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[#17] Add mapping of measurements #37

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[#17] Add mapping of measurements #37

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0ca82fc
[#17] Map to variableMeasured. Initial version.
Aug 19, 2024
05a93ac
[#17] Changed unit measurement mapping.
Aug 20, 2024
b872a81
[#17] Extract max unit measurements for ranges.
Aug 21, 2024
66ca0a2
[#17] Simplified variableMeasured mapping.
Aug 29, 2024
1cd3634
[#17] Add mapping of SiteMeaurements.
Sep 2, 2024
638e78a
[#17] Add mapping of Biotope measurements.
Sep 2, 2024
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174 changes: 172 additions & 2 deletions transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,12 @@ exclude-result-prefixes="xsl md panxslt set">
<xsl:variable name="biostratigraphic" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:Stratigraphy/abcd:BiostratigraphicTerms/abcd:BiostratigraphicTerm/abcd:Term"></xsl:variable>
<xsl:variable name="taxon_name" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Identifications/abcd:Identification/abcd:Result/abcd:TaxonIdentified/abcd:ScientificName/abcd:FullScientificNameString"></xsl:variable>
<xsl:variable name="higher_taxon" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Identifications/abcd:Identification/abcd:Result/abcd:TaxonIdentified/abcd:HigherTaxa/abcd:HigherTaxon/abcd:HigherTaxonName"></xsl:variable>

<xsl:variable name="altitude" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:Altitude"></xsl:variable>
<xsl:variable name="biotope_measure" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:Biotope/abcd:MeasurementsOrFacts"></xsl:variable>
<xsl:variable name="depth" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:Depth"></xsl:variable>
<xsl:variable name="height" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:Height"></xsl:variable>
<xsl:variable name="site_measure" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:SiteMeasurementsOrFacts"></xsl:variable>
<xsl:variable name="unit_measure" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:MeasurementsOrFacts"></xsl:variable>



Expand Down Expand Up @@ -411,9 +416,174 @@ exclude-result-prefixes="xsl md panxslt set">
<name><xsl:value-of select="$dataset_contributors"/></name>
</contributor>
</xsl:if>

<!-- variableMeasured -->
<!-- Altitude -->
<xsl:variable name="minAltitude">
<xsl:for-each select="$altitude/abcd:MeasurementOrFactAtomised/*[(self::abcd:LowerValue or self::abcd:UpperValue) and (not(../abcd:UnitOfMeasurement) or ../abcd:UnitOfMeasurement = 'm')]">
<xsl:sort select="." data-type="number" order="ascending"/>
<xsl:if test="position() = 1"><xsl:value-of select="."/></xsl:if>
</xsl:for-each>
</xsl:variable>
<xsl:variable name="maxAltitude">
<xsl:for-each select="$altitude/abcd:MeasurementOrFactAtomised/*[(self::abcd:LowerValue or self::abcd:UpperValue) and (not(../abcd:UnitOfMeasurement) or ../abcd:UnitOfMeasurement = 'm')]">
<xsl:sort select="." data-type="number" order="descending"/>
<xsl:if test="position() = 1"><xsl:value-of select="."/></xsl:if>
</xsl:for-each>
</xsl:variable>
<variableMeasured type="PropertyValue">
<name>Elevation</name>
<propertyID>https://schema.org/elevation</propertyID>
<xsl:choose>
<xsl:when test="$minAltitude = $maxAltitude">
<value xsi:type="xs:double"><xsl:value-of select="$minAltitude"/></value>
<unitText>m</unitText>
</xsl:when>
<xsl:otherwise>
<minValue xsi:type="xs:double"><xsl:value-of select="$minAltitude"/></minValue>
<xsl:if test="$maxAltitude"><maxValue xsi:type="xs:double"><xsl:value-of select="$maxAltitude"/></maxValue></xsl:if>
<unitText>m</unitText>
</xsl:otherwise>
</xsl:choose>
</variableMeasured>

