Merge branch 'remove-countries-from-UI' into pages

docs/GoogleAnalytics.js

@@ -1,34 +1,22 @@
 class GoogleAnalytics {
 
     static click_batchcode(batchcode) {
-        gtag(
+        // FK-TODO: uncomment
-            'event',
+        // gtag(
-            'click_batchcode',
+        //     'event',
-            {
+        //     'click_batchcode',
-                'batchcode': batchcode
+        //     {
-            });
+        //         'batchcode': batchcode
+        //     });
     }
 
     static view_search_results(search_term) {
-        gtag(
+        // FK-TODO: uncomment
-            'event',
+        // gtag(
-            'view_search_results',
+        //     'event',
-            {
+        //     'view_search_results',
-                'search_term': search_term
+        //     {
-            });
+        //         'search_term': search_term
-    }
+        //     });
-
-    static countrySelected(country) {
-        gtag(
-            "event",
-            "select_item",
-            {
-                item_list_id: "countrySelect",
-                items: [
-                    {
-                        item_id: country,
-                    }
-                ]
-            });
     }
 }

docs/HistoDescrsProvider.js

@@ -1,7 +1,7 @@
 class HistoDescrsProvider {
 
-    static getHistoDescrs(country, batchcode) {
+    static getHistoDescrs(batchcode) {
-        return fetch(`data/histograms/${country}/${batchcode}.json`)
+        return fetch(`data/histograms/Global/${batchcode}.json`)
             .then(response => response.json())
             .then(histoDescrs => {
                 histoDescrs.histograms.sort((histoDescr1, histoDescr2) => histoDescr1.batchcodes.length - histoDescr2.batchcodes.length);

docs/HistogramView.js

@@ -6,17 +6,17 @@ class HistogramView {
         this.#uiContainer = uiContainer
     }
 
-    displayHistogramView(country, batchcode) {
+    displayHistogramView(batchcode) {
         this
-            .#loadHistoDescrs(country, batchcode)
+            .#loadHistoDescrs(batchcode)
             .then(histoDescrs => this.#displayHistogramViewForHistoDescrs(histoDescrs));
     }
 
-    #loadHistoDescrs(country, batchcode) {
+    #loadHistoDescrs(batchcode) {
         const loadingText = document.createTextNode('Loading...');
         this.#uiContainer.appendChild(loadingText);
         return HistoDescrsProvider
-            .getHistoDescrs(country, batchcode)
+            .getHistoDescrs(batchcode)
             .then(histoDescrs => {
                 loadingText.remove();
                 return histoDescrs;

docs/batchCodeTable.js

@@ -1,30 +1,21 @@
 class BatchCodeTableInitializer {
 
-    #heading;
-    #countrySelect;
     #batchCodeTableElement;
     #batchCodeTable;
     #columnSearch;
 
-    constructor({ heading, countrySelect, batchCodeTableElement }) {
+    constructor(batchCodeTableElement) {
-        this.#heading = heading;
-        this.#countrySelect = countrySelect;
         this.#batchCodeTableElement = batchCodeTableElement;
     }
 
     initialize() {
         this.#batchCodeTable = this.#createEmptyBatchCodeTable();
         this.#columnSearch = new ColumnSearch(this.#batchCodeTable.column(this.#getColumnIndex('Company')));
-        this.#countrySelect.addEventListener('change', event => this.#displayCountry());
+        this.#display();
-        this.#displayCountry();
         this.#initializeHistogramView();
         this.#trackSearchWithGoogleAnalytics();
     }
 
-    #getCountry() {
-        return UIUtils.getSelectedOption(this.#countrySelect).value;
-    }
-
     #createEmptyBatchCodeTable() {
         return this.#batchCodeTableElement.DataTable(
             {
@@ -58,14 +49,13 @@ class BatchCodeTableInitializer {
                                 this.#getColumnIndex('Deaths'),
                                 this.#getColumnIndex('Disabilities'),
                                 this.#getColumnIndex('Life Threatening Illnesses'),
-                                this.#getColumnIndex('Countries'),
                                 this.#getColumnIndex('Severe reports'),
                                 this.#getColumnIndex('Lethality')
                             ]
                         },
                         {
                             orderable: false,
-                            targets: [this.#getColumnIndex('Countries'), this.#getColumnIndex('Company')]
+                            targets: [this.#getColumnIndex('Company')]
                         },
                         {
                             render: (data, type, row) => {
@@ -94,19 +84,16 @@ class BatchCodeTableInitializer {
                 return 5;
             case 'Company':
                 return 6;
-            case 'Countries':
-                return 7;
             case 'Severe reports':
-                return 8;
+                return 7;
             case 'Lethality':
-                return 9;
+                return 8;
         }
     }
 
