From 593cb9e1f75e13335a44a186bcbf950b1745c1c2 Mon Sep 17 00:00:00 2001
From: Adam Rauch <adam@labkey.com>
Date: Tue, 31 Dec 2024 04:28:11 -0800
Subject: [PATCH 1/2] Bump schema versions to 25.000 (#994)

---
 src/org/labkey/targetedms/TargetedMSModule.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/org/labkey/targetedms/TargetedMSModule.java b/src/org/labkey/targetedms/TargetedMSModule.java
index c1f337dea..8af31999a 100644
--- a/src/org/labkey/targetedms/TargetedMSModule.java
+++ b/src/org/labkey/targetedms/TargetedMSModule.java
@@ -225,7 +225,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 24.005;
+        return 25.000;
     }
 
     @Override

From 03988bf0688b6868996079a67f1bcf72f45e44b6 Mon Sep 17 00:00:00 2001
From: Josh Eckels <jeckels@labkey.com>
Date: Thu, 2 Jan 2025 17:15:16 -0800
Subject: [PATCH 2/2] Handle case where file is imported after the job is
 queued (#996)

---
 .../labkey/targetedms/SkylineDocImporter.java | 35 ++++++-------------
 1 file changed, 10 insertions(+), 25 deletions(-)

diff --git a/src/org/labkey/targetedms/SkylineDocImporter.java b/src/org/labkey/targetedms/SkylineDocImporter.java
index b3388a101..232d8d849 100644
--- a/src/org/labkey/targetedms/SkylineDocImporter.java
+++ b/src/org/labkey/targetedms/SkylineDocImporter.java
@@ -208,7 +208,7 @@ public TargetedMSRun importRun(RunInfo runInfo, PipelineJob job) throws IOExcept
         }
 
         // Skip if run was already fully imported
-        if (runInfo.isAlreadyImported() && run.getStatusId() == SkylineDocImporter.STATUS_SUCCESS)
+        if (run.getStatusId() == SkylineDocImporter.STATUS_SUCCESS)
         {
             _log.info(_expData.getName() + " has already been imported so it does not need to be imported again");
             return run;
@@ -2583,60 +2583,45 @@ protected static void updateRunStatus(long runId, String status, int statusId)
     public static class RunInfo implements Serializable
     {
         private final long _runId;
-        private final boolean _alreadyImported;
 
         @JsonCreator
-        private RunInfo(@JsonProperty("_runId") long runId, @JsonProperty("_alreadyImported") boolean alreadyImported)
+        private RunInfo(@JsonProperty("_runId") long runId)
         {
             _runId = runId;
-
-            _alreadyImported = alreadyImported;
         }
 
         public long getRunId()
         {
             return _runId;
         }
-
-        public boolean isAlreadyImported()
-        {
-            return _alreadyImported;
-        }
     }
 
     public RunInfo prepareRun()
     {
         try (DbScope.Transaction transaction = TargetedMSManager.getSchema().getScope().ensureTransaction(_schemaLock))
         {
-            boolean alreadyImported = false;
-
             // Don't import if we've already imported this file (undeleted run exists matching this file name)
-            _runId = getRun();
-            if (_runId != -1)
-            {
-                alreadyImported = true;
-            }
-            else
+            TargetedMSRun run = getRun();
+            if (run == null)
             {
                 _log.info("Starting import from " + _expData.getName());
-                _runId = createRun();
+                run = createRun();
             }
 
             transaction.commit();
-            return new RunInfo(_runId, alreadyImported);
+            return new RunInfo(run.getRunId());
         }
     }
 
-    protected long getRun()
+    protected TargetedMSRun getRun()
     {
         SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("DataId"), _expData.getRowId());
         filter.addCondition(FieldKey.fromParts("Container"), _container.getId());
         filter.addCondition(FieldKey.fromParts("Deleted"), Boolean.FALSE);
-        TargetedMSRun run = new TableSelector(TargetedMSManager.getTableInfoRuns(), filter, null).getObject(TargetedMSRun.class);
-        return run != null ? run.getId() : -1;
+        return new TableSelector(TargetedMSManager.getTableInfoRuns(), filter, null).getObject(TargetedMSRun.class);
     }
 
-    protected long createRun()
+    protected TargetedMSRun createRun()
     {
         TargetedMSRun run = TargetedMSManager.getRunByDataId(_expData.getRowId(), _container);
         if (run != null)
@@ -2653,7 +2638,7 @@ protected long createRun()
         run.setRepresentativeDataState(_representative == null ? RunRepresentativeDataState.NotRepresentative : _representative);
 
         run = Table.insert(_user, TargetedMSManager.getTableInfoRuns(), run);
-        return run.getId();
+        return run;
     }
 
     protected void logError(String message, Exception e)