From f8481789db9d323af3e85bdf5a0f8f8dbcf73f48 Mon Sep 17 00:00:00 2001
From: John Brestelli <jbrestell@gmail.com>
Date: Tue, 23 Dec 2025 13:17:01 -0500
Subject: [PATCH] fix paths for metabolite profiles datasets

---
 Main/lib/xml/workflow/metaboliteProfiles.xml | 15 +++++++++------
 Main/lib/xml/workflowTemplates/project.xml   | 19 +++++++++++--------
 2 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/Main/lib/xml/workflow/metaboliteProfiles.xml b/Main/lib/xml/workflow/metaboliteProfiles.xml
index 44a84872..f2a56a95 100644
--- a/Main/lib/xml/workflow/metaboliteProfiles.xml
+++ b/Main/lib/xml/workflow/metaboliteProfiles.xml
@@ -4,21 +4,24 @@
     <param name="experimentVersion"/>
     <param name="gusConfigFile"/>
 
-    <constant name="dataDir">$$parentDataDir$$/$$experimentName$$</constant>
-    <constant name="workingDir">$$dataDir$$/workingDir</constant>
-    <constant name="resultsDir">$$dataDir$$/outputDir</constant>
+    <constant name="workingDir">$$parentDataDir$$/workingDir</constant>
+    <constant name="resultsDir">$$parentDataDir$$/outputDir</constant>
+    
+    <step name="makeWorkingDir" stepClass="ReFlow::StepClasses::MakeDataDir">
+      <paramValue name="dataDir">$$workingDir$$</paramValue>
+    </step>
 
     <step name="makeProfiles" stepClass="ApiCommonWorkflow::Main::WorkflowSteps::StudyAssayResultsNextflow">
-      <paramValue name="analysisConfigFile">$$experimentName$$/final/analysisConfig.xml</paramValue>
-      <paramValue name="finalDir">$$experimentName$$/final</paramValue>
+      <paramValue name="analysisConfigFile">$$parentDataDir$$/final/analysisConfig.xml</paramValue>
+      <paramValue name="finalDir">$$parentDataDir$$/final</paramValue>
       <paramValue name="workingDir">$$workingDir$$</paramValue>
       <paramValue name="resultsDir">$$resultsDir$$</paramValue>
       <paramValue name="technologyType">metabolite_massSpec</paramValue>
       <paramValue name="nextflowWorkflow">VEuPathDB/study-assay-results-nextflow</paramValue>
       <paramValue name="isGitRepo">true</paramValue>
+      <depends name="makeWorkingDir"/>
     </step>
 
-
   <step name="loadStudyResultsFromConfig" stepClass="ApiCommonWorkflow::Main::WorkflowSteps::InsertStudyResults" stepLoadTypes="plugin">
       <paramValue name="configFile">$$dataDir$$/outputDir/insert_study_results_config.txt</paramValue>
       <paramValue name="inputDir">$$dataDir$$/outputDir</paramValue>
diff --git a/Main/lib/xml/workflowTemplates/project.xml b/Main/lib/xml/workflowTemplates/project.xml
index c17a89fa..05a20920 100644
--- a/Main/lib/xml/workflowTemplates/project.xml
+++ b/Main/lib/xml/workflowTemplates/project.xml
@@ -716,7 +716,12 @@
     </subgraph>
   </datasetTemplate>
 
-  <!-- old template deprecated-->
+  <step name="makeMetabolomicsDataDir" stepClass="ReFlow::StepClasses::MakeDataDir">
+    <paramValue name="dataDir">$$dataDir$$/metabolomics</paramValue>
+    <depends name="makeDataDir"/>
+  </step>
+  
+  <!-- old template but still in use -->
   <datasetTemplate class="metaboliteProfiles">
     <prop name="experimentName"/>
     <prop name="experimentVersion"/>
@@ -725,24 +730,22 @@
       <paramValue name="gusConfigFile">$$projectGusConfigFile$$</paramValue>
       <paramValue name="datasetName">metaboliteProfiles_${experimentName}_RSRC</paramValue>
       <paramValue name="datasetLoaderXmlFileName">$$projectName$$.xml</paramValue>
-      <paramValue name="parentDataDir">$$dataDir$$</paramValue>
+      <paramValue name="parentDataDir">$$dataDir$$/metabolomics</paramValue>      
+      <depends name="makeMetabolomicsDataDir"/>
       <!--<dependsGlobal name="chEBI_Compounds"/>-->
     </subgraph>
 
     <subgraph name="MetaboliteProfiles" xmlFile="metaboliteProfiles.xml">
       <paramValue name="gusConfigFile">$$projectGusConfigFile$$</paramValue>
-      <paramValue name="parentDataDir">$$dataDir$$</paramValue>
+      <paramValue name="parentDataDir">$$dataDir$$/metabolomics/metaboliteProfiles_${experimentName}_RSRC</paramValue>      
       <paramValue name="experimentName">metaboliteProfiles_${experimentName}_RSRC</paramValue>
       <paramValue name="experimentVersion">${experimentVersion}</paramValue>
       <depends name="metaboliteProfiles_${experimentName}_RSRC"/>
     </subgraph>
+
   </datasetTemplate>
 
-  <!-- new template for untargeted metabolomics -->
-  <step name="makeMetabolomicsDataDir" stepClass="ReFlow::StepClasses::MakeDataDir">
-    <paramValue name="dataDir">$$dataDir$$/metabolomics</paramValue>
-    <depends name="makeDataDir"/>
-  </step>
+  <!-- new template for untargeted metabolomics BUT not used on frontend yet -->
 
   <datasetTemplate class="compoundMassSpec">
     <prop name="experimentName"/>