handle kingdoms

Queries.ts

@@ -8,7 +8,7 @@ PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
 PREFIX dwcFP: <http://filteredpush.org/ontologies/oa/dwcFP#>
 PREFIX cito: <http://purl.org/spar/cito/>
 PREFIX trt: <http://plazi.org/vocab/treatment#>
-SELECT DISTINCT ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority
+SELECT DISTINCT ?kingdom ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority
   (group_concat(DISTINCT ?tcauth;separator=" / ") AS ?tcAuth)
   (group_concat(DISTINCT ?aug;separator="|") as ?augs)
   (group_concat(DISTINCT ?def;separator="|") as ?defs)
@@ -23,7 +23,7 @@ SELECT DISTINCT ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?aut
  * As its own variable to ensure consistency in the resturned bindings.
  */
 const postamble =
-  `GROUP BY ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority`;
+  `GROUP BY ?kingdom ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority`;
 
 // For unclear reasons, the queries breaks if the limit is removed.
 
@@ -38,7 +38,8 @@ BIND(<${colUri}> as ?col)
   ?col dwc:taxonRank ?rank .
   ?col dwc:scientificName ?name .
   ?col dwc:genericName ?genus .
-  # TODO # ?col dwc:parent* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?kingdom .
+  OPTIONAL { ?col (dwc:parent|dwc:acceptedName)* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?colkingdom . }
+  BIND(COALESCE(?colkingdom, "") AS ?kingdom)
   OPTIONAL {
     ?col dwc:specificEpithet ?species .
     OPTIONAL { ?col dwc:infraspecificEpithet ?infrasp . }
@@ -49,22 +50,13 @@ BIND(<${colUri}> as ?col)
     ?tn dwc:rank ?trank ;
        a dwcFP:TaxonName .
     FILTER(LCASE(?rank) = LCASE(?trank))
-    ?tn dwc:genus ?genus .
     ?tn dwc:kingdom ?kingdom .
-    {
-      ?col dwc:specificEpithet ?species .
-      ?tn dwc:species ?species .
-      {
-        ?col dwc:infraspecificEpithet ?infrasp .
-        ?tn dwc:subSpecies|dwc:variety|dwc:form ?infrasp .
-      } UNION {
-        FILTER NOT EXISTS { ?col dwc:infraspecificEpithet ?infrasp . }
-        FILTER NOT EXISTS { ?tn dwc:subSpecies|dwc:variety|dwc:form ?infrasp . }
-      }
-    } UNION {
-      FILTER NOT EXISTS { ?col dwc:specificEpithet ?species . }
-      FILTER NOT EXISTS { ?tn dwc:species ?species . }
-    }
+    ?tn dwc:genus ?genus .
+    
+    OPTIONAL { ?tn dwc:species ?tnspecies . }
+    FILTER(?species = COALESCE(?tnspecies, ""))
+    OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }
+    FILTER(?infrasp = COALESCE(?tninfrasp, ""))
 
     OPTIONAL {
       ?trtnt trt:treatsTaxonName ?tn ; trt:publishedIn/dc:date ?trtndate .
@@ -130,7 +122,8 @@ export const getNameFromTC = (tcUri: string) =>
     ?col dwc:taxonRank ?rank .
     ?col dwc:scientificName ?name . # Note: contains authority
     ?col dwc:genericName ?genus .
-    # TODO # ?col dwc:parent* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?kingdom .
+    OPTIONAL { ?col (dwc:parent|dwc:acceptedName)* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?colkingdom . }
+    FILTER(?kingdom = COALESCE(?colkingdom, ""))
 
     OPTIONAL { ?col dwc:specificEpithet ?colspecies . }
     FILTER(?species = COALESCE(?colspecies, ""))
@@ -194,7 +187,8 @@ export const getNameFromTN = (tnUri: string) =>
     ?col dwc:taxonRank ?rank .
     ?col dwc:scientificName ?name . # Note: contains authority
     ?col dwc:genericName ?genus .
-    # TODO # ?col dwc:parent* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?kingdom .
+    OPTIONAL { ?col (dwc:parent|dwc:acceptedName)* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?colkingdom . }
+    FILTER(?kingdom = COALESCE(?colkingdom, ""))
 
     OPTIONAL { ?col dwc:specificEpithet ?colspecies . }
     FILTER(?species = COALESCE(?colspecies, ""))

SparqlEndpoint.ts

@@ -1,4 +1,3 @@
-// deno-lint-ignore-file no-unused-labels
 async function sleep(ms: number): Promise<void> {
   const p = new Promise<void>((resolve) => {
     setTimeout(resolve, ms);

SynonymGroup.ts

@@ -408,6 +408,7 @@ LIMIT 500`;
     treats.forEach((t) => treatmentPromises.push(t));
 
     const name: Name = {
+      kingdom: json.results.bindings[0].kingdom!.value,
       displayName,
       rank: json.results.bindings[0].rank!.value,
       taxonNameURI,
@@ -830,8 +831,10 @@ SELECT DISTINCT ?url ?description WHERE {
  * Each `Name` is uniquely determined by its human-readable latin name (for taxa ranking below genus, this is a multi-part name — binomial or trinomial) and kingdom.
  */
 export type Name = {
-  /** taxonomic kingdom */
-  // kingdom: string;
+  /** taxonomic kingdom
+   * 
+   * may be empty for some CoL-taxa with missing ancestors */
+  kingdom: string;
   /** Human-readable name */
   displayName: string;
   /** taxonomic rank */

example/index.css

@@ -114,10 +114,6 @@ syno-treatment,
     max-height: 0;
     overflow: hidden;
     transition: all 200ms;
-
-    & img {
-      display: none;
-    }
   }
 
   &.expanded {
@@ -131,10 +127,6 @@ syno-treatment,
     .hidden {
       max-height: 200rem;
       overflow: auto;
-
-      & img {
-        display: unset;
-      }
     }
   }
 }

example/index.ts

@@ -333,7 +333,10 @@ class SynoName extends HTMLElement {
     const rank_badge = document.createElement("span");
     rank_badge.classList.add("rank");
     rank_badge.innerText = name.rank;
-    title.append(" ", rank_badge);
+    const kingdom_badge = document.createElement("span");
+    kingdom_badge.classList.add("rank");
+    kingdom_badge.innerText = name.kingdom || "Missing Kingdom";
+    title.append(" ", kingdom_badge, " ", rank_badge);
 
     if (name.taxonNameURI) {
       const name_uri = document.createElement("a");