fixed queries to be usable with lindas

plazi · Nov 5, 2024 · 9663f68 · 9663f68
1 parent 936a99c
commit 9663f68
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Showing 2 changed files with 70 additions and 58 deletions.
diff --git a/Queries.ts b/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 ?species ?infrasp ?name ?authority
+SELECT DISTINCT ?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 ?species ?infrasp ?name ?authority
  * As its own variable to ensure consistency in the resturned bindings.
  */
 const postamble =
-  `GROUP BY ?tn ?tc ?col ?rank ?genus ?species ?infrasp ?name ?authority`;
+  `GROUP BY ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority`;
 
 // For unclear reasons, the queries breaks if the limit is removed.
 
@@ -36,14 +36,14 @@ export const getNameFromCol = (colUri: string) =>
   `${preamble} WHERE {
 BIND(<${colUri}> as ?col)
   ?col dwc:taxonRank ?rank .
-  OPTIONAL { ?col dwc:scientificNameAuthorship ?colAuth . } BIND(COALESCE(?colAuth, "") as ?authority)
   ?col dwc:scientificName ?name .
   ?col dwc:genericName ?genus .
   # TODO # ?col dwc:parent* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?kingdom .
   OPTIONAL {
     ?col dwc:specificEpithet ?species .
     OPTIONAL { ?col dwc:infraspecificEpithet ?infrasp . }
   }
+  OPTIONAL { ?col dwc:scientificNameAuthorship ?authority . }
 
   OPTIONAL {
     ?tn dwc:rank ?trank ;
@@ -113,40 +113,31 @@ export const getNameFromTC = (tcUri: string) =>
       a dwcFP:TaxonConcept .
 
   ?tn a dwcFP:TaxonName .
-  ?tn dwc:rank ?rank .
+  ?tn dwc:rank ?tnrank .
   ?tn dwc:kingdom ?kingdom .
   ?tn dwc:genus ?genus .
+  OPTIONAL { ?tn dwc:subGenus ?subgenus . }
   OPTIONAL {
-    ?tn dwc:species ?species .
-    OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?infrasp . }
+    ?tn dwc:species ?tnspecies .
+    OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }
   }
   
+  BIND(LCASE(?tnrank) AS ?rank)
+  BIND(COALESCE(?tnspecies, "") AS ?species)
+  BIND(COALESCE(?tninfrasp, "") AS ?infrasp)
+  
   OPTIONAL {
-    ?col dwc:taxonRank ?crank .
-    FILTER(LCASE(?rank) = LCASE(?crank))
-    OPTIONAL { ?col dwc:scientificNameAuthorship ?colAuth . }
-    ?col dwc:scientificName ?fullName . # Note: contains authority
+    ?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 .
 
-    {
-      ?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 . }
-    }
+    OPTIONAL { ?col dwc:specificEpithet ?colspecies . }
+    FILTER(?species = COALESCE(?colspecies, ""))
+    OPTIONAL { ?col dwc:infraspecificEpithet ?colinfrasp . }
+    FILTER(?infrasp = COALESCE(?colinfrasp, ""))
+    OPTIONAL { ?col dwc:scientificNameAuthorship ?authority . }
   }
-  
-  BIND(COALESCE(?fullName, CONCAT(?genus, COALESCE(CONCAT(" (",?subgenus,")"), ""), COALESCE(CONCAT(" ",?species), ""), COALESCE(CONCAT(" ", ?infrasp), ""))) as ?name)
-  BIND(COALESCE(?colAuth, "") as ?authority)
 
   OPTIONAL {
     ?trtnt trt:treatsTaxonName ?tn ; trt:publishedIn/dc:date ?trtndate .
@@ -186,40 +177,31 @@ export const getNameFromTN = (tnUri: string) =>
   `${preamble} WHERE {
   BIND(<${tnUri}> as ?tn)
   ?tn a dwcFP:TaxonName .
-  ?tn dwc:rank ?rank .
+  ?tn dwc:rank ?tnrank .
   ?tn dwc:genus ?genus .
   ?tn dwc:kingdom ?kingdom .
+  OPTIONAL { ?tn dwc:subGenus ?subgenus . }
   OPTIONAL {
-    ?tn dwc:species ?species .
-    OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?infrasp . }
+    ?tn dwc:species ?tnspecies .
+    OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }
   }
   
