From 750de031d13c22e9451513a63c9244fb75e3c986 Mon Sep 17 00:00:00 2001
From: mernst <m.ernst@bo.berlin>
Date: Wed, 24 Jul 2024 18:16:19 +0200
Subject: [PATCH 1/4] [#20] Added recordURI mapping. Updated XML.

---
 .../abcd2bioschemas/abcd2bioschemas-xml.xslt     | 16 +++++++++++++++-
 .../example_files/HoffmannPlantsV3.xml           |  2 +-
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
index f89327a..680dde1 100644
--- a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
+++ b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
@@ -33,6 +33,7 @@ exclude-result-prefixes="xsl md panxslt set">
   <xsl:variable name="scope_taxonomic" select="/abcd:DataSets/abcd:DataSet/abcd:Metadata/abcd:Scope/abcd:TaxonomicTerms/abcd:TaxonomicTerm"></xsl:variable>
   <xsl:variable name="scope_geoecological" select="/abcd:DataSets/abcd:DataSet/abcd:Metadata/abcd:Scope/abcd:GeoecologicalTerms/*[self::abcd:GeoecologicalTerm or self::abcd:GeoEcologicalTerm]"></xsl:variable>
   
+  <xsl:variable name="unit" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit"></xsl:variable>
   <xsl:variable name="recordbasis" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:RecordBasis"></xsl:variable>
   <xsl:variable name="coordinates" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:SiteCoordinateSets/abcd:SiteCoordinates/abcd:CoordinatesLatLong"></xsl:variable>
   <xsl:variable name="country" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:Country/abcd:Name"></xsl:variable>
@@ -42,7 +43,7 @@ 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="record_uri" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:RecordURI"></xsl:variable>
 
         
 
@@ -133,6 +134,19 @@ exclude-result-prefixes="xsl md panxslt set">
           </xsl:if>
         </usageInfo>
       </xsl:for-each>
+
+    <!-- for each unit check if recordURI is a HTTP URL (contains a http). If so, use it as both identifier and url. If not, use the recordURI as identifier. -->
+    <xsl:for-each select="$unit">
+      <xsl:if test="./abcd:RecordURI">
+        <about type="BioSample">
+          <xsl:variable name="record_uri" select="./abcd:RecordURI"></xsl:variable>
+          <identifier><xsl:value-of select="$record_uri"/></identifier>
+          <xsl:if test="contains($record_uri,'http')">
+            <url><xsl:value-of select="$record_uri"/></url>
+          </xsl:if>
+        </about>
+      </xsl:if>
+    </xsl:for-each>
       
     <xsl:for-each select="$country[not(.=preceding::*)]">  
       <spatialCoverage type="Country">
diff --git a/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml b/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
index a978265..07b1e61 100644
--- a/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
+++ b/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
@@ -233,7 +233,7 @@
                         </MeasurementOrFactAtomised>
                     </MeasurementOrFact>
                 </MeasurementsOrFacts>
-                <RecordURI>https://data-rebind.bgbm.org/gfbio/biocase/page/B/HoffmannPlants/6</RecordURI>
+                <RecordURI>B/HoffmannPlants/6</RecordURI>
             </Unit>
             <Unit>
                 <SourceInstitutionID>B</SourceInstitutionID>

From c66df47398d870723f26648f0afe5c64fb24ed26 Mon Sep 17 00:00:00 2001
From: mernst <m.ernst@bo.berlin>
Date: Wed, 24 Jul 2024 18:17:12 +0200
Subject: [PATCH 2/4] [#20] Removed comment.

