HowBadIsMyBatch/src/HowBadIsMyBatch.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9de5907f-18f5-4cb1-903e-26028ff1fa03",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "\n",
    "pd.set_option('display.max_rows', 100)\n",
    "pd.set_option('display.max_columns', None)\n",
    "\n",
    "import os\n",
    "from VAERSFileDownloader import updateVAERSFiles\n",
    "from datetime import datetime\n",
    "from DateProvider import DateProvider\n",
    "from InternationalVaersCovid19Provider import getInternationalVaersCovid19, get_international_VAERSVAX_VAERSSYMPTOMS_Covid19\n",
    "from BatchCodeTableHtmlUpdater import updateBatchCodeTableHtmlFile\n",
    "from BatchCodeTablePersister import createAndSaveBatchCodeTables\n",
    "from SymptomByBatchcodeTableFactory import SymptomByBatchcodeTableFactory\n",
    "from HistogramFactoryAndPersister import createAndSaveGlobalHistograms, createAndSaveHistogramsForCountries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d1e4fa9e",
   "metadata": {},
   "outputs": [],
   "source": [
    "print(datetime.now().strftime(\"%d.%m.%Y, %H:%M:%S Uhr\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ffad1c04",
   "metadata": {},
   "outputs": [],
   "source": [
    "dateProvider = DateProvider()\n",
    "print('          lastUpdated:', dateProvider.getLastUpdated())\n",
    "print('lastUpdatedDataSource:', dateProvider.getLastUpdatedDataSource())\n",
    "needsUpdate = dateProvider.needsUpdate()\n",
    "print('needsUpdate:', needsUpdate)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "194b7357",
   "metadata": {},
   "outputs": [],
   "source": [
    "years_from_start_of_COVID_vaccination_to_present = list(range(2020, datetime.now().year + 1))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a793dff0",
   "metadata": {},
   "outputs": [],
   "source": [
    "updateVAERSFiles(\n",
    "        years = years_from_start_of_COVID_vaccination_to_present,\n",
    "        workingDirectory = os.getcwd())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "58333a19",
   "metadata": {},
   "outputs": [],
   "source": [
    "international_VAERSVAX_Covid19, international_VAERSSYMPTOMS = get_international_VAERSVAX_VAERSSYMPTOMS_Covid19(years = years_from_start_of_COVID_vaccination_to_present)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f10b558f",
   "metadata": {},
   "outputs": [],
   "source": [
    "international_VAERSVAX_Covid19"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3e0908fe",
   "metadata": {},
   "outputs": [],
   "source": [
    "international_VAERSSYMPTOMS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "204af94d",
   "metadata": {},
   "outputs": [],
   "source": [
    "symptomByBatchcodeTable = SymptomByBatchcodeTableFactory.createSymptomByBatchcodeTable(international_VAERSVAX_Covid19, international_VAERSSYMPTOMS)\n",
    "symptomByBatchcodeTable"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "23731536",
   "metadata": {},
   "outputs": [],
   "source": [
    "createAndSaveGlobalHistograms(symptomByBatchcodeTable)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f8e42955",
   "metadata": {},
   "outputs": [],
   "source": [
    "createAndSaveHistogramsForCountries(symptomByBatchcodeTable)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "781ac80e",
   "metadata": {},
   "outputs": [],
   "source": [
    "internationalVaersCovid19 = getInternationalVaersCovid19(years = years_from_start_of_COVID_vaccination_to_present)\n",
    "internationalVaersCovid19"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8d6507ca",
   "metadata": {},
   "outputs": [],
   "source": [
    "updateBatchCodeTableHtmlFile(internationalVaersCovid19, batchCodeTableHtmlFile=\"../docs/batchCodeTable.html\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0915aa5a",
   "metadata": {},
   "outputs": [],
   "source": [
    "createAndSaveBatchCodeTables(\n",
    "    internationalVaersCovid19,\n",
    "    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')"
   ]
  }
 ],
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