adopted functionality from current transf.system
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parent
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commit
2a47f5b560
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@ -1,19 +1,26 @@
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package eu.dnetlib.dhp.transformation.xslt;
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import java.util.List;
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import static org.hamcrest.Matchers.*;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertThat;
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import static org.mockito.Mockito.*;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.junit.jupiter.MockitoExtension;
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import org.hamcrest.CoreMatchers;
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import org.junit.After;
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import org.junit.Before;
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import org.junit.Test;
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import org.junit.runner.RunWith;
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import org.mockito.ArgumentCaptor;
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import org.mockito.Mock;
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import org.mockito.junit.MockitoJUnitRunner;
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@ExtendWith(MockitoExtension.class)
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@RunWith(MockitoJUnitRunner.class)
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public class PersonCleanerTest {
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private PersonCleaner personCleaner;
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@BeforeEach
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@Before
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public void setup() {
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this.personCleaner = new PersonCleaner();
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}
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@ -73,4 +80,35 @@ public class PersonCleanerTest {
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// TODO: assert scenario
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}
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@Test
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public void shouldGetName() {
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QName actualValue = personCleaner.getName();
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// TODO: assert scenario
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}
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@Test
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public void shouldGetResultType() {
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SequenceType actualValue = personCleaner.getResultType();
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// TODO: assert scenario
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}
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@Test
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public void shouldGetArgumentTypes() {
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SequenceType[] actualValue = personCleaner.getArgumentTypes();
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// TODO: assert scenario
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}
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@Test
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public void shouldCall() {
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// TODO: initialize args
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XdmValue[] xdmValues;
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XdmValue actualValue = personCleaner.call(xdmValues);
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// TODO: assert scenario
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}
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}
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@ -0,0 +1,282 @@
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<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.1"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns:oaf="http://namespace.openaire.eu/oaf"
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xmlns:dr="http://www.driver-repository.eu/namespace/dr"
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xmlns:TransformationFunction="eu.dnetlib.data.collective.transformation.core.xsl.ext.TransformationFunctionProxy"
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extension-element-prefixes="TransformationFunction"
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exclude-result-prefixes="TransformationFunction">
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<!--
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Metadata records contain no embracing resource element, but only a dataset element. Therefore, references to top element resource are adapted, and then namespaces are no copied into each single node. Resource added.
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-->
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<xsl:param name="varOfficialName" />
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<xsl:param name="varDsType" />
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<xsl:param name="varDataSourceId" />
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<xsl:param name="varFP7" select="'corda_______::'"/>
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<xsl:param name="varH2020" select="'corda__h2020::'"/>
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<xsl:param name="index" select="0"/>
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<xsl:variable name="tf" select="TransformationFunction:getInstance()"/>
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<xsl:template match="/">
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<xsl:variable name="datasourcePrefix"
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select="normalize-space(//oaf:datasourceprefix)" />
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<xsl:call-template name="validRecord" />
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</xsl:template>
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<xsl:template name="terminate">
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<xsl:message terminate="yes">
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record is not compliant, transformation is interrupted.
