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updating finalise func
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@mahaalbashir
mahaalbashir committed Oct 19, 2023
1 parent e2e1606 commit 489dffd
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Showing 2 changed files with 59 additions and 16 deletions.
10 changes: 9 additions & 1 deletion acro/acro.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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:
Expand Down
65 changes: 50 additions & 15 deletions test/test_initial.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 = (
Expand All @@ -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):
Expand All @@ -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):
Expand All @@ -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):
Expand All @@ -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):
Expand All @@ -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):
Expand All @@ -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):
Expand Down Expand Up @@ -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):
Expand Down Expand Up @@ -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)
Expand All @@ -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):
Expand All @@ -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):
Expand All @@ -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
Expand All @@ -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():
Expand Down Expand Up @@ -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):
Expand All @@ -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")
Expand All @@ -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"
Expand All @@ -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):
Expand All @@ -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):
Expand All @@ -396,14 +412,15 @@ 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)
assert output_0.summary == correct_summary
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):
Expand Down Expand Up @@ -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):
Expand All @@ -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):
Expand Down Expand Up @@ -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):
Expand All @@ -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)

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