-    #displayCountry() {
+    #display() {
-        this.#heading.textContent = this.#getCountry() == 'Global' ? 'Global Batch Codes' : `Batch Codes for ${this.#getCountry()}`;
         // FK-TODO: show "Loading.." message or spinning wheel.
-        fetch(`data/batchCodeTables/${this.#getCountry()}.json`)
+        fetch(`data/batchCodeTables/Global.json`)
             .then(response => response.json())
             .then(json => {
                 this.#_addEmptyControlColumn(json);
@@ -117,7 +104,6 @@ class BatchCodeTableInitializer {
                 this.#columnSearch.columnContentUpdated();
                 this.#selectInput();
             });
-        GoogleAnalytics.countrySelected(this.#getCountry());
     }
 
     #_addEmptyControlColumn(json) {
@@ -155,7 +141,7 @@ class BatchCodeTableInitializer {
                         row.child(uiContainer).show();
                         tr.addClass('shown');
                         const batchcode = row.data()[thisClassInstance.#getColumnIndex('Batch')];
-                        new HistogramView(uiContainer).displayHistogramView(thisClassInstance.#getCountry(), batchcode);
+                        new HistogramView(uiContainer).displayHistogramView(batchcode);
                         GoogleAnalytics.click_batchcode(batchcode);
                     }
                 });

src/BatchCodeTableFactory.py

@@ -6,13 +6,6 @@ class BatchCodeTableFactory:
 
     def __init__(self, dataFrame: pd.DataFrame):
         self.dataFrame = dataFrame
-        self.companyColumnAdder = CompanyColumnAdder(dataFrame)
-        self.countryBatchCodeTable = SummationTableFactory.createSummationTable(
-            dataFrame.groupby(
-                [
-                    dataFrame['COUNTRY'],
-                    dataFrame['VAX_LOT']
-                ]))
     
     def createGlobalBatchCodeTable(self):
         return self._postProcess(SummationTableFactory.createSummationTable(self.dataFrame.groupby('VAX_LOT')))
@@ -21,7 +14,7 @@ class BatchCodeTableFactory:
         return self._postProcess(self._getBatchCodeTableByCountry(country))
 
     def _postProcess(self, batchCodeTable):
-        batchCodeTable = self.companyColumnAdder.addCompanyColumn(batchCodeTable)
+        batchCodeTable = CompanyColumnAdder(self.dataFrame).addCompanyColumn(batchCodeTable)
         batchCodeTable = batchCodeTable[
             [
                 'Adverse Reaction Reports',
@@ -29,17 +22,22 @@ class BatchCodeTableFactory:
                 'Disabilities',
                 'Life Threatening Illnesses',
                 'Company',
-                'Countries',
                 'Severe reports',
                 'Lethality'
             ]]
         return batchCodeTable.sort_values(by = 'Severe reports', ascending = False)
 
     def _getBatchCodeTableByCountry(self, country):
-        if country in self.countryBatchCodeTable.index:
+        countryBatchCodeTable = self._getCountryBatchCodeTable()
-            return self.countryBatchCodeTable.loc[country]
+        return countryBatchCodeTable.loc[country] if country in countryBatchCodeTable.index else self._getEmptyBatchCodeTable(countryBatchCodeTable)
-        else:
-            return self._getEmptyBatchCodeTable()
 
