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
• Added context strings (e.g., "words[0:5] | sent[0:1]") to the eds.contextual_matcher component to allow for more complex patterns in the selection of the window around the trigger spans.
• Include and exclude patterns in the contextual matcher now dismiss matches that occur inside the anchor pattern (e.g. "anti" exclude pattern for anchor pattern "antibiotics" will not match the "anti" part of "antibiotics")

Changed

• Improve the contextual matcher documentation.
• Fix docs testing (since last year, we only tested that the docs run, but not that the expected output matched the actual outputs)

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).

[github-actions]

Coverage Report

Name	Stmts	Miss	∆ Miss	Cover
edsnlp/tune.py New missing coverage at line 168 ! ) - except RuntimeError as e: if "zero total variance" in str(e): # pragma: no cover	287	1	1	99.65%
edsnlp/pipes/core/contextual_matcher/contextual_matcher.py New missing coverage at lines 241-243 ! ): - to_keep = False - break	130	2	0	98.46%
TOTAL	11381	210	-4	98.15%

Files without new missing coverage

Name	Stmts	Miss	∆ Miss	Cover
edsnlp/utils/torch.py Was already missing at line 102 def load_pruned_obj(obj, _): - return obj Was already missing at line 118 def save_align_devices_hook(pickler, obj): - pickler.save_reduce(load_align_devices_hook, (obj.__dict__,), obj=obj) Was already missing at lines 121-128 def load_align_devices_hook(state): - state["execution_device"] = MAP_LOCATION ... - AlignDevicesHook = None Was already missing at line 143 if torch.Tensor in copyreg.dispatch_table: - old_dispatch[torch.Tensor] = copyreg.dispatch_table[torch.Tensor] copyreg.pickle(torch.Tensor, reduce_empty)	83	9	0	89.16%
edsnlp/utils/span_getters.py Was already missing at lines 70-73 else: - for span in candidates: - if span.label_ in span_filter: - yield span Was already missing at lines 77-79 if span_getter is None: - yield doc[:], None - return if callable(span_getter): Was already missing at lines 80-82 if callable(span_getter): - yield from span_getter(doc) - return for key, span_filter in span_getter.items(): Was already missing at line 84 if key == "*": - candidates = ( (span, group) for group in doc.spans.values() for span in group Was already missing at lines 93-96 else: - for span, group in candidates: - if span.label_ in span_filter: - yield span, group Was already missing at line 100 if callable(span_setter): - span_setter(doc, matches) else: Was already missing at line 142 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 180 elif isinstance(v, str): - new_value[k] = [v] elif isinstance(v, list) and all(isinstance(i, str) for i in v):	229	14	0	93.89%
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/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/training/trainer.py Was already missing at line 80 if result is None: - result = {} if isinstance(x, dict):	241	1	0	99.59%
edsnlp/reducers.py Was already missing at line 115 if not hasattr(module, "__file__"): - return True if module.__file__ is None: Was already missing at line 117 if module.__file__ is None: - return False # Hack to avoid copying the full module dict	67	2	0	97.01%
edsnlp/processing/spark.py Was already missing at line 50 getActiveSession = SparkSession.getActiveSession - except AttributeError:	47	1	0	97.87%
edsnlp/processing/multiprocessing.py Was already missing at lines 387-392 self.on_stop() - except BaseException as e: ... - self.main_control_queue.put(e) finally: Was already missing at lines 396-398 pass - except StopSignal: - pass for name, queue in self.consumer_queues(stage): Was already missing at line 536 while schedule[task_idx] is None: - task_idx = (task_idx + 1) % len(schedule) Was already missing at lines 600-602 if isinstance(docs, StreamSentinel): - self.active_batches[stage].append([None, None, None, docs]) - continue batch_id = str(hash(tuple(id(x) for x in docs)))[-8:] + "-" + self.uid Was already missing at lines 1115-1121 if out[0].kind == requires_sentinel: - missing_sentinels -= 1 ... - missing_sentinels = len(self.cpu_worker_names) continue	626	14	0	97.76%
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	0	96.49%
edsnlp/pipes/trainable/span_linker/span_linker.py Was already missing at lines 402-404 if self.reference_mode == "synonym": - embeds = embeds.to(new_lin.weight) - new_lin.weight.data = embeds else:	173	2	0	98.84%
edsnlp/pipes/trainable/span_classifier/span_classifier.py Was already missing at line 345 if not all(keep_bindings): - logger.warning( "Some attributes have no labels or values and have been removed:"	159	1	0	99.37%
edsnlp/pipes/trainable/ner_crf/ner_crf.py Was already missing at line 301 if self.labels is not None and not self.infer_span_setter: - return Was already missing at lines 309-311 if callable(self.target_span_getter): - for span in get_spans(doc, self.target_span_getter): - inferred_labels.add(span.label_) else:	172	3	0	98.26%