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</xsl:message>
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</xsl:template>
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<xsl:template name="validRecord">
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<record>
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<xsl:copy-of select="//*[local-name() = 'header']" />
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<metadata>
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<resource>
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<!--
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<xsl:apply-templates select="//*[local-name() = 'metadata']//*[local-name() = ('resource','dataset')]"/>
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<xsl:apply-templates select="//*[local-name() = 'metadata']"/>
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-->
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<xsl:apply-templates select="//*[local-name() = 'metadata']//*[local-name() = ('resource','dataset')]/*"/>
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<xsl:call-template name="creators" />
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<xsl:choose>
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<xsl:when test="//*[local-name() = 'datasourceprefix'][.='r3853b408a4c']">
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<xsl:copy-of copy-namespaces="no" select="//*[local-name() = 'metadata']//*[local-name() = ('resource','dataset')]/*[not(local-name()=('creators', 'alternateIdentifiers', 'relatedIdentifier'))]" />
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</xsl:when>
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<xsl:when test="//*[local-name() = 'datasourceprefix'][.='r38d07aef7b7']">
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<xsl:copy-of copy-namespaces="no" select="//*[local-name() = 'metadata']//*[local-name() = ('resource','dataset')]/*[not(local-name()=('creators', 'alternateIdentifiers', 'relatedIdentifier', 'identifier'))]" />
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</xsl:when>
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</xsl:choose>
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<xsl:call-template name="relatedIdentifiers" />
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</resource>
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<!-- OpenAIRE fields -->
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<!-- resource type, super type -->
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<xsl:choose>
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<!--
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<xsl:when test="//*[local-name()='resourceType']/@resourceTypeGeneral='Dataset' or //*[local-name()='resourceType']/@resourceTypeGeneral='Software' or //*[local-name()='resourceType']/@resourceTypeGeneral='Collection' or //*[local-name()='resourceType']/@resourceTypeGeneral='Film' or //*[local-name()='resourceType']/@resourceTypeGeneral='Sound' or //*[local-name()='resourceType']/@resourceTypeGeneral='PhysicalObject' or //*[local-name()='resourceType']/@resourceTypeGeneral='Audiovisual'">
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-->
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<xsl:when test="//*[local-name()='resourceType'][lower-case(.)='article'] or lower-case(//*[local-name()='resourceType']/@resourceTypeGeneral)=('dataset', 'software', 'collection', 'film', 'sound', 'physicalobject', 'audiovisual', 'model', 'workflow', 'service', 'image') or (//*[local-name()='resourceType'][lower-case(./@resourceTypeGeneral)='other' and lower-case(.)=('study', 'egi virtual appliance')])">
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<xsl:variable name="varCobjCategory" select="TransformationFunction:convertString($tf, distinct-values(//*[local-name()='resourceType']/@resourceTypeGeneral), 'TextTypologies')" />
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<xsl:variable name="varSuperType" select="TransformationFunction:convertString($tf, $varCobjCategory, 'SuperTypes')"/>
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<dr:CobjCategory>
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<xsl:attribute name="type" select="$varSuperType"/>
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<xsl:value-of select="$varCobjCategory" />
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</dr:CobjCategory>
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</xsl:when>
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<xsl:otherwise>
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<xsl:call-template name="terminate"/>
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</xsl:otherwise>
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</xsl:choose>
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<!-- review status -->
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<!-- no review hints found for Reactome, and kaggle collection being broken -->
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<!-- date -->
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<oaf:dateAccepted>
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<xsl:value-of select="TransformationFunction:convertString($tf, normalize-space(//*[local-name()='publicationYear']), 'DateISO8601')"/>
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</oaf:dateAccepted>
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<!-- access level, licenses -->
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<xsl:choose>
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<xsl:when test="//*[local-name() = 'rightsList']/*[local-name() = 'rights']/@rightsURI">
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<xsl:for-each select="//*[local-name() = 'rights']/@rightsURI">
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<oaf:accessrights>
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<xsl:value-of select="TransformationFunction:convertString($tf, concat('http',substring-after(., 'https')), 'AccessRights')" />
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</oaf:accessrights>
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<oaf:license>
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<xsl:value-of select="."/>
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</oaf:license>
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</xsl:for-each>
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</xsl:when>
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<xsl:otherwise>
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<oaf:accessrights>
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<xsl:value-of select="'UNKNOWN'" />
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</oaf:accessrights>
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</xsl:otherwise>
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</xsl:choose>
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<!-- language -->
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<oaf:language>
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<xsl:value-of select="TransformationFunction:convert($tf, //*[local-name()='language'], 'Languages')" />