-    def _getEmptyBatchCodeTable(self):
+    def _getCountryBatchCodeTable(self):
-        return self.countryBatchCodeTable[0:0].droplevel(0)
+        return SummationTableFactory.createSummationTable(
+            self.dataFrame.groupby(
+                [
+                    self.dataFrame['COUNTRY'],
+                    self.dataFrame['VAX_LOT']
+                ]))
+
+    def _getEmptyBatchCodeTable(self, countryBatchCodeTable):
+        return countryBatchCodeTable[0:0].droplevel(0)

src/BatchCodeTableFactoryTest.py

@@ -28,24 +28,24 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
 
         # Then
         assert_frame_equal(
-            batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Countries', 'Severe reports', 'Lethality']],
+            batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality']],
             TestHelper.createDataFrame(
-                columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Countries', 'Severe reports', 'Lethality'],
+                columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality'],
-                data = [  [2,                          1,        2,              2,                            'MODERNA', 'France',    2/2 * 100,        1/2 * 100],
+                data = [  [2,                          1,        2,              2,                            'MODERNA', 2/2 * 100,        1/2 * 100],
-                          [1,                          0,        0,              0,                            'MODERNA', 'France',    0/1 * 100,        0/1 * 100]],
+                          [1,                          0,        0,              0,                            'MODERNA', 0/1 * 100,        0/1 * 100]],
                 index = pd.Index(
                     [
                         '030L20B',
                         '030L20A'
                     ],
                     name = 'VAX_LOT')),
-            check_dtype = False)
+            check_dtype = True)
 
     def test_createGlobalBatchCodeTable(self):
         # Given
         dataFrame = TestHelper.createDataFrame(
             columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU',         'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE',                  'HOSPITAL', 'ER_VISIT', 'COUNTRY'],
-            data = [  [1,      0,          0,         'COVID19',  'PFIZER\BIONTECH',  '016M20A', '2',               'GBPFIZER INC2020486806',    0,          0,          'United Kingdom'],
+            data = [  [1,      0,          0,         'COVID19',  'PFIZER\BIONTECH',  '016M20A', '2',               'dummy',                     0,          0,          None],
                       [0,      0,          0,         'COVID19',  'MODERNA',          '030L20A', '1',               'FRMODERNATX, INC.MOD20224', 0,          0,          'France'],
                       [1,      1,          1,         'COVID19',  'MODERNA',          '030L20B', '1',               'FRMODERNATX, INC.MOD20224', 0,          0,          'France'],
                       [0,      1,          1,         'COVID19',  'MODERNA',          '030L20B', '1',               'FRMODERNATX, INC.MOD20224', 0,          0,          'United Kingdom']],
@@ -62,12 +62,12 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
 
         # Then
         assert_frame_equal(
-            batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Countries', 'Severe reports', 'Lethality']],
+            batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality']],
             TestHelper.createDataFrame(
-                columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company',         'Countries',              'Severe reports', 'Lethality'],
+                columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company',         'Severe reports', 'Lethality'],
-                data = [  [1,                          1,        0,              0,                            'PFIZER\BIONTECH', 'United Kingdom',         1/1 * 100,        1/1 * 100],
+                data = [  [1,                          1,        0,              0,                            'PFIZER\BIONTECH', 1/1 * 100,        1/1 * 100],
-                          [2,                          1,        2,              2,                            'MODERNA',         'France, United Kingdom', 2/2 * 100,        1/2 * 100],
+                          [2,                          1,        2,              2,                            'MODERNA',         2/2 * 100,        1/2 * 100],
-                          [1,                          0,        0,              0,                            'MODERNA',         'France',                 0/1 * 100,        0/1 * 100]],
+                          [1,                          0,        0,              0,                            'MODERNA',         0/1 * 100,        0/1 * 100]],
                 index = pd.Index(
                     [
                         '016M20A',
@@ -75,7 +75,7 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
                         '030L20A'
                     ],
                     name = 'VAX_LOT')),
-            check_dtype = False)
+            check_dtype = True)
 
     def test_createBatchCodeTableByNonExistingCountry(self):
         # Given
@@ -98,9 +98,9 @@ class BatchCodeTableFactoryTest(unittest.TestCase):
 
         # Then
         assert_frame_equal(
-            batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Countries', 'Severe reports', 'Lethality']],
+            batchCodeTable[['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality']],
             TestHelper.createDataFrame(
-                columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Countries', 'Severe reports', 'Lethality'],
+                columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company', 'Severe reports', 'Lethality'],
                 data = [  ],
                 index = pd.Index([], name = 'VAX_LOT')),
             check_dtype = False)

src/BatchCodeTableHtmlUpdater.py

@@ -1,30 +1,14 @@
 from bs4 import BeautifulSoup
 from HtmlTransformerUtil import HtmlTransformerUtil
-from CountryOptionsSetter import CountryOptionsSetter
 from DateProvider import DateProvider
-from HtmlUtils import getCountryOptions, getCountries
 from DateProvider import DateProvider
 
