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Merge branch 'VaccineDistributionByZipcode' into pages

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frankknoll
2023-03-10 22:09:15 +01:00
parent 513df2ce0e e3c6785513
commit 38baf5db3d
11 changed files with 249 additions and 146 deletions
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12
docs/VaccineDistributionByZipcode.html
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@@ -4,7 +4,7 @@
<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8" />
<meta content="width=device-width, initial-scale=1.0" name="viewport" /> <meta content="width=device-width, initial-scale=1.0" name="viewport" />
<title>Batch Codes of Coronavirus 2019 Vaccines</title> <title>Pfizer Vaccine Distribution by ZIP Code</title>
<link href="https://cdn.datatables.net/1.13.1/css/jquery.dataTables.css" rel="stylesheet" type="text/css" /> <link href="https://cdn.datatables.net/1.13.1/css/jquery.dataTables.css" rel="stylesheet" type="text/css" />
<link href="batchCodeTable.css" rel="stylesheet" type="text/css" /> <link href="batchCodeTable.css" rel="stylesheet" type="text/css" />
<link href="forkMeOnGitHub.css" rel="stylesheet" type="text/css" /> <link href="forkMeOnGitHub.css" rel="stylesheet" type="text/css" />
@@ -28,14 +28,14 @@
<body> <body>
<span id="forkongithub"><a href="https://github.com/KnollFrank/HowBadIsMyBatch">Fork me on GitHub</a></span> <span id="forkongithub"><a href="https://github.com/KnollFrank/HowBadIsMyBatch">Fork me on GitHub</a></span>
<h1>Batch Codes of Coronavirus 2019 Vaccines</h1> <h1>Pfizer Vaccine Distribution by ZIP Code</h1>
<table class="display" id="vaccineDistributionByZipcodeTable"> <table class="display" id="vaccineDistributionByZipcodeTable">
<thead> <thead>
<tr> <tr>
<th>PROVIDER_NAME</th> <th>Provider</th>
<th>ZIPCODE_SHP</th> <th>ZIP Code</th>
<th>LOT_NUMBER</th> <th>Lot Number</th>
<th>DOSES_SHIPPED</th> <th>Summary</th>
</tr> </tr>
</thead> </thead>
</table> </table>

48
docs/VaccineDistributionByZipcodeTableInitializer.js
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@@ -1,42 +1,39 @@
class VaccineDistributionByZipcodeTableInitializer { class VaccineDistributionByZipcodeTableInitializer {
#tableElement; #tableElement;
#table;
constructor({ tableElement }) { constructor({ tableElement }) {
this.#tableElement = tableElement; this.#tableElement = tableElement;
} }
initialize() { initialize() {
this.#table = this.#createEmptyTable(); this.#createTable();
this.#loadDataIntoTable(); this.#selectInput();
} }
#createEmptyTable() { #createTable() {
return this.#tableElement.DataTable( this.#tableElement.DataTable(
{ {
language:
{
searchPlaceholder: "Enter Batch Code"
},
search: search:
{ {
return: false return: false
}, },
ajax: 'data/vaccineDistributionByZipcode/VaccineDistributionByZipcode.json',
processing: true, processing: true,
deferRender: true, deferRender: true,
columnDefs: columnDefs:
[ [
{ {
searchable: false, searchable: false,
targets: [this.#getColumnIndex('DOSES_SHIPPED')] orderable: false,
targets: [this.#getColumnIndex('Summary')]
}, },
{ {
searchable: true, searchable: true,
targets: [ targets: [
this.#getColumnIndex('PROVIDER_NAME'), this.#getColumnIndex('Provider'),
this.#getColumnIndex('ZIPCODE_SHP'), this.#getColumnIndex('ZIP Code'),
this.#getColumnIndex('LOT_NUMBER'), this.#getColumnIndex('Lot Number'),
] ]
}, },
] ]
@@ -45,34 +42,17 @@ class VaccineDistributionByZipcodeTableInitializer {
#getColumnIndex(columnName) { #getColumnIndex(columnName) {
switch (columnName) { switch (columnName) {
case 'PROVIDER_NAME': case 'Provider':
return 0; return 0;
case 'ZIPCODE_SHP': case 'ZIP Code':
return 1; return 1;
case 'LOT_NUMBER': case 'Lot Number':
return 2; return 2;
case 'DOSES_SHIPPED': case 'Summary':
return 3; return 3;
} }
} }
#loadDataIntoTable() {
// FK-TODO: show "Loading.." message or spinning wheel.
fetch('data/vaccineDistributionByZipcode/VaccineDistributionByZipcode.json')
.then(response => response.json())
.then(json => {
this.#setTableRows(json.data);
this.#selectInput();
});
}
#setTableRows(rows) {
this.#table
.clear()
.rows.add(rows)
.draw();
}
#selectInput() { #selectInput() {
const input = document.querySelector(".dataTables_filter input"); const input = document.querySelector(".dataTables_filter input");
input.focus(); input.focus();

