francois/HowBadIsMyBatch
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refactoring

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frankknoll
2022-02-08 19:30:42 +01:00
parent 55f8f2c2ee
commit cfd44b6d8c
1 changed files with 46 additions and 41 deletions
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87
HowBadIsMyBatch.ipynb
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@@ -910,15 +910,42 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"def saveBatchCodeTable(manufacturer, excelFile):\n", "def getVaers(vaersDescrsReaderFunc):\n",
" vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n", " vaersDescrs = vaersDescrsReaderFunc()\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" DataFrameNormalizer.normalize(dataFrame)\n", " DataFrameNormalizer.normalize(dataFrame)\n",
" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, manufacturer = manufacturer, dose = '1')\n", " return dataFrame\n",
" \n",
"def getAllVaers():\n",
" return getVaers(VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs)\n",
"\n",
"def getNonDomesticVaers():\n",
" return getVaers(lambda: [VaersDescrReader(dataDir = 'VAERS').readNonDomesticVaersDescr()])\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e15bdcc0",
"metadata": {},
"outputs": [],
"source": [
"def saveBatchCodeTable(vaers, manufacturer, excelFile):\n",
" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(vaers, manufacturer = manufacturer, dose = '1')\n",
" display(batchCodeTable)\n", " display(batchCodeTable)\n",
" saveDataFrameAsExcelFile(batchCodeTable, excelFile)" " saveDataFrameAsExcelFile(batchCodeTable, excelFile)"
] ]
}, },
{
"cell_type": "code",
"execution_count": null,
"id": "9ee014eb",
"metadata": {},
"outputs": [],
"source": [
"vaers = getAllVaers()"
]
},
{ {
"cell_type": "markdown", "cell_type": "markdown",
"id": "987a04d1", "id": "987a04d1",
@@ -935,7 +962,7 @@
"outputs": [], "outputs": [],
"source": [ "source": [
"# https://www.howbadismybatch.com/moderna.html\n", "# https://www.howbadismybatch.com/moderna.html\n",
"saveBatchCodeTable(\"MODERNA\", \"results/batchCodes/moderna.xlsx\")" "saveBatchCodeTable(vaers, \"MODERNA\", \"results/batchCodes/moderna.xlsx\")"
] ]
}, },
{ {
@@ -954,7 +981,7 @@
"outputs": [], "outputs": [],
"source": [ "source": [
"# https://www.howbadismybatch.com/pfizer.html\n", "# https://www.howbadismybatch.com/pfizer.html\n",
"saveBatchCodeTable(\"PFIZER\\BIONTECH\", \"results/batchCodes/pfizer.xlsx\")" "saveBatchCodeTable(vaers, \"PFIZER\\BIONTECH\", \"results/batchCodes/pfizer.xlsx\")"
] ]
}, },
{ {
@@ -973,7 +1000,7 @@
"outputs": [], "outputs": [],
"source": [ "source": [
"# https://www.howbadismybatch.com/janssen.html\n", "# https://www.howbadismybatch.com/janssen.html\n",
"saveBatchCodeTable(\"JANSSEN\", \"results/batchCodes/janssen.xlsx\")" "saveBatchCodeTable(vaers, \"JANSSEN\", \"results/batchCodes/janssen.xlsx\")"
] ]
}, },
{ {
@@ -991,11 +1018,8 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"def saveSevereEffectsBatchCodeTable(excelFile):\n", "def saveSevereEffectsBatchCodeTable(vaers, excelFile):\n",
" vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n", " severeEffectsBatchCodeTable = BatchCodeTableFactory.createSevereEffectsBatchCodeTable(vaers, dose = '1')\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" DataFrameNormalizer.normalize(dataFrame)\n",
" severeEffectsBatchCodeTable = BatchCodeTableFactory.createSevereEffectsBatchCodeTable(dataFrame, dose = '1')\n",
" display(severeEffectsBatchCodeTable)\n", " display(severeEffectsBatchCodeTable)\n",
" saveDataFrameAsExcelFile(severeEffectsBatchCodeTable, excelFile)" " saveDataFrameAsExcelFile(severeEffectsBatchCodeTable, excelFile)"
] ]
@@ -1007,7 +1031,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"saveSevereEffectsBatchCodeTable('results/severeEffects.xlsx')" "saveSevereEffectsBatchCodeTable(vaers, 'results/severeEffects.xlsx')"
] ]
}, },
{ {
@@ -1026,28 +1050,7 @@
"outputs": [], "outputs": [],
"source": [ "source": [
"# https://www.howbadismybatch.com/firstsecond.html\n", "# https://www.howbadismybatch.com/firstsecond.html\n",
"\n", "DoseTableFactory.createDoseTable(vaers)"
"def createDoseTable():\n",
" vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" DataFrameNormalizer.normalize(dataFrame)\n",
" return DoseTableFactory.createDoseTable(dataFrame)\n",
"\n",
"def createDoseByMonthTable():\n",
" vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" DataFrameNormalizer.normalize(dataFrame)\n",
" return DoseTableFactory.createDoseByMonthTable(dataFrame)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "394fa19d",
"metadata": {},
"outputs": [],
"source": [
"createDoseTable()"
] ]
}, },
{ {
@@ -1057,7 +1060,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"doseByMonthTable = createDoseByMonthTable()\n", "doseByMonthTable = DoseTableFactory.createDoseByMonthTable(vaers)\n",
"saveDataFrameAsExcelFile(doseByMonthTable, 'results/firstsecond/doseByMonthTable.xlsx')\n", "saveDataFrameAsExcelFile(doseByMonthTable, 'results/firstsecond/doseByMonthTable.xlsx')\n",
"doseByMonthTable" "doseByMonthTable"
] ]
@@ -1079,12 +1082,6 @@
"source": [ "source": [
"# https://www.howbadismybatch.com/international.html\n", "# https://www.howbadismybatch.com/international.html\n",
"\n", "\n",
"def getNonDomesticVaers():\n",
" vaersDescr = VaersDescrReader(dataDir = 'VAERS').readNonDomesticVaersDescr()\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescr(vaersDescr)\n",
" DataFrameNormalizer.normalize(dataFrame)\n",
" return dataFrame\n",
"\n",
"nonDomesticVaers = getNonDomesticVaers()" "nonDomesticVaers = getNonDomesticVaers()"
] ]
}, },
@@ -1152,6 +1149,14 @@
" 'Australia'\n", " 'Australia'\n",
" ])" " ])"
] ]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ea8e4d13",
"metadata": {},
"outputs": [],
"source": []
} }
], ],
"metadata": { "metadata": {