/
pmc2pubmed.xsl
1337 lines (1237 loc) · 53.8 KB
/
pmc2pubmed.xsl
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<?xml version="1.0"?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:redirect="http://www.pubmedcentral.gov/redirect"
xmlns:xalan="http://xml.apache.org/xalan" extension-element-prefixes="xalan"
exclude-result-prefixes="xlink redirect">
<!--
pmc2pubmed.xsl
=============================================================
This stylesheet transforms instances of PMC Style-compliant
JATS XML to pubmed records. It has been altered from the PMC
post-processing stylesheet for more general use.
=============================================================
2014/03/20
-->
<xsl:output method="xml" omit-xml-declaration="yes" indent="yes"
doctype-public="-//NLM//DTD PubMed//EN" doctype-system="http://www.ncbi.nlm.nih.gov/corehtml/query/static/PubMed.dtd"/>
<xsl:strip-space elements="*"/>
<xsl:preserve-space elements="p"/>
<xsl:variable name="issn" select="article/front/journal-meta/issn"/>
<xsl:variable name="doi-info"/>
<xsl:template match="/">
<ArticleSet>
<Article>
<xsl:apply-templates/>
</Article>
</ArticleSet>
</xsl:template>
<xsl:template match="article">
<xsl:variable name="ppub" select="front/article-meta/pub-date[@pub-type='ppub'] | front/article-meta/pub-date[@pub-type='collection']"/>
<xsl:variable name="epub" select="front/article-meta/pub-date[@pub-type='epub']"/>
<xsl:variable name="my-lang">
<xsl:call-template name="capitalize">
<xsl:with-param name="str">
<xsl:choose>
<xsl:when test="substring-before(@xml-lang, '-')='en'">
<xsl:value-of select="'en'"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="@xml:lang"/>
</xsl:otherwise>
</xsl:choose>
</xsl:with-param>
</xsl:call-template>
</xsl:variable>
<xsl:variable name="article-title-lang">
<xsl:call-template name="capitalize">
<xsl:with-param name="str" select="descendant::article-title/@xml:lang"/>
</xsl:call-template>
</xsl:variable>
<xsl:variable name="trans-title-lang">
<xsl:call-template name="capitalize">
<xsl:with-param name="str" select="descendant::trans-title/@xml:lang"/>
</xsl:call-template>
</xsl:variable>
<xsl:variable name="alt-title-lang">
<xsl:call-template name="capitalize">
<xsl:with-param name="str" select="descendant::alt-title/@xml:lang"/>
</xsl:call-template>
</xsl:variable>
<Journal>
<xsl:choose>
<xsl:when test="front/journal-meta/publisher/publisher-name/text()">
<xsl:apply-templates select="front/journal-meta/publisher/publisher-name"/>
</xsl:when>
<xsl:otherwise>
<PublisherName>PMC</PublisherName>
</xsl:otherwise>
</xsl:choose>
<JournalTitle>
<xsl:choose>
<xsl:when test="descendant::journal-id[@journal-id-type='nlm-ta']">
<xsl:value-of select="descendant::journal-id[@journal-id-type='nlm-ta']"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="descendant::journal-id[@journal-id-type='iso-abbrev']"/>
</xsl:otherwise>
</xsl:choose>
</JournalTitle>
<Issn>
<xsl:choose>
<xsl:when test="descendant::article-meta/pub-date[@pub-type='collection']">
<xsl:value-of select="descendant::issn[@pub-type='epub']"/>
</xsl:when>
<xsl:when test="contains(descendant::issn[@pub-type='ppub'],'-')">
<xsl:value-of select="descendant::issn[@pub-type='ppub']"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="descendant::issn[@pub-type='epub']"/>
</xsl:otherwise>
</xsl:choose>
</Issn>
<xsl:apply-templates select="front/article-meta/volume"/>
<xsl:apply-templates select="front/article-meta/issue"/>
<xsl:call-template name="PubDate"/>
</Journal>
<xsl:apply-templates select="front/article-meta/title-group"/>
<xsl:choose>
<xsl:when test="front/article-meta/elocation-id">
<xsl:choose>
<xsl:when test="starts-with(front/article-meta/elocation-id,'10.')">
<ELocationID EIdType="doi">
<xsl:value-of select="front/article-meta/elocation-id"/>
</ELocationID>
</xsl:when>
<xsl:when test="translate(front/article-meta/elocation-id,'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789','')!=''">
<ELocationID EIdType="pii">
<xsl:value-of select="front/article-meta/elocation-id"/>
</ELocationID>
</xsl:when>
<xsl:otherwise>
<FirstPage LZero="save">
