IUCN

#1350
CatalogueOfLife · Sep 6, 2024 · 07ca4a5 · 07ca4a5
1 parent cb8553f
commit 07ca4a5
Show file tree

Hide file tree

Showing 5 changed files with 59 additions and 38 deletions.
diff --git a/matching-ws/src/main/java/life/catalogue/matching/controller/MatchController.java b/matching-ws/src/main/java/life/catalogue/matching/controller/MatchController.java
@@ -15,6 +15,7 @@
 import java.util.stream.Collectors;
 import life.catalogue.matching.model.*;
 import life.catalogue.matching.service.MatchingService;
+import life.catalogue.matching.util.IUCNUtils;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
@@ -671,15 +672,15 @@ public Map<String, Object> iucnRedListV1(@PathVariable(value = "usageKey", requi
       return Map.of();
     }
     NameUsageMatch.Status status = statusList.get(0);
-    String formatted = formatIucn(status.getStatus());
+    String formatted = IUCNUtils.formatIucn(status.getStatus());
     if (formatted == null || formatted.isEmpty()) {
       return Map.of();
     }
 
     String scientificName = match.getAcceptedUsage() != null ? match.getAcceptedUsage().getCanonicalName() : match.getUsage().getCanonicalName();
 
     try {
-      IUCN iucn = IUCN.valueOf(formatted); // throws IllegalArgumentException if not found
+      IUCNUtils.IUCN iucn =  IUCNUtils.IUCN.valueOf(formatted); // throws IllegalArgumentException if not found
       watch.stop();
       log("v1/species/iucnRedListCategory", usageKey, watch);
       return Map.of(
@@ -689,7 +690,7 @@ public Map<String, Object> iucnRedListV1(@PathVariable(value = "usageKey", requi
         "taxonomicStatus", NameUsageMatchV1.TaxonomicStatusV1.convert(
           match.getDiagnostics().getStatus()),
         "iucnTaxonID", status.getSourceId(),
-        "code", iucn.code
+        "code", iucn.getCode()
       );
     } catch (IllegalArgumentException e) {
       log.error("IUCN category not found: {}", formatted, e);
@@ -751,37 +752,6 @@ private static void addIfNotNull(StringJoiner joiner, Object value) {
     }
   }
 
-  String formatIucn(String original){
-    if (original == null) {
-      return null;
-    }
-    // Trim the string
-    String trimmed = original.trim();
-    // Convert to uppercase
-    String uppercased = trimmed.toUpperCase();
-    // Replace any whitespace with a single underscore
-    return uppercased.replaceAll("\\s+", "_");
-  }
-
-   enum IUCN {
-    EXTINCT("EX"),
-    EXTINCT_IN_THE_WILD("EW"),
-    CRITICALLY_ENDANGERED ("CR"),
-    ENDANGERED ("EN"),
-    VULNERABLE ("VU"),
-    NEAR_THREATENED ("NT"),
-    CONSERVATION_DEPENDENT ("CD"),
-    LEAST_CONCERN ("LC"),
-    DATA_DEFICIENT ("DD"),
-    NOT_EVALUATED ("NE");
-
-    private final String code;
-
-    IUCN(String code) {
-      this.code = code;
-    }
-  }
-
   @Data
   @Builder
   @NoArgsConstructor

diff --git a/matching-ws/src/main/java/life/catalogue/matching/index/DatasetIndex.java b/matching-ws/src/main/java/life/catalogue/matching/index/DatasetIndex.java
@@ -23,6 +23,7 @@
 import life.catalogue.api.vocab.MatchType;
 import life.catalogue.api.vocab.TaxonomicStatus;
 import life.catalogue.matching.model.*;
+import life.catalogue.matching.util.IUCNUtils;
 import life.catalogue.matching.util.LuceneUtils;
 import life.catalogue.matching.Main;
 import lombok.extern.slf4j.Slf4j;
@@ -806,9 +807,13 @@ private NameUsageMatch fromDoc(Document doc) {
         TopDocs docs = ancillarySearcher.search(query, 3);
         if (docs.totalHits.value > 0) {
           Document ancillaryDoc = ancillarySearcher.storedFields().document(docs.scoreDocs[0].doc);
-          String status = ancillaryDoc.get(FIELD_CATEGORY);
           NameUsageMatch.Status ancillaryStatus = new NameUsageMatch.Status();
-          ancillaryStatus.setStatus(status);
+          ancillaryStatus.setStatus(ancillaryDoc.get(FIELD_CATEGORY));
+          //FIXME - this needs to removed from here - use a vocab
+          String formattedIUCN = IUCNUtils.formatIucn(ancillaryDoc.get(FIELD_CATEGORY));
+          IUCNUtils.IUCN iucn = IUCNUtils.IUCN.valueOf(formattedIUCN);
+          ancillaryStatus.setStatus(formattedIUCN);
+          ancillaryStatus.setStatusCode(iucn.getCode());
           ancillaryStatus.setDatasetKey(dataset.getKey().toString());
           ancillaryStatus.setGbifKey(dataset.getGbifKey());
           ancillaryStatus.setDatasetAlias(dataset.getAlias());

