annotate COBRAxy/src/utils/model_utils.py @ 539:2fb97466e404 draft

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"""
Utilities for generating and manipulating COBRA models and related metadata.

This module includes helpers to:
- extract rules, reactions, bounds, objective coefficients, and compartments
- build a COBRA model from a tabular file
- set objective and medium from dataframes
- validate a model and convert gene identifiers
- translate model GPRs using mapping tables
"""
import os
import cobra
import pandas as pd
import re
import logging
from typing import Optional, Tuple, Union, List, Dict, Set
from collections import defaultdict
import utils.rule_parsing  as rulesUtils
import utils.reaction_parsing as reactionUtils
from cobra import Model as cobraModel, Reaction, Metabolite
import sys


############################ check_methods ####################################
def gene_type(l :str, name :str) -> str:
    """
    Determine the type of gene ID.

    Args:
        l (str): The gene identifier to check.
        name (str): The name of the dataset, used in error messages.

    Returns:
        str: The type of gene ID ('HGNC_ID', 'ENSG', 'HGNC_symbol', or 'entrez_id').

    Raises:
        sys.exit: If the gene ID type is not supported, the execution is aborted.
    """
    if check_hgnc(l):
        return 'HGNC_ID'
    elif check_ensembl(l):
        return 'ENSG'
    elif check_symbol(l):
        return 'HGNC_symbol'
    elif check_entrez(l):
        return 'entrez_id'
    else:
        sys.exit('Execution aborted:\n' +
                 'gene ID type in ' + name + ' not supported. Supported ID'+
                 'types are: HUGO ID, Ensemble ID, HUGO symbol, Entrez ID\n')

def check_hgnc(l :str) -> bool:
    """
    Check if a gene identifier follows the HGNC format.

    Args:
        l (str): The gene identifier to check.

    Returns:
        bool: True if the gene identifier follows the HGNC format, False otherwise.
    """
    if len(l) > 5:
        if (l.upper()).startswith('HGNC:'):
            return l[5:].isdigit()
        else:
            return False
    else:
        return False

def check_ensembl(l :str) -> bool:
    """
    Check if a gene identifier follows the Ensembl format.

    Args:
        l (str): The gene identifier to check.

    Returns:
        bool: True if the gene identifier follows the Ensembl format, False otherwise.
    """
    return l.upper().startswith('ENS')
 

def check_symbol(l :str) -> bool:
    """
    Check if a gene identifier follows the symbol format.

    Args:
        l (str): The gene identifier to check.

    Returns:
        bool: True if the gene identifier follows the symbol format, False otherwise.
    """
    if len(l) > 0:
        if l[0].isalpha() and l[1:].isalnum():
            return True
        else:
            return False
    else:
        return False

def check_entrez(l :str) -> bool:
    """
    Check if a gene identifier follows the Entrez ID format.

    Args:
        l (str): The gene identifier to check.

    Returns:
        bool: True if the gene identifier follows the Entrez ID format, False otherwise.
    """ 
    if len(l) > 0:
        return l.isdigit()
    else: 
        return False

################################- DATA GENERATION -################################
ReactionId = str
def generate_rules(model: cobraModel, *, asParsed = True) -> Union[Dict[ReactionId, rulesUtils.OpList], Dict[ReactionId, str]]:
    """
    Generate a dictionary mapping reaction IDs to GPR rules from the model.

    Args:
        model: COBRA model to derive data from.
        asParsed: If True, parse rules into a nested list structure; otherwise keep raw strings.

    Returns:
        Dict[ReactionId, rulesUtils.OpList]: Parsed rules by reaction ID.
        Dict[ReactionId, str]: Raw rules by reaction ID.
    """
    _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 :cobraModel, *, asParsed = True) -> Dict[ReactionId, str]:
    """
    Generate a dictionary mapping reaction IDs to reaction formulas from the model.

    Args:
        model: COBRA model to derive data from.
        asParsed: If True, convert formulas into a parsed representation; otherwise keep raw strings.

    Returns:
        Dict[ReactionId, str]: Reactions by reaction ID (parsed if requested).
    """

    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:cobraModel) -> pd.DataFrame:
    """
    Extract the uptake reactions representing the model medium.

    Returns a DataFrame with a single column 'reaction' listing exchange reactions
    with negative lower bound and no positive stoichiometric coefficients (uptake only).
    """
    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 extract_objective_coefficients(model: cobraModel) -> pd.DataFrame:
    """
    Extract objective coefficients for each reaction.

    Args:
        model: COBRA model

    Returns:
        pd.DataFrame with columns: ReactionID, ObjectiveCoefficient
    """
    coeffs = []
    # model.objective.expression is a linear expression
    objective_expr = model.objective.expression.as_coefficients_dict()
    
    for reaction in model.reactions:
        coeff = objective_expr.get(reaction.forward_variable, 0.0)
        coeffs.append({
            "ReactionID": reaction.id,
            "ObjectiveCoefficient": coeff
        })
    
    return pd.DataFrame(coeffs)

def generate_bounds(model:cobraModel) -> pd.DataFrame:
    """
    Build a DataFrame of lower/upper bounds for all reactions.

    Returns:
        pd.DataFrame indexed by reaction IDs with columns ['lower_bound', 'upper_bound'].
    """

    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: cobraModel) -> pd.DataFrame:
    """
    Generates a DataFrame containing pathway information for each reaction.
    Creates columns for each pathway position (Pathway_1, Pathway_2, etc.) only if pathways exist.
    