<xsl:value-of select="front/article-meta/elocation-id"/>
</FirstPage>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:otherwise>
<FirstPage LZero="save">
<xsl:call-template name="stripdash">
<xsl:with-param name="str" select="front/article-meta/fpage"/>
</xsl:call-template>
</FirstPage>
<xsl:if test="front/article-meta/lpage">
<LastPage>
<xsl:call-template name="stripdash">
<xsl:with-param name="str" select="front/article-meta/lpage"/>
</xsl:call-template>
</LastPage>
</xsl:if>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="$my-lang!=$trans-title-lang or $my-lang!=$alt-title-lang or $article-title-lang!=$trans-title-lang or $article-title-lang!=$alt-title-lang">
<xsl:for-each select="descendant-or-self::node()[self::article or self::article-title or self::trans-title or self::alt-title][@xml:lang and not(contains(@xml:lang, 'en') or contains(@xml:lang, 'EN'))]">
<Language>
<xsl:call-template name="capitalize">
<xsl:with-param name="str" select="@xml:lang"/>
</xsl:call-template>
</Language>
</xsl:for-each>
<xsl:if test="descendant-or-self::node()[self::article or self::article-title or self::trans-title or self::alt-title][contains(@xml:lang, 'en') or contains(@xml:lang, 'EN')]">
<Language>EN</Language>
</xsl:if>
</xsl:when>
<xsl:when test="$my-lang!='EN'">
<Language>
<xsl:call-template name="capitalize">
<xsl:with-param name="str" select="@xml:lang"/>
</xsl:call-template>
</Language>
</xsl:when>
</xsl:choose>
<xsl:apply-templates select="front/article-meta/contrib-group"/>
<!-- publicationtype -->
<xsl:if test="@article-type='correction'">
<PublicationType>Published Erratum</PublicationType>
</xsl:if>
<xsl:if test="@article-type='retraction'">
<PublicationType>Retraction of Publication</PublicationType>
</xsl:if>
<xsl:if test="@article-type='review-article'">
<PublicationType>Review</PublicationType>
</xsl:if>
<!-- pubidlist -->
<xsl:if test="front/article-meta/article-id[@pub-id-type='doi'] or
front/article-meta/article-id[@pub-id-type='knolid']">
<ArticleIdList>
<xsl:apply-templates select="front/article-meta/article-id[@pub-id-type='doi']"/>
<xsl:apply-templates select="front/article-meta/article-id[@pub-id-type='knolid']"/>
<xsl:apply-templates select="front/article-meta/article-id[@pub-id-type='publisher-id']"/>
</ArticleIdList>
</xsl:if>
<xsl:if test="front/article-meta/history/date[@date-type='received'] |
front/article-meta/history/date[@date-type='rev-recd'] |
front/article-meta/history/date[@date-type='accepted'] |
front/article-meta/pub-date[@pub-type='collection']">
<History>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='collection']"/>
<xsl:apply-templates select="front/article-meta/history/date[@date-type='received']"/>
<xsl:apply-templates select="front/article-meta/history/date[@date-type='rev-recd']"/>
<xsl:apply-templates select="front/article-meta/history/date[@date-type='accepted']"/>
<xsl:if test="$ppub!=$epub">
<xsl:if test="front/article-meta/pub-date[@pub-type='epub']/day">
<!-- Do not process if there is no epub day -->
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']"/>
</xsl:if>
</xsl:if>
</History>
</xsl:if>
<!-- == Process abstracts == -->
<xsl:choose>
<xsl:when test="front/article-meta/abstract[contains(@xml:lang, 'en') or contains(@xml:lang, 'EN')][not(@abstract-type)]
or ($my-lang='EN' and front/article-meta/abstract[not(@xml:lang)][not(@abstract-type)])">
<xsl:apply-templates select="front/article-meta/abstract[contains(@xml:lang, 'en') or contains(@xml:lang, 'EN')][not(@abstract-type)] | front/article-meta/abstract[not(@xml:lang)][not(@abstract-type)]"/>
</xsl:when>
<xsl:when test="front/article-meta/trans-abstract[contains(@xml:lang, 'en') or contains(@xml:lang, 'EN')][not(@abstract-type)]">
<xsl:apply-templates select="front/article-meta/trans-abstract[contains(@xml:lang, 'en') or contains(@xml:lang, 'EN')][not(@abstract-type)]"/>
</xsl:when>
<xsl:when test="front/article-meta/abstract[not(attribute::abstract-type)] and $my-lang='EN'">
<xsl:apply-templates select="front/article-meta/abstract[not(@abstract-type) and not(@xml:lang)]"/>
</xsl:when>
