From cd626c00e386c835aea3febdbdfcda52540c0f6a Mon Sep 17 00:00:00 2001
From: mernst <mernst@zedat.fu-berlin.de>
Date: Mon, 5 Aug 2024 19:22:15 +0200
Subject: [PATCH 1/2] [#28] Add agent mapping and example.

---
 .../abcd2bioschemas/abcd2bioschemas-xml.xslt  | 120 +++++++++++++++++-
 .../example_files/HoffmannPlantsV3.xml        |   4 +-
 2 files changed, 121 insertions(+), 3 deletions(-)

diff --git a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
index f89327a..5f503e2 100644
--- a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
+++ b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
@@ -34,6 +34,7 @@ exclude-result-prefixes="xsl md panxslt set">
   <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="recordbasis" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:RecordBasis"></xsl:variable>
+  <xsl:variable name="gathering_agents" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:Agents/abcd:GatheringAgent"></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>
   <xsl:variable name="gathering_date" select="/abcd:DataSets/abcd:DataSet/abcd:Units/abcd:Unit/abcd:Gathering/abcd:DateTime"></xsl:variable>
@@ -411,8 +412,125 @@ exclude-result-prefixes="xsl md panxslt set">
           <name><xsl:value-of select="$dataset_contributors"/></name>
         </contributor>
       </xsl:if>
+
+      <!-- After updating to XSLT 2.0, both the code below and the author mapping code can be moved to a separate function -->
+      <xsl:for-each select="$gathering_agents[not(.=preceding::*)]">  
+        <xsl:choose>
+          <xsl:when test="./abcd:Person">
+            <contributor type="Person">
+              <!-- identifier -->
+              <xsl:if test="./abcd:URIs/*[self::abcd:URI or self::abcd:URL]">
+                <xsl:choose>        
+                  <xsl:when test="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][@preferred='true']">
+                    <xsl:attribute name="id"><xsl:value-of select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][@preferred='true'][1]"/></xsl:attribute>
+                  </xsl:when>
+                  <xsl:otherwise>
+                    <xsl:attribute name="id"><xsl:value-of select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][1]"/></xsl:attribute>
+                  </xsl:otherwise>
+                </xsl:choose>
+                <xsl:for-each select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][not(.=preceding::*)]">
+                  <identifier><xsl:value-of select="."/></identifier>
+                </xsl:for-each>
+              </xsl:if>
+              
+              <!-- name -->
+              <name><xsl:value-of select="./abcd:Person/abcd:FullName"/></name>
+              <xsl:if test="./abcd:Person/abcd:AtomisedName/abcd:InheritedName">
+                <familyName><xsl:value-of select="./abcd:Person/abcd:AtomisedName/abcd:InheritedName"/></familyName>
+              </xsl:if>
+              <xsl:if test="./abcd:Person/abcd:AtomisedName/abcd:GivenNames">
+                <givenName><xsl:value-of select="./abcd:Person/abcd:AtomisedName/abcd:GivenNames"/></givenName>
+              </xsl:if>
+              
+              <!-- email -->
+              <xsl:choose>        
+                <xsl:when test="./abcd:EmailAddresses/abcd:EmailAddress[@preferred='true']">
+                  <email><xsl:value-of select="./abcd:EmailAddresses/abcd:EmailAddress[@preferred='true'][1]"/></email>
+                </xsl:when>
+                <xsl:otherwise>
+                  <xsl:for-each select="./abcd:EmailAddresses/abcd:EmailAddress">
+                    <emai1><xsl:value-of select="."/></emai1>
+                  </xsl:for-each>
+                </xsl:otherwise>
+              </xsl:choose>
+
+              <!-- phone -->
+              <xsl:choose>        
+                <xsl:when test="./abcd:TelephoneNumbers/abcd:TelephoneNumber[@preferred='true']">
+                  <telephone><xsl:value-of select="./abcd:TelephoneNumbers/abcd:TelephoneNumber[@preferred='true'][1]/abcd:Number"/></telephone>
+                </xsl:when>
+                <xsl:otherwise>
+                  <xsl:for-each select="./abcd:TelephoneNumbers/abcd:TelephoneNumber">
+                    <telephone><xsl:value-of select="./abcd:Number"/></telephone>
+                  </xsl:for-each>
+                </xsl:otherwise>
+              </xsl:choose>
+
+              <!-- affiliation: Organization -->
+              <xsl:if test="./abcd:Organisation">
+                <affiliation type="Organization">