    Args:
        model: the COBRA model to extract pathway data from.
        
    Returns:
        pd.DataFrame: DataFrame with ReactionID and pathway columns (if any pathways exist)
    """
    pathway_data = []

    # First pass: determine the maximum number of pathways any reaction has
    max_pathways = 0
    reaction_pathways = {}
    has_any_pathways = False

    for reaction in model.reactions:
        # Get unique pathways from all metabolites in the reaction
        if 'pathways' in reaction.annotation and reaction.annotation['pathways']:
            if type(reaction.annotation['pathways']) == list:
                # Filter out empty/None values
                valid_pathways = [p for p in reaction.annotation['pathways'] if p]
                if valid_pathways:
                    reaction_pathways[reaction.id] = valid_pathways
                    max_pathways = max(max_pathways, len(valid_pathways))
                    has_any_pathways = True
                else:
                    reaction_pathways[reaction.id] = []
            else:
                # Single pathway value
                if reaction.annotation['pathways']:
                    reaction_pathways[reaction.id] = [reaction.annotation['pathways']]
                    max_pathways = max(max_pathways, 1)
                    has_any_pathways = True
                else:
                    reaction_pathways[reaction.id] = []
        else:
            # No pathway annotation - use empty list
            reaction_pathways[reaction.id] = []

    # If no pathways exist in the model, return DataFrame with only ReactionID
    if not has_any_pathways:
        return None

    # Create column names for pathways only if they exist
    pathway_columns = [f"Pathway_{i+1}" for i in range(max_pathways)]

    # Second pass: create the data with pathway columns
    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

        pathway_data.append(row)

    return pd.DataFrame(pathway_data)

def set_annotation_pathways_from_data(model: cobraModel, df: pd.DataFrame):
    """Set reaction pathways based on 'Pathway_1', 'Pathway_2', ... columns in the dataframe."""
    pathway_cols = [col for col in df.columns if col.startswith('Pathway_')]
    if not pathway_cols:
        print("No 'Pathway_' columns found, skipping pathway annotation")
        return
    
    pathway_data = defaultdict(list)
    
    for idx, row in df.iterrows():
        reaction_id = str(row['ReactionID']).strip()
        if reaction_id not in model.reactions:
            continue
        
        pathways = []
        for col in pathway_cols:
            if pd.notna(row[col]) and str(row[col]).strip():
                pathways.append(str(row[col]).strip())
        
        if pathways:

            reaction = model.reactions.get_by_id(reaction_id)
            if len(pathways) == 1:
                reaction.annotation['pathways'] = pathways[0]
            else:
                reaction.annotation['pathways'] = pathways

            pathway_data[reaction_id] = pathways
    
    print(f"Annotated {len(pathway_data)} reactions with pathways.")

def build_cobra_model_from_csv(csv_path: str, model_id: str = "new_model") -> cobraModel:
    """
    Build a COBRApy model from a tabular file with reaction data.

    Args:
        csv_path: Path to the tab-separated file.
        model_id: ID for the newly created model.

    Returns:
        cobra.Model: The constructed COBRApy model.
    """
    
    # Try to detect separator
    with open(csv_path, 'r') as f:
        first_line = f.readline()
        sep = '\t' if '\t' in first_line else ','
    
    df = pd.read_csv(csv_path, sep=sep)
    
    # Check required columns
    required_cols = ['ReactionID', 'Formula']
    missing_cols = [col for col in required_cols if col not in df.columns]
    if missing_cols:
        raise ValueError(f"Missing required columns: {missing_cols}. Available columns: {list(df.columns)}")
    
    model = cobraModel(model_id)
    
    metabolites_dict = {}
    compartments_dict = {}
    
    print(f"Building model from {len(df)} reactions...")
    
    for idx, row in df.iterrows():
        reaction_formula = str(row['Formula']).strip()
        if not reaction_formula or reaction_formula == 'nan':
            continue
            
        metabolites = extract_metabolites_from_reaction(reaction_formula)
        
        for met_id in metabolites:
            compartment = extract_compartment_from_metabolite(met_id)
            
            if compartment not in compartments_dict:
                compartments_dict[compartment] = compartment
            
            if met_id not in metabolites_dict:
                metabolites_dict[met_id] = Metabolite(
                    id=met_id,
                    compartment=compartment,
                    name=met_id.replace(f"_{compartment}", "").replace("__", "_")
                )
    
    model.compartments = compartments_dict
    
    model.add_metabolites(list(metabolites_dict.values()))
    
    print(f"Added {len(metabolites_dict)} metabolites and {len(compartments_dict)} compartments")
    
    reactions_added = 0
    reactions_skipped = 0
    
    for idx, row in df.iterrows():

        reaction_id = str(row['ReactionID']).strip()
        reaction_formula = str(row['Formula']).strip()
        
        if not reaction_formula or reaction_formula == 'nan':
            raise ValueError(f"Missing reaction formula for {reaction_id}")
        
        reaction = Reaction(reaction_id)
        reaction.name = reaction_id
        
        reaction.lower_bound = float(row['lower_bound']) if pd.notna(row['lower_bound']) else -1000.0
        reaction.upper_bound = float(row['upper_bound']) if pd.notna(row['upper_bound']) else 1000.0
        
        if pd.notna(row['GPR']) and str(row['GPR']).strip():
            reaction.gene_reaction_rule = str(row['GPR']).strip()
        
        try:
            parse_reaction_formula(reaction, reaction_formula, metabolites_dict)
        except Exception as e:
            print(f"Error parsing reaction {reaction_id}: {e}")
            reactions_skipped += 1
            continue
        
        model.add_reactions([reaction])
        reactions_added += 1
            
    
    print(f"Added {reactions_added} reactions, skipped {reactions_skipped} reactions")
    