diff --git a/matching-ws/src/main/java/life/catalogue/matching/model/NameUsageMatch.java b/matching-ws/src/main/java/life/catalogue/matching/model/NameUsageMatch.java
@@ -420,7 +420,7 @@ public static class RankedName implements Serializable {
   @Data
   @JsonIgnoreProperties(ignoreUnknown = true)
   @JsonInclude(JsonInclude.Include.NON_EMPTY)
-  @Schema(description = "A status value derived from a dataset or external source. E.g. IUCN Red List status.",
+  @Schema(description = "A status value derived from a dataset or external source. E.g. IUCN Red List.",
     title = "Status", type = "object")
   public static class Status {
     @Schema(description = "The dataset key for the dataset that the status is associated with")
@@ -431,6 +431,8 @@ public static class Status {
     private String gbifKey;
     @Schema(description = "The status value")
     private String status;
+    @Schema(description = "The status code value")
+    private String statusCode;
     @Schema(description = "The ID in the source dataset for this status. e.g. the IUCN ID for this taxon")
     private String sourceId;
   }

diff --git a/matching-ws/src/main/java/life/catalogue/matching/util/IUCNUtils.java b/matching-ws/src/main/java/life/catalogue/matching/util/IUCNUtils.java
@@ -0,0 +1,40 @@
+package life.catalogue.matching.util;
+
+public class IUCNUtils {
+
+  public static String formatIucn(String original){
+    if (original == null) {
+      return null;
+    }
+    // Trim the string
+    String trimmed = original.trim();
+    // Convert to uppercase
+    String uppercased = trimmed.toUpperCase();
+    // Replace any whitespace with a single underscore
+    return uppercased.replaceAll("\\s+", "_");
+  }
+
+  public enum IUCN {
+    EXTINCT("EX"),
+    EXTINCT_IN_THE_WILD("EW"),
+    CRITICALLY_ENDANGERED ("CR"),
+    ENDANGERED ("EN"),
+    VULNERABLE ("VU"),
+    NEAR_THREATENED ("NT"),
+    CONSERVATION_DEPENDENT ("CD"),
+    LEAST_CONCERN ("LC"),
+    DATA_DEFICIENT ("DD"),
+    NOT_EVALUATED ("NE");
+
+    private final String code;
+
+    IUCN(String code) {
+      this.code = code;
+        }
+
+    public String getCode() {
+        return code;
+    }
+
+  }
+}
diff --git a/matching-ws/src/main/resources/logback.xml b/matching-ws/src/main/resources/logback.xml
@@ -7,9 +7,13 @@
       <pattern> %highlight(%boldGreen([%date{'yyyy-MM-dd HH:mm:ss'}]) %blue([${LOG_LEVEL_PATTERN:-%4p}]) %boldCyan([%logger{0}]) %boldYellow(%msg%n))</pattern>
     </encoder>
   </appender>
-  <root level="WARN">
+  <root level="INFO">
     <appender-ref ref="CONSOLE" />
   </root>
+  <!-- Suppress INFO logs from life.catalogue -->
+<!--  <logger name="com.ibatis" level="DEBUG"/>-->
+<!--  <logger name="java.sql" level="DEBUG"/>-->
+<!--  <logger name="life.catalogue.matching.db.IndexingMapper" level="TRACE"/>-->
   <logger name="life.catalogue" level="INFO"/>
   <logger name="life.catalogue.common.tax" level="ERROR"/>
   <logger name="org.springframework.web" level="ERROR"/>