From c96418d6d06e759ac3dc485d323314af5bf9caa6 Mon Sep 17 00:00:00 2001
From: Josh Eckels <jeckels@labkey.com>
Date: Fri, 26 Jul 2019 11:25:32 -0700
Subject: [PATCH] Issue 38083: PK calculations in Panorama don't render if
 SubGroup annotation isn't present (#37)

Also, don't log NPE if audit log isn't available during import
---
 resources/queries/targetedms/Pharmacokinetics.sql     | 2 +-
 src/org/labkey/targetedms/SkylineAuditLogManager.java | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/resources/queries/targetedms/Pharmacokinetics.sql b/resources/queries/targetedms/Pharmacokinetics.sql
index d32c86365..34ad36f77 100644
--- a/resources/queries/targetedms/Pharmacokinetics.sql
+++ b/resources/queries/targetedms/Pharmacokinetics.sql
@@ -17,7 +17,7 @@ SELECT
   sub.PeptideId,
   sub.MoleculeId,
   sub.Time,
-  sub.SubGroup,
+  COALESCE(sub.SubGroup, 'Default') AS SubGroup,
   (CASE WHEN MAX(sub.Dose)= MIN(sub.Dose) THEN MAX(sub.Dose) ELSE NULL END) AS Dose,
   (CASE WHEN MAX(sub.DoseUnits)= MIN(sub.DoseUnits) THEN MAX(sub.DoseUnits) ELSE NULL END) AS DoseUnits,
   (CASE WHEN MAX(sub.ROA)= MIN(sub.ROA) THEN MAX(sub.ROA) ELSE NULL END) AS ROA,
diff --git a/src/org/labkey/targetedms/SkylineAuditLogManager.java b/src/org/labkey/targetedms/SkylineAuditLogManager.java
index b942835d0..f5c605e6c 100644
--- a/src/org/labkey/targetedms/SkylineAuditLogManager.java
+++ b/src/org/labkey/targetedms/SkylineAuditLogManager.java
@@ -40,7 +40,6 @@
 import org.labkey.targetedms.parser.skyaudit.AuditLogMessageExpander;
 import org.labkey.targetedms.parser.skyaudit.AuditLogParsingException;
 import org.labkey.targetedms.parser.skyaudit.AuditLogTree;
-import org.labkey.targetedms.parser.skyaudit.DatabaseUtil;
 import org.labkey.targetedms.parser.skyaudit.SkylineAuditLogParser;
 import org.labkey.targetedms.parser.skyaudit.SkylineAuditLogSecurityManager;
 import org.labkey.targetedms.parser.skyaudit.TestRun;
@@ -122,6 +121,7 @@ private boolean verifyPreRequisites(AuditLogImportContext pContext) throws Audit
         if(pContext._logFile == null || !pContext._logFile.exists()){
             if(_securityMgr.getIntegrityLevel() == SkylineAuditLogSecurityManager.INTEGRITY_LEVEL.ANY){
                 _logger.warn("Log file is missing. Proceeding without the log.");
+                return false;
             }
             else
                 throw new AuditLogException("Current log integrity setting do not allow to upload a file without a valid audit log. ");
@@ -154,8 +154,7 @@ private boolean verifyPreRequisites(AuditLogImportContext pContext) throws Audit
                     .append(" ")
                     .append(docFilter.getSQLFragment(TargetedMSManager.getSqlDialect()));
 
-        Integer res = new SqlSelector(TargetedMSManager.getSchema(), query).getObject(Integer.class);
-        Integer docCount = (Integer)res;
+        Integer docCount = new SqlSelector(TargetedMSManager.getSchema(), query).getObject(Integer.class);
         pContext._logTree = buildLogTree(pContext._documentGUID);
 
         //verify that the tree is not empty