From 911cc52a0dd667fb52ec0e553a8614490c52b6bc Mon Sep 17 00:00:00 2001
From: Adam Rauch <adam@labkey.com>
Date: Wed, 18 Oct 2023 15:20:51 -0700
Subject: [PATCH 1/2] Sanitize maps and lists for JSONObject consumption

---
 api/src/org/labkey/api/util/JsonUtil.java | 34 +++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/api/src/org/labkey/api/util/JsonUtil.java b/api/src/org/labkey/api/util/JsonUtil.java
index 81baf1a51c0..33c8111c33c 100644
--- a/api/src/org/labkey/api/util/JsonUtil.java
+++ b/api/src/org/labkey/api/util/JsonUtil.java
@@ -43,7 +43,9 @@
 import java.util.Arrays;
 import java.util.Iterator;
 import java.util.List;
+import java.util.ListIterator;
 import java.util.Map;
+import java.util.function.Consumer;
 
 /**
  * Helper methods for working with Jackson, JSONObject, and JSONArray
@@ -262,6 +264,38 @@ else if (f == Float.NEGATIVE_INFINITY)
         return value;
     }
 
+    /**
+     * Sanitizes a mutable map by replacing +Infinity, -Infinity, and NaN values with JSON-legal values. Recursively
+     * sanitizes all embedded maps and lists as well; these must also be mutable.
+     * @param mutableMap mutable Map to sanitize
+     */
+    public static void sanitizeMap(Map<String, Object> mutableMap)
+    {
+        mutableMap.keySet().forEach(key -> sanitize(mutableMap.get(key), num -> mutableMap.put(key, translateNumber(num))));
+    }
+
+    /**
+     * Sanitizes a mutable list by replacing +Infinity, -Infinity, and NaN values with JSON-legal values. Recursively
+     * sanitizes all embedded maps and lists as well; these must also be mutable.
+     * @param mutableList mutable List to sanitize
+     */
+    public static void sanitizeList(List<Object> mutableList)
+    {
+        ListIterator<Object> iter = mutableList.listIterator();
+        while (iter.hasNext())
+            sanitize(iter.next(), num -> iter.set(translateNumber(num)));
+    }
+
+    private static void sanitize(Object obj, Consumer<Number> numberAction)
+    {
+        if (obj instanceof Map m)
+            sanitizeMap(m);
+        else if (obj instanceof List list)
+            sanitizeList(list);
+        else if (obj instanceof Number num)
+            numberAction.accept(num);
+    }
+
     public static class TestCase extends Assert
     {
         private static final String JSON_WITH_COMMENTS = """

From efff6a14c006d6968dae679c4955de71deba3122 Mon Sep 17 00:00:00 2001
From: Adam Rauch <adam@labkey.com>
Date: Wed, 18 Oct 2023 15:33:41 -0700
Subject: [PATCH 2/2] Junit test

---
 api/src/org/labkey/api/util/JsonUtil.java | 43 +++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/api/src/org/labkey/api/util/JsonUtil.java b/api/src/org/labkey/api/util/JsonUtil.java
index 33c8111c33c..fb519b73e9b 100644
--- a/api/src/org/labkey/api/util/JsonUtil.java
+++ b/api/src/org/labkey/api/util/JsonUtil.java
@@ -41,6 +41,7 @@
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.ListIterator;
@@ -456,5 +457,47 @@ public void testJsonString()
             assertEquals(html.toString(), roundTripJson.get("htmlString"));
             assertEquals(u.getUserId(), roundTripJson.get("user"));
         }
+
+        @Test
+        public void testSanitize()
+        {
+            // Rough approximation of the map GetNabRunsAction generates
+            Map<String, Object> response = new HashMap<>();
+            response.put("assayName", "foobar");
+            response.put("assayDescription", "this is my assay");
+            response.put("assayId", 1234);
+            response.put("neg", Double.NEGATIVE_INFINITY);
+            response.put("pos", Double.POSITIVE_INFINITY);
+            response.put("nan", Double.NaN);
+
+            List<Map<String, Object>> runList = new ArrayList<>();
+            response.put("runs", runList);
+            runList.add(getDoubleRun());
+            runList.add(getFloatRun());
+
+            assertThrows(JSONException.class, () -> new JSONObject(response));
+            JsonUtil.sanitizeMap(response);
+            JSONObject json = new JSONObject(response);
+        }
+
+        private Map<String, Object> getFloatRun()
+        {
+            Map<String, Object> run = new HashMap<>();
+            run.put("cutoff", Float.NaN);
+            run.put("maxDilution", Float.NEGATIVE_INFINITY);
+            run.put("minDilution", Float.POSITIVE_INFINITY);
+
+            return run;
+        }
+
+        private Map<String, Object> getDoubleRun()
+        {
+            Map<String, Object> run = new HashMap<>();
+            run.put("cutoff", Double.NaN);
+            run.put("maxDilution", Double.NEGATIVE_INFINITY);
+            run.put("minDilution", Double.POSITIVE_INFINITY);
+
+            return run;
+        }
     }
 }