francois/HowBadIsMyBatch
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showing combination of ALL doses

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frankknoll
2022-02-20 12:57:44 +01:00
parent 7d3664e213
commit 2e514149b6
2 changed files with 8 additions and 10 deletions
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2
docs/data/batchCodeTable.json
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File diff suppressed because one or more lines are too long

16
src/HowBadIsMyBatch.ipynb
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@@ -242,9 +242,8 @@
"class BatchCodeTableFactory:\n", "class BatchCodeTableFactory:\n",
"\n", "\n",
" @staticmethod\n", " @staticmethod\n",
" def createBatchCodeTable(dataFrame : pd.DataFrame, dose, minADRsForLethality = None):\n", " def createBatchCodeTable(dataFrame : pd.DataFrame, minADRsForLethality = None):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n", " dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" dataFrame = DataFrameFilter().filterBy(dataFrame, dose = dose)\n",
" batchCodeTable = BatchCodeTableFactory._createSummationTableByVAX_LOT(dataFrame)[\n", " batchCodeTable = BatchCodeTableFactory._createSummationTableByVAX_LOT(dataFrame)[\n",
" [\n", " [\n",
" 'Adverse Reaction Reports',\n", " 'Adverse Reaction Reports',\n",
@@ -917,7 +916,7 @@
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n", " }\n",
" ])\n", " ])\n",
" self._test_createBatchCodeTable(dataFrame, '1')\n", " self._test_createBatchCodeTable(dataFrame)\n",
"\n", "\n",
" def test_createBatchCodeTable_minADRsForLethality(self):\n", " def test_createBatchCodeTable_minADRsForLethality(self):\n",
" # Given\n", " # Given\n",
@@ -961,7 +960,7 @@
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n", " dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
"\n", "\n",
" # When\n", " # When\n",
" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, dose = '1', minADRsForLethality = 2)\n", " batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, minADRsForLethality = 2)\n",
"\n", "\n",
" # Then\n", " # Then\n",
" batchCodeTableExpected = pd.DataFrame(\n", " batchCodeTableExpected = pd.DataFrame(\n",
@@ -980,13 +979,13 @@
" 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, '1')\n", " self._test_createBatchCodeTable(dataFrame)\n",
"\n", "\n",
" def _test_createBatchCodeTable(self, dataFrame, dose):\n", " def _test_createBatchCodeTable(self, dataFrame):\n",
" dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n", " dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
"\n", "\n",
" # When\n", " # When\n",
" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, dose)\n", " batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame)\n",
"\n", "\n",
" # Then\n", " # Then\n",
" batchCodeTableExpected = pd.DataFrame(\n", " batchCodeTableExpected = pd.DataFrame(\n",
@@ -1263,8 +1262,7 @@
"source": [ "source": [
"def saveBatchCodeTable(vaers, file):\n", "def saveBatchCodeTable(vaers, file):\n",
" # FK-TODO: show \"Severe Reports\"\n", " # FK-TODO: show \"Severe Reports\"\n",
" # FK-TODO: show combination of ALL doses\n", " batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(vaers, minADRsForLethality = 100)\n",
" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(vaers, dose = '1', minADRsForLethality = 100)\n",
" batchCodeTable.index.set_names(\"Batch\", inplace = True)\n", " batchCodeTable.index.set_names(\"Batch\", inplace = True)\n",
" display(batchCodeTable)\n", " display(batchCodeTable)\n",
" IOUtils.saveDataFrame(batchCodeTable, file)" " IOUtils.saveDataFrame(batchCodeTable, file)"