francois/HowBadIsMyBatch
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refactoring

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frankknoll
2022-02-21 13:09:09 +01:00
parent ee333f0d1f
commit ebc58be5d9
1 changed files with 17 additions and 33 deletions
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src/HowBadIsMyBatch.ipynb
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@@ -291,26 +291,6 @@
" return manufacturerByBatchCodeTable.set_index('VAX_LOT')\n" " return manufacturerByBatchCodeTable.set_index('VAX_LOT')\n"
] ]
}, },
{
"cell_type": "code",
"execution_count": null,
"id": "09e6b511",
"metadata": {},
"outputs": [],
"source": [
"class InternationalLotTableFactory:\n",
" \n",
" def __init__(self, dataFrame : pd.DataFrame):\n",
" self.dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" self.batchCodeTableByCountryFactory = BatchCodeTableByCountryFactory(dataFrame)\n",
"\n",
" def createBatchCodeTableByCountry(self, country):\n",
" return self.batchCodeTableByCountryFactory.createBatchCodeTableByCountry(country)\n",
"\n",
" def createGlobalBatchCodeTable(self):\n",
" return self.createBatchCodeTableByCountry(None)\n"
]
},
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": null,
@@ -318,12 +298,15 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"class BatchCodeTableByCountryFactory:\n", "class BatchCodeTableFactory:\n",
"\n", "\n",
" def __init__(self, dataFrame : pd.DataFrame):\n", " def __init__(self, dataFrame : pd.DataFrame):\n",
" self.dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n", " self.dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" self.countryBatchCodeTable = None\n", " self.countryBatchCodeTable = None\n",
"\n", "\n",
" def createGlobalBatchCodeTable(self):\n",
" return self.createBatchCodeTableByCountry(None)\n",
"\n",
" def createBatchCodeTableByCountry(self, country):\n", " def createBatchCodeTableByCountry(self, country):\n",
" batchCodeTable = self._createBatchCodeTableByCountry(country)\n", " batchCodeTable = self._createBatchCodeTableByCountry(country)\n",
" batchCodeTable = CompanyColumnAdder.addCompanyColumn(batchCodeTable, CompanyColumnAdder.createCompanyByBatchCodeTable(self.dataFrame))\n", " batchCodeTable = CompanyColumnAdder.addCompanyColumn(batchCodeTable, CompanyColumnAdder.createCompanyByBatchCodeTable(self.dataFrame))\n",
@@ -555,7 +538,7 @@
"source": [ "source": [
"from pandas.testing import assert_frame_equal\n", "from pandas.testing import assert_frame_equal\n",
"\n", "\n",
"class InternationalLotTableFactoryTest(unittest.TestCase):\n", "class BatchCodeTableFactoryTest(unittest.TestCase):\n",
"\n", "\n",
" def test_createBatchCodeTableByCountry(self):\n", " def test_createBatchCodeTableByCountry(self):\n",
" # Given\n", " # Given\n",
@@ -571,10 +554,10 @@
" \"4711\",\n", " \"4711\",\n",
" \"0815\"])\n", " \"0815\"])\n",
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n", " dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
" internationalLotTableFactory = InternationalLotTableFactory(dataFrame)\n", " batchCodeTableFactory = BatchCodeTableFactory(dataFrame)\n",
" \n", " \n",
" # When\n", " # When\n",
" batchCodeTable = internationalLotTableFactory.createBatchCodeTableByCountry('France')\n", " batchCodeTable = batchCodeTableFactory.createBatchCodeTableByCountry('France')\n",
"\n", "\n",
" # Then\n", " # Then\n",
" assert_frame_equal(\n", " assert_frame_equal(\n",
@@ -605,10 +588,10 @@
" \"4711\",\n", " \"4711\",\n",
