From 489dffd87afcbd8f55406c98dcd7c8ec6b736985 Mon Sep 17 00:00:00 2001 From: mahaalbashir Date: Thu, 19 Oct 2023 15:34:40 +0100 Subject: [PATCH] updating finalise func --- acro/acro.py | 10 ++++++- test/test_initial.py | 65 ++++++++++++++++++++++++++++++++++---------- 2 files changed, 59 insertions(+), 16 deletions(-) diff --git a/acro/acro.py b/acro/acro.py index 94d81c9..922d883 100644 --- a/acro/acro.py +++ b/acro/acro.py @@ -73,7 +73,7 @@ def __init__(self, config: str = "default", suppress: bool = False) -> None: # set globals for survival analysis acro_tables.SURVIVAL_THRESHOLD = self.config["survival_safe_threshold"] - def finalise(self, path: str = "outputs", ext="json") -> Records: + def finalise(self, path: str = "outputs", ext="json") -> Records | None: """Creates a results file for checking. Parameters @@ -88,6 +88,14 @@ def finalise(self, path: str = "outputs", ext="json") -> Records: Records Object storing the outputs. """ + # check if the path exists + if os.path.exists(path): + logger.warning( + "Results file can not be created. " + "Directory %s already exists. Please choose a different directory name.", + path, + ) + return None self.results.finalise(path, ext) config_filename: str = os.path.normpath(f"{path}/config.json") try: diff --git a/test/test_initial.py b/test/test_initial.py index 12d2854..41899b7 100644 --- a/test/test_initial.py +++ b/test/test_initial.py @@ -58,7 +58,7 @@ def test_crosstab_with_aggfunc_sum(data, acro): ) acro.add_exception("output_0", "Let me have it") acro.add_exception("output_1", "I need this output") - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) output_0 = results.get_index(0) output_1 = results.get_index(1) comment_0 = ( @@ -69,6 +69,7 @@ def test_crosstab_with_aggfunc_sum(data, acro): ) assert output_0.comments == [comment_0] assert output_1.comments == [comment_1] + shutil.rmtree(PATH) def test_crosstab_threshold(data, acro): @@ -82,10 +83,11 @@ def test_crosstab_threshold(data, acro): row, col = pos assert np.isnan(output.output[0].iloc[row, col]) acro.add_exception("output_0", "Let me have it") - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) correct_summary: str = "fail; threshold: 6 cells suppressed; " output = results.get_index(0) assert output.summary == correct_summary + shutil.rmtree(PATH) def test_crosstab_multiple(data, acro): @@ -94,13 +96,14 @@ def test_crosstab_multiple(data, acro): data.year, data.grant_type, values=data.inc_grants, aggfunc="mean" ) acro.add_exception("output_0", "Let me have it") - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) correct_summary: str = ( "fail; threshold: 7 cells suppressed; p-ratio: 2 cells suppressed; " "nk-rule: 1 cells suppressed; " ) output = results.get_index(0) assert output.summary == correct_summary + shutil.rmtree(PATH) def test_negatives(data, acro): @@ -114,12 +117,13 @@ def test_negatives(data, acro): ) acro.add_exception("output_0", "Let me have it") acro.add_exception("output_1", "I want this") - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) correct_summary: str = "review; negative values found" output_0 = results.get_index(0) output_1 = results.get_index(1) assert output_0.summary == correct_summary assert output_1.summary == correct_summary + shutil.rmtree(PATH) def test_pivot_table_without_suppression(data): @@ -138,10 +142,11 @@ def test_pivot_table_pass(data, acro): _ = acro.pivot_table( data, index=["grant_type"], values=["inc_grants"], aggfunc=["mean", "std"] ) - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) correct_summary: str = "pass" output_0 = results.get_index(0) assert output_0.summary == correct_summary + shutil.rmtree(PATH) def test_pivot_table_cols(data, acro): @@ -154,13 +159,14 @@ def test_pivot_table_cols(data, acro): aggfunc=["mean", "std"], ) acro.add_exception("output_0", "Let me have it") - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) correct_summary: str = ( "fail; threshold: 14 cells suppressed; " "p-ratio: 4 cells suppressed; nk-rule: 2 cells suppressed; " ) output_0 = results.get_index(0) assert output_0.summary == correct_summary + shutil.rmtree(PATH) def test_ols(data, acro): @@ -192,12 +198,13 @@ def test_ols(data, acro): assert results.df_resid == 807 assert results.rsquared == pytest.approx(0.894, 0.001) # Finalise - results = acro.finalise() + results = acro.finalise(PATH) correct_summary: str = "pass; dof=807.0 >= 10" output_0 = results.get_index(0) output_1 = results.get_index(1) assert output_0.summary == correct_summary assert output_1.summary == correct_summary + shutil.rmtree(PATH) def test_probit_logit(data, acro): @@ -234,7 +241,7 @@ def test_probit_logit(data, acro): assert results.df_resid == 806 assert results.prsquared == pytest.approx(0.214, 0.01) # Finalise - results = acro.finalise() + results = acro.finalise(PATH) correct_summary: str = "pass; dof=806.0 >= 10" output_0 = results.get_index(0) output_1 = results.get_index(1) @@ -244,6 +251,7 @@ def test_probit_logit(data, acro): assert output_1.summary == correct_summary assert output_2.summary == correct_summary assert output_3.summary == correct_summary + shutil.rmtree(PATH) def test_finalise_excel(data, acro): @@ -257,6 +265,7 @@ def test_finalise_excel(data, acro): correct_cell: str = "_ = acro.crosstab(data.year, data.grant_type)" assert load_data.iloc[0, 0] == "Command" assert load_data.iloc[0, 1] == correct_cell + shutil.rmtree(PATH) def test_output_removal(data, acro, monkeypatch): @@ -266,12 +275,13 @@ def test_output_removal(data, acro, monkeypatch): _ = acro.crosstab(data.year, data.grant_type) exceptions = ["I want it", "Let me have it", "Please!"] monkeypatch.setattr("builtins.input", lambda _: exceptions.pop(0)) - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) output_0 = results.get("output_0") output_1 = results.get("output_1") + shutil.rmtree(PATH) # remove something that is there acro.remove_output(output_0.uid) - results = acro.finalise() + results = acro.finalise(PATH) correct_summary: str = "fail; threshold: 6 cells suppressed; " keys = results.get_keys() assert output_0.uid not in keys @@ -281,6 +291,7 @@ def test_output_removal(data, acro, monkeypatch): # remove something that is not there with pytest.raises(ValueError): acro.remove_output("123") + shutil.rmtree(PATH) def test_load_output(): @@ -329,6 +340,7 @@ def test_finalise_json(data, acro): json_data = json.load(file) results: dict = json_data["results"] assert results[orig.uid]["files"][0]["name"] == f"{orig.uid}_0.csv" + shutil.rmtree(PATH) def test_rename_output(data, acro): @@ -337,12 +349,13 @@ def test_rename_output(data, acro): _ = acro.crosstab(data.year, data.grant_type) acro.add_exception("output_0", "Let me have it") acro.add_exception("output_1", "I want this") - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) output_0 = results.get_index(0) orig_name = output_0.uid new_name = "cross_table" acro.rename_output(orig_name, new_name) - results = acro.finalise() + shutil.rmtree(PATH) + results = acro.finalise(PATH) assert output_0.uid == new_name assert orig_name not in results.get_keys() assert os.path.exists(f"outputs/{new_name}_0.csv") @@ -352,13 +365,14 @@ def test_rename_output(data, acro): # rename an output to another that already exists with pytest.raises(ValueError): acro.rename_output("output_1", "cross_table") + shutil.rmtree(PATH) def test_add_comments(data, acro): """Adding comments to output test.""" _ = acro.crosstab(data.year, data.grant_type) acro.add_exception("output_0", "Let me have it") - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) output_0 = results.get_index(0) assert output_0.comments == [] comment = "This is a cross table between year and grant_type" @@ -370,6 +384,7 @@ def test_add_comments(data, acro): # add a comment to something that is not there with pytest.raises(ValueError): acro.add_comments("123", "comment") + shutil.rmtree(PATH) def test_custom_output(acro): @@ -382,6 +397,7 @@ def test_custom_output(acro): output_0 = results.get_index(0) assert output_0.output == [file_path] assert os.path.exists(os.path.normpath(f"{PATH}/XandY.jpeg")) + shutil.rmtree(PATH) def test_missing(data, acro, monkeypatch): @@ -396,7 +412,7 @@ def test_missing(data, acro, monkeypatch): ) exceptions = ["I want it", "Let me have it"] monkeypatch.setattr("builtins.input", lambda _: exceptions.pop(0)) - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) correct_summary: str = "review; missing values found" output_0 = results.get_index(0) output_1 = results.get_index(1) @@ -404,6 +420,7 @@ def test_missing(data, acro, monkeypatch): assert output_1.summary == correct_summary assert output_0.exception == "I want it" assert output_1.exception == "Let me have it" + shutil.rmtree(PATH) def test_suppression_error(caplog): @@ -553,6 +570,7 @@ def test_surv_func(acro): results: Records = acro.finalise(path=PATH) output_1 = results.get_index(1) assert output_1.output == [filename] + shutil.rmtree(PATH) def test_zeros_are_not_disclosive(data, acro): @@ -568,13 +586,14 @@ def test_zeros_are_not_disclosive(data, acro): aggfunc=["mean", "std"], ) acro.add_exception("output_0", "Let me have it") - results: Records = acro.finalise() + results: Records = acro.finalise(PATH) correct_summary: str = ( "fail; threshold: 14 cells suppressed; " "p-ratio: 2 cells suppressed; nk-rule: 2 cells suppressed; " ) output_0 = results.get_index(0) assert output_0.summary == correct_summary + shutil.rmtree(PATH) def test_crosstab_with_totals_without_suppression(data, acro): @@ -884,6 +903,7 @@ def test_histogram_discolsive(data, acro, caplog): in caplog.text ) assert output_0.status == "fail" + shutil.rmtree(PATH) def test_histogram_non_disclosive(data, acro): @@ -896,3 +916,18 @@ def test_histogram_non_disclosive(data, acro): output_0 = results.get_index(0) assert output_0.output == [filename] assert output_0.status == "review" + shutil.rmtree(PATH) + + +def test_finalise_with_existing_path(data, acro, caplog): + """Using a path that already exists when finalising.""" + _ = acro.crosstab(data.year, data.grant_type) + acro.add_exception("output_0", "Let me have it") + acro.finalise(PATH) + _ = acro.crosstab(data.status, data.grant_type) + acro.finalise(PATH) + assert ( + "Results file can not be created. Directory RES_PYTEST " + "already exists. Please choose a different directory name." in caplog.text + ) + shutil.rmtree(PATH)