refactoring

src/BatchCodeTableHtmlUpdater.py

@@ -2,6 +2,17 @@ from bs4 import BeautifulSoup
 from HtmlTransformerUtil import HtmlTransformerUtil
 from CountryOptionsSetter import CountryOptionsSetter
 from DateProvider import DateProvider
+from HtmlUtils import getCountryOptions, getCountries
+from DateProvider import DateProvider
+from BatchCodeTablePersister import createAndSaveBatchCodeTables
+
+
+def updateBatchCodeTableHtmlFile(internationalVaersCovid19):
+    countryOptions = getCountryOptions(getCountries(internationalVaersCovid19))
+    saveCountryOptions(countryOptions)
+    saveLastUpdatedBatchCodeTable(DateProvider().getLastUpdatedDataSource())
+    createAndSaveBatchCodeTables(internationalVaersCovid19, minADRsForLethality=100)
+
 
 def saveCountryOptions(countryOptions):
     HtmlTransformerUtil().applySoupTransformerToFile(
@@ -12,6 +23,7 @@ def saveCountryOptions(countryOptions):
                     CountryOptionsSetter().setCountryOptions(html = str(soup), options = countryOptions),
                     'lxml'))
 
+
 def saveLastUpdatedBatchCodeTable(lastUpdated):
     def setLastUpdated(soup):
         soup.find(id = "last_updated").string.replace_with(lastUpdated.strftime(DateProvider.DATE_FORMAT))
@@ -20,3 +32,4 @@ def saveLastUpdatedBatchCodeTable(lastUpdated):
     HtmlTransformerUtil().applySoupTransformerToFile(
         file = "../docs/batchCodeTable.html",
         soupTransformer = setLastUpdated)
+    

src/BatchCodeTablePersister.py

@@ -1,15 +1,38 @@
 from IOUtils import IOUtils
+from BatchCodeTableFactory import BatchCodeTableFactory
 import numpy as np
+from HtmlUtils import getCountries
 
-def createAndSaveBatchCodeTableForCountry(createBatchCodeTableForCountry, country, minADRsForLethality = None):
+
+def createAndSaveBatchCodeTables(internationalVaersCovid19, minADRsForLethality):
+    batchCodeTableFactory = BatchCodeTableFactory(internationalVaersCovid19)
+    _createAndSaveBatchCodeTablesForCountries(
+        createBatchCodeTableForCountry=lambda country: batchCodeTableFactory.createBatchCodeTableByCountry(
+            country),
+        countries=getCountries(internationalVaersCovid19),
+        minADRsForLethality=minADRsForLethality)
+    _createAndSaveBatchCodeTableForCountry(
+        createBatchCodeTableForCountry=lambda country: batchCodeTableFactory.createGlobalBatchCodeTable(),
+        country='Global',
+        minADRsForLethality=minADRsForLethality)
+
+
+def _createAndSaveBatchCodeTableForCountry(createBatchCodeTableForCountry, country, minADRsForLethality=None):
     batchCodeTable = createBatchCodeTableForCountry(country)
     batchCodeTable.index.set_names("Batch", inplace=True)
     if minADRsForLethality is not None:
-        batchCodeTable.loc[batchCodeTable['Adverse Reaction Reports'] < minADRsForLethality, ['Severe reports', 'Lethality']] = [np.nan, np.nan]
+        batchCodeTable.loc[
-    IOUtils.saveDataFrame(batchCodeTable, '../docs/data/batchCodeTables/' + country)
+            batchCodeTable['Adverse Reaction Reports'] < minADRsForLethality,
+            ['Severe reports', 'Lethality']
+        ] = [np.nan, np.nan]
+    IOUtils.saveDataFrame(
+        batchCodeTable,
+        '../docs/data/batchCodeTables/' + country)
     # display(country + ":", batchCodeTable)
     display(country)
 