<xsl:when test="front/article-meta/abstract[@abstract-type='short'] and $my-lang='EN'">
<xsl:apply-templates select="front/article-meta/abstract[@abstract-type='short']"/>
</xsl:when>
<xsl:when test="front/article-meta/abstract and $my-lang='EN'">
<xsl:apply-templates select="front/article-meta/abstract[not(@xml:lang)][1]"/>
</xsl:when>
<xsl:otherwise>
<xsl:if test="//related-article[@related-article-type='corrected-article']">
<Abstract>
<xsl:for-each select="//related-article[@related-article-type='corrected-article']">
<xsl:call-template name="build-cx-relart"/>
</xsl:for-each>
</Abstract>
</xsl:if>
</xsl:otherwise>
</xsl:choose>
<!-- OtherAbstract -->
<xsl:if test="($my-lang!='EN' and front/article-meta/abstract[not(@xml:lang)])
or front/article-meta/abstract[not(contains(@xml:lang, 'en') or contains(@xml:lang, 'EN'))]
or front/article-meta/trans-abstract[not(contains(@xml:lang, 'en') or contains(@xml:lang, 'EN'))]">
<xsl:apply-templates select="front/article-meta/abstract[not(contains(@xml:lang, 'en') or contains(@xml:lang, 'EN'))] | front/article-meta/trans-abstract[not(contains(@xml:lang, 'en') or contains(@xml:lang, 'EN'))]" mode="other-abstract">
<xsl:with-param name="my-lang" select="$my-lang"/>
</xsl:apply-templates>
</xsl:if>
<xsl:if test="descendant::contract-num | descendant::grant-num">
<ObjectList>
<xsl:call-template name="build-grants">
<xsl:with-param name="nodes" select="//contract-num | //grant-num"/>
</xsl:call-template>
<xsl:call-template name="find-kwd-group">
<xsl:with-param name="nodes" select="//article-meta/kwd-group"/>
<xsl:with-param name="in-OL" select="'yes'"/>
<xsl:with-param name="my-lang" select="$my-lang"/>
</xsl:call-template>
</ObjectList>
</xsl:if>
</xsl:template>
<!-- ==== Grant Templates ==== -->
<xsl:template name="build-grants">
<xsl:param name="nodes"/>
<xsl:for-each select="$nodes">
<xsl:variable name="rid" select="@rid"/>
<Object Type="grant">
<Param Name="id">
<xsl:value-of select="."/>
</Param>
<Param Name="grantor">
<xsl:call-template name="clean-grantor">
<xsl:with-param name="str" select="descendant::contract-sponsor[@id=$rid][1]/text()|
descendant::grant-sponsor[@id=$rid][1]/text()"/>
</xsl:call-template>
</Param>
</Object>
</xsl:for-each>
</xsl:template>
<xsl:template name="clean-grantor">
<xsl:param name="str"/>
<xsl:choose>
<xsl:when test="contains($str,' : ')">
<xsl:value-of select="concat('United States ',substring-after($str,' : '))"/>
</xsl:when>
<xsl:otherwise>
<!-- If no : to delineate column, assume it's UK -->
<xsl:value-of select="concat('United Kingdom ',$str)"/>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<xsl:template name="find-kwd-group">
<xsl:param name="nodes"/>
<xsl:param name="in-OL"/>
<xsl:param name="my-lang"/>
<xsl:choose>
<xsl:when test="$nodes/@xml:lang[contains(., 'en') or contains(., 'EN')]">
<xsl:choose>
<xsl:when test="$in-OL='no'">
<ObjectList>
<xsl:apply-templates select="$nodes[contains(@xml:lang, 'en') or contains(@xml:lang, 'EN')]/kwd"/>
</ObjectList>
</xsl:when>
<xsl:otherwise>
<xsl:apply-templates select="$nodes[contains(@xml:lang, 'en') or contains(@xml:lang, 'EN')]/kwd"/>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:when test="$my-lang='EN' and $nodes[not(@xml:lang)]">
<xsl:choose>
<xsl:when test="$in-OL='no'">
<ObjectList>
<xsl:apply-templates select="$nodes[not(@xml:lang)]/kwd"/>
</ObjectList>
</xsl:when>
<xsl:otherwise>
<xsl:apply-templates select="$nodes[not(@xml:lang)]/kwd"/>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
</xsl:choose>
</xsl:template>
<xsl:template match="kwd">
<Object Type="keyword">
<Param Name="value">
<xsl:apply-templates/>
</Param>
</Object>
</xsl:template>
<xsl:template match="kwd/bold | kwd/italic | kwd/sup | kwd/sub">
<xsl:apply-templates/>
</xsl:template>
<!-- ==== Correction link ==== -->
<xsl:template name="build-cx-relart">
<xsl:text>[This corrects the article </xsl:text>
<xsl:choose>
<xsl:when test="@page">
<xsl:text>on p. </xsl:text>
<xsl:value-of select="@page"/>
<xsl:text> in vol. </xsl:text>
<xsl:value-of select="@vol"/>
</xsl:when>
<xsl:when test="@ext-link-type='doi'">
<xsl:text>DOI: </xsl:text>
