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456
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1 """
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2 Parsing utilities for gene rules (GPRs).
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3
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4 This module provides:
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5 - RuleErr: structured errors for malformed rules
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6 - RuleOp: valid logical operators (AND/OR)
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7 - OpList: nested list structure representing parsed rules with explicit operator
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8 - RuleStack: helper stack to build nested OpLists during parsing
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9 - parseRuleToNestedList: main entry to parse a rule string into an OpList
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10 """
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4
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11 from enum import Enum
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12 import utils.general_utils as utils
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13 from typing import List, Union, Optional
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14
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15 class RuleErr(utils.CustomErr):
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16 """
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456
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17 Error type for rule syntax errors.
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4
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18 """
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19 errName = "Rule Syntax Error"
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20 def __init__(self, rule :str, msg = "no further details provided") -> None:
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21 super().__init__(
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22 f"rule \"{rule}\" is malformed, {msg}",
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23 "please verify your input follows the validity guidelines")
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24
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25 class RuleOp(Enum):
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26 """
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456
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27 Valid logical operators for gene rules.
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4
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28 """
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29 OR = "or"
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30 AND = "and"
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31
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32 @classmethod
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33 def isOperator(cls, op :str) -> bool:
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34 return op.upper() in cls.__members__
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35
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36 def __str__(self) -> str: return self.value
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37
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38 class OpList(List[Union[str, "OpList"]]):
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39 """
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456
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40 Parsed rule structure: a list with an associated operator for that level.
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4
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41 """
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42 def __init__(self, op :Optional[RuleOp] = None) -> None:
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43 """
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44 (Private) Initializes an instance of OpList.
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45
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46 Args:
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47 op (str): Operator to be assigned to the OpList. Defaults to "".
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48
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49 Returns:
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50 None : practically, an OpList instance.
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51 """
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52 self.op = op
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53
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54 def setOpIfMissing(self, op :RuleOp) -> None:
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55 """
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56 Sets the operator of the OpList if it's missing.
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57
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58 Args:
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59 op (str): Operator to be assigned to the OpList.
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60
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61 Returns:
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62 None
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63 """
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64 if not self.op: self.op = op
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65
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66 def __repr__(self, indent = "") -> str:
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67 """
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68 (Private) Returns a string representation of the current OpList instance.
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69
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70 Args:
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71 indent (str): Indentation level . Defaults to "".
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72
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73 Returns:
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74 str: A string representation of the current OpList instance.
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75 """
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76 nextIndent = indent + " "
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77 return f"<{self.op}>[\n" + ",\n".join([
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78 f"{nextIndent}{item.__repr__(nextIndent) if isinstance(item, OpList) else item}"
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79 for item in self ]) + f"\n{indent}]"
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80
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81 class RuleStack:
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82 """
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456
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83 FILO stack used during parsing to build nested OpLists; the top is the current level.
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4
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84 """
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85 def __init__(self) -> None:
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86 """
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87 (Private) initializes an instance of RuleStack.
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88
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89 Returns:
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90 None : practically, a RuleStack instance.
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91 """
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92 self.__stack = [OpList()] # the stack starts out with the result list already allocated
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93 self.__updateCurrent()
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94
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95 def pop(self) -> None:
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96 """
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97 Removes the OpList on top of the stack, also flattening it once when possible.
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98
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99 Side Effects:
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100 self : mut
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101
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102 Returns:
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103 None
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104 """
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105 oldTop = self.__stack.pop()
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106 if len(oldTop) == 1 and isinstance(oldTop[0], OpList): self.__stack[-1][-1] = oldTop[0]
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107 self.__updateCurrent()
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108
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109 def push(self, operator = "") -> None:
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110 """
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111 Adds a new nesting level, in the form of a new OpList on top of the stack.
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112
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113 Args:
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114 operator : the operator assigned to the new OpList.
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115
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116 Side Effects:
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117 self : mut
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118
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119 Returns:
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120 None
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121 """
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122 newLevel = OpList(operator)
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123 self.current.append(newLevel)
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124 self.__stack.append(newLevel)
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125 self.__updateCurrent()
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126
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127 def popForward(self) -> None:
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128 """
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129 Moves the last "actual" item from the 2nd to last list to the beginning of the top list, as per
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130 the example below:
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131 stack : [list_a, list_b]
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132 list_a : [item1, item2, list_b] --> [item1, list_b]
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133 list_b : [item3, item4] --> [item2, item3, item4]
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134
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135 This is essentially a "give back as needed" operation.