    # set objective function
    set_objective_from_csv(model, df, obj_col="ObjectiveCoefficient")

    set_medium_from_data(model, df)

    set_annotation_pathways_from_data(model, df)
    
    print(f"Model completed: {len(model.reactions)} reactions, {len(model.metabolites)} metabolites")
    
    return model


# Estrae tutti gli ID metaboliti nella formula (gestisce prefissi numerici + underscore)
#def extract_metabolites_from_reaction(reaction_formula: str) -> Set[str]:
#    """
#    Extract metabolite IDs from a reaction formula.
#    Robust pattern: tokens ending with _<compartment> (e.g., _c, _m, _e),
#    allowing leading digits/underscores.
#    """
#    metabolites = set()
#    # optional coefficient followed by a token ending with _<letters>
#    if reaction_formula[-1] == ']' and reaction_formula[-3] == '[':
#        pattern = r'(?:\d+(?:\.\d+)?\s+)?([A-Za-z0-9_]+[[A-Za-z0-9]]+)'
#    else:
#        pattern = r'(?:\d+(?:\.\d+)?\s+)?([A-Za-z0-9_]+_[A-Za-z0-9]+)'
#    matches = re.findall(pattern, reaction_formula)
#    metabolites.update(matches)
#    return metabolites


def extract_metabolites_from_reaction(reaction_formula: str) -> Set[str]:
    """
    Extract metabolite IDs from a reaction formula.

    Handles:
      - optional stoichiometric coefficients (integers or decimals)
      - compartment tags at the end of the metabolite, either [c] or _c

    Returns the IDs including the compartment suffix exactly as written.
    """
    pattern = re.compile(
        r'(?:^|(?<=\s)|(?<=\+)|(?<=,)|(?<==)|(?<=:))'              # left boundary (start, space, +, comma, =, :)
        r'(?:\d+(?:\.\d+)?\s+)?'                                   # optional coefficient (requires space after)
        r'([A-Za-z0-9][A-Za-z0-9_]*(?:\[[A-Za-z0-9]+\]|_[A-Za-z0-9]+))'  # metabolite + compartment (can start with number)
    )
    return {m.group(1) for m in pattern.finditer(reaction_formula)}



def extract_compartment_from_metabolite(metabolite_id: str) -> str:
    """Extract the compartment from a metabolite ID."""
    if '_' == metabolite_id[-2]:
        return metabolite_id.split('_')[-1]
    if metabolite_id[-1] == ']' and metabolite_id[-3] == '[':
        return metabolite_id[-2]
    return 'c'  # default cytoplasm


def parse_reaction_formula(reaction: Reaction, formula: str, metabolites_dict: Dict[str, Metabolite]):
    """Parse a reaction formula and set metabolites with their coefficients."""

    if '<=>' in formula:
        parts = formula.split('<=>')
        reversible = True
    elif '<--' in formula:
        parts = formula.split('<--')
        reversible = False
    elif '-->' in formula:
        parts = formula.split('-->')
        reversible = False
    elif '<-' in formula:
        parts = formula.split('<-')
        reversible = False
    else:
        raise ValueError(f"Unrecognized reaction format: {formula}")
    
    # Handle cases where one side might be empty (exchange reactions)
    if len(parts) != 2:
        raise ValueError(f"Invalid reaction format, expected 2 parts: {formula}")
    
    left, right = parts[0].strip(), parts[1].strip()
    
    reactants = parse_metabolites_side(left) if left else {}
    products = parse_metabolites_side(right) if right else {}
    
    metabolites_to_add = {}
    
    for met_id, coeff in reactants.items():
        if met_id in metabolites_dict:
            metabolites_to_add[metabolites_dict[met_id]] = -coeff
    
    for met_id, coeff in products.items():
        if met_id in metabolites_dict:
            metabolites_to_add[metabolites_dict[met_id]] = coeff
    
    reaction.add_metabolites(metabolites_to_add)


def parse_metabolites_side(side_str: str) -> Dict[str, float]:
    """Parse one side of a reaction and extract metabolites with coefficients."""
    metabolites = {}
    if not side_str or side_str.strip() == '':
        return metabolites

    terms = side_str.split('+')
    for term in terms:
        term = term.strip()
        if not term:
            continue

        # First check if term has space-separated coefficient and metabolite
        parts = term.split()
        if len(parts) == 2:
            # Two parts: potential coefficient + metabolite
            try:
                coeff = float(parts[0])
                met_id = parts[1]
                # Verify the second part looks like a metabolite with compartment
                if re.match(r'[A-Za-z0-9_]+(?:\[[A-Za-z0-9]+\]|_[A-Za-z0-9]+)', met_id):
                    metabolites[met_id] = coeff
                    continue
            except ValueError:
                pass
        