 
-def updateBatchCodeTableHtmlFile(internationalVaersCovid19, batchCodeTableHtmlFile):
+def updateBatchCodeTableHtmlFile(batchCodeTableHtmlFile):
-    countryOptions = getCountryOptions(getCountries(internationalVaersCovid19))
-    _saveCountryOptions(countryOptions, batchCodeTableHtmlFile)
     _saveLastUpdatedBatchCodeTable(
         DateProvider().getLastUpdatedDataSource(),
         batchCodeTableHtmlFile)
 
-
-def _saveCountryOptions(countryOptions, batchCodeTableHtmlFile):
-    HtmlTransformerUtil().applySoupTransformerToFile(
-        file=batchCodeTableHtmlFile,
-        soupTransformer=lambda soup:
-            BeautifulSoup(
-                CountryOptionsSetter().setCountryOptions(
-                    html=str(soup),
-                    options=countryOptions),
-                'lxml'))
-
-
 def _saveLastUpdatedBatchCodeTable(lastUpdated, batchCodeTableHtmlFile):
     def setLastUpdated(soup):
         soup.find(id="last_updated").string.replace_with(

src/BatchCodeTablePersister.py

@@ -1,28 +1,9 @@
 from IOUtils import IOUtils
-from BatchCodeTableFactory import BatchCodeTableFactory
 import numpy as np
-from HtmlUtils import getCountries
 
 
-def createAndSaveBatchCodeTables(
+def createAndSaveGlobalBatchCodeTable(minADRsForLethality, batchCodeTableFactory):
-        internationalVaersCovid19,
+    batchCodeTable = batchCodeTableFactory.createGlobalBatchCodeTable()
-        minADRsForLethality,
-        onCountryProcessed = lambda country: None):
-    batchCodeTableFactory = BatchCodeTableFactory(internationalVaersCovid19)
-    _createAndSaveBatchCodeTablesForCountries(
-        createBatchCodeTableForCountry = lambda country: batchCodeTableFactory.createBatchCodeTableByCountry(country),
-        countries = getCountries(internationalVaersCovid19),
-        minADRsForLethality = minADRsForLethality,
-        onCountryProcessed = onCountryProcessed)
-    _createAndSaveBatchCodeTableForCountry(
-        createBatchCodeTableForCountry = lambda country: batchCodeTableFactory.createGlobalBatchCodeTable(),
-        country = 'Global',
-        minADRsForLethality = minADRsForLethality,
-        onCountryProcessed = onCountryProcessed)
-
-
-def _createAndSaveBatchCodeTableForCountry(createBatchCodeTableForCountry, country, minADRsForLethality, onCountryProcessed):
-    batchCodeTable = createBatchCodeTableForCountry(country)
     batchCodeTable.index.set_names("Batch", inplace=True)
     if minADRsForLethality is not None:
         batchCodeTable.loc[
@@ -38,16 +19,7 @@ def _createAndSaveBatchCodeTableForCountry(createBatchCodeTableForCountry, count
             'Disabilities',
             'Life Threatening Illnesses',
             'Company',
-            'Countries',
             'Severe reports',
             'Lethality'
         ]]
-    IOUtils.saveDataFrameAsJson(
+    IOUtils.saveDataFrameAsJson(batchCodeTable, '../docs/data/batchCodeTables/Global.json')
-        batchCodeTable,
-        '../docs/data/batchCodeTables/' + country + '.json')
-    onCountryProcessed(country)
-
-
-def _createAndSaveBatchCodeTablesForCountries(createBatchCodeTableForCountry, countries, minADRsForLethality, onCountryProcessed):
-    for country in countries:
-        _createAndSaveBatchCodeTableForCountry(createBatchCodeTableForCountry, country, minADRsForLethality, onCountryProcessed)

src/CountryColumnAdderTest.py

@@ -32,7 +32,7 @@ class CountryColumnAdderTest(unittest.TestCase):
                 columns = ['SPLTTYPE',                  'COUNTRY'],
                 data = [  ['GBPFIZER INC2020486806',    'United Kingdom'],
                           ['FRMODERNATX, INC.MOD20224', 'France'],
-                      ['dummy',                     'Unknown Country']],
+                          ['dummy',                     None]],
                 index = pd.Index(
                         name = 'VAERS_ID',
                         data = [