<xsl:value-of select="@xlink:href"/>
</xsl:when>
</xsl:choose>
<xsl:if test="@xlink:href and @ext-link-type='pubmed'">
<xsl:text>, PMID: </xsl:text>
<xsl:value-of select="@xlink:href"/>
</xsl:if>
<xsl:text>.]</xsl:text>
</xsl:template>
<!-- ==== Citation information ==== -->
<xsl:template match="publisher-name">
<PublisherName>
<xsl:value-of select="."/>
</PublisherName>
</xsl:template>
<xsl:template match="volume[not(ancestor::abstract)]">
<Volume>
<xsl:apply-templates/>
</Volume>
</xsl:template>
<xsl:template match="issue[not(ancestor::abstract)]">
<Issue>
<xsl:apply-templates/>
<xsl:if test="following-sibling::supplement">
<xsl:choose>
<xsl:when test="contains(.,'Sup') or contains(.,'sup') or contains(following-sibling::supplement,'Sup') or contains(following-sibling::supplement,'sup')">
<xsl:text> </xsl:text>
</xsl:when>
<xsl:otherwise>
<xsl:text> Suppl </xsl:text>
</xsl:otherwise>
</xsl:choose>
<xsl:value-of select="following-sibling::supplement"/>
</xsl:if>
</Issue>
</xsl:template>
<xsl:template name="PubDate">
<xsl:choose>
<xsl:when test="front/article-meta/pub-date/@pub-type='ppub' and front/article-meta/pub-date/@pub-type='epub'">
<!-- When ppub and epub both exist, write ppub as PubDate and epub in History.
PubMed loader picks up epub date from history and converts it to PubDate PubStatus="epub" -->
<PubDate PubStatus="ppublish">
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='ppub']/year"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='ppub']/month"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='ppub']/day"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='ppub']/season"/>
</PubDate>
</xsl:when>
<xsl:when test="(count(front/article-meta/pub-date[@pub-type!='pmc-release'])>1 and front/article-meta/pub-date[@pub-type='epub'] and front/article-meta/pub-date[@pub-type='collection'] and not(front/article-meta/pub-date[@pub-type='epub']/day)) or (count(front/article-meta/pub-date[@pub-type!='pmc-release'])=1 and front/article-meta/pub-date[@pub-type='epub'] and not(front/article-meta/pub-date/day))">
<!-- When only pub-date is epub and there is no day, do not write @PubStatus.
PubStatus="epublish" requires Day element which we don't have. -->
<PubDate>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/year"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/month"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/season"/>
</PubDate>
</xsl:when>
<xsl:when test="count(front/article-meta/pub-date[@pub-type!='pmc-release'][@pub-type!='epreprint'])=1 and front/article-meta/pub-date[@pub-type='epub']">
<!-- When there's only 1 pub-date and it's an epub date, send as epublish and do
not send ppublish value -->
<PubDate PubStatus="epublish">
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/year"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/month"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/day"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/season"/>
</PubDate>
</xsl:when>
<xsl:when test="count(front/article-meta/pub-date[@pub-type!='pmc-release'])>1
and front/article-meta/pub-date[@pub-type='epub'] and front/article-meta/pub-date[@pub-type='collection']">
<!-- Send collection date as ppublish in history -->
<PubDate PubStatus="epublish">
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/year"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/month"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/day"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/season"/>
</PubDate>
</xsl:when>
<xsl:when test="front/article-meta/pub-date[@pub-type='nihms-submitted'] and not(front/article-meta-pub-date[@pub-type='ppub'])
and front/article-meta/pub-date[@pub-type='epub']">
<!-- When there's an nihms-submitted date, no ppub date, but an epub date, send that without PubStatus -->
<PubDate>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/year"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/month"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub']/day"/>
</PubDate>
</xsl:when>
<xsl:when test="front/article-meta/pub-date[@pub-type='collection']">
