Revision 55116
Added by Alessia Bardi over 4 years ago
| modules/dnet-openaireplus-profiles/trunk/src/main/resources/eu/dnetlib/test/profiles/TransformationRuleDSResources/TransformationRuleDSResourceType/xslt_cleaning_ORP-biotools.xml | ||
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<SCRIPT> |
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<TITLE>xslt_cleaning_ORP-biotools</TITLE> |
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<CODE><![CDATA[ |
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<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="2.0" |
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xmlns:oaf="http://namespace.openaire.eu/oaf" xmlns:xs="http://www.w3.org/2001/XMLSchema" |
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xmlns:dr="http://www.driver-repository.eu/namespace/dr" |
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xmlns:datacite="http://datacite.org/schema/kernel-4" xmlns:functx="http://www.functx.com" |
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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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<xsl:function xmlns:functx="http://www.functx.com" name="functx:value-intersect" as="xs:anyAtomicType*"> |
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<xsl:param name="arg1" as="xs:anyAtomicType*"/> |
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<xsl:param name="arg2" as="xs:anyAtomicType*"/> |
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<xsl:sequence select=" distinct-values($arg1[.=$arg2]) "/> |
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</xsl:function> |
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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="index" select="0"/> |
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<xsl:param name="transDate" select="current-dateTime()"/> |
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<xsl:variable name="tf" select="TransformationFunction:getInstance()"/> |
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<!-- TODO: ADD HERE THE LIST OF AUTHORS' EMAILS--> |
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<xsl:variable name="elixirGRAuthorMails" select="()"/> |
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<xsl:template match="/"> |
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<xsl:variable name="datasourcePrefix" 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"> record is not compliant, transformation is interrupted. |
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<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:oaf="http://namespace.openaire.eu/oaf" xmlns:datacite="http://datacite.org/schema/kernel-4" xmlns:functx="http://www.functx.com" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:TransformationFunction="eu.dnetlib.data.collective.transformation.core.xsl.ext.TransformationFunctionProxy" xmlns:dr="http://www.driver-repository.eu/namespace/dr" exclude-result-prefixes="TransformationFunction" extension-element-prefixes="TransformationFunction" version="2.0"> |
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<xsl:function as="xs:anyAtomicType*" name="functx:value-intersect"> |
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<xsl:param as="xs:anyAtomicType*" name="arg1"/> |
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<xsl:param as="xs:anyAtomicType*" name="arg2"/> |
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<xsl:sequence select=" distinct-values($arg1[.=$arg2]) "/> |
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</xsl:function> |
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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="index" select="0"/> |
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<xsl:param name="transDate" select="current-dateTime()"/> |
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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" 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"> 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:apply-templates select="//*[local-name() = 'header']"/> |
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<metadata> |
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<!-- |
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</xsl:template> |
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<xsl:template name="validRecord"> |
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<record> |
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<xsl:apply-templates select="//*[local-name() = 'header']"/> |
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<metadata><!-- |
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<xsl:apply-templates select="//*[local-name() = 'metadata']//*[local-name() = 'list']"/> |
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--> |
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<datacite:resource> |
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<datacite:resourceType> |
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<xsl:attribute name="resourceTypeGeneral" select="'Software'"/> |
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<xsl:value-of select="//*[local-name() = 'toolType']"/> |
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</datacite:resourceType> |