src/CountryOptionsSetter.py

@@ -1,21 +0,0 @@
-from bs4 import BeautifulSoup
-
-
-class CountryOptionsSetter:
-
-    def setCountryOptions(self, html, options):
-        soup = self._setCountryOptions(self._parse(html), self._parseOptions(options))
-        return str(soup)
-
-    def _setCountryOptions(self, soup, options):
-        countrySelect = soup.find(id = "countrySelect")
-        countrySelect.clear()
-        for option in options:
-            countrySelect.append(option)
-        return soup
-
-    def _parseOptions(self, options):
-        return [self._parse(option).option for option in options]
-
-    def _parse(self, html):
-        return BeautifulSoup(html, 'lxml')

src/CountryOptionsSetterTest.py

@@ -1,73 +0,0 @@
-import unittest
-from CountryOptionsSetter import CountryOptionsSetter
-
-class CountryOptionsSetterTest(unittest.TestCase):
-
-    def test_setCountryOptions(self):
-        # Given
-        countryOptionsSetter = CountryOptionsSetter()
-
-        # When
-        htmlActual = countryOptionsSetter.setCountryOptions(
-            html='''
-            <html>
-              <body>
-                <p>Test<p/>
-                <select id="countrySelect" name="country">
-                  <option value="Global" selected>Global</option>
-                  <option value="Afghanistan">Afghanistan</option>
-                  <option value="Albania">Albania</option>
-                  <option value="Algeria">Algeria</option>
-                </select>
-              </body>
-            </html>
-            ''',
-            options=[
-                '<option value="Global" selected>Global</option>',
-                '<option value="Azerbaijan">Azerbaijan</option>',
-                '<option value="Bahrain">Bahrain</option>'])
-
-        # Then
-        assertEqualHTML(
-            htmlActual,
-            '''
-            <html>
-              <body>
-                <p>Test<p/>
-                <select id="countrySelect" name="country">
-                  <option value="Global" selected>Global</option>
-                  <option value="Azerbaijan">Azerbaijan</option>
-                  <option value="Bahrain">Bahrain</option>
-                </select>
-              </body>
-            </html>
-            ''')
-
-# adapted from https://stackoverflow.com/questions/8006909/pretty-print-assertequal-for-html-strings
-def assertEqualHTML(string1, string2, file1='', file2=''):
-    u'''
-    Compare two unicode strings containing HTML.
-    A human friendly diff goes to logging.error() if they
-    are not equal, and an exception gets raised.
-    '''
-    from bs4 import BeautifulSoup as bs
-    import difflib
-
-    def short(mystr):
-        max = 20
-        if len(mystr) > max:
-            return mystr[:max]
-        return mystr
-    p = []
-    for mystr, file in [(string1, file1), (string2, file2)]:
-        if not isinstance(mystr, str):
-            raise Exception(u'string ist not unicode: %r %s' %
-                            (short(mystr), file))
-        soup = bs(mystr, 'lxml')
-        pretty = soup.prettify()
-        p.append(pretty)
-    if p[0] != p[1]:
-        for line in difflib.unified_diff(p[0].splitlines(), p[1].splitlines(), fromfile=file1, tofile=file2):
-            display(line)
-        display(p[0], ' != ', p[1])
-        raise Exception('Not equal %s %s' % (file1, file2))

src/HistogramFactoryAndPersister.py

@@ -6,10 +6,6 @@ from HistogramDescriptionTableFactory import HistogramDescriptionTableFactory
 
 def createAndSaveGlobalHistograms(symptomByBatchcodeTable):
     symptomByBatchcodeTable = symptomByBatchcodeTable.assign(COUNTRY = 'Global')
-    createAndSaveHistogramsForCountries(symptomByBatchcodeTable)
-
-
-def createAndSaveHistogramsForCountries(symptomByBatchcodeTable):
     dictByBatchcodeTable = createHistograms(symptomByBatchcodeTable)
     explodedTable = MultiIndexExploder.explodeMultiIndexOfTable(dictByBatchcodeTable)
     histogramDescriptionTable = HistogramDescriptionTableFactory.createHistogramDescriptionTable(explodedTable)