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 98 if learnable_transitions: - self.transitions = torch.nn.Parameter( torch.zeros_like(forbidden_transitions, dtype=torch.float) Was already missing at line 108 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 117 if learnable_transitions and with_start_end_transitions: - self.end_transitions = torch.nn.Parameter( torch.zeros(num_tags, dtype=torch.float)	137	5	0	96.35%
edsnlp/pipes/trainable/embeddings/transformer/transformer.py Was already missing at line 165 if quantization is not None: - kwargs["quantization_config"] = quantization Was already missing at line 185 if self.cls_token_id is None: - [self.cls_token_id] = self.tokenizer.convert_tokens_to_ids( [self.tokenizer.special_tokens_map["bos_token"]] Was already missing at line 189 if self.sep_token_id is None: - [self.sep_token_id] = self.tokenizer.convert_tokens_to_ids( [self.tokenizer.special_tokens_map["eos_token"]]	166	3	0	98.19%
edsnlp/pipes/qualifiers/reported_speech/reported_speech.py Was already missing at lines 24-28 return "REPORTED" - elif token._.rspeech is False: - return "DIRECT" - else: - return None	100	3	0	97.00%
edsnlp/pipes/qualifiers/negation/negation.py Was already missing at line 28 else: - return None	100	1	0	99.00%
edsnlp/pipes/qualifiers/hypothesis/hypothesis.py Was already missing at line 27 else: - return None	97	1	0	98.97%
edsnlp/pipes/qualifiers/history/history.py Was already missing at lines 26-32 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 349-355 ) - except ValueError: ... - note_datetime = None Was already missing at lines 364-370 ) - except ValueError: ... - birth_datetime = None Was already missing at lines 436-439 ) - except ValueError as e: - absolute_date = None - logger.warning( "In doc {}, the following date {} raises this error: {}. "	178	14	0	92.13%
edsnlp/pipes/qualifiers/family/family.py Was already missing at line 27 else: - return None	82	1	0	98.78%
edsnlp/pipes/qualifiers/base.py Was already missing at line 178 def __call__(self, doc: Doc) -> Doc: - results = self.process(doc) raise NotImplementedError(f"{type(results)} should be used to tag the document")	50	1	0	98.00%
edsnlp/pipes/ner/tnm/model.py Was already missing at line 147 def __str__(self): - return self.norm() Was already missing at line 171 ) - exclude_unset = skip_defaults	112	2	0	98.21%
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/disorders/solid_tumor/solid_tumor.py Was already missing at lines 131-137 for span in spans: - span.label_ = "solid_tumor" ... - yield span	38	6	0	84.21%
edsnlp/pipes/ner/disorders/peripheral_vascular_disease/peripheral_vascular_disease.py Was already missing at line 108 if "peripheral" not in span._.assigned.keys(): - continue	16	1	0	93.75%
edsnlp/pipes/ner/disorders/diabetes/diabetes.py Was already missing at line 131 # Mostly FP - continue Was already missing at line 134 elif self.has_far_complications(span): - span._.status = 2 Was already missing at line 145 if next(iter(self.complication_matcher(context)), None) is not None: - return True return False	30	3	0	90.00%
edsnlp/pipes/ner/disorders/connective_tissue_disease/connective_tissue_disease.py Was already missing at line 104 # Huge change of FP / Title section - continue	15	1	0	93.33%
edsnlp/pipes/ner/disorders/ckd/ckd.py Was already missing at lines 121-124 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	30	3	0	90.00%
edsnlp/pipes/ner/disorders/cerebrovascular_accident/cerebrovascular_accident.py Was already missing at lines 112-114 if span._.source == "ischemia": - if "brain" not in span._.assigned.keys(): - continue	18	2	0	88.89%
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()	16	2	0	87.50%
edsnlp/pipes/misc/split/split.py Was already missing at lines 183-185 if max_length <= 0 and self.regex is None: - yield doc - return	73	2	0	97.26%
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/quantities/quantities.py Was already missing at lines 147-149 def __getitem__(self, item: int): - assert isinstance(item, int) - return [self][item] Was already missing at lines 160-163 def __eq__(self, other: Any): - if isinstance(other, SimpleQuantity): - return self.convert_to(other.unit) == other.value - return False Was already missing at line 166 if other.unit == self.unit: - return SimpleQuantity(self.value + other.value, self.unit, self.registry) return SimpleQuantity( Was already missing at line 193 return self.convert_to(other_unit) - except KeyError: raise AttributeError(f"Unit {other_unit} not found") Was already missing at line 198 def verify(cls, ent): - return True Was already missing at line 264 def __lt__(self, other: Union[SimpleQuantity, "RangeQuantity"]): - return max(self.convert_to(other.unit)) < min((part.value for part in other)) Was already missing at line 275 return self.convert_to(other.unit) == other.value - return False Was already missing at line 289 def verify(cls, ent): - return True Was already missing at line 888 if snippet.end != last and doclike.doc[last: snippet.end].text.strip() == "": - pseudo.append("w") pseudo = "".join(pseudo) Was already missing at line 1069 if start_line is None: - continue Was already missing at lines 1100-1102 unit_norm = self.unit_followers[unit_before.label_] - except (KeyError, AttributeError, IndexError): - pass Was already missing at line 1145 ): - ent = doc[unit_text.start: number.end] else: Was already missing at lines 1152-1154 dims = self.unit_registry.parse_unit(unit_norm)[0] - except KeyError: - continue Was already missing at lines 1260-1262 last._.set(last.label_, new_value) - except (AttributeError, TypeError): - merged.append(ent) else:	440	20	0	95.45%