---
 transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
index 680dde1..41400c3 100644
--- a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
+++ b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
@@ -135,7 +135,6 @@ exclude-result-prefixes="xsl md panxslt set">
         </usageInfo>
       </xsl:for-each>
 
-    <!-- for each unit check if recordURI is a HTTP URL (contains a http). If so, use it as both identifier and url. If not, use the recordURI as identifier. -->
     <xsl:for-each select="$unit">
       <xsl:if test="./abcd:RecordURI">
         <about type="BioSample">

From aca75b2bb2aecd4df6de85da15c2922a0faa0cd0 Mon Sep 17 00:00:00 2001
From: mernst <mernst@zedat.fu-berlin.de>
Date: Mon, 5 Aug 2024 11:44:29 +0200
Subject: [PATCH 3/4] [#27] Added mapping of additional IDs to BioSample

---
 .../abcd2bioschemas/abcd2bioschemas-xml.xslt      | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
index 41400c3..3705af1 100644
--- a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
+++ b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
@@ -140,6 +140,21 @@ exclude-result-prefixes="xsl md panxslt set">
         <about type="BioSample">
           <xsl:variable name="record_uri" select="./abcd:RecordURI"></xsl:variable>
           <identifier><xsl:value-of select="$record_uri"/></identifier>
+          <xsl:if test="./abcd:SourceInstitutionID">
+            <identifier><xsl:value-of select="./abcd:SourceInstitutionID"/></identifier>
+          </xsl:if>
+          <xsl:if test="./abcd:SourceID">
+            <identifier><xsl:value-of select="./abcd:SourceID"/></identifier>
+          </xsl:if>
+          <xsl:if test="./abcd:UnitID">
+            <identifier><xsl:value-of select="./abcd:UnitID"/></identifier>
+          </xsl:if>
+          <xsl:if test="./abcd:UnitIDNumeric">
+            <identifier><xsl:value-of select="./abcd:UnitIDNumeric"/></identifier>
+          </xsl:if>
+          <xsl:if test="./abcd:UnitGUID">
+            <identifier><xsl:value-of select="./abcd:UnitGUID"/></identifier>
+          </xsl:if>
           <xsl:if test="contains($record_uri,'http')">
             <url><xsl:value-of select="$record_uri"/></url>
           </xsl:if>

From 832201c73cef4c9b3fc6a1872f787d02716489d1 Mon Sep 17 00:00:00 2001
From: mernst <mernst@zedat.fu-berlin.de>
Date: Mon, 5 Aug 2024 15:25:45 +0200
Subject: [PATCH 4/4] [#29] Add collectors field no. mapping & examples

---
 transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt       | 3 +++
 .../abcd2bioschemas/example_files/HoffmannPlantsV3.xml         | 2 ++
 2 files changed, 5 insertions(+)

diff --git a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
index 3705af1..2ba57c3 100644
--- a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
+++ b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
@@ -155,6 +155,9 @@ exclude-result-prefixes="xsl md panxslt set">
           <xsl:if test="./abcd:UnitGUID">
             <identifier><xsl:value-of select="./abcd:UnitGUID"/></identifier>
           </xsl:if>
+          <xsl:if test="./abcd:CollectorsFieldNumber">
+            <identifier><xsl:value-of select="./abcd:CollectorsFieldNumber"/></identifier>
+          </xsl:if>
           <xsl:if test="contains($record_uri,'http')">
             <url><xsl:value-of select="$record_uri"/></url>
           </xsl:if>
diff --git a/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml b/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
index 07b1e61..1a95b95 100644
--- a/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
+++ b/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
@@ -437,6 +437,7 @@
                 <SourceInstitutionID>B</SourceInstitutionID>
                 <SourceID>HoffmannPlants</SourceID>
                 <UnitID>16</UnitID>
+                <CollectorsFieldNumber>160</CollectorsFieldNumber>
                 <Identifications>
                     <Identification>
                         <Result>
@@ -503,6 +504,7 @@
                 <SourceInstitutionID>B</SourceInstitutionID>
                 <SourceID>HoffmannPlants</SourceID>
                 <UnitID>17</UnitID>
+                <CollectorsFieldNumber>170</CollectorsFieldNumber>
                 <Identifications>
                     <Identification>
                         <Result>