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Fix pandas bug after upgrade in reciepe in matchid backend upgrade #142

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merged 4 commits into from
Jul 21, 2024
Merged

Fix pandas bug after upgrade in reciepe in matchid backend upgrade #142

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a8f7567
fix bug correction side effect on NUM_DECES - permalink
rhanka May 8, 2024
0398a59
Merge pull request #140 from matchID-project/fix/num-deces-permalink
rhanka May 8, 2024
3a6ade9
Fix: The support for using Y (years) and M (months) in np.timedelta64…
rhanka Jul 20, 2024
d551457
Merge pull request #141 from matchID-project/fix/numpy-timedelta
rhanka Jul 21, 2024
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3 changes: 1 addition & 2 deletions projects/deces-dataprep/datasets/deces_src.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ datasets:
compression: gzip
type: fwf
encoding: latin1
widths: [80, 1, 8, 5, 30, 30, 8, 5, 9, 1]
widths: [80, 1, 8, 5, 30, 30, 8, 5, 10]
names:
- NOM_PRENOMS
- SEXE
Expand All @@ -19,4 +19,3 @@ datasets:
- DATE_DECES
- CODE_INSEE_DECES
- NUM_DECES
- END_OF_LINE
10 changes: 7 additions & 3 deletions projects/deces-dataprep/recipes/deces_dataprep.yml
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Expand Up @@ -7,8 +7,6 @@ recipes:
dataset: deces_index
threads: !ENV ${RECIPE_THREADS}
steps:
- delete:
select: END_OF_LINE
- normalize:
select: (NOM_PRENOMS|COMMUNE_NAISSANCE|PAYS_NAISSANCE|NUM_DECES)$
- exec:
Expand All @@ -17,6 +15,11 @@ recipes:
- df['_id'] = df['UID']
- df['SOURCE'] = str(desc['source']['name'])
- df['SOURCE_LINE'] = 1+df.index
- replace:
select: NUM_DECES
regex:
- '(.{9}).*': '\1'
- '\s*$': ''
- replace:
select: SOURCE
regex:
Expand Down Expand Up @@ -93,8 +96,9 @@ recipes:
select: DATE.*NORM
format: "%Y%m%d"
- exec:
# Year = 365.25 * 24 * 60 * 60 seconds
- df['AGE_DECES'] = np.where(df['DATE_DECES'] > df['DATE_NAISSANCE'],
(df['DATE_DECES_NORM'] - df['DATE_NAISSANCE_NORM']).astype('<m8[Y]'),
((df['DATE_DECES_NORM'] - df['DATE_NAISSANCE_NORM']).astype('timedelta64[s]').astype(int) / 31557600).round().astype(int),
None)
- df['DATE_NAISSANCE_NORM'] = df['DATE_NAISSANCE_NORM'].dt.strftime('%Y%m%d')
- df['DATE_DECES_NORM'] = df['DATE_DECES_NORM'].dt.strftime('%Y%m%d')
Expand Down
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