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<?xml version="1.0" encoding="utf-8"?>
<!-- Creates macros for repeated cv, cvterm and organism elements -->
<!-- Macro IDs correspond to unique key constraints in chado db -->
<!-- UK constraints are combined using double-underscore: '__' -->
<!-- AUTHOR: Chris Mungall cjm at fruitfly dot org -->
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
version="1.0">
<xsl:output indent="yes" method="xml"/>
<!-- INDEXES -->
<!-- create an index of every element by its database unique key -->
<!-- ORGANISM INDEX -->
<xsl:key name="k-organism_id" match="//organism_id[*]" use="concat(organism/genus,'__',organism/species)"/>
<!-- DB INDEX -->
<xsl:key name="k-db_id" match="//db_id[*]" use="db/name"/>
<!-- CV INDEX -->
<xsl:key name="k-cv_id" match="//cv_id[*]" use="cv/name"/>
<!-- CVTERM-BY-TYPE_ID INDEX -->
<xsl:key name="k-type_id" match="//type_id[*]" use="concat(cvterm/cv_id/cv/name,'__',cvterm/name)"/>
<!-- UNIQUE NODESETS -->
<!-- create a unique instance of each macroifyable element -->
<!-- DISTINCT ORGANISMs -->
<xsl:variable
name="u-organism_id"
select="//organism_id[generate-id(.)=generate-id(key('k-organism_id',concat(organism/genus,'__',organism/species))[1])]"/>
<!-- DISTINCT CVTERMs (by type_id) -->
<xsl:variable
name="u-type_id"
select="//type_id[generate-id(.)=generate-id(key('k-type_id',concat(cvterm/cv_id/cv/name,'__',cvterm/name))[1])]"/>
<!-- DISTINCT CVs -->
<xsl:variable
name="u-cv_id"
select="//cv_id[generate-id(.)=generate-id(key('k-cv_id',cv/name)[1])]"/>
<!-- DISTINCT DBs -->
<xsl:variable
name="u-db_id"
select="//db_id[generate-id(.)=generate-id(key('k-db_id',db/name)[1])]"/>
<!-- ** TEMPLATES ** -->
<!-- INITIAL MATCH -->
<xsl:template match="/chado">
<chado>
<!-- insect organism macro -->
<xsl:for-each select="$u-organism_id">
<xsl:apply-templates mode="insert-macro" select="organism">
<xsl:with-param name="macro-id" select="concat(organism/genus,'__',organism/species)"/>
</xsl:apply-templates>
</xsl:for-each>
<!-- insect db macro -->
<xsl:for-each select="$u-db_id">
<xsl:apply-templates mode="insert-macro" select="db">
<xsl:with-param name="macro-id" select="concat('db__',db/name)"/>
</xsl:apply-templates>
</xsl:for-each>
<!-- insect cv macro -->
<xsl:for-each select="$u-cv_id">
<xsl:apply-templates mode="insert-macro" select="cv">
<xsl:with-param name="macro-id" select="concat('cv__',cv/name)"/>
</xsl:apply-templates>
</xsl:for-each>
<!-- insect cvterm macro -->
<xsl:for-each select="$u-type_id">
<xsl:apply-templates mode="insert-macro" select="cvterm">
<xsl:with-param name="macro-id" select="concat(cvterm/cv_id/cv/name,'__',cvterm/name)"/>
</xsl:apply-templates>
</xsl:for-each>
<!-- process everything else as normal -->
<xsl:apply-templates mode="main" select="*"/>
</chado>
</xsl:template>
<!-- INSERT MACRO DEFINITION -->
<xsl:template mode="insert-macro" match="*">
<xsl:param name="macro-id"/>
<xsl:copy>
<xsl:attribute name="id">
<xsl:value-of select="$macro-id"/>
</xsl:attribute>
<xsl:apply-templates mode="main" select="*"/>
</xsl:copy>
</xsl:template>
<!-- NORMAL PROCESSING (RECURSIVE) -->
<xsl:template mode="main" match="/ | @* | node()">
<xsl:choose>
<xsl:when test="name(.)='organism_id'">
<xsl:copy>
<xsl:value-of select="concat(organism/genus,'__',organism/species)"/>
</xsl:copy>
</xsl:when>
<xsl:when test="name(.)='type_id'">
<xsl:copy>
<xsl:value-of select="concat(cvterm/cv_id/cv/name,'__',cvterm/name)"/>
</xsl:copy>
</xsl:when>
<xsl:when test="name(.)='cv_id'">
<xsl:copy>
<xsl:value-of select="concat('cv__',cv/name)"/>
</xsl:copy>
</xsl:when>
<xsl:when test="name(.)='db_id'">
<xsl:copy>
<xsl:value-of select="concat('db__',db/name)"/>
</xsl:copy>
</xsl:when>
<xsl:otherwise>
<xsl:copy>
<xsl:apply-templates mode="main" select="@* | node()" />
</xsl:copy>
</xsl:otherwise>
</xsl:choose>
</xsl:template>
</xsl:stylesheet>
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