<PubDate PubStatus="ecollection">
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='collection']/year"/>
<xsl:apply-templates
select="front/article-meta/pub-date[@pub-type='collection']/month"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='collection']/day"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='ppub']/season"/>
</PubDate>
</xsl:when>
<xsl:otherwise>
<PubDate PubStatus="ppublish">
<xsl:choose>
<xsl:when test="front/article-meta/pub-date[@pub-type='ppub']">
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='ppub']/year"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='ppub']/month"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='ppub']/day"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='ppub']/season"/>
</xsl:when>
<xsl:when test="front/article-meta/pub-date[@pub-type='epub-ppub']">
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub-ppub']/year"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub-ppub']/month"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub-ppub']/day"/>
<xsl:apply-templates select="front/article-meta/pub-date[@pub-type='epub-ppub']/season"/>
</xsl:when>
</xsl:choose>
</PubDate>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<xsl:template match="title-group">
<xsl:choose>
<xsl:when test="ancestor::article/@xml:lang='EN' or ancestor::article/@xml:lang='en'">
<ArticleTitle>
<xsl:choose>
<xsl:when test="ancestor::article/@article-type='correction'">
<xsl:choose>
<xsl:when test="starts-with(article-title,'CORRIGEND')
or starts-with(article-title,'Corrigend')
or starts-with(article-title,'CORRECTION')
or starts-with(article-title,'Correction')
or starts-with(article-title, 'ERRATA')
or starts-with(article-title, 'Errata')
or starts-with(article-title, 'ERRATUM')
or starts-with(article-title, 'Erratum')"/>
<xsl:otherwise>
<xsl:text>Erratum: </xsl:text>
</xsl:otherwise>
</xsl:choose>
<xsl:apply-templates select="article-title"/>
<xsl:if test="subtitle">
<xsl:text>: </xsl:text>
<xsl:apply-templates select="subtitle"/>
</xsl:if>
</xsl:when>
<xsl:otherwise>
<xsl:apply-templates select="article-title"/>
<xsl:if test="subtitle">
<xsl:text>: </xsl:text>
<xsl:apply-templates select="subtitle"/>
</xsl:if>
</xsl:otherwise>
</xsl:choose>
</ArticleTitle>
</xsl:when>
<xsl:otherwise>
<xsl:if test="trans-title[@xml:lang='en' or @xml:lang='EN']">
<ArticleTitle>
<xsl:apply-templates select="trans-title"/>
</ArticleTitle>
</xsl:if>
<xsl:if test="trans-title-group[@xml:lang='en' or @xml:lang='EN'] or trans-title-group/trans-title[@xml:lang='en' or @xml:lang='EN'] ">
<ArticleTitle>
<xsl:apply-templates select="trans-title-group/trans-title"/>
</ArticleTitle>
</xsl:if>
<VernacularTitle>
<xsl:apply-templates select="article-title"/>
<xsl:if test="subtitle">
<xsl:text>: </xsl:text>
<xsl:apply-templates select="subtitle"/>
</xsl:if>
</VernacularTitle>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<xsl:template match="article-title | subtitle | trans-title">
<xsl:apply-templates select="*[not(self::fnr) and not(self::xref)]|text()"/>
</xsl:template>
<!-- ==== Date Templates ==== -->
<xsl:template name="get_pubmonth">
<xsl:param name="month"/>
<Month>
<xsl:choose>
<xsl:when test="$month='1' or $month='01'">Jan</xsl:when>
<xsl:when test="$month='2' or $month='02'">Feb</xsl:when>
<xsl:when test="$month='3' or $month='03'">Mar</xsl:when>
<xsl:when test="$month='4' or $month='04'">Apr</xsl:when>
<xsl:when test="$month='5' or $month='05'">May</xsl:when>
<xsl:when test="$month='6' or $month='06'">Jun</xsl:when>
<xsl:when test="$month='7' or $month='07'">Jul</xsl:when>
<xsl:when test="$month='8' or $month='08'">Aug</xsl:when>
<xsl:when test="$month='9' or $month='09'">Sept</xsl:when>
<xsl:when test="$month='10'">Oct</xsl:when>
<xsl:when test="$month='11'">Nov</xsl:when>
<xsl:when test="$month='12'">Dec</xsl:when>
</xsl:choose>
</Month>
</xsl:template>
<xsl:template match="date[@date-type='received']">
<xsl:if test="day">
<PubDate PubStatus="received">
<xsl:apply-templates select="year"/>
<xsl:apply-templates select="month"/>
<xsl:apply-templates select="day"/>