2
docs/data/vaccineDistributionByZipcode/VaccineDistributionByZipcode.json
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File diff suppressed because one or more lines are too long

15
src/ADRColumnAdder.py Normal file
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@@ -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')

5
src/ADR_by_Batchcode_Table_Factory.py Normal file
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@@ -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']]

150
src/HowBadIsMyBatch.ipynb
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@@ -163,6 +163,156 @@
" minADRsForLethality = 100,\n", " minADRsForLethality = 100,\n",
" onCountryProcessed = display)" " 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",
" dtype = {'DOSES_SHIPPED': 'int'})\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": "8cd250f7",
"metadata": {},
"outputs": [],
"source": [
"OVERALL_DOSES_SHIPPED_by_LOT_NUMBER = vaccineDistributionByZipcode.groupby('LOT_NUMBER').agg(OVERALL_DOSES_SHIPPED = pd.NamedAgg(column = 'DOSES_SHIPPED', aggfunc = sum))\n",
"OVERALL_DOSES_SHIPPED_by_LOT_NUMBER"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "1a5667be",
"metadata": {},
"outputs": [],
"source": [
"from OVERALL_DOSES_SHIPPEDColumnAdder import OVERALL_DOSES_SHIPPEDColumnAdder\n",
"\n",
"vaccineDistributionByZipcode = OVERALL_DOSES_SHIPPEDColumnAdder(OVERALL_DOSES_SHIPPED_by_LOT_NUMBER).addColumn(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": "3276cce7",
"metadata": {},
"outputs": [],
"source": [
"def summarize(row):\n",
" ADRs = row['DOSES_SHIPPED'] / row['OVERALL_DOSES_SHIPPED'] * row['Adverse Reaction Reports']\n",
" return f\"{row['DOSES_SHIPPED']} (out of {row['OVERALL_DOSES_SHIPPED']}) shipped doses are statistically responsible for <b>{ADRs:.2f}</b> (out of {row['Adverse Reaction Reports']}) adverse reaction reports\"\n",
"\n",
"vaccineDistributionByZipcode['Summary'] = vaccineDistributionByZipcode.apply(summarize, axis = 'columns')\n",
"vaccineDistributionByZipcode"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "10cf731f",
"metadata": {},
"outputs": [],
"source": [
"vaccineDistributionByZipcode = vaccineDistributionByZipcode[['PROVIDER_NAME', 'ZIPCODE_SHP', 'LOT_NUMBER', 'Summary']]\n",
"vaccineDistributionByZipcode"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0c2020e9",
"metadata": {},
"outputs": [],
"source": [
"vaccineDistributionByZipcode = vaccineDistributionByZipcode.rename(\n",
" columns = {\n",
" 'PROVIDER_NAME': 'Provider',\n",
" 'ZIPCODE_SHP': 'ZIP Code',\n",
" 'LOT_NUMBER': 'Lot Number'\n",
" })\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": { "metadata": {

16
src/OVERALL_DOSES_SHIPPEDColumnAdder.py Normal file
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@@ -0,0 +1,16 @@
import pandas as pd
# FK-TODO: DRY with ADRColumnAdder
class OVERALL_DOSES_SHIPPEDColumnAdder:
def __init__(self, OVERALL_DOSES_SHIPPED_by_LOT_NUMBER):
self.OVERALL_DOSES_SHIPPED_by_LOT_NUMBER = OVERALL_DOSES_SHIPPED_by_LOT_NUMBER
def addColumn(self, vaccineDistributionByZipcode):
return pd.merge(
vaccineDistributionByZipcode,
self.OVERALL_DOSES_SHIPPED_by_LOT_NUMBER,
how = 'left',
left_on = 'LOT_NUMBER',
right_index = True,
validate = 'many_to_one')

