/FOSDataModel.java
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@ -1,71 +1,71 @@
package eu.dnetlib.dhp.bypassactionset.model;
import com.opencsv.bean.CsvBindByPosition;
package eu.dnetlib.dhp.bypassactionset.model;
import java.io.Serializable;
import com.opencsv.bean.CsvBindByPosition;
public class FOSDataModel implements Serializable {
@CsvBindByPosition(position = 1)
@CsvBindByPosition(position = 1)
// @CsvBindByName(column = "doi")
private String doi;
private String doi;
@CsvBindByPosition(position = 2)
@CsvBindByPosition(position = 2)
// @CsvBindByName(column = "level1")
private String level1;
private String level1;
@CsvBindByPosition(position = 3)
@CsvBindByPosition(position = 3)
// @CsvBindByName(column = "level2")
private String level2;
private String level2;
@CsvBindByPosition(position = 4)
@CsvBindByPosition(position = 4)
// @CsvBindByName(column = "level3")
private String level3;
private String level3;
public FOSDataModel() {
public FOSDataModel() {
}
}
public FOSDataModel(String doi, String level1, String level2, String level3) {
this.doi = doi;
this.level1 = level1;
this.level2 = level2;
this.level3 = level3;
}
public FOSDataModel(String doi, String level1, String level2, String level3) {
this.doi = doi;
this.level1 = level1;
this.level2 = level2;
this.level3 = level3;
}
public static FOSDataModel newInstance(String d, String level1, String level2, String level3) {
return new FOSDataModel(d, level1, level2, level3);
}
public static FOSDataModel newInstance(String d, String level1, String level2, String level3) {
return new FOSDataModel(d, level1, level2, level3);
}
public String getDoi() {
return doi;
}
public String getDoi() {
return doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public String getLevel1() {
return level1;
}
public String getLevel1() {
return level1;
}
public void setLevel1(String level1) {
this.level1 = level1;
}
public void setLevel1(String level1) {
this.level1 = level1;
}
public String getLevel2() {
return level2;
}
public String getLevel2() {
return level2;
}
public void setLevel2(String level2) {
this.level2 = level2;
}
public void setLevel2(String level2) {
this.level2 = level2;
}
public String getLevel3() {
return level3;
}
public String getLevel3() {
return level3;
}
public void setLevel3(String level3) {
this.level3 = level3;
}
public void setLevel3(String level3) {
this.level3 = level3;
}
}

95
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/opencitations/GetOpenCitationsRefs.java
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@ -1,3 +1,4 @@
package eu.dnetlib.dhp.bypassactionset.opencitations;
import java.io.*;
@ -20,73 +21,73 @@ import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class GetOpenCitationsRefs implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetOpenCitationsRefs.class);
private static final Logger log = LoggerFactory.getLogger(GetOpenCitationsRefs.class);
public static void main(final String[] args) throws IOException, ParseException {
public static void main(final String[] args) throws IOException, ParseException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
GetOpenCitationsRefs.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bypassactionset/opencitations/input_parameters.json"))));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
GetOpenCitationsRefs.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bypassactionset/opencitations/input_parameters.json"))));
parser.parseArgument(args);
parser.parseArgument(args);
final String[] inputFile = parser.get("inputFile").split(";");
log.info("inputFile {}", inputFile.toString());
final String[] inputFile = parser.get("inputFile").split(";");
log.info("inputFile {}", inputFile.toString());
final String workingPath = parser.get("workingPath");
log.info("workingPath {}", workingPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath {}", workingPath);
final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode);
final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
FileSystem fileSystem = FileSystem.get(conf);
GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
for (String file : inputFile) {
ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem);
}
for (String file : inputFile) {
ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem);
}
}
}
private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
throws IOException {
private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
throws IOException {
final Path path = new Path(inputFile);
final Path path = new Path(inputFile);
FSDataInputStream oc_zip = fileSystem.open(path);
FSDataInputStream oc_zip = fileSystem.open(path);
int count = 1;
try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
ZipEntry entry = null;
while ((entry = zis.getNextEntry()) != null) {
int count = 1;
try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
ZipEntry entry = null;
while ((entry = zis.getNextEntry()) != null) {
if (!entry.isDirectory()) {
String fileName = entry.getName();
fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
count++;
try (
FSDataOutputStream out = fileSystem
.create(new Path(workingPath + "/COCI/" + fileName + ".gz"));
GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
if (!entry.isDirectory()) {
String fileName = entry.getName();
fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
count++;
try (
FSDataOutputStream out = fileSystem
.create(new Path(workingPath + "/COCI/" + fileName + ".gz"));
GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
IOUtils.copy(zis, gzipOs);
IOUtils.copy(zis, gzipOs);
}
}
}
}
}
}
}
}
}
}
}

