From a0253849f29ad6b002fbf3c86c78c6705d324658 Mon Sep 17 00:00:00 2001
From: Adam Rauch <adam@labkey.com>
Date: Tue, 1 Oct 2024 14:57:07 -0700
Subject: [PATCH] Use WritablePropertyMap

---
 .../targetedms/TargetedMSController.java      | 31 ++++++++++---------
 .../chromlib/ChromatogramLibraryUtils.java    |  3 +-
 .../folderImport/PanoramaQCSettings.java      |  4 +--
 3 files changed, 21 insertions(+), 17 deletions(-)

diff --git a/src/org/labkey/targetedms/TargetedMSController.java b/src/org/labkey/targetedms/TargetedMSController.java
index 61c975106..965dea45a 100644
--- a/src/org/labkey/targetedms/TargetedMSController.java
+++ b/src/org/labkey/targetedms/TargetedMSController.java
@@ -77,6 +77,8 @@
 import org.labkey.api.data.DataRegion;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.PropertyMap;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.data.RenderContext;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SimpleFilter;
@@ -751,12 +753,12 @@ public Object execute(LeveyJenningsPlotOptions form, BindException errors)
         {
             ApiSimpleResponse response = new ApiSimpleResponse();
 
-            PropertyManager.PropertyMap properties = null;
+            PropertyMap properties = null;
 
-            // only stash and retrieve plot option properties for logged in users
+            // only stash and retrieve plot option properties for logged-in users
             if (!getUser().isGuest())
             {
-                properties = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, true);
+                WritablePropertyMap writable = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, true);
 
                 Map<String, String> valuesToPersist = form.getAsMapOfStrings();
                 if (!valuesToPersist.isEmpty())
@@ -766,20 +768,21 @@ public Object execute(LeveyJenningsPlotOptions form, BindException errors)
                     valuesToPersist.put("endDate", form.getEndDate());
                     valuesToPersist.put("selectedAnnotations", form.getSelectedAnnotationsString());
 
-                    properties.putAll(valuesToPersist);
-                    properties.save();
+                    writable.putAll(valuesToPersist);
+                    writable.save();
                 }
                 else
                 {
-                    if (properties.containsKey("selectedAnnotations") && (ReplicateManager.getReplicateAnnotationNameValues(getContainer()).size() == 0))
+                    if (writable.containsKey("selectedAnnotations") && (ReplicateManager.getReplicateAnnotationNameValues(getContainer()).isEmpty()))
                     {
                         // If there are no replicate annotations in this folder anymore, remove any saved annotation filters
                         // Issue 35726: No way to clear previously saved replicate annotation values in QC plots if folder no longer contains annotations
-                        properties.remove("selectedAnnotations");
-                        properties.save();
+                        writable.remove("selectedAnnotations");
+                        writable.save();
                     }
                 }
 
+                properties = writable;
             }
 
             if (properties == null || properties.isEmpty())
@@ -802,8 +805,8 @@ public static class SaveQCPlotSettingsAsDefaultAction extends MutatingApiAction<
         @Override
         public Object execute(LeveyJenningsPlotOptions form, BindException errors)
         {
-            PropertyManager.PropertyMap current = PropertyManager.getProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY);
-            PropertyManager.PropertyMap defaults = PropertyManager.getWritableProperties(getContainer(), QCFolderConstants.CATEGORY, true);
+            PropertyMap current = PropertyManager.getProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY);
+            WritablePropertyMap defaults = PropertyManager.getWritableProperties(getContainer(), QCFolderConstants.CATEGORY, true);
             defaults.clear(); // Clear the map. There may be properties that are no longer applicable (e.g. selectedAnnotations, startDate, endDate).
             defaults.putAll(current);
             defaults.save();
@@ -825,7 +828,7 @@ public static class RevertToDefaultQCPlotSettingsAction extends MutatingApiActio
         @Override
         public Object execute(LeveyJenningsPlotOptions form, BindException errors)
         {
-            PropertyManager.PropertyMap current = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, false);
+            WritablePropertyMap current = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, false);
             if (current != null)
             {
                 current.delete();
@@ -837,7 +840,7 @@ public Object execute(LeveyJenningsPlotOptions form, BindException errors)
         }
     }
 
-    private static class LeveyJenningsPlotOptions
+    public static class LeveyJenningsPlotOptions
     {
         private String _metric;
         private String _yAxisScale;
@@ -1306,7 +1309,7 @@ public Object execute(QCMetricOutliersForm form, BindException errors)
                 response.put("offlineAnnotationTypeId", ts2.getObject(Integer.class));
             }
 
-            PropertyManager.PropertyMap properties = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, false);
+            WritablePropertyMap properties = PropertyManager.getWritableProperties(getUser(), getContainer(), QCFolderConstants.CATEGORY, false);
             if (properties != null)
             {
                 Map<String, Object> toSend = new HashMap<>(properties);
@@ -4158,7 +4161,7 @@ public static class PharmacokineticsOptionsAction extends MutatingApiAction<PKOp
         @Override
         public Object execute(PKOptions form, BindException errors)
         {
-            PropertyManager.PropertyMap properties = PropertyManager.getWritableProperties(getContainer(), getPropMapName(form), true);
+            WritablePropertyMap properties = PropertyManager.getWritableProperties(getContainer(), getPropMapName(form), true);
 
             // only stash option properties for users with editor role (i.e. UpdatePermissions)
             if (form.getSubgroups() != null && getContainer().hasPermission(getUser(), UpdatePermission.class))
diff --git a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
index 2f0be57f8..eb5f6e410 100644
--- a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
+++ b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
@@ -20,6 +20,7 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.pipeline.LocalDirectory;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineService;
@@ -119,7 +120,7 @@ else if (run.getCreated().after(new Date(Files.getLastModifiedTime(clibFile).toM
 
     public static int incrementLibraryRevision(Container container, User user, LocalDirectory localDirectory)
     {
-        PropertyManager.PropertyMap propMap = PropertyManager.getWritableProperties(container, "TargetedMS", true);
+        WritablePropertyMap propMap = PropertyManager.getWritableProperties(container, "TargetedMS", true);
         String revisionVal = propMap.get(PROP_CHROM_LIB_REVISION);
         int newRevision;
         if(revisionVal == null)
diff --git a/src/org/labkey/targetedms/folderImport/PanoramaQCSettings.java b/src/org/labkey/targetedms/folderImport/PanoramaQCSettings.java
index 0a7afd409..c5b101c6c 100644
--- a/src/org/labkey/targetedms/folderImport/PanoramaQCSettings.java
+++ b/src/org/labkey/targetedms/folderImport/PanoramaQCSettings.java
@@ -1,7 +1,6 @@
 package org.labkey.targetedms.folderImport;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.jasper.tagplugins.jstl.core.Import;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.admin.FolderImportContext;
@@ -12,6 +11,7 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.data.Results;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SimpleFilter;
@@ -253,7 +253,7 @@ public int importSettingsFromFile(FolderImportContext ctx, VirtualFile panoramaQ
                         props.load(is);
                         if (!ctx.getUser().isGuest())
                         {
-                            PropertyManager.PropertyMap properties = PropertyManager.getWritableProperties(ctx.getUser(), ctx.getContainer(), QCFolderConstants.CATEGORY, true);
+                            WritablePropertyMap properties = PropertyManager.getWritableProperties(ctx.getUser(), ctx.getContainer(), QCFolderConstants.CATEGORY, true);
                             for (Map.Entry<Object, Object> entry : props.entrySet())
                             {
                                 if (entry.getKey() instanceof String && entry.getValue() instanceof String)