Frailty migration

[theoimbert-aphp]

Summary

This PR implements NER pipelines for mentions of frailty across several domains of the Geriatric Assessment, along with some clinically validated geriatric scores for these domains.

Description

The following new NER components were added:

• eds.autonomy
• eds.cognition
• eds.frailty
• eds.general_status
• eds.geriatric_assessment
• eds.incontinence
• eds.mobility
• eds.nutrition
• eds.pain
• eds.polymed
• eds.sensory
• eds.social
• eds.thymic
• eds.adl
• eds.iadl
• eds.bref
• eds.chair_stand
• eds.en_eva
• eds.g8
• eds.gait_speed
• eds.gds
• eds.mini_gds
• eds.mini_cog
• eds.mms
• eds.moca
• eds.ps
• eds.rockwood
• eds.sppb
• eds.tug

Those components are the result of the work done on the PASSAGE cohort and project (article yet to come).

Behavior

All these pipelines are based on ContextualMatchers, and work similarly to other NER pipelines already present in EDS-NLP. The "basic" frailty domain pipelines store their matches in doc.ents and doc.spans[{domain}] by default. The score pipelines store their matches in doc.ents, doc.spans[{score}] and doc.spans[{domain}], where {domain} is their corresponding frailty domain. For example, the eds.adl pipeline stores its matches in doc.ents, doc.spans["adl"] and doc.spans["autonomy"].

For each match, a severity attribute is set for the corresponding domain. Here is an example :

nlp = edsnlp.blank("eds")
nlp.add_pipe(eds.normalizer())
nlp.add_pipe(eds.sentences())
nlp.add_pipe(eds.adl())

doc = nlp("ADL 6/6")

spans = doc.spans["adl"]
spans
# Out: ['ADL 6/6']

span = spans[0]
span._.autonomy
# Out: 'healthy'

Tests

Added unit tests for all these pipelines.

Documentation

Added documentation for all these pipelines. The documentation may need to be updated later on, notably when the article releases, and to provide some additional information on the scores.

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]

Docs preview URL

https://edsnlp-frailty-migration.vercel.app

[github-actions]

Coverage Report

Name	Stmts	Miss	∆ Miss	Cover
edsnlp/pipes/ner/frailty/utils.py New missing coverage at line 131 ! if current_window[0] < window[0]: - window[0] = current_window[0] if current_window[1] > window[1]: New missing coverage at line 133 ! if current_window[1] > window[1]: - window[1] = current_window[1] new_regex = make_assign_regex(regex_list)	41	2	2	95.12%
edsnlp/pipes/ner/frailty/scores/base.py New missing coverage at line 76 ! if isinstance(score_normalization, str): - self.score_normalization = registry.misc.get(score_normalization) else: New missing coverage at line 183 ! if assign.span_getter is not None: - assigned = [ (matched_span, matched_span)	91	2	2	97.80%
edsnlp/pipes/ner/frailty/base.py New missing coverage at line 50 ! if name is None: - name = domain if label is None: New missing coverage at line 52 ! if label is None: - label = domain self.domain = domain	39	2	2	94.87%
edsnlp/pipes/ner/frailty/scores/iadl_score/factory.py New missing coverage at line 25 ! elif value == 0: - return "altered_severe" else:	20	1	1	95.00%
edsnlp/pipes/ner/frailty/scores/chair_stand_score/factory.py New missing coverage at line 31 ! if kept_value is None: - return	36	1	1	97.22%
TOTAL	14453	265	4	98.17%

