Merge branch 'master' into fct_project_id_replacement

This commit is contained in:
Claudio Atzori 2021-07-29 11:38:22 +02:00
commit 5f7330d407
8 changed files with 160 additions and 61 deletions

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@ -25,6 +25,11 @@
<groupId>com.github.sisyphsu</groupId> <groupId>com.github.sisyphsu</groupId>
<artifactId>dateparser</artifactId> <artifactId>dateparser</artifactId>
</dependency> </dependency>
<dependency>
<groupId>me.xuender</groupId>
<artifactId>unidecode</artifactId>
</dependency>
<dependency> <dependency>
<groupId>org.apache.spark</groupId> <groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId> <artifactId>spark-core_2.11</artifactId>

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@ -7,22 +7,19 @@ import java.time.format.DateTimeFormatter;
import java.time.format.DateTimeParseException; import java.time.format.DateTimeParseException;
import java.util.*; import java.util.*;
import java.util.function.Function; import java.util.function.Function;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import java.util.stream.Stream; import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.jetbrains.annotations.NotNull;
import com.github.sisyphsu.dateparser.DateParserUtils; import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists; import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets; import com.google.common.collect.Sets;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import me.xuender.unidecode.Unidecode;
public class GraphCleaningFunctions extends CleaningFunctions { public class GraphCleaningFunctions extends CleaningFunctions {
@ -194,11 +191,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(Objects::nonNull) .filter(Objects::nonNull)
.filter(sp -> StringUtils.isNotBlank(sp.getValue())) .filter(sp -> StringUtils.isNotBlank(sp.getValue()))
.filter( .filter(
sp -> sp sp -> {
.getValue() final String title = sp
.toLowerCase() .getValue()
.replaceAll(TITLE_FILTER_REGEX, "") .toLowerCase();
.length() > TITLE_FILTER_RESIDUAL_LENGTH) final String residual = Unidecode
.decode(title)
.replaceAll(TITLE_FILTER_REGEX, "");
return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH;
})
.map(GraphCleaningFunctions::cleanValue) .map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }

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@ -4,12 +4,8 @@ package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.*; import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException; import java.io.IOException;
import java.time.LocalDate;
import java.time.format.DateTimeFormatter;
import java.util.HashSet; import java.util.HashSet;
import java.util.List; import java.util.List;
import java.util.Locale;
import java.util.Optional;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
@ -19,13 +15,32 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Result;
import me.xuender.unidecode.Unidecode;
public class OafMapperUtilsTest { public class OafMapperUtilsTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
public void testUnidecode() {
assertEquals("Liu Ben Mu hiruzuSen tawa", Unidecode.decode("六本木ヒルズ森タワ"));
assertEquals("Nan Wu A Mi Tuo Fo", Unidecode.decode("南无阿弥陀佛"));
assertEquals("Yi Tiao Hui Zou Lu De Yu", Unidecode.decode("一条会走路的鱼"));
assertEquals("amidaniyorai", Unidecode.decode("あみだにょらい"));
assertEquals("T`owrk`iayi", Unidecode.decode("Թուրքիայի"));
assertEquals("Obzor tematiki", Unidecode.decode("Обзор тематики"));
assertEquals("GERMANSKIE IaZYKI", Unidecode.decode("ГЕРМАНСКИЕ ЯЗЫКИ"));
assertEquals("Diereunese tes ikanopoieses", Unidecode.decode("Διερεύνηση της ικανοποίησης"));
assertEquals("lqDy l'wly@", Unidecode.decode("القضايا الأولية"));
assertEquals("abc def ghi", Unidecode.decode("abc def ghi"));
}
@Test @Test
public void testDateValidation() { public void testDateValidation() {