+                  <!-- name -->
+                  <name><xsl:value-of select="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Text"/></name>
+                  <xsl:if test="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Abbreviation">
+                    <alternateName><xsl:value-of select="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Abbreviation"/></alternateName>
+                  </xsl:if>
+                </affiliation>
+              </xsl:if>
+            </contributor>
+          </xsl:when>
+          <xsl:otherwise>
+          <!-- organisation as contributor -->
+            <contributor type="Organization">
+              <!-- identifier -->
+              <xsl:if test="./abcd:URIs/*[self::abcd:URI or self::abcd:URL]">
+                <xsl:choose>        
+                  <xsl:when test="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][@preferred='true']">
+                    <xsl:attribute name="id"><xsl:value-of select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][@preferred='true'][1]"/></xsl:attribute>
+                  </xsl:when>
+                  <xsl:otherwise>
+                    <xsl:attribute name="id"><xsl:value-of select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][1]"/></xsl:attribute>
+                  </xsl:otherwise>
+                </xsl:choose>
+                <xsl:for-each select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][not(.=preceding::*)]">
+                  <identifier><xsl:value-of select="."/></identifier>
+                </xsl:for-each>
+              </xsl:if>
+              
+              <!-- name -->
+              <name><xsl:value-of select="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Text"/></name>
+              <xsl:if test="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Abbreviation">
+                <alternateName><xsl:value-of select="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Abbreviation"/></alternateName>
+              </xsl:if>
+              
+              <!-- email -->
+              <xsl:choose>        
+                <xsl:when test="./abcd:EmailAddresses/abcd:EmailAddress[@preferred='true']">
+                  <email><xsl:value-of select="./abcd:EmailAddresses/abcd:EmailAddress[@preferred='true'][1]"/></email>
+                </xsl:when>
+                <xsl:otherwise>
+                  <xsl:for-each select="./abcd:EmailAddresses/abcd:EmailAddress">
+                    <emai1><xsl:value-of select="."/></emai1>
+                  </xsl:for-each>
+                </xsl:otherwise>
+              </xsl:choose>
+
+              <!-- phone -->
+              <xsl:choose>        
+                <xsl:when test="./abcd:TelephoneNumbers/abcd:TelephoneNumber[@preferred='true']">
+                  <telephone><xsl:value-of select="./abcd:TelephoneNumbers/abcd:TelephoneNumber[@preferred='true'][1]/abcd:Number"/></telephone>
+                </xsl:when>
+                <xsl:otherwise>
+                  <xsl:for-each select="./abcd:TelephoneNumbers/abcd:TelephoneNumber">
+                    <telephone><xsl:value-of select="./abcd:Number"/></telephone>
+                  </xsl:for-each>
+                </xsl:otherwise>
+              </xsl:choose>
+            </contributor>
+          </xsl:otherwise>
+        </xsl:choose>
+      </xsl:for-each>
+
      <!-- TODO:
-       - Gathering Agents as contributors?
        - variableMeasured
      -->
     </jsonld>
diff --git a/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml b/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
index a978265..3023032 100644
--- a/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
+++ b/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
@@ -157,7 +157,7 @@
                     <Agents>
                         <GatheringAgent>
                             <Person>
-                                <FullName>Anke Hoffmann</FullName>
+                                <FullName>Max Mustermann</FullName>
                             </Person>
                         </GatheringAgent>
                     </Agents>
@@ -215,7 +215,7 @@
                     <Agents>
                         <GatheringAgent>
                             <Person>
-                                <FullName>Anke Hoffmann</FullName>
+                                <FullName>Anna Förster</FullName>
                             </Person>
                         </GatheringAgent>
                     </Agents>