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<xsl:for-each select="//*[local-name() = 'language']"> |
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<datacite:format> |
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<xsl:value-of select="."/> |
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</datacite:format> |
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</xsl:for-each> |
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<!-- DOE CODE does not state languages; projects/funding: funders not known to OpenAIRE |
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<datacite:resource> |
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<datacite:resourceType> |
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<xsl:attribute name="resourceTypeGeneral" select="'Software'"/> |
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<xsl:value-of select="//*[local-name() = 'toolType']"/> |
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</datacite:resourceType> |
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<xsl:for-each select="//*[local-name() = 'language']"> |
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<datacite:format> |
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<xsl:value-of select="."/> |
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</datacite:format> |
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</xsl:for-each><!-- DOE CODE does not state languages; projects/funding: funders not known to OpenAIRE |
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--> |
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<datacite:publisher> |
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<xsl:value-of select="$varOfficialName"/> |
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</datacite:publisher> |
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<datacite:relatedIdentifiers> |
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<xsl:for-each |
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select="//*[local-name() = 'documentation'][not(./*[local-name() = 'type'] = ('Terms of use', 'Citation instructions', 'Contributions policy', 'Governance'))]">
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<datacite:relatedIdentifier> |
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<xsl:attribute name="relatedIdentifierType" select="'URL'"/> |
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<xsl:attribute name="relationType" select="'IsDocumentedBy'"/> |
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<xsl:value-of select="./*[local-name() = 'url']"/> |
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</datacite:relatedIdentifier> |
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</xsl:for-each> |
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<!-- paper references --> |
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<xsl:call-template name="relatedPaper"/> |
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</datacite:relatedIdentifiers> |
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<datacite:alternateIdentifiers> |
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<!-- landing page, documentation, distribution --> |
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<datacite:alternateIdentifier> |
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<xsl:attribute name="alternateIdentifierType" select="'LandingPage'"/> |
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<xsl:value-of |
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select="concat('https://bio.tools/', //*[local-name() = 'id'])"/>
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</datacite:alternateIdentifier> |
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<!-- |
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<datacite:publisher> |
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<xsl:value-of select="$varOfficialName"/> |
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</datacite:publisher> |
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<datacite:relatedIdentifiers> |
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<xsl:for-each select="//*[local-name() = 'documentation'][not(./*[local-name() = 'type'] = ('Terms of use', 'Citation instructions', 'Contributions policy', 'Governance'))]">
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<datacite:relatedIdentifier> |
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<xsl:attribute name="relatedIdentifierType" select="'URL'"/> |
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<xsl:attribute name="relationType" select="'IsDocumentedBy'"/> |
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<xsl:value-of select="./*[local-name() = 'url']"/> |
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</datacite:relatedIdentifier> |
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</xsl:for-each><!-- paper references --> |
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<xsl:call-template name="relatedPaper"/> |
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</datacite:relatedIdentifiers> |
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<datacite:alternateIdentifiers><!-- landing page, documentation, distribution --> |
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<datacite:alternateIdentifier> |
