WIP - further work for multi taxonomy support

taxon depth facet support facetting on any rank level for a checklist query on any rank level for a checklist #342
gbif · Sep 17, 2024 · dbacac7 · dbacac7
1 parent df83959
commit dbacac7
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Showing 16 changed files with 323 additions and 135 deletions.
diff --git a/event-ws/src/main/java/org/gbif/event/search/es/EventSearchEs.java b/event-ws/src/main/java/org/gbif/event/search/es/EventSearchEs.java
@@ -97,7 +97,7 @@ public EventSearchEs(
     this.nameUsageMatchingService = nameUsageMatchingService;
     eventEsFieldMapper = EventEsField.buildFieldMapper();
     occurrenceEsFieldMapper = OccurrenceEventEsField.buildFieldMapper();
-    this.esSearchRequestBuilder = new EsSearchRequestBuilder(eventEsFieldMapper, conceptClient);
+    this.esSearchRequestBuilder = new EsSearchRequestBuilder(eventEsFieldMapper, conceptClient, null); ///FIXME
     searchHitEventConverter = new SearchHitEventConverter(eventEsFieldMapper, true);
     searchHitOccurrenceConverter = new SearchHitOccurrenceConverter(occurrenceEsFieldMapper, true);
     this.esResponseParser = new EsResponseParser<>(eventEsFieldMapper, searchHitEventConverter);

diff --git a/...download-service/src/main/java/org/gbif/occurrence/download/service/PredicateFactory.java b/...download-service/src/main/java/org/gbif/occurrence/download/service/PredicateFactory.java
@@ -70,16 +70,18 @@ public static Predicate build(Map<String, String[]> params) {
     List<Predicate> groupedByParam = new ArrayList<>();
     for (Map.Entry<String,String[]> p : params.entrySet()) {
       // recognize valid params by enum name, ignore others
-      OccurrenceSearchParameter param = toEnumParam(p.getKey());
-      boolean matchCase = Optional.ofNullable(params.get("matchCase")).map(vals -> Boolean.parseBoolean(vals[0])).orElse(false);
-      String[] values = p.getValue();
-      if (param != null && values != null && values.length > 0) {
-        // valid parameter
-        Predicate predicate = buildParamPredicate(param, matchCase, values);
-        if (predicate != null) {
-          groupedByParam.add(predicate);
+      toEnumParam(p.getKey()).ifPresent(param -> {
+        boolean matchCase = Optional.ofNullable(params.get("matchCase"))
+          .map(vals -> Boolean.parseBoolean(vals[0])).orElse(false);
+        String[] values = p.getValue();
+        if (values != null && values.length > 0) {
+          // valid parameter
+          Predicate predicate = buildParamPredicate(param, matchCase, values);
+          if (predicate != null) {
+            groupedByParam.add(predicate);
+          }
         }
-      }
+      });
     }
 
     if (groupedByParam.isEmpty()) {
@@ -98,9 +100,9 @@ public static Predicate build(Map<String, String[]> params) {
   /**
    * @return the search enum or null if it cant be converted
    */
-  private static OccurrenceSearchParameter toEnumParam(String name) {
+  private static Optional<OccurrenceSearchParameter> toEnumParam(String name) {
     try {
-      return VocabularyUtils.lookupEnum(name, OccurrenceSearchParameter.class);
+      return OccurrenceSearchParameter.lookup(name);
     } catch (IllegalArgumentException e) {
       return null;
     }

diff --git a/occurrence-es-mapping/src/main/java/org/gbif/occurrence/search/es/EsResponseParser.java b/occurrence-es-mapping/src/main/java/org/gbif/occurrence/search/es/EsResponseParser.java
@@ -121,7 +121,10 @@ private Optional<List<Facet<OccurrenceSearchParameter>>> parseFacets(
       List<? extends Terms.Bucket> buckets = getBuckets(aggs);
 
       // get facet of the agg
-      OccurrenceSearchParameter facet =  occurrenceBaseEsFieldMapper.getSearchParameter(aggs.getName());
+      OccurrenceSearchParameter facet = occurrenceBaseEsFieldMapper.getSearchParameter(aggs.getName());
+      if (facet == null) {
+        facet = new OccurrenceSearchParameter(aggs.getName(), String.class);
+      }
 
       // check for paging in facets
       long facetOffset = extractFacetOffset(request, facet);

diff --git a/...-es-mapping/src/main/java/org/gbif/occurrence/search/es/SearchHitOccurrenceConverter.java b/...-es-mapping/src/main/java/org/gbif/occurrence/search/es/SearchHitOccurrenceConverter.java
@@ -407,36 +407,35 @@ private void setTaxonFields(SearchHit hit, Occurrence occ) {
 
   private void setClassifications(SearchHit hit, Occurrence occ) {
 
-    getMapValue(hit, "classifications")
-      .ifPresent(
-        classifications -> Optional.of(classifications.entrySet().stream().map(m -> {
+    getMapValue(hit, "classifications").flatMap(classifications -> Optional.of(classifications.entrySet().stream().map(m -> {
 
-            String datasetKey = m.getKey();
-            Map<String, Object> value = (Map<String, Object>) m.getValue();
+      String datasetKey = m.getKey();
+      Map<String, Object> value = (Map<String, Object>) m.getValue();
 
-            Classification cl = new Classification();
-            cl.setDatasetKey(datasetKey);
+      Classification cl = new Classification();
+      cl.setDatasetKey(datasetKey);
 