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@ -1,13 +1,15 @@
package eu.dnetlib.dhp.oa.graph.raw; package eu.dnetlib.dhp.oa.graph.raw;
import com.fasterxml.jackson.databind.ObjectMapper; import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.cleanup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.fixVocabularyNames;
import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; import static org.junit.jupiter.api.Assertions.*;
import eu.dnetlib.dhp.schema.common.ModelConstants; import static org.mockito.Mockito.lenient;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.PidType; import java.io.IOException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
@ -16,12 +18,14 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock; import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import java.io.IOException; import com.fasterxml.jackson.databind.ObjectMapper;
import java.util.List;
import java.util.Optional;
import static org.junit.jupiter.api.Assertions.*; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import static org.mockito.Mockito.lenient; import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class MappersTest { public class MappersTest {
@ -340,7 +344,7 @@ public class MappersTest {
assertEquals(2, p.getOriginalId().size()); assertEquals(2, p.getOriginalId().size());
assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:pub.uni-bielefeld.de:2949739"))); assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:pub.uni-bielefeld.de:2949739")));
//assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); // assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0));
assertValidId(p.getCollectedfrom().get(0).getKey()); assertValidId(p.getCollectedfrom().get(0).getKey());
assertTrue(p.getAuthor().size() > 0); assertTrue(p.getAuthor().size() > 0);
@ -557,31 +561,6 @@ public class MappersTest {
assertNotNull(d.getInstance().get(0).getUrl()); assertNotNull(d.getInstance().get(0).getUrl());
} }
@Test
void testEnermaps() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("enermaps.xml"));
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
System.out.println("***************");
System.out.println(new ObjectMapper().writeValueAsString(list));
System.out.println("***************");
assertEquals(1, list.size());
assertTrue(list.get(0) instanceof Dataset);
final Dataset d = (Dataset) list.get(0);
assertValidId(d.getId());
assertValidId(d.getCollectedfrom().get(0).getKey());
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
assertEquals(1, d.getAuthor().size());
assertEquals(1, d.getInstance().size());
assertNotNull(d.getInstance().get(0).getUrl());
assertNotNull(d.getContext());
assertTrue(StringUtils.isNotBlank(d.getContext().get(0).getId()));
assertEquals("enermaps::selection::tgs00004", d.getContext().get(0).getId());
}
@Test @Test
void testClaimFromCrossref() throws IOException { void testClaimFromCrossref() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml")); final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml"));
@ -663,6 +642,30 @@ public class MappersTest {
System.out.println(p.getTitle().get(0).getValue()); System.out.println(p.getTitle().get(0).getValue());
} }
@Test
void testJairo() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_jairo.xml"));
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
System.out.println("***************");
System.out.println(new ObjectMapper().writeValueAsString(list));
System.out.println("***************");
final Publication p = (Publication) list.get(0);
assertValidId(p.getId());
assertValidId(p.getCollectedfrom().get(0).getKey());
assertNotNull(p.getTitle());
assertFalse(p.getTitle().isEmpty());
assertTrue(p.getTitle().size() == 1);
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
final Publication p_cleaned = cleanup(fixVocabularyNames(p));
assertNotNull(p_cleaned.getTitle());
assertFalse(p_cleaned.getTitle().isEmpty());
}
@Test @Test
void testOdfFromHdfs() throws IOException { void testOdfFromHdfs() throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_from_hdfs.xml")); final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_from_hdfs.xml"));

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@ -0,0 +1,70 @@
<?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:xsi="http://www.w3.org/2001/XMLSchema-instance">
<header xmlns="http://namespace.openaire.eu/">
<dri:objIdentifier>jairo_______::000012e58ed836576ef2a0d38b0f726f</dri:objIdentifier>
<dri:recordIdentifier>oai:irdb.nii.ac.jp:01221:0000010198</dri:recordIdentifier>
<dri:dateOfCollection/>
<dri:mdFormat/>
<dri:mdFormatInterpretation/>
<dri:repositoryId/>
<dr:objectIdentifier/>
<dr:dateOfCollection>2021-05-10T11:31:09.424Z</dr:dateOfCollection>
<dr:dateOfTransformation>2021-06-03T01:45:42.536Z</dr:dateOfTransformation>
<oaf:datasourceprefix>jairo_______</oaf:datasourceprefix>
</header>
<metadata xmlns="http://namespace.openaire.eu/">
<dc:title>多項式GCDを用いた復号法に関する研究</dc:title>
<dc:creator>上原, 剛</dc:creator>
<dc:creator>甲斐, 博</dc:creator>
<dc:creator>野田, 松太郎</dc:creator>
<dc:format>application/pdf</dc:format>
<dc:identifier>http://hdl.handle.net/2433/25934</dc:identifier>
<dc:language>jpn</dc:language>
<dc:publisher>京都大学数理解析研究所</dc:publisher>
<dc:subject classid="ndc" classname="ndc"
schemeid="dnet:subject_classification_typologies" schemename="dnet:subject_classification_typologies">410</dc:subject>
<dc:type>Departmental Bulletin Paper</dc:type>
<dr:CobjCategory type="publication">0014</dr:CobjCategory>
<oaf:dateAccepted>2004-10-01</oaf:dateAccepted>
<oaf:projectid/>
<oaf:collectedDatasourceid>openaire____::554c7c2873</oaf:collectedDatasourceid>
<oaf:accessrights>OPEN</oaf:accessrights>
<oaf:hostedBy id="openaire____::554c7c2873" name="JAIRO"/>
<oaf:collectedFrom id="openaire____::554c7c2873" name="JAIRO"/>
<oaf:identifier identifierType="handle">2433/25934</oaf:identifier>
<oaf:identifier identifierType="ncid">AN00061013</oaf:identifier>
<oaf:identifier identifierType="LandingPage">http://hdl.handle.net/2433/25934</oaf:identifier>
<oaf:fulltext>http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/25934/1/1395-16.pdf</oaf:fulltext>
<oaf:journal ep="110" iss="" issn="1880-2818" sp="104" vol="1395">数理解析研究所講究録</oaf:journal>
</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="2021-05-10T11:31:09.424Z">
<baseURL>https%3A%2F%2Firdb.nii.ac.jp%2Foai</baseURL>
<identifier>oai:irdb.nii.ac.jp:01221:0000010198</identifier>
<datestamp>2021-04-13T13:36:29Z</datestamp>
<metadataNamespace/>
<originDescription altered="true" harvestDate="2021-04-13T13:36:29Z">
<baseURL>http://repository.kulib.kyoto-u.ac.jp/dspace-oai/request</baseURL>
<identifier>oai:repository.kulib.kyoto-u.ac.jp:2433/25934</identifier>
<datestamp>2012-07-12T14:15:41Z</datestamp>
<metadataNamespace>http://irdb.nii.ac.jp/oai</metadataNamespace>
</originDescription>
</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>

