--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COBRAxy/src/utils/rule_parsing.py	Sat Oct 25 14:55:13 2025 +0000
@@ -0,0 +1,250 @@
+"""
+Parsing utilities for gene rules (GPRs).
+
+This module provides:
+- RuleErr: structured errors for malformed rules
+- RuleOp: valid logical operators (AND/OR)
+- OpList: nested list structure representing parsed rules with explicit operator
+- RuleStack: helper stack to build nested OpLists during parsing
+- parseRuleToNestedList: main entry to parse a rule string into an OpList
+"""
+from enum import Enum
+import utils.general_utils as utils
+from typing import List, Union, Optional
+
+class RuleErr(utils.CustomErr):
+    """
+    Error type for rule syntax errors.
+    """
+    errName = "Rule Syntax Error"
+    def __init__(self, rule :str, msg = "no further details provided") -> None:
+        super().__init__(
+            f"rule \"{rule}\" is malformed, {msg}",
+            "please verify your input follows the validity guidelines")
+
+class RuleOp(Enum):
+    """
+    Valid logical operators for gene rules.
+    """
+    OR  = "or"
+    AND = "and"
+
+    @classmethod
+    def isOperator(cls, op :str) -> bool:
+        return op.upper() in cls.__members__
+
+    def __str__(self) -> str: return self.value
+
+class OpList(List[Union[str, "OpList"]]):
+    """
+    Parsed rule structure: a list with an associated operator for that level.
+    """
+    def __init__(self, op :Optional[RuleOp] = None) -> None:
+        """
+        (Private) Initializes an instance of OpList.
+
+        Args:
+            op (str): Operator to be assigned to the OpList. Defaults to "".
+        
+        Returns:
+            None : practically, an OpList instance.
+        """
+        self.op = op
+
+    def setOpIfMissing(self, op :RuleOp) -> None:
+        """
+        Sets the operator of the OpList if it's missing.
+
+        Args:
+            op (str): Operator to be assigned to the OpList.
+        
+        Returns:
+            None
+        """
+        if not self.op: self.op = op
+
+    def __repr__(self, indent = "") -> str:
+        """
+        (Private) Returns a string representation of the current OpList instance.
+
+        Args:
+            indent (str): Indentation level . Defaults to "".
+
+        Returns:
+            str: A string representation of the current OpList instance.
+        """
+        nextIndent = indent + "  "
+        return f"<{self.op}>[\n" + ",\n".join([
+            f"{nextIndent}{item.__repr__(nextIndent) if isinstance(item, OpList) else item}"
+            for item in self ]) + f"\n{indent}]"
+
+class RuleStack:
+    """
+    FILO stack used during parsing to build nested OpLists; the top is the current level.
+    """
+    def __init__(self) -> None:
+        """
+        (Private) initializes an instance of RuleStack.
+
+        Returns:
+            None : practically, a RuleStack instance.
+        """
+        self.__stack = [OpList()] # the stack starts out with the result list already allocated
+        self.__updateCurrent()
+
+    def pop(self) -> None:
+        """
+        Removes the OpList on top of the stack, also flattening it once when possible.
+
+        Side Effects:
+            self : mut
+
+        Returns:
+            None
+        """
+        oldTop = self.__stack.pop()
+        if len(oldTop) == 1 and isinstance(oldTop[0], OpList): self.__stack[-1][-1] = oldTop[0]
+        self.__updateCurrent()
+
+    def push(self, operator = "") -> None:
+        """
+        Adds a new nesting level, in the form of a new OpList on top of the stack.
+
+        Args:
+            operator : the operator assigned to the new OpList.
