From 7c439bc09226f62b25a84dabc210a3608079d84e Mon Sep 17 00:00:00 2001
From: Jon Van Oast <jon@wildme.org>
Date: Thu, 6 Feb 2025 10:36:08 -0700
Subject: [PATCH] limit (manual) indexing to only do Annotations with
 matchAgainst=true and acmId set

---
 src/main/java/org/ecocean/Annotation.java   |  1 +
 src/main/java/org/ecocean/Shepherd.java     | 20 ++++++++++++++++++++
 src/main/webapp/appadmin/opensearchSync.jsp |  2 +-
 3 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/ecocean/Annotation.java b/src/main/java/org/ecocean/Annotation.java
index 7ec2e193a3..fe337c5393 100644
--- a/src/main/java/org/ecocean/Annotation.java
+++ b/src/main/java/org/ecocean/Annotation.java
@@ -189,6 +189,7 @@ public void opensearchDocumentSerializer(JsonGenerator jgen, Shepherd myShepherd
         }
     }
 
+    // TODO should this also be limited by matchAgainst and acmId?
     @Override public String getAllVersionsSql() {
         return "SELECT \"ID\", \"VERSION\" AS version FROM \"ANNOTATION\" ORDER BY version";
     }
diff --git a/src/main/java/org/ecocean/Shepherd.java b/src/main/java/org/ecocean/Shepherd.java
index 6c903d354b..96e860f811 100644
--- a/src/main/java/org/ecocean/Shepherd.java
+++ b/src/main/java/org/ecocean/Shepherd.java
@@ -2063,6 +2063,26 @@ public Iterator getAllAnnotationsNoQuery() {
         }
     }
 
+    // note: where clause can also contain " ORDER BY xxx"
+    public Iterator getAnnotationsFilter(String jdoWhereClause) {
+        Query query = null;
+
+        try {
+            query = pm.newQuery("SELECT FROM org.ecocean.Annotation WHERE " + jdoWhereClause);
+            Collection c = (Collection)(query.execute());
+            List list = new ArrayList(c);
+            Iterator it = list.iterator();
+            query.closeAll();
+            return it;
+        } catch (Exception npe) {
+            System.out.println(
+                "Error encountered when trying to execute getAllAnnotationsFilter. Returning a null iterator.");
+            npe.printStackTrace();
+            if (query != null) query.closeAll();
+            return null;
+        }
+    }
+
     public Iterator<Encounter> getAllAnnotations(String order) {
         Extent extClass = pm.getExtent(Annotation.class, true);
         Query q = pm.newQuery(extClass);
diff --git a/src/main/webapp/appadmin/opensearchSync.jsp b/src/main/webapp/appadmin/opensearchSync.jsp
index d97aa91d89..a2f5394460 100644
--- a/src/main/webapp/appadmin/opensearchSync.jsp
+++ b/src/main/webapp/appadmin/opensearchSync.jsp
@@ -88,7 +88,7 @@ if (endNum > 0) {
     if (indexName.equals("encounter")) {
         itr = myShepherd.getAllEncounters("catalogNumber");
     } else if (indexName.equals("annotation")) {
-        itr = myShepherd.getAllAnnotations("id");
+        itr = myShepherd.getAnnotationsFilter("matchAgainst == true && acmId != null ORDER BY id");
     } else if (indexName.equals("individual")) {
         itr = myShepherd.getAllMarkedIndividuals();
     }