francois/HowBadIsMyBatch
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refactoring

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frankknoll
2022-02-01 08:33:24 +01:00
parent 360cbb3b25
commit b025bf2aae
1 changed files with 35 additions and 28 deletions
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63
HowBadIsMyBatch.ipynb
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@@ -21,34 +21,41 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"def read_csv(file, usecols, dtype = {}):\n", "import pandas as pd\n",
" return pd.read_csv(\n",
" file,\n",
" index_col = 'VAERS_ID',\n",
" encoding = 'latin1',\n",
" low_memory = False,\n",
" usecols = usecols,\n",
" dtype = dtype)\n",
"\n", "\n",
"def readVaersDescr(dataDir, year):\n", "class VaersDescrReader:\n",
" folder = dataDir + \"/\" + year + \"VAERSData/\"\n", " \n",
" return {\n", " def __init__(self, dataDir):\n",
" 'VAERSDATA':\n", " self.dataDir = dataDir \n",
" read_csv(\n",
" folder + year + \"VAERSDATA.csv\",\n",
" ['VAERS_ID', 'DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT']),\n",
" 'VAERSVAX':\n",
" read_csv(\n",
" folder + year + \"VAERSVAX.csv\",\n",
" ['VAERS_ID', 'VAX_DOSE_SERIES', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT'],\n",
" dtype = {\"VAX_DOSE_SERIES\": \"string\"})\n",
" }\n",
"\n", "\n",
"def readVaersDescrs(dataDir, years):\n", " def readAllVaersDescrs(self):\n",
" return [readVaersDescr(dataDir, year) for year in years]\n", " return self.readVaersDescrs([\"2021\", \"2022\"])\n",
" \n",
" def readVaersDescrs(self, years):\n",
" return [self.readVaersDescr(year) for year in years]\n",
"\n", "\n",
"def readAllVaersDescrs(dataDir):\n", " def readVaersDescr(self, year):\n",
" return readVaersDescrs(dataDir, [\"2021\", \"2022\"])" " folder = self.dataDir + \"/\" + year + \"VAERSData/\"\n",
" return {\n",
" 'VAERSDATA':\n",
" self._read_csv(\n",
" folder + year + \"VAERSDATA.csv\",\n",
" ['VAERS_ID', 'DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT']),\n",
" 'VAERSVAX':\n",
" self._read_csv(\n",
" folder + year + \"VAERSVAX.csv\",\n",
" ['VAERS_ID', 'VAX_DOSE_SERIES', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT'],\n",
" dtype = {\"VAX_DOSE_SERIES\": \"string\"})\n",
" }\n",
"\n",
" def _read_csv(self, file, usecols, dtype = {}):\n",
" return pd.read_csv(\n",
" file,\n",
" index_col = 'VAERS_ID',\n",
" encoding = 'latin1',\n",
" low_memory = False,\n",
" usecols = usecols,\n",
" dtype = dtype)\n"
] ]
}, },
{ {
@@ -383,7 +390,7 @@
" self._test_createBatchCodeTable(\n", " self._test_createBatchCodeTable(\n",
" filterDataFrame(\n", " filterDataFrame(\n",
" createDataFrameFromDescrs(\n", " createDataFrameFromDescrs(\n",
" readAllVaersDescrs(\"test/VAERS\")),\n", " VaersDescrReader(\"test/VAERS\").readAllVaersDescrs()),\n",
" manufacturer = \"MODERNA\",\n", " manufacturer = \"MODERNA\",\n",
" dose = '1'))\n", " dose = '1'))\n",
"\n", "\n",
@@ -484,7 +491,7 @@
" batchCodeTable = createBatchCodeTable(\n", " batchCodeTable = createBatchCodeTable(\n",
" filterDataFrame(\n", " filterDataFrame(\n",
" createDataFrameFromDescrs(\n", " createDataFrameFromDescrs(\n",
" readAllVaersDescrs(\"VAERS\")),\n", " VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n",
" manufacturer = manufacturer,\n", " manufacturer = manufacturer,\n",
" dose = '1'))\n", " dose = '1'))\n",
" display(manufacturer, batchCodeTable)\n", " display(manufacturer, batchCodeTable)\n",
@@ -514,7 +521,7 @@
" severeEffectsBatchCodeTable = createSevereEffectsBatchCodeTable(\n", " severeEffectsBatchCodeTable = createSevereEffectsBatchCodeTable(\n",
" filterDataFrameForSevereEffects(\n", " filterDataFrameForSevereEffects(\n",
" createDataFrameFromDescrs(\n", " createDataFrameFromDescrs(\n",
" readAllVaersDescrs(\"VAERS\")),\n", " VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n",
" dose = '1'))\n", " dose = '1'))\n",
" display('severeEffectsBatchCodeTable', severeEffectsBatchCodeTable)\n", " display('severeEffectsBatchCodeTable', severeEffectsBatchCodeTable)\n",
" severeEffectsBatchCodeTable.to_excel(excelFile)" " severeEffectsBatchCodeTable.to_excel(excelFile)"