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refactoring

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frankknoll
2022-02-20 18:55:02 +01:00
parent 9d44215c37
commit be1f4e613e
23 changed files with 68 additions and 62 deletions
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MANUFACTURER",null,null],["EA3599",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ6798",1,0,0,0,"PFIZER\\BIONTECH",null,null],["300042698",1,0,0,0,"MODERNA",null,null],["ER9470",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EL1491",11,0,0,0,"PFIZER\\BIONTECH",null,null],["EL0725",5,0,0,0,"PFIZER\\BIONTECH",null,null],["EL 9127",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EL 0725",2,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ6796",7,0,0,0,"PFIZER\\BIONTECH",null,null],["EF9470",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ6790",3,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ6136",3,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ6134",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ 6797",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ 6136",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EI0725",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ET7205",1,0,0,0,"PFIZER\\BIONTECH",null,null]]} {"columns":["Batch","Adverse Reaction Reports","Deaths","Disabilities","Life Threatening Illnesses","Company","Severe reports","Lethality"],"data":[["EW2243",1,1,0,0,"PFIZER\\BIONTECH",null,null],["EW 9012",1,0,0,1,"PFIZER\\BIONTECH",null,null],["EW9217",1,1,0,0,"PFIZER\\BIONTECH",null,null],["EN6200",1,1,0,0,"PFIZER\\BIONTECH",null,null],["300042723",2,0,1,0,"MODERNA",null,null],["ACA5778",2,0,0,1,"JANSSEN",null,null],["EP2166",5,1,0,1,"PFIZER\\BIONTECH",null,null],["XE393",3,0,0,1,"JANSSEN",null,null],["ET3620",3,0,1,0,"PFIZER\\BIONTECH",null,null],["FG4442",3,1,0,0,"PFIZER\\BIONTECH",null,null],["EW9127",10,0,0,3,"PFIZER\\BIONTECH",null,null],["FE4728",4,0,1,0,"PFIZER\\BIONTECH",null,null],["ET6956",9,0,0,2,"PFIZER\\BIONTECH",null,null],["3001650",5,1,0,0,"MODERNA",null,null],["FE6208",11,0,2,0,"PFIZER\\BIONTECH",null,null],["NOT PROVIDED",11,0,2,0,"MODERNA",null,null],["FA7083",6,1,0,0,"PFIZER\\BIONTECH",null,null],["EX6537",14,2,0,1,"PFIZER\\BIONTECH",null,null],["EX8680",8,0,0,1,"PFIZER\\BIONTECH",null,null],["FC8736",8,0,0,1,"PFIZER\\BIONTECH",null,null],["EW2246",9,1,0,0,"PFIZER\\BIONTECH",null,null],["EJ6797",13,0,0,1,"PFIZER\\BIONTECH",null,null],["UNKNOWN",63,1,2,3,"PFIZER\\BIONTECH",null,null],["FE6840",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FK6304",2,0,0,0,"PFIZER\\BIONTECH",null,null],["XD975",3,0,0,0,"JANSSEN",null,null],["EW9129",1,0,0,0,"PFIZER\\BIONTECH",null,null],["XD955",1,0,0,0,"JANSSEN",null,null],["EX3599",7,0,0,0,"PFIZER\\BIONTECH",null,null],["UNKNOW",1,0,0,0,"MODERNA",null,null],["PD6840",1,0,0,0,"PFIZER\\BIONTECH",null,null],["KT8736",1,0,0,0,"PFIZER\\BIONTECH",null,null],["G26761A",1,0,0,0,"MODERNA",null,null],["G267619",1,0,0,0,"MODERNA",null,null],["EX6737",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FA4632",22,0,0,0,"PFIZER\\BIONTECH",null,null],["FE4442",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FH0161",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FC1435",7,0,0,0,"PFIZER\\BIONTECH",null,null],["FC4442",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FE8235",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FD 4555",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FD1435",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FD1921",2,0,0,0,"PFIZER\\BIONTECH",null,null],["FD4555",14,0,0,0,"PFIZER\\BIONTECH",null,null],["FE7083",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FE3065",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FD6840",13,0,0,0,"PFIZER\\BIONTECH",null,null],["1091557",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EW2239",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EW 2246",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ASKED