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<xsl:attribute name="alternateIdentifierType" select="'LandingPage'"/> |
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<xsl:value-of select="concat('https://bio.tools/', //*[local-name() = 'id'])"/>
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</datacite:alternateIdentifier><!-- |
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<xsl:for-each select="distinct-values((//*[local-name() = 'link'][./*[local-name() = 'type' and . = 'Repository']]/*[local-name() = 'url'], //*[local-name() = 'link'][./*[local-name() = 'url' and starts-with(., 'https://github.com/')]]/*[local-name() = 'url']/replace(., '(https://github.com/[^/]*/[^/]*)(/.*)?', '$1')))"> |
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--> |
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<xsl:for-each |
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select="distinct-values((//*[local-name() = 'link'][./*[local-name() = 'type' and . = 'Repository']]/*[local-name() = 'url'], //*[starts-with(., 'https://github.com/') and contains(., concat('/', //*[local-name() = 'id']))]/replace(., '(https://github.com/[^/]*/[^/]*)(/.*)?', '$1')))">
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<datacite:alternateIdentifier> |
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<xsl:attribute name="alternateIdentifierType" |
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select="'DistributionLocation'"/> |
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<xsl:value-of select="."/> |
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</datacite:alternateIdentifier> |
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</xsl:for-each> |
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<!-- identifier --> |
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<datacite:alternateIdentifier> |
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<xsl:attribute name="alternateIdentifierType" |
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select="'local accession id'"/> |
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<xsl:value-of select="//*[local-name() = 'id']"/> |
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</datacite:alternateIdentifier> |
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</datacite:alternateIdentifiers> |
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<datacite:identifier> |
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<xsl:attribute name="identifierType" select="'URL'"/> |
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<xsl:value-of |
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select="concat('https://bio.tools/', //*[local-name() = 'id'])"/>
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</datacite:identifier> |
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<!-- title --> |
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<datacite:titles> |
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<datacite:title> |
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<xsl:value-of |
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select="//*[local-name() = 'list']/*[local-name() = 'name']"/> |
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</datacite:title> |
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</datacite:titles> |
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<!-- version --> |
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<xsl:if |
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test="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]"> |
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<datacite:version> |
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<xsl:value-of |
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select="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]" |
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/> |
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</datacite:version> |
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</xsl:if> |
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<!-- bio.tools' credit/typeRole Developer/... is not identical with statements on GitHub ??? (Scoary) --> |
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<xsl:call-template name="authors"/> |
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<datacite:contributors> |
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<xsl:for-each |
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select="//*[local-name() = 'contact']/*[local-name() = 'name' and not(. = 'null')]"> |
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<xsl:variable name="varContributorName" |
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select="TransformationFunction:convertString($tf, ., 'Person')"/> |
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<datacite:contributor> |
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<xsl:attribute name="contributorType" select="'ContactPerson'"/> |
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<datacite:contributorName> |
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<xsl:value-of select="$varContributorName"/> |
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</datacite:contributorName> |
