--- a/COBRAxy/ras_to_bounds_beta.py	Mon Sep 08 21:37:14 2025 +0000
+++ b/COBRAxy/ras_to_bounds_beta.py	Mon Sep 08 21:54:14 2025 +0000
@@ -10,6 +10,7 @@
 import sys
 import csv
 from joblib import Parallel, delayed, cpu_count
+import utils.rule_parsing  as rulesUtils
 
 # , medium
 
@@ -149,6 +150,126 @@
                 new_bounds.loc[reaction, "upper_bound"] = valMax
     return new_bounds
 
+################################- DATA GENERATION -################################
+ReactionId = str
+def generate_rules(model: cobra.Model, *, asParsed = True) -> Union[Dict[ReactionId, rulesUtils.OpList], Dict[ReactionId, str]]:
+    """
+    Generates a dictionary mapping reaction ids to rules from the model.
+
+    Args:
+        model : the model to derive data from.
+        asParsed : if True parses the rules to an optimized runtime format, otherwise leaves them as strings.
+
+    Returns:
+        Dict[ReactionId, rulesUtils.OpList] : the generated dictionary of parsed rules.
+        Dict[ReactionId, str] : the generated dictionary of raw rules.
+    """
+    # Is the below approach convoluted? yes
+    # Ok but is it inefficient? probably
+    # Ok but at least I don't have to repeat the check at every rule (I'm clinically insane)
+    _ruleGetter   =  lambda reaction : reaction.gene_reaction_rule
+    ruleExtractor = (lambda reaction :
+        rulesUtils.parseRuleToNestedList(_ruleGetter(reaction))) if asParsed else _ruleGetter
+
+    return {
+        reaction.id : ruleExtractor(reaction)
+        for reaction in model.reactions
+        if reaction.gene_reaction_rule }
+
+def generate_reactions(model :cobra.Model, *, asParsed = True) -> Dict[ReactionId, str]:
+    """
+    Generates a dictionary mapping reaction ids to reaction formulas from the model.
+
+    Args:
+        model : the model to derive data from.
+        asParsed : if True parses the reactions to an optimized runtime format, otherwise leaves them as they are.
+
+    Returns:
+        Dict[ReactionId, str] : the generated dictionary.
+    """
+
+    unparsedReactions = {
+        reaction.id : reaction.reaction
+        for reaction in model.reactions
+        if reaction.reaction 
+    }
+
+    if not asParsed: return unparsedReactions
+    
+    return reactionUtils.create_reaction_dict(unparsedReactions)
+
+def get_medium(model:cobra.Model) -> pd.DataFrame:
+    trueMedium=[]
+    for r in model.reactions:
+        positiveCoeff=0
+        for m in r.metabolites:
+            if r.get_coefficient(m.id)>0:
+                positiveCoeff=1;
+        if (positiveCoeff==0 and r.lower_bound<0):
+            trueMedium.append(r.id)
+
+    df_medium = pd.DataFrame()
+    df_medium["reaction"] = trueMedium
+    return df_medium
+
+def generate_bounds(model:cobra.Model) -> pd.DataFrame:
+
+    rxns = []
+    for reaction in model.reactions:
+        rxns.append(reaction.id)
+
+    bounds = pd.DataFrame(columns = ["lower_bound", "upper_bound"], index=rxns)
+
+    for reaction in model.reactions:
+        bounds.loc[reaction.id] = [reaction.lower_bound, reaction.upper_bound]
+    return bounds
+
+
+
+def generate_compartments(model: cobra.Model) -> pd.DataFrame:
+    """
+    Generates a DataFrame containing compartment information for each reaction.
+    Creates columns for each compartment position (Compartment_1, Compartment_2, etc.)
+    
+    Args:
+        model: the COBRA model to extract compartment data from.
+        
+    Returns:
+        pd.DataFrame: DataFrame with ReactionID and compartment columns
+    """
+    pathway_data = []
+
+    # First pass: determine the maximum number of pathways any reaction has
+    max_pathways = 0
+    reaction_pathways = {}
+
+    for reaction in model.reactions:
+        # Get unique pathways from all metabolites in the reaction
+        if type(reaction.annotation['pathways']) == list:
+            reaction_pathways[reaction.id] = reaction.annotation['pathways']
+            max_pathways = max(max_pathways, len(reaction.annotation['pathways']))
+        else:
+            reaction_pathways[reaction.id] = [reaction.annotation['pathways']]
+
+    # Create column names for pathways
+    pathway_columns = [f"Pathway_{i+1}" for i in range(max_pathways)]
+
+    # Second pass: create the data
+    for reaction_id, pathways in reaction_pathways.items():
+        row = {"ReactionID": reaction_id}
+        
+        # Fill pathway columns
+        for i in range(max_pathways):
+            col_name = pathway_columns[i]
+            if i < len(pathways):
+                row[col_name] = pathways[i]
+            else:
+                row[col_name] = None  # or "" if you prefer empty strings
+
+        pathway_data.append(row)
+
+    return pd.DataFrame(pathway_data)
+
 def save_model(model, filename, output_folder, file_format='csv'):
     """
     Save a COBRA model to file in the specified format.
@@ -170,10 +291,10 @@
             # Special handling for tabular format using utils functions
             filepath = os.path.join(output_folder, f"{filename}.csv")
             
-            rules = utils.generate_rules(model, asParsed = False)
-            reactions = utils.generate_reactions(model, asParsed = False)
-            bounds = utils.generate_bounds(model)
-            medium = utils.get_medium(model)
+            rules = generate_rules(model, asParsed = False)
+            reactions = generate_reactions(model, asParsed = False)
+            bounds = generate_bounds(model)
+            medium = get_medium(model)
             
             try:
                 compartments = utils.generate_compartments(model)
@@ -269,7 +390,7 @@
     
     pass
 
-def generate_bounds(model: cobra.Model, ras=None, output_folder='output/', save_models=False, save_models_path='saved_models/', save_models_format='csv') -> pd.DataFrame:
+def generate_bounds_model(model: cobra.Model, ras=None, output_folder='output/', save_models=False, save_models_path='saved_models/', save_models_format='csv') -> pd.DataFrame:
     """
     Generate reaction bounds for a metabolic model based on medium conditions and optional RAS adjustments.
     
@@ -369,12 +490,12 @@
         print(f"{key}: {value}")
 
     if(ARGS.ras_selector == True):
-        generate_bounds(model, ras=ras_combined, output_folder=ARGS.output_path,
+        generate_bounds_model(model, ras=ras_combined, output_folder=ARGS.output_path,
                        save_models=ARGS.save_models, save_models_path=ARGS.save_models_path,
                        save_models_format=ARGS.save_models_format)
         class_assignments.to_csv(ARGS.cell_class, sep='\t', index=False)
     else:
-        generate_bounds(model, output_folder=ARGS.output_path,
+        generate_bounds_model(model, output_folder=ARGS.output_path,
                        save_models=ARGS.save_models, save_models_path=ARGS.save_models_path,
                        save_models_format=ARGS.save_models_format)