AtlasOfLivingAustralia/biocollect#1596

- updated species search of bulk import - added species format code
AtlasOfLivingAustralia · Sep 4, 2024 · d112b94 · d112b94
1 parent aa2d51f
commit d112b94
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Showing 4 changed files with 75 additions and 12 deletions.
diff --git a/grails-app/services/au/org/ala/ecodata/MetadataService.groovy b/grails-app/services/au/org/ala/ecodata/MetadataService.groovy
@@ -41,6 +41,7 @@ class MetadataService {
  SpeciesReMatchService speciesReMatchService
  HubService hubService
  ProjectService projectService
+ RecordService recordService
 
  /**
  * @deprecated use versioned API to retrieve activity form definitions
@@ -896,17 +897,13 @@ class MetadataService {
  data
  }
 
- Map autoPopulateSpeciesData (Map data, int limit = 10) {
+ Map autoPopulateSpeciesData (Map data) {
  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)
- || name.equalsIgnoreCase(data.name)
- || name.equalsIgnoreCase(data.commonName)
- }
+ Map bestMatch = speciesReMatchService.searchByName(searchName)
+ if(!bestMatch && data.commonName) {
+ String commonName = data.commonName
+ bestMatch = speciesReMatchService.searchByName(commonName, false, true)
  }
 
  if (bestMatch) {
@@ -917,7 +914,7 @@ class MetadataService {
  }
 
  if(!data?.name) {
- data.name = data?.commonName ? data?.scientificName + '(' + data?.commonName + ')' : data?.scientificName
+ data.name = recordService.formatTaxonName(data, RecordService.SCIENTIFIC_NAME_COMMON_NAME)
  }
 
  data

diff --git a/grails-app/services/au/org/ala/ecodata/RecordService.groovy b/grails-app/services/au/org/ala/ecodata/RecordService.groovy
@@ -45,6 +45,10 @@ class RecordService {
 
  final def ignores = ["action", "controller", "associatedMedia"]
  private static final List<String> EXCLUDED_RECORD_PROPERTIES = ["_id", "activityId", "dateCreated", "json", "outputId", "projectActivityId", "projectId", "status", "dataResourceUid"]
+ static final String COMMON_NAME = 'COMMONNAME'
+ static final String SCIENTIFIC_NAME = 'SCIENTIFICNAME'
+ static final String COMMON_NAME_SCIENTIFIC_NAME = 'COMMONNAME(SCIENTIFICNAME)'
+ static final String SCIENTIFIC_NAME_COMMON_NAME = 'SCIENTIFICNAME(COMMONNAME)'
 
  def getProjectActivityService() {
  grailsApplication.mainContext.projectActivityService
@@ -1119,4 +1123,37 @@ class RecordService {
  commonService.updateProperties(output, props)
  }
  }
+
+ /** format species by specific type **/
+ String formatTaxonName (Map data, String displayType) {
+ String name = ''
+ switch (displayType){
+ case COMMON_NAME_SCIENTIFIC_NAME:
+ if (data.commonName && data.scientificName) {
+ name = "${data.commonName} (${data.scientificName})"
+ } else if (data.commonName) {
+ name = data.commonName
+ } else if (data.scientificName) {
+ name = data.scientificName
+ }
+ break
+ case SCIENTIFIC_NAME_COMMON_NAME:
+ if (data.scientificName && data.commonName) {
+ name = "${data.scientificName} (${data.commonName})"
+ } else if (data.scientificName) {
+ name = data.scientificName
+ } else if (data.commonName) {
+ name = data.commonName
+ }
+ break
+ case COMMON_NAME:
+ name = data.commonName ?: data.scientificName ?: ""
+ break
+ case SCIENTIFIC_NAME:
+ name = data.scientificName ?: ""
+ break
+ }
+
+ name
+ }
 }
diff --git a/grails-app/services/au/org/ala/ecodata/SpeciesReMatchService.groovy b/grails-app/services/au/org/ala/ecodata/SpeciesReMatchService.groovy
@@ -125,7 +125,7 @@ class SpeciesReMatchService {
  }
 
  resp
- })
+ }) as Map
  }
 
  Map searchByVernacularNameOnNameMatchingServer (String name) {
@@ -139,6 +139,6 @@ class SpeciesReMatchService {
  }
 
  resp
- })
+ }) as Map
  }
 }
diff --git a/src/test/groovy/au/org/ala/ecodata/RecordServiceSpec.groovy b/src/test/groovy/au/org/ala/ecodata/RecordServiceSpec.groovy
@@ -68,5 +68,34 @@ class RecordServiceSpec extends MongoSpec implements ServiceUnitTest<RecordServi
  recordMap.recordNumber == "${prefix}/bioActivity/index/a1"
  }
 
+ def "formatTaxonName should format name based on displayType"() {
+ setup:
+ Map data = [commonName: commonName, scientificName: scientificName]
+
+ when:
+ String result = service.formatTaxonName(data, displayType)
+
+ then:
+ result == expectedName
+
+ where:
+ commonName | scientificName | displayType | expectedName
+ 'Blackbird' | 'Turdus merula' | service.COMMON_NAME_SCIENTIFIC_NAME | 'Blackbird (Turdus merula)'
+ 'Blackbird' | 'Turdus merula' | service.SCIENTIFIC_NAME_COMMON_NAME | 'Turdus merula (Blackbird)'
+ 'Blackbird' | 'Turdus merula' | service.COMMON_NAME | 'Blackbird'
+ null | 'Turdus merula' | service.COMMON_NAME | 'Turdus merula'
+ 'Blackbird' | 'Turdus merula' | service.SCIENTIFIC_NAME | 'Turdus merula'
+ null | 'Turdus merula' | service.SCIENTIFIC_NAME | 'Turdus merula'
+ null | 'Turdus merula' | service.COMMON_NAME_SCIENTIFIC_NAME | 'Turdus merula'
+ null | 'Turdus merula' | service.SCIENTIFIC_NAME_COMMON_NAME | 'Turdus merula'
+ 'Blackbird' | null | service.COMMON_NAME_SCIENTIFIC_NAME | 'Blackbird'
+ 'Blackbird' | null | service.SCIENTIFIC_NAME_COMMON_NAME | 'Blackbird'
+ 'Blackbird' | null | service.COMMON_NAME | 'Blackbird'
+ null | null | service.COMMON_NAME | ''
+ null | null | service.SCIENTIFIC_NAME | ''
+ null | null | service.COMMON_NAME_SCIENTIFIC_NAME | ''
+ null | null | service.SCIENTIFIC_NAME_COMMON_NAME | ''
+ }
+
 }