Merge remote-tracking branch 'origin/beta' into orcid_import
This commit is contained in:
Sandro La Bruzzo
commit
5e22b67b8a
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@ -3,6 +3,8 @@ package eu.dnetlib.dhp.schema.oaf.utils;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.time.LocalDate;
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import java.time.ZoneId;
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import java.time.format.DateTimeFormatter;
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@ -36,6 +38,13 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
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private static final String NAME_CLEANING_REGEX = "[\\r\\n\\t\\s]+";
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private static final Set<String> INVALID_AUTHOR_NAMES = new HashSet<>();
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private static final Set<String> INVALID_URLS = new HashSet<>();
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private static final Set<String> INVALID_URL_HOSTS = new HashSet<>();
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private static final HashSet<String> PEER_REVIEWED_TYPES = new HashSet<>();
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static {
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@ -48,6 +57,47 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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PEER_REVIEWED_TYPES.add("Thesis");
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PEER_REVIEWED_TYPES.add("Bachelor thesis");
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PEER_REVIEWED_TYPES.add("Conference object");
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INVALID_AUTHOR_NAMES.add("(:null)");
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INVALID_AUTHOR_NAMES.add("(:unap)");
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INVALID_AUTHOR_NAMES.add("(:tba)");
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INVALID_AUTHOR_NAMES.add("(:unas)");
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INVALID_AUTHOR_NAMES.add("(:unav)");
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INVALID_AUTHOR_NAMES.add("(:unkn)");
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INVALID_AUTHOR_NAMES.add("(:unkn) unknown");
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INVALID_AUTHOR_NAMES.add(":none");
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INVALID_AUTHOR_NAMES.add(":null");
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INVALID_AUTHOR_NAMES.add(":unas");
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INVALID_AUTHOR_NAMES.add(":unav");
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INVALID_AUTHOR_NAMES.add(":unkn");
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INVALID_AUTHOR_NAMES.add("[autor desconocido]");
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INVALID_AUTHOR_NAMES.add("[s. n.]");
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INVALID_AUTHOR_NAMES.add("[s.n]");
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INVALID_AUTHOR_NAMES.add("[unknown]");
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INVALID_AUTHOR_NAMES.add("anonymous");
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INVALID_AUTHOR_NAMES.add("n.n.");
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INVALID_AUTHOR_NAMES.add("nn");
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INVALID_AUTHOR_NAMES.add("no name supplied");
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INVALID_AUTHOR_NAMES.add("none");
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INVALID_AUTHOR_NAMES.add("none available");
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INVALID_AUTHOR_NAMES.add("not available not available");
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INVALID_AUTHOR_NAMES.add("null &na;");
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INVALID_AUTHOR_NAMES.add("null anonymous");
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INVALID_AUTHOR_NAMES.add("unbekannt");
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INVALID_AUTHOR_NAMES.add("unknown");
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INVALID_URL_HOSTS.add("creativecommons.org");
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INVALID_URL_HOSTS.add("www.academia.edu");
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INVALID_URL_HOSTS.add("academia.edu");
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INVALID_URL_HOSTS.add("researchgate.net");
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INVALID_URL_HOSTS.add("www.researchgate.net");
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INVALID_URLS.add("http://repo.scoap3.org/api");
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INVALID_URLS.add("http://ora.ox.ac.uk/objects/uuid:");
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INVALID_URLS.add("http://ntur.lib.ntu.edu.tw/news/agent_contract.pdf");
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INVALID_URLS.add("https://media.springer.com/full/springer-instructions-for-authors-assets/pdf/SN_BPF_EN.pdf");
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INVALID_URLS.add("http://www.tobaccoinduceddiseases.org/dl/61aad426c96519bea4040a374c6a6110/");
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INVALID_URLS.add("https://www.bilboard.nl/verenigingsbladen/bestuurskundige-berichten");
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}
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public static <T extends Oaf> T cleanContext(T value, String contextId, String verifyParam) {
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@ -558,6 +608,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) {
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i.setFulltext(null);
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}
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if (Objects.nonNull(i.getUrl())) {
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i
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.setUrl(
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i
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.getUrl()
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.stream()
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.filter(GraphCleaningFunctions::urlFilter)
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.collect(Collectors.toList()));
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}
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}
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}
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if (Objects.isNull(r.getBestaccessright())
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@ -580,8 +639,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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.getAuthor()
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.stream()
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.filter(Objects::nonNull)
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.filter(a -> StringUtils.isNotBlank(a.getFullname()))
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.filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")))
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.filter(GraphCleaningFunctions::isValidAuthorName)
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.map(GraphCleaningFunctions::cleanupAuthor)
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.collect(Collectors.toList()));
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@ -739,12 +797,30 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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// HELPERS
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private static boolean isValidAuthorName(Author a) {
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return !Stream
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.of(a.getFullname(), a.getName(), a.getSurname())
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.filter(s -> s != null && !s.isEmpty())
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.collect(Collectors.joining(""))
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.toLowerCase()
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.matches(INVALID_AUTHOR_REGEX);
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return StringUtils.isNotBlank(a.getFullname()) &&
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StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")) &&
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!INVALID_AUTHOR_NAMES.contains(StringUtils.lowerCase(a.getFullname()).trim()) &&
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!Stream
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.of(a.getFullname(), a.getName(), a.getSurname())
