Extend geocode utility to actually support the state to state mappings #310
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- state_x -> state_y where x,y are in {code, id, name}
| # state_name -> state_id | ||
| new_data = gmpr.add_geocode(self.zip_data, "zip", "state_name") | ||
| new_data2 = gmpr.add_geocode(new_data, "state_name", "state_id") | ||
| assert new_data2.shape == (12, 6) |
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should there also be an assert statement for new_data?
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Nah, new_data is just the test data for state_name to state_id, but it starts in zip form
* update replace_geocode documentation to be clear about data columns * add test cases for renaming columns in replace_geocode * fix the state to state conversion dropped columns issue
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not specifically related to this PR, I just missed this in the previous one: |
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Ahhh, thanks, might as well take care of that here. |
Refactor cdc_covidnet to use geo utils
| new_data = gmpr.add_population_column(self.zip_data, "zip") | ||
| assert new_data["population"].sum() == 274902 |
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any reason not to keep both of these checks?
Also, if it's 5x5 output it may be simpler juts to do a direct df comparison on values
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This is an old test I don't see anymore. Pull again?
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I was just asking why it was deleted
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Ah. I decided to move away from tests based on data-derived population counts. I figured the tests should catch whether the underlying logic or arithmetic breaks, not whether the data file changed. Am open to reasons for keeping though.
| # hrr -> nation | ||
| with pytest.raises(ValueError): | ||
| new_data = gmpr.replace_geocode(self.zip_data, "zip", "hrr") | ||
| new_data2 = gmpr.replace_geocode(new_data, "hrr", "nation") | ||
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| # hrr -> nation | ||
| with pytest.raises(ValueError): | ||
| new_data = gmpr.replace_geocode(self.zip_data, "zip", "hrr") | ||
| new_data2 = gmpr.replace_geocode(new_data, "hrr", "nation") | ||
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| # hrr -> nation | ||
| with pytest.raises(ValueError): | ||
| new_data = gmpr.replace_geocode(self.zip_data, "zip", "hrr") | ||
| new_data2 = gmpr.replace_geocode(new_data, "hrr", "nation") | ||
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Oops, this is a new one 😄
| @@ -411,6 +420,23 @@ def test_add_geocode(self): | |||
| ) | |||
| ) | |||
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| # hrr -> nation | |||
| with pytest.raises(ValueError): | |||
| new_data = gmpr.replace_geocode(self.zip_data, "zip", "hrr") | |||
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I'm pretty sure if the first line valueerrors but the second one doesnt, it still passes, so may want to split this into two with pytest raises.... statements
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Wouldn't that have been caught in the zip -> hrr test some lines before that though?
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Maybe im understanding this test wrong. I read it as testing that both
new_data = gmpr.replace_geocode(self.zip_data, "zip", "hrr")
and
new_data2 = gmpr.replace_geocode(new_data, "hrr", "nation")
raise valueerrors. Is that right?
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It's testing the second one, since we should not be mapping hrr -> nation (it's an incomplete mapping, so it's unsupported).
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Ohhh got it, didn't see the second line calls new_data. Thanks.
| new_code="state_id", | ||
| dropna=False) | ||
| # To use the original column name, reassign original column and drop new one | ||
| hosp_df[APIConfig.STATE_COL] = hosp_df["state_id"].str.upper() |
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@chinandrew btw, this may be cdc_covidnet specific, but the state abbreviation in other indicators (like JHU) is assumed to be lower case. Are we sure this is what we want?
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For some reason cdc covidnet was uppercase, so i kept it consistent. if it's something we can change, would definitely recommend we standardize, but haven't looked into it.
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@krivard thoughts?
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Slacked Katie on this while discussing a similar issue, apparently downstream ingestion will standardize everything and accepts lower or uppercase, so this can be removed and we can just move to lowercase for the indicator code.
Add support for the state_x -> state_y where x,y are in {code, id, name} mappings