+  BIND(LCASE(?tnrank) AS ?rank)
+  BIND(COALESCE(?tnspecies, "") AS ?species)
+  BIND(COALESCE(?tninfrasp, "") AS ?infrasp)
+  
   OPTIONAL {
-    ?col dwc:taxonRank ?crank .
-    FILTER(LCASE(?rank) = LCASE(?crank))
-    OPTIONAL { ?col dwc:scientificNameAuthorship ?colAuth . }
-    ?col dwc:scientificName ?fullName . # Note: contains authority
+    ?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 .
 
-    {
-      ?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 . }
-    }
+    OPTIONAL { ?col dwc:specificEpithet ?colspecies . }
+    FILTER(?species = COALESCE(?colspecies, ""))
+    OPTIONAL { ?col dwc:infraspecificEpithet ?colinfrasp . }
+    FILTER(?infrasp = COALESCE(?colinfrasp, ""))
+    OPTIONAL { ?col dwc:scientificNameAuthorship ?authority . }
   }
-  
-  BIND(COALESCE(?fullName, CONCAT(?genus, COALESCE(CONCAT(" (",?subgenus,")"), ""), COALESCE(CONCAT(" ",?species), ""), COALESCE(CONCAT(" ", ?infrasp), ""))) as ?name)
-  BIND(COALESCE(?colAuth, "") as ?authority)
 
   OPTIONAL {
     ?trtnt trt:treatsTaxonName ?tn ; trt:publishedIn/dc:date ?trtndate .

diff --git a/SynonymGroup.ts b/SynonymGroup.ts
@@ -281,11 +281,41 @@ LIMIT 500`;
   ): Promise<void> {
     const treatmentPromises: Treatment[] = [];
 
-    const displayName: string = json.results.bindings[0].name!.value
-      .replace(
-        json.results.bindings[0].authority?.value ?? "",
-        "",
-      ).trim();
+    const abbreviateRank = (rank: string) => {
+      switch (rank) {
+        case "variety":
+          return "var.";
+        case "subspecies":
+          return "subsp.";
+        case "form":
+          return "f.";
+        default:
+          return rank;
+      }
+    };
+
+    const displayName: string = (json.results.bindings[0].name
+      ? (
+        json.results.bindings[0].authority
+          ? json.results.bindings[0].name.value
+            .replace(
+              json.results.bindings[0].authority.value,
+              "",
+            )
+          : json.results.bindings[0].name.value
+      )
+      : json.results.bindings[0].genus!.value +
+        (json.results.bindings[0].subgenus?.value
+          ? ` (${json.results.bindings[0].subgenus.value})`
+          : "") +
+        (json.results.bindings[0].species?.value
+          ? ` ${json.results.bindings[0].species.value}`
+          : "") +
+        (json.results.bindings[0].infrasp?.value
+          ? ` ${abbreviateRank(json.results.bindings[0].rank!.value)} ${
+            json.results.bindings[0].infrasp.value
+          }`
+          : "")).trim();
 
     // Case where the CoL-taxon has no authority. There should only be one of these.
     let unathorizedCol: string | undefined;
@@ -469,11 +499,11 @@ SELECT DISTINCT ?current ?current_status (GROUP_CONCAT(DISTINCT ?dpr; separator=
   {
     ?col dwc:acceptedName ?current .
     ?dpr dwc:acceptedName ?current .
-    ?current dwc:taxonomicStatus ?current_status .
+    OPTIONAL { ?current dwc:taxonomicStatus ?current_status . }
   } UNION {
     ?col dwc:taxonomicStatus ?current_status .
     OPTIONAL { ?dpr dwc:acceptedName ?col . }
-    FILTER NOT EXISTS { ?col dwc:acceptedName ?current . }
+    FILTER NOT EXISTS { ?col dwc:acceptedName ?_ . }
     BIND(?col AS ?current)
   }
 }