--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COBRAxy/utils/rule_parsing.py	Wed Sep 18 10:59:10 2024 +0000
@@ -0,0 +1,243 @@
+from enum import Enum
+import utils.general_utils as utils
+from typing import List, Union, Optional
+
+class RuleErr(utils.CustomErr):
+    """
+    CustomErr subclass 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):
+    """
+    Encodes all operators valid in 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"]]):
+    """
+    Represents a parsed rule and each of its nesting levels, including the operator that level uses.
+    """
+    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 structure to save the intermediate representation of a Rule during parsing, with the
+    current nesting level at the top of the stack.
+    """
+    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 single rule from its string representation to an OpList, making all priority explicit
+    through nesting levels.
+
+    Args:
+        rule : the string representation of a rule to be parsed.
+    
+    Raises:
+        RuleErr : whenever something goes wrong during parsing.
+    
+    Returns:
+        OpList : the parsed rule.
+    """
+    source = iter(rule
+        .replace("(", "( ").replace(")", " )") # Single out parens as words
+        .strip()  # remove whitespace at extremities
+        .split()) # split by spaces
+
+    stack = RuleStack()
+    nestingErr = RuleErr(rule, "mismatch between open and closed parentheses")
+    try:
+        while True: # keep reading until source ends
+            while True:
+                operand = next(source, None) # expected name or rule opening
+                if operand is None: raise RuleErr(rule, "found trailing open parentheses")
+                if operand == "and" or operand == "or" or operand == ")": # found operator instead, panic
+                    raise RuleErr(rule, f"found \"{operand}\" in unexpected position")
+
+                if operand != "(": break # found name
+
+                # found rule opening, we add new nesting level but don't know the operator
+                stack.push()
+
+            stack.current.append(operand)
+
+            while True: # keep reading until operator is found or source ends
+                operator = next(source, None) # expected operator or rule closing
+                if operator and operator != ")": break # found operator
+
+                if stack.currentIsAnd(): stack.pop() # we close the "and" chain
+
+                if not operator: break
+                stack.pop() # we close the parentheses
+
+            # we proceed with operator:
+            if not operator: break # there is no such thing as a double loop break.. yet
+            
+            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) # buffer now knows what operator its data had
+
+    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
\ No newline at end of file