# HG changeset patch
# User francesco_lapi
# Date 1757276963 0
# Node ID 6c7ddf68381ad9a7fe612bee0f673b93052496b3
# Parent  e94735cb40fa8581007b394220f05adb15cdbbe7
Uploaded

diff -r e94735cb40fa -r 6c7ddf68381a COBRAxy/ras_generator.py
--- a/COBRAxy/ras_generator.py	Sun Sep 07 20:07:44 2025 +0000
+++ b/COBRAxy/ras_generator.py	Sun Sep 07 20:29:23 2025 +0000
@@ -647,15 +647,41 @@
     #if filenamePath.ext is utils.FileFormat.PICKLE: return utils.readPickle(datFilePath)
 
     dict_rule = {}
-    for line in utils.readCsv(datFilePath, delimiter = "\t"):
-        if line[2] == "":
-            dict_rule[line[0]] = ruleUtils.OpList([""])
-        else:
-            dict_rule[line[0]] = ruleUtils.parseRuleToNestedList(line[2])
 
+    try:
+        # Proviamo prima con delimitatore tab
+        for line in utils.readCsv(datFilePath, delimiter = "\t"):
+            if len(line) < 3:  # Controlliamo che ci siano almeno 3 colonne
+                utils.logWarning(f"Skipping malformed line: {line}", ARGS.out_log)
+                continue
+            
+            if line[2] == "":
+                dict_rule[line[0]] = ruleUtils.OpList([""])
+            else:
+                dict_rule[line[0]] = ruleUtils.parseRuleToNestedList(line[2])
+                
+    except Exception as e:
+        # Se fallisce con tab, proviamo con virgola
+        try:
+            dict_rule = {}
+            for line in utils.readCsv(datFilePath, delimiter = ","):
+                if len(line) < 3:
+                    utils.logWarning(f"Skipping malformed line: {line}", ARGS.out_log)
+                    continue
+                
+                if line[2] == "":
+                    dict_rule[line[0]] = ruleUtils.OpList([""])
+                else:
+                    dict_rule[line[0]] = ruleUtils.parseRuleToNestedList(line[2])
+        except Exception as e2:
+            raise ValueError(f"Unable to parse rules file. Tried both tab and comma delimiters. Original errors: Tab: {e}, Comma: {e2}")
+
+    if not dict_rule:
+            raise ValueError("No valid rules found in the uploaded file. Please check the file format.")
     # csv rules need to be parsed, those in a pickle format are taken to be pre-parsed.
     return dict_rule
 
+
 def main(args:List[str] = None) -> None:
     """
     Initializes everything and sets the program in motion based on the fronted input arguments.
diff -r e94735cb40fa -r 6c7ddf68381a COBRAxy/ras_generator.xml
--- a/COBRAxy/ras_generator.xml	Sun Sep 07 20:07:44 2025 +0000
+++ b/COBRAxy/ras_generator.xml	Sun Sep 07 20:29:23 2025 +0000
@@ -24,9 +24,11 @@
         ]]>
     </command>
     <inputs>
-        <param name="model_upload" argument="--model_upload" type="data" format="csv, tsv, tabular" label="Custom model (optional)" help="If not provided, the selected model will be used." />
-        <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
-        <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset_RAS" help="Default: Dataset_RAS. Do not use white spaces or special symbols." />
+        <param name="model_upload" argument="--model_upload" type="data" format="csv,tsv,tabular" 
+                label="Model rules file:" help="Upload a CSV/TSV file containing reaction rules generated by the Model Initialization tool." />
+        <param name="input" argument="--input" type="data" format="tabular,csv,tsv" label="Gene Expression dataset:" />
+        <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset_RAS" 
+                help="Default: Dataset_RAS. Do not use white spaces or special symbols." />
         <param name="none" argument="--none" type="boolean" checked="true" label="(A and NaN) solved as (A)?" /> 
     </inputs>