refactoring

src/BatchCodeTableHtmlUpdater.py

@@ -0,0 +1,22 @@
+from bs4 import BeautifulSoup
+from HtmlTransformerUtil import HtmlTransformerUtil
+from CountryOptionsSetter import CountryOptionsSetter
+from DateProvider import DateProvider
+
+def saveCountryOptions(countryOptions):
+    HtmlTransformerUtil().applySoupTransformerToFile(
+        file = "../docs/batchCodeTable.html",
+        soupTransformer =
+            lambda soup:
+                BeautifulSoup(
+                    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))
+        return soup
+
+    HtmlTransformerUtil().applySoupTransformerToFile(
+        file = "../docs/batchCodeTable.html",
+        soupTransformer = setLastUpdated)

src/BatchCodeTablePersister.py

@@ -0,0 +1,15 @@
+from IOUtils import IOUtils
+import numpy as np
+
+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]
+    IOUtils.saveDataFrame(batchCodeTable, '../docs/data/batchCodeTables/' + country)
+    # display(country + ":", batchCodeTable)
+    display(country)
+
+def createAndSaveBatchCodeTablesForCountries(createBatchCodeTableForCountry, countries, minADRsForLethality = None):
+    for country in countries:
+        createAndSaveBatchCodeTableForCountry(createBatchCodeTableForCountry, country, minADRsForLethality)

src/HowBadIsMyBatch.ipynb

@@ -7,7 +7,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import pandas as pd\n",
     "\n",
     "pd.set_option('display.max_rows', 100)\n",
@@ -124,26 +123,6 @@
     "from BatchCodeTableFactory import BatchCodeTableFactory"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4db36933",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from HtmlTransformerUtil import HtmlTransformerUtil"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "32d4eecf",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from CountryOptionsSetter import CountryOptionsSetter"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -151,44 +130,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from bs4 import BeautifulSoup\n",
+    "from BatchCodeTableHtmlUpdater import saveCountryOptions, saveLastUpdatedBatchCodeTable"
-    "\n",
-    "\n",
-    "def saveCountryOptions(countryOptions):\n",
-    "    HtmlTransformerUtil().applySoupTransformerToFile(\n",
-    "        file = \"../docs/batchCodeTable.html\",\n",
-    "        soupTransformer =\n",
-    "            lambda soup:\n",
-    "                BeautifulSoup(\n",
-    "                    CountryOptionsSetter().setCountryOptions(html = str(soup), options = countryOptions),\n",
-    "                    'lxml'))\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f02dddfe",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def saveLastUpdatedBatchCodeTable(lastUpdated):\n",
-    "    def setLastUpdated(soup):\n",
-    "        soup.find(id = \"last_updated\").string.replace_with(lastUpdated.strftime(DateProvider.DATE_FORMAT))\n",
-    "        return soup\n",
-    "\n",
-    "    HtmlTransformerUtil().applySoupTransformerToFile(\n",
-    "        file = \"../docs/batchCodeTable.html\",\n",
-    "        soupTransformer = setLastUpdated)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6aa28541",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from IOUtils import IOUtils"
    ]
   },
   {
@@ -220,18 +162,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def createAndSaveBatchCodeTableForCountry(createBatchCodeTableForCountry, country, minADRsForLethality = None):\n",
+    "from BatchCodeTablePersister import createAndSaveBatchCodeTableForCountry, createAndSaveBatchCodeTablesForCountries"
-    "    batchCodeTable = createBatchCodeTableForCountry(country)\n",
-    "    batchCodeTable.index.set_names(\"Batch\", inplace = True)\n",
-    "    if minADRsForLethality is not None:\n",
-    "        batchCodeTable.loc[batchCodeTable['Adverse Reaction Reports'] < minADRsForLethality, ['Severe reports', 'Lethality']] = [np.nan, np.nan]\n",
-    "    IOUtils.saveDataFrame(batchCodeTable, '../docs/data/batchCodeTables/' + country)\n",
-    "    # display(country + \":\", batchCodeTable)\n",
-    "    display(country)\n",
-    "\n",
-    "def createAndSaveBatchCodeTablesForCountries(createBatchCodeTableForCountry, countries, minADRsForLethality = None):\n",
-    "    for country in countries:\n",
-    "        createAndSaveBatchCodeTableForCountry(createBatchCodeTableForCountry, country, minADRsForLethality)"
    ]
   },
   {
@@ -241,11 +172,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def getCountryOptions(countries):\n",
+    "from HtmlUtils import getCountryOptions"
-    "    return [getCountryOption(country) for country in countries]\n",
-    "\n",
-    "def getCountryOption(country):\n",
-    "    return '<option value=\"{country}\">{country}</option>'.format(country = country)"
    ]
   },
   {
@@ -256,7 +183,7 @@
    "outputs": [],
    "source": [
     "countries = sorted(internationalVaersCovid19['COUNTRY'].unique())\n",
-    "countryOptions = ['<option value=\"Global\" selected>Global</option>']  + getCountryOptions(countries)"
+    "countryOptions = getCountryOptions(countries)\n"
    ]
   },
   {

src/HtmlUtils.py

@@ -0,0 +1,10 @@
+def getCountryOptions(countries):
+    return ['<option value="Global" selected>Global</option>'] + _getCountryOptions(countries)
+
+
+def _getCountryOptions(countries):
+    return [_getCountryOption(country) for country in countries]
+
+
+def _getCountryOption(country):
+    return '<option value="{country}">{country}</option>'.format(country=country)