Skip to content

Commit

Permalink
[#17] Map to variableMeasured. Initial version.
Browse files Browse the repository at this point in the history
  • Loading branch information
mernst committed Aug 19, 2024
1 parent e33e81a commit 0ca82fc
Show file tree
Hide file tree
Showing 2 changed files with 248 additions and 3 deletions.
169 changes: 167 additions & 2 deletions transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
View file
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 +416,169 @@ 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:for-each select="$biotope_measure/abcd:MeasurementOrFact[not(.=preceding::*)]">
<variableMeasured type="PropertyValue">
<xsl:if test="./abcd:MeasurementOrFactText">
<name><xsl:value-of select="./abcd:MeasurementOrFactText"/></name>
</xsl:if>
<xsl:if test="./abcd:MeasurementOrFactAtomised">
<xsl:if test="./abcd:MeasurementOrFactAtomised/abcd:Parameter">
<name><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:Parameter"/></name>
</xsl:if>
<xsl:if test="./abcd:MeasurementOrFactAtomised/abcd:Method">
<measurementTechnique><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:Method"/></measurementTechnique>
</xsl:if>
<xsl:choose>
<xsl:when test="(./abcd:MeasurementOrFactAtomised/abcd:UpperValue) and not(./abcd:MeasurementOrFactAtomised/abcd:LowerValue = ./abcd:MeasurementOrFactAtomised/abcd:UpperValue)">
<maxValue xsi:type="xs:double"><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:UpperValue"/></maxValue>
<minValue xsi:type="xs:double"><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:LowerValue"/></minValue>
</xsl:when>
<xsl:otherwise>
<value xsi:type="xs:double"><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:LowerValue"/></value>
</xsl:otherwise>
</xsl:choose>
<xsl:if test="./abcd:MeasurementOrFactAtomised/abcd:UnitOfMeasurement">
<unitText><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:UnitOfMeasurement"/></unitText>
</xsl:if>
</xsl:if>
</variableMeasured>
</xsl:for-each>

<!-- Unit measurements -->
<xsl:for-each select="$unit_measure/abcd:MeasurementOrFact[not(.=preceding::*)]">
<variableMeasured type="PropertyValue">
<xsl:if test="./abcd:MeasurementOrFactText">
<name><xsl:value-of select="./abcd:MeasurementOrFactText"/></name>
</xsl:if>
<xsl:if test="./abcd:MeasurementOrFactAtomised">
<xsl:if test="./abcd:MeasurementOrFactAtomised/abcd:Parameter">
<name><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:Parameter"/></name>
</xsl:if>
<xsl:if test="./abcd:MeasurementOrFactAtomised/abcd:Method">
<measurementTechnique><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:Method"/></measurementTechnique>
</xsl:if>
<xsl:choose>
<xsl:when test="(./abcd:MeasurementOrFactAtomised/abcd:UpperValue) and not(./abcd:MeasurementOrFactAtomised/abcd:LowerValue = ./abcd:MeasurementOrFactAtomised/abcd:UpperValue)">
<maxValue xsi:type="xs:double"><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:UpperValue"/></maxValue>
<minValue xsi:type="xs:double"><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:LowerValue"/></minValue>
</xsl:when>
<xsl:otherwise>
<!-- TODO: Check if LowerValue is a number -->
<xsl:choose>
<xsl:when test="number(./abcd:MeasurementOrFactAtomised/abcd:LowerValue)">
<value xsi:type="xs:double"><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:LowerValue"/></value>
</xsl:when>
<xsl:otherwise>
<!-- TODO: extract numbers from string. If there are multiple numbers, add multiple value elements -->
<xsl:for-each select="for $n in tokenize(./abcd:MeasurementOrFactAtomised/abcd:LowerValue, '[^0-9]+' )[.] return xs:double($n)">
<value xsi:type="xs:double"><xsl:value-of select="."/></value>
</xsl:for-each>
</xsl:otherwise>
</xsl:choose>
</xsl:otherwise>
</xsl:choose>
<xsl:if test="./abcd:MeasurementOrFactAtomised/abcd:UnitOfMeasurement">
<unitText><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:UnitOfMeasurement"/></unitText>
</xsl:if>
</xsl:if>
</variableMeasured>
</xsl:for-each>