</PubDate>
</xsl:if>
</xsl:template>
<xsl:template match="date[@date-type='rev-recd']">
<xsl:if test="day">
<PubDate PubStatus="revised">
<xsl:apply-templates select="year"/>
<xsl:apply-templates select="month"/>
<xsl:apply-templates select="day"/>
</PubDate>
</xsl:if>
</xsl:template>
<xsl:template match="date[@date-type='accepted']">
<xsl:if test="day">
<PubDate PubStatus="accepted">
<xsl:apply-templates select="year"/>
<xsl:apply-templates select="month"/>
<xsl:apply-templates select="day"/>
</PubDate>
</xsl:if>
</xsl:template>
<xsl:template match="pub-date[@pub-type='collection']">
<PubDate PubStatus="ecollection">
<xsl:apply-templates select="year"/>
<xsl:apply-templates select="month"/>
<xsl:apply-templates select="day"/>
<xsl:apply-templates select="season"/>
</PubDate>
</xsl:template>
<xsl:template match="pub-date[@pub-type='epub']">
<PubDate PubStatus="epublish">
<xsl:apply-templates select="year"/>
<xsl:apply-templates select="month"/>
<xsl:apply-templates select="day"/>
</PubDate>
</xsl:template>
<xsl:template match="year">
<Year>
<xsl:apply-templates/>
</Year>
</xsl:template>
<xsl:template match="day">
<Day>
<xsl:apply-templates/>
</Day>
</xsl:template>
<xsl:template match="month">
<Month>
<xsl:apply-templates/>
</Month>
</xsl:template>
<xsl:template match="season">
<Season>
<xsl:apply-templates/>
</Season>
</xsl:template>
<!-- ==== Contrib templates ==== -->
<xsl:template match="contrib-group[1]">
<AuthorList>
<xsl:for-each select="contrib[not(attribute::contrib-type='editor')]">
<xsl:apply-templates select=".">
<xsl:with-param name="position" select="position()"/>
</xsl:apply-templates>
</xsl:for-each>
<!-- grab authors from other contrib groups in article-meta -->
<xsl:for-each select="following-sibling::contrib-group/contrib[not(attribute::contrib-type='editor')]">
<xsl:apply-templates select=".">
<xsl:with-param name="position" select="position()"/>
</xsl:apply-templates>
</xsl:for-each>
</AuthorList>
<xsl:if test="contrib/collab/contrib-group">
<GroupList>
<xsl:for-each select="contrib/collab[contrib-group]">
<Group>
<GroupName>
<xsl:apply-templates select="text()"/>
</GroupName>
<xsl:for-each select="contrib-group/contrib">
<IndividualName>
<xsl:apply-templates select="name/given-names"/>
<xsl:apply-templates select="name/surname"/>
<xsl:apply-templates select="name/suffix"/>
<xsl:apply-templates select="aff[1]" mode="group-list"/>
</IndividualName>
</xsl:for-each>
</Group>
</xsl:for-each>
</GroupList>
</xsl:if>
</xsl:template>
<xsl:template match="contrib-group[position()!=1]"/>
<xsl:template match="contrib[not(attribute::contrib-type='editor')]">
<xsl:param name="position"/>
<xsl:variable name="clean-fname" select="normalize-space(name/given-names)"/>
<xsl:variable name="fname" select="substring($clean-fname,2,1)"/>
<xsl:variable name="ftest">
<xsl:call-template name="capitalize">
<xsl:with-param name="str" select="substring($clean-fname,2,1)"/>
</xsl:call-template>
</xsl:variable>
<xsl:variable name="refid" select="xref[@ref-type='aff'][1]/@rid"/>
<Author>
<xsl:choose>
<xsl:when test="collab">
<CollectiveName>
<xsl:apply-templates select="collab/*[not(self::contrib-group)] | collab/text()"/>
</CollectiveName>
</xsl:when>
<xsl:otherwise>
<FirstName>
<xsl:choose>
<xsl:when test="name[@name-style='given-only']">
<xsl:attribute name="EmptyYN">
<xsl:value-of select="'Y'"/>
</xsl:attribute>
</xsl:when>
<xsl:when test="name[@content-type='index']/given-names/node()">
<xsl:choose>
<xsl:when test="name[@content-type='index']/given-names/@initials">
<xsl:choose>
<xsl:when test="string-length(name[@content-type='index']/given-names) > string-length(name[@content-type='index']/given-names/@initials)">
<xsl:value-of select="normalize-space(name[@content-type='index']/given-names)"/>
</xsl:when>
<xsl:otherwise>
<xsl:call-template name="process-initials">
<xsl:with-param name="str" select="name[@content-type='index']/given-names/@initials"/>
</xsl:call-template>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="normalize-space(name[@content-type='index']/given-names)"/>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:when test="name/given-names/node()">