BUT NOT P",1,0,0,0,"PFIZER\\BIONTECH",null,null],["AD1921",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ACA5775",1,0,0,0,"JANSSEN",null,null],["ABZ5320",1,0,0,0,"JANSSEN",null,null],["8X8680",1,0,0,0,"PFIZER\\BIONTECH",null,null],["626761A",1,0,0,0,"MODERNA",null,null],["3003652",3,0,0,0,"MODERNA",null,null],["3003604",1,0,0,0,"MODERNA",null,null],["3003185",4,0,0,0,"MODERNA",null,null],["3002913",1,0,0,0,"MODERNA",null,null],["3002622",1,0,0,0,"MODERNA",null,null],["3002546",2,0,0,0,"MODERNA",null,null],["3002336",1,0,0,0,"MODERNA",null,null],["3001946",3,0,0,0,"MODERNA",null,null],["3000489",1,0,0,0,"MODERNA",null,null],["ASKED BUT UNKNO",5,0,0,0,"PFIZER\\BIONTECH",null,null],["DC8736",1,0,0,0,"UNKNOWN MANUFACTURER",null,null],["EA3599",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ6798",1,0,0,0,"PFIZER\\BIONTECH",null,null],["300042698",1,0,0,0,"MODERNA",null,null],["ER9470",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EL1491",11,0,0,0,"PFIZER\\BIONTECH",null,null],["EL0725",5,0,0,0,"PFIZER\\BIONTECH",null,null],["EL 9127",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EL 0725",2,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ6796",7,0,0,0,"PFIZER\\BIONTECH",null,null],["EF9470",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ6790",3,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ6136",3,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ6134",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ 6797",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ 6136",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EI0725",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ET7205",1,0,0,0,"PFIZER\\BIONTECH",null,null]]}

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{"columns":["Batch","Adverse Reaction Reports","Deaths","Disabilities","Life Threatening Illnesses","Company","Severe reports","Lethality"],"data":[["EX2405",2,0,0,1,"PFIZER\\BIONTECH",null,null],["041A21A",1,0,0,0,"JANSSEN",null,null],["EW0216",1,0,0,0,"PFIZER\\BIONTECH",null,null],["UNKNOWN",2,0,0,0,"PFIZER\\BIONTECH",null,null],["FM2954",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FH8021",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FD7207",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FA7483",4,0,0,0,"PFIZER\\BIONTECH",null,null],["FA4597",3,0,0,0,"PFIZER\\BIONTECH",null,null],["EWO175",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EW0182",1,0,0,0,"PFIZER\\BIONTECH",null,null],["204A21A",1,0,0,0,"JANSSEN",null,null],["EW0171",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EW0151",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ET9096",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ER7449",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ER2659",3,0,0,0,"PFIZER\\BIONTECH",null,null],["EQ0168",1,0,0,0,"PFIZER\\BIONTECH",null,null],["87663",1,0,0,0,"PFIZER\\BIONTECH",null,null],["34030BD",1,0,0,0,"PFIZER\\BIONTECH",null,null],["XD985",1,0,0,0,"JANSSEN",null,null]]} {"columns":["Batch","Adverse Reaction Reports","Deaths","Disabilities","Life Threatening Illnesses","Company","Severe reports","Lethality"],"data":[["EX2405",2,0,0,1,"PFIZER\\BIONTECH",null,null],["041A21A",1,0,0,0,"MODERNA",null,null],["EW0216",1,0,0,0,"PFIZER\\BIONTECH",null,null],["UNKNOWN",2,0,0,0,"PFIZER\\BIONTECH",null,null],["FM2954",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FH8021",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FD7207",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FA7483",4,0,0,0,"PFIZER\\BIONTECH",null,null],["FA4597",3,0,0,0,"PFIZER\\BIONTECH",null,null],["EWO175",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EW0182",1,0,0,0,"PFIZER\\BIONTECH",null,null],["204A21A",1,0,0,0,"JANSSEN",null,null],["EW0171",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EW0151",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ET9096",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ER7449",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ER2659",3,0,0,0,"PFIZER\\BIONTECH",null,null],["EQ0168",1,0,0,0,"PFIZER\\BIONTECH",null,null],["87663",1,0,0,0,"PFIZER\\BIONTECH",null,null],["34030BD",1,0,0,0,"PFIZER\\BIONTECH",null,null],["XD985",1,0,0,0,"JANSSEN",null,null]]}