src/HowBadIsMyBatch.ipynb

@@ -18,9 +18,10 @@
     "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 BatchCodeTablePersister import createAndSaveGlobalBatchCodeTable\n",
     "from SymptomByBatchcodeTableFactory import SymptomByBatchcodeTableFactory\n",
-    "from HistogramFactoryAndPersister import createAndSaveGlobalHistograms, createAndSaveHistogramsForCountries"
+    "from HistogramFactoryAndPersister import createAndSaveGlobalHistograms\n",
+    "from BatchCodeTableFactory import BatchCodeTableFactory"
    ]
   },
   {
@@ -120,16 +121,6 @@
     "createAndSaveGlobalHistograms(symptomByBatchcodeTable)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f8e42955",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "createAndSaveHistogramsForCountries(symptomByBatchcodeTable)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -137,7 +128,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "internationalVaersCovid19 = getInternationalVaersCovid19(years = years_from_start_of_COVID_vaccination_to_present)\n",
+    "internationalVaersCovid19 = getInternationalVaersCovid19(dataDir = 'VAERS', years = years_from_start_of_COVID_vaccination_to_present)\n",
     "internationalVaersCovid19"
    ]
   },
@@ -148,7 +139,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "updateBatchCodeTableHtmlFile(internationalVaersCovid19, batchCodeTableHtmlFile=\"../docs/batchCodeTable.html\")"
+    "updateBatchCodeTableHtmlFile(batchCodeTableHtmlFile=\"../docs/batchCodeTable.html\")"
    ]
   },
   {
@@ -158,10 +149,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "createAndSaveBatchCodeTables(\n",
+    "createAndSaveGlobalBatchCodeTable(\n",
-    "    internationalVaersCovid19,\n",
     "    minADRsForLethality = 100,\n",
-    "    onCountryProcessed = display)"
+    "    batchCodeTableFactory = BatchCodeTableFactory(internationalVaersCovid19))"
    ]
   },
   {

src/HtmlUtils.py

@@ -1,14 +0,0 @@
-def getCountries(internationalVaersCovid19):
-    return sorted(internationalVaersCovid19['COUNTRY'].unique())
-
-
-def getCountryOptions(countries):
-    return ['<option value="Global" selected>Global</option>'] + _getCountryOptions(countries)
-
-
-def _getCountryOptions(countries):
-    return [_getCountryOption(country) for country in countries]
-
-
-def _getCountryOption(country):
-    return '<option value="{country}">{country}</option>'.format(country=country)

src/InternationalVaersCovid19Provider.py

@@ -5,11 +5,11 @@ from VaersDescrReader import VaersDescrReader
 from CountryColumnAdder import CountryColumnAdder
 
 
-def getInternationalVaersCovid19(years):
+def getInternationalVaersCovid19(dataDir, years):
     internationalVaers = pd.concat(
         [
-            VaersReader.getVaersForYears(years),
+            VaersReader.getVaersForYears(dataDir, years),
-            VaersReader.getNonDomesticVaers()
+            VaersReader.getNonDomesticVaers(dataDir)
         ])
     internationalVaersCovid19 = DataFrameFilter().filterByCovid19(internationalVaers)
     return internationalVaersCovid19

src/Splttype2CountryConverter.py

@@ -16,7 +16,7 @@ class Splttype2CountryConverter:
                     lambda splttype:
                         Splttype2CountryConverter._getCountryNameOfSplttypeOrDefault(
                             splttype = splttype,
-                            default = 'Unknown Country'))
+                            default = None))
                 .astype("string"))
 