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136
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137 Side Effects:
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138 self : mut
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139
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140 Returns:
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141 None
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142 """
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143 self.current.insert(0, self.__stack[-2].pop(-2))
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144
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145 def currentIsAnd(self) -> bool:
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146 """
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147 Checks if the current OpList's assigned operator is "and".
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148
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149 Returns:
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150 bool : True if the current OpList's assigned operator is "and", False otherwise.
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151 """
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152 return self.current.op is RuleOp.AND
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153
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154 def obtain(self, err :Optional[utils.CustomErr] = None) -> Optional[OpList]:
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155 """
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156 Obtains the first OpList on the stack, only if it's the only element.
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157
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158 Args:
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159 err : The error to raise if obtaining the result is not possible.
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160
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161 Side Effects:
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162 self : mut
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163
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164 Raises:
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165 err: If given, otherwise None is returned.
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166
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167 Returns:
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168 Optional[OpList]: The first OpList on the stack, only if it's the only element.
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169 """
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170
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171 if len(self.__stack) == 1: return self.__stack.pop()
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172 if err: raise err
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173 return None
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174
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175 def __updateCurrent(self) -> None:
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176 """
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177 (Private) Updates the current OpList to the one on top of the stack.
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178
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179 Side Effects:
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180 self : mut
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181
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182 Returns:
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183 None
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184 """
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185 self.current = self.__stack[-1]
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186
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187 def parseRuleToNestedList(rule :str) -> OpList:
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188 """
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456
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189 Parse a rule string into an OpList, making operator precedence explicit via nesting.
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4
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190
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191 Args:
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456
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192 rule: Rule string to parse (supports parentheses, 'and', 'or').
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4
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193
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194 Raises:
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456
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195 RuleErr: If the rule is malformed (e.g., mismatched parentheses or misplaced operators).
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4
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196
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197 Returns:
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456
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198 OpList: Parsed rule as an OpList structure.
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4
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199 """
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200 source = iter(rule
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456
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201 .replace("(", "( ").replace(")", " )") # single out parentheses as words
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202 .strip() # trim edges
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4
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203 .split()) # split by spaces
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204
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205 stack = RuleStack()
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206 nestingErr = RuleErr(rule, "mismatch between open and closed parentheses")
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207 try:
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456
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208 while True: # read until source ends
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4
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209 while True:
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456
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210 operand = next(source, None) # expect operand or '('
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211 if operand is None: raise RuleErr(rule, "found trailing open parentheses")
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456
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212 if operand in ("and", "or", ")"): # unexpected operator position
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213 raise RuleErr(rule, f"found \"{operand}\" in unexpected position")
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214
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456
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215 if operand != "(": break # got a name
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216
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456
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217 # found rule opening: add a new nesting level
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218 stack.push()
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219
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220 stack.current.append(operand)
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221
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456
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222 while True: # read until operator found or source ends
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223 operator = next(source, None) # expect operator or ')'
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224 if operator and operator != ")": break # got operator
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225
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456
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226 if stack.currentIsAnd(): stack.pop() # close current AND chain
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227
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228 if not operator: break
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456
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229 stack.pop() # close parentheses
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230
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456
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231 if not operator: break
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232
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233 if not RuleOp.isOperator(operator): raise RuleErr(
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234 rule, f"found \"{operator}\" in unexpected position, expected operator")
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235
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236 operator = RuleOp(operator)
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237 if operator is RuleOp.OR and stack.currentIsAnd():
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238 stack.pop()
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239
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240 elif operator is RuleOp.AND and not stack.currentIsAnd():
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241 stack.push(operator)
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242 stack.popForward()
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243
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456
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244 stack.current.setOpIfMissing(operator)
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4
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245
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246 except RuleErr as err: raise err # bubble up proper errors
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247 except: raise nestingErr # everything else is interpreted as a nesting error.
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248
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249 parsedRule = stack.obtain(nestingErr)
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250 return parsedRule[0] if len(parsedRule) == 1 and isinstance(parsedRule[0], list) else parsedRule |
