mergin with branch beta

This commit is contained in:
Miriam Baglioni 2023-11-27 15:10:55 +01:00
commit e3cce9a5a0
11 changed files with 238 additions and 35 deletions

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@ -3,6 +3,8 @@ package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
import java.net.MalformedURLException;
import java.net.URL;
import java.time.LocalDate;
import java.time.ZoneId;
import java.time.format.DateTimeFormatter;
@ -36,6 +38,13 @@ public class GraphCleaningFunctions extends CleaningFunctions {
public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
private static final String NAME_CLEANING_REGEX = "[\\r\\n\\t\\s]+";
private static final Set<String> INVALID_AUTHOR_NAMES = new HashSet<>();
private static final Set<String> INVALID_URLS = new HashSet<>();
private static final Set<String> INVALID_URL_HOSTS = new HashSet<>();
private static final HashSet<String> PEER_REVIEWED_TYPES = new HashSet<>();
static {
@ -48,6 +57,47 @@ public class GraphCleaningFunctions extends CleaningFunctions {
PEER_REVIEWED_TYPES.add("Thesis");
PEER_REVIEWED_TYPES.add("Bachelor thesis");
PEER_REVIEWED_TYPES.add("Conference object");
INVALID_AUTHOR_NAMES.add("(:null)");
INVALID_AUTHOR_NAMES.add("(:unap)");
INVALID_AUTHOR_NAMES.add("(:tba)");
INVALID_AUTHOR_NAMES.add("(:unas)");
INVALID_AUTHOR_NAMES.add("(:unav)");
INVALID_AUTHOR_NAMES.add("(:unkn)");
INVALID_AUTHOR_NAMES.add("(:unkn) unknown");
INVALID_AUTHOR_NAMES.add(":none");
INVALID_AUTHOR_NAMES.add(":null");
INVALID_AUTHOR_NAMES.add(":unas");
INVALID_AUTHOR_NAMES.add(":unav");
INVALID_AUTHOR_NAMES.add(":unkn");
INVALID_AUTHOR_NAMES.add("[autor desconocido]");
INVALID_AUTHOR_NAMES.add("[s. n.]");
INVALID_AUTHOR_NAMES.add("[s.n]");
INVALID_AUTHOR_NAMES.add("[unknown]");
INVALID_AUTHOR_NAMES.add("anonymous");
INVALID_AUTHOR_NAMES.add("n.n.");
INVALID_AUTHOR_NAMES.add("nn");
INVALID_AUTHOR_NAMES.add("no name supplied");
INVALID_AUTHOR_NAMES.add("none");
INVALID_AUTHOR_NAMES.add("none available");
INVALID_AUTHOR_NAMES.add("not available not available");
INVALID_AUTHOR_NAMES.add("null &na;");
INVALID_AUTHOR_NAMES.add("null anonymous");
INVALID_AUTHOR_NAMES.add("unbekannt");
INVALID_AUTHOR_NAMES.add("unknown");
INVALID_URL_HOSTS.add("creativecommons.org");
INVALID_URL_HOSTS.add("www.academia.edu");
INVALID_URL_HOSTS.add("academia.edu");
INVALID_URL_HOSTS.add("researchgate.net");
INVALID_URL_HOSTS.add("www.researchgate.net");
INVALID_URLS.add("http://repo.scoap3.org/api");
INVALID_URLS.add("http://ora.ox.ac.uk/objects/uuid:");
INVALID_URLS.add("http://ntur.lib.ntu.edu.tw/news/agent_contract.pdf");
INVALID_URLS.add("https://media.springer.com/full/springer-instructions-for-authors-assets/pdf/SN_BPF_EN.pdf");
INVALID_URLS.add("http://www.tobaccoinduceddiseases.org/dl/61aad426c96519bea4040a374c6a6110/");
INVALID_URLS.add("https://www.bilboard.nl/verenigingsbladen/bestuurskundige-berichten");
}
public static <T extends Oaf> T cleanContext(T value, String contextId, String verifyParam) {
@ -558,6 +608,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) {
i.setFulltext(null);
}
if (Objects.nonNull(i.getUrl())) {
i
.setUrl(
i
.getUrl()
.stream()
.filter(GraphCleaningFunctions::urlFilter)
.collect(Collectors.toList()));
}
}
}
if (Objects.isNull(r.getBestaccessright())
@ -580,8 +639,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.getAuthor()
.stream()
.filter(Objects::nonNull)
.filter(a -> StringUtils.isNotBlank(a.getFullname()))
.filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")))
.filter(GraphCleaningFunctions::isValidAuthorName)
.map(GraphCleaningFunctions::cleanupAuthor)
.collect(Collectors.toList()));
@ -739,12 +797,30 @@ public class GraphCleaningFunctions extends CleaningFunctions {
// HELPERS
private static boolean isValidAuthorName(Author a) {
return !Stream
.of(a.getFullname(), a.getName(), a.getSurname())
.filter(s -> s != null && !s.isEmpty())
.collect(Collectors.joining(""))
.toLowerCase()
.matches(INVALID_AUTHOR_REGEX);
return StringUtils.isNotBlank(a.getFullname()) &&
StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")) &&
!INVALID_AUTHOR_NAMES.contains(StringUtils.lowerCase(a.getFullname()).trim()) &&
!Stream
.of(a.getFullname(), a.getName(), a.getSurname())
.filter(StringUtils::isNotBlank)
.collect(Collectors.joining(""))
.toLowerCase()
.matches(INVALID_AUTHOR_REGEX);
}
private static boolean urlFilter(String u) {
try {
final URL url = new URL(u);
if (StringUtils.isBlank(url.getPath()) || "/".equals(url.getPath())) {
return false;
}
if (INVALID_URL_HOSTS.contains(url.getHost())) {
return false;
}
return !INVALID_URLS.contains(url.toString());
} catch (MalformedURLException ex) {
return false;
}
}
private static List<StructuredProperty> processPidCleaning(List<StructuredProperty> pids) {

