cobraxy: COBRAxy/utils/rule_parsing.py comparison

comparison COBRAxy/utils/rule_parsing.py @ 4:41f35c2f0c7b draft

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author	luca_milaz
date	Wed, 18 Sep 2024 10:59:10 +0000
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-:1f3ac6fd9867
+:41f35c2f0c7b
+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

Mercurial > repos > bimib > cobraxy

comparison COBRAxy/utils/rule_parsing.py @ 4:41f35c2f0c7b draft