from __future__ import annotations
__all__ = ["FamilyDetector", "FamilyDetectorRule", "FamilyMetadata"]
import dataclasses
import logging
from pathlib import Path
import re
from typing import List, Optional, Union
from typing_extensions import TypedDict
import yaml
from medkit.core import Attribute
from medkit.core.text import ContextOperation, Segment
from medkit.text.utils.decoding import get_ascii_from_unicode
logger = logging.getLogger(__name__)
_PATH_TO_DEFAULT_RULES = Path(__file__).parent / "family_detector_default_rules.yml"
[docs]@dataclasses.dataclass
class FamilyDetectorRule:
"""Regexp-based rule to use with `FamilyDetector`
Input text may be converted before detecting rule.
Parameters
----------
regexp:
The regexp pattern used to match a family reference
exclusion_regexps:
Optional exclusion patterns
id:
Unique identifier of the rule to store in the metadata of the entities
case_sensitive:
Whether to consider case when running `regexp and `exclusion_regexs`
unicode_sensitive:
If True, rule matches are searched on unicode text.
So, `regexp` and `exclusion_regexps` shall not contain non-ASCII chars because
they would never be matched.
If False, rule matches are searched on closest ASCII text when possible.
(cf. FamilyDetector)
"""
regexp: str
exclusion_regexps: List[str] = dataclasses.field(default_factory=list)
id: Optional[str] = None
case_sensitive: bool = False
unicode_sensitive: bool = False
def __post_init__(self):
assert self.unicode_sensitive or (
self.regexp.isascii() and all(r.isascii() for r in self.exclusion_regexps)
), (
"FamilyDetectorRule regexps shouldn't contain non-ASCII chars when"
" unicode_sensitive is False"
)
[docs]class FamilyDetector(ContextOperation):
"""Annotator creating family attributes with boolean values
indicating if a family reference has been detected.
Because family attributes will be attached to whole annotations,
each input annotation should be "local"-enough rather than
a big chunk of text (ie a sentence or a syntagma).
For detecting family references, the module uses rules that may be sensitive to unicode or
not. When the rule is not sensitive to unicode, we try to convert unicode chars to
the closest ascii chars. However, some characters need to be pre-processed before
(e.g., `n°` -> `number`). So, if the text lengths are different, we fall back on
initial unicode text for detection even if rule is not unicode-sensitive.
In this case, a warning is logged for recommending to pre-process data.
Note that for better results, family detection should be run at the sentence
level (ie on sentence segments) rather than at the syntagma level [1].
[1] N. Garcelon, A. Neuraz, V. Benoit, R. Salomon, A. Burgun, "Improving a
full-text search engine: the importance of negation detection and family
history context to identify cases in a biomedical data warehouse", Journal
of the American Medical Informatics Association, Volume 24, Issue 3, May
2017
"""
def __init__(
self,
output_label: str,
rules: Optional[List[FamilyDetectorRule]] = None,
uid: Optional[str] = None,
):
"""
Parameters
----------
output_label:
The label of the created attributes
rules:
The set of rules to use when detecting family references. If none provided,
the rules in "family_detector_default_rules.yml" will be used
uid:
Identifier of the detector
"""
# Pass all arguments to super (remove self)
init_args = locals()
init_args.pop("self")
super().__init__(**init_args)
if rules is None:
rules = self.load_rules(_PATH_TO_DEFAULT_RULES, encoding="utf-8")
self.check_rules_sanity(rules)
self.output_label = output_label
self.rules = rules
# pre-compile patterns
self._non_empty_text_pattern = re.compile(r"[a-z]", flags=re.IGNORECASE)
self._patterns = [
re.compile(rule.regexp, flags=0 if rule.case_sensitive else re.IGNORECASE)
for rule in self.rules
]
self._exclusion_patterns = [
re.compile(
"|".join(
f"(?:{r})" for r in rule.exclusion_regexps
), # join all exclusions in one pattern
flags=0 if rule.case_sensitive else re.IGNORECASE,
)
if rule.exclusion_regexps
else None
for rule in self.rules
]
self._has_non_unicode_sensitive_rule = any(
not r.unicode_sensitive for r in rules
)
[docs] def run(self, segments: List[Segment]):
"""Add a family attribute to each segment with a boolean value
indicating if a family reference has been detected.
Family attributes with a `True` value have a metadata dict with
fields described in :class:`.FamilyMetadata`.
Parameters
----------
segments:
List of segments to detect as being family references or not
"""
for segment in segments:
family_attr = self._detect_family_ref_in_segment(segment)
if family_attr is not None:
segment.attrs.add(family_attr)
def _detect_family_ref_in_segment(self, segment: Segment) -> Optional[Attribute]:
rule_id = self._find_matching_rule(segment.text)
if rule_id is not None:
family_attr = Attribute(
label=self.output_label,
value=True,
metadata=FamilyMetadata(rule_id=rule_id),
)
else:
family_attr = Attribute(label=self.output_label, value=False)
if self._prov_tracer is not None:
self._prov_tracer.add_prov(
family_attr, self.description, source_data_items=[segment]
)
return family_attr
def _find_matching_rule(self, text: str) -> Optional[Union[str, int]]:
# skip empty text
if self._non_empty_text_pattern.search(text) is None:
return None
text_unicode = text
text_ascii = None
if self._has_non_unicode_sensitive_rule:
text_ascii = get_ascii_from_unicode(text, logger=logger)
# try all rules until we have a match
for rule_index, rule in enumerate(self.rules):
pattern = self._patterns[rule_index]
exclusion_pattern = self._exclusion_patterns[rule_index]
text = text_unicode if rule.unicode_sensitive else text_ascii
if pattern.search(text) is not None:
if exclusion_pattern is None or exclusion_pattern.search(text) is None:
# return the rule id or the rule index if no id has been set
rule_id = rule.id if rule.id is not None else rule_index
return rule_id
return None
[docs] @staticmethod
def load_rules(
path_to_rules: Path, encoding: Optional[str] = None
) -> List[FamilyDetectorRule]:
"""
Load all rules stored in a yml file
Parameters
----------
path_to_rules
Path to a yml file containing a list of mappings
with the same structure as `FamilyDetectorRule`
encoding
Encoding of the file to open
Returns
-------
List[FamilyDetectorRule]
List of all the rules in `path_to_rules`,
can be used to init a `FamilyDetector`
"""
with open(path_to_rules, mode="r", encoding=encoding) as f:
rules_data = yaml.safe_load(f)
rules = [FamilyDetectorRule(**d) for d in rules_data]
return rules
[docs] @staticmethod
def check_rules_sanity(rules: List[FamilyDetectorRule]):
"""Check consistency of a set of rules"""
if any(r.id is not None for r in rules):
if not all(r.id is not None for r in rules):
raise ValueError(
"Some rules have ids and other do not. Please provide either ids"
" for all rules or no ids at all"
)
if len(set(r.id for r in rules)) != len(rules):
raise ValueError(
"Some rules have the same id, each rule must have a unique id"
)
[docs] @staticmethod
def save_rules(
rules: List[FamilyDetectorRule],
path_to_rules: Path,
encoding: Optional[str] = None,
):
"""
Store rules in a yml file
Parameters
----------
rules
The rules to save
path_to_rules
Path to a .yml file that will contain the rules
encoding
Encoding of the .yml file
"""
with open(path_to_rules, mode="w", encoding=encoding) as f:
rules_data = [dataclasses.asdict(r) for r in rules]
rules = yaml.safe_dump(rules_data, f)