Files without new missing coverage

Name	Stmts	Miss	∆ Miss	Cover
edsnlp/utils/typing.py Was already missing at line 44 def __get_validators__(cls): - yield cls.validate	48	1	0	97.92%
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)	81	9	0	88.89%
edsnlp/utils/span_getters.py Was already missing at lines 73-75 if span_getter is None: - yield doclike[:], None - return if callable(span_getter): Was already missing at lines 76-78 if callable(span_getter): - yield from span_getter(doclike) - return for key, span_filter in span_getter.items(): Was already missing at lines 99-102 else: - for span, group in candidates: - if span.label_ in span_filter: - yield span, group Was already missing at line 107 if callable(span_setter): - span_setter(doc, matches) else: Was already missing at line 138 if callable(value): - return value if isinstance(value, str): Was already missing at line 187 elif isinstance(v, str): - new_value[k] = [v] elif isinstance(v, list) and all(isinstance(i, str) for i in v):	241	10	0	95.85%
edsnlp/utils/resources.py Was already missing at line 33 if not verbs: - return conjugated_verbs	25	1	0	96.00%
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/fuzzy_alignment.py Was already missing at line 70 if len(other.begins) == 0: - return self begins = self.unapply(other.begins, side="left")	191	1	0	99.48%
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/file_system.py Was already missing at line 39 if isinstance(filesystem, str): - filesystem = fsspec.filesystem(filesystem) Was already missing at line 50 if not isinstance(inferred_protocols, (list, tuple, set)): - inferred_protocols = [inferred_fs.protocol] if not isinstance(filesystem_protocols, (list, tuple, set)): Was already missing at line 52 if not isinstance(filesystem_protocols, (list, tuple, set)): - filesystem_protocols = [filesystem.protocol] assert set(filesystem_protocols) & set(inferred_protocols), (	31	3	0	90.32%
edsnlp/training/trainer.py Was already missing at line 59 if result is None: - result = {} if isinstance(x, dict): Was already missing at line 118 # fmt: off - autocast = { "fp16": torch.float16, "float16": torch.float16, Was already missing at lines 379-385 if self.sub_batch_size and self.sub_batch_size[1] == "splits": - data = data.batchify( ... - data = data.map(lambda b: [nlp.collate(sb, device=device) for sb in b]) elif self.sub_batch_size: Was already missing at lines 938-945 raise - except Exception: ... - raise Was already missing at lines 972-974 ) > grad_max_dev * math.sqrt(grad_var): - spike = True - spikes += 1 else: Was already missing at line 981 if spike and grad_dev_policy == "clip_mean": - torch.nn.utils.clip_grad_norm_( grad_params, grad_mean, norm_type=2 Was already missing at line 985 elif spike and grad_dev_policy == "clip_threshold": - torch.nn.utils.clip_grad_norm_( grad_params,	357	13	0	96.36%
edsnlp/training/loggers.py Was already missing at line 65 if self._file is not None: - return os.makedirs(self.logging_dir, exist_ok=True) Was already missing at line 102 if col not in values and col != "step": - row.append("") else: Was already missing at line 225 def tracker(self): - return self.printer Was already missing at line 293 ) - logging_dir = env_logging_dir assert logging_dir is not None, (	160	4	0	97.50%
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	68	2	0	97.06%
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 222-230 return re.findall(r"/[^\s]+\.so[^\s]*", f.read()) - except Exception: ... - return [] Was already missing at lines 233-235 loaded = loaded_libs() - except Exception: - return False return any(any(k in os.path.basename(p).lower() for k in libs) for p in loaded) Was already missing at line 254 ) - method = "spawn" Was already missing at lines 258-264 if has_hdfs and method == "fork": - safe = "forkserver" if "forkserver" in methods else "spawn" ... - method = safe Was already missing at lines 454-457 for _ in self.iter_tasks(stage=stage, stop_mode=True): - pass - except StopSignal: - pass for name, queue in self.consumer_queues(stage): Was already missing at lines 672-674 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 line 1144 if self.error: - raise self.error finally: Was already missing at lines 1202-1208 if out[0].kind == requires_sentinel: - missing_sentinels -= 1 ... - missing_sentinels = len(self.cpu_worker_names) continue	671	24	0	96.42%
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]	53	2	0	96.23%
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:	175	2	0	98.86%
