392 lines
11 KiB
Plaintext
392 lines
11 KiB
Plaintext
{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "9de5907f-18f5-4cb1-903e-26028ff1fa03",
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"metadata": {},
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"outputs": [],
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"source": [
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"import pandas as pd\n",
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"\n",
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"pd.set_option('display.max_rows', 100)\n",
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"pd.set_option('display.max_columns', None)\n",
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"\n",
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"import os\n",
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"from IOUtils import IOUtils\n",
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"from VAERSFileDownloader import updateVAERSFiles\n",
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"from datetime import datetime\n",
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"from DateProvider import DateProvider\n",
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"from InternationalVaersCovid19Provider import getInternationalVaersCovid19, get_international_VAERSVAX_VAERSSYMPTOMS_Covid19\n",
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"from BatchCodeTableHtmlUpdater import updateBatchCodeTableHtmlFile, saveLastUpdatedBatchCodeTable\n",
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"from BatchCodeTablePersister import createGlobalBatchCodeTable\n",
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"from SymptomByBatchcodeTableFactory import SymptomByBatchcodeTableFactory\n",
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"from HistogramFactoryAndPersister import createAndSaveGlobalHistograms\n",
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"from BatchCodeTableFactory import BatchCodeTableFactory\n",
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"from Column2DataframeAdder import addColumn2Dataframe\n",
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"from CountriesByBatchcodeProvider import getCountryCountsByBatchcodeTable\n",
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"from CountryCountsByBatchcodeTable2BarChartDescriptionTableConverter import CountryCountsByBatchcodeTable2BarChartDescriptionTableConverter\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "d1e4fa9e",
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"metadata": {},
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"outputs": [],
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"source": [
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"print(datetime.now().strftime(\"%d.%m.%Y, %H:%M:%S Uhr\"))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "ffad1c04",
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"metadata": {},
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"outputs": [],
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"source": [
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"dateProvider = DateProvider()\n",
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"print(' lastUpdated:', dateProvider.getLastUpdated())\n",
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"print('lastUpdatedDataSource:', dateProvider.getLastUpdatedDataSource())\n",
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"needsUpdate = dateProvider.needsUpdate()\n",
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"print('needsUpdate:', needsUpdate)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "194b7357",
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"metadata": {},
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"outputs": [],
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"source": [
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"years_from_start_of_COVID_vaccination_to_present = list(range(2020, datetime.now().year + 1))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "a793dff0",
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"metadata": {},
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"outputs": [],
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"source": [
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"updateVAERSFiles(\n",
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" years = years_from_start_of_COVID_vaccination_to_present,\n",
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" workingDirectory = os.getcwd())"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "58333a19",
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"metadata": {},
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"outputs": [],
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"source": [
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"international_VAERSVAX_Covid19, international_VAERSSYMPTOMS = get_international_VAERSVAX_VAERSSYMPTOMS_Covid19(years = years_from_start_of_COVID_vaccination_to_present)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "f10b558f",
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"metadata": {},
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"outputs": [],
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"source": [
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"international_VAERSVAX_Covid19"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "3e0908fe",
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"metadata": {},
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"outputs": [],
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"source": [
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"international_VAERSSYMPTOMS"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "781ac80e",
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"metadata": {},
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"outputs": [],
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"source": [
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"internationalVaersCovid19 = getInternationalVaersCovid19(dataDir = 'VAERS', years = years_from_start_of_COVID_vaccination_to_present)\n",
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"internationalVaersCovid19"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "0915aa5a",
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"metadata": {},
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"outputs": [],
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"source": [
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"batchCodeTable = createGlobalBatchCodeTable(\n",
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" deleteEntriesWithADRsLessThanOrEqual = 2,\n",
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" minADRsForLethality = 100,\n",
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" batchCodeTableFactory = BatchCodeTableFactory(internationalVaersCovid19))\n",
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"batchCodeTable"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "d8e81ffc",
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"metadata": {},
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"outputs": [],
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"source": [
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"IOUtils.saveDataFrameAsJson(batchCodeTable, '../docs/data/batchCodeTables/Global.json')\n",
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"saveLastUpdatedBatchCodeTable(\n",
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" DateProvider().getLastUpdatedDataSource(),\n",
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" batchCodeTableHtmlFile=\"../docs/batchCodes.html\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "189a639e",
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"metadata": {},
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"outputs": [],
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"source": [
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"updateBatchCodeTableHtmlFile(batchCodeTable, batchCodeTableHtmlFile=\"../docs/HowBadIsMyBatch.html\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "19fa050b",
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"metadata": {},
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"outputs": [],
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"source": [
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"symptomByBatchcodeTable = SymptomByBatchcodeTableFactory.createSymptomByBatchcodeTable(\n",
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" VAERSVAX = international_VAERSVAX_Covid19[international_VAERSVAX_Covid19['VAX_LOT'].isin(batchCodeTable['Batch'])],\n",
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" VAERSSYMPTOMS = international_VAERSSYMPTOMS)\n",
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"symptomByBatchcodeTable"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "ec2a692e",
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"metadata": {},
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"outputs": [],
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"source": [
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"createAndSaveGlobalHistograms(symptomByBatchcodeTable, batchCodeTable)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "9588a10c",
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"metadata": {},
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"outputs": [],
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"source": [
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"countryCountsByBatchcode = getCountryCountsByBatchcodeTable()\n",
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"countryCountsByBatchcode"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "70fcc420",
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"metadata": {},
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"outputs": [],
