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Use fix-new-dashboard-ver branch #184

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609dd54
Use fix-new-dashboard-ver branch
stefanb Jul 8, 2022
f24dc3c
Merge branch 'master' into cepimose-fix-new-dashboard
stefanb Jul 8, 2022
96639f2
Merge branch 'master' into cepimose-fix-new-dashboard
stefanb Jul 13, 2022
8d22e27
Merge branch 'master' into cepimose-fix-new-dashboard
stefanb Jul 20, 2022
7528548
Merge branch 'master' into cepimose-fix-new-dashboard
stefanb Aug 20, 2022
45e1232
Prepare for 4th dose
stefanb Aug 20, 2022
010642a
Merge branch 'master' into cepimose-fix-new-dashboard
stefanb Sep 9, 2022
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4 changes: 2 additions & 2 deletions requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -6,5 +6,5 @@ pandas==1.4.*
pyquery==1.4.*
python-dateutil==2.8.*
requests==2.28.*
cepimose==0.1.34
# git+https://github.com/sledilnik/py-cepimose@master#egg=cepimose
# cepimose==0.1.34
git+https://github.com/sledilnik/py-cepimose@fix-new-dashboard-ver#egg=cepimose
1 change: 1 addition & 0 deletions update_stats.py
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Expand Up @@ -78,6 +78,7 @@ def computeStats(update_time):
'vaccination.administered', 'vaccination.administered.todate',
'vaccination.administered2nd', 'vaccination.administered2nd.todate',
'vaccination.administered3rd', 'vaccination.administered3rd.todate',
# 'vaccination.administered4th', 'vaccination.administered4th.todate',
'vaccination.used.todate', 'vaccination.delivered.todate'
], axis='columns')

