From f9237099b05fbeb5a5b9d5d6af10487a6cf543ff Mon Sep 17 00:00:00 2001
From: Josh Eckels <jeckels@labkey.com>
Date: Mon, 3 Mar 2025 14:03:24 -0800
Subject: [PATCH 1/2] Handle bad peptide_group_id values more gracefully (#212)

---
 .../org/scharp/atlas/pepdb/PepDBController.java    | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/pepdb/src/org/scharp/atlas/pepdb/PepDBController.java b/pepdb/src/org/scharp/atlas/pepdb/PepDBController.java
index c0998ff6..a45484b0 100644
--- a/pepdb/src/org/scharp/atlas/pepdb/PepDBController.java
+++ b/pepdb/src/org/scharp/atlas/pepdb/PepDBController.java
@@ -33,6 +33,7 @@
 import org.labkey.api.view.InsertView;
 import org.labkey.api.view.JspView;
 import org.labkey.api.view.NavTree;
+import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.UpdateView;
 import org.labkey.api.view.VBox;
 import org.labkey.api.view.ViewContext;
@@ -442,7 +443,18 @@ public class DisplayPeptideGroupInformationAction extends SimpleViewAction<Pepti
         public ModelAndView getView(PeptideAndGroupForm form, BindException errors) throws Exception
         {
             _log.debug("PeptideAndGroupForm: " + form.toString());
-            PeptideGroup pg = PepDBManager.getPeptideGroupByID(Integer.parseInt(form.getPeptide_group_id()));
+            PeptideGroup pg = null;
+            try
+            {
+                int peptideGroupId = Integer.parseInt(form.getPeptide_group_id());
+                pg = PepDBManager.getPeptideGroupByID(peptideGroupId);
+            }
+            catch (NumberFormatException ignored) {}
+            if (pg == null || !getContainer().getId().equalsIgnoreCase(pg.getContainerId()))
+            {
+                throw new NotFoundException();
+            }
+
             DataRegion rgn1 = new DataRegion();
             TableInfo tableInfo1 = PepDBSchema.getInstance().getTableInfoPeptideGroups();
             rgn1.setColumns(tableInfo1.getColumns("peptide_group_id,peptide_group_name,pathogen_id,seq_ref,clade_id,pep_align_ref_id,group_type_id,createdby,created,modifiedby,modified"));

From 4ed7ed58371788ba7d3763490ee1881ca6c1daf9 Mon Sep 17 00:00:00 2001
From: Trey Chadick <tchad@labkey.com>
Date: Tue, 18 Mar 2025 10:27:37 -0700
Subject: [PATCH 2/2] Don't use error log for non-error (#215)

---
 pepdb/src/org/scharp/atlas/pepdb/PepDBController.java | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pepdb/src/org/scharp/atlas/pepdb/PepDBController.java b/pepdb/src/org/scharp/atlas/pepdb/PepDBController.java
index a45484b0..ae4a8760 100644
--- a/pepdb/src/org/scharp/atlas/pepdb/PepDBController.java
+++ b/pepdb/src/org/scharp/atlas/pepdb/PepDBController.java
@@ -1,5 +1,8 @@
 package org.scharp.atlas.pepdb;
 
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpSession;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.action.ExportAction;
@@ -46,9 +49,6 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import jakarta.servlet.http.HttpServletRequest;
-import jakarta.servlet.http.HttpServletResponse;
-import jakarta.servlet.http.HttpSession;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.ArrayList;
@@ -912,7 +912,7 @@ public void export(Object bean, HttpServletResponse response, BindException erro
             ViewContext ctx = getViewContext();
             HttpSession session = ctx.getRequest().getSession();
             PeptideQueryForm form = (PeptideQueryForm) session.getAttribute("PEPTIDE_QUERY_FORM");
-            _log.error("Form " + form.getMessage() + " had filter : " + form.getFilter());
+            _log.info("Form " + form.getMessage() + " had filter : " + form.getFilter());
             printExcel(bean, response, errors, form);
         }
     }