Remove Relation From AS #466
|
|
@ -0,0 +1,244 @@
|
||||||
|
package eu.dnetlib.dhp.actionmanager.webcrawl;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
import eu.dnetlib.dhp.actionmanager.Constants;
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
|
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.apache.hadoop.io.Text;
|
||||||
|
import org.apache.hadoop.io.compress.GzipCodec;
|
||||||
|
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
|
||||||
|
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.*;
|
||||||
|
import org.apache.spark.sql.types.StructType;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
import scala.Tuple2;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
import java.util.Arrays;
|
||||||
|
import java.util.List;
|
||||||
|
import java.util.Optional;
|
||||||
|
|
||||||
|
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||||
|
|
||||||
|
public class RemoveRelationFromActionSet
|
||||||
|
implements Serializable {
|
||||||
|
private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class);
|
||||||
|
private static final String DOI_PREFIX = "50|doi_________::";
|
||||||
|
|
||||||
|
|
||||||
|
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||||
|
|
||||||
|
public static void main(String[] args) throws Exception {
|
||||||
|
String jsonConfiguration = IOUtils
|
||||||
|
.toString(
|
||||||
|
CreateActionSetFromWebEntries.class
|
||||||
|
.getResourceAsStream(
|
||||||
|
"/eu/dnetlib/dhp/actionmanager/webcrawl/as_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("actionSetPath");
|
||||||
|
log.info("inputPath: {}", inputPath);
|
||||||
|
|
||||||
|
final String outputPath = parser.get("outputPath");
|
||||||
|
log.info("outputPath: {}", outputPath);
|
||||||
|
|
||||||
|
final String blackListInputPath = parser.get("blackListPath");
|
||||||
|
log.info("blackListInputPath: {}", blackListInputPath);
|
||||||
|
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
|
||||||
|
runWithSparkSession(
|
||||||
|
conf,
|
||||||
|
isSparkSessionManaged,
|
||||||
|
spark -> {
|
||||||
|
|
||||||
|
removeFromActionSet(spark, inputPath, outputPath, blackListInputPath);
|
||||||
|
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
private static void removeFromActionSet(SparkSession spark, String inputPath, String outputPath, String blackListInputPath) {
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public static void createActionSet(SparkSession spark, String inputPath,
|
||||||
|
String outputPath, String blackListInputPath) {
|
||||||
|
|
||||||
|
final Dataset<Row> dataset = readWebCrawl(spark, inputPath)
|
||||||
|
.filter("country_code=='IE'")
|
||||||
|
.drop("publication_year");
|
||||||
|
|
||||||
|
final Dataset<Row> blackList = readBlackList(spark, blackListInputPath);
|
||||||
|
|
||||||
|
dataset
|
||||||
|
.join(blackList, dataset.col("id").equalTo(blackList.col("OpenAlexId")), "left")
|
||||||
|
.filter((FilterFunction<Row>) r -> r.getAs("OpenAlexId") == null)
|
||||||
|
.drop("OpenAlexId")
|
||||||
|
.flatMap((FlatMapFunction<Row, Relation>) row -> {
|
||||||
|
List<Relation> ret = new ArrayList<>();
|
||||||
|
final String ror = ROR_PREFIX
|
||||||
|
+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
|
||||||
|
ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
|
||||||
|
|
||||||
|
return ret
|
||||||
|
.iterator();
|
||||||
|
}, Encoders.bean(Relation.class))
|
||||||
|
.toJavaRDD()
|
||||||
|
.map(p -> new AtomicAction(p.getClass(), p))
|
||||||
|
.mapToPair(
|
||||||
|
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
|
||||||
|
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
|
||||||
|
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Dataset<Row> readWebCrawl(SparkSession spark, String inputPath) {
|
||||||
|
StructType webInfo = StructType
|
||||||
|
.fromDDL(
|
||||||
|
"`id` STRING , `doi` STRING, `ids` STRUCT<`pmid` :STRING, `pmcid`: STRING >, `publication_year` STRING, "
|
||||||
|
+
|
||||||
|
"`authorships` ARRAY<STRUCT <`institutions`: ARRAY <STRUCT <`ror`: STRING, `country_code` :STRING>>>>");
