From 3f38e066a5d16c376352d7dc14f74526ae5af2cc Mon Sep 17 00:00:00 2001 From: frankknoll Date: Fri, 10 Mar 2023 11:17:21 +0100 Subject: [PATCH] adding ADR column to vaccineDistributionByZipcode table --- src/ADRColumnAdder.py | 15 +++++ src/ADR_by_Batchcode_Table_Factory.py | 5 ++ src/HowBadIsMyBatch.ipynb | 83 ++++++++++++++++++++++++++ src/VaccineDistributionByZipcode.ipynb | 72 ---------------------- 4 files changed, 103 insertions(+), 72 deletions(-) create mode 100644 src/ADRColumnAdder.py create mode 100644 src/ADR_by_Batchcode_Table_Factory.py delete mode 100644 src/VaccineDistributionByZipcode.ipynb diff --git a/src/ADRColumnAdder.py b/src/ADRColumnAdder.py new file mode 100644 index 00000000000..259980fbbff --- /dev/null +++ b/src/ADRColumnAdder.py @@ -0,0 +1,15 @@ +import pandas as pd + +class ADRColumnAdder: + + def __init__(self, ADR_by_Batchcode): + self.ADR_by_Batchcode = ADR_by_Batchcode + + def addADRColumn(self, vaccineDistributionByZipcode): + return pd.merge( + vaccineDistributionByZipcode, + self.ADR_by_Batchcode, + how = 'left', + left_on = 'LOT_NUMBER', + right_index = True, + validate = 'many_to_one') diff --git a/src/ADR_by_Batchcode_Table_Factory.py b/src/ADR_by_Batchcode_Table_Factory.py new file mode 100644 index 00000000000..5b36504cda3 --- /dev/null +++ b/src/ADR_by_Batchcode_Table_Factory.py @@ -0,0 +1,5 @@ +from BatchCodeTableFactory import BatchCodeTableFactory + +def create_ADR_by_Batchcode_Table_4USA(internationalVaersCovid19): + batchCodeTable4USA = BatchCodeTableFactory(internationalVaersCovid19).createBatchCodeTableByCountry('United States') + return batchCodeTable4USA[['Adverse Reaction Reports']] diff --git a/src/HowBadIsMyBatch.ipynb b/src/HowBadIsMyBatch.ipynb index 5df524c3b91..437ab0d3f13 100644 --- a/src/HowBadIsMyBatch.ipynb +++ b/src/HowBadIsMyBatch.ipynb @@ -163,6 +163,89 @@ " minADRsForLethality = 100,\n", " onCountryProcessed = display)" ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "id": "2d93b511", + "metadata": {}, + "source": [ + "# Vaccine Distribution by Zipcode" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "cfcbad44", + "metadata": {}, + "outputs": [], + "source": [ + "vaccineDistributionByZipcode = pd.read_excel(\n", + " io = 'tmp/Amended-22-01962-Pfizer-2022-0426-pulled-2022-0823.xlsx',\n", + " usecols = ['PROVIDER_NAME', 'ZIPCODE_SHP', 'LOT_NUMBER', 'DOSES_SHIPPED'])\n", + "vaccineDistributionByZipcode" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "59c745d2", + "metadata": {}, + "outputs": [], + "source": [ + "from VaccineDistributionByZipcodeSimplifier import VaccineDistributionByZipcodeSimplifier\n", + "\n", + "vaccineDistributionByZipcode = VaccineDistributionByZipcodeSimplifier.sumDoses(vaccineDistributionByZipcode)\n", + "vaccineDistributionByZipcode" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f77505c6", + "metadata": {}, + "outputs": [], + "source": [ + "from ADR_by_Batchcode_Table_Factory import create_ADR_by_Batchcode_Table_4USA\n", + "\n", + "ADR_by_Batchcode_Table_4USA = create_ADR_by_Batchcode_Table_4USA(internationalVaersCovid19)\n", + "ADR_by_Batchcode_Table_4USA" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "99120c77", + "metadata": {}, + "outputs": [], + "source": [ + "from ADRColumnAdder import ADRColumnAdder\n", + "\n", + "vaccineDistributionByZipcode = ADRColumnAdder(ADR_by_Batchcode_Table_4USA).addADRColumn(vaccineDistributionByZipcode)\n", + "vaccineDistributionByZipcode" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f68c72d0", + "metadata": {}, + "outputs": [], + "source": [ + "vaccineDistributionByZipcode.to_excel('tmp/Amended-22-01962-Pfizer-2022-0426-pulled-2022-0823_sumDoses.xlsx')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9b8f0b6e", + "metadata": {}, + "outputs": [], + "source": [ + "from IOUtils import IOUtils\n", + "\n", + "IOUtils.saveDataFrameAsJson(vaccineDistributionByZipcode, '../docs/data/vaccineDistributionByZipcode/VaccineDistributionByZipcode.json')" + ] } ], "metadata": { diff --git a/src/VaccineDistributionByZipcode.ipynb b/src/VaccineDistributionByZipcode.ipynb deleted file mode 100644 index f89184752d4..00000000000 --- a/src/VaccineDistributionByZipcode.ipynb +++ /dev/null @@ -1,72 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "import pandas as pd\n", - "\n", - "vaccineDistributionByZipcode = pd.read_excel(\n", - " io = 'tmp/Amended-22-01962-Pfizer-2022-0426-pulled-2022-0823.xlsx',\n", - " usecols = ['PROVIDER_NAME', 'ZIPCODE_SHP', 'LOT_NUMBER', 'DOSES_SHIPPED'])\n", - "vaccineDistributionByZipcode" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from VaccineDistributionByZipcodeSimplifier import VaccineDistributionByZipcodeSimplifier\n", - "\n", - "vaccineDistributionByZipcode = VaccineDistributionByZipcodeSimplifier.sumDoses(vaccineDistributionByZipcode)\n", - "vaccineDistributionByZipcode" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "vaccineDistributionByZipcode.to_excel('tmp/Amended-22-01962-Pfizer-2022-0426-pulled-2022-0823_sumDoses.xlsx')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "from IOUtils import IOUtils\n", - "\n", - "IOUtils.saveDataFrameAsJson(vaccineDistributionByZipcode, '../docs/data/vaccineDistributionByZipcode/VaccineDistributionByZipcode.json')" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "howbadismybatch-venv-kernel", - "language": "python", - "name": "howbadismybatch-venv-kernel" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.8" - }, - "orig_nbformat": 4 - }, - "nbformat": 4, - "nbformat_minor": 2 -}