Improve contextual matcher

[percevalw]

Added

• Expose the defaults patterns of eds.negation, eds.hypothesis, eds.family, eds.history and eds.reported_speech under a eds.negation.default_patterns attribute
• Added a context_getter SpanGetter argument to the eds.matcher class to only retrieve entities inside the spans returned by the getter
• Added a filter_expr parameter to scorers to filter the documents to score
• Added a new required field to eds.contextual_matcher assign patterns to only match if the required field has been found, and an include parameter (similar to exclude) to search for required patterns without assigning them to the entity

Checklist

• If this PR is a bug fix, the bug is documented in the test suite.
• Changes were documented in the changelog (pending section).
• If necessary, changes were made to the documentation (eg new pipeline).

[codecov]

Codecov Report

Attention: Patch coverage is 89.81481% with 11 lines in your changes are missing coverage. Please review.

Project coverage is 96.97%. Comparing base (ad16e9b) to head (53bcc0e).
Report is 23 commits behind head on master.

❗ Current head 53bcc0e differs from pull request most recent head 465ba39

Please upload reports for the commit 465ba39 to get more accurate results.

Files	Patch %	Lines
...ipes/core/contextual_matcher/contextual_matcher.py	87.27%	7 Missing ⚠️
edsnlp/pipes/core/contextual_matcher/models.py	89.18%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #289      +/-   ##
==========================================
+ Coverage   96.94%   96.97%   +0.03%     
==========================================
  Files         262      262              
  Lines        9022     9048      +26     
==========================================
+ Hits         8746     8774      +28     
+ Misses        276      274       -2     

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[github-actions]

Coverage Report

Name	Stmts	Miss	∆ Miss	Cover
edsnlp/pipes/core/contextual_matcher/contextual_matcher.py Was already missing at line 111 ) - label = label_name if label is None: New missing coverage at lines 188-197 ! for include in p.include: - include.matcher = RegexMatcher( - attr=include.regex_attr or p.regex_attr or self.attr, - flags=include.regex_flags or p.regex_flags or self.regex_flags, - ignore_excluded=ignore_excluded, - ignore_space_tokens=ignore_space_tokens, - alignment_mode="expand", - ) - - include.matcher.build_patterns(regex={"include": include.regex}) New missing coverage at lines 262-268 ! for include in self.patterns[source].include: - snippet = include.window(span) - - if next(include.matcher(snippet, as_spans=True), None) is None: - to_keep = False - logger.trace(f"Entity {span} was filtered out") - break New missing coverage at line 329 ! else: - assigned_list = [ (matched_span, matched_span, assign.name, assign) New missing coverage at lines 341-343 ! if assign.required and not assigned_list: - logger.trace(f"Entity {span} was filtered out") - return New missing coverage at line 348 ! if assigned is None: - continue group_span, full_match_span, value_key, assign = assigned	150	12	18	92.00%
edsnlp/utils/span_getters.py Was already missing at lines 53-56 else: - for span in candidates: - if span.label_ in span_filter: - yield span Was already missing at lines 60-62 if span_getter is None: - yield doc[:], None - return if callable(span_getter): Was already missing at lines 63-65 if callable(span_getter): - yield from span_getter(doc) - return for key, span_filter in span_getter.items(): Was already missing at line 67 if key == "*": - candidates = ( (span, group) for group in doc.spans.values() for span in group Was already missing at lines 76-79 else: - for span, group in candidates: - if span.label_ in span_filter: - yield span, group Was already missing at line 83 if callable(span_setter): - span_setter(doc, matches) else: Was already missing at line 125 elif isinstance(v, str): - new_value[k] = [v] elif isinstance(v, list) and all(isinstance(i, str) for i in v): Was already missing at line 163 elif isinstance(v, str): - new_value[k] = [v] elif isinstance(v, list) and all(isinstance(i, str) for i in v): New missing coverage at line 328 ! def __rand__(self, other: "Context"): - return self & other if other is not None else self New missing coverage at line 332 ! # fmt: off - return UnionContext([ *(self.contexts if isinstance(self, UnionContext) else (self,)), New missing coverage at line 339 ! def __ror__(self, other: "Context"): - return self & other if other is not None else self New missing coverage at line 343 ! def parse(cls, query): - return eval( query, New missing coverage at line 357 ! if isinstance(obj, str): - return cls.parse(obj) if isinstance(obj, tuple): New missing coverage at lines 373-377 ! def __getitem__(cls, item) -> Span: - assert isinstance(item, slice) - before = item.start - after = item.stop - return cls(before, after) New missing coverage at line 437 ! ): - self.contexts = contexts New missing coverage at lines 440-444 ! def __call__(self, span): - results = [context(span) for context in self.contexts] - min_word = min([span.start for span in results]) - max_word = max([span.end for span in results]) - return span.doc[min_word:max_word]	220	28	14	87.27%
edsnlp/package.py New missing coverage at line 55 ! if isinstance(obj, ModuleType): - module_name = obj.__name__ else: New missing coverage at line 67 ! return package, version - except (ImportError, AttributeError): raise Exception(f"Cound not find package of type {obj}") New missing coverage at lines 86-90 ! def save_module(pickler, obj, *args, **kwargs): - package_name = get_package(obj) - if package_name is not None: - pickler.packages.add(package_name) - return dill_save_module(pickler, obj, *args, **kwargs) New missing coverage at line 473 ! if isinstance(pipeline, Path): - pipeline = edsnlp.load(pipeline) dependencies = get_deep_dependencies(pipeline)	202	7	7	96.53%
TOTAL	9380	245	33	97.39%

