francois/HowBadIsMyBatch
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

combining batch code tables of all companies

Browse Source
This commit is contained in:
frankknoll
2022-02-12 21:06:49 +01:00
parent e7ae087108
commit 732c273095
7 changed files with 24 additions and 105 deletions
Download Patch File Download Diff File Expand all files Collapse all files

73
src/HowBadIsMyBatch.ipynb
View File

@@ -228,10 +228,10 @@
"class BatchCodeTableFactory:\n",
"\n",
" @staticmethod\n",
" def createBatchCodeTable(dataFrame : pd.DataFrame, manufacturer, dose):\n",
" def createBatchCodeTable(dataFrame : pd.DataFrame, dose):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" dataFrame = DataFrameFilter().filterBy(dataFrame, manufacturer = manufacturer, dose = dose)\n",
" return BatchCodeTableFactory._createSummationTableByVAX_LOT(dataFrame)[['ADRs', 'DEATHS', 'DISABILITIES', 'LIFE THREATENING ILLNESSES']]\n",
" dataFrame = DataFrameFilter().filterBy(dataFrame, dose = dose)\n",
" return BatchCodeTableFactory._createSummationTableByVAX_LOT(dataFrame)[['ADRs', 'DEATHS', 'DISABILITIES', 'LIFE THREATENING ILLNESSES', 'COMPANY']]\n",
"\n",
" # create table from https://www.howbadismybatch.com/combined.html\n",
" @staticmethod\n",
@@ -740,17 +740,17 @@
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n",
" ])\n",
" self._test_createBatchCodeTable(dataFrame, \"MODERNA\", '1')\n",
" self._test_createBatchCodeTable(dataFrame, '1')\n",
"\n",
" def test_createBatchCodeTable(self):\n",
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescrReader(dataDir = \"test/VAERS\").readAllVaersDescrs())\n",
" DataFrameNormalizer.normalize(dataFrame)\n",
" self._test_createBatchCodeTable(dataFrame, \"MODERNA\", '1')\n",
" self._test_createBatchCodeTable(dataFrame, '1')\n",
"\n",
" def _test_createBatchCodeTable(self, dataFrame, manufacturer, dose):\n",
" def _test_createBatchCodeTable(self, dataFrame, dose):\n",
" # When\n",
" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, manufacturer, dose)\n",
" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, dose)\n",
"\n",
" # Then\n",
" batchCodeTableExpected = pd.DataFrame(\n",
@@ -758,7 +758,8 @@
" 'ADRs': [2, 1],\n",
" 'DEATHS': [0, 1],\n",
" 'DISABILITIES': [2, 0],\n",
" 'LIFE THREATENING ILLNESSES': [0, 0]\n",
" 'LIFE THREATENING ILLNESSES': [0, 0],\n",
" 'COMPANY': ['MODERNA', 'MODERNA']\n",
" },\n",
" index = pd.Index(['025L20A', '037K20A'], name = 'VAX_LOT'))\n",
" assert_frame_equal(batchCodeTable, batchCodeTableExpected, check_dtype = False)\n"
@@ -961,8 +962,8 @@
"metadata": {},
"outputs": [],
"source": [
"def saveBatchCodeTable(vaers, manufacturer, file):\n",
" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(vaers, manufacturer = manufacturer, dose = '1')\n",
"def saveBatchCodeTable(vaers, file):\n",
" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(vaers, dose = '1')\n",
" display(batchCodeTable)\n",
" IOUtils.saveDataFrame(batchCodeTable, file)"
]
@@ -997,22 +998,12 @@
"internationalVaers = getInternationalVaers()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f74475e8",
"metadata": {},
"outputs": [],
"source": [
"internationalVaers"
]
},
{
"cell_type": "markdown",
"id": "987a04d1",
"metadata": {},
"source": [
"### Moderna batch codes"
"### Batch codes"
]
},
{
@@ -1023,45 +1014,7 @@
"outputs": [],
"source": [
"# https://www.howbadismybatch.com/moderna.html\n",
"saveBatchCodeTable(internationalVaers, \"MODERNA\", \"../data/moderna\")"
]
},
{
"cell_type": "markdown",
"id": "29dd4daa",
"metadata": {},
"source": [
"### Pfizer batch codes"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6121e2b3",
"metadata": {},
"outputs": [],
"source": [
"# https://www.howbadismybatch.com/pfizer.html\n",
"saveBatchCodeTable(internationalVaers, \"PFIZER\\BIONTECH\", \"../data/pfizer\")"
]
},
{
"cell_type": "markdown",
"id": "7e83a551",
"metadata": {},
"source": [
"### Janssen batch codes"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "1a64eef5",
"metadata": {},
"outputs": [],
"source": [
"# https://www.howbadismybatch.com/janssen.html\n",
"saveBatchCodeTable(internationalVaers, \"JANSSEN\", \"../data/janssen\")"
"saveBatchCodeTable(internationalVaers, \"../data/batchCodeTable\")"
]
},
{