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<datacite:givenName> |
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<xsl:value-of |
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select="substring-after($varContributorName, ', ')"/> |
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</datacite:givenName> |
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<datacite:familyName> |
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<xsl:value-of |
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select="substring-before($varContributorName, ', ')"/> |
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</datacite:familyName> |
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</datacite:contributor> |
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</xsl:for-each> |
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</datacite:contributors> |
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<datacite:descriptions> |
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<datacite:description> |
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<xsl:attribute name="descriptionType"> |
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<xsl:value-of select="'Abstract'"/> |
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</xsl:attribute> |
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<xsl:value-of select="//*[local-name() = 'description']"/> |
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</datacite:description> |
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<!-- |
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<xsl:for-each select="distinct-values((//*[local-name() = 'link'][./*[local-name() = 'type' and . = 'Repository']]/*[local-name() = 'url'], //*[starts-with(., 'https://github.com/') and contains(., concat('/', //*[local-name() = 'id']))]/replace(., '(https://github.com/[^/]*/[^/]*)(/.*)?', '$1')))">
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<datacite:alternateIdentifier> |
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<xsl:attribute name="alternateIdentifierType" select="'DistributionLocation'"/> |
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<xsl:value-of select="."/> |
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</datacite:alternateIdentifier> |
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</xsl:for-each><!-- identifier --> |
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<datacite:alternateIdentifier> |
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<xsl:attribute name="alternateIdentifierType" select="'local accession id'"/> |
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<xsl:value-of select="//*[local-name() = 'id']"/> |
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</datacite:alternateIdentifier> |
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</datacite:alternateIdentifiers> |
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<datacite:identifier> |
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<xsl:attribute name="identifierType" select="'URL'"/> |
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<xsl:value-of select="concat('https://bio.tools/', //*[local-name() = 'id'])"/>
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</datacite:identifier><!-- title --> |
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<datacite:titles> |
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<datacite:title> |
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<xsl:value-of select="//*[local-name() = 'list']/*[local-name() = 'name']"/> |
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</datacite:title> |
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</datacite:titles><!-- version --> |
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<xsl:if test="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]"> |
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<datacite:version> |
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<xsl:value-of select="//*[local-name() = 'list']/*[local-name() = 'version'][not(. = 'null')]"/> |
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</datacite:version> |
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</xsl:if><!-- bio.tools' credit/typeRole Developer/... is not identical with statements on GitHub ??? (Scoary) --> |
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<xsl:call-template name="authors"/> |
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<datacite:contributors> |
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<xsl:for-each select="//*[local-name() = 'contact']/*[local-name() = 'name' and not(. = 'null')]"> |
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<xsl:variable name="varContributorName" select="TransformationFunction:convertString($tf, ., 'Person')"/> |
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<datacite:contributor> |
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<xsl:attribute name="contributorType" select="'ContactPerson'"/> |
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<datacite:contributorName> |
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<xsl:value-of select="$varContributorName"/> |
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</datacite:contributorName> |
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<datacite:givenName> |