<xsl:choose>
<xsl:when test="name/given-names/@initials">
<xsl:choose>
<xsl:when test="string-length(name/given-names) > string-length(name/given-names/@initials)">
<xsl:value-of select="normalize-space(name/given-names)"/>
</xsl:when>
<xsl:otherwise>
<xsl:call-template name="process-initials">
<xsl:with-param name="str" select="name/given-names/@initials"/>
</xsl:call-template>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="normalize-space(name/given-names)"/>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:otherwise>
<xsl:attribute name="EmptyYN">
<xsl:value-of select="'Y'"/>
</xsl:attribute>
</xsl:otherwise>
</xsl:choose>
</FirstName>
<LastName>
<xsl:choose>
<xsl:when test="name[@name-style='given-only']">
<xsl:value-of select="normalize-space(name/given-names)"/>
</xsl:when>
<xsl:when test="name[@content-type='index']">
<xsl:value-of select="normalize-space(name[@content-type='index']/surname)"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="normalize-space(name/surname)"/>
</xsl:otherwise>
</xsl:choose>
</LastName>
<xsl:apply-templates select="name/suffix"/>
<xsl:choose>
<xsl:when test="aff">
<xsl:choose>
<xsl:when test="count(//article-meta//aff[@id]) > 1 and xref[@ref-type='aff']">
<xsl:apply-templates select="aff[@id=$refid]"/>
</xsl:when>
<xsl:otherwise>
<xsl:apply-templates select="aff[1]"/>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:otherwise>
<xsl:choose>
<xsl:when test="count(//article-meta//aff) > 1 and xref[@ref-type='aff']">
<xsl:choose>
<xsl:when test="count(xref[@ref-type='aff']) > 1">
<xsl:choose>
<xsl:when test="ancestor::contrib-group/aff">
<Affiliation>
<xsl:for-each select="xref[@ref-type='aff']">
<xsl:variable name="my-rid" select="@rid"/>
<xsl:apply-templates select="ancestor::contrib-group/aff[@id=$my-rid]">
<xsl:with-param name="in-aff" select="'yes'"/>
</xsl:apply-templates>
<xsl:if test="following-sibling::xref[@ref-type='aff']">
<xsl:text>; </xsl:text>
</xsl:if>
</xsl:for-each>
</Affiliation>
</xsl:when>
<xsl:otherwise>
<Affiliation>
<xsl:for-each select="xref[@ref-type='aff']">
<xsl:variable name="my-rid" select="@rid"/>
<xsl:apply-templates select="ancestor::contrib-group/following-sibling::aff[@id=$my-rid]">
<xsl:with-param name="in-aff" select="'yes'"/>
</xsl:apply-templates>
<xsl:if test="following-sibling::xref[@ref-type='aff']">
<xsl:text>; </xsl:text>
</xsl:if>
</xsl:for-each>
</Affiliation>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:otherwise>
<xsl:choose>
<xsl:when test="ancestor::contrib-group/aff">
<xsl:apply-templates select="ancestor::contrib-group/aff[@id=$refid]"/>
</xsl:when>
<xsl:otherwise>
<xsl:apply-templates select="ancestor::contrib-group/following-sibling::aff[@id=$refid]"/>
</xsl:otherwise>
</xsl:choose>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:when test="following-sibling::aff">
<xsl:apply-templates select="following-sibling::aff[1]"/>
</xsl:when>
<xsl:otherwise>
<xsl:apply-templates select="ancestor::contrib-group/following-sibling::aff[1]"/>
</xsl:otherwise>
</xsl:choose>
</xsl:otherwise>
</xsl:choose>
</xsl:otherwise>
</xsl:choose>
<xsl:if test="contrib-id[@contrib-id-type='orcid']">
<Identifier Source="ORCID">
<xsl:choose>
<xsl:when test="contains(contrib-id[@contrib-id-type='orcid'], 'http://orcid.org/')">
<xsl:value-of select="substring-after(contrib-id[@contrib-id-type='orcid'],'http://orcid.org/')"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="contrib-id[@contrib-id-type='orcid']"/>
</xsl:otherwise>
</xsl:choose>
</Identifier>
</xsl:if>
</Author>
</xsl:template>
<xsl:template name="process-initials">
<xsl:param name="str"/>
<xsl:if test="$str">
<xsl:choose>
<xsl:when test="string-length($str) > 1">
<xsl:value-of select="substring($str,1,1)"/>
<xsl:text> </xsl:text>
<xsl:call-template name="process-initials">
<xsl:with-param name="str" select="substring($str,2)"/>
</xsl:call-template>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="$str"/>
</xsl:otherwise>
</xsl:choose>
</xsl:if>
</xsl:template>
<xsl:template match="given-names">
<xsl:choose>