        # Single term - check if it's a metabolite (no coefficient)  
        # Updated pattern to include metabolites starting with numbers
        if re.match(r'[A-Za-z0-9][A-Za-z0-9_]*(?:\[[A-Za-z0-9]+\]|_[A-Za-z0-9]+)', term):
            metabolites[term] = 1.0
        else:
            print(f"Warning: Could not parse metabolite term: '{term}'")

    return metabolites



def set_objective_from_csv(model: cobra.Model, df: pd.DataFrame, obj_col: str = "ObjectiveCoefficient"):
    """
    Sets the model's objective function based on a column of coefficients in the CSV.
    Can be any reaction(s), not necessarily biomass.
    """
    obj_dict = {}
    
    for idx, row in df.iterrows():
        reaction_id = str(row['ReactionID']).strip()
        coeff = float(row[obj_col]) if pd.notna(row[obj_col]) else 0.0
        if coeff != 0:
            if reaction_id in model.reactions:
                obj_dict[model.reactions.get_by_id(reaction_id)] = coeff
            else:
                print(f"Warning: reaction {reaction_id} not found in model, skipping for objective.")

    if not obj_dict:
        raise ValueError("No reactions found with non-zero objective coefficient.")

    model.objective = obj_dict
    print(f"Objective set with {len(obj_dict)} reactions.")




def set_medium_from_data(model: cobraModel, df: pd.DataFrame):
    """Set the medium based on the 'InMedium' column in the dataframe."""
    if 'InMedium' not in df.columns:
        print("No 'InMedium' column found, skipping medium setup")
        return
        
    medium_reactions = df[df['InMedium'] == True]['ReactionID'].tolist()
    
    medium_dict = {}
    for rxn_id in medium_reactions:
        if rxn_id in [r.id for r in model.reactions]:
            reaction = model.reactions.get_by_id(rxn_id)
            if reaction.lower_bound < 0: 
                medium_dict[rxn_id] = abs(reaction.lower_bound)
    
    if medium_dict:
        model.medium = medium_dict
        print(f"Medium set with {len(medium_dict)} components")
    else:
        print("No medium components found")
def validate_model(model: cobraModel) -> Dict[str, any]:
    """Validate the model and return basic statistics."""
    validation = {
        'num_reactions': len(model.reactions),
        'num_metabolites': len(model.metabolites),
        'num_genes': len(model.genes),
        'num_compartments': len(model.compartments),
        'objective': str(model.objective),
        'medium_size': len(model.medium),
        'reversible_reactions': len([r for r in model.reactions if r.reversibility]),
        'exchange_reactions': len([r for r in model.reactions if r.id.startswith('EX_')]),
    }
    
    try:
        # Growth test
        solution = model.optimize()
        validation['growth_rate'] = solution.objective_value
        validation['status'] = solution.status
    except Exception as e:
        validation['growth_rate'] = None
        validation['status'] = f"Error: {e}"
    
    return validation

def convert_genes(model, annotation):
    """Rename genes using a selected annotation key in gene.notes; returns a model copy."""
    from cobra.manipulation import rename_genes
    model2=model.copy()
    try:
        dict_genes={gene.id:gene.notes[annotation]  for gene in model2.genes}
    except:
        print("No annotation in gene dict!")
        return -1
    rename_genes(model2,dict_genes)

    return model2

# ---------- Utility helpers ----------
def _normalize_colname(col: str) -> str:
    return col.strip().lower().replace(' ', '_')

def _choose_columns(mapping_df: 'pd.DataFrame') -> Dict[str, str]:
    """
    Find useful columns and return a dict {ensg: colname1, hgnc_id: colname2, ...}.
    Raise ValueError if no suitable mapping is found.
    """
    cols = { _normalize_colname(c): c for c in mapping_df.columns }
    chosen = {}
    # candidate names for each category
    candidates = {
        'ensg': ['ensg', 'ensembl_gene_id', 'ensembl'],
        'hgnc_id': ['hgnc_id', 'hgnc', 'hgnc:'],
        'hgnc_symbol': ['hgnc_symbol', 'hgnc symbol', 'symbol'],
        'entrez_id': ['entrez', 'entrez_id', 'entrezgene'],
        'gene_number': ['gene_number']
    }
    for key, names in candidates.items():
        for n in names:
            if n in cols:
                chosen[key] = cols[n]
                break
    return chosen

def _validate_target_uniqueness(mapping_df: 'pd.DataFrame',
                                source_col: str,
                                target_col: str,
                                model_source_genes: Optional[Set[str]] = None,
                                logger: Optional[logging.Logger] = None) -> None:
    """
        Check that, within the filtered mapping_df, each target maps to at most one source.
        Log examples if duplicates are found.
    """
    if logger is None:
        logger = logging.getLogger(__name__)

    if mapping_df.empty:
        logger.warning("Mapping dataframe is empty for the requested source genes; skipping uniqueness validation.")
        return

    # normalize temporary columns for grouping (without altering the original df)
    tmp = mapping_df[[source_col, target_col]].copy()
    tmp['_src_norm'] = tmp[source_col].astype(str).apply(_normalize_gene_id)
    tmp['_tgt_norm'] = tmp[target_col].astype(str).str.strip()

    # optionally filter to the set of model source genes
    if model_source_genes is not None:
        tmp = tmp[tmp['_src_norm'].isin(model_source_genes)]

    if tmp.empty:
        logger.warning("After filtering to model source genes, mapping table is empty — nothing to validate.")
        return