-            //set the usage
-            Map<String, String> usage = (Map<String, String>) value.get("usage");
-            cl.setUsage(new RankedName(usage.get("key"), usage.get("name"), usage.get("rank"), usage.get("authorship")));
+      //set the usage
+      Map<String, String> usage = (Map<String, String>) value.get("usage");
+      cl.setUsage(new RankedName(usage.get("key"), usage.get("name"), usage.get("rank"), usage.get("authorship")));
 
-            //set the accepted usage
-            Map<String, String> acceptedusage = (Map<String, String>) value.get("acceptedUsage");
-            Optional.ofNullable(acceptedusage).ifPresent(au -> cl.setAcceptedUsage(new RankedName(au.get("key"), au.get("name"), au.get("rank"), au.get("authorship"))));
+      //set the accepted usage
+      Map<String, String> acceptedusage = (Map<String, String>) value.get("acceptedUsage");
+      Optional.ofNullable(acceptedusage).ifPresent(au -> cl.setAcceptedUsage(new RankedName(au.get("key"), au.get("name"), au.get("rank"), au.get("authorship"))));
 
-            //set the classification
-            Map<String, String> tree = (Map<String, String>) value.get("classification");
-            Map<String, String> treeKeys = (Map<String, String>) value.get("classificationKeys");
+      //set the classification
+      Map<String, String> tree = (Map<String, String>) value.get("classification");
+      Map<String, String> treeKeys = (Map<String, String>) value.get("classificationKeys");
 
-            cl.setIucnRedListCategory((String) value.get("iucnRedListCategory"));
+      cl.setIucnRedListCategory((String) value.get("iucnRedListCategory"));
 
-            cl.setClassification(
-              treeKeys.entrySet().stream()
-                .map(entry -> new RankedName((String) entry.getValue(), (String) tree.get(entry.getKey()), entry.getKey(), null))
-                .collect(Collectors.toList()));
-            return cl;
-          }).collect(Collectors.toList())).ifPresent(occ::setClassifications));
+      cl.setClassification(
+        treeKeys.entrySet().stream()
+          .map(entry -> new RankedName((String) entry.getValue(), (String) tree.get(entry.getKey()), entry.getKey(), null))
+          .collect(Collectors.toList())
+      );
+      return cl;
+    }).collect(Collectors.toList()))).ifPresent(occ::setClassifications);
   }
 
   private void setGrscicollFields(SearchHit hit, Occurrence occ) {

diff --git a/...ps/src/main/java/org/gbif/occurrence/search/heatmap/OccurrenceHeatmapRequestProvider.java b/...ps/src/main/java/org/gbif/occurrence/search/heatmap/OccurrenceHeatmapRequestProvider.java
@@ -127,17 +127,15 @@ private static OccurrenceHeatmapRequest.Mode getMode(HttpServletRequest request)
           .orElse(OccurrenceHeatmapRequest.Mode.GEO_BOUNDS);
   }
 
-
   private static Optional<OccurrenceSearchParameter> findSearchParam(String name) {
     try {
-      return Optional.ofNullable((OccurrenceSearchParameter) VocabularyUtils.lookupEnum(name, OccurrenceSearchParameter.class));
+      return  OccurrenceSearchParameter.lookup(name);
     } catch (IllegalArgumentException e) {
       // we have all params here, not only the enum ones, so this is ok to end up here a few times
     }
     return Optional.empty();
   }
 
-
   /**
    * Removes all empty and null parameters from the list.
    * Each value is trimmed(String.trim()) in order to remove all sizes of empty parameters.

diff --git a/...heatmaps/src/main/java/org/gbif/occurrence/search/heatmap/es/EsHeatmapRequestBuilder.java b/...heatmaps/src/main/java/org/gbif/occurrence/search/heatmap/es/EsHeatmapRequestBuilder.java
@@ -45,7 +45,7 @@ class EsHeatmapRequestBuilder {
 
   EsHeatmapRequestBuilder(OccurrenceBaseEsFieldMapper occurrenceBaseEsFieldMapper, ConceptClient conceptClient) {
     this.occurrenceBaseEsFieldMapper = occurrenceBaseEsFieldMapper;
-    this.esSearchRequestBuilder = new EsSearchRequestBuilder(occurrenceBaseEsFieldMapper, conceptClient);
+    this.esSearchRequestBuilder = new EsSearchRequestBuilder(occurrenceBaseEsFieldMapper, conceptClient, null);
   }
 
   @VisibleForTesting

diff --git a/...h/src/main/java/org/gbif/occurrence/search/configuration/NameUsageMatchServiceTriage.java b/...h/src/main/java/org/gbif/occurrence/search/configuration/NameUsageMatchServiceTriage.java
@@ -6,9 +6,8 @@
 import org.gbif.ws.client.ClientBuilder;
 import org.gbif.ws.json.JacksonJsonObjectMapperProvider;
 import org.springframework.stereotype.Service;
-import java.util.LinkedHashMap;
-import java.util.Map;
-import java.util.Optional;
+
+import java.util.*;
 
 /**
  * Name usage match service triage.
@@ -51,6 +50,15 @@ public NameUsageMatchResponse match(String checklistKey, NameUsageMatchRequest m
       .orElseThrow(() -> new IllegalArgumentException("No service for checklist key " + checklistKey));
   }
 
+  public Collection<String> getChecklistRanks(String checklistKey) {
+    if (checklistKey == null) {
+      return List.of();
+    }
+    return Optional.ofNullable(serviceByChecklistKey.get(checklistKey))
+      .orElseThrow(() -> new IllegalArgumentException("No service for checklist key " + checklistKey))
+      .getMetadata().getMainIndex().getNameUsageByRankCount().keySet();
+  }
+
   /**
    * Match a name usage against the default service
    * @param matchRequest the match request