AtlasOfLivingAustralia/fieldcapture#3049

- better species matching against bie
AtlasOfLivingAustralia · Apr 9, 2024 · e68ecec · e68ecec
1 parent 5c5e786
commit e68ecec
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Showing 3 changed files with 20 additions and 10 deletions.
diff --git a/grails-app/services/au/org/ala/ecodata/MetadataService.groovy b/grails-app/services/au/org/ala/ecodata/MetadataService.groovy
@@ -844,14 +844,16 @@ class MetadataService {
         data
     }
 
-    Map autoPopulateSpeciesData(Map data){
-        if (!data?.guid && (data?.scientificName ?: data?.commonName)) {
-            def result = speciesReMatchService.searchBie(data.scientificName?: data.commonName, 10)
-            // only if there is a single match
-            if (result?.autoCompleteList?.size() == 1) {
-                data.guid = result?.autoCompleteList[0]?.guid
-                data.commonName = data.commonName ?: result?.autoCompleteList[0]?.commonName
-                data.scientificName = data.scientificName ?: result?.autoCompleteList[0]?.name
+    Map autoPopulateSpeciesData (Map data, int limit = 10) {
+        String searchName = (data?.scientificName)?.trim()
+        if (!data?.guid && (searchName)) {
+            def result = speciesReMatchService.searchBie(searchName, limit)
+            // find the name that exactly matches the search name
+            def bestMatch = result?.autoCompleteList?.find { it.matchedNames?.findResult { String name -> name.equalsIgnoreCase(searchName) } }
+            if (bestMatch) {
+                data.guid = bestMatch?.guid
+                data.commonName = data.commonName ?: bestMatch?.commonName
+                data.scientificName = data.scientificName ?: bestMatch?.name
             }
         }
 

diff --git a/grails-app/services/au/org/ala/ecodata/ParatooService.groovy b/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
@@ -1932,6 +1932,14 @@ class ParatooService {
         }
 
         metadataService.autoPopulateSpeciesData(result)
+        // try again with common name
+        if ((result.guid == null) && result.commonName) {
+            def speciesObject = [scientificName: result.commonName]
+            metadataService.autoPopulateSpeciesData(speciesObject)
+            result.guid = speciesObject.guid
+            result.scientificName = result.scientificName ?: speciesObject.scientificName
+        }
+
         // record is only created if guid is present
         result.guid = result.guid ?: "A_GUID"
         result

diff --git a/src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy b/src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy
@@ -487,7 +487,7 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         then:
         outputSpeciesId != null
         result == [name: "Acacia glauca Willd.", scientificName: "Acacia glauca Willd.", guid: "A_GUID", commonName: "Acacia glauca", taxonRank: "Species"]
-        1 * metadataService.autoPopulateSpeciesData(_) >> null
+        2 * metadataService.autoPopulateSpeciesData(_) >> null
 
         when: // no scientific name
         result = service.transformSpeciesName("Frogs [Class] (scientific: )")
@@ -496,7 +496,7 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         then:
         outputSpeciesId != null
         result == [name: "Frogs", scientificName: "", guid: "A_GUID", commonName: "Frogs", taxonRank: "Class"]
-        1 * metadataService.autoPopulateSpeciesData(_) >> null
+        2 * metadataService.autoPopulateSpeciesData(_) >> null
     }
 
     void "buildRelationshipTree should build relationship tree correctly"() {