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adding global batch code table

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frankknoll
2022-02-20 19:56:11 +01:00
parent 48befecfd3
commit ace0ce843f
3 changed files with 78 additions and 7 deletions
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75
src/HowBadIsMyBatch.ipynb
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@@ -421,6 +421,9 @@
" def createBatchCodeTableByCountry(self, country):\n",
" return self.batchCodeTableByCountryFactory.createBatchCodeTableByCountry(country)\n",
"\n",
" def createGlobalBatchCodeTable(self):\n",
" return self.createBatchCodeTableByCountry(None)\n",
"\n",
" def _createInternationalLotTable(self):\n",
" return SummationTableFactory.createSummationTableHavingSevereReportsColumn(self.dataFrame.groupby(self.dataFrame['COUNTRY']))\n"
]
@@ -453,9 +456,14 @@
" ]]\n",
" return batchCodeTable.sort_values(by = 'Severe reports', ascending = False)\n",
"\n",
" # FK-TODO: refactor\n",
" def _createBatchCodeTableByCountry(self, country):\n",
" if country is None:\n",
" return SummationTableFactory.createSummationTableHavingSevereReportsColumn(self.dataFrame.groupby('VAX_LOT'))\n",
"\n",
" if self.countryBatchCodeTable is None:\n",
" self.countryBatchCodeTable = self._getCountryBatchCodeTable()\n",
" \n",
" return self._getCountry(self.countryBatchCodeTable, country)\n",
"\n",
" def _getCountryBatchCodeTable(self):\n",
@@ -1192,6 +1200,42 @@
" name = 'VAX_LOT')),\n",
" check_dtype = False)\n",
"\n",
" def test_createGlobalBatchCodeTable(self):\n",
" # Given\n",
" dataFrame = TestHelper.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE', 'HOSPITAL', 'ER_VISIT', 'COUNTRY'],\n",
" data = [ [1, 0, 0, 'COVID19', 'PFIZER\\BIONTECH', '016M20A', '2', 'GBPFIZER INC2020486806', 0, 0, 'United Kingdom'],\n",
" [0, 0, 0, 'COVID19', 'MODERNA', '030L20A', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France'],\n",
" [1, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France'],\n",
" [0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France']],\n",
" index = [\n",
" \"1048786\",\n",
" \"1048786\",\n",
" \"4711\",\n",
" \"0815\"])\n",
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
" internationalLotTableFactory = InternationalLotTableFactory(dataFrame)\n",
" \n",
" # When\n",
" batchCodeTable = internationalLotTableFactory.createGlobalBatchCodeTable()\n",
"\n",
" # Then\n",
" assert_frame_equal(\n",
" batchCodeTable,\n",
" TestHelper.createDataFrame(\n",
" columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality'],\n",
" data = [ [1, 1, 0, 0, 'PFIZER\\BIONTECH', 1/1 * 100, 1/1 * 100],\n",
" [2, 1, 2, 2, 'MODERNA', 2/2 * 100, 1/2 * 100],\n",
" [1, 0, 0, 0, 'MODERNA', 0/1 * 100, 0/1 * 100]],\n",
" index = pd.Index(\n",
" [\n",
" '016M20A',\n",
" '030L20B',\n",
" '030L20A'\n",
" ],\n",
" name = 'VAX_LOT')),\n",
" check_dtype = False)\n",
"\n",
" def test_createBatchCodeTableByNonExistingCountry(self):\n",
" # Given\n",
" dataFrame = TestHelper.createDataFrame(\n",
@@ -1464,8 +1508,8 @@
" IOUtils.saveDataFrame(batchCodeTable, '../docs/data/' + country)\n",
" display(country + \":\", batchCodeTable)\n",
"\n",
"def createAndSaveAndDisplayBatchCodeTablesByCountry(nonDomesticVaers, countries, minADRsForLethality = None):\n",
" internationalLotTableFactory = InternationalLotTableFactory(nonDomesticVaers)\n",
"def createAndSaveAndDisplayBatchCodeTablesByCountry(vaers, countries, minADRsForLethality = None):\n",
" internationalLotTableFactory = InternationalLotTableFactory(vaers)\n",
" for country in countries:\n",
" createAndSaveAndDisplayBatchCodeTableByCountry(internationalLotTableFactory, country, minADRsForLethality)"
]
@@ -1518,6 +1562,33 @@
" minADRsForLethality = 100)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "106c0d91",
"metadata": {},
"outputs": [],
"source": [
"internationalLotTableFactory = InternationalLotTableFactory(internationalVaers)\n",
"globalBatchCodeTable = internationalLotTableFactory.createGlobalBatchCodeTable()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e75bd993",
"metadata": {},
"outputs": [],
"source": [
" # FK-TODO: DRY with createAndSaveAndDisplayBatchCodeTableByCountry()\n",
" minADRsForLethality = 100\n",
" globalBatchCodeTable.index.set_names(\"Batch\", inplace = True)\n",
" if minADRsForLethality is not None:\n",
" globalBatchCodeTable.loc[globalBatchCodeTable['Adverse Reaction Reports'] < minADRsForLethality, ['Severe reports', 'Lethality']] = [np.nan, np.nan]\n",
" IOUtils.saveDataFrame(globalBatchCodeTable, '../docs/data/Global')\n",
" display('Global' + \":\", globalBatchCodeTable)\n"
]
},
{
"cell_type": "markdown",
"id": "ba02139d",