edsnlp/pipes/trainable/span_classifier/span_classifier.py Was already missing at line 380 if not all(keep_bindings): - logger.warning( "Some attributes have no labels or values and have been removed:"	171	1	0	99.42%
edsnlp/pipes/trainable/ner_crf/ner_crf.py Was already missing at line 302 if self.labels is not None and not self.infer_span_setter: - return Was already missing at lines 310-312 if callable(self.target_span_getter): - for span in get_spans(doc, self.target_span_getter): - inferred_labels.add(span.label_) else: Was already missing at line 447 ) - self._has_warned = True	177	4	0	97.74%
edsnlp/pipes/trainable/layers/crf.py Was already missing at line 80 if learnable_transitions: - self.transitions = torch.nn.Parameter( torch.zeros_like(forbidden_transitions, dtype=torch.float) Was already missing at line 90 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 99 if learnable_transitions and with_start_end_transitions: - self.end_transitions = torch.nn.Parameter( torch.zeros(num_tags, dtype=torch.float)	138	3	0	97.83%
edsnlp/pipes/trainable/embeddings/transformer/transformer.py Was already missing at line 167 if quantization is not None: - kwargs["quantization_config"] = quantization Was already missing at line 192 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 196 if self.sep_token_id is None: - [self.sep_token_id] = self.tokenizer.convert_tokens_to_ids( [self.tokenizer.special_tokens_map["eos_token"]]	168	3	0	98.21%
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	101	1	0	99.01%
edsnlp/pipes/qualifiers/hypothesis/hypothesis.py Was already missing at line 27 else: - return None	98	1	0	98.98%
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 351-357 ) - except ValueError: ... - note_datetime = None Was already missing at lines 366-372 ) - except ValueError: ... - birth_datetime = None Was already missing at lines 438-441 ) - except ValueError as e: - absolute_date = None - logger.warning( "In doc {}, the following date {} raises this error: {}. "	180	14	0	92.22%
edsnlp/pipes/qualifiers/family/family.py Was already missing at line 27 else: - return None	83	1	0	98.80%
edsnlp/pipes/qualifiers/base.py Was already missing at line 123 elif on_ents_only is not True: - assert span_getter is None, ( "Cannot use both `span_getter` and `on_ents_only` as a span "	52	1	0	98.08%
edsnlp/pipes/ner/tnm/model.py Was already missing at line 143 def __str__(self): - return self.norm() Was already missing at line 167 ) - exclude_unset = skip_defaults	109	2	0	98.17%
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/disorders/base.py Was already missing at lines 119-122 if span._.status is not None and span._.status not in all_detailed_status: - default_status = 1 if 1 in all_detailed_status else None ... - span._.status = default_status span._.detailed_status = self.detailed_status_mapping.get(	31	2	0	93.55%
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/split/split.py Was already missing at lines 186-188 if max_length <= 0 and self.regex is None: - yield doc - return	74	2	0	97.30%
edsnlp/pipes/misc/sections/sections.py Was already missing at line 126 if sections is None: - sections = patterns.sections sections = dict(sections)	46	1	0	97.83%
edsnlp/pipes/misc/quantities/quantities.py Was already missing at lines 195-197 def __getitem__(self, item: int): - assert isinstance(item, int) - return [self][item] Was already missing at lines 209-215 def __eq__(self, other: Any): - if isinstance(other, SimpleQuantity): ... - return False Was already missing at line 218 if other.unit == self.unit: - return SimpleQuantity( self.value + other.value, Was already missing at line 272 def verify(cls, ent): - return True Was already missing at line 338 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 361 return self.convert_to(other.unit) == other.value - return False Was already missing at line 375 def verify(cls, ent): - return True Was already missing at line 1357 if snippet.end != last and doclike.doc[last : snippet.end].text.strip() == "": - pseudo.append("w") pseudo = "".join(pseudo) Was already missing at lines 1738-1742 ): - unitless_pattern = self.unitless_patterns[ ... - unit_norm = next( scope["unit"] Was already missing at line 1783 ): - ent = doc[min(ent_start, unit_text.start) : number.end] else:	702	14	0	98.01%
edsnlp/pipes/misc/dates/models.py Was already missing at line 157 else: - d["month"] = note_datetime.month if self.day is None: Was already missing at lines 161-167 else: - if self.year is None: ... - d["day"] = default_day Was already missing at lines 175-177 return dt - except ValueError: - return None Was already missing at line 193 else: - return None Was already missing at line 209 if self.second: - norm += f"{self.second:02}s"	203	11	0	94.58%
