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[Backfill corrections] Align daily and rollup file formats; make dates portable #1760

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Merged
merged 2 commits into from
Jan 23, 2023
Merged

[Backfill corrections] Align daily and rollup file formats; make dates portable #1760

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ff9d515
move lag and issue_date setting to daily files in change
nmdefries Jan 12, 2023
f3a2e33
move lag and issue_date setting to daily files in quidel_covidtest
nmdefries Jan 12, 2023
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15 changes: 12 additions & 3 deletions changehc/delphi_changehc/backfill.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,18 @@ def store_backfill_file(df, _end_date, backfill_dir, numtype, geo, weekday):
'num', 'den']
backfilldata = backfilldata.loc[backfilldata["time_value"] >= _start_date,
selected_columns]

backfilldata["lag"] = [(_end_date - x).days for x in backfilldata["time_value"]]
backfilldata["time_value"] = backfilldata.time_value.dt.strftime("%Y-%m-%d")
backfilldata["issue_date"] = datetime.strftime(_end_date, "%Y-%m-%d")

backfilldata = backfilldata.astype({
"time_value": "string",
"issue_date": "string",
"fips": "string",
"state_id": "string"
})

path = backfill_dir + \
"/changehc_%s_as_of_%s.parquet"%(numtype, datetime.strftime(_end_date, "%Y%m%d"))
# Store intermediate file into the backfill folder
Expand Down Expand Up @@ -109,9 +121,6 @@ def get_date(file_link):
pdList = []
for fn in new_files:
df = pd.read_parquet(fn, engine='pyarrow')
issue_date = get_date(fn)
df["issue_date"] = issue_date
df["lag"] = [(issue_date - x).days for x in df["time_value"]]
pdList.append(df)
merged_file = pd.concat(pdList).sort_values(["time_value", "fips"])
path = backfill_dir + "/changehc_%s_from_%s_to_%s.parquet"%(
Expand Down
7 changes: 2 additions & 5 deletions changehc/tests/test_backfill.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@
class TestBackfill:

def test_store_backfill_file(self):

fn = "changehc_covid_as_of_20200101.parquet"
dropdate = datetime(2020, 1, 1)
numtype = "covid"
Expand Down Expand Up @@ -69,7 +69,7 @@ def test_store_backfill_file(self):
backfill_df = pd.read_parquet(backfill_dir + "/"+ fn, engine='pyarrow')

selected_columns = ['time_value', 'fips', 'state_id',
'num', 'den']
'num', 'den', 'lag', 'issue_date']
assert set(selected_columns) == set(backfill_df.columns)

os.remove(backfill_dir + "/" + fn)
Expand Down Expand Up @@ -114,9 +114,6 @@ def test_merge_backfill_file(self):
if "from" in file:
continue
df = pd.read_parquet(file, engine='pyarrow')
issue_date = datetime.strptime(file[-16:-8], "%Y%m%d")
df["issue_date"] = issue_date
df["lag"] = [(issue_date - x).days for x in df["time_value"]]
pdList.append(df)
os.remove(file)
new_files = glob.glob(backfill_dir + "/changehc_%s*.parquet"%numtype)
Expand Down
14 changes: 11 additions & 3 deletions quidel_covidtest/delphi_quidel_covidtest/backfill.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,17 @@ def store_backfill_file(df, _end_date, backfill_dir):
'num_age_0_17', 'den_age_0_17']
backfilldata = backfilldata.loc[backfilldata["time_value"] >= _start_date,
selected_columns]
backfilldata["lag"] = [(_end_date - x).days for x in backfilldata["time_value"]]
backfilldata["time_value"] = backfilldata.time_value.dt.strftime("%Y-%m-%d")
backfilldata["issue_date"] = datetime.strftime(_end_date, "%Y-%m-%d")

backfilldata = backfilldata.astype({
"time_value": "string",
"issue_date": "string",
"fips": "string",
"state_id": "string"
})

path = backfill_dir + \
"/quidel_covidtest_as_of_%s.parquet"%datetime.strftime(_end_date, "%Y%m%d")
# Store intermediate file into the backfill folder
Expand Down Expand Up @@ -108,9 +119,6 @@ def get_date(file_link):
pdList = []
for fn in new_files:
df = pd.read_parquet(fn, engine='pyarrow')
issue_date = get_date(fn)
df["issue_date"] = issue_date
df["lag"] = [(issue_date - x).days for x in df["time_value"]]
pdList.append(df)
merged_file = pd.concat(pdList).sort_values(["time_value", "fips"])
path = backfill_dir + "/quidel_covidtest_from_%s_to_%s.parquet"%(
Expand Down
6 changes: 2 additions & 4 deletions quidel_covidtest/tests/test_backfill.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,8 @@ def test_store_backfill_file(self):
'num_age_18_49', 'den_age_18_49',
'num_age_50_64', 'den_age_50_64',
'num_age_65plus', 'den_age_65plus',
'num_age_0_17', 'den_age_0_17']
'num_age_0_17', 'den_age_0_17',
'lag', 'issue_date']
assert set(selected_columns) == set(backfill_df.columns)

os.remove(backfill_dir + "/" + fn)
Expand Down Expand Up @@ -86,9 +87,6 @@ def test_merge_backfill_file(self):
if "from" in file:
continue
df = pd.read_parquet(file, engine='pyarrow')
issue_date = datetime.strptime(file[-16:-8], "%Y%m%d")
df["issue_date"] = issue_date
df["lag"] = [(issue_date - x).days for x in df["time_value"]]
pdList.append(df)
os.remove(file)
new_files = glob.glob(backfill_dir + "/quidel_covidtest*.parquet")
Expand Down