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Merge branch 'Symptoms-caused-by-Lots'

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frankknoll
2023-11-09 12:23:27 +01:00
parent f34b171f09 b34b8f1b03
commit fdd58ffda5
14 changed files with 29365 additions and 17643 deletions
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26378
docs/SymptomsCausedByCOVIDLots/index.html
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docs/SymptomsCausedByCOVIDLots/js/PageInitializer.js
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@@ -1,8 +1,9 @@
class PageInitializer {
static initializePage({ symptom, vaccine }) {
static initializePage({ symptom, vaccine, symptomVsSymptomChart }) {
PageInitializer.#configureSymptom(symptom);
PageInitializer.#configureVaccine(vaccine);
PageInitializer.#configureSymptomVsSymptomChart(symptomVsSymptomChart);
}
static #configureSymptom({ symptomSelectElement, prrByVaccineTableElement, downloadPrrByVaccineTableButton }) {
@@ -25,6 +26,12 @@ class PageInitializer {
});
}
static #configureSymptomVsSymptomChart(symptomVsSymptomChart) {
new SymptomVsSymptomChartViewInitializer().configureSymptomVsSymptomChart(
symptomVsSymptomChart,
PageInitializer.#initializeSelectElement);
}
static #initializeSelectElement({ selectElement, onValueSelected, minimumInputLength }) {
selectElement.select2({ minimumInputLength: minimumInputLength });
selectElement.on(

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docs/SymptomsCausedByCOVIDLots/js/Sets.js Normal file
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@@ -0,0 +1,20 @@
class Sets {
static filterSet(set, predicate) {
return new Set([...set].filter(predicate));
}
static union(sets) {
return sets.reduce(
(union, set) => new Set([...union, ...set]),
new Set());
}
static intersection(set1, set2) {
return new Set([...set1].filter(x => set2.has(x)));
}
static isEmpty(set) {
return set.size == 0;
}
}

48
docs/SymptomsCausedByCOVIDLots/js/SymptomVsSymptomChartDataProvider.js Normal file
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@@ -0,0 +1,48 @@
class SymptomVsSymptomChartDataProvider {
// FK-TODO: extract utility class and test
static retainCommonKeys({ dict1, dict2 }) {
const commonKeys = SymptomVsSymptomChartDataProvider.#getCommonKeys(dict1, dict2);
return {
dict1: SymptomVsSymptomChartDataProvider.#retainKeysOfDict(dict1, commonKeys),
dict2: SymptomVsSymptomChartDataProvider.#retainKeysOfDict(dict2, commonKeys)
};
}
static getChartData({ prrByLotX, prrByLotY }) {
const { dict1: prrByLotXCommon, dict2: prrByLotYCommon } =
SymptomVsSymptomChartDataProvider.retainCommonKeys(
{
dict1: prrByLotX,
dict2: prrByLotY
});
const lots = Object.keys(prrByLotXCommon);
return {
labels: lots,
data:
lots.map(
lot => ({
x: prrByLotXCommon[lot],
y: prrByLotYCommon[lot]
}))
};
}
static #getCommonKeys(dict1, dict2) {
return Sets.intersection(
SymptomVsSymptomChartDataProvider.#getKeySet(dict1),
SymptomVsSymptomChartDataProvider.#getKeySet(dict2));
}
static #getKeySet(dict) {
return new Set(Object.keys(dict));
}
static #retainKeysOfDict(dict, keys2Retain) {
const entries2Retain =
Object
.entries(dict)
.filter(([key, _]) => keys2Retain.has(key));
return Object.fromEntries(entries2Retain);
}
}

