Merge branch 'main' into all_filters_encounter_search

Author: erinz2020

src/main/java/org/ecocean/Annotation.java

@@ -134,7 +134,7 @@ public long setVersion() {
 
     public JSONObject opensearchMapping() {
         JSONObject map = super.opensearchMapping();
-        JSONObject keywordType = new org.json.JSONObject("{\"type\": \"keyword\"}");
+        JSONObject keywordType = new JSONObject("{\"type\": \"keyword\"}");
 
 /*
         JSONObject keywordNormalType = new org.json.JSONObject(
@@ -1373,7 +1373,7 @@ public static Base createFromApi(JSONObject payload, List<File> files, Shepherd
     public static Object validateFieldValue(String fieldName, JSONObject data)
     throws ApiException {
         if (data == null) throw new ApiException("empty payload");
-        org.json.JSONObject error = new org.json.JSONObject();
+        JSONObject error = new JSONObject();
         error.put("fieldName", fieldName);
         String exMessage = "invalid value for " + fieldName;
         Object returnValue = null;

src/main/java/org/ecocean/Encounter.java

@@ -4350,6 +4350,51 @@ public void opensearchDocumentSerializer(JsonGenerator jgen, Shepherd myShepherd
         }
     }
 
+    public void opensearchIndexDeep()
+    throws IOException {
+        this.opensearchIndex();
+
+        final String encId = this.getId();
+        ExecutorService executor = Executors.newFixedThreadPool(4);
+        Runnable rn = new Runnable() {
+            public void run() {
+                Shepherd bgShepherd = new Shepherd("context0");
+                bgShepherd.setAction("Encounter.opensearchIndexDeep_" + encId);
+                bgShepherd.beginDBTransaction();
+                try {
+                    Encounter enc = bgShepherd.getEncounter(encId);
+                    if ((enc == null) || !enc.hasMarkedIndividual()) {
+                        // bgShepherd.rollbackAndClose();
+                        executor.shutdown();
+                        return;
+                    }
+                    MarkedIndividual indiv = enc.getIndividual();
+                    System.out.println("opensearchIndexDeep() background indexing indiv " +
+                        indiv.getId() + " via enc " + encId);
+                    try {
+                        indiv.opensearchIndex();
+                    } catch (Exception ex) {
+                        System.out.println("opensearchIndexDeep() background indexing " +
+                            indiv.getId() + " FAILED: " + ex.toString());
+                        ex.printStackTrace();
+                    }
+                } catch (Exception e) {
+                    System.out.println("opensearchIndexDeep() backgrounding Encounter " + encId +
+                        " hit an exception.");
+                    e.printStackTrace();
+                } finally {
+                    bgShepherd.rollbackAndClose();
+                }
+                System.out.println("opensearchIndexDeep() backgrounding Encounter " + encId +
+                    " finished.");
+                executor.shutdown();
+            }
+        };
+        System.out.println("opensearchIndexDeep() begin backgrounding indiv for " + this);
+        executor.execute(rn);
+        System.out.println("opensearchIndexDeep() [foreground] finished for Encounter " + encId);
+    }
+
     // given a doc from opensearch, can user access it?
     public static boolean opensearchAccess(org.json.JSONObject doc, User user,
         Shepherd myShepherd) {