From 3600d042c922b3b88075b9c57a86dad0bf20df29 Mon Sep 17 00:00:00 2001
From: mernst <mernst@zedat.fu-berlin.de>
Date: Mon, 5 Aug 2024 20:02:20 +0200
Subject: [PATCH 2/2] [#28] Reduced mapping. Added abcd:AgentText.

---
 .../abcd2bioschemas/abcd2bioschemas-xml.xslt  | 137 +++++-------------
 .../example_files/HoffmannPlantsV3.xml        |   4 +-
 2 files changed, 37 insertions(+), 104 deletions(-)

diff --git a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
index 5f503e2..7bbe446 100644
--- a/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
+++ b/transformations/abcd2bioschemas/abcd2bioschemas-xml.xslt
@@ -416,116 +416,51 @@ exclude-result-prefixes="xsl md panxslt set">
       <!-- After updating to XSLT 2.0, both the code below and the author mapping code can be moved to a separate function -->
       <xsl:for-each select="$gathering_agents[not(.=preceding::*)]">  
         <xsl:choose>
-          <xsl:when test="./abcd:Person">
-            <contributor type="Person">
-              <!-- identifier -->
-              <xsl:if test="./abcd:URIs/*[self::abcd:URI or self::abcd:URL]">
-                <xsl:choose>        
-                  <xsl:when test="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][@preferred='true']">
-                    <xsl:attribute name="id"><xsl:value-of select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][@preferred='true'][1]"/></xsl:attribute>
-                  </xsl:when>
-                  <xsl:otherwise>
-                    <xsl:attribute name="id"><xsl:value-of select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][1]"/></xsl:attribute>
-                  </xsl:otherwise>
-                </xsl:choose>
-                <xsl:for-each select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][not(.=preceding::*)]">
-                  <identifier><xsl:value-of select="."/></identifier>
-                </xsl:for-each>
-              </xsl:if>
-              
-              <!-- name -->
-              <name><xsl:value-of select="./abcd:Person/abcd:FullName"/></name>
-              <xsl:if test="./abcd:Person/abcd:AtomisedName/abcd:InheritedName">
-                <familyName><xsl:value-of select="./abcd:Person/abcd:AtomisedName/abcd:InheritedName"/></familyName>
-              </xsl:if>
-              <xsl:if test="./abcd:Person/abcd:AtomisedName/abcd:GivenNames">
-                <givenName><xsl:value-of select="./abcd:Person/abcd:AtomisedName/abcd:GivenNames"/></givenName>
-              </xsl:if>
-              
-              <!-- email -->
-              <xsl:choose>        
-                <xsl:when test="./abcd:EmailAddresses/abcd:EmailAddress[@preferred='true']">
-                  <email><xsl:value-of select="./abcd:EmailAddresses/abcd:EmailAddress[@preferred='true'][1]"/></email>
-                </xsl:when>
-                <xsl:otherwise>
-                  <xsl:for-each select="./abcd:EmailAddresses/abcd:EmailAddress">
-                    <emai1><xsl:value-of select="."/></emai1>
-                  </xsl:for-each>
-                </xsl:otherwise>
-              </xsl:choose>
+          <xsl:when test="./abcd:Person or ./abcd:Organisation">
+            <xsl:choose>
+              <xsl:when test="./abcd:Person">
+                <contributor type="Person">
+                  
+                  <!-- name -->
+                  <name><xsl:value-of select="./abcd:Person/abcd:FullName"/></name>
+                  <xsl:if test="./abcd:Person/abcd:AtomisedName/abcd:InheritedName">
+                    <familyName><xsl:value-of select="./abcd:Person/abcd:AtomisedName/abcd:InheritedName"/></familyName>
+                  </xsl:if>
+                  <xsl:if test="./abcd:Person/abcd:AtomisedName/abcd:GivenNames">
+                    <givenName><xsl:value-of select="./abcd:Person/abcd:AtomisedName/abcd:GivenNames"/></givenName>
+                  </xsl:if>
 
-              <!-- phone -->
-              <xsl:choose>        
-                <xsl:when test="./abcd:TelephoneNumbers/abcd:TelephoneNumber[@preferred='true']">
-                  <telephone><xsl:value-of select="./abcd:TelephoneNumbers/abcd:TelephoneNumber[@preferred='true'][1]/abcd:Number"/></telephone>
-                </xsl:when>
-                <xsl:otherwise>
-                  <xsl:for-each select="./abcd:TelephoneNumbers/abcd:TelephoneNumber">
-                    <telephone><xsl:value-of select="./abcd:Number"/></telephone>
-                  </xsl:for-each>
-                </xsl:otherwise>
-              </xsl:choose>
+                  <!-- affiliation: Organization -->
+                  <xsl:if test="./abcd:Organisation">
+                    <affiliation type="Organization">
+                      <!-- name -->
+                      <name><xsl:value-of select="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Text"/></name>
+                      <xsl:if test="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Abbreviation">
+                        <alternateName><xsl:value-of select="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Abbreviation"/></alternateName>
+                      </xsl:if>
+                    </affiliation>
+                  </xsl:if>
+                </contributor>
+              </xsl:when>
 