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</oaf:language>
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<!-- hostedBy, collectedFrom -->
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<oaf:hostedBy>
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<xsl:attribute name="name">
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<xsl:value-of select="$varOfficialName"/>
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</xsl:attribute>
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<xsl:attribute name="id">
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<xsl:value-of select="$varDataSourceId"/>
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</xsl:attribute>
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</oaf:hostedBy>
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<oaf:collectedFrom>
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<xsl:attribute name="name">
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<xsl:value-of select="$varOfficialName"/>
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</xsl:attribute>
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<xsl:attribute name="id">
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<xsl:value-of select="$varDataSourceId"/>
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</xsl:attribute>
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</oaf:collectedFrom>
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</metadata>
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<xsl:copy-of select="//*[local-name() = 'about']" />
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</record>
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</xsl:template>
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<xsl:template match="node()|@*">
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<!--
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<xsl:copy copy-namespaces="no">
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<xsl:apply-templates select="node()|@*"/>
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</xsl:copy>
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-->
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</xsl:template>
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<xsl:template match="//*[local-name() = ('resource','dataset')]/*[local-name()='alternateIdentifiers']">
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<!--
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<xsl:element name="alternateIdentifiers" namespace="http://www.openarchives.org/OAI/2.0/">
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-->
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<xsl:if test="//*[local-name() = 'datasourceprefix'][.='r3853b408a4c']">
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<alternateIdentifiers>
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<!--
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<xsl:copy-of select="./*" copy-namespaces="no"/>
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-->
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<alternateIdentifier>
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<xsl:attribute name="alternateIdentifierType" select="'LandingPage'"/>
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<xsl:value-of select="concat('https://reactome.org/content/detail/', substring-after(//*[local-name() = 'recordIdentifier'], 'https://reactome.org/PathwayBrowser/#/'))" />
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</alternateIdentifier>
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</alternateIdentifiers>
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</xsl:if>
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<xsl:if test="//*[local-name() = 'datasourceprefix'][.='r38d07aef7b7']">
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<alternateIdentifiers>
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<!--
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<xsl:copy-of select="./*" copy-namespaces="no"/>
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-->
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<alternateIdentifier>
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<xsl:attribute name="alternateIdentifierType" select="'local accession id'"/>
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<xsl:value-of select="//*[local-name() = 'recordIdentifier']" />
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</alternateIdentifier>
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</alternateIdentifiers>
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<identifier>
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<xsl:attribute name="identifierType" select="'URL'"/>
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<xsl:value-of select="//*[local-name() = 'alternateIdentifiers']/*[local-name() = 'alternateIdentifier'][./@*[local-name()='alternateIdentifierType']='URL']" />
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</identifier>
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</xsl:if>
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</xsl:template>
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<!--
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<xsl:template match="//*[local-name() = ('resource','dataset')]/*[local-name()='identifier']">
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<xsl:copy-of select="." copy-namespaces="no" />
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<xsl:if test="not(//*[local-name() = ('resource','dataset')]/*[local-name()='alternateIdentifiers'])">
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<xsl:element name="alternateIdentifiers" namespace="http://www.openarchives.org/OAI/2.0/">
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</xsl:element>
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</xsl:if>
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</xsl:template>
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-->
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<!--
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<xsl:template match="//*[local-name()='language']">
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<oaf:language>
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<xsl:value-of select="TransformationFunction:convert($tf, //*[local-name()='language'], 'Languages')" />
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</oaf:language>
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</xsl:template>
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-->
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<xsl:template name="relatedIdentifiers">
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<relatedIdentifiers>
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<xsl:copy-of select="//*[local-name()='relatedIdentifier']" copy-namespaces="no"/>
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<xsl:for-each select="//*[local-name() = ('resource','dataset')]/*[local-name()='relatedIdentifier'][starts-with(.,'http://www.ncbi.nlm.nih.gov/pubmed/')]">
