simple services for ID lookup #1318

matching-ws/src/main/java/life/catalogue/matching/DatasetIndex.java

@@ -494,6 +494,90 @@ public static class IDMatchResult {
     boolean matchOnlyInJoinIndex;
   }
 
+  /**
+   * Matches an external ID. Intended for debug purposes only, to quickly
+   * check if ids are present and joined to main index or not.
+   *
+   * @param identifier the identifier to match
+   * @return IDMatchResult with the document, datasetKey, and flags
+   */
+  public List<ExternalID> lookupIdentifier(@NotNull String identifier)  {
+    List<ExternalID> results = new ArrayList<>();
+
+    try {
+      // if join indexes are present, add them to the match
+      if (identifierSearchers != null && !identifierSearchers.isEmpty()) {
+        for (Dataset dataset : identifierSearchers.keySet()) {
+          // find the index and search it
+          IndexSearcher identifierSearcher = identifierSearchers.get(dataset);
+          Query identifierQuery = new TermQuery(new Term(FIELD_ID, identifier));
+          TopDocs identifierDocs = identifierSearcher.search(identifierQuery, 3);
+
+          if (identifierDocs.totalHits.value > 0) {
+            Document identifierDoc = identifierSearcher.storedFields().document(identifierDocs.scoreDocs[0].doc);
+            results.add(toExternalID(identifierDoc, dataset.getKey().toString()));
+          }
+        }
+      }
+    } catch (IOException e) {
+      log.error("Problem querying external ID indexes with {}", identifier, e);
+    }
+    // no indexes available
+    return results;
+  }
+
+  /**
+   * Matches an external ID. Intended for debug purposes only, to quickly
+   * check if ids are present and joined to main index or not.
+   *
+   * @param datasetID the datasetKey to match
+   * @param identifier the identifier to match
+   * @return IDMatchResult with the document, datasetKey, and flags
+   */
+  public List<ExternalID> lookupIdentifier(@NotNull String datasetID, @NotNull String identifier)  {
+    List<ExternalID> results = new ArrayList<>();
+
+    try {
+      // if join indexes are present, add them to the match
+      if (identifierSearchers != null && !identifierSearchers.isEmpty()) {
+        for (Dataset dataset : identifierSearchers.keySet()) {
+
+          // use the prefix mapping
+          if (dataset.getKey().toString().equals(datasetID) || (dataset.getGbifKey() != null && dataset.getGbifKey().equals(datasetID))) {
+
+            // find the index and search it
+            IndexSearcher identifierSearcher = identifierSearchers.get(dataset);
+            Query identifierQuery = new TermQuery(new Term(FIELD_ID, identifier));
+            TopDocs identifierDocs = identifierSearcher.search(identifierQuery, 3);
+
+            if (identifierDocs.totalHits.value > 0) {
+              Document identifierDoc = identifierSearcher.storedFields().
+                document(identifierDocs.scoreDocs[0].doc);
+
+              results.add(toExternalID(identifierDoc, dataset.getKey().toString()));
+            }
+          }
+        }
+      }
+    } catch (IOException e) {
+      log.error("Problem querying external ID indexes with {}", identifier, e);
+    }
+    // no indexes available
+    return results;
+  }
+
+  private static ExternalID toExternalID(Document doc, String datasetKey) {
+    return ExternalID.builder()
+      .id(doc.get(FIELD_ID))
+      .datasetKey(datasetKey)
+      .scientificName(doc.get(FIELD_SCIENTIFIC_NAME))
+      .rank(doc.get(FIELD_RANK))
+      .parentID(doc.get(FIELD_PARENT_ID))
+      .status(doc.get(FIELD_STATUS))
+      .mainIndexID(doc.get(FIELD_JOIN_ID))
+      .build();
+  }
+
   /**
    * Matches an external ID
    * @param key the external ID to match

matching-ws/src/main/java/life/catalogue/matching/ExternalID.java

@@ -0,0 +1,31 @@
+package life.catalogue.matching;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import io.swagger.v3.oas.annotations.media.Schema;
+import lombok.Builder;
+import lombok.Data;
+
+@Schema(description = "An identifier from another checklist that may be associated with a name usage in the main index", title = "ExternalID", type = "object")
+@Data
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@Builder
+public class ExternalID {
+    @Schema(description = "The external identifier that may or may not have been associated with the main index")
+    private String id;
+    @Schema(description = "The main index identifier that the external identifier was matched to")
+    private String mainIndexID;
+    @Schema(description = "The dataset key of the main index identifier")
+    private String datasetKey;
+    @Schema(description = "The parent ID of the external identifier")
+    private String parentID;
+    @Schema(description = "The scientific name associated with the external identifier")
+    private String scientificName;
+    @Schema(description = "The accepted taxon ID of the external identifier")
+    private String acceptedTaxonID;
+    @Schema(description = "The rank of the external identifier")
+    private String rank;
+    @Schema(description = "The status of the external identifier")
+    private String status;
+}

matching-ws/src/main/java/life/catalogue/matching/IDController.java

@@ -0,0 +1,36 @@
+package life.catalogue.matching;
+
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RestController;
+
+@RestController
+public class IDController {
+
+  @Autowired
+  MatchingService matchingService;
+
+  @ApiResponse(responseCode = "200", description = "Name usage suggestions found")
+  @Tag(name = "ID lookup")
+  @GetMapping(
+    value = {"v2/id/{datasetId}/{identifier}"},
+    produces = "application/json")
+  public Object matchV2(
+    @PathVariable(value = "datasetId", required = false) String datasetId,
+    @PathVariable(value = "identifier", required = false) String identifier) {
+    return matchingService.matchID(datasetId, identifier);
+  }
+
+  @ApiResponse(responseCode = "200", description = "Name usage suggestions found")
+  @Tag(name = "ID lookup")
+  @GetMapping(
+    value = {"v2/id/{identifier}"},
+    produces = "application/json")
+  public Object matchV2(
+    @PathVariable(value = "identifier", required = false) String identifier) {
+    return matchingService.matchID(identifier);
+  }
+}

matching-ws/src/main/java/life/catalogue/matching/MatchController.java

@@ -30,6 +30,7 @@
 import org.springframework.boot.web.servlet.error.ErrorController;
 import org.springframework.util.Assert;
 import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.context.request.WebRequest;

matching-ws/src/main/java/life/catalogue/matching/MatchingService.java

@@ -233,6 +233,14 @@ private static void setAlternatives(NameUsageMatch match, List<NameUsageMatch> a
     match.setAlternatives(alts);
   }
 
+  public List<ExternalID> matchID(String identifier){
+    return datasetIndex.lookupIdentifier(identifier);
+  }
+
+  public List<ExternalID> matchID(String datasetID, String identifier){
+    return datasetIndex.lookupIdentifier(datasetID, identifier);
+  }
+
   public NameUsageMatch match(
       @Nullable String scientificName,
       @Nullable LinneanClassification classification,