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<xsl:value-of select="substring-after($varContributorName, ', ')"/> |
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</datacite:givenName> |
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<datacite:familyName> |
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<xsl:value-of select="substring-before($varContributorName, ', ')"/> |
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</datacite:familyName> |
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</datacite:contributor> |
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</xsl:for-each> |
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</datacite:contributors> |
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<datacite:descriptions> |
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<datacite:description> |
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<xsl:attribute name="descriptionType"> |
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<xsl:value-of select="'Abstract'"/> |
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</xsl:attribute> |
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<xsl:value-of select="//*[local-name() = 'description']"/> |
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</datacite:description><!-- |
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<xsl:for-each select="//*[local-name() = 'operatingSystem'], //*[local-name() = 'function']/*[local-name() = 'comment' and not(. = 'null')]"> |
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--> |
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<xsl:for-each |
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select="//*[local-name() = 'function']/*[local-name() = 'comment' and not(. = 'null')]"> |
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<datacite:description> |
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<xsl:attribute name="descriptionType" select="'Abstract'"/> |
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<xsl:value-of select="."/> |
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</datacite:description> |
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</xsl:for-each> |
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<xsl:for-each select="//*[local-name() = 'operatingSystem']"> |
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<datacite:description> |
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<xsl:attribute name="descriptionType" select="'TechnicalInfo'"/> |
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<xsl:value-of select="."/> |
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</datacite:description> |
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</xsl:for-each> |
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</datacite:descriptions> |
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<!-- subject --> |
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<!-- dropping duplicate topics - funny that this seemingly works --> |
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<datacite:subjects> |
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<xsl:for-each |
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select="//*[local-name() = 'topic'][index-of(distinct-values(//*[local-name() = 'topic']/*[local-name() = 'uri']), ./*[local-name() = 'uri'])]"> |
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<xsl:if test="."> |
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<datacite:subject> |
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<xsl:attribute name="subjectScheme" select="'EDAM Ontology'"/> |
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<xsl:attribute name="schemeURI" |
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select="'http://edamontology.org'"/> |
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<xsl:attribute name="valueURI" |
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select="./*[local-name() = 'uri']"/> |
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<xsl:value-of select="./*[local-name() = 'term']"/> |
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</datacite:subject> |
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</xsl:if> |
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</xsl:for-each> |
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</datacite:subjects> |
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</datacite:resource> |
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<!-- |
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<xsl:for-each select="//*[local-name() = 'function']/*[local-name() = 'comment' and not(. = 'null')]"> |
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<datacite:description> |
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<xsl:attribute name="descriptionType" select="'Abstract'"/> |
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<xsl:value-of select="."/> |
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</datacite:description> |
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</xsl:for-each> |
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<xsl:for-each select="//*[local-name() = 'operatingSystem']"> |
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<datacite:description> |