    # build reverse mapping: target -> set(sources)
    grouped = tmp.groupby('_tgt_norm')['_src_norm'].agg(lambda s: set(s.dropna()))
    # find targets with more than one source
    problematic = {t: sorted(list(s)) for t, s in grouped.items() if len(s) > 1}

    if problematic:
    # prepare warning message with examples (limited subset)
        sample_items = list(problematic.items())
        msg_lines = ["Mapping validation failed: some target IDs are associated with multiple source IDs."]
        for tgt, sources in sample_items:
            msg_lines.append(f"  - target '{tgt}' <- sources: {', '.join(sources)}")
        full_msg = "\n".join(msg_lines)
    # log warning
        logger.warning(full_msg)

    # if everything is fine
    logger.info("Mapping validation passed: no target ID is associated with multiple source IDs (within filtered set).")


def _normalize_gene_id(g: str) -> str:
    """Normalize a gene ID for use as a key (removes prefixes like 'HGNC:' and strips)."""
    if g is None:
        return ""
    g = str(g).strip()
    # remove common prefixes
    g = re.sub(r'^(HGNC:)', '', g, flags=re.IGNORECASE)
    g = re.sub(r'^(ENSG:)', '', g, flags=re.IGNORECASE)
    return g

def _is_or_only_expression(expr: str) -> bool:
    """
    Check if a GPR expression contains only OR operators (no AND operators).
    
    Args:
        expr: GPR expression string
        
    Returns:
        bool: True if expression contains only OR (and parentheses) and has multiple genes, False otherwise
    """
    if not expr or not expr.strip():
        return False
        
    # Normalize the expression
    normalized = expr.replace(' AND ', ' and ').replace(' OR ', ' or ')
    
    # Check if it contains any AND operators
    has_and = ' and ' in normalized.lower()
    
    # Check if it contains OR operators
    has_or = ' or ' in normalized.lower()
    
    # Must have OR operators and no AND operators
    return has_or and not has_and


def _flatten_or_only_gpr(expr: str) -> str:
    """
    Flatten a GPR expression that contains only OR operators by:
    1. Removing all parentheses
    2. Extracting unique gene names
    3. Joining them with ' or '
    
    Args:
        expr: GPR expression string with only OR operators
        
    Returns:
        str: Flattened GPR expression
    """
    if not expr or not expr.strip():
        return expr
        
    # Extract all gene tokens (exclude logical operators and parentheses)
    gene_pattern = r'\b[A-Za-z0-9:_.-]+\b'
    logical = {'and', 'or', 'AND', 'OR', '(', ')'}
    
    tokens = re.findall(gene_pattern, expr)
    genes = [t for t in tokens if t not in logical]
    
    # Create set to remove duplicates, then convert back to list to maintain some order
    unique_genes = list(dict.fromkeys(genes))  # Preserves insertion order
    
    if len(unique_genes) == 0:
        return expr
    elif len(unique_genes) == 1:
        return unique_genes[0]
    else:
        return ' or '.join(unique_genes)


def _simplify_boolean_expression(expr: str) -> str:
    """
    Simplify a boolean expression by removing duplicates while strictly preserving semantics.
    This function handles simple duplicates within parentheses while being conservative about
    complex expressions that could change semantics.
    """
    if not expr or not expr.strip():
        return expr
    
    # Normalize operators and whitespace
    expr = expr.replace(' AND ', ' and ').replace(' OR ', ' or ')
    expr = ' '.join(expr.split())  # Normalize whitespace
    
    def simplify_parentheses_content(match_obj):
        """Helper function to simplify content within parentheses."""
        content = match_obj.group(1)  # Content inside parentheses
        
        # Only simplify if it's a pure OR or pure AND chain
        if ' or ' in content and ' and ' not in content:
            # Pure OR chain - safe to deduplicate
            parts = [p.strip() for p in content.split(' or ') if p.strip()]
            unique_parts = []
            seen = set()
            for part in parts:
                if part not in seen:
                    unique_parts.append(part)
                    seen.add(part)
            
            if len(unique_parts) == 1:
                return unique_parts[0]  # Remove unnecessary parentheses for single items
            else:
                return '(' + ' or '.join(unique_parts) + ')'
                
        elif ' and ' in content and ' or ' not in content:
            # Pure AND chain - safe to deduplicate  
            parts = [p.strip() for p in content.split(' and ') if p.strip()]
            unique_parts = []
            seen = set()
            for part in parts:
                if part not in seen:
                    unique_parts.append(part)
                    seen.add(part)
            
            if len(unique_parts) == 1:
                return unique_parts[0]  # Remove unnecessary parentheses for single items
            else:
                return '(' + ' and '.join(unique_parts) + ')'
        else:
            # Mixed operators or single item - return with parentheses as-is
            return '(' + content + ')'
    
    def remove_duplicates_simple(parts_str: str, separator: str) -> str:
        """Remove duplicates from a simple chain of operations."""
        parts = [p.strip() for p in parts_str.split(separator) if p.strip()]
        
        # Remove duplicates while preserving order
        unique_parts = []
        seen = set()
        for part in parts:
            if part not in seen:
                unique_parts.append(part)
                seen.add(part)
        
        if len(unique_parts) == 1:
            return unique_parts[0]
        else:
            return f' {separator} '.join(unique_parts)
    
    try:
        import re
        
        # First, simplify content within parentheses
        # This handles cases like (A or A) -> A and (B and B) -> B
        expr_simplified = re.sub(r'\(([^()]+)\)', simplify_parentheses_content, expr)
        
