Merge branch 'main' into pages

merging EudraVigilance into pages branch

src/HowBadIsMyBatch.ipynb

@@ -441,16 +441,16 @@
   },
   {
    "cell_type": "markdown",
-   "id": "3e47c62c",
+   "id": "6c302a04",
    "metadata": {},
    "source": [
-    "# Symptoms caused by Vaccines\n"
+    "# Symptoms caused by Drugs (EudraVigilance)\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5cd9935f",
+   "id": "fb02ce7c",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -460,12 +460,112 @@
     "from SymptomsCausedByVaccines.PrrSeriesTransformer import PrrSeriesTransformer\n",
     "from SymptomsCausedByVaccines.ProportionalReportingRatiosPersister import saveProportionalReportingRatios\n",
     "import os\n",
-    "import pandas as pd"
+    "import pandas as pd\n",
+    "import gc"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "f38924ec",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def saveProportionalReportingRatios4PrrByVaccineBySymptomWithoutZeroPrrs(prrByVaccineAndSymptom, webAppBaseDir):\n",
+    "    prrByVaccineBySymptom = PrrSeriesFactory.getPrrByVaccineBySymptom(prrByVaccineAndSymptom)\n",
+    "\n",
+    "    prrByVaccineBySymptomWithoutZeroPrrs = PrrSeriesTransformer.filterByNonZeroPrrs(prrByVaccineBySymptom)\n",
+    "    del prrByVaccineBySymptom\n",
+    "    gc.collect()\n",
+    "\n",
+    "    filenameBySymptom = saveProportionalReportingRatios(\n",
+    "        prrByVaccineBySymptomWithoutZeroPrrs,\n",
+    "        directory = os.path.normpath(webAppBaseDir + '/data/ProportionalReportingRatios/symptoms'))\n",
+    "\n",
+    "    del prrByVaccineBySymptomWithoutZeroPrrs\n",
+    "    gc.collect()\n",
+    "    return filenameBySymptom"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e1237c0b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def saveProportionalReportingRatios4PrrBySymptomByVaccineWithHighPrrs(prrByVaccineAndSymptom, webAppBaseDir):\n",
+    "    prrBySymptomByVaccine = PrrSeriesFactory.getPrrBySymptomByVaccine(prrByVaccineAndSymptom)\n",
+    "    prrBySymptomByVaccineWithHighPrrs = PrrSeriesTransformer.filterPrrs(prrBySymptomByVaccine, lambda prr: prr >= 2)\n",
+    "    del prrBySymptomByVaccine\n",
+    "    gc.collect()\n",
+    "\n",
+    "    filenameByDrug = saveProportionalReportingRatios(\n",
+    "        prrBySymptomByVaccineWithHighPrrs,\n",
+    "        directory = os.path.normpath(webAppBaseDir + '/data/ProportionalReportingRatios/vaccines'))\n",
+    "\n",
+    "    del prrBySymptomByVaccineWithHighPrrs\n",
+    "    gc.collect()\n",
+    "    return filenameByDrug"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "64ccf3c9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def saveProportionalReportingRatiosAndUpdateHtmlFile(prrByVaccineAndSymptom, webAppBaseDir):\n",
+    "    prrByVaccineAndSymptom = DataFrameFilter.withoutZeroRowsAndZeroColumns(prrByVaccineAndSymptom)\n",
+    "    filenameBySymptom = saveProportionalReportingRatios4PrrByVaccineBySymptomWithoutZeroPrrs(prrByVaccineAndSymptom, webAppBaseDir)\n",
+    "    filenameByDrug = saveProportionalReportingRatios4PrrBySymptomByVaccineWithHighPrrs(prrByVaccineAndSymptom, webAppBaseDir)\n",
+    "    updateHtmlFile(\n",
+    "        symptomsDescr = {\n",
+    "            'symptoms': list(prrByVaccineAndSymptom.columns),\n",
+    "            'filenameBySymptom': filenameBySymptom },\n",
+    "        vaccinesDescr = {\n",
+    "            'vaccines': list(prrByVaccineAndSymptom.index),\n",