244
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/opencitations/SparkUpdateOCRels.java
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@ -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;
@ -23,136 +22,129 @@ 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);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws IOException, ParseException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
SparkUpdateOCRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json"))));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}", inputPath.toString());
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final boolean shouldDuplicateRels =
Optional.ofNullable(parser.get("shouldDuplicateRels"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark ->
addOCRelations(spark, inputPath, outputPath, shouldDuplicateRels)
);
}
private static void addOCRelations(SparkSession spark, String inputPath, String outputPath,
boolean shouldDuplicateRels) {
spark
.sqlContext()
.createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
.flatMap(
(FlatMapFunction<String, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) value -> value != null)
.write()
.mode(SaveMode.Append)
.option("compression", "gzip")
.json(outputPath);
}
private static List<Relation> createRelation(String value, boolean duplicate) {
String[] line = value.split(",");
if (!line[1].startsWith("10.")) {
return new ArrayList<>();
}
List<Relation> relationList = new ArrayList<>();
String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue(DOI, line[1]));
final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue(DOI, line[2]));
relationList
.addAll(
getRelations(
citing,
cited));
if (duplicate && line[1].endsWith(REF_DOI)) {
citing = ID_PREFIX + IdentifierFactory
.md5(CleaningFunctions.normalizePidValue(DOI, line[1].substring(0, line[1].indexOf(REF_DOI))));
relationList.addAll(getRelations(citing, cited));
}
return relationList;
}
private static Collection<Relation> getRelations(String citing, String cited) {
return Arrays
.asList(
getRelation(citing, cited, ModelConstants.CITES),
getRelation(cited, citing, ModelConstants.IS_CITED_BY));
}
public static Relation getRelation(
String source,
String target,
String relclass) {
Relation r = new Relation();
r.setCollectedfrom(getCollectedFrom());
r.setSource(source);
r.setTarget(target);
r.setRelClass(relclass);
r.setRelType(ModelConstants.RESULT_RESULT);
r.setSubRelType(ModelConstants.CITATION);
r
.setDataInfo(
getDataInfo(UPDATE_DATA_INFO_TYPE, OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME,
ModelConstants.DNET_PROVENANCE_ACTIONS, OC_TRUST, false));
return r;
}
public static List<KeyValue> getCollectedFrom() {
KeyValue kv = new KeyValue();
kv.setKey(ModelConstants.OPENOCITATIONS_ID);
kv.setValue(ModelConstants.OPENOCITATIONS_NAME);
return Arrays.asList(kv);
}
private static final Logger log = LoggerFactory.getLogger(SparkUpdateOCRels.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws IOException, ParseException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
SparkUpdateOCRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json"))));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}", inputPath.toString());
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final boolean shouldDuplicateRels = Optional
.ofNullable(parser.get("shouldDuplicateRels"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> addOCRelations(spark, inputPath, outputPath, shouldDuplicateRels));
}
private static void addOCRelations(SparkSession spark, String inputPath, String outputPath,
boolean shouldDuplicateRels) {
spark
.sqlContext()
.createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
.flatMap(
(FlatMapFunction<String, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) value -> value != null)
.write()
.mode(SaveMode.Append)
.option("compression", "gzip")
.json(outputPath);
}
private static List<Relation> createRelation(String value, boolean duplicate) {
String[] line = value.split(",");
if (!line[1].startsWith("10.")) {
return new ArrayList<>();
}
List<Relation> relationList = new ArrayList<>();
String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue(DOI, line[1]));
final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue(DOI, line[2]));
relationList
.addAll(
getRelations(
citing,
cited));
if (duplicate && line[1].endsWith(REF_DOI)) {
citing = ID_PREFIX + IdentifierFactory
.md5(CleaningFunctions.normalizePidValue(DOI, line[1].substring(0, line[1].indexOf(REF_DOI))));
relationList.addAll(getRelations(citing, cited));
}
return relationList;
}
private static Collection<Relation> getRelations(String citing, String cited) {
return Arrays
.asList(
getRelation(citing, cited, ModelConstants.CITES),
getRelation(cited, citing, ModelConstants.IS_CITED_BY));
}
public static Relation getRelation(
String source,
String target,
String relclass) {
Relation r = new Relation();
r.setCollectedfrom(getCollectedFrom());
r.setSource(source);
r.setTarget(target);
r.setRelClass(relclass);
r.setRelType(ModelConstants.RESULT_RESULT);
r.setSubRelType(ModelConstants.CITATION);
r
.setDataInfo(
getDataInfo(
UPDATE_DATA_INFO_TYPE, OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME,
ModelConstants.DNET_PROVENANCE_ACTIONS, OC_TRUST, false));
return r;
}
public static List<KeyValue> getCollectedFrom() {
KeyValue kv = new KeyValue();
kv.setKey(ModelConstants.OPENOCITATIONS_ID);
kv.setValue(ModelConstants.OPENOCITATIONS_NAME);
return Arrays.asList(kv);
}
}

20
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bypassactionset/bip_prepare_parameters.json
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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
}
]

32
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bypassactionset/bip_update_parameters.json
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@ -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
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@ -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
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@ -0,0 +1,250 @@
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)));
}
}

253
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bypassactionset/FOSTest.java
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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
Unescape Escape View File

@ -0,0 +1,86 @@
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{"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"}]}]}
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{"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"}]}]}
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{"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"}]}]}
{"10.0000/geoekonomi.v4i02.38": [{"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.v6i01.24": [{"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.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"}]}]}
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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"}]}]}
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{"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"}]}]}
{"10.0000/hoplos.v1i1.13210": [{"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.v1i1.13211": [{"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.v1i1.13212": [{"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.v1i2.13231": [{"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.v2i2.28782": [{"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.v2i2.28783": [{"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.v2i2.28784": [{"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.v2i2.28786": [{"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.v2i2.28787": [{"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"}]}]}
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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>[2.8.21]</dhp-schemas.version>
<dhp-schemas.version>[2.8.22-SNAPSHOT]</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>

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