Mercurial > repos > bimib > cobraxy
view COBRAxy/utils/rule_parsing.py @ 218:8d1988935e1f draft
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author | luca_milaz |
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date | Sat, 14 Dec 2024 18:50:08 +0000 |
parents | 41f35c2f0c7b |
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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