Adding possibility to select cim10 and atc in eds.cim10 and eds.drugs #314

svittoz · 2024-08-21T15:57:10Z

Description

Currently, eds.cim10 and eds.drugs does not allow to select cim10 or ATC of interest, resulting in high computational time when used.

TODO : see also eds.umls ?

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 · 2024-08-28T15:41:14Z

Coverage Report

Name

Stmts

Miss

∆ Miss

Cover

edsnlp/pipes/misc/quantities/quantities.py

New missing coverage at lines 147-149 !

     def __getitem__(self, item: int):
-         assert isinstance(item, int)
-         return [self][item]

New missing coverage at lines 160-163 !

     def __eq__(self, other: Any):
-         if isinstance(other, SimpleQuantity):
-             return self.convert_to(other.unit) == other.value
-         return False

New missing coverage at line 166 !

         if other.unit == self.unit:
-             return self.__class__(self.value + other.value, self.unit, self.registry)
         return self.__class__(

New missing coverage at line 193 !

             return self.convert_to(other_unit)
-         except KeyError:
             raise AttributeError(f"Unit {other_unit} not found")

New missing coverage at line 198 !

     def verify(cls, ent):
-         return True

New missing coverage at line 237 !

     def __lt__(self, other: Union[SimpleQuantity, "RangeQuantity"]):
-         return max(self.convert_to(other.unit)) < min((part.value for part in other))

New missing coverage at line 248 !

             return self.convert_to(other.unit) == other.value
-         return False

New missing coverage at line 262 !

     def verify(cls, ent):
-         return True

New missing coverage at line 857 !

         if snippet.end != last and doclike.doc[last: snippet.end].text.strip() == "":
-             pseudo.append("w")
         pseudo = "".join(pseudo)

New missing coverage at line 1031 !

                             if start_line is None:
-                                 continue

New missing coverage at lines 1062-1064 !

                         unit_norm = self.unit_followers[unit_before.label_]
-                 except (KeyError, AttributeError, IndexError):
-                     pass

New missing coverage at line 1107 !

             ):
-                 ent = doc[unit_text.start: number.end]
             else:

New missing coverage at lines 1114-1116 !

                 dims = self.unit_registry.parse_unit(unit_norm)[0]
-             except KeyError:
-                 continue

New missing coverage at lines 1227-1229 !

                     last._.set(last.label_, new_value)
-                 except (AttributeError, TypeError):
-                     merged.append(ent)
             else:

429

20

95.34%

TOTAL

9316

209

20

97.76%

Files without new missing coverage

Name	Stmts	Miss	Cover
edsnlp/utils/span_getters.py Was already missing at lines 52-55 else: - for span in candidates: - if span.label_ in span_filter: - yield span Was already missing at lines 59-61 if span_getter is None: - yield doc[:], None - return if callable(span_getter): Was already missing at lines 62-64 if callable(span_getter): - yield from span_getter(doc) - return for key, span_filter in span_getter.items(): Was already missing at line 66 if key == "*": - candidates = ( (span, group) for group in doc.spans.values() for span in group Was already missing at lines 75-78 else: - for span, group in candidates: - if span.label_ in span_filter: - yield span, group Was already missing at line 82 if callable(span_setter): - span_setter(doc, matches) else: Was already missing at line 124 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 162 elif isinstance(v, str): - new_value[k] = [v] elif isinstance(v, list) and all(isinstance(i, str) for i in v):	153	14	90.85%
edsnlp/utils/resources.py Was already missing at line 33 if not verbs: - return conjugated_verbs	24	1	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	75.00%
edsnlp/utils/lazy_module.py Was already missing at line 46 ): - continue for import_node in node.body:	31	1	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	98.65%
edsnlp/utils/bindings.py Was already missing at line 22 return "." + path - return path	66	1	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	96.89%
edsnlp/processing/spark.py Was already missing at line 51 getActiveSession = SparkSession.getActiveSession - except AttributeError:	43	1	97.67%
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 570-572 else: - batch = gpu_pipe.prepare_batch(docs, device=device) - inputs = None active_batches[batch_id] = (docs, task_id, inputs) Was already missing at line 949 if isinstance(outputs, BaseException): - raise outputs Was already missing at line 1017 if v is not None: - os.environ[k] = v	420	16	96.19%
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	96.49%
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	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	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)	137	5	96.35%
edsnlp/pipes/trainable/embeddings/transformer/transformer.py Was already missing at line 165 if quantization is not None: - kwargs["quantization_config"] = quantization	157	1	99.36%
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	73	3	95.89%
edsnlp/pipes/qualifiers/negation/negation.py Was already missing at line 22 else: - return None	77	1	98.70%
edsnlp/pipes/qualifiers/hypothesis/hypothesis.py Was already missing at line 21 else: - return None	74	1	98.65%
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 310-316 ) - except ValueError: ... - note_datetime = None Was already missing at lines 325-331 ) - except ValueError: ... - birth_datetime = None Was already missing at lines 397-400 ) - except ValueError as e: - absolute_date = None - logger.warning( "In doc {}, the following date {} raises this error: {}. "	154	14	90.91%
edsnlp/pipes/qualifiers/family/family.py Was already missing at line 21 else: - return None	59	1	98.31%
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	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	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	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	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	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	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	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	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	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	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	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	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	85.71%
edsnlp/pipes/misc/sections/sections.py Was already missing at line 126 if sections is None: - sections = patterns.sections sections = dict(sections)	45	1	97.78%
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	94.39%
edsnlp/pipes/misc/dates/dates.py Was already missing at line 248 if isinstance(absolute, str): - absolute = [absolute] if isinstance(relative, str): Was already missing at line 250 if isinstance(relative, str): - relative = [relative] if isinstance(duration, str): Was already missing at line 252 if isinstance(duration, str): - relative = [duration] if isinstance(false_positive, str): Was already missing at lines 356-365 if self.merge_mode == "align": - alignments = align_spans(matches, spans, sort_by_overlap=True) ... - matches.append(span) Was already missing at line 450 elif d1 in seen or v1.bound is None or v2.bound is None: - continue Was already missing at lines 461-463 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:	152	15	90.13%
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	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	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	91.95%
edsnlp/pipes/core/contextual_matcher/models.py Was already missing at lines 19-23 if isinstance(v, list): - assert ( - len(v) == 2 - ), "`window` should be a tuple/list of two integer, or a single integer" - v = tuple(v) if isinstance(v, int):	115	2	98.26%
edsnlp/pipes/core/contextual_matcher/contextual_matcher.py Was already missing at line 94 ) - label = label_name if label is None: Was already missing at line 343 if assigned is None: - continue if replace_entity:	143	2	98.60%
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	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	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	98.63%
edsnlp/language.py Was already missing at line 103 if last != begin: - logger.warning( "Missed some characters during"	51	1	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	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	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	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	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	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	98.88%
edsnlp/core/registries.py Was already missing at line 78 if obj.error is not None: - raise obj.error	164	1	99.39%
edsnlp/core/pipeline.py Was already missing at line 552 if name in exclude: - continue if name not in components:	410	1	99.76%
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 448 for name, pipe, _ in self.torch_components(): - pipe.to(device) return self	151	2	98.68%
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	95.24%

264 files skipped due to complete coverage.

Coverage success: total of 97.76% is above 97.76% 🎉

sonarcloud · 2024-08-28T16:27:46Z

Quality Gate passed

Issues
7 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

percevalw

Hi @svittoz, thank you ! I've left a few comments and suggestions

percevalw · 2024-10-04T14:05:09Z

edsnlp/pipes/ner/cim10/patterns.py

@@ -30,4 +30,6 @@ def get_patterns() -> Dict[str, List[str]]:

    patterns = df.groupby("code")["patterns"].agg(list).to_dict()

+    patterns = {k: v for k, v in patterns.items() if k in cim10} if cim10 else patterns


Why not (which would fail for unknown cim10 codes) and might be a bit faster

Suggested change

patterns = {k: v for k, v in patterns.items() if k in cim10} if cim10 else patterns

patterns = {k: patterns[k] for k in codes} if codes else patterns

percevalw · 2024-10-04T14:06:17Z

edsnlp/pipes/ner/cim10/patterns.py

@@ -5,7 +5,7 @@
 from edsnlp import BASE_DIR


-def get_patterns() -> Dict[str, List[str]]:
+def get_patterns(cim10: List[str] = None) -> Dict[str, List[str]]:


Maybe standardize the cim10/atc into a "code" parameter ?

Suggested change

def get_patterns(cim10: List[str] = None) -> Dict[str, List[str]]:

def get_patterns(codes: List[str] = None) -> Dict[str, List[str]]:

percevalw · 2024-10-04T14:06:26Z

edsnlp/pipes/ner/cim10/factory.py

@@ -28,6 +28,7 @@ def create_component(
    name: str = "cim10",
    *,
    attr: str = "NORM",
+    cim10: List[str] = None,


Suggested change

cim10: List[str] = None,

codes: List[str] = None,

percevalw · 2024-10-04T14:07:55Z

edsnlp/pipes/ner/cim10/factory.py

+    cim10 : str
+        List of cim10 to retrieve. If None, all cim10 will be searched,
+        resulting in higher computation time.


Standardize cim10/atc/codes

Suggested change

cim10 : str

List of cim10 to retrieve. If None, all cim10 will be searched,

resulting in higher computation time.

codes : str

CIM10 codes to retrieve. If None, synonyms for all codes will be searched

resulting in higher computation time.

percevalw · 2024-10-04T14:08:08Z

edsnlp/pipes/ner/cim10/factory.py

@@ -104,7 +108,7 @@ def create_component(
        nlp=nlp,
        name=name,
        regex=dict(),
-        terms=get_patterns(),
+        terms=get_patterns(cim10),


Suggested change

terms=get_patterns(cim10),

terms=get_patterns(codes),

percevalw · 2024-10-04T14:09:19Z

edsnlp/pipes/ner/drugs/factory.py

@@ -83,6 +84,9 @@ def create_component(
        The name of the component
    attr : str
        The default attribute to use for matching.
+    atc : str
+        List of atc to retrieve. If None, all atc will be searched,


Suggested change

List of atc to retrieve. If None, all atc will be searched,

codes : str

ATC codes to retrieve. If None, synonyms for all codes will be searched

resulting in higher computation time.

percevalw · 2024-10-04T14:09:26Z

edsnlp/pipes/ner/drugs/factory.py

@@ -111,7 +115,7 @@ def create_component(
        nlp=nlp,
        name=name,
        regex=dict(),
-        terms=get_patterns(),
+        terms=get_patterns(atc),


Suggested change

terms=get_patterns(atc),

terms=get_patterns(codes),

percevalw · 2024-10-04T14:09:35Z

edsnlp/pipes/ner/drugs/patterns.py

@@ -6,6 +6,8 @@
 drugs_file = BASE_DIR / "resources" / "drugs.json"


-def get_patterns() -> Dict[str, List[str]]:
+def get_patterns(atc: List[str] = None) -> Dict[str, List[str]]:


Suggested change

def get_patterns(atc: List[str] = None) -> Dict[str, List[str]]:

def get_patterns(codes: List[str] = None) -> Dict[str, List[str]]:

percevalw · 2024-10-04T14:18:34Z

edsnlp/pipes/ner/drugs/patterns.py

    with open(drugs_file, "r") as f:
-        return json.load(f)
+        patterns = json.load(f)
+        patterns = {k: v for k, v in patterns.items() if k in atc} if atc else patterns


Suggested change

patterns = {k: v for k, v in patterns.items() if k in atc} if atc else patterns

patterns = {k: patterns[k] for k in codes} if codes else patterns

percevalw · 2024-10-07T12:30:33Z

tests/pipelines/misc/test_quantities.py

    text = """
        Leucocytes ¦ ¦ ¦4.2 ¦ ¦4.0-10.0
        Hémoglobine ¦ ¦9.0 - ¦ ¦13-14
        """
    doc = blank_nlp(text)
    doc = matcher(doc)

-    assert len(doc.spans["measurements"]) == 0
+    assert len(doc.spans["quantities"]) == 0


Add a backward compatibility test ?

Suggested change

assert len(doc.spans["quantities"]) == 0

assert len(doc.spans["quantities"]) == 0

def test_measurements(blank_nlp):

blank_nlp.add_pipe("eds.measurements")

assert blank_nlp("La tumeur fait 4 cm").spans["measurements"][0]._.value.mm == 40

VITTOZ Simon and others added 2 commits August 28, 2024 13:21

rename eds.measurements pipe to eds.quantities

fff384a

adding possibility to select cim10 and atc in eds.cim10 and eds.drugs

c804921

svittoz force-pushed the terminology-subset branch from 55433ab to c804921 Compare August 28, 2024 15:17

svittoz added 2 commits August 28, 2024 18:24

Update patterns.py

e2fc805

Update patterns.py

b4d8dfb

svittoz requested a review from percevalw August 28, 2024 17:12

percevalw reviewed Oct 7, 2024

View reviewed changes

percevalw force-pushed the master branch 2 times, most recently from ae75dc5 to 430ef22 Compare October 10, 2024 20:17

percevalw force-pushed the master branch 4 times, most recently from 2038fb9 to 232ca91 Compare November 4, 2024 21:23

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Adding possibility to select cim10 and atc in eds.cim10 and eds.drugs #314

Adding possibility to select cim10 and atc in eds.cim10 and eds.drugs #314

svittoz commented Aug 21, 2024 •

edited

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github-actions bot commented Aug 28, 2024 •

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sonarcloud bot commented Aug 28, 2024

percevalw left a comment

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percevalw Oct 4, 2024

percevalw Oct 7, 2024

		@@ -30,4 +30,6 @@ def get_patterns() -> Dict[str, List[str]]:

		patterns = df.groupby("code")["patterns"].agg(list).to_dict()

		patterns = {k: v for k, v in patterns.items() if k in cim10} if cim10 else patterns

	patterns = {k: v for k, v in patterns.items() if k in cim10} if cim10 else patterns
	patterns = {k: patterns[k] for k in codes} if codes else patterns

	def get_patterns(cim10: List[str] = None) -> Dict[str, List[str]]:
	def get_patterns(codes: List[str] = None) -> Dict[str, List[str]]:

	def get_patterns(atc: List[str] = None) -> Dict[str, List[str]]:
	def get_patterns(codes: List[str] = None) -> Dict[str, List[str]]:

-    assert len(doc.spans["quantities"]) == 0
+    assert len(doc.spans["quantities"]) == 0
+def test_measurements(blank_nlp):
+    blank_nlp.add_pipe("eds.measurements")
+    assert blank_nlp("La tumeur fait 4 cm").spans["measurements"][0]._.value.mm == 40

Adding possibility to select cim10 and atc in eds.cim10 and eds.drugs #314

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Adding possibility to select cim10 and atc in eds.cim10 and eds.drugs #314

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svittoz commented Aug 21, 2024 • edited Loading

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sonarcloud bot commented Aug 28, 2024

Quality Gate passed

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svittoz commented Aug 21, 2024 •

edited

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github-actions bot commented Aug 28, 2024 •

edited

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