Files without new missing coverage

Name	Stmts	Miss	∆ Miss	Cover
edsnlp/viz/quick_examples.py Was already missing at lines 88-91 if end > istart: - interval = (start, iend) - del intervals[idx] - break	80	3	0	96.25%
edsnlp/utils/resources.py Was already missing at line 33 if not verbs: - return conjugated_verbs	24	1	0	95.83%
edsnlp/utils/numbers.py Was already missing at line 34 else: - string = s string = string.lower().strip() Was already missing at lines 38-41 return int(string) - except ValueError: - parsed = DIGITS_MAPPINGS.get(string, None) - return parsed	16	4	0	75.00%
edsnlp/utils/lazy_module.py Was already missing at line 46 ): - continue for import_node in node.body:	31	1	0	96.77%
edsnlp/utils/filter.py Was already missing at line 206 if isinstance(label, int): - return [span for span in spans if span.label == label] else:	74	1	0	98.65%
edsnlp/utils/bindings.py Was already missing at line 22 return "." + path - return path	66	1	0	98.48%
edsnlp/train.py Was already missing at line 190 else: - sample_len = lambda idx, noise=True: 1 # noqa: E731 Was already missing at lines 257-263 if total + num_tokens > self.grad_accumulation_max_tokens: - print( ... - mini_batches.append([]) total += num_tokens Was already missing at line 349 if 0 <= self.limit <= count: - break if not (len(doc) and (filter_fn is None or filter_fn(doc))): Was already missing at line 351 if not (len(doc) and (filter_fn is None or filter_fn(doc))): - continue count += 1 Was already missing at lines 385-387 for ent in doc.ents: - for token in ent: - token.is_sent_start = False for sent in doc.sents if doc.has_annotation("SENT_START") else (doc[:],):	257	8	0	96.89%
edsnlp/processing/spark.py Was already missing at line 51 getActiveSession = SparkSession.getActiveSession - except AttributeError:	43	1	0	97.67%
edsnlp/processing/simple.py Was already missing at lines 28-30 no_grad = sys.modules["torch"].no_grad - except (KeyError, AttributeError): - no_grad = nullcontext reader = lc.reader	52	2	0	96.15%
edsnlp/processing/multiprocessing.py Was already missing at lines 227-231 if os.environ.get("TORCH_SHARING_STRATEGY"): - try: - torch.multiprocessing.set_sharing_strategy(os.environ["TORCH_SHARING_STRATEGY"]) - except NameError: - pass Was already missing at line 249 def save_align_devices_hook(pickler: Any, obj: Any): - pickler.save_reduce(load_align_devices_hook, (obj.__dict__,), obj=obj) Was already missing at lines 252-259 def load_align_devices_hook(state): - state["execution_device"] = MAP_LOCATION ... - AlignDevicesHook = None Was already missing at line 452 - new_batch_iterator = None Was already missing at lines 573-575 else: - batch = gpu_pipe.prepare_batch(docs, device=device) - inputs = None active_batches[batch_id] = (docs, task_id, inputs) Was already missing at line 939 if isinstance(outputs, BaseException): - raise outputs Was already missing at line 1007 if v is not None: - os.environ[k] = v	417	16	0	96.16%
edsnlp/pipes/trainable/span_linker/span_linker.py Was already missing at lines 401-403 if self.reference_mode == "synonym": - embeds = embeds.to(new_lin.weight) - new_lin.weight.data = embeds else:	172	2	0	98.84%
edsnlp/pipes/trainable/ner_crf/ner_crf.py Was already missing at line 250 if self.labels is not None and not self.infer_span_setter: - return Was already missing at lines 258-260 if callable(self.target_span_getter): - for span in get_spans(doc, self.target_span_getter): - inferred_labels.add(span.label_) else:	157	3	0	98.09%