-              <!-- affiliation: Organization -->
-              <xsl:if test="./abcd:Organisation">
-                <affiliation type="Organization">
+              <!-- organisation as contributor -->
+              <xsl:otherwise>
+                <contributor type="Organization">
                   <!-- name -->
                   <name><xsl:value-of select="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Text"/></name>
                   <xsl:if test="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Abbreviation">
                     <alternateName><xsl:value-of select="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Abbreviation"/></alternateName>
                   </xsl:if>
-                </affiliation>
-              </xsl:if>
-            </contributor>
+                </contributor>
+              </xsl:otherwise>
+            </xsl:choose>
           </xsl:when>
           <xsl:otherwise>
-          <!-- organisation as contributor -->
-            <contributor type="Organization">
-              <!-- identifier -->
-              <xsl:if test="./abcd:URIs/*[self::abcd:URI or self::abcd:URL]">
-                <xsl:choose>        
-                  <xsl:when test="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][@preferred='true']">
-                    <xsl:attribute name="id"><xsl:value-of select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][@preferred='true'][1]"/></xsl:attribute>
-                  </xsl:when>
-                  <xsl:otherwise>
-                    <xsl:attribute name="id"><xsl:value-of select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][1]"/></xsl:attribute>
-                  </xsl:otherwise>
-                </xsl:choose>
-                <xsl:for-each select="./abcd:URIs/*[self::abcd:URI or self::abcd:URL][not(.=preceding::*)]">
-                  <identifier><xsl:value-of select="."/></identifier>
-                </xsl:for-each>
-              </xsl:if>
-              
-              <!-- name -->
-              <name><xsl:value-of select="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Text"/></name>
-              <xsl:if test="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Abbreviation">
-                <alternateName><xsl:value-of select="./abcd:Organisation/abcd:Name/abcd:Representation/abcd:Abbreviation"/></alternateName>
-              </xsl:if>
-              
-              <!-- email -->
-              <xsl:choose>        
-                <xsl:when test="./abcd:EmailAddresses/abcd:EmailAddress[@preferred='true']">
-                  <email><xsl:value-of select="./abcd:EmailAddresses/abcd:EmailAddress[@preferred='true'][1]"/></email>
-                </xsl:when>
-                <xsl:otherwise>
-                  <xsl:for-each select="./abcd:EmailAddresses/abcd:EmailAddress">
-                    <emai1><xsl:value-of select="."/></emai1>
-                  </xsl:for-each>
-                </xsl:otherwise>
-              </xsl:choose>
-
-              <!-- phone -->
-              <xsl:choose>        
-                <xsl:when test="./abcd:TelephoneNumbers/abcd:TelephoneNumber[@preferred='true']">
-                  <telephone><xsl:value-of select="./abcd:TelephoneNumbers/abcd:TelephoneNumber[@preferred='true'][1]/abcd:Number"/></telephone>
-                </xsl:when>
-                <xsl:otherwise>
-                  <xsl:for-each select="./abcd:TelephoneNumbers/abcd:TelephoneNumber">
-                    <telephone><xsl:value-of select="./abcd:Number"/></telephone>
-                  </xsl:for-each>
-                </xsl:otherwise>
-              </xsl:choose>
-            </contributor>
+            <xsl:if test="./abcd:AgentText">
+              <contributor type="Thing">
+                <name><xsl:value-of select="./abcd:AgentText"/></name>
+              </contributor>
+            </xsl:if>
           </xsl:otherwise>
         </xsl:choose>
       </xsl:for-each>
diff --git a/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml b/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
index 3023032..d63c63e 100644
--- a/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
+++ b/transformations/abcd2bioschemas/example_files/HoffmannPlantsV3.xml
@@ -280,9 +280,7 @@
                     </DateTime>
                     <Agents>
                         <GatheringAgent>
-                            <Person>
-                                <FullName>Anke Hoffmann</FullName>
-                            </Person>
+                            <AgentText>Anna Förster, Arno Förster</AgentText>
                         </GatheringAgent>
                     </Agents>
                     <LocalityText>Queen Elizabeth National Park; Crater Road</LocalityText>