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{"columns":["Batch","Adverse Reaction Reports","Deaths","Disabilities","Life Threatening Illnesses","Company","Severe reports","Lethality"],"data":[["FF2154",1,0,0,1,"PFIZER\\BIONTECH",null,null],["UNKNOWN",6,1,0,0,"PFIZER\\BIONTECH",null,null],["EK4245",13,0,0,1,"PFIZER\\BIONTECH",null,null],["EY5456",2,0,0,0,"PFIZER\\BIONTECH",null,null],["UNK",2,0,0,0,"PFIZER\\BIONTECH",null,null],["FK8892",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FJ8198",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FJ1926",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FG1657",2,0,0,0,"PFIZER\\BIONTECH",null,null],["FF3319",1,0,0,0,"UNKNOWN MANUFACTURER",null,null],["FE8087",2,0,0,0,"PFIZER\\BIONTECH",null,null],["1E022A",2,0,0,0,"PFIZER\\BIONTECH",null,null],["3002336",1,0,0,0,"MODERNA",null,null],["ER6166",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ER0866",4,0,0,0,"PFIZER\\BIONTECH",null,null],["EP6775",3,0,0,0,"PFIZER\\BIONTECH",null,null],["EN1196",19,0,0,0,"PFIZER\\BIONTECH",null,null],["EL0200",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EK4237",14,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ3002",4,0,0,0,"PFIZER\\BIONTECH",null,null],["ER9449",1,0,0,0,"PFIZER\\BIONTECH",null,null]]} {"columns":["Batch","Adverse Reaction Reports","Deaths","Disabilities","Life Threatening Illnesses","Company","Severe reports","Lethality"],"data":[["FF2154",1,0,0,1,"PFIZER\\BIONTECH",null,null],["UNKNOWN",6,1,0,0,"PFIZER\\BIONTECH",null,null],["EK4245",13,0,0,1,"PFIZER\\BIONTECH",null,null],["EY5456",2,0,0,0,"PFIZER\\BIONTECH",null,null],["UNK",2,0,0,0,"PFIZER\\BIONTECH",null,null],["FK8892",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FJ8198",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FJ1926",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FG1657",2,0,0,0,"PFIZER\\BIONTECH",null,null],["FF3319",1,0,0,0,"PFIZER\\BIONTECH",null,null],["FE8087",2,0,0,0,"PFIZER\\BIONTECH",null,null],["1E022A",2,0,0,0,"PFIZER\\BIONTECH",null,null],["3002336",1,0,0,0,"MODERNA",null,null],["ER6166",1,0,0,0,"PFIZER\\BIONTECH",null,null],["ER0866",4,0,0,0,"PFIZER\\BIONTECH",null,null],["EP6775",3,0,0,0,"PFIZER\\BIONTECH",null,null],["EN1196",19,0,0,0,"PFIZER\\BIONTECH",null,null],["EL0200",1,0,0,0,"PFIZER\\BIONTECH",null,null],["EK4237",14,0,0,0,"PFIZER\\BIONTECH",null,null],["EJ3002",4,0,0,0,"PFIZER\\BIONTECH",null,null],["ER9449",1,0,0,0,"PFIZER\\BIONTECH",null,null]]}

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@@ -33,14 +33,14 @@
"\n", "\n",
" def readVaersDescrForYear(self, year):\n", " def readVaersDescrForYear(self, year):\n",
" return {\n", " return {\n",
" 'VAERSDATA': self._readVAERSDATA(self.dataDir + \"/\" + year + \"VAERSDATA.csv\"),\n", " 'VAERSDATA': self._readVAERSDATA('{dataDir}/{year}VAERSDATA.csv'.format(dataDir = self.dataDir, year = year)),\n",
" 'VAERSVAX': self._readVAERSVAX(self.dataDir + \"/\" + year + \"VAERSVAX.csv\")\n", " 'VAERSVAX': self._readVAERSVAX('{dataDir}/{year}VAERSVAX.csv'.format(dataDir = self.dataDir, year = year))\n",
" }\n", " }\n",
"\n", "\n",
" def readNonDomesticVaersDescr(self):\n", " def readNonDomesticVaersDescr(self):\n",
" return {\n", " return {\n",
" 'VAERSDATA': self._readVAERSDATA(self.dataDir + \"/\" + \"NonDomesticVAERSDATA.csv\"),\n", " 'VAERSDATA': self._readVAERSDATA(self.dataDir + \"/NonDomesticVAERSDATA.csv\"),\n",
" 'VAERSVAX': self._readVAERSVAX(self.dataDir + \"/\" + \"NonDomesticVAERSVAX.csv\")\n", " 'VAERSVAX': self._readVAERSVAX(self.dataDir + \"/NonDomesticVAERSVAX.csv\")\n",
" }\n", " }\n",
"\n", "\n",
