#951

- checks species match using name matching server

Author: temi

grails-app/conf/application.groovy

@@ -503,6 +503,7 @@ if (!ala.baseURL) {
 }
 bie.ws.url = "https://bie-ws.ala.org.au/"
 bie.url = "https://bie.ala.org.au/"
+namesmatching.url = "https://namematching-ws-test.ala.org.au/"
 
 if (!collectory.baseURL) {
     //collectory.baseURL = "https://collectory-dev.ala.org.au/"

grails-app/services/au/org/ala/ecodata/ParatooService.groovy

@@ -77,6 +77,7 @@ class ParatooService {
     RecordService recordService
     MetadataService metadataService
     UserService userService
+    SpeciesReMatchService speciesReMatchService
 
     /**
      * The rules we use to find projects eligible for use by paratoo are:
@@ -2053,7 +2054,7 @@ class ParatooService {
     /**
      * Transforms a species name to species object used by ecodata.
      * e.g. Acacia glauca [Species] (scientific: Acacia glauca Willd.)
-     * [name: "Acacia glauca Willd.", scientificName: "Acacia glauca Willd.", guid: "A_GUID"]
+     * [name: "Acacia glauca Willd.", scientificName: "Acacia glauca Willd.", commonName: "Acacia glauca", guid: "A_GUID"]
      * Guid is necessary to generate species occurrence record. Guid is found by searching the species name with BIE. If not found, then a default value is added.
      * @param name
      * @return
@@ -2064,28 +2065,34 @@ class ParatooService {
         }
 
         String regex = "([^\\[\\(]*)(?:\\[(.*)\\])?\\s*(?:\\(scientific:\\s*(.*?)\\))?"
+        String commonName, scientificName = name
         Pattern pattern = Pattern.compile(regex)
         Matcher matcher = pattern.matcher(name)
-        Map result = [name: name, scientificName: name, commonName: name, outputSpeciesId: UUID.randomUUID().toString()]
+        Map result = [scientificName: name, commonName: name, outputSpeciesId: UUID.randomUUID().toString()]
 
         if (matcher.find()) {
-            String commonName = matcher.group(1)?.trim()
-            String scientificName = matcher.group(3)?.trim()
-            result.commonName = commonName ?: result.commonName
+            commonName = matcher.group(1)?.trim()
+            scientificName = matcher.group(3)?.trim()
             result.taxonRank = matcher.group(2)?.trim()
-            result.scientificName = scientificName ?: commonName ?: result.scientificName
-            result.name = scientificName ?: commonName ?: result.name
+            result.scientificName = scientificName
+            result.commonName = commonName
         }
 
-        metadataService.autoPopulateSpeciesData(result)
+        Map resp = speciesReMatchService.searchByName(scientificName)
+        if (resp) {
+            result.putAll(resp)
+        }
         // 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
+        if ((result.guid == null) && commonName) {
+            resp = speciesReMatchService.searchByName(commonName)
+            if (resp) {
+                result.putAll(resp)
+                result.commonName = commonName
+            }
         }
 
+        result.name = result.commonName ? result.scientificName ? "${result.scientificName} (${result.commonName})" : result.commonName : result.scientificName
+
         // record is only created if guid is present
         result.guid = result.guid ?: Record.UNMATCHED_GUID
         result

grails-app/services/au/org/ala/ecodata/SpeciesReMatchService.groovy

@@ -90,4 +90,36 @@ class SpeciesReMatchService {
             webService.getJson(url)
         })
     }
+
+    Map searchByName (String name, boolean addDetails = false) {
+        Map result = searchNameMatchingServer(name)
+        if (result) {
+            Map resp = [
+                    scientificName: result.scientificName,
+                    commonName: result.vernacularName,
+                    guid: result.taxonConceptID,
+                    taxonRank: result.rank
+            ]
+
+            if(addDetails) {
+                resp.put('details', result)
+            }
+
+            return resp
+        }
+    }
+
+    Map searchNameMatchingServer(String name) {
+        name = name?.toLowerCase() ?: ""
+        cacheService.get('name-matching-server-' + name, {
+            def encodedQuery = URLEncoder.encode(name ?: '', "UTF-8")
+            def url = "${grailsApplication.config.getProperty('namesmatching.url')}api/search?q=${encodedQuery}"
+            def resp = webService.getJson(url)
+            if (!resp.success) {
+                return null
+            }
+
+            resp
+        })
+    }
 }

src/test/groovy/au/org/ala/ecodata/ParatooServiceSpec.groovy

@@ -26,6 +26,7 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
     TokenService tokenService = Mock(TokenService)
     SettingService settingService = Mock(SettingService)
     MetadataService metadataService = Mock(MetadataService)
+    SpeciesReMatchService speciesReMatchService = Mock(SpeciesReMatchService)
     ActivityService activityService = Mock(ActivityService)
     RecordService recordService = Mock(RecordService)
     UserService userService = Mock(UserService)
@@ -55,6 +56,7 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         service.recordService = recordService
         service.cacheService = new CacheService()
         service.userService = userService
+        service.speciesReMatchService = speciesReMatchService
 