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docs/SymptomsCausedByCOVIDLots/js/SymptomVsSymptomChartView.js Normal file
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@@ -0,0 +1,84 @@
class SymptomVsSymptomChartView {
#canvas;
#chart;
constructor(canvas) {
this.#canvas = canvas;
}
loadAndDisplayChart(symptomX, symptomY) {
Promise
.all([symptomX, symptomY].map(symptom => PrrByVaccineProvider.getPrrByVaccine(symptom)))
.then(
([prrByLotX, prrByLotY]) => {
const { labels, data } = SymptomVsSymptomChartDataProvider.getChartData({ prrByLotX, prrByLotY });
this.#displayChart(symptomX, symptomY, labels, data);
});
}
#displayChart(symptomX, symptomY, labels, data) {
if (this.#chart != null) {
this.#chart.destroy();
}
this.#chart =
new Chart(
this.#canvas,
this.#getConfig(symptomX, symptomY, labels, data));
}
#getConfig(symptomX, symptomY, labels, data) {
return {
type: 'scatter',
data: this.#getData(labels, data),
options: this.#getOptions(symptomX, symptomY)
};
}
#getData(labels, data) {
return {
datasets:
[
{
labels: labels,
data: data,
backgroundColor: 'rgb(0, 0, 255)'
}
]
};
}
#getOptions(symptomX, symptomY) {
return {
scales: {
x: {
type: 'linear',
position: 'bottom',
title: this.#getAxisTitle(symptomX)
},
y: {
title: this.#getAxisTitle(symptomY)
}
},
plugins: {
legend: {
display: false
},
tooltip: {
callbacks: {
label: function (context) {
return 'Batch: ' + context.dataset.labels[context.dataIndex];
}
}
}
}
};
}
#getAxisTitle(symptom) {
return {
display: true,
text: 'PRR ratio of Batch for ' + symptom
}
}
}

44
docs/SymptomsCausedByCOVIDLots/js/SymptomVsSymptomChartViewInitializer.js Normal file
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@@ -0,0 +1,44 @@
class SymptomVsSymptomChartViewInitializer {
#symptomVsSymptomChartView;
#symptomX;
#symptomY;
configureSymptomVsSymptomChart(
{ symptomSelectXElement, symptomSelectYElement, symptomVsSymptomChartViewElement },
initializeSelectElement) {
this.#symptomVsSymptomChartView = new SymptomVsSymptomChartView(symptomVsSymptomChartViewElement);
{
initializeSelectElement(
{
selectElement: symptomSelectXElement,
onValueSelected: symptomX => {
this.#symptomX = symptomX;
this.#loadAndDisplayChart();
},
minimumInputLength: 4
});
this.#symptomX = null;
}
{
initializeSelectElement(
{
selectElement: symptomSelectYElement,
onValueSelected: symptomY => {
this.#symptomY = symptomY;
this.#loadAndDisplayChart();
},
minimumInputLength: 4
});
this.#symptomY = null;
}
this.#loadAndDisplayChart();
}
#loadAndDisplayChart() {
if (this.#symptomX != null && this.#symptomY != null) {
this.#symptomVsSymptomChartView.loadAndDisplayChart(this.#symptomX, this.#symptomY);
}
}
}

80
docs/SymptomsCausedByCOVIDLots/test/SymptomVsSymptomChartDataProviderTest.js Normal file
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@@ -0,0 +1,80 @@
QUnit.module('SymptomVsSymptomChartDataProviderTest', function () {
QUnit.test.each(
'shouldRetainCommonLots',
[
[
{
dict1: {
"lotX": 1.0
},
dict2: {
"lotY": 2.0
}
},
{
dict1: {
},
dict2: {
}
}
],
[
{
dict1: {
"lotX": 1.0,
"lotCommon": 2.0
},
dict2: {
"lotCommon": 3.0,
"lotY": 4.0
}
},
{
dict1: {
"lotCommon": 2.0
},
dict2: {
"lotCommon": 3.0
}
}
]
],
(assert, [dicts, dictsHavingCommonKeys]) => {
// Given
// When
const dictsHavingCommonKeysActual = SymptomVsSymptomChartDataProvider.retainCommonKeys(dicts);
// Then
assert.deepEqual(dictsHavingCommonKeysActual, dictsHavingCommonKeys);
});
QUnit.test('shouldProvideChartData', function (assert) {
// Given
const prrByLotX = {
"lotX": 1.0,
"lotCommon": 2.0
};
const prrByLotY = {
"lotCommon": 3.0,
"lotY": 4.0
};
// When
const chartData = SymptomVsSymptomChartDataProvider.getChartData({ prrByLotX, prrByLotY });
// Then
assert.deepEqual(
chartData,
{
labels: ["lotCommon"],
data: [
{
x: 2.0,
y: 3.0
}
]
});
});
});

