forked from D-Net/dnet-hadoop
Merge pull request '[WebCrawl] adding affiliation relations from web information' (#428) from WebCrowlBeta into beta
Reviewed-on: D-Net/dnet-hadoop#428
This commit is contained in:
commit
c57cff2d6d
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package eu.dnetlib.dhp.actionmanager.webcrawl;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.*;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FlatMapFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.types.StructType;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
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import eu.dnetlib.dhp.schema.oaf.utils.PidType;
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import scala.Tuple2;
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/**
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* @author miriam.baglioni
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* @Date 18/04/24
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*/
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public class CreateActionSetFromWebEntries implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class);
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private static final String DOI_PREFIX = "50|doi_________::";
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private static final String ROR_PREFIX = "20|ror_________::";
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private static final String PMID_PREFIX = "50|pmid________::";
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private static final String PMCID_PREFIX = "50|pmc_________::";
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private static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b";
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private static final String WEB_CRAWL_NAME = "Web Crawl";
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public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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CreateActionSetFromWebEntries.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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createActionSet(spark, inputPath, outputPath );
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});
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}
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public static void createActionSet(SparkSession spark, String inputPath,
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String outputPath) {
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final Dataset<Row> dataset = readWebCrawl(spark, inputPath)
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.filter("publication_year <= 2020 or country_code=='IE'")
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.drop("publication_year");
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dataset.flatMap((FlatMapFunction<Row, Relation>) row -> {
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List<Relation> ret = new ArrayList<>();
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final String ror = ROR_PREFIX
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+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
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ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
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ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
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ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
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return ret
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.iterator();
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}, Encoders.bean(Relation.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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}
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private static Dataset<Row> readWebCrawl(SparkSession spark, String inputPath) {
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StructType webInfo = StructType
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.fromDDL(
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"`id` STRING , `doi` STRING, `ids` STRUCT<`pmid` :STRING, `pmcid`: STRING >, `publication_year` STRING, "
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+
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"`authorships` ARRAY<STRUCT <`institutions`: ARRAY <STRUCT <`ror`: STRING, `country_code` :STRING>>>>");
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return spark
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.read()
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.schema(webInfo)
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.json(inputPath)
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.withColumn(
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"authors", functions
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.explode(
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functions.col("authorships")))
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.selectExpr("id", "doi", "ids", "publication_year", "authors.institutions as institutions")
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.withColumn(
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"institution", functions
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.explode(
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functions.col("institutions")))
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.selectExpr(
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"id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
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"institution.country_code as country_code", "publication_year")
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.distinct();
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}
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private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
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if (pmcid == null)
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return new ArrayList<>();
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return createAffiliatioRelationPair(
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PMCID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC" , pmcid))),
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ror);
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}
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private static List<Relation> createAffiliationRelationPairPMID(String pmid, String ror) {
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if (pmid == null)
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return new ArrayList<>();
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return createAffiliatioRelationPair(
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PMID_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), removeResolver("PMID", pmid))),
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ror);
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}
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private static String removeResolver(String pidType, String pid) {
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switch (pidType){
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case "PMID":
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return pid.substring(33);
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case "PMC":
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return "PMC" + pid.substring(43);
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case "DOI":
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return pid.substring(16);
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}
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throw new RuntimeException();
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}
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private static List<Relation> createAffiliationRelationPairDOI(String doi, String ror) {
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if (doi == null)
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return new ArrayList<>();
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return createAffiliatioRelationPair(
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DOI_PREFIX
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), removeResolver("DOI" ,doi))),
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ror);
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}
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private static List<Relation> createAffiliatioRelationPair(String resultId, String orgId) {
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ArrayList<Relation> newRelations = new ArrayList();
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newRelations
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.add(
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OafMapperUtils
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.getRelation(
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orgId, resultId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION,
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ModelConstants.IS_AUTHOR_INSTITUTION_OF,
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Arrays
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.asList(
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OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
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OafMapperUtils
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.dataInfo(
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false, null, false, false,
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OafMapperUtils
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.qualifier(
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"sysimport:crasswalk:webcrawl", "Imported from Webcrawl",
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ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
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"0.9"),