edsnlp/pipes/trainable/layers/crf.py Was already missing at line 21 # out: 2 * N * O - return (log_A.unsqueeze(-1) + log_B.unsqueeze(-3)).logsumexp(-2) Was already missing at line 29 # out: 2 * N * O - return (log_A.unsqueeze(-1) + log_B.unsqueeze(-3)).max(-2) Was already missing at line 97 if learnable_transitions: - self.transitions = torch.nn.Parameter( torch.zeros_like(forbidden_transitions, dtype=torch.float) Was already missing at line 107 if learnable_transitions and with_start_end_transitions: - self.start_transitions = torch.nn.Parameter( torch.zeros(num_tags, dtype=torch.float) Was already missing at line 116 if learnable_transitions and with_start_end_transitions: - self.end_transitions = torch.nn.Parameter( torch.zeros(num_tags, dtype=torch.float)	136	5	0	96.32%
edsnlp/pipes/trainable/embeddings/span_pooler/span_pooler.py Was already missing at line 200 if len(batch["begins"]) == 0: - return { "embeddings": torch.empty(0, self.output_size, device=device),	67	1	0	98.51%
edsnlp/pipes/qualifiers/reported_speech/reported_speech.py Was already missing at lines 18-22 return "REPORTED" - elif token._.rspeech is False: - return "DIRECT" - else: - return None	74	3	0	95.95%
edsnlp/pipes/qualifiers/negation/negation.py Was already missing at line 22 else: - return None	78	1	0	98.72%
edsnlp/pipes/qualifiers/hypothesis/hypothesis.py Was already missing at line 21 else: - return None	75	1	0	98.67%
edsnlp/pipes/qualifiers/history/history.py Was already missing at lines 20-26 def history_getter(token: Union[Token, Span]) -> Optional[str]: - if token._.history is True: - return "ATCD" - elif token._.history is False: - return "CURRENT" - else: - return None Was already missing at lines 312-318 ) - except ValueError: ... - note_datetime = None Was already missing at lines 327-333 ) - except ValueError: ... - birth_datetime = None Was already missing at lines 399-402 ) - except ValueError as e: - absolute_date = None - logger.warning( "In doc {}, the following date {} raises this error: {}. "	155	14	0	90.97%
edsnlp/pipes/qualifiers/family/family.py Was already missing at line 21 else: - return None	60	1	0	98.33%
edsnlp/pipes/qualifiers/base.py Was already missing at line 21 if normalizer and not normalizer.lowercase: - logger.warning( "You have chosen the NORM attribute, but disabled lowercasing "	44	1	0	97.73%
edsnlp/pipes/ner/tnm/tnm.py Was already missing at lines 156-158 value = TNM.parse_obj(groupdict) - except ValidationError: - value = TNM.parse_obj({})	44	2	0	95.45%
edsnlp/pipes/ner/tnm/model.py Was already missing at line 139 def __str__(self): - return self.norm() Was already missing at line 163 ) - exclude_unset = skip_defaults	104	2	0	98.08%
edsnlp/pipes/ner/scores/sofa/sofa.py Was already missing at line 32 if not assigned: - continue if assigned.get("method_max") is not None: Was already missing at line 40 else: - method = "Non précisée"	25	2	0	92.00%
edsnlp/pipes/ner/scores/elston_ellis/patterns.py Was already missing at line 26 if x <= 5: - return 1 Was already missing at lines 32-36 else: - return 3 - - except ValueError: - return None	21	4	0	80.95%
edsnlp/pipes/ner/scores/charlson/patterns.py Was already missing at lines 21-23 return int(extracted_score) - except ValueError: - return None	13	2	0	84.62%