Expand Down
55 changes: 33 additions & 22 deletions update_vaccination.py
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Expand Up @@ -42,6 +42,7 @@ def computeVaccination(update_time):
'vaccination.administered', 'vaccination.administered.todate',
'vaccination.administered2nd', 'vaccination.administered2nd.todate',
'vaccination.administered3rd', 'vaccination.administered3rd.todate',
# 'vaccination.administered4th', 'vaccination.administered4th.todate',
'vaccination.used.todate',
'vaccination.pfizer.used.todate',
'vaccination.moderna.used.todate',
Expand All @@ -54,23 +55,23 @@ def computeVaccination(update_time):
'vaccination.az.delivered', 'vaccination.az.delivered.todate',
'vaccination.janssen.delivered', 'vaccination.janssen.delivered.todate',
'vaccination.novavax.delivered', 'vaccination.novavax.delivered.todate',
'vaccination.age.0-11.1st.todate','vaccination.age.0-11.2nd.todate','vaccination.age.0-11.3rd.todate',
'vaccination.age.12-17.1st.todate','vaccination.age.12-17.2nd.todate','vaccination.age.12-17.3rd.todate',
'vaccination.age.18-24.1st.todate','vaccination.age.18-24.2nd.todate','vaccination.age.18-24.3rd.todate',
'vaccination.age.25-29.1st.todate','vaccination.age.25-29.2nd.todate','vaccination.age.25-29.3rd.todate',
'vaccination.age.30-34.1st.todate','vaccination.age.30-34.2nd.todate','vaccination.age.30-34.3rd.todate',
'vaccination.age.35-39.1st.todate','vaccination.age.35-39.2nd.todate','vaccination.age.35-39.3rd.todate',
'vaccination.age.40-44.1st.todate','vaccination.age.40-44.2nd.todate','vaccination.age.40-44.3rd.todate',
'vaccination.age.45-49.1st.todate','vaccination.age.45-49.2nd.todate','vaccination.age.45-49.3rd.todate',
'vaccination.age.50-54.1st.todate','vaccination.age.50-54.2nd.todate','vaccination.age.50-54.3rd.todate',
'vaccination.age.55-59.1st.todate','vaccination.age.55-59.2nd.todate','vaccination.age.55-59.3rd.todate',
'vaccination.age.60-64.1st.todate','vaccination.age.60-64.2nd.todate','vaccination.age.60-64.3rd.todate',
'vaccination.age.65-69.1st.todate','vaccination.age.65-69.2nd.todate','vaccination.age.65-69.3rd.todate',
'vaccination.age.70-74.1st.todate','vaccination.age.70-74.2nd.todate','vaccination.age.70-74.3rd.todate',
'vaccination.age.75-79.1st.todate','vaccination.age.75-79.2nd.todate','vaccination.age.75-79.3rd.todate',
'vaccination.age.80-84.1st.todate','vaccination.age.80-84.2nd.todate','vaccination.age.80-84.3rd.todate',
'vaccination.age.85-89.1st.todate','vaccination.age.85-89.2nd.todate','vaccination.age.85-89.3rd.todate',
'vaccination.age.90+.1st.todate','vaccination.age.90+.2nd.todate','vaccination.age.90+.3rd.todate'
'vaccination.age.0-11.1st.todate' ,'vaccination.age.0-11.2nd.todate' ,'vaccination.age.0-11.3rd.todate' ,#'vaccination.age.0-11.4th.todate',
'vaccination.age.12-17.1st.todate','vaccination.age.12-17.2nd.todate','vaccination.age.12-17.3rd.todate',#'vaccination.age.12-17.4th.todate',
'vaccination.age.18-24.1st.todate','vaccination.age.18-24.2nd.todate','vaccination.age.18-24.3rd.todate',#'vaccination.age.18-24.4th.todate',
'vaccination.age.25-29.1st.todate','vaccination.age.25-29.2nd.todate','vaccination.age.25-29.3rd.todate',#'vaccination.age.25-29.4th.todate',
'vaccination.age.30-34.1st.todate','vaccination.age.30-34.2nd.todate','vaccination.age.30-34.3rd.todate',#'vaccination.age.30-34.4th.todate',
'vaccination.age.35-39.1st.todate','vaccination.age.35-39.2nd.todate','vaccination.age.35-39.3rd.todate',#'vaccination.age.35-39.4th.todate',
'vaccination.age.40-44.1st.todate','vaccination.age.40-44.2nd.todate','vaccination.age.40-44.3rd.todate',#'vaccination.age.40-44.4th.todate',
'vaccination.age.45-49.1st.todate','vaccination.age.45-49.2nd.todate','vaccination.age.45-49.3rd.todate',#'vaccination.age.45-49.4th.todate',
'vaccination.age.50-54.1st.todate','vaccination.age.50-54.2nd.todate','vaccination.age.50-54.3rd.todate',#'vaccination.age.50-54.4th.todate',
'vaccination.age.55-59.1st.todate','vaccination.age.55-59.2nd.todate','vaccination.age.55-59.3rd.todate',#'vaccination.age.55-59.4th.todate',
'vaccination.age.60-64.1st.todate','vaccination.age.60-64.2nd.todate','vaccination.age.60-64.3rd.todate',#'vaccination.age.60-64.4th.todate',
'vaccination.age.65-69.1st.todate','vaccination.age.65-69.2nd.todate','vaccination.age.65-69.3rd.todate',#'vaccination.age.65-69.4th.todate',
'vaccination.age.70-74.1st.todate','vaccination.age.70-74.2nd.todate','vaccination.age.70-74.3rd.todate',#'vaccination.age.70-74.4th.todate',
'vaccination.age.75-79.1st.todate','vaccination.age.75-79.2nd.todate','vaccination.age.75-79.3rd.todate',#'vaccination.age.75-79.4th.todate',
'vaccination.age.80-84.1st.todate','vaccination.age.80-84.2nd.todate','vaccination.age.80-84.3rd.todate',#'vaccination.age.80-84.4th.todate',
'vaccination.age.85-89.1st.todate','vaccination.age.85-89.2nd.todate','vaccination.age.85-89.3rd.todate',#'vaccination.age.85-89.4th.todate',
'vaccination.age.90+.1st.todate' ,'vaccination.age.90+.2nd.todate' ,'vaccination.age.90+.3rd.todate' #,'vaccination.age.90+.4th.todate'
], axis='columns')
merged.to_csv(filename, float_format='%.0f', line_terminator='\r\n')
write_timestamp_file(filename=filename, old_hash=old_hash)
Expand All @@ -82,22 +83,25 @@ def import_nijz_dash_vacc_administred():
df = pd.DataFrame.from_dict(cepimose.vaccinations_by_day()).set_index('date').rename(columns={
'first_dose': 'vaccination.administered.todate',
'second_dose': 'vaccination.administered2nd.todate',
'third_dose': 'vaccination.administered3rd.todate'
'third_dose': 'vaccination.administered3rd.todate'#,
# 'fourth_dose': 'vaccination.administered4th.todate'
})