        # Check if the resulting expression has mixed operators  
        has_and = ' and ' in expr_simplified
        has_or = ' or ' in expr_simplified
        
        # Only simplify top-level if it's pure AND or pure OR
        if has_and and not has_or and '(' not in expr_simplified:
            # Pure AND chain at top level - safe to deduplicate
            return remove_duplicates_simple(expr_simplified, 'and')
        elif has_or and not has_and and '(' not in expr_simplified:
            # Pure OR chain at top level - safe to deduplicate  
            return remove_duplicates_simple(expr_simplified, 'or')
        else:
            # Mixed operators or has parentheses - return the simplified version (with parentheses content cleaned)
            return expr_simplified
            
    except Exception:
        # If anything goes wrong, return the original expression
        return expr


def translate_model_genes(model: 'cobra.Model',
                         mapping_df: 'pd.DataFrame',
                         target_nomenclature: str,
                         source_nomenclature: str = 'hgnc_id',
                         allow_many_to_one: bool = False,
                         logger: Optional[logging.Logger] = None) -> Tuple['cobra.Model', Dict[str, str]]:
    """
    Translate model genes from source_nomenclature to target_nomenclature using a mapping table.
    mapping_df should contain columns enabling mapping (e.g., ensg, hgnc_id, hgnc_symbol, entrez).

    Args:
        model: COBRA model to translate.
        mapping_df: DataFrame containing the mapping information.
        target_nomenclature: Desired target key (e.g., 'hgnc_symbol').
        source_nomenclature: Current source key in the model (default 'hgnc_id').
        allow_many_to_one: If True, allow many-to-one mappings and handle duplicates in GPRs.
        logger: Optional logger.
    
    Returns:
        Tuple containing:
        - Translated COBRA model
        - Dictionary mapping reaction IDs to translation issue descriptions
    """
    if logger is None:
        logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
        logger = logging.getLogger(__name__)

    logger.info(f"Translating genes from '{source_nomenclature}' to '{target_nomenclature}'")

    # normalize column names and choose relevant columns
    chosen = _choose_columns(mapping_df)
    if not chosen:
        raise ValueError("Could not detect useful columns in mapping_df. Expected at least one of: ensg, hgnc_id, hgnc_symbol, entrez.")

    # map source/target to actual dataframe column names (allow user-specified source/target keys)
    # normalize input args
    src_key = source_nomenclature.strip().lower()
    tgt_key = target_nomenclature.strip().lower()

    # try to find the actual column names for requested keys
    col_for_src = None
    col_for_tgt = None
    # first, try exact match
    for k, actual in chosen.items():
        if k == src_key:
            col_for_src = actual
        if k == tgt_key:
            col_for_tgt = actual

    # if not found, try mapping common names
    if col_for_src is None:
        possible_src_names = {k: v for k, v in chosen.items()}
        # try to match by contained substring
        for k, actual in possible_src_names.items():
            if src_key in k:
                col_for_src = actual
                break

    if col_for_tgt is None:
        for k, actual in chosen.items():
            if tgt_key in k:
                col_for_tgt = actual
                break

    if col_for_src is None:
        raise ValueError(f"Source column for '{source_nomenclature}' not found in mapping dataframe.")
    if col_for_tgt is None:
        raise ValueError(f"Target column for '{target_nomenclature}' not found in mapping dataframe.")

    model_source_genes = { _normalize_gene_id(g.id) for g in model.genes }
    logger.info(f"Filtering mapping to {len(model_source_genes)} source genes present in model (normalized).")

    tmp_map = mapping_df[[col_for_src, col_for_tgt]].dropna().copy()
    tmp_map[col_for_src + "_norm"] = tmp_map[col_for_src].astype(str).apply(_normalize_gene_id)

    filtered_map = tmp_map[tmp_map[col_for_src + "_norm"].isin(model_source_genes)].copy()

    if filtered_map.empty:
        logger.warning("No mapping rows correspond to source genes present in the model after filtering. Proceeding with empty mapping (no translation will occur).")

    if not allow_many_to_one:
        _validate_target_uniqueness(filtered_map, col_for_src, col_for_tgt, model_source_genes=model_source_genes, logger=logger)

    # Crea il mapping
    gene_mapping = _create_gene_mapping(filtered_map, col_for_src, col_for_tgt, logger)

    # copy model
    model_copy = model.copy()

    # statistics
    stats = {'translated': 0, 'one_to_one': 0, 'one_to_many': 0, 'not_found': 0, 'simplified_gprs': 0, 'flattened_or_gprs': 0}
    unmapped = []
    multi = []
    
    # Dictionary to store translation issues per reaction
    reaction_translation_issues = {}

    original_genes = {g.id for g in model_copy.genes}
    logger.info(f"Original genes count: {len(original_genes)}")