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<xsl:attribute name="descriptionType" select="'TechnicalInfo'"/> |
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<xsl:value-of select="."/> |
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</datacite:description> |
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</xsl:for-each> |
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</datacite:descriptions><!-- subject --><!-- dropping duplicate topics - funny that this seemingly works --> |
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<datacite:subjects> |
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<xsl:for-each select="//*[local-name() = 'topic'][index-of(distinct-values(//*[local-name() = 'topic']/*[local-name() = 'uri']), ./*[local-name() = 'uri'])]"> |
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<xsl:if test="."> |
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<datacite:subject> |
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<xsl:attribute name="subjectScheme" select="'EDAM Ontology'"/> |
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<xsl:attribute name="schemeURI" select="'http://edamontology.org'"/> |
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<xsl:attribute name="valueURI" select="./*[local-name() = 'uri']"/> |
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<xsl:value-of select="./*[local-name() = 'term']"/> |
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</datacite:subject> |
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</xsl:if> |
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</xsl:for-each> |
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</datacite:subjects> |
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</datacite:resource><!-- |
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CobjCategory, SuperType |
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--> |
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<xsl:variable name="varCobjCategory" select="'0029'"/> |
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<xsl:variable name="varSuperType" |
|
| 224 |
select="TransformationFunction:convertString($tf, $varCobjCategory, 'SuperTypes')"/> |
|
| 225 |
<dr:CobjCategory> |
|
| 226 |
<xsl:attribute name="type" select="$varSuperType"/> |
|
| 227 |
<xsl:value-of select="$varCobjCategory"/> |
|
| 228 |
</dr:CobjCategory> |
|
| 229 |
|
|
| 230 |
<!-- |
|
| 152 |
<xsl:variable name="varCobjCategory" select="'0029'"/> |
|
| 153 |
<xsl:variable name="varSuperType" select="TransformationFunction:convertString($tf, $varCobjCategory, 'SuperTypes')"/> |
|
| 154 |
<dr:CobjCategory> |
|
| 155 |
<xsl:attribute name="type" select="$varSuperType"/> |
|
| 156 |
<xsl:value-of select="$varCobjCategory"/> |
|
| 157 |
</dr:CobjCategory><!-- |
|
| 231 | 158 |
access rights, licenses |
| 232 | 159 |
--> |
| 233 |
<xsl:for-each |
|
| 234 |
select="//*[local-name() = ('license', 'accessibility') and not(. = 'null')]">
|
|
| 235 |
<oaf:accessrights> |
|
| 236 |
<xsl:variable name="varAccessRights" |
|
| 237 |
select="TransformationFunction:convertString($tf, ., 'AccessRights')"/> |
|
| 238 |
<xsl:choose> |
|
| 239 |
<xsl:when |
|
| 240 |
test="$varAccessRights = ('OPEN', 'OPEN SOURCE') and $varSuperType = 'software'">
|
|
| 241 |
<xsl:value-of select="'OPEN SOURCE'"/> |
|
| 242 |
</xsl:when> |
|
| 243 |
<xsl:otherwise> |
|
| 244 |
<xsl:value-of select="$varAccessRights"/> |
|
| 245 |
</xsl:otherwise> |
|
| 246 |
</xsl:choose> |
|
| 247 |
</oaf:accessrights> |
|
| 248 |
</xsl:for-each> |
|
| 249 |
|
|
| 250 |
<xsl:for-each select="//*[local-name() = 'license' and not(. = 'null')]"> |
|
| 251 |
<oaf:license> |
|
| 252 |
<xsl:value-of select="."/> |
|
| 253 |
</oaf:license> |
|
| 254 |
</xsl:for-each> |
|
| 255 |
|
|
| 256 |
<oaf:hostedBy> |
|
| 257 |
<xsl:attribute name="name" select="$varOfficialName"/> |
|
| 258 |
<xsl:attribute name="id" select="$varDataSourceId"/> |
|
| 259 |
</oaf:hostedBy> |
|
| 260 |
<oaf:collectedFrom> |
|
| 261 |
<xsl:attribute name="name" select="$varOfficialName"/> |
|
| 262 |
<xsl:attribute name="id" select="$varDataSourceId"/> |
|
| 263 |
</oaf:collectedFrom> |
|
| 264 |
|
|
| 265 |
<!-- |
|
| 160 |
<xsl:for-each select="//*[local-name() = ('license', 'accessibility') and not(. = 'null')]">
|
|
| 161 |
<oaf:accessrights> |
|
| 162 |
<xsl:variable name="varAccessRights" select="TransformationFunction:convertString($tf, ., 'AccessRights')"/> |
|
| 163 |
<xsl:choose> |
|
| 164 |
<xsl:when test="$varAccessRights = ('OPEN', 'OPEN SOURCE') and $varSuperType = 'software'">
|
|
| 165 |
<xsl:value-of select="'OPEN SOURCE'"/> |
|
| 166 |
</xsl:when> |
|
| 167 |
<xsl:otherwise> |
|
| 168 |
<xsl:value-of select="$varAccessRights"/> |
|
| 169 |
</xsl:otherwise> |
|
| 170 |
</xsl:choose> |
|
| 171 |
</oaf:accessrights> |
|
| 172 |
</xsl:for-each> |
|
| 173 |
<xsl:for-each select="//*[local-name() = 'license' and not(. = 'null')]"> |
|
| 174 |
<oaf:license> |
|
| 175 |
<xsl:value-of select="."/> |
|
| 176 |
</oaf:license> |
|
| 177 |
</xsl:for-each> |
|
| 178 |
<oaf:hostedBy> |
|
| 179 |
<xsl:attribute name="name" select="$varOfficialName"/> |
|
| 180 |
<xsl:attribute name="id" select="$varDataSourceId"/> |
|
| 181 |
</oaf:hostedBy> |
|
| 182 |
<oaf:collectedFrom> |
|
