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ingestion: fix datetime parsing error on NK #18

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merged 1 commit into from
Apr 18, 2023
Merged

ingestion: fix datetime parsing error on NK #18

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15 changes: 6 additions & 9 deletions scripts/ingestion/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import logging
import os
import sys
import re

import boto3
import pandas as pd
Expand Down Expand Up @@ -105,19 +106,15 @@ def get_data_with_estimated_onset(df: pd.DataFrame) -> pd.DataFrame:
)

def estimate_onset(row):
if isinstance(row.Date_onset, str) and (
"NA" not in row.Date_onset or "NK" not in row.Date_onset
):
if isinstance(row.Date_onset, str) and re.match(REGEX_DATE, row.Date_onset):
return pd.to_datetime(row.Date_onset)
if isinstance(row.Date_death, str) and (
"NA" not in row.Date_death or "NK" not in row.Date_death
):
if isinstance(row.Date_death, str) and re.match(REGEX_DATE, row.Date_death):
return pd.to_datetime(row.Date_death) - delay_death
if (
isinstance(row.Date_of_first_consult, str)
and "NA" not in row.Date_of_first_consult
if isinstance(row.Date_of_first_consult, str) and re.match(
REGEX_DATE, row.Date_of_first_consult
):
return pd.to_datetime(row.Date_of_first_consult) - delay_to_consult_hosp
return None

df["Date_onset_estimated"] = df.apply(estimate_onset, axis=1)
return df
Expand Down
2 changes: 1 addition & 1 deletion scripts/ingestion/test_data.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,6 @@ ID,Case_status,Age,Gender,Date_onset,Date_death,Date_of_first_consult,Data_up_to
2,probable,40-46,female,2023-02-06,2023-02-14,,2023-04-04,Bata,1,ZZ,household contact
3,confirmed,20,male,2023-02-19,,2023-02-25,2023-04-04,Nsoc Nsomo,2,AA,
4,confirmed,99,female,2023-01-05,2023-01-11,,2023-04-04,Nsoc Nsomo,,ZK,school
5,probable,65,male,,2023-01-19,,2023-04-04,Ebiebyin,,KR,household contact
5,probable,65,male,NK,2023-01-19,,2023-04-04,Ebiebyin,,KR,household contact
6,confirmed,59,female,,,2023-04-02,2023-04-04,Ebiebyin,,ZZ,
7,confirmed,0,male,2023-02-11,,2023-02-13,2023-04-04,Nsork,,ZZ,
4 changes: 2 additions & 2 deletions scripts/ingestion/test_run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
2,probable,female,40-46,2023-02-06,2023-02-06,,2023-02-14,Bata,2023-04-04,1
3,confirmed,male,20,2023-02-19,2023-02-19,2023-02-25,,Nsoc Nsomo,2023-04-04,2
4,confirmed,female,99,2023-01-05,2023-01-05,,2023-01-11,Nsoc Nsomo,2023-04-04,
5,probable,male,65,,2023-01-13,,2023-01-19,Ebiebyin,2023-04-04,
5,probable,male,65,NK,2023-01-13,,2023-01-19,Ebiebyin,2023-04-04,
6,confirmed,female,59,,2023-03-29,2023-04-02,,Ebiebyin,2023-04-04,
7,confirmed,male,0,2023-02-11,2023-02-11,2023-02-13,,Nsork,2023-04-04,
"""
Expand All @@ -40,7 +40,7 @@
2,probable,female,40-46,2023-02-06,2023-02-06,,2023-02-14,Bata,2023-04-04
3,confirmed,male,20,2023-02-19,2023-02-19,2023-02-25,,Nsoc Nsomo,2023-04-04
4,confirmed,female,99,2023-01-05,2023-01-05,,2023-01-11,Nsoc Nsomo,2023-04-04
5,probable,male,65,,2023-01-13,,2023-01-19,Ebiebyin,2023-04-04
5,probable,male,65,NK,2023-01-13,,2023-01-19,Ebiebyin,2023-04-04
6,confirmed,female,59,,2023-03-29,2023-04-02,,Ebiebyin,2023-04-04
7,confirmed,male,0,2023-02-11,2023-02-11,2023-02-13,,Nsork,2023-04-04
"""
Expand Down