edsnlp/pipes/misc/dates/models.py Was already missing at line 165 else: - d["month"] = note_datetime.month if self.day is None: Was already missing at lines 169-175 else: - if self.year is None: ... - d["day"] = default_day Was already missing at lines 183-185 return dt - except ValueError: - return None Was already missing at line 201 else: - return None Was already missing at line 217 if self.second: - norm += f"{self.second:02}s"	205	11	0	94.63%
edsnlp/pipes/misc/dates/dates.py Was already missing at line 249 if isinstance(absolute, str): - absolute = [absolute] if isinstance(relative, str): Was already missing at line 251 if isinstance(relative, str): - relative = [relative] if isinstance(duration, str): Was already missing at line 253 if isinstance(duration, str): - relative = [duration] if isinstance(false_positive, str): Was already missing at lines 357-366 if self.merge_mode == "align": - alignments = align_spans(matches, spans, sort_by_overlap=True) ... - matches.append(span) Was already missing at lines 462-464 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:	153	14	0	90.85%
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 160-164 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 167-169 self.model = pickle.load(inp) - elif isinstance(end_lines_model, EndLinesModel): - self.model = end_lines_model else: Was already missing at line 200 ): - return "ENUMERATION" Was already missing at line 287 if np.isnan(sigma): - sigma = 1	89	7	0	92.13%
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/package.py Was already missing at lines 474-476 version = version or pyproject["project"]["version"] - except (KeyError, TypeError): - version = "0.1.0" name = name or pyproject["project"]["name"] Was already missing at line 480 else: - main_package = None model_package = snake_case(name.lower())	214	3	0	98.60%
edsnlp/metrics/span_attributes.py Was already missing at lines 56-58 ) - assert attributes is None - attributes = kwargs.pop("qualifiers") if attributes is None:	71	2	0	97.18%
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 38 def __init__(self, ann_file, line): - super().__init__(f"File {ann_file}, unrecognized Brat line {line}") Was already missing at line 192 ) - except Exception: raise Exception(	186	2	0	98.92%
edsnlp/data/polars.py Was already missing at line 36 if hasattr(data, "collect"): - data = data.collect() assert isinstance(data, pl.DataFrame)	55	1	0	98.18%
edsnlp/data/json.py Was already missing at line 81 return records - except Exception as e: raise Exception(f"Cannot read {file}: {e}")	112	1	0	99.11%
edsnlp/data/converters.py Was already missing at line 427 elif key == "XPOS": - word.tag_ = value elif key == "FEATS": Was already missing at line 734 if isinstance(converter, type): - return converter(**kwargs), {} return converter, validate_kwargs(converter, kwargs)	235	2	0	99.15%
edsnlp/data/conll.py Was already missing at lines 81-83 ) - except StopIteration: - cols = DEFAULT_COLUMNS warnings.warn( Was already missing at lines 92-96 if not line: - if doc["words"]: - yield doc - doc = {"words": []} - continue if line.startswith("#"):	76	6	0	92.11%
edsnlp/core/torch_component.py Was already missing at line 392 if hasattr(self, "compiled"): - res = self.compiled(batch) else: Was already missing at line 438 """ - return self.preprocess(doc) Was already missing at line 463 if object.__repr__(self) in exclude: - return exclude.add(object.__repr__(self))	187	3	0	98.40%
edsnlp/core/stream.py Was already missing at lines 190-192 if isinstance(batch, StreamSentinel): - yield batch - continue results = [] Was already missing at lines 1007-1009 elif op.batch_fn is None: - batch_size = op.size - batch_fn = batchify else:	356	4	0	98.88%
edsnlp/core/pipeline.py Was already missing at line 605 if name in exclude: - continue if name not in components: Was already missing at lines 716-719 """ - res = Stream.ensure_stream(docs) - res = res.map(functools.partial(self.preprocess, supervision=supervision)) - return res	446	4	0	99.10%
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%

275 files skipped due to complete coverage.

Coverage success: total of 98.15% is above 98.13% 🎉

[aricohen93]

why everything under negation? eds.negation.default_patterns

[aricohen93]

@percevalw ?

[percevalw]

It's not everything under negation, eds.hypothesis patterns will be under eds.hypothesis.default_patterns

[github-actions]

Docs preview URL

https://edsnlp-improve-contextual-matcher.vercel.app/

[sonarqubecloud]

Quality Gate passed

Issues
11 New issues
1 Accepted issue

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

See analysis details on SonarQube Cloud