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"source": [
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"countryCountsByBatchcode.to_excel('tmp/countryCountsByBatchcode.xlsx')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "7a67b1f6",
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"metadata": {},
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"outputs": [],
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"source": [
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"barChartDescriptionTable = CountryCountsByBatchcodeTable2BarChartDescriptionTableConverter.convert2BarChartDescriptionTable(countryCountsByBatchcode)\n",
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"barChartDescriptionTable"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "8e1b471a",
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"metadata": {},
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"outputs": [],
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"source": [
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"barChartDescriptionTable['BAR_CHART_DESCRIPTION'].to_json('../docs/data/barChartDescriptionTable.json')"
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]
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},
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{
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"attachments": {},
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"cell_type": "markdown",
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"id": "2d93b511",
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"metadata": {},
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"source": [
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"# Vaccine Distribution by Zipcode"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "cfcbad44",
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"metadata": {},
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"outputs": [],
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"source": [
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"vaccineDistributionByZipcode = pd.read_excel(\n",
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" io = 'data/Amended-22-01962-Pfizer-2022-0426-pulled-2022-0823.xlsx',\n",
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" usecols = ['PROVIDER_NAME', 'ZIPCODE_SHP', 'LOT_NUMBER', 'DOSES_SHIPPED'],\n",
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" dtype = {'DOSES_SHIPPED': 'int'})\n",
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"vaccineDistributionByZipcode"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "59c745d2",
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"metadata": {},
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"outputs": [],
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"source": [
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"from VaccineDistributionByZipcodeSimplifier import VaccineDistributionByZipcodeSimplifier\n",
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"\n",
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"vaccineDistributionByZipcode = VaccineDistributionByZipcodeSimplifier.sumDoses(vaccineDistributionByZipcode)\n",
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"vaccineDistributionByZipcode"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "8cd250f7",
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"metadata": {},
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"outputs": [],
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"source": [
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"OVERALL_DOSES_SHIPPED_by_LOT_NUMBER = vaccineDistributionByZipcode.groupby('LOT_NUMBER').agg(OVERALL_DOSES_SHIPPED = pd.NamedAgg(column = 'DOSES_SHIPPED', aggfunc = sum))\n",
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"OVERALL_DOSES_SHIPPED_by_LOT_NUMBER"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "1a5667be",
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"metadata": {},
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"outputs": [],
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"source": [
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"vaccineDistributionByZipcode = addColumn2Dataframe(dataframe = vaccineDistributionByZipcode, column = OVERALL_DOSES_SHIPPED_by_LOT_NUMBER)\n",
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"vaccineDistributionByZipcode"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "f77505c6",
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"metadata": {},
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"outputs": [],
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"source": [
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"from ADR_by_Batchcode_Table_Factory import create_ADR_by_Batchcode_Table_4USA\n",
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"\n",
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"ADR_by_Batchcode_Table_4USA = create_ADR_by_Batchcode_Table_4USA(internationalVaersCovid19)\n",
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"ADR_by_Batchcode_Table_4USA"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "99120c77",
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"metadata": {},
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"outputs": [],
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"source": [
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"vaccineDistributionByZipcode = addColumn2Dataframe(dataframe = vaccineDistributionByZipcode, column = ADR_by_Batchcode_Table_4USA)\n",
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"vaccineDistributionByZipcode"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "3276cce7",
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"metadata": {},
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"outputs": [],
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"source": [
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"vaccineDistributionByZipcode['Statistical Number of Adverse Reaction Reports'] = (vaccineDistributionByZipcode['DOSES_SHIPPED'] / vaccineDistributionByZipcode['OVERALL_DOSES_SHIPPED'] * vaccineDistributionByZipcode['Adverse Reaction Reports']).round(2)\n",
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"vaccineDistributionByZipcode['Statistical Number of Adverse Reaction Reports (per 100,000)'] = (vaccineDistributionByZipcode['DOSES_SHIPPED'] / vaccineDistributionByZipcode['OVERALL_DOSES_SHIPPED'] * 100000).round().astype(int)\n",
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"vaccineDistributionByZipcode"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "10cf731f",
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"metadata": {},
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"outputs": [],
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"source": [
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"vaccineDistributionByZipcode = vaccineDistributionByZipcode[['PROVIDER_NAME', 'ZIPCODE_SHP', 'LOT_NUMBER', 'DOSES_SHIPPED', 'Statistical Number of Adverse Reaction Reports', 'Statistical Number of Adverse Reaction Reports (per 100,000)']]\n",
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"vaccineDistributionByZipcode"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "0c2020e9",
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"metadata": {},
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"outputs": [],
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"source": [
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"vaccineDistributionByZipcode = vaccineDistributionByZipcode.rename(\n",
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" columns = {\n",
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" 'PROVIDER_NAME': 'Provider',\n",
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" 'ZIPCODE_SHP': 'ZIP Code',\n",
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" 'LOT_NUMBER': 'Lot Number',\n",
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" 'DOSES_SHIPPED': 'Doses Shipped'\n",
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" })\n",
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"vaccineDistributionByZipcode"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "f68c72d0",
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"metadata": {},
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"outputs": [],
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"source": [
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"# vaccineDistributionByZipcode.to_excel('tmp/Amended-22-01962-Pfizer-2022-0426-pulled-2022-0823_sumDoses.xlsx')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "9b8f0b6e",
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"metadata": {},
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"outputs": [],
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"source": [
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"from IOUtils import IOUtils\n",
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"\n",
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"IOUtils.saveDataFrameAsJson(vaccineDistributionByZipcode, '../docs/data/vaccineDistributionByZipcode/VaccineDistributionByZipcode.json')"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "howbadismybatch-venv-kernel",
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"language": "python",
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"name": "howbadismybatch-venv-kernel"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.15"
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},
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"vscode": {
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"interpreter": {
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"hash": "1bce2b9b19ce5f16d695ff75ac05095b3e564c169ff454b58b87cb796c0695b8"
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}
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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