| 183 |
<xsl:attribute name="name" select="$varOfficialName"/> |
|
| 184 |
<xsl:attribute name="id" select="$varDataSourceId"/> |
|
| 185 |
</oaf:collectedFrom><!-- |
|
| 266 | 186 |
<oaf:identifier> |
| 267 | 187 |
<xsl:value-of select="//*[local-name() = 'id']"/> |
| 268 | 188 |
</oaf:identifier> |
| 269 | 189 |
--> |
| 270 |
|
|
| 271 |
<!-- Check for person emails and elixirNode if we can set the concept for ELIXIR-GR --> |
|
| 272 |
<xsl:variable name="authorMails" select="//credit/email"/> |
|
| 273 |
<xsl:if test="//elixirNode/text() = 'Greece' or /list/name/text() or count(functx:value-intersect($authorMails, $elixirGRAuthorMails)) > 0"> |
|
| 274 |
<oaf:concept> |
|
| 275 |
<xsl:attribute name="id" select="'elixir-gr'"/> |
|
| 276 |
</oaf:concept> |
|
| 277 |
</xsl:if> |
|
| 278 |
|
|
| 279 |
|
|
| 280 |
<!-- date --> |
|
| 281 |
<oaf:dateAccepted> |
|
| 282 |
<xsl:value-of |
|
| 283 |
select="//*[local-name() = 'additionDate']/substring-before(., 'T')"/> |
|
| 284 |
</oaf:dateAccepted> |
|
| 285 |
|
|
| 286 |
</metadata> |
|
| 287 |
<xsl:copy-of select="//*[local-name() = 'about']"/> |
|
| 288 |
</record> |
|
| 289 |
|
|
| 290 |
</xsl:template> |
|
| 291 |
|
|
| 292 |
<xsl:template match="node() | @*"> |
|
| 293 |
<xsl:copy> |
|
| 294 |
<xsl:apply-templates select="node() | @*"/> |
|
| 295 |
</xsl:copy> |
|
| 296 |
</xsl:template> |
|
| 297 |
|
|
| 298 |
<xsl:template match="//*[local-name() = 'metadata']//*[local-name() = 'resource']"> |
|
| 299 |
<xsl:copy> |
|
| 300 |
<xsl:apply-templates select="node() | @*"/> |
|
| 301 |
</xsl:copy> |
|
| 302 |
</xsl:template> |
|
| 303 |
|
|
| 304 |
<xsl:template match="//*[local-name() = 'header']"> |
|
| 305 |
<xsl:copy> |
|
| 306 |
<xsl:apply-templates select="node() | @*"/> |
|
| 307 |
<xsl:element name="dr:dateOfTransformation"> |
|
| 308 |
<xsl:value-of select="$transDate"/> |
|
| 309 |
</xsl:element> |
|
| 310 |
</xsl:copy> |
|
| 311 |
</xsl:template> |
|
| 312 |
|
|
| 313 |
<xsl:template name="authors"> |
|
| 314 |
<!-- Allowed roles : |
|
| 190 |
<xsl:variable name="elixirGRAuthorMails" select="()"/> |
|
| 191 |
<xsl:variable name="elixirGRTools" select="('FINDbase','DruGeVar','ePGA','easyFRAP','CHRONOS','DEsubs','PICKLE','ANASTASIA','BioTranslator','metaseqR','recoup','ACT','Proteosign','BioTextQuest(+)','SCENERY','MXM','PRED-TMBB2','PRED-TAT','PRED-SIGNAL','PRED-LIPO','OMPdb','GWAR','METAGEN','DIANA-mirExTra','DIANA-mirPath','DIANA-microT','microTSS','DIANA-miRGen','DIANA-LNCBase','Network Analyzer','Variant Ranker','','GWAS Training','GprotPRED','AMYL-PRED 2','SymCurv','RNEA','BUFET','BiP finder','MR-microT ','M-IOLITE','PICKLE','MESBL GC-MS metabolite peak database','3DMem-enzyme','Micro-CTvlab','g-Class','Align Paths','BPM','haplotypeAnalysisPipeline','Mutations-Meta-Analyser ','TRES','MiGA')"/>
|
|
| 192 |
<xsl:variable name="authorMails" select="//credit/email"/> |
|
| 193 |
<xsl:if test="//elixirNode/text() = 'Greece' or $elixirGRTools=/list/name/text() or count(functx:value-intersect($authorMails, $elixirGRAuthorMails)) > 0"> |
|
| 194 |
<oaf:concept> |
|
| 195 |
<xsl:attribute name="id" select="'elixir-gr'"/> |
|
| 196 |
</oaf:concept> |
|
| 197 |
</xsl:if><!-- date --> |
|
| 198 |
<oaf:dateAccepted> |
|
| 199 |
<xsl:value-of select="//*[local-name() = 'additionDate']/substring-before(., 'T')"/> |
|
| 200 |
</oaf:dateAccepted> |
|
| 201 |
</metadata> |
|
| 202 |
<xsl:copy-of select="//*[local-name() = 'about']"/> |
|
| 203 |
</record> |
|
| 204 |
</xsl:template> |
|
| 205 |
<xsl:template match="node() | @*"> |
|
| 206 |
<xsl:copy> |
|
| 207 |
<xsl:apply-templates select="node() | @*"/> |
|
| 208 |
</xsl:copy> |
|
| 209 |
</xsl:template> |
|
| 210 |
<xsl:template match="//*[local-name() = 'metadata']//*[local-name() = 'resource']"> |
|
| 211 |
<xsl:copy> |
|
| 212 |
<xsl:apply-templates select="node() | @*"/> |
|
| 213 |
</xsl:copy> |
|
| 214 |
</xsl:template> |
|
| 215 |
<xsl:template match="//*[local-name() = 'header']"> |
|
| 216 |
<xsl:copy> |
|
| 217 |
<xsl:apply-templates select="node() | @*"/> |
|
| 218 |
<xsl:element name="dr:dateOfTransformation"> |
|
| 219 |
<xsl:value-of select="$transDate"/> |
|
| 220 |
</xsl:element> |
|
| 221 |
</xsl:copy> |
|
| 222 |
</xsl:template> |
|
| 223 |
<xsl:template name="authors"><!-- Allowed roles : |
|
| 315 | 224 |
Developer |
| 316 | 225 |
Maintainer |
| 317 | 226 |
Provider |
| ... | ... | |
| 321 | 230 |
Primary contact |
| 322 | 231 |
We'll consider Developer and Primary Contact as authors. |
| 323 | 232 |
--> |
| 324 |
<xsl:choose> |
|
| 325 |
<xsl:when |
|
| 326 |
test="not(//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and (. = 'Developer' or . = 'Primary contact')]][./*[local-name() = 'name' and not(. = 'null')]])"> |
|
| 327 |
<xsl:call-template name="terminate"/> |
|
| 328 |
</xsl:when> |
|
| 329 |
<xsl:otherwise> |
|
| 330 |
<creators> |
|
| 331 |
<xsl:for-each |
|
| 332 |
select="//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and (. = 'Developer' or . = 'Primary contact')]]/*[local-name() = 'name' and not(. = 'null')]"> |
|
| 333 |
<xsl:for-each select="tokenize(., ', ')"> |
|
| 334 |
<xsl:variable name="varDeveloperName" |
|
| 335 |
select="TransformationFunction:convertString($tf, normalize-space(.), 'Person')"/> |
|
| 336 |
<creator> |
|
| 337 |
<creatorName> |
|
| 338 |
