starting Safety Signal (All drugs)

src/HowBadIsMyBatch.ipynb

@@ -439,6 +439,145 @@
     "    lastUpdatedElementId = 'last_updated')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "6c302a04",
+   "metadata": {},
+   "source": [
+    "# Symptoms caused by Drugs (EudraVigilance)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fb02ce7c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from SymptomsCausedByVaccines.DataFrameFilter import DataFrameFilter\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",
+    "import os\n",
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4ad05656",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prrByVaccineAndSymptom = pd.read_csv(\n",
+    "    'data/prrByDrugAndSymptom-EudraVigilance-10.csv',\n",
+    "    index_col = 'DRUG')\n",
+    "prrByVaccineAndSymptom"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7aed1621",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prrByVaccineAndSymptom = DataFrameFilter.withoutZeroRowsAndZeroColumns(prrByVaccineAndSymptom)\n",
+    "prrByVaccineAndSymptom"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "588aaa2b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prrByVaccineBySymptom = PrrSeriesFactory.getPrrByVaccineBySymptom(prrByVaccineAndSymptom)\n",
+    "prrByVaccineBySymptom"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "379d9730",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prrBySymptomByVaccine = PrrSeriesFactory.getPrrBySymptomByVaccine(prrByVaccineAndSymptom)\n",
+    "prrBySymptomByVaccine"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0cfd4c66",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prrByVaccineBySymptomWithoutZeroPrrs = PrrSeriesTransformer.filterByNonZeroPrrs(prrByVaccineBySymptom)\n",
+    "prrByVaccineBySymptomWithoutZeroPrrs"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "86da9cb7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prrBySymptomByVaccineWithHighPrrs = PrrSeriesTransformer.filterPrrs(prrBySymptomByVaccine, lambda prr: prr >= 2)\n",
+    "prrBySymptomByVaccineWithHighPrrs"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b41b60c7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "webAppBaseDir = os.getcwd() + '/../docs/SymptomsCausedByDrugs'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "26f72e75",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "saveProportionalReportingRatios(\n",
+    "    prrByVaccineBySymptomWithoutZeroPrrs,\n",
+    "    directory = os.path.normpath(webAppBaseDir + '/data/ProportionalReportingRatios/symptoms'))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5bfdcbdd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "saveProportionalReportingRatios(\n",
+    "    prrBySymptomByVaccineWithHighPrrs,\n",
+    "    directory = os.path.normpath(webAppBaseDir + '/data/ProportionalReportingRatios/vaccines'))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cc97b8d4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "updateHtmlFile(\n",
+    "    symptoms = list(prrByVaccineAndSymptom.columns),\n",
+    "    vaccines = list(prrByVaccineAndSymptom.index),\n",
+    "    htmlFile = os.path.normpath(webAppBaseDir + '/index.html'))"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "3e47c62c",

src/SymptomsCausedByVaccines/HtmlUtils.py

@@ -1,3 +1,5 @@
+import html
+
 def getVaccineOptions(vaccines, defaultOptionText):
     return _getOptionsWithDefaultOption(defaultOptionText = defaultOptionText, values = vaccines)
 
@@ -15,4 +17,4 @@ def _getOptions(values):
 
 
 def _getOption(value):
-    return '<option value="{value}">{value}</option>'.format(value=value)
+    return '<option value="{value}">{value}</option>'.format(value = html.escape(value))