" def _readVAERSDATA(self, file):\n", " def _readVAERSDATA(self, file):\n",
@@ -331,9 +331,9 @@
"class CountryColumnAdder:\n", "class CountryColumnAdder:\n",
" \n", " \n",
" @staticmethod\n", " @staticmethod\n",
" def addCountryColumn(dataFrame, countryColumnName):\n", " def addCountryColumn(dataFrame):\n",
" dataFrame[countryColumnName] = CountryColumnAdder.getCountryColumn(dataFrame)\n", " dataFrame['Country'] = CountryColumnAdder.getCountryColumn(dataFrame)\n",
" return dataFrame.astype({countryColumnName: \"string\"})\n", " return dataFrame.astype({'Country': \"string\"})\n",
"\n", "\n",
" @staticmethod\n", " @staticmethod\n",
" def getCountryColumn(dataFrame):\n", " def getCountryColumn(dataFrame):\n",
@@ -422,9 +422,7 @@
" return self.batchCodeTableByCountryFactory.createBatchCodeTableByCountry(country)\n", " return self.batchCodeTableByCountryFactory.createBatchCodeTableByCountry(country)\n",
"\n", "\n",
" def _createInternationalLotTable(self):\n", " def _createInternationalLotTable(self):\n",
" countryColumnName = 'Country'\n", " return SummationTableFactory.createSummationTableHavingSevereReportsColumn(self.dataFrame.groupby(self.dataFrame['Country']))\n"
" dataFrame = CountryColumnAdder.addCountryColumn(self.dataFrame, countryColumnName = countryColumnName)\n",
" return SummationTableFactory.createSummationTableHavingSevereReportsColumn(dataFrame.groupby(dataFrame[countryColumnName]))\n"
] ]
}, },
{ {
@@ -461,13 +459,11 @@
" return self._getCountry(self.countryBatchCodeTable, country)\n", " return self._getCountry(self.countryBatchCodeTable, country)\n",
"\n", "\n",
" def _getCountryBatchCodeTable(self):\n", " def _getCountryBatchCodeTable(self):\n",
" countryColumnName = 'Country'\n",
" dataFrame = CountryColumnAdder.addCountryColumn(self.dataFrame, countryColumnName = countryColumnName)\n",
" return SummationTableFactory.createSummationTableHavingSevereReportsColumn(\n", " return SummationTableFactory.createSummationTableHavingSevereReportsColumn(\n",
" dataFrame.groupby(\n", " self.dataFrame.groupby(\n",
" [\n", " [\n",
" dataFrame[countryColumnName],\n", " self.dataFrame['Country'],\n",
" dataFrame['VAX_LOT']\n", " self.dataFrame['VAX_LOT']\n",
" ]))\n", " ]))\n",
"\n", "\n",
" def _getCountry(self, countryBatchCodeTable, country):\n", " def _getCountry(self, countryBatchCodeTable, country):\n",
@@ -1009,7 +1005,7 @@
"\n", "\n",
" def test_createBatchCodeTableFromFiles(self):\n", " def test_createBatchCodeTableFromFiles(self):\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescrReader(dataDir = \"test/VAERS\").readVaersDescrsForYears([\"2021\", \"2022\"]))\n", " VaersDescrReader(dataDir = \"test/VAERS\").readVaersDescrsForYears([2021, 2022]))\n",
" DataFrameNormalizer.normalize(dataFrame)\n", " DataFrameNormalizer.normalize(dataFrame)\n",
" self._test_createBatchCodeTable(dataFrame)\n", " self._test_createBatchCodeTable(dataFrame)\n",
"\n", "\n",
@@ -1128,12 +1124,12 @@
" def test_createInternationalLotTable(self):\n", " def test_createInternationalLotTable(self):\n",
" # Given\n", " # Given\n",
" dataFrame = TestHelper.createDataFrame(\n", " dataFrame = TestHelper.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE', 'HOSPITAL', 'ER_VISIT'],\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', 'MODERNA', '016M20A', '2', 'GBPFIZER INC2020486806', 0, 0],\n", " data = [ [1, 0, 0, 'COVID19', 'MODERNA', '016M20A', '2', 'GBPFIZER INC2020486806', 0, 0, 'United Kingdom'],\n",
" [1, 0, 0, 'COVID19', 'MODERNA', '030L20A', '1', 'FRMODERNATX, INC.MOD20224', 0, 0],\n", " [1, 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],\n", " [1, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France'],\n",
" [0, 0, 0, 'COVID19', 'MODERNA', '030L20B', '1', 'dummy'],\n", " [0, 0, 0, 'COVID19', 'MODERNA', '030L20B', '1', 'dummy', 0, 0, 'Unknown Country'],\n",
" [0, 0, 0, 'COVID19', 'MODERNA', '030L20B', '1', 123]],\n", " [0, 0, 0, 'COVID19', 'MODERNA', '030L20B', '1', 123, 0, 0, 'Unknown Country']],\n",