     @staticmethod

src/SummationTableFactory.py

@@ -10,8 +10,7 @@ class SummationTableFactory:
                 'Adverse Reaction Reports':   pd.NamedAgg(column = 'DIED',     aggfunc = 'size'),
                 'Life Threatening Illnesses': pd.NamedAgg(column = 'L_THREAT', aggfunc = 'sum'), 
                 'Disabilities':               pd.NamedAgg(column = 'DISABLE',  aggfunc = 'sum'),
-                'Severities':                 pd.NamedAgg(column = 'SEVERE',   aggfunc = 'sum'),
+                'Severities':                 pd.NamedAgg(column = 'SEVERE',   aggfunc = 'sum')
-                'Countries':                  pd.NamedAgg(column = 'COUNTRY',  aggfunc = SummationTableFactory.countries2str)
             })
         summationTable['Severe reports'] = summationTable['Severities'] / summationTable['Adverse Reaction Reports'] * 100
         summationTable['Lethality'] = summationTable['Deaths'] / summationTable['Adverse Reaction Reports'] * 100
@@ -22,10 +21,5 @@ class SummationTableFactory:
                 'Disabilities',
                 'Life Threatening Illnesses',
                 'Severe reports',
-                'Lethality',
+                'Lethality'
-                'Countries'
             ]]
-
-    @staticmethod
-    def countries2str(countries):
-        return  ', '.join(sorted(set(countries)))

src/VaersDescrReader.py

@@ -19,9 +19,9 @@ class VaersDescrReader:
 
     def readNonDomesticVaersDescr(self):
         return {
-                    'VAERSDATA': self._readVAERSDATA(self.dataDir + "/NonDomesticVAERSDATA.csv"),
+                    'VAERSDATA': self._readVAERSDATA(self.dataDir + '/NonDomesticVAERSDATA.csv'),
-                    'VAERSVAX': self._readVAERSVAX(self.dataDir + "/NonDomesticVAERSVAX.csv"),
+                    'VAERSVAX': self._readVAERSVAX(self.dataDir + '/NonDomesticVAERSVAX.csv'),
-                    'VAERSSYMPTOMS': self._readVAERSSYMPTOMS(self.dataDir + "/NonDomesticVAERSSYMPTOMS.csv")
+                    'VAERSSYMPTOMS': self._readVAERSSYMPTOMS(self.dataDir + '/NonDomesticVAERSSYMPTOMS.csv')
                }
 
     def _readVAERSDATA(self, file):
@@ -29,7 +29,7 @@ class VaersDescrReader:
             file = file,
             usecols = ['VAERS_ID', 'RECVDATE', 'DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT', 'SPLTTYPE'],
             parse_dates = ['RECVDATE'],
-            date_parser = lambda dateStr: pd.to_datetime(dateStr, format = "%m/%d/%Y"))
+            date_parser = lambda dateStr: pd.to_datetime(dateStr, format = '%m/%d/%Y'))
         DataFrameNormalizer._convertColumnsOfDataFrame_Y_to_1_else_0(
             VAERSDATA,
             ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'])
@@ -41,8 +41,8 @@ class VaersDescrReader:
             usecols = ['VAERS_ID', 'VAX_DOSE_SERIES', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT'],
             dtype =
                 {
-                    "VAX_DOSE_SERIES": "string",
+                    'VAX_DOSE_SERIES': 'string',
-                    "VAX_LOT": "string"
+                    'VAX_LOT': 'string'
                 })
         DataFrameNormalizer.removeUnknownBatchCodes(VAERSVAX)
         DataFrameNormalizer.convertVAX_LOTColumnToUpperCase(VAERSVAX)

src/VaersReader.py

@@ -3,23 +3,20 @@ from VaersDescrReader import VaersDescrReader
 from VaersDescr2DataFrameConverter import VaersDescr2DataFrameConverter
 from SevereColumnAdder import SevereColumnAdder
 
-def getVaersForYears(years):
+def getVaersForYears(dataDir, years):
     def addCountryColumn(dataFrame):
         dataFrame['COUNTRY'] = 'United States'
         return dataFrame
 
     return _getVaers(
-        _getVaersDescrReader().readVaersDescrsForYears(years),
+        VaersDescrReader(dataDir).readVaersDescrsForYears(years),
         addCountryColumn)
 
-def getNonDomesticVaers():
+def getNonDomesticVaers(dataDir):
     return _getVaers(
-        [_getVaersDescrReader().readNonDomesticVaersDescr()],
+        [VaersDescrReader(dataDir).readNonDomesticVaersDescr()],
         addCountryColumn = lambda dataFrame: CountryColumnAdder(dataFrame).addCountryColumn(dataFrame))
 
-def _getVaersDescrReader():
-    return VaersDescrReader(dataDir = "VAERS")
-
 def _getVaers(vaersDescrs, addCountryColumn):
     dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)
     dataFrame = addCountryColumn(dataFrame)