<xsl:when test="contains(normalize-space(.),' ')">
<FirstName>
<xsl:value-of select="substring-before(normalize-space(.),' ')"/>
</FirstName>
<MiddleName>
<xsl:call-template name="nodot">
<xsl:with-param name="str" select="substring-after(normalize-space(.),' ')"/>
</xsl:call-template>
</MiddleName>
</xsl:when>
<xsl:otherwise>
<FirstName>
<xsl:value-of select="normalize-space(.)"/>
</FirstName>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<xsl:template match="surname[not(ancestor::abstract)]">
<LastName>
<xsl:value-of select="normalize-space(.)"/>
</LastName>
</xsl:template>
<xsl:template match="suffix">
<Suffix>
<xsl:apply-templates/>
</Suffix>
</xsl:template>
<xsl:template match="aff">
<xsl:param name="insr"/>
<xsl:param name="in-aff"/>
<xsl:choose>
<!-- Affiliation element already written in contrib match -->
<xsl:when test="$in-aff='yes'">
<xsl:choose>
<xsl:when test="count(label) > 1 and label[1]=$insr">
<xsl:call-template name="fix-aff-punct">
<xsl:with-param name="str" select="normalize-space(text()[1])"/>
</xsl:call-template>
</xsl:when>
<xsl:when test="count(sup) > 1 and sup[1]=$insr">
<xsl:call-template name="fix-aff-punct">
<xsl:with-param name="str" select="normalize-space(text()[1])"/>
</xsl:call-template>
</xsl:when>
<xsl:otherwise>
<xsl:for-each select="*[not(self::label) and not(self::sup) and not(self::bold)]|text()">
<xsl:apply-templates select="self::node()"/>
<xsl:text> </xsl:text>
</xsl:for-each>
</xsl:otherwise>
</xsl:choose>
</xsl:when>
<xsl:otherwise>
<Affiliation>
<xsl:choose>
<xsl:when test="count(label) > 1 and label[1]=$insr">
<xsl:call-template name="fix-aff-punct">
<xsl:with-param name="str" select="normalize-space(text()[1])"/>
</xsl:call-template>
</xsl:when>
<xsl:when test="count(sup) > 1 and sup[1]=$insr">
<xsl:call-template name="fix-aff-punct">
<xsl:with-param name="str" select="normalize-space(text()[1])"/>
</xsl:call-template>
</xsl:when>
<xsl:otherwise>
<xsl:for-each select="*[not(self::label) and not(self::sup) and not(self::bold)]|text()">
<xsl:apply-templates select="self::node()"/>
<xsl:text> </xsl:text>
</xsl:for-each>
</xsl:otherwise>
</xsl:choose>
</Affiliation>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<xsl:template match="aff" mode="group-list">
<!-- only 1 aff allowed, combine if multiple -->
<Affiliation>
<xsl:apply-templates/>
<xsl:for-each select="following-sibling::aff">
<xsl:text>; </xsl:text>
<xsl:apply-templates/>
</xsl:for-each>
</Affiliation>
</xsl:template>
<xsl:template name="fix-aff-punct">
<xsl:param name="str"/>
<xsl:variable name="charcount" select="string-length($str)"/>
<xsl:variable name="lastchar" select="substring($str,$charcount,1)"/>
<xsl:choose>
<xsl:when test="$lastchar = ':' or $lastchar = ';' or $lastchar = ','">
<xsl:value-of select="substring($str,1,$charcount - 1)"/>
<xsl:text>.</xsl:text>
</xsl:when>
<xsl:when test="$lastchar = '.' or $lastchar = '!' or $lastchar = '?'">
<xsl:value-of select="$str"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="$str"/>
<xsl:text>.</xsl:text>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<!-- ==== Article front templates ==== -->
<xsl:template match="xref[@ref-type='fn']"/>
<xsl:template match="article-id[@pub-id-type='doi']">
<ArticleId IdType="doi">
<xsl:apply-templates/>
</ArticleId>
</xsl:template>
<xsl:template match="article-id[@pub-id-type='knolid']">
<ArticleId IdType="pii">
<xsl:value-of select="substring-after(.,'http://knol.google.com/')"/>
</ArticleId>
</xsl:template>
<xsl:template match="article-id[@pub-id-type='publisher-id']">
<ArticleId IdType="pii">
<xsl:apply-templates/>
</ArticleId>
</xsl:template>
<xsl:template match="abstract | trans-abstract">
<Abstract>
<xsl:choose>
<xsl:when test="sec[not(title='Electronic supplementary material') and not(title='Images') and normalize-space(title)] and p">
<AbstractText Label="">
<xsl:apply-templates select="p"/>
</AbstractText>
<xsl:apply-templates select="sec"/>
</xsl:when>
<xsl:otherwise>
<xsl:apply-templates/>
</xsl:otherwise>
</xsl:choose>
<xsl:if test="//related-article[@related-article-type='corrected-article']">
<xsl:choose>