From d96f08bc65ce7b5012d970549a9af1a9a13cf355 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Thu, 19 Dec 2024 15:30:07 -0800
Subject: [PATCH 1/2] Delete MS2 GWT code. Switch to simple job launcher

---
 .../org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java b/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java
index 2c137f1f5..cd8097215 100644
--- a/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java
+++ b/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java
@@ -122,7 +122,7 @@ private void startCalculation(User u, Container c, boolean allowRunningDuringDay
             if (!inputFile.exists())
                 inputFile.createNewFile();
 
-            AbstractFileAnalysisJob job = protocol.createPipelineJob(bg, root, Collections.singletonList(inputFile), fileParameters, null);
+            AbstractFileAnalysisJob job = protocol.createPipelineJob(bg, root, Collections.singletonList(inputFile.toPath()), fileParameters.toPath(), null);
             PipelineService.get().queueJob(job);
 
             String dateFormat = "yyyy_MM_dd_hh_mm_ss";

From b33d334898e0e38f368778017a85d3dc9b94ffe6 Mon Sep 17 00:00:00 2001
From: labkey-jeckels <jeckels@labkey.com>
Date: Sun, 22 Dec 2024 12:31:26 -0800
Subject: [PATCH 2/2] Fix CometTest. Trim now unused code

---
 .../org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java b/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java
index cd8097215..c803e43cb 100644
--- a/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java
+++ b/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java
@@ -89,7 +89,7 @@ private void startCalculation(User u, Container c, boolean allowRunningDuringDay
                     "\t<note label=\"jobCreateTime\" type=\"input\">" + new Date().getTime() + "</note>" +
                 "</bioml>";
 
-            AbstractFileAnalysisProtocol<?> protocol = factory.createProtocolInstance(protocolName, "", xml);
+            AbstractFileAnalysisProtocol<?> protocol = factory.createProtocolInstance(protocolName, "", xml, c);
             if (protocol == null)
             {
                 return;