Merge branch 'Symptoms-caused-by-Lots'

docs/SymptomsCausedByCOVIDLots/js/PageInitializer.js

@@ -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(

docs/SymptomsCausedByCOVIDLots/js/Sets.js

@@ -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;
+    }
+}

docs/SymptomsCausedByCOVIDLots/js/SymptomVsSymptomChartDataProvider.js

@@ -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);
+    }
+}

docs/SymptomsCausedByCOVIDLots/js/SymptomVsSymptomChartView.js

@@ -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
+        }
+    }
+}

docs/SymptomsCausedByCOVIDLots/js/SymptomVsSymptomChartViewInitializer.js

@@ -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);
+        }
+    }
+}

docs/SymptomsCausedByCOVIDLots/test/SymptomVsSymptomChartDataProviderTest.js

@@ -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
+                    }
+                ]
+            });
+    });
+});

docs/SymptomsCausedByCOVIDLots/test/index.test.html

@@ -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>

src/HowBadIsMyBatch.ipynb

@@ -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",
+    "    batches = list(prrByLotAndSymptom.index),\n",
-    "    htmlFile = \"../docs/SymptomsCausedByCOVIDLots/index.html\",\n",
+    "    htmlFile = \"../docs/SymptomsCausedByCOVIDLots/index.html\")"
-    "    defaultSelectVaccineOptionText = 'Select Batch')"
    ]
   },
   {

src/SymptomsCausedByVaccines/HtmlUpdater.py

@@ -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,

src/help.txt

@@ -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