<!-- Depth -->
<xsl:variable name="minDepth">
<xsl:for-each select="$depth/abcd:MeasurementOrFactAtomised/*[(self::abcd:LowerValue or self::abcd:UpperValue) and (not(../abcd:UnitOfMeasurement) or ../abcd:UnitOfMeasurement = 'm')]">
<xsl:sort select="." data-type="number" order="ascending"/>
<xsl:if test="position() = 1"><xsl:value-of select="."/></xsl:if>
</xsl:for-each>
</xsl:variable>
<xsl:variable name="maxDepth">
<xsl:for-each select="$depth/abcd:MeasurementOrFactAtomised/*[(self::abcd:LowerValue or self::abcd:UpperValue) and (not(../abcd:UnitOfMeasurement) or ../abcd:UnitOfMeasurement = 'm')]">
<xsl:sort select="." data-type="number" order="descending"/>
<xsl:if test="position() = 1"><xsl:value-of select="."/></xsl:if>
</xsl:for-each>
</xsl:variable>
<variableMeasured type="PropertyValue">
<name>Depth</name>
<propertyID>https://schema.org/depth</propertyID>
<xsl:choose>
<xsl:when test="$minDepth = $maxDepth">
<value xsi:type="xs:double"><xsl:value-of select="$minDepth"/></value>
<unitText>m</unitText>
</xsl:when>
<xsl:otherwise>
<minValue xsi:type="xs:double"><xsl:value-of select="$minDepth"/></minValue>
<xsl:if test="$maxDepth"><maxValue xsi:type="xs:double"><xsl:value-of select="$maxDepth"/></maxValue></xsl:if>
<unitText>m</unitText>
</xsl:otherwise>
</xsl:choose>
</variableMeasured>

<!-- Biotope -->
<xsl:variable name="parameters">
<xsl:for-each select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:Biotope/abcd:MeasurementsOrFacts/abcd:MeasurementOrFact/abcd:MeasurementOrFactAtomised/abcd:Parameter[not(.=preceding::*)]">
<parameter><xsl:value-of select="."/></parameter>
</xsl:for-each>
</xsl:variable>
<xsl:for-each select="$parameters/parameter">
<test><xsl:value-of select="."/></test>
<xsl:variable name="param" select="."/>
<xsl:variable name="minValue">
<xsl:for-each select="$biotope_measure/abcd:MeasurementOrFact[abcd:MeasurementOrFactAtomised/abcd:Parameter=$param]/abcd:MeasurementOrFactAtomised/*[(self::abcd:LowerValue or self::abcd:UpperValue) and number(.)]">
<xsl:sort select="." data-type="number" order="ascending"/>
<xsl:if test="position() = 1"><xsl:value-of select="."/></xsl:if>
</xsl:for-each>
</xsl:variable>
<xsl:variable name="maxValue">
<xsl:for-each select="$biotope_measure/abcd:MeasurementOrFact[abcd:MeasurementOrFactAtomised/abcd:Parameter=$param]/abcd:MeasurementOrFactAtomised/*[(self::abcd:LowerValue or self::abcd:UpperValue) and number(.)]">
<xsl:sort select="." data-type="number" order="descending"/>
<xsl:if test="position() = 1"><xsl:value-of select="."/></xsl:if>
</xsl:for-each>
</xsl:variable>
<variableMeasured type="PropertyValue">
<name><xsl:value-of select="$param"/></name>
<xsl:choose>
<xsl:when test="$minValue = $maxValue">
<value xsi:type="xs:double"><xsl:value-of select="$minValue"/></value>
</xsl:when>
<xsl:otherwise>
<minValue xsi:type="xs:double"><xsl:value-of select="$minValue"/></minValue>
<maxValue xsi:type="xs:double"><xsl:value-of select="$maxValue"/></maxValue>
</xsl:otherwise>
</xsl:choose>
</variableMeasured>
</xsl:for-each>