edsnlp/pipes/ner/scores/base_score.py Was already missing at line 154 if value is None: - continue normalized_value = self.score_normalization(value)	47	1	0	97.87%
edsnlp/pipes/ner/disorders/solid_tumor/solid_tumor.py Was already missing at lines 114-117 if use_tnm: - from edsnlp.pipes.ner.tnm import TNM - - self.tnm = TNM(nlp, pattern=None, attr="TEXT") Was already missing at lines 119-129 def process_tnm(self, doc): - spans = self.tnm.process(doc) ... - yield span Was already missing at line 149 if self.use_tnm: - yield from self.process_tnm(doc)	35	12	0	65.71%
edsnlp/pipes/ner/disorders/peripheral_vascular_disease/peripheral_vascular_disease.py Was already missing at line 106 if "peripheral" not in span._.assigned.keys(): - continue	15	1	0	93.33%
edsnlp/pipes/ner/disorders/diabetes/diabetes.py Was already missing at line 133 # Mostly FP - continue Was already missing at line 136 elif self.has_far_complications(span): - span._.status = 2 Was already missing at line 148 if next(iter(self.complication_matcher(context)), None) is not None: - return True return False	31	3	0	90.32%
edsnlp/pipes/ner/disorders/connective_tissue_disease/connective_tissue_disease.py Was already missing at line 102 # Huge change of FP / Title section - continue	14	1	0	92.86%
edsnlp/pipes/ner/disorders/ckd/ckd.py Was already missing at lines 119-122 dfg_value = float(dfg_span.text.replace(",", ".").strip()) - except ValueError: - logger.trace(f"DFG value couldn't be extracted from {dfg_span.text}") - return False	29	3	0	89.66%
edsnlp/pipes/ner/disorders/cerebrovascular_accident/cerebrovascular_accident.py Was already missing at lines 110-112 if span._.source == "ischemia": - if "brain" not in span._.assigned.keys(): - continue	17	2	0	88.24%
edsnlp/pipes/ner/adicap/models.py Was already missing at line 15 def norm(self) -> str: - return self.code Was already missing at line 18 def __str__(self): - return self.norm()	14	2	0	85.71%
edsnlp/pipes/misc/tables/tables.py Was already missing at line 129 else: - self.tables_pattern = tables_pattern Was already missing at line 134 else: - self.sep = sep_pattern	28	2	0	92.86%
edsnlp/pipes/misc/sections/sections.py Was already missing at line 126 if sections is None: - sections = patterns.sections sections = dict(sections)	45	1	0	97.78%
edsnlp/pipes/misc/measurements/measurements.py Was already missing at lines 146-148 def __getitem__(self, item: int): - assert isinstance(item, int) - return [self][item] Was already missing at lines 159-162 def __eq__(self, other: Any): - if isinstance(other, SimpleMeasurement): - return self.convert_to(other.unit) == other.value - return False Was already missing at line 165 if other.unit == self.unit: - return self.__class__(self.value + other.value, self.unit, self.registry) return self.__class__( Was already missing at line 194 def verify(cls, ent): - return True Was already missing at line 233 def __lt__(self, other: Union[SimpleMeasurement, "RangeMeasurement"]): - return max(self.convert_to(other.unit)) < min((part.value for part in other)) Was already missing at line 244 return self.convert_to(other.unit) == other.value - return False Was already missing at line 258 def verify(cls, ent): - return True Was already missing at line 498 if isinstance(measurements, str): - measurements = [measurements] if