francois/HowBadIsMyBatch
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

starting to add Hospitalization

Browse Source
This commit is contained in:
Frank Knoll
2024-04-23 17:15:58 +02:00
parent d84b86ed20
commit 91fd2084bd
4 changed files with 35 additions and 15 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
src/BatchCodeTableFactory.py
View File

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

28
src/BatchCodeTableFactoryTest.py
View File

@@ -12,7 +12,7 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
dataFrame = TestHelper.createDataFrame( dataFrame = TestHelper.createDataFrame(
columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE', 'HOSPITAL', 'ER_VISIT', 'COUNTRY'], 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'], 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'], [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']], [0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France']],
index = [ index = [
@@ -28,11 +28,11 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
# Then # Then
assert_frame_equal( 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( 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 = [ [2, 1, 2, 2, 'MODERNA', 2/2 * 100, 1/2 * 100], data = [ [2, 1, 2, 2, 0, 'MODERNA', 2/2 * 100, 1/2 * 100],
[1, 0, 0, 0, 'MODERNA', 0/1 * 100, 0/1 * 100]], [1, 0, 0, 0, 1, 'MODERNA', 0/1 * 100, 0/1 * 100]],
index = pd.Index( index = pd.Index(
[ [
'030L20B', '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'], 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], 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'], [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'], [1, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 1, 0, 'France'],
[0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'United Kingdom']], [0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 1, 0, 'United Kingdom']],
index = [ index = [
"1048786", "1048786",
"1048786", "1048786",
@@ -62,12 +62,12 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
# Then # Then
assert_frame_equal( 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( 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 = [ [1, 1, 0, 0, 'PFIZER\BIONTECH', 1/1 * 100, 1/1 * 100], data = [ [1, 1, 0, 0, 0, 'PFIZER\BIONTECH', 1/1 * 100, 1/1 * 100],
[2, 1, 2, 2, 'MODERNA', 2/2 * 100, 1/2 * 100], [2, 1, 2, 2, 2, 'MODERNA', 2/2 * 100, 1/2 * 100],
[1, 0, 0, 0, 'MODERNA', 0/1 * 100, 0/1 * 100]], [1, 0, 0, 0, 0, 'MODERNA', 0/1 * 100, 0/1 * 100]],
index = pd.Index( index = pd.Index(
[ [
'016M20A', '016M20A',
@@ -98,9 +98,9 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
# Then # Then
assert_frame_equal( 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( 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 = [ ], data = [ ],
index = pd.Index([], name = 'VAX_LOT')), index = pd.Index([], name = 'VAX_LOT')),
check_dtype = False) check_dtype = False)

4
src/SummationTableFactory.py
View File

@@ -8,7 +8,8 @@ class SummationTableFactory:
**{ **{
'Deaths': pd.NamedAgg(column = 'DIED', aggfunc = 'sum'), 'Deaths': pd.NamedAgg(column = 'DIED', aggfunc = 'sum'),
'Adverse Reaction Reports': pd.NamedAgg(column = 'DIED', aggfunc = 'size'), 'Adverse Reaction Reports': pd.NamedAgg(column = 'DIED', aggfunc = 'size'),
'Life Threatening Illnesses': pd.NamedAgg(column = 'L_THREAT', aggfunc = 'sum'), 'Life Threatening Illnesses': pd.NamedAgg(column = 'L_THREAT', aggfunc = 'sum'),
'Hospitalization': pd.NamedAgg(column = 'HOSPITAL', aggfunc = 'sum'),
'Disabilities': pd.NamedAgg(column = 'DISABLE', aggfunc = 'sum'), 'Disabilities': pd.NamedAgg(column = 'DISABLE', aggfunc = 'sum'),
'Severities': pd.NamedAgg(column = 'SEVERE', aggfunc = 'sum') 'Severities': pd.NamedAgg(column = 'SEVERE', aggfunc = 'sum')
}) })
@@ -20,6 +21,7 @@ class SummationTableFactory:
'Deaths', 'Deaths',
'Disabilities', 'Disabilities',
'Life Threatening Illnesses', 'Life Threatening Illnesses',
'Hospitalization',
'Severe reports', 'Severe reports',
'Lethality' 'Lethality'
]] ]]

17
src/help.txt
View File

@@ -21,6 +21,23 @@ jupyter notebook
FK-FIXME: FK-FIXME:
FK-TODO: 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: anacron job:
sudo cp src/intensivstationen_howbadismybatch.sh /etc/cron.daily/intensivstationen_howbadismybatch sudo cp src/intensivstationen_howbadismybatch.sh /etc/cron.daily/intensivstationen_howbadismybatch