+    "            'filenameByDrug': filenameByDrug },\n",
+    "        htmlFile = os.path.normpath(webAppBaseDir + '/index.html'))\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cc2cf05f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "os.system('cd data; 7z x -y prrByDrugAndSymptom-EudraVigilance.7z')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3db1a115",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "saveProportionalReportingRatiosAndUpdateHtmlFile(\n",
+    "    prrByVaccineAndSymptom = pd.read_csv(\n",
+    "        'data/prrByDrugAndSymptom-EudraVigilance.csv',\n",
+    "        index_col = 'DRUG'),\n",
+    "    webAppBaseDir = os.getcwd() + '/../docs/SymptomsCausedByDrugs')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3e47c62c",
+   "metadata": {},
+   "source": [
+    "# Symptoms caused by Vaccines\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0974c307",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -480,101 +580,13 @@
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "dfa98cd9",
    "metadata": {},
    "outputs": [],
    "source": [
-    "prrByVaccineAndSymptom = DataFrameFilter.withoutZeroRowsAndZeroColumns(prrByVaccineAndSymptom)\n",
-    "prrByVaccineAndSymptom"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "640868c7",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "prrByVaccineBySymptom = PrrSeriesFactory.getPrrByVaccineBySymptom(prrByVaccineAndSymptom)\n",
-    "prrByVaccineBySymptom"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0f247c64",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "prrBySymptomByVaccine = PrrSeriesFactory.getPrrBySymptomByVaccine(prrByVaccineAndSymptom)\n",
-    "prrBySymptomByVaccine"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "760ac423",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "prrByVaccineBySymptomWithoutZeroPrrs = PrrSeriesTransformer.filterByNonZeroPrrs(prrByVaccineBySymptom)\n",
-    "prrByVaccineBySymptomWithoutZeroPrrs"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f07203e4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "prrBySymptomByVaccineWithHighPrrs = PrrSeriesTransformer.filterPrrs(prrBySymptomByVaccine, lambda prr: prr >= 2)\n",
-    "prrBySymptomByVaccineWithHighPrrs"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "webAppBaseDir = os.getcwd() + '/../docs/SymptomsCausedByVaccines'"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0b40071c",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "saveProportionalReportingRatios(\n",
-    "    prrByVaccineBySymptomWithoutZeroPrrs,\n",
-    "    directory = os.path.normpath(webAppBaseDir + '/data/ProportionalReportingRatios/symptoms'))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "fac4b34f",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "saveProportionalReportingRatios(\n",
-    "    prrBySymptomByVaccineWithHighPrrs,\n",
-    "    directory = os.path.normpath(webAppBaseDir + '/data/ProportionalReportingRatios/vaccines'))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "803dfbef",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "updateHtmlFile(\n",
-    "    symptoms = list(prrByVaccineAndSymptom.columns),\n",
-    "    vaccines = list(prrByVaccineAndSymptom.index),\n",
-    "    htmlFile = os.path.normpath(webAppBaseDir + '/index.html'))"
+    "saveProportionalReportingRatiosAndUpdateHtmlFile(\n",
+    "    prrByVaccineAndSymptom = prrByVaccineAndSymptom,\n",
+    "    webAppBaseDir = os.getcwd() + '/../docs/SymptomsCausedByVaccines')"
    ]
   },
   {