isinstance(measurements, (list, tuple)): Was already missing at line 711 if snippet.end != last and doclike.doc[last: snippet.end].text.strip() == "": - pseudo.append("w") pseudo = "".join(pseudo) Was already missing at lines 875-877 unit_norm = self.unit_followers[unit_before.label_] - except (KeyError, AttributeError, IndexError): - pass Was already missing at line 920 ): - ent = doc[unit_text.start: number.end] else: Was already missing at lines 927-929 dims = self.unit_registry.parse_unit(unit_norm)[0] - except KeyError: - continue Was already missing at lines 1034-1036 last._.set(last.label_, new_value) - except (AttributeError, TypeError): - merged.append(ent) else:	388	19	0	95.10%
edsnlp/pipes/misc/dates/models.py Was already missing at line 152 else: - d["month"] = note_datetime.month if self.day is None: Was already missing at lines 156-162 else: - if self.year is None: ... - d["day"] = default_day Was already missing at lines 170-172 return dt - except ValueError: - return None Was already missing at line 188 else: - return None Was already missing at line 204 if self.second: - norm += f"{self.second:02}s"	196	11	0	94.39%
edsnlp/pipes/misc/dates/dates.py Was already missing at line 243 if isinstance(absolute, str): - absolute = [absolute] if isinstance(relative, str): Was already missing at line 245 if isinstance(relative, str): - relative = [relative] if isinstance(duration, str): Was already missing at line 247 if isinstance(duration, str): - relative = [duration] if isinstance(false_positive, str): Was already missing at lines 348-357 if self.merge_mode == "align": - alignments = align_spans(matches, spans, sort_by_overlap=True) ... - matches.append(span) Was already missing at line 439 elif d1 in seen or v1.bound is None or v2.bound is None: - continue Was already missing at lines 450-452 if v1.mode == Mode.DURATION: - m1 = Bound.FROM if v2.bound == Bound.UNTIL else Bound.UNTIL - m2 = v2.mode or Bound.FROM elif v2.mode == Mode.DURATION:	148	15	0	89.86%
edsnlp/pipes/misc/consultation_dates/consultation_dates.py Was already missing at line 131 else: - self.date_matcher = None Was already missing at line 134 if not consultation_mention: - consultation_mention = [] elif consultation_mention is True:	48	2	0	95.83%
edsnlp/pipes/core/normalizer/__init__.py Was already missing at line 7 def excluded_or_space_getter(t): - return t.is_space or t.tag_ == "EXCLUDED"	5	1	0	80.00%
edsnlp/pipes/core/endlines/endlines.py Was already missing at lines 151-155 if end_lines_model is None: - path = build_path(__file__, "base_model.pkl") - - with open(path, "rb") as inp: - self.model = pickle.load(inp) elif isinstance(end_lines_model, str): Was already missing at lines 158-160 self.model = pickle.load(inp) - elif isinstance(end_lines_model, EndLinesModel): - self.model = end_lines_model else: Was already missing at line 191 ): - return "ENUMERATION" Was already missing at line 278 if np.isnan(sigma): - sigma = 1	87	7	0	91.95%
edsnlp/patch_spacy.py Was already missing at lines 67-69 # if module is reloaded. - existing_func = registry.factories.get(internal_name) - if not util.is_same_func(factory_func, existing_func): raise ValueError(	31	2	0	93.55%
