Merge branch 'fct_project_id_replacement' of https://code-repo.d4science.org/D-Net/dnet-hadoop into fct_project_id_replacement

2021-07-30 10:13:56 +02:00 · 2021-07-30 10:13:56 +02:00 · 081fe92a21
parent 576693d782 5f7330d407
commit 081fe92a21
8 changed files with 160 additions and 61 deletions
--- a/dhp-common/pom.xml
+++ b/dhp-common/pom.xml
@ -25,6 +25,11 @@
 			<groupId>com.github.sisyphsu</groupId>
 			<artifactId>dateparser</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>me.xuender</groupId>
+			<artifactId>unidecode</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>org.apache.spark</groupId>
 			<artifactId>spark-core_2.11</artifactId>
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
@ -7,22 +7,19 @@ import java.time.format.DateTimeFormatter;
 import java.time.format.DateTimeParseException;
 import java.util.*;
 import java.util.function.Function;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;

 import org.apache.commons.lang3.StringUtils;
-import org.jetbrains.annotations.NotNull;

 import com.github.sisyphsu.dateparser.DateParserUtils;
 import com.google.common.collect.Lists;
-import com.google.common.collect.Maps;
 import com.google.common.collect.Sets;

 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
+import me.xuender.unidecode.Unidecode;

 public class GraphCleaningFunctions extends CleaningFunctions {

@ -194,11 +191,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 							.filter(Objects::nonNull)
 							.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
 							.filter(
-								sp -> sp
-									.getValue()
-									.toLowerCase()
-									.replaceAll(TITLE_FILTER_REGEX, "")
-									.length() > TITLE_FILTER_RESIDUAL_LENGTH)
+								sp -> {
+									final String title = sp
+										.getValue()
+										.toLowerCase();
+									final String residual = Unidecode
+										.decode(title)
+										.replaceAll(TITLE_FILTER_REGEX, "");
+									return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH;
+								})
 							.map(GraphCleaningFunctions::cleanValue)
 							.collect(Collectors.toList()));
 			}
--- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
+++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
@ -4,12 +4,8 @@ package eu.dnetlib.dhp.schema.oaf.utils;
 import static org.junit.jupiter.api.Assertions.*;

 import java.io.IOException;
-import java.time.LocalDate;
-import java.time.format.DateTimeFormatter;
 import java.util.HashSet;
 import java.util.List;
-import java.util.Locale;
-import java.util.Optional;
 import java.util.stream.Collectors;

 import org.apache.commons.io.IOUtils;
@ -19,13 +15,32 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;

 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 {

 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
 		.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
 	public void testDateValidation() {

--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
@ -1,13 +1,15 @@

 package eu.dnetlib.dhp.oa.graph.raw;

-import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
-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;
+import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.cleanup;
+import static eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions.fixVocabularyNames;
+import static org.junit.jupiter.api.Assertions.*;
+import static org.mockito.Mockito.lenient;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Optional;
+
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.junit.jupiter.api.BeforeEach;
@ -16,12 +18,14 @@ import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;

-import java.io.IOException;
-import java.util.List;
-import java.util.Optional;
+import com.fasterxml.jackson.databind.ObjectMapper;

-import static org.junit.jupiter.api.Assertions.*;
-import static org.mockito.Mockito.lenient;
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+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)
 public class MappersTest {
@ -340,7 +344,7 @@ public class MappersTest {
 		assertEquals(2, p.getOriginalId().size());

 		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());
 		assertTrue(p.getAuthor().size() > 0);
@ -557,31 +561,6 @@ public class MappersTest {
 		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
 	void testClaimFromCrossref() throws IOException {
 		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());
 	}

+	@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
 	void testOdfFromHdfs() throws IOException {
 		final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_from_hdfs.xml"));
--- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_jairo.xml
@ -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>
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
@ -16,7 +16,6 @@ import javax.xml.transform.*;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;

-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.util.LongAccumulator;
 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.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;

 public class XmlRecordFactory implements Serializable {

--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
@ -7,8 +7,6 @@ import java.io.IOException;
 import java.io.StringReader;
 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.dom4j.Document;
 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.utils.ContextMapper;
 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.Publication;
 import eu.dnetlib.dhp.schema.oaf.Relation;
@ -137,17 +136,18 @@ public class XmlRecordFactoryTest {
 	@Test
 	public void testEnermapsRecord() throws IOException, DocumentException {

-		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\"/>"+
-				"</entries>";
+		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\"/>" +
+			"</entries>";

 		ContextMapper contextMapper = ContextMapper.fromXml(contextmap);
 		XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, XmlConverterJob.schemaLocation,
-				otherDsTypeId);
+			otherDsTypeId);

 		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);

--- a/pom.xml
+++ b/pom.xml
@ -205,6 +205,11 @@
 				<artifactId>dateparser</artifactId>
 				<version>1.0.7</version>
 			</dependency>
+			<dependency>
+				<groupId>me.xuender</groupId>
+				<artifactId>unidecode</artifactId>
+				<version>0.0.7</version>
+			</dependency>

 			<dependency>
 				<groupId>com.google.guava</groupId>