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renaming 'Life Threatening Illnesses' to 'Life-Threatening Illnesses'

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Frank Knoll
2024-04-23 23:00:34 +02:00
parent 450a55c9c9 2f6aee2157
commit 6951ac6ca2
10 changed files with 40 additions and 39 deletions
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6
docs/AdverseReactionReportsChartView.js
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@@ -32,7 +32,7 @@ class AdverseReactionReportsChartView {
labels: [ labels: [
'Deaths', 'Deaths',
'Disabilities', 'Disabilities',
'Life Threatening Illnesses', 'Life-Threatening Illnesses',
'Hospitalizations', 'Hospitalizations',
'Other Adverse Events' 'Other Adverse Events'
], ],
@@ -42,9 +42,9 @@ class AdverseReactionReportsChartView {
data: [ data: [
ADRDescr['Deaths'], ADRDescr['Deaths'],
ADRDescr['Disabilities'], ADRDescr['Disabilities'],
ADRDescr['Life Threatening Illnesses'], ADRDescr['Life-Threatening Illnesses'],
ADRDescr['Hospitalizations'], ADRDescr['Hospitalizations'],
ADRDescr['Adverse Reaction Reports'] - (ADRDescr['Deaths'] + ADRDescr['Disabilities'] + ADRDescr['Life Threatening Illnesses'] + ADRDescr['Hospitalizations']) ADRDescr['Adverse Reaction Reports'] - (ADRDescr['Deaths'] + ADRDescr['Disabilities'] + ADRDescr['Life-Threatening Illnesses'] + ADRDescr['Hospitalizations'])
], ],
backgroundColor: '#1a73e8' backgroundColor: '#1a73e8'
}] }]

4
docs/BatchCodeTableInitializer.js
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@@ -49,7 +49,7 @@ class BatchCodeTableInitializer {
this.#getColumnIndex('Adverse Reaction Reports'), this.#getColumnIndex('Adverse Reaction Reports'),
this.#getColumnIndex('Deaths'), this.#getColumnIndex('Deaths'),
this.#getColumnIndex('Disabilities'), this.#getColumnIndex('Disabilities'),
this.#getColumnIndex('Life Threatening Illnesses'), this.#getColumnIndex('Life-Threatening Illnesses'),
this.#getColumnIndex('Hospitalizations'), this.#getColumnIndex('Hospitalizations'),
this.#getColumnIndex('Severe reports'), this.#getColumnIndex('Severe reports'),
this.#getColumnIndex('Lethality') this.#getColumnIndex('Lethality')
@@ -108,7 +108,7 @@ class BatchCodeTableInitializer {
return 2; return 2;
case 'Disabilities': case 'Disabilities':
return 3; return 3;
case 'Life Threatening Illnesses': case 'Life-Threatening Illnesses':
return 4; return 4;
case 'Hospitalizations': case 'Hospitalizations':
return 5; return 5;

2
docs/batchCodes.html
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@@ -49,7 +49,7 @@
<th>Adverse Reaction Reports</th> <th>Adverse Reaction Reports</th>
<th>Deaths</th> <th>Deaths</th>
<th>Disabilities</th> <th>Disabilities</th>
<th>Life Threatening Illnesses</th> <th>Life-Threatening Illnesses</th>
<th>Hospitalizations</th> <th>Hospitalizations</th>
<th>Company</th> <th>Company</th>
<th>Severe reports</th> <th>Severe reports</th>

1
docs/data/histograms/Global/0321A.json Normal file
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@@ -0,0 +1 @@
{"batchcode": "0321A", "histogram": {"Ageusia": 1, "Anosmia": 1, "Immunisation reaction": 1, "Pneumonia": 1, "Rash": 1, "Rash pruritic": 1}, "Disabilities": 0, "Adverse Reaction Reports": 3, "Hospitalizations": 0, "Life-Threatening Illnesses": 0, "Company": "MODERNA", "Deaths": 0}

2
src/BatchCodeTableFactory.py
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@@ -20,7 +20,7 @@ class BatchCodeTableFactory:
'Adverse Reaction Reports', 'Adverse Reaction Reports',
'Deaths', 'Deaths',
'Disabilities', 'Disabilities',
'Life Threatening Illnesses', 'Life-Threatening Illnesses',
'Hospitalizations', 'Hospitalizations',
'Company', 'Company',
'Severe reports', 'Severe reports',

12
src/BatchCodeTableFactoryTest.py
View File

@@ -28,9 +28,9 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
# Then # Then
assert_frame_equal( assert_frame_equal(
batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalizations', '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', 'Hospitalizations', '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(
@@ -62,9 +62,9 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
# Then # Then
assert_frame_equal( assert_frame_equal(
batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalizations', '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', 'Hospitalizations', '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]],
@@ -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', 'Hospitalizations', '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', 'Hospitalizations', '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

@@ -27,7 +27,7 @@ class BatchCodeTableIntoHistogramDescriptionTableMerger:
'Adverse Reaction Reports', 'Adverse Reaction Reports',
'Deaths', 'Deaths',
'Disabilities', 'Disabilities',
'Life Threatening Illnesses', 'Life-Threatening Illnesses',
'Hospitalizations', 'Hospitalizations',
'Company' 'Company'
]] ]]

4
src/BatchCodeTableIntoHistogramDescriptionTableMergerTest.py
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@@ -33,7 +33,7 @@ class BatchCodeTableIntoHistogramDescriptionTableMergerTest(unittest.TestCase):
data = ['1808982'])) data = ['1808982']))
batchCodeTable = TestHelper.createDataFrame( batchCodeTable = TestHelper.createDataFrame(
columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Hospitalizations', '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',
@@ -53,7 +53,7 @@ class BatchCodeTableIntoHistogramDescriptionTableMergerTest(unittest.TestCase):
'Adverse Reaction Reports': 2, 'Adverse Reaction Reports': 2,
'Deaths': 1, 'Deaths': 1,
'Disabilities': 2, 'Disabilities': 2,
'Life Threatening Illnesses': 2, 'Life-Threatening Illnesses': 2,
'Hospitalizations': 3, 'Hospitalizations': 3,
'Company': 'MODERNA', 'Company': 'MODERNA',
'histograms': [ 'histograms': [

2
src/BatchCodeTablePersister.py
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@@ -16,7 +16,7 @@ def createGlobalBatchCodeTable(deleteEntriesWithADRsLessThanOrEqual, minADRsForL
'Adverse Reaction Reports', 'Adverse Reaction Reports',
'Deaths', 'Deaths',
'Disabilities', 'Disabilities',
'Life Threatening Illnesses', 'Life-Threatening Illnesses',
'Hospitalizations', 'Hospitalizations',
'Company', 'Company',
'Severe reports', 'Severe reports',

4
src/SummationTableFactory.py
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@@ -8,7 +8,7 @@ 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'),
'Hospitalizations': 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')
@@ -20,7 +20,7 @@ class SummationTableFactory:
'Adverse Reaction Reports', 'Adverse Reaction Reports',
'Deaths', 'Deaths',
'Disabilities', 'Disabilities',
'Life Threatening Illnesses', 'Life-Threatening Illnesses',
'Hospitalizations', 'Hospitalizations',
'Severe reports', 'Severe reports',
'Lethality' 'Lethality'