+
+        Side Effects:
+            self : mut
+        
+        Returns:
+            None
+        """
+        newLevel = OpList(operator)
+        self.current.append(newLevel)
+        self.__stack.append(newLevel)
+        self.__updateCurrent()
+
+    def popForward(self) -> None:
+        """
+        Moves the last "actual" item from the 2nd to last list to the beginning of the top list, as per
+        the example below:
+        stack  : [list_a, list_b]
+        list_a : [item1, item2, list_b] --> [item1, list_b]
+        list_b : [item3, item4]         --> [item2, item3, item4]
+
+        This is essentially a "give back as needed" operation.
+
+        Side Effects:
+            self : mut
+        
+        Returns:
+            None
+        """
+        self.current.insert(0, self.__stack[-2].pop(-2))
+
+    def currentIsAnd(self) -> bool:
+        """
+        Checks if the current OpList's assigned operator is "and".
+
+        Returns:
+            bool : True if the current OpList's assigned operator is "and", False otherwise.
+        """
+        return self.current.op is RuleOp.AND
+
+    def obtain(self, err :Optional[utils.CustomErr] = None) -> Optional[OpList]:
+        """
+        Obtains the first OpList on the stack, only if it's the only element.
+
+        Args:
+            err : The error to raise if obtaining the result is not possible.
+
+        Side Effects:
+            self : mut    
+        
+        Raises:
+            err: If given, otherwise None is returned.
+
+        Returns:
+            Optional[OpList]: The first OpList on the stack, only if it's the only element.
+        """
+
+        if len(self.__stack) == 1: return self.__stack.pop()
+        if err: raise err
+        return None
+
+    def __updateCurrent(self) -> None:
+        """
+        (Private) Updates the current OpList to the one on top of the stack.
+
+        Side Effects:
+            self : mut
+        
+        Returns:
+            None
+        """
+        self.current = self.__stack[-1]
+
+def parseRuleToNestedList(rule :str) -> OpList:
+    """
+    Parse a rule string into an OpList, making operator precedence explicit via nesting.
+
+    Args:
+        rule: Rule string to parse (supports parentheses, 'and', 'or').
+    
+    Raises:
+        RuleErr: If the rule is malformed (e.g., mismatched parentheses or misplaced operators).
+    
+    Returns:
+        OpList: Parsed rule as an OpList structure.
+    """
+    source = iter(rule
+        .replace("(", "( ").replace(")", " )") # single out parentheses as words
+        .strip()  # trim edges
+        .split()) # split by spaces
+
+    stack = RuleStack()
+    nestingErr = RuleErr(rule, "mismatch between open and closed parentheses")
+    try:
+        while True: # read until source ends
+            while True:
+                operand = next(source, None) # expect operand or '('
+                if operand is None: raise RuleErr(rule, "found trailing open parentheses")
+                if operand in ("and", "or", ")"): # unexpected operator position
+                    raise RuleErr(rule, f"found \"{operand}\" in unexpected position")
+
+                if operand != "(": break # got a name
+
+                # found rule opening: add a new nesting level
+                stack.push()
+
+            stack.current.append(operand)
+
+            while True: # read until operator found or source ends
+                operator = next(source, None) # expect operator or ')'
+                if operator and operator != ")": break # got operator
+
+                if stack.currentIsAnd(): stack.pop() # close current AND chain
+
+                if not operator: break
+                stack.pop() # close parentheses
+
+            if not operator: break
+            
+            if not RuleOp.isOperator(operator): raise RuleErr(
+                rule, f"found \"{operator}\" in unexpected position, expected operator")
+            
+            operator = RuleOp(operator)
+            if operator is RuleOp.OR and stack.currentIsAnd():
+                stack.pop()
+
+            elif operator is RuleOp.AND and not stack.currentIsAnd():
+                stack.push(operator)
+                stack.popForward()
+
+            stack.current.setOpIfMissing(operator)
+
+    except RuleErr as err: raise err # bubble up proper errors
+    except: raise nestingErr # everything else is interpreted as a nesting error.
+
+    parsedRule = stack.obtain(nestingErr)
+    return parsedRule[0] if len(parsedRule) == 1 and isinstance(parsedRule[0], list) else parsedRule
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