#376 rankID updates

AtlasOfLivingAustralia · Jan 3, 2024 · a00cbe2 · a00cbe2
1 parent 62295d4
commit a00cbe2
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Showing 4 changed files with 71 additions and 13 deletions.
diff --git a/build.gradle b/build.gradle
@@ -110,7 +110,7 @@ dependencies {
     }
 
     implementation "org.grails.plugins:grails-spring-websocket:2.3.0"
-    implementation group: "au.org.ala", name: "ala-name-matching-model", version:"4.2"
+    implementation group: "au.org.ala", name: "ala-name-matching-model", version:"4.3"
     implementation "org.jsoup:jsoup:1.15.4"
     implementation 'net.sf.opencsv:opencsv:2.3'
     implementation "org.apache.solr:solr-solrj:8.1.0"

diff --git a/grails-app/conf/application.yml b/grails-app/conf/application.yml
@@ -222,10 +222,17 @@ vernacularListsUrl: /default-vernacular-lists.json
 # Location of locality keywords (null for default)
 localityKeywordsUrl: /default-locality-keywords.json
 #nationalSpeciesDatasets: dr2699,dr2700,dr2702,dr2704,dr2703,dr3118
-defaultDownloadFields: guid,rank,scientificName,scientificNameAuthorship,taxonomicStatus,establishmentMeans,rk_genus,rk_family,rk_order,rk_class,rk_phylum,rk_kingdom,datasetName,parentGuid,acceptedConceptName,acceptedConceptID,idxtype,name
+
+# all available rk_ and rkid_ fields in SOLR are added to defaultDownloadFields when no rk_ field is defined in defaultDownloadFields
+defaultDownloadFields: guid,rank,scientificName,scientificNameAuthorship,taxonomicStatus,establishmentMeans,datasetName,parentGuid,acceptedConceptName,acceptedConceptID,idxtype,name
+downloadMaxRows: 10000
+
 additionalResultFields: ""
 #toggle for the population of occurrence counts
 
+# override the taxon ranks taxonRanksFile with an external file
+taxonRanksFile:
+
 # Score normal value (divides integer priority by the norm to give solr boosts)
 
 # SOLR additional params and connections

diff --git a/grails-app/controllers/au/org/ala/bie/MiscController.groovy b/grails-app/controllers/au/org/ala/bie/MiscController.groovy
@@ -40,9 +40,32 @@ class MiscController {
         return
     }
 
-    // Documented in openapi.yml, not migrating to annotations because no recent use
+    @Operation(
+            method = "GET",
+            tags = "rank",
+            operationId = "ranks",
+            summary = "Gets a description of the ranks used to classify levels of taxa",
+            responses = [
+                    @ApiResponse(
+                            responseCode = "200",
+                            headers = [
+                                    @Header(name = 'Access-Control-Allow-Headers', description = "CORS header", schema = @Schema(type = "String")),
+                                    @Header(name = 'Access-Control-Allow-Methods', description = "CORS header", schema = @Schema(type = "String")),
+                                    @Header(name = 'Access-Control-Allow-Origin', description = "CORS header", schema = @Schema(type = "String"))
+                            ]
+                    )
+            ]
+    )
+    @Path("/ranks")
+    @Produces("application/json")
     def ranks() {
-        render importService.ranks() as JSON
+        def indexedFields = indexService.getIndexFieldDetails().collect {
+            it.name.replaceAll("^[^_]+_", "")
+        }
+        def activeRanks = importService.ranks().findAll {
+            indexedFields.contains(it.value.rank)
+        }
+        render activeRanks as JSON
     }
 
     def indexFields() {

diff --git a/grails-app/services/au/org/ala/bie/ImportService.groovy b/grails-app/services/au/org/ala/bie/ImportService.groovy
@@ -1594,6 +1594,15 @@ class ImportService implements GrailsConfigurationAware {
         }
     }
 
+    def getTaxonRankID(taxonRanks, taxonRank) {
+        def tr = taxonRanks.get(taxonRank)
+        if (!tr) {
+            tr = taxonRanks.find { it.value.otherNames?.contains(taxonRank) }
+        }
+
+        return tr ? tr.rankID : -1
+    }
+
     def buildTaxonRecord(Record record, Map doc, Map attributionMap, Map datasetMap, Map taxonRanks, String defaultTaxonomicStatus, String defaultDatasetName) {
         def datasetID = record.value(DwcTerm.datasetID)
         def taxonRank = (record.value(DwcTerm.taxonRank) ?: "").toLowerCase()
@@ -1602,7 +1611,9 @@ class ImportService implements GrailsConfigurationAware {
         def scientificNameAuthorship = record.value(DwcTerm.scientificNameAuthorship)
         def nameComplete = record.value(ALATerm.nameComplete)
         def nameFormatted = record.value(ALATerm.nameFormatted)
-        def taxonRankID = taxonRanks.get(taxonRank) ? taxonRanks.get(taxonRank).rankID : -1
+        // TODO: use ALATerm.taxonRankID, or the alternative, when it exists in ala-name-matching-model
+        //def taxonRankID = record.value(ALATerm.taxonRankID) ?: getTaxonRankID(taxonRanks, taxonRank)
+        def taxonRankID = getTaxonRankID(taxonRanks, taxonRank)
         def taxonomicStatus = record.value(DwcTerm.taxonomicStatus) ?: defaultTaxonomicStatus
         def nameType = record.value(GbifTerm.nameType)
         String taxonRemarks = record.value(DwcTerm.taxonRemarks)
@@ -2942,15 +2953,32 @@ class ImportService implements GrailsConfigurationAware {
      * @return
      */
     def ranks() {
-        JsonSlurper slurper = new JsonSlurper()
-        def ranks = slurper.parse(this.class.getResource("/taxonRanks.json"))
-        def idMap = [:]
-        def iter = ranks.iterator()
-        while (iter.hasNext()) {
-            def entry = iter.next()
-            idMap.put(entry.rank, entry)
+        String path = grailsApplication.config.taxonRanksFile
+        File taxonRanksFile = new File(path)
+        if (path && taxonRanksFile.exists()) {
+            JsonSlurper slurper = new JsonSlurper()
+            def ranks = slurper.parse(taxonRanksFile.text)
+            def idMap = [:]
+            def iter = ranks.iterator()
+            while (iter.hasNext()) {
+                def entry = iter.next()
+                idMap.put(entry.rank, entry)
+            }
+            idMap
+        } else {
+            def idMap = [:]
+            RankType.values().each { rankType ->
+                idMap.put(rankType.field, [
+                        branch: null,
+                        notes: null,
+                        otherNames: [],
+                        rank: rankType.field,
+                        rankGroup: rankType.cbRank?.name()?.toLowerCase(),
+                        rankID: rankType.sortOrder
+                ])
+            }
+            idMap
         }
-        idMap
     }
 
     /**