-def createAndSaveBatchCodeTablesForCountries(createBatchCodeTableForCountry, countries, minADRsForLethality = None):
+
+def _createAndSaveBatchCodeTablesForCountries(createBatchCodeTableForCountry, countries, minADRsForLethality=None):
     for country in countries:
-        createAndSaveBatchCodeTableForCountry(createBatchCodeTableForCountry, country, minADRsForLethality)
+        _createAndSaveBatchCodeTableForCountry(
+            createBatchCodeTableForCountry, country, minADRsForLethality)

src/HowBadIsMyBatch.ipynb

@@ -103,26 +103,6 @@
     "    downloadVAERSFileAndUnzip('NonDomesticVAERSData.zip', workingDirectory)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "3ebcba86",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from DataFrameFilter import DataFrameFilter"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "71456a79",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from BatchCodeTableFactory import BatchCodeTableFactory"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -130,17 +110,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from BatchCodeTableHtmlUpdater import saveCountryOptions, saveLastUpdatedBatchCodeTable"
+    "from BatchCodeTableHtmlUpdater import updateBatchCodeTableHtmlFile"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "86e0e4f2",
+   "id": "62132e68",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from VaersReader import getVaersForYears, getNonDomesticVaers"
+    "from InternationalVaersCovid19Provider import getInternationalVaersCovid19"
    ]
   },
   {
@@ -150,42 +130,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "internationalVaers = pd.concat([getVaersForYears([2020, 2021, 2022]), getNonDomesticVaers()])\n",
+    "internationalVaersCovid19 = getInternationalVaersCovid19([2020, 2021, 2022])\n",
-    "internationalVaersCovid19 = DataFrameFilter().filterByCovid19(internationalVaers)\n",
     "internationalVaersCovid19"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ff259a35",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from BatchCodeTablePersister import createAndSaveBatchCodeTableForCountry, createAndSaveBatchCodeTablesForCountries"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "cc1ef82a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from HtmlUtils import getCountryOptions"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0c4d04fb",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "countries = sorted(internationalVaersCovid19['COUNTRY'].unique())\n",
-    "countryOptions = getCountryOptions(countries)\n"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -193,38 +141,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "saveCountryOptions(countryOptions)"
+    "updateBatchCodeTableHtmlFile(internationalVaersCovid19)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "9c7485b5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "saveLastUpdatedBatchCodeTable(dateProvider.getLastUpdatedDataSource())"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7e7e01a5",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "minADRsForLethality = 100\n",
-    "batchCodeTableFactory = BatchCodeTableFactory(internationalVaersCovid19)\n",
-    "\n",
-    "createAndSaveBatchCodeTablesForCountries(\n",
-    "    createBatchCodeTableForCountry = lambda country: batchCodeTableFactory.createBatchCodeTableByCountry(country),\n",
-    "    countries = countries,\n",
-    "    minADRsForLethality = minADRsForLethality)\n",
-    "\n",
-    "createAndSaveBatchCodeTableForCountry(\n",
-    "    createBatchCodeTableForCountry = lambda country: batchCodeTableFactory.createGlobalBatchCodeTable(),\n",
-    "    country = 'Global',\n",
-    "    minADRsForLethality = minADRsForLethality)"
    ]
   },
   {

src/HtmlUtils.py

@@ -1,3 +1,7 @@
+def getCountries(internationalVaersCovid19):
+    return sorted(internationalVaersCovid19['COUNTRY'].unique())
+
+
 def getCountryOptions(countries):
     return ['<option value="Global" selected>Global</option>'] + _getCountryOptions(countries)
 

src/InternationalVaersCovid19Provider.py

@@ -0,0 +1,8 @@
+from DataFrameFilter import DataFrameFilter
+from VaersReader import getVaersForYears, getNonDomesticVaers
+import pandas as pd
+
+def getInternationalVaersCovid19(years):
+    internationalVaers = pd.concat([getVaersForYears(years), getNonDomesticVaers()])
+    internationalVaersCovid19 = DataFrameFilter().filterByCovid19(internationalVaers)
+    return internationalVaersCovid19