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/llm/llm_span_qualifier/llm_span_qualifier.py Was already missing at line 579 if isinstance(formatted_context, Doc): - context_text = formatted_context.text else: Was already missing at line 657 if start == -1 or end <= 0 or end <= start: - return None try: Was already missing at line 750 if next_yield >= len(doc_states): - return for state in doc_states[next_yield:]:	249	3	0	98.80%
edsnlp/pipes/llm/llm_markup_extractor/llm_markup_extractor.py Was already missing at line 309 if seed is not None: - api_kwargs["seed"] = seed self.retriever = None Was already missing at line 355 if span is None: - continue spans.append(span) Was already missing at lines 467-469 if not contexts: - remaining_ctx_counts[doc_idx] = 0 - buffer[doc_idx] = doc else: Was already missing at line 490 if result is None: - pass else:	157	5	0	96.82%
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_attribute.py Was already missing at lines 68-70 ) - assert attributes is None - attributes = kwargs.pop("qualifiers") if attributes is None:	93	2	0	97.85%
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"	52	1	0	98.08%
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/huggingface_dataset.py Was already missing at line 259 if isinstance(item, DatasetEndSentinel): - continue else:	99	1	0	98.99%
edsnlp/data/converters.py Was already missing at line 427 elif key == "XPOS": - word.tag_ = value elif key == "FEATS": Was already missing at line 835 if self.keep_raw_attribute_values: - return value try: Was already missing at line 897 if not attr: - continue if "=" in attr: Was already missing at line 928 if span is None: - continue for k, v in attrs.items(): Was already missing at line 998 if isinstance(value, (bool, int, float)): - return repr(value) s = str(value) Was already missing at line 1307 if current_type is not None: - entities.append((start_idx, i, current_type)) start_idx = i Was already missing at line 1401 if start < 0 or start >= len(tags): - continue tags[start] = f"B-{label}" Was already missing at line 1445 if isinstance(converter, type): - return converter(**kwargs), {} return converter, validate_kwargs(converter, kwargs)	500	8	0	98.40%
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 407 if hasattr(self, "compiled"): - res = self.compiled(batch) else: Was already missing at line 453 """ - return self.preprocess(doc)	190	2	0	98.95%
edsnlp/core/stream.py Was already missing at line 155 else: - yield res return Was already missing at lines 203-205 if isinstance(batch, StreamSentinel): - yield batch - continue results = [] Was already missing at lines 1030-1032 elif op.batch_fn is None: - batch_size = op.size - batch_fn = batchify else:	383	5	0	98.69%
edsnlp/core/registries.py Was already missing at line 138 if isinstance(obj, DraftPipe): - return obj elif isinstance(obj, dict): Was already missing at line 143 if result is not None: - return result elif isinstance(obj, (tuple, list, set)): Was already missing at line 148 if result is not None: - return result return None	221	3	0	98.64%
edsnlp/core/pipeline.py Was already missing at line 607 if name in exclude: - continue if name not in components: Was already missing at lines 715-718 """ - res = Stream.ensure_stream(docs) - res = res.map(functools.partial(self.preprocess, supervision=supervision)) - return res	463	4	0	99.14%
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/_version.py Was already missing at line 21 if repo_root is None: - return base_version Was already missing at line 39 - return ( base_version	15	2	0	86.67%
edsnlp/tune.py Was already missing at line 221 return logger_config.get("@loggers") == "json" - return False Was already missing at line 291 continue - raise for feature, importance in importance_scores.items(): Was already missing at line 399 ): - resolved_key = int(key) try: Was already missing at lines 650-652 return os.path.join(info.root_dir, metrics_relpath) - time.sleep(1) - return None Was already missing at line 834 if was_pruned: - _handle_pruned_dvc_runs(queue, entries, entry) if not (result and result.exp_hash and result.ref_info): Was already missing at line 1062 else: - config = copy.deepcopy(raw_config) updated_config = update_config( Was already missing at line 1197 else: - config_path_phase_2 = os.path.join(output_dir_phase_1, "config.cfg")	626	8	-2	98.72%