         JSON.registerObjectMarshaller(new MapMarshaller())
         JSON.registerObjectMarshaller(new CollectionMarshaller())
@@ -654,25 +656,6 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         result == ""
     }
 
-    void "transformSpeciesName should convert paratoo species name to object correctly"() {
-        when:
-        Map result = service.transformSpeciesName("Acacia glauca [Species] (scientific: Acacia glauca Willd.)")
-        String outputSpeciesId = result.remove("outputSpeciesId")
-        then:
-        outputSpeciesId != null
-        result == [name: "Acacia glauca Willd.", scientificName: "Acacia glauca Willd.", guid: "A_GUID", commonName: "Acacia glauca", taxonRank: "Species"]
-        2 * metadataService.autoPopulateSpeciesData(_) >> null
-
-        when: // no scientific name
-        result = service.transformSpeciesName("Frogs [Class] (scientific: )")
-        outputSpeciesId = result.remove("outputSpeciesId")
-
-        then:
-        outputSpeciesId != null
-        result == [name: "Frogs", scientificName: "Frogs", guid: "A_GUID", commonName: "Frogs", taxonRank: "Class"]
-        2 * metadataService.autoPopulateSpeciesData(_) >> null
-    }
-
     void "buildRelationshipTree should build relationship tree correctly"() {
         given:
         def properties = [
@@ -723,6 +706,25 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         relationships["fauna-survey"].contains("fauna-observation")
     }
 
+    void "transformSpeciesName should convert paratoo species name to object correctly"() {
+        when:
+        Map result = service.transformSpeciesName("Acacia glauca [Species] (scientific: Acacia glauca Willd.)")
+        String outputSpeciesId = result.remove("outputSpeciesId")
+        then:
+        outputSpeciesId != null
+        result == [name: "Acacia glauca Willd. (Acacia glauca)", scientificName: "Acacia glauca Willd.", guid: "A_GUID", commonName: "Acacia glauca", taxonRank: "Species"]
+        2 * speciesReMatchService.searchByName(_) >> null
+
+        when: // no scientific name
+        result = service.transformSpeciesName("Frogs [Class] (scientific: )")
+        outputSpeciesId = result.remove("outputSpeciesId")
+
+        then:
+        outputSpeciesId != null
+        result == [name: "Frogs", scientificName: "", guid: "A_GUID", commonName: "Frogs", taxonRank: "Class"]
+        2 * speciesReMatchService.searchByName(_) >> null
+    }
+
     void "buildTreeFromParentChildRelationships should build tree correctly"() {
         given:
         def relationships = [
@@ -1399,13 +1401,19 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
         result.lut.remove('outputSpeciesId')
 
         then:
+        1 * speciesReMatchService.searchByName(_) >> [
+                commonName: "Cat",
+                scientificName: "Felis catus",
+                guid: "TAXON_ID",
+                taxonRank: "species"
+        ]
         result == [
                 lut: [
                         commonName: "Cat",
-                        name: "Cat",
-                        taxonRank: null,
-                        scientificName: "Cat",
-                        guid: "A_GUID"
+                        name: "Felis catus (Cat)",
+                        taxonRank: "species",
+                        scientificName: "Felis catus",
+                        guid: "TAXON_ID"
                 ]
         ]
 
@@ -1417,18 +1425,25 @@ class ParatooServiceSpec extends MongoSpec implements ServiceUnitTest<ParatooSer
                 ]
         ]
         output = [
-                lut: "Cat"
+                lut: "Cats [Species] (scientific: Felis catus)"
         ]
         result = service.recursivelyTransformData(dataModel, output, formName, 1, null)
         result.lut.remove('outputSpeciesId')
         then:
+        1 * speciesReMatchService.searchByName("Felis catus") >> null
+        1 * speciesReMatchService.searchByName("Cats") >> [
+                commonName: "Cat",
+                scientificName: "Felis catus",
+                guid: "TAXON_ID",
+                taxonRank: "species"
+        ]
         result == [
                 lut: [
-                        commonName: "Cat",
-                        name: "Cat",
-                        taxonRank: null,
-                        scientificName: "Cat",
-                        guid: "A_GUID"
+                        commonName: "Cats",
+                        name: "Felis catus (Cats)",
+                        taxonRank: "species",
+                        scientificName: "Felis catus",
+                        guid: "TAXON_ID"
                 ]
         ]
     }