edsnlp/optimization.py Was already missing at line 32 def param_groups(self, value): - self.optim.param_groups = value Was already missing at line 36 def state(self): - return self.optim.state Was already missing at line 40 def state(self, value): - self.optim.state = value Was already missing at line 89 def __init__(self, groups): - self.param_groups = groups	77	4	0	94.81%
edsnlp/matchers/simstring.py Was already missing at line 280 if custom: - attr = attr[1:].lower() Was already missing at line 295 if custom: - token_text = getattr(token._, attr) else:	146	2	0	98.63%
edsnlp/language.py Was already missing at line 103 if last != begin: - logger.warning( "Missed some characters during"	51	1	0	98.04%
edsnlp/data/standoff.py Was already missing at line 43 def __init__(self, ann_file, line): - super().__init__(f"File {ann_file}, unrecognized Brat line {line}") Was already missing at line 83 if not len(ann_paths): - return { "text": text, Was already missing at line 197 ) - except Exception: raise Exception(	172	3	0	98.26%
edsnlp/data/polars.py Was already missing at line 26 if hasattr(data, "collect"): - data = data.collect() assert isinstance(data, pl.DataFrame)	44	1	0	97.73%
edsnlp/data/json.py Was already missing at line 94 if not is_jsonl: - obj[FILENAME] = filename results.append(obj) Was already missing at line 96 results.append(obj) - except Exception: raise Exception(f"Cannot parse {filename}")	107	2	0	98.13%
edsnlp/data/converters.py Was already missing at line 659 if isinstance(converter, type) or kwargs_to_init: - return converter(**kwargs), {} return converter, validate_kwargs(converter, kwargs)	192	1	0	99.48%
edsnlp/data/base.py Was already missing at lines 174-180 """ - data = LazyCollection.ensure_lazy(data) - if converter: - converter, kwargs = get_doc2dict_converter(converter, kwargs) - data = data.map(converter, kwargs=kwargs) - - return data	39	5	0	87.18%
edsnlp/core/torch_component.py Was already missing at line 390 if hasattr(self, "compiled"): - res = self.compiled(batch) else: Was already missing at line 436 """ - return self.preprocess(doc)	179	2	0	98.88%
edsnlp/core/registries.py Was already missing at line 76 if obj.error is not None: - raise obj.error	165	1	0	99.39%
edsnlp/core/pipeline.py Was already missing at line 550 if name in exclude: - continue if name not in components:	404	1	0	99.75%
edsnlp/core/lazy_collection.py Was already missing at line 51 def __call__(self, *args, **kwargs): - return self.forward(*args, **kwargs) Was already missing at line 436 for name, pipe, *_ in self.torch_components(): - pipe.to(device) return self	149	2	0	98.66%
edsnlp/connectors/omop.py Was already missing at line 69 if not isinstance(row.ents, list): - continue Was already missing at line 87 else: - doc.spans[span.label_].append(span) Was already missing at line 127 if df.note_id.isna().any(): - df["note_id"] = range(len(df)) Was already missing at line 171 if i > 0: - df.term_modifiers += ";" df.term_modifiers += ext + "=" + df[ext].astype(str)	84	4	0	95.24%
edsnlp/processing/deprecated_pipe.py Was already missing at lines 207-209 def converter(doc): - res = results_extractor(doc) - return ( [{"note_id": doc._.note_id, **row} for row in res]	57	2	-2	96.49%

258 files skipped due to complete coverage.

Coverage failure: total of 97.39% is less than 97.58% ❌

[sonarqubecloud]

Quality Gate passed

Issues
6 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[aricohen93]

why everything under negation? eds.negation.default_patterns