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docs/SymptomsCausedByCOVIDLots/test/index.test.html Normal file
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@@ -0,0 +1,38 @@
<!DOCTYPE html>
<html lang="de">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Safety Signals for COVID Batches</title>
<script src="../../Utils.js"></script>
<script src="../../UIUtils.js"></script>
<script src="../../NumberWithBarElementFactory.js"></script>
<script src="../js/Sets.js"></script>
<script src="../js/PrrByKey2CsvConverter.js"></script>
<script src="../js/PageInitializer.js"></script>
<script src="../js/PrrByVaccineProvider.js"></script>
<script src="../js/PrrByKeyTable.js"></script>
<script src="../js/PrrByKeyTableView.js"></script>
<script src="../js/PrrByVaccineTableView.js"></script>
<script src="../js/PrrBySymptomTableView.js"></script>
<script src="../js/SymptomVsSymptomChartView.js"></script>
<script src="../js/SymptomVsSymptomChartDataProvider.js"></script>
<script src="../js/SymptomVsSymptomChartViewInitializer.js"></script>
<link rel="stylesheet" href="https://code.jquery.com/qunit/qunit-2.17.2.css">
<script src="https://code.jquery.com/qunit/qunit-2.17.2.js"></script>
<script type="text/javascript" src="./jshamcrest.js"></script>
<script type="text/javascript" src="./jsmockito-1.0.4.js"></script>
<script>
JsHamcrest.Integration.QUnit();
JsMockito.Integration.QUnit();
</script>
<script src="./SymptomVsSymptomChartDataProviderTest.js"></script>
</head>
<body>
<div id="qunit"></div>
<div id="qunit-fixture"></div>
</body>
</html>

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docs/SymptomsCausedByCOVIDLots/test/jsmockito-1.0.4.js Normal file
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docs/SymptomsCausedByVaccines/index.html
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src/HowBadIsMyBatch.ipynb
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@@ -438,7 +438,7 @@
"metadata": {},
"outputs": [],
"source": [
"from SymptomsCausedByVaccines.HtmlUpdater import updateHtmlFile\n",
"from SymptomsCausedByVaccines.HtmlUpdater import updateHtmlFile, updateHtmlFile4SymptomsCausedByCOVIDLots\n",
"from SymptomsCausedByVaccines.PrrSeriesFactory import PrrSeriesFactory\n",
"from SymptomsCausedByVaccines.PrrSeriesTransformer import PrrSeriesTransformer\n",
"from SymptomsCausedByVaccines.ProportionalReportingRatiosPersister import saveProportionalReportingRatios\n",
@@ -627,11 +627,10 @@
"metadata": {},
"outputs": [],
"source": [
"updateHtmlFile(\n",
"updateHtmlFile4SymptomsCausedByCOVIDLots(\n",
" symptoms = list(prrByLotAndSymptom.columns),\n",
" vaccines = list(prrByLotAndSymptom.index),\n",
" htmlFile = \"../docs/SymptomsCausedByCOVIDLots/index.html\",\n",
" defaultSelectVaccineOptionText = 'Select Batch')"
" batches = list(prrByLotAndSymptom.index),\n",
" htmlFile = \"../docs/SymptomsCausedByCOVIDLots/index.html\")"
]
},
{

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src/SymptomsCausedByVaccines/HtmlUpdater.py
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@@ -16,6 +16,19 @@ def updateHtmlFile(symptoms, vaccines, htmlFile, defaultSelectVaccineOptionText
htmlFile = htmlFile,
selectElementId = 'vaccineSelect')
def updateHtmlFile4SymptomsCausedByCOVIDLots(symptoms, batches, htmlFile):
symptomOptions = getSymptomOptions(symptoms)
for selectElementId in ['symptomSelect', 'symptomSelectX', 'symptomSelectY']:
_saveOptions(
options = symptomOptions,
htmlFile = htmlFile,
selectElementId = selectElementId)
_saveOptions(
options = getVaccineOptions(batches, 'Select Batch'),
htmlFile = htmlFile,
selectElementId = 'vaccineSelect')
def _saveOptions(options, htmlFile, selectElementId):
HtmlTransformerUtil().applySoupTransformerToFile(
file=htmlFile,

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src/help.txt
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@@ -7,6 +7,7 @@ FK-TODO:
- Symptomhistogramm
- http://www.howbadismybatch.info/SymptomsCausedByVaccines/index.html
- http://www.howbadismybatch.info/SymptomsCausedByCOVIDLots/index.html
http://www.howbadismybatch.info/SymptomsCausedByCOVIDLots/test/index.test.html
anacron job:
sudo cp src/intensivstationen_howbadismybatch.sh /etc/cron.daily/intensivstationen_howbadismybatch