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<xsl:element name="relatedIdentifier">
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<xsl:attribute name="relatedIdentifierType" select="'PMID'"/>
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<xsl:attribute name="relationType" select="./@*[local-name()='relationType']"/>
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<xsl:value-of select="substring-after(., 'http://www.ncbi.nlm.nih.gov/pubmed/')" />
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</xsl:element>
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</xsl:for-each>
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</relatedIdentifiers>
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</xsl:template>
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<xsl:template name="creators">
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<xsl:choose>
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<xsl:when test="//*[local-name() = 'datasourceprefix'][.='r3853b408a4c']">
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<creators>
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<xsl:for-each select="//*[local-name() = 'creators']/*[local-name()='creator']">
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<creator>
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<xsl:choose>
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<xsl:when test="contains(./*[local-name() = 'creatorName'], ',')">
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<xsl:variable name="varContributorNameReverse" select="TransformationFunction:convertString($tf, ./*[local-name()='creatorName'], 'Person')"/>
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<xsl:variable name="varFamilyName" select="normalize-space(substring-after($varContributorNameReverse, ','))"/>
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<xsl:variable name="varGivenName" select="normalize-space(substring-before($varContributorNameReverse, ','))"/>
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<creatorName>
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<xsl:value-of select="concat($varFamilyName, ', ', $varGivenName)" />
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</creatorName>
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<givenName>
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<xsl:value-of select="$varGivenName" />
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</givenName>
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<familyName>
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<xsl:value-of select="$varFamilyName" />
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</familyName>
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</xsl:when>
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<xsl:when test="string-length(./*[local-name() = 'creatorName']) > 0 and not(contains(./*[local-name() = 'creatorName'], ','))">
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<creatorName>
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<xsl:value-of select="TransformationFunction:convertString($tf, ./*[local-name()='creatorName'], 'Person')" />
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</creatorName>
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</xsl:when>
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</xsl:choose>
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<xsl:for-each select="./*[local-name()='affiliation']">
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<affiliation>
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<xsl:value-of select="." />
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</affiliation>
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</xsl:for-each>
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</creator>
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</xsl:for-each>
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<xsl:if test="not(//*[local-name() = 'creators']/*[local-name()='creator'])">
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<xsl:call-template name="terminate"/>
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</xsl:if>
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</creators>
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</xsl:when>
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<xsl:when test="//*[local-name() = 'datasourceprefix'][.='r38d07aef7b7']">
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<creators>
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<xsl:for-each select="//*[local-name() = 'creators']/*[local-name()='creator']">
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<creator>
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<xsl:choose>
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<xsl:when test="string-length(./*[local-name() = 'creatorName']) > 0">
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<creatorName>
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<xsl:value-of select="./*[local-name()='creatorName']" />
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</creatorName>
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</xsl:when>
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</xsl:choose>
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</creator>
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</xsl:for-each>
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<!--
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<xsl:if test="not(//*[local-name() = 'creators']/*[local-name()='creator']) or //*[local-name() = 'creators']/*[local-name()='creator']/*[local-name()='creatorName'][starts-with(., 'test ') and ends-with(., ' + eval(location.hash.slice(1)), //')]">
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-->
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<xsl:if test="not(//*[local-name() = 'creators']/*[local-name()='creator'])">
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<xsl:call-template name="terminate"/>
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</xsl:if>
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<xsl:if test="//*[local-name() = 'creators']/*[local-name()='creator']/*[local-name()='creatorName'][starts-with(., 'test ') and ends-with(., ' + eval(location.hash.slice(1)), //')]">
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<xsl:call-template name="terminate"/>
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</xsl:if>
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</creators>
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</xsl:when>
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<xsl:otherwise>
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<xsl:copy-of select="//*[local-name() = ('resource','dataset')]/*[local-name()='creators']" copy-namespaces="no"/>
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</xsl:otherwise>
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</xsl:choose>
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</xsl:template>
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</xsl:stylesheet>
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