Merge remote-tracking branch 'origin/develop'

# Conflicts: # build.gradle
AtlasOfLivingAustralia · Jul 12, 2023 · bfbd8d9 · bfbd8d9
2 parents e98de8e + ce1795e
commit bfbd8d9
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Showing 5 changed files with 48 additions and 14 deletions.
diff --git a/build.gradle b/build.gradle
@@ -40,7 +40,7 @@ repositories {
 }
 
 group = 'au.org.ala'
-version = '3.2.0'
+version = '3.2.1'
 
 
 boolean inplace = false

diff --git a/src/main/java/au/org/ala/biocache/dao/SolrIndexDAOImpl.java b/src/main/java/au/org/ala/biocache/dao/SolrIndexDAOImpl.java
@@ -14,7 +14,6 @@
 import com.fasterxml.jackson.core.type.TypeReference;
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.lang.StringUtils;
-import org.apache.commons.lang3.Streams;
 import org.apache.commons.lang3.tuple.Pair;
 import org.apache.http.client.config.RequestConfig;
 import org.apache.http.impl.client.CloseableHttpClient;
@@ -522,6 +521,24 @@ public Set<IndexFieldDTO> getIndexFieldDetails(String... fields) throws Exceptio
             indexFieldMap.remove(indexFieldToHide);
         }
 
+        // Insert entries for cl* and el* items
+        Map<String, String> layerNameMap = layersService.getLayerNameMap();
+        for (Map.Entry<String, String> item : layerNameMap.entrySet()) {
+            IndexFieldDTO field = new IndexFieldDTO();
+            field.setDocvalue(true);
+            field.setIndexed(true);
+            field.setStored(true);
+            field.setDescription(item.getValue());
+            field.setName(item.getKey());
+            field.setDownloadName(item.getKey());
+            if (item.getKey().startsWith("cl")) {
+                field.setDataType("string");
+            } else {
+                field.setDataType("float");
+            }
+            indexFieldMap.put(item.getKey(), field);
+        }
+
         if (fields != null && fields.length > 0) {
             return Arrays.stream(fields)
                     .map(fieldName -> indexFieldMap.get(fieldName))

diff --git a/src/main/java/au/org/ala/biocache/service/AlaLayersService.java b/src/main/java/au/org/ala/biocache/service/AlaLayersService.java
@@ -1,12 +1,12 @@
 /**************************************************************************
  *  Copyright (C) 2013 Atlas of Living Australia
  *  All Rights Reserved.
- * 
+ *
  *  The contents of this file are subject to the Mozilla Public
  *  License Version 1.1 (the "License"); you may not use this file
  *  except in compliance with the License. You may obtain a copy of
  *  the License at http://www.mozilla.org/MPL/
- * 
+ *
  *  Software distributed under the License is distributed on an "AS
  *  IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or
  *  implied. See the License for the specific language governing
@@ -36,7 +36,7 @@
 /**
  * The ALA Spatial portal implementation for the layer service.
  * Metadata information will be cached from spatial webservices.
- * 
+ *
  * @author Natasha Carter ([email protected])
  */
 @Component("layersService")
@@ -47,11 +47,11 @@ public class AlaLayersService implements LayersService {
     private Map<String,String> idToNameMap = RestartDataService.get(this, "idToNameMap", new TypeReference<HashMap<String, String>>(){}, HashMap.class);
     private List<Map<String,Object>> layers = RestartDataService.get(this, "layers", new TypeReference<ArrayList<Map<String, Object>>>(){}, ArrayList.class);
     private Map<String,String> extraLayers = new HashMap<String,String>();
-    
+
     //NC 20131018: Allow cache to be disabled via config (enabled by default)
     @Value("${caches.layers.enabled:true}")
     protected Boolean enabled = null;
-    
+
     @Value("${spatial.layers.url:https://spatial.ala.org.au/ws/fields}")
     protected String spatialUrl;
 
