htsworkflow/templates/sra.rdfxml.xsl

   1 <?xml version="1.0"?>
   2 <xsl:stylesheet version="1.0"
   3                 xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
   4                 xmlns:xs="http://www.w3.org/2001/XMLSchema#"
   5                 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   6                 xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
   7                 xmlns:submission="http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#"
   8                 xmlns:sra="http://www.ncbi.nlm.nih.gov/sra"
   9                 xmlns:sras="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-3/SRA.package.xsd#"
  10                 xmlns:sraa="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-3/SRA.attribute#"
  11                 >
  12
  13 <xsl:output method="xml" indent="yes"/>
  14
  15 <xsl:template match="/">
  16   <rdf:RDF xmlns:ddf="http://encodesubmit.ucsc.edu/pipeline/download_ddf#"
  17            xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
  18            xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
  19            xmlns:submission="http://jumpgate.caltech.edu/wiki/UcscSubmissionOntology#"
  20            xmlns:pipeline="http://encodesubmit.ucsc.edu/pipeline/"
  21            xmlns:sra="http://www.ncbi.nlm.nih.gov/sra"
  22            xmlns:sras="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-3/SRA.package.xsd#"
  23            xmlns:sraa="http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-3/SRA.attribute#"
  24 >
  25     <xsl:apply-templates select="*"/>
  26   </rdf:RDF>
  27 </xsl:template>
  28
  29 <xsl:template match="EXPERIMENT_PACKAGE">
  30   <xsl:apply-templates select="./EXPERIMENT"/>
  31   <!-- xsl:for-each select="./EXPERIMENT/EXPERIMENT_ATTRIBUTES/EXPERIMENT_ATTRIBUTE">
  32     <xsl:call-template name="node_detail"/>
  33   </xsl:for-each -->
  34   <xsl:apply-templates select="./SUBMISSION"/>
  35   <xsl:apply-templates select="./STUDY"/>
  36   <xsl:apply-templates select="./SAMPLE"/>
  37   <!-- xsl:for-each select="./SAMPLE/SAMPLE_ATTRIBUTES/SAMPLE_ATTRIBUTE">
  38     <xsl:call-template name="node_detail"/>
  39   </xsl:for-each -->
  40   <xsl:apply-templates select="./RUN_SET"/>
  41 </xsl:template>
  42
  43 <xsl:template match="EXPERIMENT">
  44   <sras:experiment>
  45     <xsl:attribute name="rdf:about">http://www.ncbi.nlm.nih.gov/sra/<xsl:value-of select="@accession"/></xsl:attribute>
  46     <sras:experiment_alias><xsl:value-of select="@alias"/></sras:experiment_alias>
  47     <sras:center_name><xsl:value-of select="@center_name"/></sras:center_name>
  48     <xsl:apply-templates select="STUDY_REF"/>
  49     <xsl:apply-templates select="DESIGN"/>
  50     <xsl:apply-templates select="PLATFORM"/>
  51     <xsl:for-each select="./EXPERIMENT_ATTRIBUTES/EXPERIMENT_ATTRIBUTE">
  52       <xsl:call-template name="node_simple"/>
  53     </xsl:for-each>
  54     <sras:submission>
  55       <xsl:attribute name="rdf:resource">http://www.ncbi.nlm.nih.gov/sra/<xsl:value-of select="../SUBMISSION/@accession"/></xsl:attribute>
  56     </sras:submission>
  57   </sras:experiment>
  58 </xsl:template>
  59
  60 <xsl:template match="STUDY_REF">
  61   <sras:study>
  62     <xsl:attribute name="rdf:resource">http://www.ncbi.nlm.nih.gov/sra/<xsl:value-of select="@accession"/></xsl:attribute>
  63   </sras:study>
  64 </xsl:template>
  65
  66 <xsl:template match="DESIGN">
  67   <xsl:apply-templates select="SAMPLE_DESCRIPTOR"/>
  68   <xsl:apply-templates select="LIBRARY_DESCRIPTOR"/>
  69 </xsl:template>
  70
  71 <xsl:template match="SAMPLE_DESCRIPTOR">
  72   <sras:sample>
  73     <xsl:attribute name="rdf:resource">http://www.ncbi.nlm.nih.gov/sra/<xsl:value-of select="@accession"/></xsl:attribute>
  74   </sras:sample>
  75 </xsl:template>
  76
  77 <xsl:template match="LIBRARY_DESCRIPTOR">
  78   <sras:library_name><xsl:value-of select="LIBRARY_NAME"/></sras:library_name>
  79   <sras:library_strategy><xsl:value-of select="LIBRARY_STRATEGY"/></sras:library_strategy>
  80   <sras:library_source><xsl:value-of select="LIBRARY_SOURCE"/></sras:library_source>
  81   <sras:library_selection><xsl:value-of select="LIBRARY_SELECTION"/></sras:library_selection>
  82   <sras:library_protocol>
  83     <xsl:attribute name="rdf:resource">http:<xsl:value-of select="substring-after(LIBRARY_CONSTRUCTION_PROTOCOL, 'http')"/></xsl:attribute></sras:library_protocol>
  84 </xsl:template>
  85
  86 <xsl:template match="PLATFORM">