    # translate GPRs
    for rxn in model_copy.reactions:
        gpr = rxn.gene_reaction_rule
        if gpr and gpr.strip():
            new_gpr, rxn_issues = _translate_gpr(gpr, gene_mapping, stats, unmapped, multi, logger, track_issues=True)
            if rxn_issues:
                reaction_translation_issues[rxn.id] = rxn_issues
            
            if new_gpr != gpr:
                # Check if this GPR has translation issues and contains only OR operators
                if rxn_issues and _is_or_only_expression(new_gpr):
                    # Flatten the GPR: remove parentheses and create set of unique genes
                    flattened_gpr = _flatten_or_only_gpr(new_gpr)
                    if flattened_gpr != new_gpr:
                        stats['flattened_or_gprs'] += 1
                        logger.debug(f"Flattened OR-only GPR with issues for {rxn.id}: '{new_gpr}' -> '{flattened_gpr}'")
                        new_gpr = flattened_gpr
                
                simplified_gpr = _simplify_boolean_expression(new_gpr)
                if simplified_gpr != new_gpr:
                    stats['simplified_gprs'] += 1
                    logger.debug(f"Simplified GPR for {rxn.id}: '{new_gpr}' -> '{simplified_gpr}'")
                rxn.gene_reaction_rule = simplified_gpr
                logger.debug(f"Reaction {rxn.id}: '{gpr}' -> '{simplified_gpr}'")

    # update model genes based on new GPRs
    _update_model_genes(model_copy, logger)

    # final logging
    _log_translation_statistics(stats, unmapped, multi, original_genes, model_copy.genes, logger)

    logger.info("Translation finished")
    return model_copy, reaction_translation_issues


# ---------- helper functions ----------
def _create_gene_mapping(mapping_df, source_col: str, target_col: str, logger: logging.Logger) -> Dict[str, List[str]]:
    """
    Build mapping dict: source_id -> list of target_ids
    Normalizes IDs (removes prefixes like 'HGNC:' etc).
    """
    df = mapping_df[[source_col, target_col]].dropna().copy()
    # normalize to string
    df[source_col] = df[source_col].astype(str).apply(_normalize_gene_id)
    df[target_col] = df[target_col].astype(str).str.strip()

    df = df.drop_duplicates()

    logger.info(f"Creating mapping from {len(df)} rows")

    mapping = defaultdict(list)
    for _, row in df.iterrows():
        s = row[source_col]
        t = row[target_col]
        if t not in mapping[s]:
            mapping[s].append(t)

    # stats
    one_to_one = sum(1 for v in mapping.values() if len(v) == 1)
    one_to_many = sum(1 for v in mapping.values() if len(v) > 1)
    logger.info(f"Mapping: {len(mapping)} source keys, {one_to_one} 1:1, {one_to_many} 1:many")
    return dict(mapping)


def _translate_gpr(gpr_string: str,
                   gene_mapping: Dict[str, List[str]],
                   stats: Dict[str, int],
                   unmapped_genes: List[str],
                   multi_mapping_genes: List[Tuple[str, List[str]]],
                   logger: logging.Logger,
                   track_issues: bool = False) -> Union[str, Tuple[str, str]]:
    """
    Translate genes inside a GPR string using gene_mapping.
    Returns new GPR string, and optionally translation issues if track_issues=True.
    """
    # Generic token pattern: letters, digits, :, _, -, ., (captures HGNC:1234, ENSG000..., symbols)
    token_pattern = r'\b[A-Za-z0-9:_.-]+\b'
    tokens = re.findall(token_pattern, gpr_string)

    logical = {'and', 'or', 'AND', 'OR', '(', ')'}
    tokens = [t for t in tokens if t not in logical]

    new_gpr = gpr_string
    issues = []

    for token in sorted(set(tokens), key=lambda x: -len(x)):  # longer tokens first to avoid partial replacement
        norm = _normalize_gene_id(token)
        if norm in gene_mapping:
            targets = gene_mapping[norm]
            stats['translated'] += 1
            if len(targets) == 1:
                stats['one_to_one'] += 1
                replacement = targets[0]
            else:
                stats['one_to_many'] += 1
                multi_mapping_genes.append((token, targets))
                replacement = "(" + " or ".join(targets) + ")"
                if track_issues:
                    issues.append(f"{token} -> {' or '.join(targets)}")

            pattern = r'\b' + re.escape(token) + r'\b'
            new_gpr = re.sub(pattern, replacement, new_gpr)
        else:
            stats['not_found'] += 1
            if token not in unmapped_genes:
                unmapped_genes.append(token)
            logger.debug(f"Token not found in mapping (left as-is): {token}")

    # Check for many-to-one cases (multiple source genes mapping to same target)
    if track_issues:
        # Build reverse mapping to detect many-to-one cases from original tokens
        original_to_target = {}
        
        for orig_token in tokens:
            norm = _normalize_gene_id(orig_token)
            if norm in gene_mapping:
                targets = gene_mapping[norm]
                for target in targets:
                    if target not in original_to_target:
                        original_to_target[target] = []
                    if orig_token not in original_to_target[target]:
                        original_to_target[target].append(orig_token)
        
        # Identify many-to-one mappings in this specific GPR
        for target, original_genes in original_to_target.items():
            if len(original_genes) > 1:
                issues.append(f"{' or '.join(original_genes)} -> {target}")
    
    issue_text = "; ".join(issues) if issues else ""
    
    if track_issues:
        return new_gpr, issue_text
    else:
        return new_gpr


def _update_model_genes(model: 'cobra.Model', logger: logging.Logger):
    """
    Rebuild model.genes from gene_reaction_rule content.
    Removes genes not referenced and adds missing ones.
    """
    # collect genes in GPRs
    gene_pattern = r'\b[A-Za-z0-9:_.-]+\b'
    logical = {'and', 'or', 'AND', 'OR', '(', ')'}
    genes_in_gpr: Set[str] = set()

    for rxn in model.reactions:
        gpr = rxn.gene_reaction_rule
        if gpr and gpr.strip():
            toks = re.findall(gene_pattern, gpr)
            toks = [t for t in toks if t not in logical]
            # normalize IDs consistent with mapping normalization
            toks = [_normalize_gene_id(t) for t in toks]
            genes_in_gpr.update(toks)