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null));
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newRelations
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.add(
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OafMapperUtils
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.getRelation(
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resultId, orgId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION,
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ModelConstants.HAS_AUTHOR_INSTITUTION,
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Arrays
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.asList(
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OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
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OafMapperUtils
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.dataInfo(
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false, null, false, false,
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OafMapperUtils
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.qualifier(
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"sysimport:crasswalk:webcrawl", "Imported from Webcrawl",
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ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
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"0.9"),
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null));
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return newRelations;
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}
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}
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@ -0,0 +1,20 @@
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[
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{
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"paramName": "sp",
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"paramLongName": "sourcePath",
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"paramDescription": "the zipped opencitations file",
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"paramRequired": true
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},
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{
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"paramName": "op",
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"paramLongName": "outputPath",
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"paramDescription": "the working path",
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"paramRequired": true
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},
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "the hdfs name node",
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"paramRequired": false
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}
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]
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sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
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outputPath=/tmp/miriam/webcrawlComplete/
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>hive_metastore_uris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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<property>
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<name>sparkExecutorNumber</name>
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<value>4</value>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<value>15G</value>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<value>6G</value>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<value>1</value>
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</property>
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</configuration>
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@ -0,0 +1,53 @@
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<workflow-app name="WebCrawl Integration" xmlns="uri:oozie:workflow:0.5">
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="create_actionset"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="create_actionset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Produces the AS for WC</name>
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<class>eu.dnetlib.dhp.actionmanager.webcrawl.CreateActionSetFromWebEntries</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
|
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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||||
<arg>--outputPath</arg><arg>${outputPath}</arg>
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||||
</spark>
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||||
<ok to="End"/>
|
||||
<error to="Kill"/>
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||||
</action>
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||||
<end name="End"/>
|
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</workflow-app>
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|
|
@ -0,0 +1,287 @@
|
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package eu.dnetlib.dhp.actionmanager.webcrawl;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
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import org.apache.hadoop.io.Text;
|
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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.schema.action.AtomicAction;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 22/04/24
|
||||
*/
|
||||
public class CreateASTest {
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
private static final Logger log = LoggerFactory
|
||||
.getLogger(CreateASTest.class);
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files
|
||||
.createTempDirectory(CreateASTest.class.getSimpleName());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(CreateASTest.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(CreateASTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
void testNumberofRelations() throws Exception {
|
||||
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/webcrawl/")
|
||||
.getPath();
|
||||
|
||||
CreateActionSetFromWebEntries
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-sourcePath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet1"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
Assertions.assertEquals(64, tmp.count());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void testRelations() throws Exception {
|
||||
|
||||
// , "doi":"https://doi.org/10.1126/science.1188021", "pmid":"https://pubmed.ncbi.nlm.nih.gov/20448178", https://www.ncbi.nlm.nih.gov/pmc/articles/5100745
|
||||
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/webcrawl/")
|
||||
.getPath();
|
||||
|
||||
CreateActionSetFromWebEntries
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-sourcePath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet1"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1, tmp
|
||||
.filter(
|
||||
r -> r
|
||||
.getSource()
|
||||
.equals(
|
||||
"50|doi_________::" + IdentifierFactory
|
||||
.md5(
|
||||
PidCleaner
|
||||
.normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023"))))
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1, tmp
|
||||
.filter(
|
||||
r -> r
|
||||
.getTarget()
|
||||
.equals(
|
||||
"50|doi_________::" + IdentifierFactory
|
||||
.md5(
|
||||
PidCleaner
|
||||
.normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023"))))
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1, tmp
|
||||
.filter(
|
||||
r -> r
|
||||
.getSource()
|
||||
.equals(
|
||||
"20|ror_________::" + IdentifierFactory
|
||||
.md5(
|
||||
PidCleaner
|
||||
.normalizePidValue("ROR", "https://ror.org/03argrj65"))))
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1, tmp
|
||||
.filter(
|
||||
r -> r
|
||||
.getTarget()
|
||||
.equals(
|
||||
"20|ror_________::" + IdentifierFactory
|
||||
.md5(
|
||||
PidCleaner
|
||||
.normalizePidValue("ROR", "https://ror.org/03argrj65"))))
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
5, tmp
|
||||
.filter(
|
||||
r -> r
|
||||
.getSource()
|
||||
.equals(
|
||||
"20|ror_________::" + IdentifierFactory
|
||||
.md5(
|
||||
PidCleaner
|
||||
.normalizePidValue("ROR", "https://ror.org/03265fv13"))))
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
5, tmp
|
||||
.filter(
|
||||
r -> r
|
||||
.getTarget()
|
||||
.equals(
|
||||
"20|ror_________::" + IdentifierFactory
|
||||
.md5(
|
||||
PidCleaner
|
||||
.normalizePidValue("ROR", "https://ror.org/03265fv13"))))
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
2, tmp
|
||||
.filter(
|
||||
r -> r
|
||||
.getTarget()
|
||||
.equals(
|
||||
"20|ror_________::" + IdentifierFactory
|
||||
.md5(
|
||||
PidCleaner
|
||||
.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
|
||||
&& r.getSource().startsWith("50|doi"))
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
2, tmp
|
||||
.filter(
|
||||
r -> r
|
||||
.getTarget()
|
||||
.equals(
|
||||
"20|ror_________::" + IdentifierFactory
|
||||
.md5(
|
||||
PidCleaner
|
||||
.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
|
||||
&& r.getSource().startsWith("50|pmid"))
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1, tmp
|
||||
.filter(
|
||||
r -> r
|
||||
.getTarget()
|
||||
.equals(
|
||||
"20|ror_________::" + IdentifierFactory
|
||||
.md5(
|
||||
PidCleaner
|
||||
.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
|
||||
&& r.getSource().startsWith("50|pmc"))
|
||||
.count());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testRelationsCollectedFrom() throws Exception {
|
||||
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/webcrawl")
|
||||
.getPath();
|
||||
|
||||
CreateActionSetFromWebEntries
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-sourcePath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet1"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
tmp.foreach(r -> {
|
||||
assertEquals("Web Crawl", r.getCollectedfrom().get(0).getValue());
|
||||
assertEquals("10|openaire____::fb98a192f6a055ba495ef414c330834b", r.getCollectedfrom().get(0).getKey());
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
Loading…
Reference in New Issue