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

renaming Hospitalization to Hospitalizations

Browse Source
This commit is contained in:
Frank Knoll
2024-04-23 18:14:22 +02:00
parent a2d4c356be
commit dd01d7cd18
10 changed files with 25 additions and 42 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
docs/AdverseReactionReportsChartView.js
View File

@@ -33,7 +33,7 @@ class AdverseReactionReportsChartView {
'Deaths', 'Deaths',
'Disabilities', 'Disabilities',
'Life Threatening Illnesses', 'Life Threatening Illnesses',
'Hospitalization', 'Hospitalizations',
'Other Adverse Events' 'Other Adverse Events'
], ],
datasets: [{ datasets: [{
@@ -43,8 +43,8 @@ class AdverseReactionReportsChartView {
ADRDescr['Deaths'], ADRDescr['Deaths'],
ADRDescr['Disabilities'], ADRDescr['Disabilities'],
ADRDescr['Life Threatening Illnesses'], ADRDescr['Life Threatening Illnesses'],
ADRDescr['Hospitalization'], ADRDescr['Hospitalizations'],
ADRDescr['Adverse Reaction Reports'] - (ADRDescr['Deaths'] + ADRDescr['Disabilities'] + ADRDescr['Life Threatening Illnesses'] + ADRDescr['Hospitalization']) ADRDescr['Adverse Reaction Reports'] - (ADRDescr['Deaths'] + ADRDescr['Disabilities'] + ADRDescr['Life Threatening Illnesses'] + ADRDescr['Hospitalizations'])
], ],
backgroundColor: '#1a73e8' backgroundColor: '#1a73e8'
}] }]

4
docs/BatchCodeTableInitializer.js
View File

@@ -50,7 +50,7 @@ class BatchCodeTableInitializer {
this.#getColumnIndex('Deaths'), this.#getColumnIndex('Deaths'),
this.#getColumnIndex('Disabilities'), this.#getColumnIndex('Disabilities'),
this.#getColumnIndex('Life Threatening Illnesses'), this.#getColumnIndex('Life Threatening Illnesses'),
this.#getColumnIndex('Hospitalization'), this.#getColumnIndex('Hospitalizations'),
this.#getColumnIndex('Severe reports'), this.#getColumnIndex('Severe reports'),
this.#getColumnIndex('Lethality') this.#getColumnIndex('Lethality')
] ]
@@ -110,7 +110,7 @@ class BatchCodeTableInitializer {
return 3; return 3;
case 'Life Threatening Illnesses': case 'Life Threatening Illnesses':
return 4; return 4;
case 'Hospitalization': case 'Hospitalizations':
return 5; return 5;
case 'Company': case 'Company':
return 6; return 6;

2
docs/batchCodes.html
View File

@@ -58,7 +58,7 @@
<th>Deaths</th> <th>Deaths</th>
<th>Disabilities</th> <th>Disabilities</th>
<th>Life Threatening Illnesses</th> <th>Life Threatening Illnesses</th>
<th>Hospitalization</th> <th>Hospitalizations</th>
<th>Company</th> <th>Company</th>
<th>Severe reports</th> <th>Severe reports</th>
<th>Lethality</th> <th>Lethality</th>