    # existing gene ids
    existing = {g.id for g in model.genes}

    # remove obsolete genes
    to_remove = [gid for gid in existing if gid not in genes_in_gpr]
    removed = 0
    for gid in to_remove:
        try:
            gene_obj = model.genes.get_by_id(gid)
            model.genes.remove(gene_obj)
            removed += 1
        except Exception:
            # safe-ignore
            pass

    # add new genes
    added = 0
    for gid in genes_in_gpr:
        if gid not in existing:
            new_gene = cobra.Gene(gid)
            try:
                model.genes.add(new_gene)
            except Exception:
                # fallback: if model.genes doesn't support add, try append or model.add_genes
                try:
                    model.genes.append(new_gene)
                except Exception:
                    try:
                        model.add_genes([new_gene])
                    except Exception:
                        logger.warning(f"Could not add gene object for {gid}")
            added += 1

    logger.info(f"Model genes updated: removed {removed}, added {added}")


def export_model_to_tabular(model: cobraModel, 
                           output_path: str,
                           translation_issues: Dict = None,
                           include_objective: bool = True,
                           save_function = None) -> pd.DataFrame:
    """
    Export a COBRA model to tabular format with optional components.
    
    Args:
        model: COBRA model to export
        output_path: Path where to save the tabular file
        translation_issues: Optional dict of {reaction_id: issues} from gene translation
        include_objective: Whether to include objective coefficient column
        save_function: Optional custom save function, if None uses pd.DataFrame.to_csv
        
    Returns:
        pd.DataFrame: The merged tabular data
    """
    # Generate model data
    rules = generate_rules(model, asParsed=False)
    
    reactions = generate_reactions(model, asParsed=False)
    bounds = generate_bounds(model)
    medium = get_medium(model)
    compartments = generate_compartments(model)
    
    # Create base DataFrames
    df_rules = pd.DataFrame(list(rules.items()), columns=["ReactionID", "GPR"])
    df_reactions = pd.DataFrame(list(reactions.items()), columns=["ReactionID", "Formula"])
    df_bounds = bounds.reset_index().rename(columns={"index": "ReactionID"})
    df_medium = medium.rename(columns={"reaction": "ReactionID"})
    df_medium["InMedium"] = True
    
    # Start merging
    merged = df_reactions.merge(df_rules, on="ReactionID", how="outer")
    merged = merged.merge(df_bounds, on="ReactionID", how="outer")
    
    # Add objective coefficients if requested
    if include_objective:
        objective_function = extract_objective_coefficients(model)
        merged = merged.merge(objective_function, on="ReactionID", how="outer")
    
    # Add compartments/pathways if they exist
    if compartments is not None:
        merged = merged.merge(compartments, on="ReactionID", how="outer")
    
    # Add medium information
    merged = merged.merge(df_medium, on="ReactionID", how="left")
    
    # Add translation issues if provided
    if translation_issues:
        df_translation_issues = pd.DataFrame([
            {"ReactionID": rxn_id, "TranslationIssues": issues}
            for rxn_id, issues in translation_issues.items()
        ])
        if not df_translation_issues.empty:
            merged = merged.merge(df_translation_issues, on="ReactionID", how="left")
            merged["TranslationIssues"] = merged["TranslationIssues"].fillna("")
    
    # Final processing
    merged["InMedium"] = merged["InMedium"].fillna(False)
    merged = merged.sort_values(by="InMedium", ascending=False)
    
    # Save the file
    if save_function:
        save_function(merged, output_path)
    else:
        merged.to_csv(output_path, sep="\t", index=False)
    
    return merged


def _log_translation_statistics(stats: Dict[str, int],
                               unmapped_genes: List[str],
                               multi_mapping_genes: List[Tuple[str, List[str]]],
                               original_genes: Set[str],
                               final_genes,
                               logger: logging.Logger):
    logger.info("=== TRANSLATION STATISTICS ===")
    logger.info(f"Translated: {stats.get('translated', 0)} (1:1 = {stats.get('one_to_one', 0)}, 1:many = {stats.get('one_to_many', 0)})")
    logger.info(f"Not found tokens: {stats.get('not_found', 0)}")
    logger.info(f"Simplified GPRs: {stats.get('simplified_gprs', 0)}")
    logger.info(f"Flattened OR-only GPRs with issues: {stats.get('flattened_or_gprs', 0)}")

    final_ids = {g.id for g in final_genes}
    logger.info(f"Genes in model: {len(original_genes)} -> {len(final_ids)}")

    if unmapped_genes:
        logger.warning(f"Unmapped tokens ({len(unmapped_genes)}): {', '.join(unmapped_genes[:20])}{(' ...' if len(unmapped_genes)>20 else '')}")
    if multi_mapping_genes:
        logger.info(f"Multi-mapping examples ({len(multi_mapping_genes)}):")
        for orig, targets in multi_mapping_genes[:10]:
            logger.info(f"  {orig} -> {', '.join(targets)}")
    
    # Log summary of flattened GPRs if any
    if stats.get('flattened_or_gprs', 0) > 0:
        logger.info(f"Flattened {stats['flattened_or_gprs']} OR-only GPRs that had translation issues (removed parentheses, created unique gene sets)")