adding global batch code table

docs/internationalBatchCodeTables.html

@@ -68,7 +68,7 @@
     }
 
     function displayCountry(country, batchCodeTable) {
-      document.querySelector('.heading').textContent = `Batch Codes for ${country}`;
+      document.querySelector('.heading').textContent = country == 'Global' ? 'Global Batch Codes' : `Batch Codes for ${country}`;
       batchCodeTable.ajax.url(`data/${country}.json`).load();
       selectInput();
     }
@@ -79,10 +79,9 @@
         'change',
         event => {
           const country = event.target.value;
-          if (country != 'Select country ...') {
+          displayCountry(country, batchCodeTable);
-            displayCountry(country, batchCodeTable);
-          }
         });
+      displayCountry('Global', batchCodeTable)
     });
   </script>
 </head>
@@ -93,7 +92,7 @@
   <p>
     <label>Select country:
       <select id="countrySelect" name="country">
-        <option value="Select country ...">Select country ...</option>
+        <option value="Global" selected>Global</option>
         <option value="Afghanistan">Afghanistan</option>
         <option value="Albania">Albania</option>
         <option value="Algeria">Algeria</option>

src/HowBadIsMyBatch.ipynb

@@ -421,6 +421,9 @@
     "    def createBatchCodeTableByCountry(self, country):\n",
     "        return self.batchCodeTableByCountryFactory.createBatchCodeTableByCountry(country)\n",
     "\n",
+    "    def createGlobalBatchCodeTable(self):\n",
+    "        return self.createBatchCodeTableByCountry(None)\n",
+    "\n",
     "    def _createInternationalLotTable(self):\n",
     "        return SummationTableFactory.createSummationTableHavingSevereReportsColumn(self.dataFrame.groupby(self.dataFrame['COUNTRY']))\n"
    ]
@@ -453,9 +456,14 @@
     "            ]]\n",
     "        return batchCodeTable.sort_values(by = 'Severe reports', ascending = False)\n",
     "\n",
+    "    # FK-TODO: refactor\n",
     "    def _createBatchCodeTableByCountry(self, country):\n",
+    "        if country is None:\n",
+    "            return SummationTableFactory.createSummationTableHavingSevereReportsColumn(self.dataFrame.groupby('VAX_LOT'))\n",
+    "\n",
     "        if self.countryBatchCodeTable is None:\n",
     "            self.countryBatchCodeTable = self._getCountryBatchCodeTable()\n",
+    "            \n",
     "        return self._getCountry(self.countryBatchCodeTable, country)\n",
     "\n",
     "    def _getCountryBatchCodeTable(self):\n",
@@ -1192,6 +1200,42 @@
     "                    name = 'VAX_LOT')),\n",
     "            check_dtype = False)\n",
     "\n",
+    "    def test_createGlobalBatchCodeTable(self):\n",
+    "        # Given\n",
+    "        dataFrame = TestHelper.createDataFrame(\n",
+    "            columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU',         'VAX_LOT', 'VAX_DOSE_SERIES', 'SPLTTYPE',                  'HOSPITAL', 'ER_VISIT', 'COUNTRY'],\n",
+    "            data = [  [1,      0,          0,         'COVID19',  'PFIZER\\BIONTECH',  '016M20A', '2',               'GBPFIZER INC2020486806',    0,          0,          'United Kingdom'],\n",
+    "                      [0,      0,          0,         'COVID19',  'MODERNA',          '030L20A', '1',               'FRMODERNATX, INC.MOD20224', 0,          0,          'France'],\n",
+    "                      [1,      1,          1,         'COVID19',  'MODERNA',          '030L20B', '1',               'FRMODERNATX, INC.MOD20224', 0,          0,          'France'],\n",
+    "                      [0,      1,          1,         'COVID19',  'MODERNA',          '030L20B', '1',               'FRMODERNATX, INC.MOD20224', 0,          0,          'France']],\n",
+    "            index = [\n",
+    "                \"1048786\",\n",
+    "                \"1048786\",\n",
+    "                \"4711\",\n",
+    "                \"0815\"])\n",
+    "        dataFrame = SevereColumnAdder.addSevereColumn(dataFrame)\n",
+    "        internationalLotTableFactory = InternationalLotTableFactory(dataFrame)\n",
+    "        \n",
+    "        # When\n",
+    "        batchCodeTable = internationalLotTableFactory.createGlobalBatchCodeTable()\n",
+    "\n",
+    "        # Then\n",
+    "        assert_frame_equal(\n",
+    "            batchCodeTable,\n",
+    "            TestHelper.createDataFrame(\n",
+    "                columns = ['Adverse Reaction Reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses', 'Company',         'Severe reports', 'Lethality'],\n",
+    "                data = [  [1,                          1,        0,              0,                            'PFIZER\\BIONTECH', 1/1 * 100,        1/1 * 100],\n",
+    "                          [2,                          1,        2,              2,                            'MODERNA',         2/2 * 100,        1/2 * 100],\n",
+    "                          [1,                          0,        0,              0,                            'MODERNA',         0/1 * 100,        0/1 * 100]],\n",
+    "                index = pd.Index(\n",
+    "                    [\n",
+    "                        '016M20A',\n",
+    "                        '030L20B',\n",
+    "                        '030L20A'\n",
+    "                    ],\n",
+    "                    name = 'VAX_LOT')),\n",
+    "            check_dtype = False)\n",
+    "\n",
     "    def test_createBatchCodeTableByNonExistingCountry(self):\n",
     "        # Given\n",
     "        dataFrame = TestHelper.createDataFrame(\n",
@@ -1464,8 +1508,8 @@
     "    IOUtils.saveDataFrame(batchCodeTable, '../docs/data/' + country)\n",
     "    display(country + \":\", batchCodeTable)\n",
     "\n",
-    "def createAndSaveAndDisplayBatchCodeTablesByCountry(nonDomesticVaers, countries, minADRsForLethality = None):\n",
+    "def createAndSaveAndDisplayBatchCodeTablesByCountry(vaers, countries, minADRsForLethality = None):\n",
-    "    internationalLotTableFactory = InternationalLotTableFactory(nonDomesticVaers)\n",
+    "    internationalLotTableFactory = InternationalLotTableFactory(vaers)\n",
     "    for country in countries:\n",
     "        createAndSaveAndDisplayBatchCodeTableByCountry(internationalLotTableFactory, country, minADRsForLethality)"
    ]
@@ -1518,6 +1562,33 @@
     "    minADRsForLethality = 100)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "106c0d91",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "internationalLotTableFactory = InternationalLotTableFactory(internationalVaers)\n",
+    "globalBatchCodeTable = internationalLotTableFactory.createGlobalBatchCodeTable()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e75bd993",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "    # FK-TODO: DRY with createAndSaveAndDisplayBatchCodeTableByCountry()\n",
+    "    minADRsForLethality = 100\n",
+    "    globalBatchCodeTable.index.set_names(\"Batch\", inplace = True)\n",
+    "    if minADRsForLethality is not None:\n",
+    "        globalBatchCodeTable.loc[globalBatchCodeTable['Adverse Reaction Reports'] < minADRsForLethality, ['Severe reports', 'Lethality']] = [np.nan, np.nan]\n",
+    "    IOUtils.saveDataFrame(globalBatchCodeTable, '../docs/data/Global')\n",
+    "    display('Global' + \":\", globalBatchCodeTable)\n"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "ba02139d",