@@ -64,12 +64,12 @@ public class AlaLayersService implements LayersService {
     protected Map<String, Integer> distributions = RestartDataService.get(this, "distributions", new TypeReference<HashMap<String, Integer>>(){}, HashMap.class);
     protected Map<String, Integer> checklists = RestartDataService.get(this, "checklists", new TypeReference<HashMap<String, Integer>>(){}, HashMap.class);
     protected Map<String, Integer> tracks = RestartDataService.get(this, "tracks", new TypeReference<HashMap<String, Integer>>(){}, HashMap.class);
-    
+
     @Inject
     private RestOperations restTemplate; // NB MappingJacksonHttpMessageConverter() injected by Spring
 
     private CountDownLatch wait = new CountDownLatch(1);
-    
+
     @Override
     public Map<String, String> getLayerNameMap() {
         try {
@@ -78,7 +78,7 @@ public Map<String, String> getLayerNameMap() {
         }
         return idToNameMap;
     }
-    
+
     @Scheduled(fixedDelay = 43200000)// schedule to run every 12 hours
     public void refreshCache(){
         init();
@@ -102,7 +102,9 @@ public void run() {
                         List list = restTemplate.getForObject(spatialUrl, List.class);
                         if (list != null && list.size() > 0) layers = list;
                         for (Map<String, Object> values : layers) {
-                            tmpMap.put((String) values.get("id"), (String) values.get("desc"));
+                            if ((Boolean) values.get("enabled") && (Boolean) values.get("indb")) {
+                                tmpMap.put((String) values.get("id"), (String) values.get("desc"));
+                            }
                         }
 
                         if (tmpMap.size() > 0) idToNameMap = tmpMap;

diff --git a/src/main/java/au/org/ala/biocache/stream/StreamFacet.java b/src/main/java/au/org/ala/biocache/stream/StreamFacet.java
@@ -9,6 +9,7 @@
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.log4j.Logger;
 import org.apache.solr.client.solrj.io.Tuple;
+import org.bouncycastle.util.Arrays;
 
 import java.io.OutputStream;
 import java.util.ArrayList;
@@ -18,6 +19,11 @@ public class StreamFacet implements ProcessInterface {
 
     private final static Logger logger = Logger.getLogger(StreamFacet.class);
 
+    private final static String [] lsidFields = {"taxonConceptID", "kingdomID", "classID", "phylumID", "orderID",
+            "familyID", "genusID", "speciesID", "subspeciesID",
+            "raw_taxonConceptID", "raw_kingdomID", "raw_classID", "raw_phylumID", "raw_orderID",
+            "raw_familyID", "raw_genusID", "raw_speciesID"};
+
     SearchDAOImpl searchDAO;
     DownloadDetailsDTO downloadDetails;
     SpatialSearchRequestDTO request;
@@ -48,8 +54,14 @@ public StreamFacet(SearchDAOImpl searchDAO, DownloadDetailsDTO downloadDetails,
         String facetName = request.getFacets()[0];
 
         // shouldLookup is valid for 1.0 and 2.0 SOLR schema
-        boolean isGuid = request.getFacets()[0].contains("_guid") ||
-                request.getFacets()[0].endsWith("ID");
+        boolean isGuid = request.getFacets()[0].contains("_guid");
+        for (String field : lsidFields) {
+            if (field.equals(request.getFacets()[0])) {
+                isGuid = true;
+                break;
+            }
+        }
+
         boolean isLsid = request.getFacets()[0].contains("_lsid") || request.getFacets()[0].contains(OccurrenceIndex.TAXON_CONCEPT_ID);
         boolean shouldLookupTaxon = lookupName && (isLsid || isGuid);
         boolean isUid = request.getFacets()[0].contains("_uid") || request.getFacets()[0].endsWith("Uid");

diff --git a/src/test/java/au/org/ala/biocache/controller/OccurrenceControllerIT.java b/src/test/java/au/org/ala/biocache/controller/OccurrenceControllerIT.java
@@ -15,6 +15,8 @@
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.mockito.ArgumentCaptor;
+import org.mockito.internal.matchers.GreaterOrEqual;
+import org.mockito.internal.matchers.LessOrEqual;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.test.context.ContextConfiguration;
@@ -33,6 +35,7 @@
 import java.security.Principal;
 import java.util.*;
 
+import static org.hamcrest.Matchers.*;
 import static org.mockito.Mockito.*;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
@@ -309,7 +312,7 @@ public void getIndexFieldsTest() throws Exception {
         this.mockMvc.perform(get("/index/fields")
                 .contentType(MediaType.APPLICATION_JSON))
                 .andExpect(status().isOk())
-                .andExpect(jsonPath("$.length()").value(INDEXED_FIELD_SIZE));
+                .andExpect(jsonPath("$", hasSize(greaterThanOrEqualTo(INDEXED_FIELD_SIZE))));
     }
 
     @Test