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@ -12,6 +12,7 @@ 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.JavaPairRDD;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
@ -57,11 +58,14 @@ public class PrepareAffiliationRelations implements Serializable {
Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String crossrefInputPath = parser.get("crossrefInputPath");
log.info("crossrefInputPath: {}", crossrefInputPath);
final String pubmedInputPath = parser.get("pubmedInputPath");
log.info("pubmedInputPath: {}", pubmedInputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
@ -70,12 +74,28 @@ public class PrepareAffiliationRelations implements Serializable {
isSparkSessionManaged,
spark -> {
Constants.removeOutputDir(spark, outputPath);
prepareAffiliationRelations(spark, inputPath, outputPath);
List<KeyValue> collectedFromCrossref = OafMapperUtils
.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
spark, crossrefInputPath, collectedFromCrossref);
List<KeyValue> collectedFromPubmed = OafMapperUtils
.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
spark, pubmedInputPath, collectedFromPubmed);
crossrefRelations
.union(pubmedRelations)
.saveAsHadoopFile(
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
});
}
private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath,
String outputPath) {
private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
String inputPath,
List<KeyValue> collectedfrom) {
// load and parse affiliation relations from HDFS
Dataset<Row> df = spark
@ -92,7 +112,7 @@ public class PrepareAffiliationRelations implements Serializable {
new Column("matching.Confidence").as("confidence"));
// prepare action sets for affiliation relations
df
return df
.toJavaRDD()
.flatMap((FlatMapFunction<Row, Relation>) row -> {
@ -120,8 +140,6 @@ public class PrepareAffiliationRelations implements Serializable {
qualifier,
Double.toString(row.getAs("confidence")));
List<KeyValue> collectedfrom = OafMapperUtils.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
// return bi-directional relations
return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
@ -129,9 +147,7 @@ public class PrepareAffiliationRelations implements Serializable {
.map(p -> new AtomicAction(Relation.class, 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);
new Text(OBJECT_MAPPER.writeValueAsString(aa))));
}
private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,

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@ -6,9 +6,15 @@
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramName": "cip",
"paramLongName": "crossrefInputPath",
"paramDescription": "the path to get the input data from Crossref",
"paramRequired": true
},
{
"paramName": "pip",
"paramLongName": "pubmedInputPath",
"paramDescription": "the path to get the input data from Pubmed",
"paramRequired": true
},
{

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@ -31,5 +31,6 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
# The following is needed as a property of a workflow
oozie.wf.application.path=${oozieTopWfApplicationPath}
inputPath=/data/bip-affiliations/data.json
crossrefInputPath=/data/bip-affiliations/data.json
pubmedInputPath=/data/bip-affiliations/pubmed-data.json
outputPath=/tmp/crossref-affiliations-output-v5

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@ -2,8 +2,12 @@
<parameters>
<property>
<name>inputPath</name>
<description>the path where to find the inferred affiliation relations</description>
<name>crossrefInputPath</name>
<description>the path where to find the inferred affiliation relations from Crossref</description>
</property>
<property>
<name>pubmedInputPath</name>
<description>the path where to find the inferred affiliation relations from Pubmed</description>
</property>
<property>
<name>outputPath</name>
@ -83,7 +87,7 @@
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the inferred by BIP! affiliation relations from Crossref</name>
<name>Produces the atomic action with the inferred by BIP! affiliation relations (from Crossref and Pubmed)</name>
<class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
@ -96,7 +100,8 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}</arg>
<arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
<arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>