2
src/BatchCodeTableFactory.py
View File

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

22
src/BatchCodeTableFactoryTest.py
View File

@@ -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', 'Hospitalization', 'Company', 'Severe reports', 'Lethality']], batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalizations', 'Company', 'Severe reports', 'Lethality']],
TestHelper.createDataFrame( TestHelper.createDataFrame(
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalization', 'Company', 'Severe reports', 'Lethality'], columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalizations', 'Company', 'Severe reports', 'Lethality'],
data = [ [2, 1, 2, 2, 0, 'MODERNA', 2/2 * 100, 1/2 * 100], 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]], [1, 0, 0, 0, 1, 'MODERNA', 0/1 * 100, 0/1 * 100]],
index = pd.Index( index = pd.Index(
[ [
'030L20B', '030L20B',
@@ -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', 'Hospitalization', 'Company', 'Severe reports', 'Lethality']], batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalizations', 'Company', 'Severe reports', 'Lethality']],
TestHelper.createDataFrame( TestHelper.createDataFrame(
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalization', 'Company', 'Severe reports', 'Lethality'], columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalizations', 'Company', 'Severe reports', 'Lethality'],
data = [ [1, 1, 0, 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, 2, 'MODERNA', 2/2 * 100, 1/2 * 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]], [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', 'Hospitalization', 'Company', 'Severe reports', 'Lethality']], batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalizations', 'Company', 'Severe reports', 'Lethality']],
TestHelper.createDataFrame( TestHelper.createDataFrame(
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalization', 'Company', 'Severe reports', 'Lethality'], columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalizations', 'Company', 'Severe reports', 'Lethality'],
data = [ ], data = [ ],
index = pd.Index([], name = 'VAX_LOT')), index = pd.Index([], name = 'VAX_LOT')),
check_dtype = False) check_dtype = False)

2
src/BatchCodeTableIntoHistogramDescriptionTableMerger.py
View File

@@ -28,7 +28,7 @@ class BatchCodeTableIntoHistogramDescriptionTableMerger:
'Deaths', 'Deaths',
'Disabilities', 'Disabilities',
'Life Threatening Illnesses', 'Life Threatening Illnesses',
'Hospitalization', 'Hospitalizations',
'Company' 'Company'
]] ]]

6
src/BatchCodeTableIntoHistogramDescriptionTableMergerTest.py
View File

@@ -33,8 +33,8 @@ class BatchCodeTableIntoHistogramDescriptionTableMergerTest(unittest.TestCase):
data = ['1808982'])) data = ['1808982']))
batchCodeTable = TestHelper.createDataFrame( batchCodeTable = TestHelper.createDataFrame(
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalization', 'Company', 'Severe reports', 'Lethality'], columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalizations', 'Company', 'Severe reports', 'Lethality'],
data = [ [2, 1, 2, 2, 3, 'MODERNA', 2/2 * 100, np.nan]], data = [ [2, 1, 2, 2, 3, 'MODERNA', 2/2 * 100, np.nan]],
index = pd.Index( index = pd.Index(
name = 'VAX_LOT', name = 'VAX_LOT',
data = ['1808982'])) data = ['1808982']))
@@ -54,7 +54,7 @@ class BatchCodeTableIntoHistogramDescriptionTableMergerTest(unittest.TestCase):
'Deaths': 1, 'Deaths': 1,
'Disabilities': 2, 'Disabilities': 2,
'Life Threatening Illnesses': 2, 'Life Threatening Illnesses': 2,
'Hospitalization': 3, 'Hospitalizations': 3,
'Company': 'MODERNA', 'Company': 'MODERNA',
'histograms': [ 'histograms': [
{ {

2
src/BatchCodeTablePersister.py
View File

@@ -17,7 +17,7 @@ def createGlobalBatchCodeTable(deleteEntriesWithADRsLessThanOrEqual, minADRsForL
'Deaths', 'Deaths',
'Disabilities', 'Disabilities',
'Life Threatening Illnesses', 'Life Threatening Illnesses',
'Hospitalization', 'Hospitalizations',
'Company', 'Company',
'Severe reports', 'Severe reports',
'Lethality' 'Lethality'

4
src/SummationTableFactory.py
View File

@@ -9,7 +9,7 @@ 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'), 'Hospitalizations': 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')
}) })
@@ -21,7 +21,7 @@ class SummationTableFactory:
'Deaths', 'Deaths',
'Disabilities', 'Disabilities',
'Life Threatening Illnesses', 'Life Threatening Illnesses',
'Hospitalization', 'Hospitalizations',
'Severe reports', 'Severe reports',
'Lethality' 'Lethality'
]] ]]

17
src/help.txt
View File

@@ -21,23 +21,6 @@ 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