380 files skipped due to complete coverage.

Coverage success: total of 98.17% is above 98.07% 🎉

[percevalw]

Hi @theoimbert-aphp, congratulations on this massive work!

1. Names:

Some component names are a bit short and ambiguous (e.g., eds.ps). I suggest making them more explicit, e.g., eds.ecog_performance_status_score instead of eds.ps).

For example:

• eds.autonomy -> eds.autonomy_status
• eds.cognition -> eds.cognitive_status
• eds.frailty -> eds.frailty
• eds.general_status -> eds.global_health_status
• eds.geriatric_assessment -> eds.geriatric_assessment
• eds.incontinence -> eds.incontinence_status
• eds.mobility -> eds.mobility_status
• eds.nutrition -> eds.nutritional_status
• eds.pain -> eds.pain_status
• eds.polymed -> eds.polypharmacy_status
• eds.sensory -> eds.sensory_status
• eds.social -> eds.social_status
• eds.thymic -> eds.mood_status
• eds.adl -> eds.adl_score
• eds.bref -> eds.bref_score
• eds.chair_stand -> eds.chair_stand_score
• eds.en_eva -> eds.pain_rating_score
• eds.g8_score -> eds.g8_score
• eds.gait_speed -> eds.gait_speed_score
• eds.gds -> eds.geriatric_depression_scale_score
• eds.iadl -> eds.iadl_score
• eds.mini_cog -> eds.mini_cog_score
• eds.mini_gds -> eds.mini_gds_score
• eds.mms -> eds.mini_mental_state_score
• eds.moca -> eds.moca_score
• eds.ps -> eds.ecog_performance_status_score
• eds.rockwood -> eds.clinical_frailty_scale_score
• eds.sppb -> eds.sppb_score
• eds.tug -> eds.timed_up_and_go_score

What do you think about this ? we can discuss this mapping here and I can handle the refactoring if you want to.

2. Coverage

Some pipes have missing coverage, which can be quite easily improved by adding specific tests : could you handle that ?

To use the rebased PR, run the following commands:

⚠️ This will erase any local changes made to the branch

git fetch
git reset origin/frailty_migration --hard

[theoimbert-aphp]

Hi @percevalw, thanks for the feedback !

1. Regarding names I understand and I think it's a good idea, but I have a few remarks:

• I used autonomy as a short-hand way to talk about what geriatricians call "functional status", so I think since we are renaming things it would be best to rename eds.autonomy to eds.functional_status
• I think a better name for eds.thymic would be eds.psychological_status, as it fits better to the geriatricians' jargon than eds.mood_status
• I'm a bit skeptical about leaving eds.frailty as is if everything else is renamed, as I'm afraid it could be misleading and implying this is a "one fits all" magical component that would extract everything related to frailty, whereas in reality it only captures explicit mentions of frailty (e.g : "Le patient est fragile") and misses out on basically everything else that is covered by the other components. Perhaps something along the lines of eds.frailty_mentions ? Let me know what you think

As for the rest, your propositions seem great to me !

2. Regarding coverage, sure, I can look into that !

[percevalw]

I'm ok with all your comments. Regarding the pipe names, can I let you edit and suggest a final mapping that would go in the same direction of being more explicit ?

[theoimbert-aphp]

Sure, the final mapping would be like so :

• eds.autonomy -> eds.functional_status
• eds.cognition -> eds.cognitive_status
• eds.frailty -> eds.frailty_mentions
• eds.general_status -> eds.global_health_status
• eds.geriatric_assessment -> eds.geriatric_assessment
• eds.incontinence -> eds.incontinence_status
• eds.mobility -> eds.mobility_status
• eds.nutrition -> eds.nutritional_status
• eds.pain -> eds.pain_status
• eds.polymed -> eds.polypharmacy_status
• eds.sensory -> eds.sensory_status
• eds.social -> eds.social_status
• eds.thymic -> eds.psychological_status
• eds.adl -> eds.adl_score
• eds.bref -> eds.bref_score
• eds.chair_stand -> eds.chair_stand_score
• eds.en_eva -> eds.pain_rating_score
• eds.g8_score -> eds.g8_score
• eds.gait_speed -> eds.gait_speed_score
• eds.gds -> eds.geriatric_depression_scale_score
• eds.iadl -> eds.iadl_score
• eds.mini_cog -> eds.mini_cog_score
• eds.mini_gds -> eds.mini_gds_score
• eds.mms -> eds.mini_mental_state_score
• eds.moca -> eds.moca_score
• eds.ps -> eds.ecog_performance_status_score
• eds.rockwood -> eds.clinical_frailty_scale_score
• eds.sppb -> eds.sppb_score
• eds.tug -> eds.timed_up_and_go_score

[sonarqubecloud]

Quality Gate passed

Issues
343 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
1.9% Duplication on New Code

See analysis details on SonarQube Cloud