From 7354fe6a1feae079a79f2f657362dcb722672b5d Mon Sep 17 00:00:00 2001
From: temi <temi.varghese@csiro.au>
Date: Fri, 10 Jan 2025 07:06:17 +1100
Subject: [PATCH] #1053 - support species manual entry

---
 .../au/org/ala/ecodata/ParatooService.groovy  | 21 ++++++++++++-------
 .../org/ala/ecodata/ParatooServiceSpec.groovy | 17 ++++++++++++++-
 2 files changed, 30 insertions(+), 8 deletions(-)

diff --git a/grails-app/services/au/org/ala/ecodata/ParatooService.groovy b/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
index febfb3aff..4dceb8afa 100644
--- a/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
+++ b/grails-app/services/au/org/ala/ecodata/ParatooService.groovy
@@ -2097,7 +2097,7 @@ class ParatooService {
         }
 
         String regex = "([^\\[\\(]*)(?:\\[(.*)\\])?\\s*(?:\\(scientific:\\s*(.*?)\\))?"
-        String commonName, scientificName = name
+        String commonName, scientificName, taxonRank
         Pattern pattern = Pattern.compile(regex)
         Matcher matcher = pattern.matcher(name)
         Map result = [scientificName: name, commonName: name, outputSpeciesId: UUID.randomUUID().toString()]
@@ -2105,17 +2105,18 @@ class ParatooService {
         if (matcher.find()) {
             commonName = matcher.group(1)?.trim()
             scientificName = matcher.group(3)?.trim()
-            result.taxonRank = matcher.group(2)?.trim()
-            result.scientificName = scientificName
-            result.commonName = commonName
+            taxonRank = matcher.group(2)?.trim()
+            result.taxonRank = taxonRank
+            result.scientificName = scientificName == null ? result.scientificName : scientificName
+            result.commonName = commonName == null ? result.commonName : commonName
         }
 
-        Map resp = speciesReMatchService.searchByName(scientificName)
+        Map resp = speciesReMatchService.searchByName(result.scientificName)
         if (resp) {
             result.putAll(resp)
         }
         // try again with common name
-        if ((result.guid == null) && commonName) {
+        if ((result.guid == null) && result.commonName) {
             resp = speciesReMatchService.searchByName(commonName, false, true)
             if (resp) {
                 result.putAll(resp)
@@ -2123,7 +2124,13 @@ class ParatooService {
             }
         }
 
-        result.name = result.commonName ? result.scientificName ? "${result.scientificName} (${result.commonName})" : result.commonName : result.scientificName
+        if (result.commonName != result.scientificName) {
+            result.name = result.commonName ? result.scientificName ? "${result.scientificName} (${result.commonName})" : result.commonName : result.scientificName
+        }
+        else {
+            result.name = result.scientificName ?: result.commonName
+        }
+
         List specialCases = grailsApplication.config.getProperty("paratoo.species.specialCases", List)
         // do not create record for special cases
         if (specialCases.contains(name)) {
diff --git a/src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy b/src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy
index eecefa9dc..1b4cb2cfc 100644
--- a/src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy
+++ b/src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy
@@ -800,13 +800,28 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         1 * speciesReMatchService.searchByName(_) >> null
         1 * speciesReMatchService.searchByName(_, false, true) >> null
 
+        when: // user inputs scientific name to field
+        result = service.transformSpeciesName("Centipeda cunninghamii")
+        outputSpeciesId = result.remove("outputSpeciesId")
+
+        then:
+        outputSpeciesId != null
+        result == [name: "Centipeda cunninghamii (Common Sneezeweed)", scientificName: "Centipeda cunninghamii", guid: "https://id.biodiversity.org.au/node/apni/2916674", commonName: "Common Sneezeweed", taxonRank: "species"]
+        1 * speciesReMatchService.searchByName(_) >> [
+                scientificName: "Centipeda cunninghamii",
+                commonName: "Common Sneezeweed",
+                guid: "https://id.biodiversity.org.au/node/apni/2916674",
+                taxonRank: "species"
+        ]
+        0 * speciesReMatchService.searchByName(_, false, true)
+
         when: // Do not create record when value equals special cases. Therefore, removes guid.
         result = service.transformSpeciesName("Other")
         outputSpeciesId = result.remove("outputSpeciesId")
 
         then:
         outputSpeciesId != null
-        result == [name: "Other", scientificName: null, commonName: "Other", taxonRank: null]
+        result == [name: "Other", scientificName: "Other", commonName: "Other", taxonRank: null]
         1 * speciesReMatchService.searchByName(_) >> null
         1 * speciesReMatchService.searchByName(_, false, true) >> null