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.filter(StringUtils::isNotBlank)
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.collect(Collectors.joining(""))
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.toLowerCase()
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.matches(INVALID_AUTHOR_REGEX);
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}
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private static boolean urlFilter(String u) {
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try {
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final URL url = new URL(u);
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if (StringUtils.isBlank(url.getPath()) || "/".equals(url.getPath())) {
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return false;
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}
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if (INVALID_URL_HOSTS.contains(url.getHost())) {
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return false;
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}
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return !INVALID_URLS.contains(url.toString());
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} catch (MalformedURLException ex) {
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return false;
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}
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}
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private static List<StructuredProperty> processPidCleaning(List<StructuredProperty> pids) {
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@ -12,6 +12,7 @@ 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.JavaPairRDD;
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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.Dataset;
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@ -57,11 +58,14 @@ public class PrepareAffiliationRelations implements Serializable {
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Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("inputPath");
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log.info("inputPath {}: ", inputPath);
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final String crossrefInputPath = parser.get("crossrefInputPath");
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log.info("crossrefInputPath: {}", crossrefInputPath);
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final String pubmedInputPath = parser.get("pubmedInputPath");
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log.info("pubmedInputPath: {}", pubmedInputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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@ -70,12 +74,28 @@ public class PrepareAffiliationRelations implements Serializable {
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isSparkSessionManaged,
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spark -> {
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Constants.removeOutputDir(spark, outputPath);
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prepareAffiliationRelations(spark, inputPath, outputPath);
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List<KeyValue> collectedFromCrossref = OafMapperUtils
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.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
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JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
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spark, crossrefInputPath, collectedFromCrossref);
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List<KeyValue> collectedFromPubmed = OafMapperUtils
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.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
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JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
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spark, pubmedInputPath, collectedFromPubmed);
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crossrefRelations
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.union(pubmedRelations)
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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});
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}
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private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath,
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String outputPath) {
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private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
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String inputPath,
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List<KeyValue> collectedfrom) {
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// load and parse affiliation relations from HDFS
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Dataset<Row> df = spark
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@ -92,7 +112,7 @@ public class PrepareAffiliationRelations implements Serializable {
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new Column("matching.Confidence").as("confidence"));
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// prepare action sets for affiliation relations
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df
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return df
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.toJavaRDD()
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.flatMap((FlatMapFunction<Row, Relation>) row -> {
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@ -120,8 +140,6 @@ public class PrepareAffiliationRelations implements Serializable {
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qualifier,
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Double.toString(row.getAs("confidence")));
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List<KeyValue> collectedfrom = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
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// return bi-directional relations
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return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
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@ -129,9 +147,7 @@ public class PrepareAffiliationRelations implements Serializable {
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.map(p -> new AtomicAction(Relation.class, 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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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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}
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private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,
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@ -6,9 +6,15 @@
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"paramRequired": false
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},
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{
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"paramName": "ip",
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"paramLongName": "inputPath",
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"paramDescription": "the URL from where to get the programme file",
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"paramName": "cip",
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"paramLongName": "crossrefInputPath",
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"paramDescription": "the path to get the input data from Crossref",
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"paramRequired": true
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},
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{
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"paramName": "pip",
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"paramLongName": "pubmedInputPath",
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"paramDescription": "the path to get the input data from Pubmed",
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"paramRequired": true
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},
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{
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|
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@ -31,5 +31,6 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
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# The following is needed as a property of a workflow
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oozie.wf.application.path=${oozieTopWfApplicationPath}
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inputPath=/data/bip-affiliations/data.json
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crossrefInputPath=/data/bip-affiliations/data.json