4
src/TestHelper.py
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@@ -4,5 +4,5 @@ import pandas as pd
class TestHelper: class TestHelper:
@staticmethod @staticmethod
def createDataFrame(index, columns, data, dtypes={}): def createDataFrame(columns, data, dtypes={}, **kwargs):
return pd.DataFrame(index=index, columns=columns, data=data).astype(dtypes) return pd.DataFrame(columns=columns, data=data, **kwargs).astype(dtypes)

103
src/VaccineDistributionByZipcode.ipynb
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@@ -1,103 +0,0 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import pandas as pd\n",
"\n",
"vaccineDistributionByZipcode = pd.read_excel('tmp/Amended-22-01962-Pfizer-2022-0426-pulled-2022-0823_edited.xlsx')\n",
"vaccineDistributionByZipcode"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"len(vaccineDistributionByZipcode['PROVIDER_NAME'].unique())"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"len(vaccineDistributionByZipcode['ZIPCODE_SHP'].unique())"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"vaccineDistributionByZipcode['AWARDEE'].unique()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"vaccineDistributionByZipcode['STATE_SHP'].unique()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"vaccineDistributionByZipcode[vaccineDistributionByZipcode['ZIPCODE_SHP'] == '37801']"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from IOUtils import IOUtils\n",
"\n",
"IOUtils.saveDataFrameAsJson(vaccineDistributionByZipcode, '../docs/data/vaccineDistributionByZipcode/VaccineDistributionByZipcode.json')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"IOUtils.saveDataFrameAsHtml(vaccineDistributionByZipcode, '../docs/data/vaccineDistributionByZipcode/VaccineDistributionByZipcode.html')"
]
}
],
"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
}

10
src/VaccineDistributionByZipcodeSimplifier.py Normal file
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@@ -0,0 +1,10 @@
import pandas as pd
class VaccineDistributionByZipcodeSimplifier:
@staticmethod
def sumDoses(vaccineDistributionByZipcode):
return (vaccineDistributionByZipcode
.groupby(['PROVIDER_NAME', 'ZIPCODE_SHP', 'LOT_NUMBER'])
.agg(DOSES_SHIPPED = pd.NamedAgg(column = 'DOSES_SHIPPED', aggfunc = sum))
.reset_index())

30
src/VaccineDistributionByZipcodeSimplifierTest.py Normal file
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@@ -0,0 +1,30 @@
import unittest
from VaccineDistributionByZipcodeSimplifier import VaccineDistributionByZipcodeSimplifier
from TestHelper import TestHelper
from pandas.testing import assert_frame_equal
import pandas as pd
class VaccineDistributionByZipcodeSimplifierTest(unittest.TestCase):
def test_sumDoses(self):
# Given
doses_shipped1 = 300.0
doses_shipped2 = 400.0
vaccineDistributionByZipcode = TestHelper.createDataFrame(
columns = ['PROVIDER_NAME', 'ZIPCODE_SHP', 'LOT_NUMBER', 'DOSES_SHIPPED'],
data = [ ['@PHARMACY.COM', '97206-2314', 'FK9893', 300.0],
['@PHARMACY.COM - 82ND AVE', '97266-4885', 'FK9893', doses_shipped1],
['@PHARMACY.COM - 82ND AVE', '97266-4885', 'FK9893', doses_shipped2],
['@PHARMACY.COM - 82ND AVE', '97266-4885', 'FL8095', 200.0]])
# When
vaccineDistributionByZipcodeSimplified = VaccineDistributionByZipcodeSimplifier.sumDoses(vaccineDistributionByZipcode)
# Then
assert_frame_equal(
vaccineDistributionByZipcodeSimplified,
TestHelper.createDataFrame(
columns = ['PROVIDER_NAME', 'ZIPCODE_SHP', 'LOT_NUMBER', 'DOSES_SHIPPED'],
data = [ ['@PHARMACY.COM', '97206-2314', 'FK9893', 300.0],
['@PHARMACY.COM - 82ND AVE', '97266-4885', 'FK9893', doses_shipped1 + doses_shipped2],
['@PHARMACY.COM - 82ND AVE', '97266-4885', 'FL8095', 200.0]]))