" \"0815\"])\n", " \"0815\"])\n",
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n", " dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
" internationalLotTableFactory = InternationalLotTableFactory(dataFrame)\n", " batchCodeTableFactory = BatchCodeTableFactory(dataFrame)\n",
" \n", " \n",
" # When\n", " # When\n",
" batchCodeTable = internationalLotTableFactory.createGlobalBatchCodeTable()\n", " batchCodeTable = batchCodeTableFactory.createGlobalBatchCodeTable()\n",
"\n", "\n",
" # Then\n", " # Then\n",
" assert_frame_equal(\n", " assert_frame_equal(\n",
@@ -641,10 +624,10 @@
" \"4711\",\n", " \"4711\",\n",
" \"0815\"])\n", " \"0815\"])\n",
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n", " dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
" internationalLotTableFactory = InternationalLotTableFactory(dataFrame)\n", " batchCodeTableFactory = BatchCodeTableFactory(dataFrame)\n",
" \n", " \n",
" # When\n", " # When\n",
" batchCodeTable = internationalLotTableFactory.createBatchCodeTableByCountry('non existing country')\n", " batchCodeTable = batchCodeTableFactory.createBatchCodeTableByCountry('non existing country')\n",
"\n", "\n",
" # Then\n", " # Then\n",
" assert_frame_equal(\n", " assert_frame_equal(\n",
@@ -748,7 +731,8 @@
" if minADRsForLethality is not None:\n", " if minADRsForLethality is not None:\n",
" batchCodeTable.loc[batchCodeTable['Adverse Reaction Reports'] < minADRsForLethality, ['Severe reports', 'Lethality']] = [np.nan, np.nan]\n", " batchCodeTable.loc[batchCodeTable['Adverse Reaction Reports'] < minADRsForLethality, ['Severe reports', 'Lethality']] = [np.nan, np.nan]\n",
" IOUtils.saveDataFrame(batchCodeTable, '../docs/data/' + country)\n", " IOUtils.saveDataFrame(batchCodeTable, '../docs/data/' + country)\n",
" display(country + \":\", batchCodeTable)\n", " # display(country + \":\", batchCodeTable)\n",
" display(country)\n",
"\n", "\n",
"def createAndSaveBatchCodeTablesForCountries(createBatchCodeTableForCountry, countries, minADRsForLethality = None):\n", "def createAndSaveBatchCodeTablesForCountries(createBatchCodeTableForCountry, countries, minADRsForLethality = None):\n",
" for country in countries:\n", " for country in countries:\n",
@@ -789,17 +773,17 @@
"outputs": [], "outputs": [],
"source": [ "source": [
"minADRsForLethality = 100\n", "minADRsForLethality = 100\n",
"internationalLotTableFactory = InternationalLotTableFactory(internationalVaers)\n", "batchCodeTableFactory = BatchCodeTableFactory(internationalVaers)\n",
"\n", "\n",
"createAndSaveBatchCodeTablesForCountries(\n", "createAndSaveBatchCodeTablesForCountries(\n",
" createBatchCodeTableForCountry = lambda country: internationalLotTableFactory.createBatchCodeTableByCountry(country),\n", " createBatchCodeTableForCountry = lambda country: batchCodeTableFactory.createBatchCodeTableByCountry(country),\n",
" countries = countries,\n", " countries = countries,\n",
" minADRsForLethality = minADRsForLethality)\n", " minADRsForLethality = minADRsForLethality)\n",
"\n", "\n",
"createAndSaveBatchCodeTableForCountry(\n", "createAndSaveBatchCodeTableForCountry(\n",
" createBatchCodeTableForCountry = lambda country: internationalLotTableFactory.createGlobalBatchCodeTable(),\n", " createBatchCodeTableForCountry = lambda country: batchCodeTableFactory.createGlobalBatchCodeTable(),\n",
" country = 'Global',\n", " country = 'Global',\n",
" minADRsForLethality = minADRsForLethality)\n" " minADRsForLethality = minADRsForLethality)"
] ]
} }
], ],