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@ -74,17 +74,22 @@ public class PrepareAffiliationRelationsTest {
@Test
void testMatch() throws Exception {
String affiliationRelationsPath = getClass()
String crossrefAffiliationRelationPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
.getPath();
String pubmedAffiliationRelationsPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
.getPath();
String outputPath = workingDir.toString() + "/actionSet";
PrepareAffiliationRelations
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-inputPath", affiliationRelationsPath,
"-crossrefInputPath", crossrefAffiliationRelationPath,
"-pubmedInputPath", pubmedAffiliationRelationsPath,
"-outputPath", outputPath
});
@ -101,7 +106,7 @@ public class PrepareAffiliationRelationsTest {
// );
// }
// count the number of relations
assertEquals(20, tmp.count());
assertEquals(40, tmp.count());
Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
dataset.createOrReplaceTempView("result");
@ -112,7 +117,7 @@ public class PrepareAffiliationRelationsTest {
// verify that we have equal number of bi-directional relations
Assertions
.assertEquals(
10, execVerification
20, execVerification
.filter(
"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
.collectAsList()
@ -120,7 +125,7 @@ public class PrepareAffiliationRelationsTest {
Assertions
.assertEquals(
10, execVerification
20, execVerification
.filter(
"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
.collectAsList()

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@ -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;

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@ -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

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@ -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")));

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@ -0,0 +1,65 @@
<?xml version="1.0" encoding="UTF-8"?>
<record xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dr="http://www.driver-repository.eu/namespace/dr"
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:oaf="http://namespace.openaire.eu/oaf"
xmlns:oai="http://www.openarchives.org/OAI/2.0/"
xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance"
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<header xmlns="http://namespace.openaire.eu/">
<dri:objIdentifier>od______3272::6a4d00217a024a46ce9697ce98b13c2a</dri:objIdentifier>
<dri:recordIdentifier>oai:idus.us.es:11441/118940</dri:recordIdentifier>
<dri:dateOfCollection/>
<dri:mdFormat/>
<dri:mdFormatInterpretation/>
<dri:repositoryId/>
<dr:objectIdentifier/>
<dr:dateOfCollection>2021-08-20T12:32:32.826Z</dr:dateOfCollection>
<dr:dateOfTransformation>2023-07-04T15:47:55.397Z</dr:dateOfTransformation>
<oaf:datasourceprefix>od______3272</oaf:datasourceprefix>
</header>
<metadata xmlns="http://namespace.openaire.eu/">
<dc:title>El museo pictorico y escala optica : tomo I : theorica de la pintura en que se describe su origen ... y se aprueban con demonstraciomes mathematicas y filosoficas, sus mas radicales fundamentos</dc:title>
<dc:creator>Palomino de Castro y Velasco, Antonio, 1653-1726</dc:creator>
<dc:contributor>Rovira y Brocandel, Hipólito, 1693-1765</dc:contributor>
<dc:contributor>Palomino de Castro y Velasco, Antonio, 1653-1726</dc:contributor>
<dc:date>2021-08-12T08:59:53Z</dc:date>
<dc:date>1715</dc:date>
<dc:description>A 042(a)/063</dc:description>
<dc:format>application/pdf</dc:format>
<dc:identifier>https://idus.us.es/handle//11441/118940</dc:identifier>
<dc:language>spa</dc:language>
<dc:publisher>En Madrid : por Lucas Antonio de Bedmar ... : vendese en casa de Don Joseph de Villar y Villanueva, 1715</dc:publisher>
<dc:type>info:eu-repo/semantics/book</dc:type>
<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
<dr:CobjCategory type="publication">0002</dr:CobjCategory>
<oaf:dateAccepted>1715-01-01</oaf:dateAccepted>
<oaf:embargoenddate/>
<oaf:collectedDatasourceid>opendoar____::3272</oaf:collectedDatasourceid>
<oaf:accessrights>OPEN</oaf:accessrights>
<oaf:hostedBy id="opendoar____::3272" name="idUS. Depósito de Investigación de la Universidad de Sevilla."/>
<oaf:collectedFrom id="opendoar____::3272" name="idUS. Depósito de Investigación de la Universidad de Sevilla."/>
<oaf:identifier identifierType="landingPage">https://idus.us.es/handle//11441/118940</oaf:identifier>
<oaf:journal eissn="" ep="" iss="" issn="" sp="" vol=""/>
<oaf:license>http://creativecommons.org/licenses/by-nc-nd/4.0/</oaf:license>
</metadata>
<about>
<provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
<originDescription altered="true" harvestDate="2021-08-20T12:32:32.826Z">
<baseURL>http%3A%2F%2Fidus.us.es%2Foai%2Fdriver</baseURL>
<identifier>oai:idus.us.es:11441/118940</identifier>
<datestamp>2021-08-12T08:59:54Z</datestamp>
<metadataNamespace>http://www.openarchives.org/OAI/2.0/oai_dc/</metadataNamespace>
</originDescription>
</provenance>
<oaf:datainfo>
<oaf:inferred>false</oaf:inferred>
<oaf:deletedbyinference>false</oaf:deletedbyinference>
<oaf:trust>0.9</oaf:trust>
<oaf:inferenceprovenance/>
<oaf:provenanceaction classid="sysimport:crosswalk:repository"
classname="sysimport:crosswalk:repository"
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
</oaf:datainfo>
</about>
</record>