src/SymptomsCausedByVaccines/HtmlUpdater.py

@@ -5,14 +5,19 @@ from SymptomsCausedByVaccines.HtmlUtils import getSymptomOptions, getVaccineOpti
 from SymptomsCausedByVaccines.OptionsSetter import OptionsSetter
 
 
-def updateHtmlFile(symptoms, vaccines, htmlFile, defaultSelectVaccineOptionText = 'Select Vaccine'):
+def updateHtmlFile(symptomsDescr, vaccinesDescr, htmlFile, defaultSelectVaccineOptionText = 'Select Vaccine'):
     _saveOptions(
-        options = getSymptomOptions(symptoms),
+        options = getSymptomOptions(
+            symptoms = symptomsDescr['symptoms'],
+            filenameBySymptom = symptomsDescr['filenameBySymptom']),
         htmlFile = htmlFile,
         selectElementId = 'symptomSelect')
     
     _saveOptions(
-        options = getVaccineOptions(vaccines, defaultSelectVaccineOptionText),
+        options = getVaccineOptions(
+            vaccines = vaccinesDescr['vaccines'],
+            filenameByDrug = vaccinesDescr['filenameByDrug'],
+            defaultOptionText = defaultSelectVaccineOptionText),
         htmlFile = htmlFile,
         selectElementId = 'vaccineSelect')
 

src/SymptomsCausedByVaccines/HtmlUtils.py

@@ -1,18 +1,28 @@
-def getVaccineOptions(vaccines, defaultOptionText):
-    return _getOptionsWithDefaultOption(defaultOptionText = defaultOptionText, values = vaccines)
+import html
+
+def getVaccineOptions(vaccines, filenameByDrug, defaultOptionText):
+    return _getOptionsWithDefaultOption(
+        defaultOptionText = defaultOptionText,
+        values = vaccines,
+        filenameByValue = filenameByDrug)
 
 
-def getSymptomOptions(symptoms):
-    return _getOptionsWithDefaultOption(defaultOptionText = 'Select Symptom', values = symptoms)
+def getSymptomOptions(symptoms, filenameBySymptom):
+    return _getOptionsWithDefaultOption(
+        defaultOptionText = 'Select Symptom',
+        values = symptoms,
+        filenameByValue = filenameBySymptom)
 
 
-def _getOptionsWithDefaultOption(defaultOptionText, values):
-    return ['<option hidden disabled selected value>{defaultOptionText}</option>'.format(defaultOptionText = defaultOptionText)] + _getOptions(values)
+def _getOptionsWithDefaultOption(defaultOptionText, values, filenameByValue):
+    return ['<option hidden disabled selected value>{defaultOptionText}</option>'.format(defaultOptionText = defaultOptionText)] + _getOptions(values, filenameByValue)
 
 
-def _getOptions(values):
-    return [_getOption(value) for value in values]
+def _getOptions(values, filenameByValue):
+    return [_getOption(filename = filenameByValue[value], displayValue = value) for value in values]
 
 
-def _getOption(value):
-    return '<option value="{value}">{value}</option>'.format(value=value)
+def _getOption(filename, displayValue):
+    return '<option value="{value}">{displayValue}</option>'.format(
+        value = filename,
+        displayValue = html.escape(str(displayValue)))

src/SymptomsCausedByVaccines/ProportionalReportingRatiosPersister.py

@@ -1,7 +1,12 @@
 import shutil
 from IOUtils import IOUtils
 
-def saveProportionalReportingRatios(prrByVaccineBySymptom, directory):
+def saveProportionalReportingRatios(prrBySymptomByDrug, directory):
     shutil.rmtree(directory, ignore_errors = True)
-    for symptom, prrByVaccine in prrByVaccineBySymptom.items():
-        IOUtils.saveDictAsJson(prrByVaccine, f'{directory}/{symptom}.json')
+    filenameByDrug = {}
+    i = 0
+    for drug, prrBySymptom in prrBySymptomByDrug.items():
+        i += 1
+        filenameByDrug[drug] = f'{i}'
+        IOUtils.saveDictAsJson(prrBySymptom, f'{directory}/{i}.json')
+    return filenameByDrug    

src/SymptomsCausedByVaccines/ProportionalReportingRatiosPersisterTest.py

@@ -0,0 +1,33 @@
+import unittest
+from pandas.testing import assert_series_equal
+from TestHelper import TestHelper
+import pandas as pd
+import simplejson as json
+from SymptomsCausedByVaccines.ProportionalReportingRatiosPersister import saveProportionalReportingRatios
+
+
+class ProportionalReportingRatiosPersisterTest(unittest.TestCase):
+
+    def test_saveProportionalReportingRatios(self):
+        # Given
+        drug = '"GENERIC COLD ACID" '
+        prrBySymptom = { 'Sepsis ': 366.3084378480811 }
+        prrBySymptomByDrug = TestHelper.createSeries(
+                indexName = 'DRUG',
+                data = { drug: prrBySymptom })
+        directory = 'src/tmp/vaccines'
+        
+        # When
+        filenameByDrug = saveProportionalReportingRatios(prrBySymptomByDrug, directory)
+        
+        # Then
+        drugFilename = '1'
+        self.assertDictEqual(
+            ProportionalReportingRatiosPersisterTest.readJsonFile(f'{directory}/{drugFilename}.json'),
+            prrBySymptom)
+        self.assertDictEqual(filenameByDrug, { drug: drugFilename })
+
+    @staticmethod
+    def readJsonFile(file):
+        with open(file) as fp:
+            return json.load(fp)