<xsl:value-of select="$varDeveloperName"/> |
|
| 339 |
</creatorName> |
|
| 340 |
<givenName> |
|
| 341 |
<xsl:value-of select="substring-after($varDeveloperName, ', ')" |
|
| 342 |
/> |
|
| 343 |
</givenName> |
|
| 344 |
<familyName> |
|
| 345 |
<xsl:value-of select="substring-before($varDeveloperName, ', ')" |
|
| 346 |
/> |
|
| 347 |
</familyName> |
|
| 348 |
<!-- TODO: change the loop so we can set the ORICD id --> |
|
| 349 |
<!--<xsl:if |
|
| 350 |
test="string-length(./*[local-name() = 'orcidId']) > 0 and ./*[local-name() = 'orcidId'] != 'null'"> |
|
| 351 |
<nameIdentifier nameIdentifierScheme="ORCID" |
|
| 352 |
schemeURI="https://orcid.org"> |
|
| 353 |
<xsl:value-of select="./*[local-name() = 'orcidId']"/> |
|
| 354 |
</nameIdentifier> |
|
| 355 |
</xsl:if> |
|
| 356 |
--> |
|
| 357 |
</creator> |
|
| 358 |
</xsl:for-each> |
|
| 359 |
</xsl:for-each> |
|
| 360 |
</creators> |
|
| 361 |
</xsl:otherwise> |
|
| 362 |
</xsl:choose> |
|
| 363 |
</xsl:template> |
|
| 364 |
|
|
| 365 |
<!-- |
|
| 233 |
<xsl:choose> |
|
| 234 |
<xsl:when test="not(//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and (. = 'Developer' or . = 'Primary contact')]][./*[local-name() = 'name' and not(. = 'null')]])"> |
|
| 235 |
<xsl:call-template name="terminate"/> |
|
| 236 |
</xsl:when> |
|
| 237 |
<xsl:otherwise> |
|
| 238 |
<creators> |
|
| 239 |
<xsl:for-each select="//*[local-name() = 'credit'][./*[local-name() = 'typeRole' and (. = 'Developer' or . = 'Primary contact')]]/*[local-name() = 'name' and not(. = 'null')]"> |
|
| 240 |
<xsl:for-each select="tokenize(., ', ')"> |
|
| 241 |
<xsl:variable name="varDeveloperName" select="TransformationFunction:convertString($tf, normalize-space(.), 'Person')"/> |
|
| 242 |
<creator> |
|
| 243 |
<creatorName> |
|
| 244 |
<xsl:value-of select="$varDeveloperName"/> |
|
| 245 |
</creatorName> |
|
| 246 |
<givenName> |
|
| 247 |
<xsl:value-of select="substring-after($varDeveloperName, ', ')"/> |
|
| 248 |
</givenName> |
|
| 249 |
<familyName> |
|
| 250 |
<xsl:value-of select="substring-before($varDeveloperName, ', ')"/> |
|
| 251 |
</familyName> |
|
| 252 |
</creator> |
|
| 253 |
</xsl:for-each> |
|
| 254 |
</xsl:for-each> |
|
| 255 |
</creators> |
|
| 256 |
</xsl:otherwise> |
|
| 257 |
</xsl:choose> |
|
| 258 |
</xsl:template><!-- |
|
| 366 | 259 |
<xsl:template match="//*[local-name() = 'DOI']"> |
| 367 | 260 |
--> |
| 368 |
<xsl:template name="relatedPaper"> |
|
| 369 |
<xsl:for-each |
|
| 370 |
select="//*[local-name() = 'publication']/*[local-name() = ('doi', 'pmid', 'pmcid') and not(. = 'null')]">
|
|
| 371 |
<xsl:element name="datacite:relatedIdentifier"> |
|
| 372 |
<xsl:attribute name="relatedIdentifierType" select="upper-case(local-name())"/> |
|
| 373 |
<xsl:attribute name="relationType"> |
|
| 374 |
<xsl:choose> |
|
| 375 |
<xsl:when test="../*[local-name() = 'type'] = 'Primary'"> |
|
| 376 |
<xsl:value-of select="'isSupplementTo'"/> |
|
| 377 |
</xsl:when> |
|
| 378 |
<xsl:when |
|
| 379 |
test="../*[local-name() = 'type'] = ('Review', 'Benchmark', 'Comparison')">
|
|
| 380 |
<xsl:value-of select="'isReviewedBy'"/> |
|
| 381 |
</xsl:when> |
|
| 382 |
<xsl:when test="../*[local-name() = 'type'] = 'Usage'"> |
|
| 383 |
<xsl:value-of select="'isReferencedBy'"/> |
|
| 384 |
</xsl:when> |
|
| 385 |
<xsl:when test="../*[local-name() = 'type'] = 'Method'"> |
|
| 386 |
<xsl:value-of select="'references'"/> |
|
| 387 |
</xsl:when> |
|
| 388 |
<xsl:otherwise> |
|
| 389 |
<xsl:value-of select="'isReferencedBy'"/> |
|
| 390 |
</xsl:otherwise> |
|
| 391 |
</xsl:choose> |
|
| 392 |
</xsl:attribute> |
|
| 393 |
<xsl:value-of select="."/> |
|
| 394 |
</xsl:element> |
|
| 395 |
</xsl:for-each> |
|
| 396 |
</xsl:template> |
|
| 397 |
|
|
| 398 |
</xsl:stylesheet> |
|
| 261 |
<xsl:template name="relatedPaper"> |
|
| 262 |
<xsl:for-each select="//*[local-name() = 'publication']/*[local-name() = ('doi', 'pmid', 'pmcid') and not(. = 'null')]">
|
|
| 263 |
<xsl:element name="datacite:relatedIdentifier"> |
|
| 264 |
<xsl:attribute name="relatedIdentifierType" select="upper-case(local-name())"/> |
|
| 265 |
<xsl:attribute name="relationType"> |
|
| 266 |
<xsl:choose> |
|
| 267 |
<xsl:when test="../*[local-name() = 'type'] = 'Primary'"> |
|
| 268 |
<xsl:value-of select="'isSupplementTo'"/> |
|
| 269 |
</xsl:when> |
|
| 270 |
<xsl:when test="../*[local-name() = 'type'] = ('Review', 'Benchmark', 'Comparison')">
|
|
| 271 |
<xsl:value-of select="'isReviewedBy'"/> |
|
| 272 |
</xsl:when> |
|
| 273 |
<xsl:when test="../*[local-name() = 'type'] = 'Usage'"> |
|
| 274 |
<xsl:value-of select="'isReferencedBy'"/> |
|
| 275 |
</xsl:when> |
|
| 276 |
<xsl:when test="../*[local-name() = 'type'] = 'Method'"> |
|
| 277 |
<xsl:value-of select="'references'"/> |
|
| 278 |
</xsl:when> |
|
| 279 |
<xsl:otherwise> |
|
| 280 |
<xsl:value-of select="'isReferencedBy'"/> |
|
| 281 |
</xsl:otherwise> |
|
| 282 |
</xsl:choose> |
|
| 283 |
</xsl:attribute> |
|
| 284 |
<xsl:value-of select="."/> |
|
| 285 |
</xsl:element> |
|
| 286 |
</xsl:for-each> |
|
| 287 |
</xsl:template> |
|
| 288 |
</xsl:stylesheet> |
|
| 399 | 289 |
]]> |
| 400 | 290 |
</CODE> |
| 401 | 291 |
</SCRIPT> |
Also available in: Unified diff
Tagging for elixir-gr based on the list of tools. Everything related to the concept has been grouped in the same section of the xslt.