" index = [\n", " index = [\n",
" \"1048786\",\n", " \"1048786\",\n",
" \"1048786\",\n", " \"1048786\",\n",
@@ -1160,17 +1156,16 @@
" 'United Kingdom',\n", " 'United Kingdom',\n",
" 'Unknown Country'\n", " 'Unknown Country'\n",
" ],\n", " ],\n",
" dtype = \"string\",\n",
" name = 'Country')))\n", " name = 'Country')))\n",
"\n", "\n",
" def test_createBatchCodeTableByCountry(self):\n", " def test_createBatchCodeTableByCountry(self):\n",
" # Given\n", " # Given\n",
" dataFrame = TestHelper.createDataFrame(\n", " dataFrame = TestHelper.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE', 'HOSPITAL', 'ER_VISIT'],\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],\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],\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],\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]],\n", " [0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France']],\n",
" index = [\n", " index = [\n",
" \"1048786\",\n", " \"1048786\",\n",
" \"1048786\",\n", " \"1048786\",\n",
@@ -1200,11 +1195,11 @@
" def test_createBatchCodeTableByNonExistingCountry(self):\n", " def test_createBatchCodeTableByNonExistingCountry(self):\n",
" # Given\n", " # Given\n",
" dataFrame = TestHelper.createDataFrame(\n", " dataFrame = TestHelper.createDataFrame(\n",
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE', 'HOSPITAL', 'ER_VISIT'],\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],\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],\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],\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]],\n", " [0, 1, 1, 'COVID19', 'MODERNA', '030L20B', '1', 'FRMODERNATX, INC.MOD20224', 0, 0, 'France']],\n",
" index = [\n", " index = [\n",
" \"1048786\",\n", " \"1048786\",\n",
" \"1048786\",\n", " \"1048786\",\n",
@@ -1243,14 +1238,25 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"def getVaersForYears(years):\n",
" return _getVaers(_getVaersDescrReader().readVaersDescrsForYears(years))\n",
"\n",
"def getVaersForYear(year):\n", "def getVaersForYear(year):\n",
" return getVaersForYears([year])\n", " return getVaersForYears([year])\n",
"\n", "\n",
"# FK-TODO: DRY with getNonDomesticVaers()\n",
"def getVaersForYears(years):\n",
" vaersDescrs = _getVaersDescrReader().readVaersDescrsForYears(years)\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" dataFrame['Country'] = 'United States'\n",
" DataFrameNormalizer.normalize(dataFrame)\n",
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
" return dataFrame\n",
"\n",
"def getNonDomesticVaers():\n", "def getNonDomesticVaers():\n",
" return _getVaers([_getVaersDescrReader().readNonDomesticVaersDescr()])\n", " vaersDescrs = [_getVaersDescrReader().readNonDomesticVaersDescr()]\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" dataFrame = CountryColumnAdder.addCountryColumn(dataFrame)\n",
" DataFrameNormalizer.normalize(dataFrame)\n",
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
" return dataFrame\n",
"\n", "\n",
"def _getVaersDescrReader():\n", "def _getVaersDescrReader():\n",
" return VaersDescrReader(dataDir = \"VAERS\")\n", " return VaersDescrReader(dataDir = \"VAERS\")\n",
@@ -1270,7 +1276,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"vaers = getVaersForYears([\"2020\", \"2021\", \"2022\"])\n", "vaers = getVaersForYears([2020, 2021, 2022])\n",
"vaers" "vaers"
] ]
}, },
@@ -1486,7 +1492,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"countries = sorted(CountryColumnAdder.getCountryColumn(nonDomesticVaers).unique())" "countries = sorted(internationalVaers['Country'].unique())"
] ]
}, },
{ {
@@ -1507,7 +1513,7 @@
"outputs": [], "outputs": [],
"source": [ "source": [
"createAndSaveAndDisplayBatchCodeTablesByCountry(\n", "createAndSaveAndDisplayBatchCodeTablesByCountry(\n",
" nonDomesticVaers,\n", " internationalVaers,\n",
" countries,\n", " countries,\n",
" minADRsForLethality = 100)" " minADRsForLethality = 100)"
] ]