|
||||||
|
|
||||||
|
return spark
|
||||||
|
.read()
|
||||||
|
.schema(webInfo)
|
||||||
|
.json(inputPath)
|
||||||
|
.withColumn(
|
||||||
|
"authors", functions
|
||||||
|
.explode(
|
||||||
|
functions.col("authorships")))
|
||||||
|
.selectExpr("id", "doi", "ids", "publication_year", "authors.institutions as institutions")
|
||||||
|
.withColumn(
|
||||||
|
"institution", functions
|
||||||
|
.explode(
|
||||||
|
functions.col("institutions")))
|
||||||
|
|
||||||
|
.selectExpr(
|
||||||
|
"id", "doi", "institution.ror as ror",
|
||||||
|
"institution.country_code as country_code", "publication_year")
|
||||||
|
.distinct();
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
|
||||||
|
|
||||||
|
return spark
|
||||||
|
.read()
|
||||||
|
.option("header", true)
|
||||||
|
.csv(inputPath)
|
||||||
|
.select("OpenAlexId");
|
||||||
|
}
|
||||||
|
|
||||||
|
private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
|
||||||
|
if (pmcid == null)
|
||||||
|
return new ArrayList<>();
|
||||||
|
|
||||||
|
return createAffiliatioRelationPair(
|
||||||
|
PMCID_PREFIX
|
||||||
|
+ IdentifierFactory
|
||||||
|
.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC", pmcid))),
|
||||||
|
ror);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static List<Relation> createAffiliationRelationPairPMID(String pmid, String ror) {
|
||||||
|
if (pmid == null)
|
||||||
|
return new ArrayList<>();
|
||||||
|
|
||||||
|
return createAffiliatioRelationPair(
|
||||||
|
PMID_PREFIX
|
||||||
|
+ IdentifierFactory
|
||||||
|
.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), removeResolver("PMID", pmid))),
|
||||||
|
ror);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static String removeResolver(String pidType, String pid) {
|
||||||
|
switch (pidType) {
|
||||||
|
case "PMID":
|
||||||
|
return pid.substring(33);
|
||||||
|
case "PMC":
|
||||||
|
return "PMC" + pid.substring(43);
|
||||||
|
case "DOI":
|
||||||
|
return pid.substring(16);
|
||||||
|
}
|
||||||
|
|
||||||
|
throw new RuntimeException();
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private static List<Relation> createAffiliationRelationPairDOI(String doi, String ror) {
|
||||||
|
if (doi == null)
|
||||||
|
return new ArrayList<>();
|
||||||
|
|
||||||
|
return createAffiliatioRelationPair(
|
||||||
|
DOI_PREFIX
|
||||||
|
+ IdentifierFactory
|
||||||
|
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), removeResolver("DOI", doi))),
|
||||||
|
ror);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private static List<Relation> createAffiliatioRelationPair(String resultId, String orgId) {
|
||||||
|
ArrayList<Relation> newRelations = new ArrayList();
|
||||||
|
|
||||||
|
newRelations
|
||||||
|
.add(
|
||||||
|
OafMapperUtils
|
||||||
|
.getRelation(
|
||||||
|
orgId, resultId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION,
|
||||||
|
ModelConstants.IS_AUTHOR_INSTITUTION_OF,
|
||||||
|
Arrays
|
||||||
|
.asList(
|
||||||
|
OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
|
||||||
|
OafMapperUtils
|
||||||
|
.dataInfo(
|
||||||
|
false, null, false, false,
|
||||||
|
OafMapperUtils
|
||||||
|
.qualifier(
|
||||||
|
"sysimport:crasswalk:webcrawl", "Imported from Webcrawl",
|
||||||
|
ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
|
||||||
|
"0.9"),
|
||||||
|
null));
|
||||||
|
|
||||||
|
newRelations
|
||||||
|
.add(
|
||||||
|
OafMapperUtils
|
||||||
|
.getRelation(
|
||||||
|
resultId, orgId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION,
|
||||||
|
ModelConstants.HAS_AUTHOR_INSTITUTION,
|
||||||
|
Arrays
|
||||||
|
.asList(
|
||||||
|
OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
|
||||||
|
OafMapperUtils
|
||||||
|
.dataInfo(
|
||||||
|
false, null, false, false,
|
||||||
|
OafMapperUtils
|
||||||
|
.qualifier(
|
||||||
|
"sysimport:crasswalk:webcrawl", "Imported from Webcrawl",
|
||||||
|
ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
|
||||||
|
"0.9"),
|
||||||
|
null));
|
||||||
|
|
||||||
|
return newRelations;
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue