OMOP explorer

[svittoz]

Description

Add Altair visualization tools for any OMOP table in the model of the Biology module.

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).

[Thomzoy]

LGTM ! Very nice addition

[github-actions]

Coverage Report

Name	Stmts	Miss	∆ Miss	Cover
eds_scikit/plot/omop_teva.py New missing coverage at line 108 ! if drop_columns: - table = table.merge( visit_occurrence.drop(columns=drop_columns),	40	1	1	98%
TOTAL	2434	154	1	94%

Files without new missing coverage

Name	Stmts	Miss	∆ Miss	Cover
eds_scikit/utils/test_utils.py Was already missing at line 50 def date(s): - return dt.strptime(s, "%Y-%m-%d") Was already missing at lines 88-90 args = tuple(args) - elif type(index_or_key) == str: - kwargs[index_or_key] = inputs Was already missing at lines 114-116 else: - normalized_sum_sq_diff = sum_sq_diff / np.sqrt(sum_sq_diff) - assert normalized_sum_sq_diff < 0.001	54	5	0	91%
eds_scikit/utils/flowchart/flowchart.py Was already missing at line 152 def __str__(self) -> str: - return self.__repr__()	131	1	0	99%
eds_scikit/utils/custom_implem/custom_implem.py Was already missing at line 54 """ - return cut( x,	22	1	0	95%
eds_scikit/utils/checks.py Was already missing at line 127 if return_index_or_key: - return kwargs[argname], argname return kwargs[argname] Was already missing at line 149 else: - to_display_per_concept = [f"- {concept}" for concept in required_concepts] str_to_display = "\n".join(to_display_per_concept) Was already missing at lines 172-189 - if all(isinstance(table, tuple) for table in required_tables): ... - super().__init__(message)	71	10	0	86%
eds_scikit/utils/bunch.py Was already missing at line 32 def __setattr__(self, key, value): - self[key] = value Was already missing at line 35 def __dir__(self): - return self.keys() Was already missing at lines 38-41 def __getattr__(self, key): - try: - return self[key] - except KeyError: raise AttributeError(key)	11	5	0	55%
eds_scikit/resources/utils.py Was already missing at line 19 if len(splited) == 1: - return None return splited[-1]	6	1	0	83%
eds_scikit/resources/reg.py Was already missing at lines 50-78 # Looking for a match excluding version string - candidates = [ ... - func = r.get(candidates[0]) return func	16	4	0	75%
eds_scikit/period/tagging_functions.py Was already missing at lines 60-63 # TODO: is this necessary ? - logger.warning("No matching were found between the 2 DataFrames") - - return framework.DataFrame( columns=["person_id", "t_start", "t_end", "concept", "value"] Was already missing at lines 119-123 return (B_start >= A_start) & (B_end <= A_end) - elif algo == interval_algos.from_before_to: - return B_end <= A_start - elif algo == interval_algos.to_before_from: - return A_end <= B_start else:	36	6	0	83%
eds_scikit/period/stays.py Was already missing at line 409 if open_stay_end_datetime is None: - open_stay_end_datetime = datetime.now() vo["visit_end_datetime_calc"] = open_stay_end_datetime	86	1	0	99%
eds_scikit/io/i2b2_mapping.py Was already missing at lines 38-211 - i2b2_table_name = i2b2_tables[db_source][table] ... - return df Was already missing at lines 230-234 - def f(x): - return mapping.get(x, default) - - return F.udf(f)	79	69	0	13%
eds_scikit/io/base.py Was already missing at line 13 def __str__(self): - return self.__repr__()	9	1	0	89%
eds_scikit/event/from_code.py Was already missing at lines 108-111 else: - event.loc[:, "t_start"] = event.loc[:, columns["code_start_datetime"]] ... - event = event.drop( columns=[columns["code_start_datetime"], columns["code_end_datetime"]]	42	3	0	93%
eds_scikit/event/diabetes.py Was already missing at lines 88-102 """ - diabetes = conditions_from_icd10( ... - - return diabetes	10	4	0	60%
eds_scikit/event/consultations.py Was already missing at line 68 if type(algo) == str: - algo = [algo]	61	1	0	98%
eds_scikit/emergency/emergency_care_site.py Was already missing at line 54 if algo == "from_regex_on_parent_UF": - return from_regex_on_parent_UF(care_site) elif algo == "from_regex_on_care_site_description": Was already missing at line 166 """ - return attributes.get_parent_attributes( care_site,	31	2	0	94%
eds_scikit/datasets/synthetic/biology.py Was already missing at lines 37-44 def reset_to_pandas(self): - if self.module == "koalas": ... - self.module = "pandas"	132	7	0	95%
eds_scikit/datasets/__init__.py Was already missing at line 38 def __dir__(): - return known_datasets + [func.__name__ for func in __all__] Was already missing at lines 52-56 def add_dataset(table: pd.DataFrame, name: str): - dataset_path = os.path.abspath( - os.path.join(os.path.dirname(__file__), name + ".csv") - ) - table.to_csv(dataset_path, index=False) Was already missing at line 67 """ - return [func.__name__ for func in __all__]	26	4	0	85%
eds_scikit/biology/viz/plot.py Was already missing at line 72 else: - logger.error( "The folder {} has not been found", Was already missing at lines 718-720 else: - terminologies_hist = alt.Chart().mark_text() - terminologies_time_series = ( alt.Chart(measurement)	130	3	0	98%
eds_scikit/biology/viz/aggregate.py Was already missing at line 83 if stats_only: - return {"measurement_stats": measurement_stats} Was already missing at line 208 if overall_only: - return measurement_stats_overall	97	2	0	98%
eds_scikit/biology/utils/config.py Was already missing at lines 30-66 """ - my_custom_config = pd.DataFrame() ... - register_configs() Was already missing at lines 73-75 for config in glob.glob(os.path.join(CONFIGS_PATH, "*.csv")): - config_name = Path(config).stem - registry.data.register( f"get_biology_config.{config_name}", Was already missing at lines 89-94 """ - registered = list(registry.data.get_all().keys()) - configs = [ - r.split(".")[-1] for r in registered if r.startswith("get_biology_config") - ] - return configs	35	22	0	37%
eds_scikit/biology/cleaning/cohort.py Was already missing at line 28 if isinstance(studied_pop, DataFrame.__args__): - filtered_measures = measurement.merge( studied_pop,	9	1	0	89%

62 files skipped due to complete coverage.

Coverage success: total of 94% is above 93% 🎉

[codecov]

Codecov Report

Attention: Patch coverage is 52.26131% with 95 lines in your changes missing coverage. Please review.

Project coverage is 81.92%. Comparing base (b7c19e6) to head (c731ca4).
Report is 7 commits behind head on main.

❗ Current head c731ca4 differs from pull request most recent head 874010b

Please upload reports for the commit 874010b to get more accurate results.

Files	Patch %	Lines
eds_scikit/plot/omop_teva.py	8.00%	92 Missing ⚠️
eds_scikit/plot/table_viz.py	95.94%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #61      +/-   ##
==========================================
- Coverage   84.23%   81.92%   -2.32%     
==========================================
  Files          86       91       +5     
  Lines        2550     2749     +199     
==========================================
+ Hits         2148     2252     +104     
- Misses        402      497      +95     

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