# dummy row for diff calculation remowed afterwards
dummy_date = datetime.datetime(2020, 12, 26)
dummy_row = pd.DataFrame({
'vaccination.administered.todate': 0,
'vaccination.administered2nd.todate': 0,
'vaccination.administered3rd.todate': 0
'vaccination.administered3rd.todate': 0#,
# 'vaccination.administered4th.todate': 0
}, index=[dummy_date])

# calculate diffs from cumulative values (vaccinations per day)
df_diff = pd.concat([dummy_row, df]).diff().drop(labels=[dummy_date]).rename(columns={
'vaccination.administered.todate': 'vaccination.administered',
'vaccination.administered2nd.todate': 'vaccination.administered2nd',
'vaccination.administered3rd.todate': 'vaccination.administered3rd'
'vaccination.administered3rd.todate': 'vaccination.administered3rd'#,
# 'vaccination.administered4th.todate': 'vaccination.administered4th'
}).astype('Int64')

# merge dataframes (cumulative and per day)
Expand All @@ -106,7 +110,8 @@ def import_nijz_dash_vacc_administred():
# sort cols
df = df[['vaccination.administered', 'vaccination.administered.todate',
'vaccination.administered2nd', 'vaccination.administered2nd.todate',
'vaccination.administered3rd', 'vaccination.administered3rd.todate']]
'vaccination.administered3rd', 'vaccination.administered3rd.todate']]#,
# 'vaccination.administered4th', 'vaccination.administered4th.todate']]
df = df.astype('Int64')

# write csv
Expand Down Expand Up @@ -251,6 +256,7 @@ def import_nijz_dash_vacc_by_age():
for ag in vByAgeGroups:
print(f"Joining {ageGroups[ag]} ({ag}): {len(vByAgeGroups[ag])} rows:")
agData = pd.DataFrame.from_dict(vByAgeGroups[ag]).set_index('date')
agData.drop(columns=['fourth_dose'], inplace=True) # TODO: remove
# agData["first_diff"] = agData["first_dose"].diff()
# agData["second_diff"] = agData["second_dose"].diff()
# agData = agData[['first_diff', 'first_dose', 'second_diff', 'second_dose']]
Expand All @@ -261,6 +267,8 @@ def import_nijz_dash_vacc_by_age():
'second_dose': f'vaccination.age.{ageGroups[ag]}.2nd.todate',
# 'third_diff': f'vaccination.region.{ageGroups[ag]}.3rd',
'third_dose': f'vaccination.age.{ageGroups[ag]}.3rd.todate',
# 'fourth_diff': f'vaccination.region.{ageGroups[ag]}.4th',
# 'fourth_dose': f'vaccination.age.{ageGroups[ag]}.4th.todate',
})
print(agData)
print(agData.describe())
Expand Down Expand Up @@ -303,14 +311,17 @@ def import_nijz_dash_vacc_by_region():
regData["first_diff"] = regData["first_dose"].diff()
regData["second_diff"] = regData["second_dose"].diff()
regData["third_diff"] = regData["third_dose"].diff()
regData = regData[['first_diff', 'first_dose', 'second_diff', 'second_dose', 'third_diff', 'third_dose']]
# regData["fourth_diff"] = regData["fourth_dose"].diff()
regData = regData[['first_diff', 'first_dose', 'second_diff', 'second_dose', 'third_diff', 'third_dose']]#, 'fourth_diff', 'fourth_dose']]
regData.rename(inplace=True, columns={
'first_diff': 'vaccination.region.{}.1st'.format(regions[reg]),
'first_dose': 'vaccination.region.{}.1st.todate'.format(regions[reg]),
'second_diff': 'vaccination.region.{}.2nd'.format(regions[reg]),
'second_dose': 'vaccination.region.{}.2nd.todate'.format(regions[reg]),
'third_diff': 'vaccination.region.{}.3rd'.format(regions[reg]),
'third_dose': 'vaccination.region.{}.3rd.todate'.format(regions[reg]),
# 'fourth_diff': 'vaccination.region.{}.4th'.format(regions[reg]),
# 'fourth_dose': 'vaccination.region.{}.4th.todate'.format(regions[reg]),
})
print(regData)
print(regData.describe())
Expand Down