<!-- Site measurements -->
<xsl:for-each select="$site_measure/abcd:SiteMeasurementOrFact[not(.=preceding::*)]">
<variableMeasured type="PropertyValue">
<xsl:if test="./abcd:MeasurementOrFactText">
<name><xsl:value-of select="./abcd:MeasurementOrFactText"/></name>
</xsl:if>
<xsl:if test="./abcd:MeasurementOrFactAtomised">
<xsl:if test="./abcd:MeasurementOrFactAtomised/abcd:Parameter">
<name><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:Parameter"/></name>
</xsl:if>
<xsl:if test="./abcd:MeasurementOrFactAtomised/abcd:Method">
<measurementTechnique><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:Method"/></measurementTechnique>
</xsl:if>
<xsl:choose>
<xsl:when test="(./abcd:MeasurementOrFactAtomised/abcd:UpperValue) and not(./abcd:MeasurementOrFactAtomised/abcd:LowerValue = ./abcd:MeasurementOrFactAtomised/abcd:UpperValue)">
<maxValue xsi:type="xs:double"><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:UpperValue"/></maxValue>
<minValue xsi:type="xs:double"><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:LowerValue"/></minValue>
</xsl:when>
<xsl:otherwise>
<value xsi:type="xs:double"><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:LowerValue"/></value>
</xsl:otherwise>
</xsl:choose>
<xsl:if test="./abcd:MeasurementOrFactAtomised/abcd:UnitOfMeasurement">
<unitText><xsl:value-of select="./abcd:MeasurementOrFactAtomised/abcd:UnitOfMeasurement"/></unitText>
</xsl:if>
</xsl:if>
</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
82 changes: 81 additions & 1 deletion transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -100,6 +100,11 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<Altitude>
<MeasurementOrFactAtomised>
<LowerValue>1250</LowerValue>
</MeasurementOrFactAtomised>
</Altitude>
</Gathering>
<MeasurementsOrFacts>
<MeasurementOrFact>
Expand Down Expand Up @@ -166,6 +171,11 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<Altitude>
<MeasurementOrFactAtomised>
<LowerValue>950</LowerValue>
</MeasurementOrFactAtomised>
</Altitude>
</Gathering>
<RecordURI>https://data-rebind.bgbm.org/gfbio/biocase/page/B/HoffmannPlants/4</RecordURI>
</Unit>
Expand Down Expand Up @@ -224,6 +234,13 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<Altitude>
<MeasurementOrFactAtomised>
<LowerValue>2500</LowerValue>
<UpperValue>2900</UpperValue>
<UnitOfMeasurement>m</UnitOfMeasurement>
</MeasurementOrFactAtomised>
</Altitude>
</Gathering>
<MeasurementsOrFacts>
<MeasurementOrFact>
Expand Down Expand Up @@ -290,6 +307,11 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<Altitude>
<MeasurementOrFactAtomised>
<LowerValue>2600</LowerValue>
</MeasurementOrFactAtomised>
</Altitude>
</Gathering>
<MeasurementsOrFacts>
<MeasurementOrFact>
Expand Down Expand Up @@ -356,6 +378,11 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<Altitude>
<MeasurementOrFactAtomised>
<LowerValue>200</LowerValue>
</MeasurementOrFactAtomised>
</Altitude>
</Gathering>
<MeasurementsOrFacts>
<MeasurementOrFact>
Expand Down Expand Up @@ -422,6 +449,11 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<Altitude>
<MeasurementOrFactAtomised>
<LowerValue>300</LowerValue>
</MeasurementOrFactAtomised>
</Altitude>
</Gathering>
<MeasurementsOrFacts>
<MeasurementOrFact>
Expand Down Expand Up @@ -554,6 +586,11 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<Depth>
<MeasurementOrFactAtomised>
<LowerValue>0.5</LowerValue>
</MeasurementOrFactAtomised>
</Depth>
</Gathering>
<MeasurementsOrFacts>
<MeasurementOrFact>
Expand Down Expand Up @@ -620,6 +657,12 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<Depth>
<MeasurementOrFactAtomised>
<LowerValue>1.2</LowerValue>
<UpperValue>1.5</UpperValue>
</MeasurementOrFactAtomised>
</Depth>
</Gathering>
<RecordURI>https://data-rebind.bgbm.org/gfbio/biocase/page/B/HoffmannPlants/26</RecordURI>
</Unit>
Expand Down Expand Up @@ -1266,6 +1309,14 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<SiteMeasurementsOrFacts>
<SiteMeasurementOrFact>
<MeasurementOrFactAtomised>
<Parameter>Temperature</Parameter>
<LowerValue>20</LowerValue>
</MeasurementOrFactAtomised>
</SiteMeasurementOrFact>
</SiteMeasurementsOrFacts>
</Gathering>
<MeasurementsOrFacts>
<MeasurementOrFact>
Expand Down Expand Up @@ -1332,6 +1383,14 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<SiteMeasurementsOrFacts>
<SiteMeasurementOrFact>
<MeasurementOrFactAtomised>
<Parameter>Temperature</Parameter>
<LowerValue>20</LowerValue>
</MeasurementOrFactAtomised>
</SiteMeasurementOrFact>
</SiteMeasurementsOrFacts>
</Gathering>
<MeasurementsOrFacts>
<MeasurementOrFact>
Expand Down Expand Up @@ -1464,6 +1523,16 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<Biotope>
<MeasurementsOrFacts>
<MeasurementOrFact>
<MeasurementOrFactAtomised>
<Parameter>Salinity</Parameter>
<LowerValue>0.1</LowerValue>
</MeasurementOrFactAtomised>
</MeasurementOrFact>
</MeasurementsOrFacts>
</Biotope>
</Gathering>
<MeasurementsOrFacts>
<MeasurementOrFact>
Expand Down Expand Up @@ -1530,6 +1599,17 @@
<Name> Uganda</Name>
<ISO3166Code>UG </ISO3166Code>
</Country>
<Biotope>
<MeasurementsOrFacts>
<MeasurementOrFact>
<MeasurementOrFactAtomised>
<Parameter>Vegetation Height</Parameter>
<LowerValue>10</LowerValue>
<UnitOfMeasurement>cm</UnitOfMeasurement>
</MeasurementOrFactAtomised>
</MeasurementOrFact>
</MeasurementsOrFacts>
</Biotope>
</Gathering>
<RecordURI>https://data-rebind.bgbm.org/gfbio/biocase/page/B/HoffmannPlants/113</RecordURI>
</Unit>
Expand Down Expand Up @@ -2181,7 +2261,7 @@
<MeasurementOrFact>
<MeasurementOrFactAtomised>
<Method>height of plant or bush in cm</Method>
<LowerValue>34--64</LowerValue>
<LowerValue>0.01--1064</LowerValue>
</MeasurementOrFactAtomised>
</MeasurementOrFact>
</MeasurementsOrFacts>
Expand Down

0 comments on commit 0ca82fc

Please sign in to comment.