  87   <sras:instrument_model><xsl:value-of select="ILLUMINA/INSTRUMENT_MODEL"/></sras:instrument_model>
  88   <sras:sequence_length rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal"><xsl:value-of select="ILLUMINA/SEQUENCE_LENGTH"/></sras:sequence_length>
  89 </xsl:template>
  90
  91 <!-- xsl:template select="EXPERIMENT" mode="ref" -->
  92 <xsl:template name="node_ref">
  93   <sras:has_attribute>
  94     <xsl:attribute rdf:name="rdf:nodeID"><xsl:value-of select="generate-id(node())"/></xsl:attribute>
  95   </sras:has_attribute>
  96 </xsl:template>
  97
  98 <!-- xsl:template name="attribute" mode="nodedetail" -->
  99 <xsl:template name="node_detail">
 100   <sras:attribute>
 101     <xsl:attribute rdf:name="rdf:nodeID"><xsl:value-of select="generate-id(node())"/></xsl:attribute>
 102     <sras:attribute_name><xsl:value-of select="TAG"/></sras:attribute_name>
 103   </sras:attribute>
 104   <sras:attribute>
 105     <xsl:attribute rdf:name="rdf:nodeID"><xsl:value-of select="generate-id(node())"/></xsl:attribute>
 106     <sras:attribute_value><xsl:value-of select="VALUE"/></sras:attribute_value>
 107   </sras:attribute>
 108 </xsl:template>
 109
 110 <!-- try to generate attributes with non blank nodes -->
 111 <xsl:template name="node_simple">
 112   <xsl:variable name="spacelessTag">
 113     <xsl:call-template name="string-replace-all">
 114       <xsl:with-param name="text" select="TAG" />
 115       <xsl:with-param name="replace" select="' '" />
 116       <xsl:with-param name="by" select="'_'" />
 117     </xsl:call-template>
 118   </xsl:variable>
 119   <xsl:element name="sraa:{$spacelessTag}"><xsl:value-of select="VALUE"/></xsl:element>
 120 </xsl:template>
 121
 122 <!-- SUBMISSION TOP LEVEL -->
 123 <xsl:template match="SUBMISSION">
 124   <sras:submission>
 125     <xsl:attribute name="rdf:about">http://www.ncbi.nlm.nih.gov/sra/<xsl:value-of select="@accession"/></xsl:attribute>
 126     <sras:alias><xsl:value-of select="@alias"/></sras:alias>
 127     <sras:comment><xsl:value-of select="@submission_comment"/></sras:comment>
 128     <sras:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime"><xsl:value-of select="@submission_date"/></sras:date>
 129     <sras:lab_name><xsl:value-of select="@lab_name"/></sras:lab_name>
 130     <sras:accession><xsl:value-of select="@accession"/></sras:accession>
 131   </sras:submission>
 132 </xsl:template>
 133
 134 <xsl:template match="STUDY">
 135   <sras:study>
 136     <xsl:attribute name="rdf:about">http://www.ncbi.nlm.nih.gov/sra/<xsl:value-of select="@accession"/></xsl:attribute>
 137     <sras:study_alias><xsl:value-of select="@alias"/></sras:study_alias>
 138     <sras:title><xsl:value-of select="DESCRIPTOR/STUDY_TITLE"/></sras:title>
 139     <sras:description><xsl:value-of select="normalize-space(DESCRIPTOR/STUDY_DESCRIPTION)"/></sras:description>
 140   </sras:study>
 141 </xsl:template>
 142
 143 <xsl:template match="SAMPLE">
 144   <sras:sample>
 145     <xsl:attribute name="rdf:about">http://www.ncbi.nlm.nih.gov/sra/<xsl:value-of select="@accession"/></xsl:attribute>
 146     <sras:sample_alias><xsl:value-of select="@alias"/></sras:sample_alias>
 147     <sras:common_name><xsl:value-of select="SAMPLE_NAME/COMMON_NAME"/></sras:common_name>
 148     <sras:description><xsl:value-of select="DESCRIPTION"/></sras:description>
 149     <xsl:for-each select="./SAMPLE_ATTRIBUTES/SAMPLE_ATTRIBUTE">
 150       <xsl:call-template name="node_simple"/>
 151     </xsl:for-each>
 152   </sras:sample>
 153 </xsl:template>
 154 <xsl:template match="RUN_SET">
 155 </xsl:template>
 156
 157 <!-- from http://geekswithblogs.net/Erik/archive/2008/04/01/120915.aspx -->
 158 <xsl:template name="string-replace-all">
 159     <xsl:param name="text" />
 160     <xsl:param name="replace" />
 161     <xsl:param name="by" />
 162     <xsl:choose>
 163       <xsl:when test="contains($text, $replace)">
 164         <xsl:value-of select="substring-before($text,$replace)" />
 165         <xsl:value-of select="$by" />
 166         <xsl:call-template name="string-replace-all">
 167           <xsl:with-param name="text"
 168           select="substring-after($text,$replace)" />
 169           <xsl:with-param name="replace" select="$replace" />
 170           <xsl:with-param name="by" select="$by" />
 171         </xsl:call-template>
 172       </xsl:when>
 173       <xsl:otherwise>
 174         <xsl:value-of select="$text" />
 175       </xsl:otherwise>
 176     </xsl:choose>
 177   </xsl:template>
 178
 179 </xsl:stylesheet>