# HG changeset patch
# User francesco_lapi
# Date 1757078554 0
# Node ID 64563ca68ace95a9eb2dc2708b02656a2291ce10
# Parent  a0b53ccc73a8b6ecdaf596cab33f199188da5c35
Uploaded

diff -r a0b53ccc73a8 -r 64563ca68ace COBRAxy/custom_data_generator.py
--- a/COBRAxy/custom_data_generator.py	Fri Sep 05 13:05:29 2025 +0000
+++ b/COBRAxy/custom_data_generator.py	Fri Sep 05 13:22:34 2025 +0000
@@ -229,7 +229,9 @@
     # Determine final model name: explicit --name overrides, otherwise use the model id
     
     model_name = ARGS.name if ARGS.name else ARGS.model
-    
+    print(ARGS.name)
+    print(model_name)
+    print(ARGS.medium_selector)
     
     if ARGS.name == "ENGRO2" and ARGS.medium_selector != "Default":
         df_mediums = pd.read_csv(ARGS.tool_dir + "/local/medium/medium.csv", index_col = 0)
@@ -247,7 +249,7 @@
                 model.reactions.get_by_id(reaction).lower_bound = -float(value)
 
     if ARGS.name == "ENGRO2" and ARGS.gene_format != "Default":
-        utils.convert_genes(model, ARGS.gene_format)
+        model = utils.convert_genes(model, ARGS.gene_format)
 
     # generate data
     rules = generate_rules(model, asParsed = False)
diff -r a0b53ccc73a8 -r 64563ca68ace COBRAxy/custom_data_generator.xml
--- a/COBRAxy/custom_data_generator.xml	Fri Sep 05 13:05:29 2025 +0000
+++ b/COBRAxy/custom_data_generator.xml	Fri Sep 05 13:22:34 2025 +0000
@@ -15,7 +15,7 @@
         <![CDATA[
       	python $__tool_directory__/custom_data_generator.py
         --tool_dir $__tool_directory__
-        --medium_selector $cond_model.medium_selector
+        --medium_selector $cond_model.cond_medium.medium_selector
         #if $cond_model.model_selector == 'Custom_model'
             --input $cond_model.input
             --name $cond_model.name
@@ -37,7 +37,7 @@
             <!-- ENGRO2 -->
             <when value="ENGRO2">
                 <param name="name" argument="--name" type="text" value="ENGRO2" hidden="true" />
-                <conditional name="medium_selector">
+                <conditional name="cond_medium">
                     <expand macro="options_ras_to_bounds_medium"/>
                 </conditional>
             </when>
@@ -45,7 +45,7 @@
             <!-- Recon -->
             <when value="Recon">
                 <param name="name" argument="--name" type="text" value="Recon" hidden="true" />
-                <conditional name="medium_selector">
+                <conditional name="cond_medium">
                     <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
                         <option value="Default" selected="true">Default (Recon built-in medium)</option>
                     </param>
@@ -59,7 +59,7 @@
             <when value="Custom_model">
                 <param name="input" argument="--input" type="data" format="json,xml" label="Custom model file:" />
                 <param name="name" argument="--name" type="text" label="Model's name:" value="CustomModel" />
-                <conditional name="medium_selector">
+                <conditional name="cond_medium">
                     <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
                         <option value="Default" selected="true">Don't use a separate medium file (use model defaults)</option>
                     </param>