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@ -16,7 +16,6 @@ import javax.xml.transform.*;
import javax.xml.transform.dom.DOMSource; import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult; import javax.xml.transform.stream.StreamResult;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.spark.util.LongAccumulator; import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document; import org.dom4j.Document;
@ -43,6 +42,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class XmlRecordFactory implements Serializable { public class XmlRecordFactory implements Serializable {

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@ -7,8 +7,6 @@ import java.io.IOException;
import java.io.StringReader; import java.io.StringReader;
import java.util.List; import java.util.List;
import eu.dnetlib.dhp.oa.provision.utils.ContextDef;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.dom4j.Document; import org.dom4j.Document;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
@ -25,6 +23,7 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
@ -137,17 +136,18 @@ public class XmlRecordFactoryTest {
@Test @Test
public void testEnermapsRecord() throws IOException, DocumentException { public void testEnermapsRecord() throws IOException, DocumentException {
String contextmap = "<entries><entry id=\"enermaps\" label=\"Energy Research\" name=\"context\" type=\"community\"/>" + String contextmap = "<entries><entry id=\"enermaps\" label=\"Energy Research\" name=\"context\" type=\"community\"/>"
"<entry id=\"enermaps::selection\" label=\"Featured dataset\" name=\"category\"/>"+ +
"<entry id=\"enermaps::selection::tgs00004\" label=\"Dataset title\" name=\"concept\"/>"+ "<entry id=\"enermaps::selection\" label=\"Featured dataset\" name=\"category\"/>" +
"</entries>"; "<entry id=\"enermaps::selection::tgs00004\" label=\"Dataset title\" name=\"concept\"/>" +
"</entries>";
ContextMapper contextMapper = ContextMapper.fromXml(contextmap); ContextMapper contextMapper = ContextMapper.fromXml(contextmap);
XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation, XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation,
otherDsTypeId); otherDsTypeId);
Dataset d = OBJECT_MAPPER Dataset d = OBJECT_MAPPER
.readValue(IOUtils.toString(getClass().getResourceAsStream("enermaps.json")), Dataset.class); .readValue(IOUtils.toString(getClass().getResourceAsStream("enermaps.json")), Dataset.class);
JoinedEntity je = new JoinedEntity<>(d); JoinedEntity je = new JoinedEntity<>(d);

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@ -205,6 +205,11 @@
<artifactId>dateparser</artifactId> <artifactId>dateparser</artifactId>
<version>1.0.7</version> <version>1.0.7</version>
</dependency> </dependency>
<dependency>
<groupId>me.xuender</groupId>
<artifactId>unidecode</artifactId>
<version>0.0.7</version>
</dependency>
<dependency> <dependency>
<groupId>com.google.guava</groupId> <groupId>com.google.guava</groupId>