#622 fix(urlencode lsid)

gbif · Feb 3, 2022 · 11f3a4e · 11f3a4e
1 parent 8a46afe
commit 11f3a4e
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Showing 5 changed files with 338 additions and 16 deletions.
diff --git a/livingatlas/pipelines/src/main/java/au/org/ala/distribution/DistributionService.java b/livingatlas/pipelines/src/main/java/au/org/ala/distribution/DistributionService.java
@@ -12,16 +12,21 @@ public interface DistributionService {
   @GET("distribution/")
   Call<List<DistributionLayer>> getLayers();
 
+  /**
+   * @param id the species id MUST be URLEncoded
+   * @param nowkt
+   * @return
+   */
   @GET("distribution/lsids/{id}")
   Call<List<DistributionLayer>> getLayersByLsid(
-      @Path("id") String id, @Query("nowkt") String nowkt);
+      @Path(value = "id") String id, @Query("nowkt") String nowkt);
 
   /**
-   * @param lsid
+   * @param id the species id MUST be URLEncoded
    * @param points Map<uuid, <decimalLatitude,decimalLongitude>>
    * @return
    */
   @POST("distribution/outliers/{id}")
   Call<Map<String, Double>> outliers(
-      @Path("id") String lsid, @Body Map<String, Map<String, Double>> points);
+      @Path(value = "id") String id, @Body Map<String, Map<String, Double>> points);
 }
diff --git a/livingatlas/pipelines/src/main/java/au/org/ala/distribution/DistributionServiceImpl.java b/livingatlas/pipelines/src/main/java/au/org/ala/distribution/DistributionServiceImpl.java
@@ -4,6 +4,8 @@
 import com.fasterxml.jackson.databind.PropertyNamingStrategy;
 import java.io.IOException;
 import java.io.Serializable;
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
 import java.util.List;
 import java.util.Map;
 import lombok.extern.slf4j.Slf4j;
@@ -50,19 +52,22 @@ public List<DistributionLayer> getLayers() throws IOException, ExpertDistributio
 
   public List<DistributionLayer> findLayersByLsid(String lsid)
       throws IOException, ExpertDistributionException {
+    lsid = URLEncoder.encode(lsid, StandardCharsets.UTF_8.toString());
     Response<List<DistributionLayer>> response = service.getLayersByLsid(lsid, "false").execute();
     int code = response.code();
     if (code >= 200 && code < 300) {
       List<au.org.ala.distribution.DistributionLayer> layers = response.body();
       return layers;
     } else {
+      log.error("Error in finding the expert distribution layer of " + lsid);
       errorHandler(code, response);
       return null;
     }
   }
 
   public Map<String, Double> outliers(String lsid, Map<String, Map<String, Double>> points)
       throws IOException, ExpertDistributionException {
+    lsid = URLEncoder.encode(lsid, StandardCharsets.UTF_8.toString());
     Response<Map<String, Double>> response = service.outliers(lsid, points).execute();
     int code = response.code();
     if (code >= 200 && code < 300) {

diff --git a/...pipelines/src/main/java/au/org/ala/pipelines/transforms/DistributionOutlierTransform.java b/...pipelines/src/main/java/au/org/ala/pipelines/transforms/DistributionOutlierTransform.java
@@ -65,20 +65,22 @@ public MapElements<IndexRecord, KV<String, IndexRecord>> toKv() {
           public Iterable<DistributionOutlierRecord> apply(
               KV<String, Iterable<IndexRecord>> input) {
             String lsid = input.getKey();
+
             Iterable<IndexRecord> records = input.getValue();
             Iterator<IndexRecord> iter = records.iterator();
             List<DistributionOutlierRecord> outputs = new ArrayList();
-
+            Map points = new HashMap();
             try {
               DistributionServiceImpl distributionService =
                   DistributionServiceImpl.init(spatialUrl);
+
               List<DistributionLayer> edl = distributionService.findLayersByLsid(lsid);
+
               boolean hasEDL = edl.size() > 0 ? true : false;
               double distanceToEDL = hasEDL ? 0 : -1; // 0 -inside, -1: no EDL
               // Available EDLD of this species
 
               if (hasEDL) {
-                Map points = new HashMap();
                 while (iter.hasNext()) {
                   IndexRecord record = iter.next();
                   DistributionOutlierRecord dr = convertToDistribution(record, distanceToEDL);
@@ -104,14 +106,11 @@ public Iterable<DistributionOutlierRecord> apply(
               }
             } catch (ExpertDistributionException e) {
               log.error("Error in processing the species: " + lsid + " . Ignored");
+              log.error("Points: " + points);
               log.error(e.getMessage());
-              // throw new RuntimeException(
-              //  "Expert distribution service throws a runtime error, please check
-              // logs");
             } catch (Exception e) {
-              log.error("Error in processing the species: " + lsid + " . Ignored");
+              log.error("Runtime error in processing the species: " + lsid + " . Ignored");
               log.error(e.getMessage());
-              // throw new RuntimeException("Runtime error: " + e.getMessage());
             }
 
             return outputs;

diff --git a/livingatlas/pipelines/src/main/resources/logback.xml b/livingatlas/pipelines/src/main/resources/logback.xml
@@ -3,7 +3,7 @@
         <resetJUL>true</resetJUL>
     </contextListener>
     <!-- Stop output INFO at start -->
-    <statusListener class="ch.qos.logback.core.status.NopStatusListener" />
+<!--    <statusListener class="ch.qos.logback.core.status.NopStatusListener" />-->
 
     <property name="defaultPattern" value="%-5level [%date{'yyyy-MM-dd HH:mm:ss,SSSZ'}] [%thread] %logger: %msg%n%xEx"/>