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starting to add Hospitalization

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Frank Knoll
2024-04-23 17:15:58 +02:00
parent d84b86ed20
commit 91fd2084bd
4 changed files with 35 additions and 15 deletions
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1
src/BatchCodeTableFactory.py
View File

@@ -21,6 +21,7 @@ class BatchCodeTableFactory:
'Deaths',
'Disabilities',
'Life Threatening Illnesses',
'Hospitalization',
'Company',
'Severe reports',
'Lethality'

28
src/BatchCodeTableFactoryTest.py
View File

@@ -12,7 +12,7 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
dataFrame = TestHelper.createDataFrame(
columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE', 'HOSPITAL', 'ER_VISIT', 'COUNTRY'],
data = [ [1, 0, 0, 'COVID19', 'PFIZER\BIONTECH', '016M20A', '2', 'GBPFIZER INC2020486806', 0, 0, 'United Kingdom'],
[0, 0, 0, 'COVID19', 'MODERNA', '030L20A', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France'],
[0, 0, 0, 'COVID19', 'MODERNA', '030L20A', '1', 'FRMODERNATX, INC.MOD20224', 1, 0, 'France'],
[1, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France'],
[0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France']],
index = [
@@ -28,11 +28,11 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
# Then
assert_frame_equal(
batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality']],
batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalization', 'Company', 'Severe reports', 'Lethality']],
TestHelper.createDataFrame(
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality'],
data = [ [2, 1, 2, 2, 'MODERNA', 2/2 * 100, 1/2 * 100],
[1, 0, 0, 0, 'MODERNA', 0/1 * 100, 0/1 * 100]],
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalization', 'Company', 'Severe reports', 'Lethality'],
data = [ [2, 1, 2, 2, 0, 'MODERNA', 2/2 * 100, 1/2 * 100],
[1, 0, 0, 0, 1, 'MODERNA', 0/1 * 100, 0/1 * 100]],
index = pd.Index(
[
'030L20B',
@@ -47,8 +47,8 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE', 'HOSPITAL', 'ER_VISIT', 'COUNTRY'],
data = [ [1, 0, 0, 'COVID19', 'PFIZER\BIONTECH', '016M20A', '2', 'dummy', 0, 0, None],
[0, 0, 0, 'COVID19', 'MODERNA', '030L20A', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France'],
[1, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France'],
[0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'United Kingdom']],
[1, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 1, 0, 'France'],
[0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 1, 0, 'United Kingdom']],
index = [
"1048786",
"1048786",
@@ -62,12 +62,12 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
# Then
assert_frame_equal(
batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality']],
batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalization', 'Company', 'Severe reports', 'Lethality']],
TestHelper.createDataFrame(
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality'],
data = [ [1, 1, 0, 0, 'PFIZER\BIONTECH', 1/1 * 100, 1/1 * 100],
[2, 1, 2, 2, 'MODERNA', 2/2 * 100, 1/2 * 100],
[1, 0, 0, 0, 'MODERNA', 0/1 * 100, 0/1 * 100]],
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalization', 'Company', 'Severe reports', 'Lethality'],
data = [ [1, 1, 0, 0, 0, 'PFIZER\BIONTECH', 1/1 * 100, 1/1 * 100],
[2, 1, 2, 2, 2, 'MODERNA', 2/2 * 100, 1/2 * 100],
[1, 0, 0, 0, 0, 'MODERNA', 0/1 * 100, 0/1 * 100]],
index = pd.Index(
[
'016M20A',
@@ -98,9 +98,9 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
# Then
assert_frame_equal(
batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality']],
batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalization', 'Company', 'Severe reports', 'Lethality']],
TestHelper.createDataFrame(
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality'],
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalization', 'Company', 'Severe reports', 'Lethality'],
data = [ ],
index = pd.Index([], name = 'VAX_LOT')),
check_dtype = False)

2
src/SummationTableFactory.py
View File

@@ -9,6 +9,7 @@ class SummationTableFactory:
'Deaths': pd.NamedAgg(column = 'DIED', aggfunc = 'sum'),
'Adverse Reaction Reports': pd.NamedAgg(column = 'DIED', aggfunc = 'size'),
'Life Threatening Illnesses': pd.NamedAgg(column = 'L_THREAT', aggfunc = 'sum'),
'Hospitalization': pd.NamedAgg(column = 'HOSPITAL', aggfunc = 'sum'),
'Disabilities': pd.NamedAgg(column = 'DISABLE', aggfunc = 'sum'),
'Severities': pd.NamedAgg(column = 'SEVERE', aggfunc = 'sum')
})
@@ -20,6 +21,7 @@ class SummationTableFactory:
'Deaths',
'Disabilities',
'Life Threatening Illnesses',
'Hospitalization',
'Severe reports',
'Lethality'
]]

17
src/help.txt
View File

@@ -21,6 +21,23 @@ jupyter notebook
FK-FIXME:
FK-TODO:
- add HOSPITAL, 'Hospitalization':
see: L_THREAT, 'Life Threatening Illnesses'
+ BatchCodeTableFactoryTest
- DataFrameFilterTest
- SevereColumnAdder
+ SummationTableFactory
- VaersDescrReaderTest
- VaersDescrReader
- AdverseReactionReportsChartView
- batchCodes.html
- BatchCodeTableInitializer
+ BatchCodeTableFactory
- BatchCodeTableIntoHistogramDescriptionTableMergerTest
- BatchCodeTableIntoHistogramDescriptionTableMerger
- BatchCodeTablePersister.py
anacron job:
sudo cp src/intensivstationen_howbadismybatch.sh /etc/cron.daily/intensivstationen_howbadismybatch