<!-- Unit measurements -->
<xsl:variable name="parameters">
<xsl:for-each select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:MeasurementsOrFacts/abcd:MeasurementOrFact/abcd:MeasurementOrFactAtomised/abcd:Parameter[not(.=preceding::*)]">
<parameter><xsl:value-of select="."/></parameter>
</xsl:for-each>
</xsl:variable>
<xsl:for-each select="$parameters/parameter">
<xsl:variable name="param" select="."/>
<xsl:variable name="minValue">
<xsl:for-each select="$unit_measure/abcd:MeasurementOrFact[abcd:MeasurementOrFactAtomised/abcd:Parameter=$param]/abcd:MeasurementOrFactAtomised/*[(self::abcd:LowerValue or self::abcd:UpperValue) and number(.)]">
<xsl:sort select="." data-type="number" order="ascending"/>
<xsl:if test="position() = 1"><xsl:value-of select="."/></xsl:if>
</xsl:for-each>
</xsl:variable>
<xsl:variable name="maxValue">
<xsl:for-each select="$unit_measure/abcd:MeasurementOrFact[abcd:MeasurementOrFactAtomised/abcd:Parameter=$param]/abcd:MeasurementOrFactAtomised/*[(self::abcd:LowerValue or self::abcd:UpperValue) and number(.)]">
<xsl:sort select="." data-type="number" order="descending"/>
<xsl:if test="position() = 1"><xsl:value-of select="."/></xsl:if>
</xsl:for-each>
</xsl:variable>
<variableMeasured type="PropertyValue">
<name><xsl:value-of select="$param"/></name>
<xsl:choose>
<xsl:when test="$minValue = $maxValue">
<value xsi:type="xs:double"><xsl:value-of select="$minValue"/></value>
</xsl:when>
<xsl:otherwise>
<minValue xsi:type="xs:double"><xsl:value-of select="$minValue"/></minValue>
<maxValue xsi:type="xs:double"><xsl:value-of select="$maxValue"/></maxValue>
</xsl:otherwise>
</xsl:choose>
</variableMeasured>
</xsl:for-each>

<!-- Site measurements -->
<xsl:variable name="parameters">
<xsl:for-each select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:SiteMeasurementsOrFacts/abcd:SiteMeasurementOrFact/abcd:MeasurementOrFactAtomised/abcd:Parameter[not(.=preceding::*)]">
<parameter><xsl:value-of select="."/></parameter>
</xsl:for-each>
</xsl:variable>
<xsl:for-each select="$parameters/parameter">
<xsl:variable name="param" select="."/>
<xsl:variable name="minValue">
<xsl:for-each select="$site_measure/abcd:SiteMeasurementOrFact[abcd:MeasurementOrFactAtomised/abcd:Parameter=$param]/abcd:MeasurementOrFactAtomised/*[(self::abcd:LowerValue or self::abcd:UpperValue) and number(.)]">
<xsl:sort select="." data-type="number" order="ascending"/>
<xsl:if test="position() = 1"><xsl:value-of select="."/></xsl:if>
</xsl:for-each>
</xsl:variable>
<xsl:variable name="maxValue">
<xsl:for-each select="$site_measure/abcd:SiteMeasurementOrFact[abcd:MeasurementOrFactAtomised/abcd:Parameter=$param]/abcd:MeasurementOrFactAtomised/*[(self::abcd:LowerValue or self::abcd:UpperValue) and number(.)]">
<xsl:sort select="." data-type="number" order="descending"/>
<xsl:if test="position() = 1"><xsl:value-of select="."/></xsl:if>
</xsl:for-each>
</xsl:variable>
<variableMeasured type="PropertyValue">
<name><xsl:value-of select="$param"/></name>
<xsl:choose>
<xsl:when test="$minValue = $maxValue">
<value xsi:type="xs:double"><xsl:value-of select="$minValue"/></value>
</xsl:when>
<xsl:otherwise>
<minValue xsi:type="xs:double"><xsl:value-of select="$minValue"/></minValue>
<maxValue xsi:type="xs:double"><xsl:value-of select="$maxValue"/></maxValue>
</xsl:otherwise>
</xsl:choose>
</variableMeasured>
</xsl:for-each>

<!-- TODO:
- Gathering Agents as contributors?
- variableMeasured
- variableMeasured:
- Identify variants with multiple values in the same element (e.g. in LowerValue)
- Add examples
-->
</jsonld>
</xsl:template>
Expand Down
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