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[BypassAS] addition of OC relations

This commit is contained in:
Miriam Baglioni 2021-11-09 12:07:19 +01:00
parent 6f7ca539c6
commit 9e214ce0eb
6 changed files with 270 additions and 12 deletions
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20
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java
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@ -25,18 +25,23 @@ public class PropagationConstant {
private PropagationConstant() {
}
public static final String DOI = "doi";
public static final String REF_DOI = ".refs";
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_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_ID = "FOS";
public static final String FOS_CLASS_NAME = "Subject from fos classification";
public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
public static final String ID_PREFIX = "50|doi_________::";
public static final String OC_TRUST = "0.91";
public final static String NULL = "NULL";
public static final String INSTITUTIONAL_REPO_TYPE = "pubsrepository::institutional";
@ -95,8 +100,15 @@ 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);
}
public static DataInfo getDataInfo(
String inference_provenance, String inference_class_id, String inference_class_name, String qualifierSchema,
String trust, boolean inferred) {
DataInfo di = new DataInfo();
di.setInferred(true);
di.setInferred(inferred);
di.setDeletedbyinference(false);
di.setTrust(trust);
di.setInferenceprovenance(inference_provenance);

1
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/bipfinder/PrepareBipFinder.java
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@ -2,7 +2,6 @@ package eu.dnetlib.dhp.bypassactionset.bipfinder;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bypassactionset.SparkUpdateBip;
import eu.dnetlib.dhp.bypassactionset.model.BipDeserialize;
import eu.dnetlib.dhp.bypassactionset.model.BipScore;
import eu.dnetlib.dhp.schema.oaf.Result;

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/SparkUpdateBip.java → dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/bipfinder/SparkUpdateBip.java
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@ -1,5 +1,5 @@
package eu.dnetlib.dhp.bypassactionset;
package eu.dnetlib.dhp.bypassactionset.bipfinder;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bypassactionset.model.BipScore;

9
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/SparkUpdateFOS.java → dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/fos/SparkUpdateFOS.java
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@ -1,11 +1,9 @@
package eu.dnetlib.dhp.bypassactionset;
package eu.dnetlib.dhp.bypassactionset.fos;
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.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Measure;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import org.apache.commons.io.IOUtils;
@ -28,8 +26,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
public class SparkUpdateFOS implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkUpdateFOS.class);
private final static String NULL = "NULL";
private final static String DNET_RESULT_SUBJECT = "dnet:result_subject";
public static <I extends Result> void main(String[] args) throws Exception {
@ -108,7 +105,7 @@ public class SparkUpdateFOS implements Serializable {
return null;
StructuredProperty sp = new StructuredProperty();
sp.setValue(sbj);
sp.setQualifier(getQualifier(FOS_CLASS_ID, FOS_CLASS_NAME, DNET_RESULT_SUBJECT));
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,

92
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/opencitations/GetOpenCitationsRefs.java Normal file
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@ -0,0 +1,92 @@
package eu.dnetlib.dhp.bypassactionset.opencitations;
import java.io.*;
import java.io.Serializable;
import java.util.Objects;
import java.util.zip.GZIPOutputStream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class GetOpenCitationsRefs implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetOpenCitationsRefs.class);
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"))));
parser.parseArgument(args);
final String[] inputFile = parser.get("inputFile").split(";");
log.info("inputFile {}", inputFile.toString());
final String workingPath = parser.get("workingPath");
log.info("workingPath {}", workingPath);
final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
for (String file : inputFile) {
ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem);
}
}
private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
throws IOException {
final Path path = new Path(inputFile);
FSDataInputStream oc_zip = fileSystem.open(path);
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))) {
IOUtils.copy(zis, gzipOs);
}
}
}
}
}
}

158
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bypassactionset/opencitations/SparkUpdateOCRels.java Normal file
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@ -0,0 +1,158 @@
package eu.dnetlib.dhp.bypassactionset.opencitations;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.io.Serializable;
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;
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 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);
}
}