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pubmedInputPath=/data/bip-affiliations/pubmed-data.json
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outputPath=/tmp/crossref-affiliations-output-v5
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|
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@ -2,8 +2,12 @@
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<parameters>
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<property>
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<name>inputPath</name>
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<description>the path where to find the inferred affiliation relations</description>
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<name>crossrefInputPath</name>
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<description>the path where to find the inferred affiliation relations from Crossref</description>
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</property>
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<property>
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<name>pubmedInputPath</name>
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<description>the path where to find the inferred affiliation relations from Pubmed</description>
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</property>
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<property>
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<name>outputPath</name>
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@ -83,7 +87,7 @@
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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 atomic action with the inferred by BIP! affiliation relations from Crossref</name>
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<name>Produces the atomic action with the inferred by BIP! affiliation relations (from Crossref and Pubmed)</name>
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<class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -96,7 +100,8 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--inputPath</arg><arg>${inputPath}</arg>
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<arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
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<arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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</spark>
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<ok to="End"/>
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|
|
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@ -74,17 +74,22 @@ public class PrepareAffiliationRelationsTest {
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@Test
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void testMatch() throws Exception {
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String affiliationRelationsPath = getClass()
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String crossrefAffiliationRelationPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
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.getPath();
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String pubmedAffiliationRelationsPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
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.getPath();
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String outputPath = workingDir.toString() + "/actionSet";
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PrepareAffiliationRelations
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath", affiliationRelationsPath,
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"-crossrefInputPath", crossrefAffiliationRelationPath,
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"-pubmedInputPath", pubmedAffiliationRelationsPath,
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"-outputPath", outputPath
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});
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@ -101,7 +106,7 @@ public class PrepareAffiliationRelationsTest {
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// );
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// }
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// count the number of relations
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assertEquals(20, tmp.count());
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assertEquals(40, tmp.count());
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Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
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dataset.createOrReplaceTempView("result");
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|
@ -112,7 +117,7 @@ public class PrepareAffiliationRelationsTest {
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// verify that we have equal number of bi-directional relations
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Assertions
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.assertEquals(
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10, execVerification
|
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20, execVerification
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.filter(
|
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"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
|
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.collectAsList()
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||||
|
|
@ -120,7 +125,7 @@ public class PrepareAffiliationRelationsTest {
|
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|
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Assertions
|
||||
.assertEquals(
|
||||
10, execVerification
|
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20, execVerification
|
||||
.filter(
|
||||
"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
|
||||
.collectAsList()
|
||||
|
|
|
|||
|
|
@ -29,7 +29,7 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
|
||||
protected final VocabularyGroup vocs;
|
||||
|
||||
protected static final UrlValidator URL_VALIDATOR = UrlValidator.getInstance();
|
||||
protected static final UrlValidator URL_VALIDATOR = new UrlValidator(UrlValidator.ALLOW_2_SLASHES);
|
||||
|
||||
private final boolean invisible;
|
||||
|
||||
|
|
|
|||
|
|
@ -251,9 +251,19 @@ public class CleanGraphSparkJobTest {
|
|||
.filter(String.format("id = '%s'", id))
|
||||
.first();
|
||||
|
||||
final Set<String> invalidURLs = new HashSet<>();
|
||||
invalidURLs.add("http://academia.edu/abcd");
|
||||
invalidURLs.add("http://repo.scoap3.org/api");
|
||||
invalidURLs.add("http://hdl.handle.net/");
|
||||
|
||||
assertNull(p_in.getBestaccessright());
|
||||
assertTrue(p_in instanceof Result);
|
||||
assertTrue(p_in instanceof Publication);
|
||||
assertNotNull(p_in.getAuthor());
|
||||
assertEquals(14, p_in.getAuthor().size());
|
||||
assertNotNull(p_in.getInstance());
|
||||
assertNotNull(p_in.getInstance().get(0));
|
||||
assertEquals(3, p_in.getInstance().get(0).getUrl().stream().filter(invalidURLs::contains).count());
|
||||
|
||||
new CleanGraphSparkJob(
|
||||
args(
|
||||
|
|
@ -273,6 +283,9 @@ public class CleanGraphSparkJobTest {
|
|||
|
||||
assertNull(p.getPublisher());
|
||||
|
||||
assertNotNull(p.getAuthor());
|
||||
assertEquals(12, p.getAuthor().size());
|
||||
|
||||
assertEquals("und", p.getLanguage().getClassid());
|
||||
assertEquals("Undetermined", p.getLanguage().getClassname());
|
||||
|
||||
|
|
@ -364,6 +377,8 @@ public class CleanGraphSparkJobTest {
|
|||
.stream()
|
||||
.anyMatch(s -> s.getValue().equals("10.1009/qwerty")));
|
||||
|
||||
assertTrue(p.getInstance().get(0).getUrl().stream().noneMatch(invalidURLs::contains));
|
||||
|
||||
assertNotNull(p.getSubject());
|
||||
|
||||
List<Subject> fos_subjects = p
|
||||
|
|
|
|||
|
|
@ -797,6 +797,20 @@ class MappersTest {
|
|||
assertFalse(p_cleaned.getTitle().isEmpty());
|
||||
}
|
||||
|
||||
@Test
|
||||
void test_instance_url_validation() throws IOException {
|
||||
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("idus_sevilla.xml")));
|
||||
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
|
||||
|
||||
final Publication p = (Publication) list.get(0);
|
||||
|
||||
assertNotNull(p.getInstance());
|
||||
assertFalse(p.getInstance().isEmpty());
|
||||
assertNotNull(p.getInstance().get(0).getUrl());
|
||||
assertFalse(p.getInstance().get(0).getUrl().isEmpty());
|
||||
assertEquals("https://idus.us.es/handle//11441/118940", p.getInstance().get(0).getUrl().get(0));
|
||||
}
|
||||
|
||||
@Test
|
||||
void testZenodo() throws IOException, DocumentException {
|
||||
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml")));
|
||||
|
|
|
|||
File diff suppressed because one or more lines are too long
|
|
@ -0,0 +1,65 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
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Loading…
Reference in New Issue