Remove hard coded covid hotfixes (#10)

* Final cleanup * Fix location code * Fix tests * fix cypress tests * fix missing type * Fix make superuser file
globaldothealth · Jul 14, 2023 · cd68be1 · cd68be1
1 parent f2c1b88
commit cd68be1
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Showing 11 changed files with 35 additions and 28 deletions.
diff --git a/data-serving/data-service/src/controllers/case.ts b/data-serving/data-service/src/controllers/case.ts
@@ -398,11 +398,14 @@ export class CasesController {
                 if (numCases === 1) {
                     result = await c.save();
                 } else {
-                    const cases = Array.from(
-                        { length: numCases },
-                        () => new Day0Case(req.body),
-                    );
-                    result = { cases: await Day0Case.insertMany(cases) };
+                    const newCases: CaseDocument[] = [];
+                    for (let i = 0; i < numCases; i++) {
+                        const multiCaseInstance = new Day0Case(
+                            await caseFromDTO(receivedCase),
+                        );
+                        newCases.push(await multiCaseInstance.save());
+                    }
+                    result = { cases: newCases };
                 }
             }
 

diff --git a/dev/README.md b/dev/README.md
@@ -66,7 +66,7 @@ token, or if you'd like to use a different GMail account for mailing notificatio
 Give your user all the permissions to access the portal and make CRUD updates.
 
 ```shell
-./dev/make_superuser.sh $YOUR_GOOGLE_EMAIL
+./dev/make_superuser.sh $DATABASE_NAME $YOUR_GOOGLE_EMAIL
 ```
 
 Note that **the user must be logged-in into the portal before you can issue this command**. To run it against a different instance/database, set `$GDH_DATABASE` to the appropriate connection string.

diff --git a/dev/make_superuser.sh b/dev/make_superuser.sh
@@ -7,8 +7,9 @@ pushd `pwd`
 # We have to run docker-compose from this directory for it to pick up the .env file.
 cd `dirname "$0"`
 
-# Tell us what database to use — default is covid19 but you can override it for other instances
-DB="${GDH_DATABASE:-$MONGO_DB_NAME}"
-docker-compose -f docker-compose.yml -f docker-compose.dev.yml exec mongo mongo "${DB}" --eval "var email='$1'; var roles=['admin', 'curator'];" /verification/scripts/roles.js
+# Pass database name as the first parameter
+DB="${GDH_DATABASE:-$1}"
+# Pass email of user to grant an admin role as second parameter
+docker-compose -f docker-compose.yml -f docker-compose.dev.yml exec mongo mongo "${DB}" --eval "var email='$2'; var roles=['admin', 'curator'];" /verification/scripts/roles.js
 # Restore directory.
 popd
diff --git a/verification/curator-service/ui/cypress/e2e/components/AppTest.spec.ts b/verification/curator-service/ui/cypress/e2e/components/AppTest.spec.ts
@@ -6,43 +6,43 @@ describe('App', function () {
     beforeEach(() => {
         cy.task('clearSourcesDB', {});
         cy.seedLocation({
-            country: 'DEU',
+            country: 'DE',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'Germany',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'FRA',
+            country: 'FR',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'France',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'ESP',
+            country: 'ES',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'Spain',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'ITA',
+            country: 'IT',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'Italy',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'POL',
+            country: 'PL',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'Poland',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'RUS',
+            country: 'RU',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'Russia',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'PER',
+            country: 'PE',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'Peru',
             geoResolution: 'Country',

diff --git a/verification/curator-service/ui/cypress/e2e/components/BulkCaseForm.spec.ts b/verification/curator-service/ui/cypress/e2e/components/BulkCaseForm.spec.ts
@@ -5,13 +5,13 @@ describe('Bulk upload form', function () {
         cy.task('clearCasesDB', {});
         cy.login();
         cy.seedLocation({
-            country: 'FRA',
+            country: 'FR',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'France',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'CAN',
+            country: 'CA',
             geometry: { latitude: 51.1784, longitude: 115.5708 },
             name: 'Canada',
             geoResolution: 'Country',

diff --git a/verification/curator-service/ui/cypress/e2e/components/Curator.spec.ts b/verification/curator-service/ui/cypress/e2e/components/Curator.spec.ts
@@ -77,7 +77,7 @@ describe('Curator', function () {
         cy.get('li[data-value="N"]').click();
 
         // LOCATION
-        cy.get('div[data-testid="location.geocodeLocation"]').type('France');
+        cy.get('div[data-testid="location.geocodeLocation"]').type('France', { delay: 0});
         cy.wait('@geolocationFranceSuggest');
         cy.contains('France').click();
         /* Change France to something else to check we can edit geocode results.

diff --git a/verification/curator-service/ui/cypress/e2e/components/LinelistTableTest.spec.ts b/verification/curator-service/ui/cypress/e2e/components/LinelistTableTest.spec.ts
@@ -11,31 +11,31 @@ describe('Linelist table', function () {
             roles: ['admin', 'curator'],
         });
         cy.seedLocation({
-            country: 'FRA',
+            country: 'FR',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'France',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'DEU',
+            country: 'DE',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'Germany',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'ESP',
+            country: 'ES',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'Spain',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'GBR',
+            country: 'GB',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'United Kingdom',
             geoResolution: 'Country',
         });
         cy.seedLocation({
-            country: 'ARG',
+            country: 'AR',
             geometry: { latitude: 51.5072, longitude: -0.1275 },
             name: 'Argentina',
             geoResolution: 'Country',

diff --git a/verification/curator-service/ui/cypress/e2e/components/NewCaseForm.spec.ts b/verification/curator-service/ui/cypress/e2e/components/NewCaseForm.spec.ts
@@ -11,7 +11,7 @@ describe('New case form', function () {
             fixture: 'geolocation_france_suggest.json',
         }).as('geolocationFranceSuggest');
         cy.seedLocation({
-            country: 'FRA',
+            country: 'FR',
             geometry: { latitude: 45.75889, longitude: 4.84139 },
             name: 'France',
             geoResolution: 'Country',

diff --git a/verification/curator-service/ui/src/api/models/Day0Case.ts b/verification/curator-service/ui/src/api/models/Day0Case.ts
@@ -51,6 +51,7 @@ export interface Demographics {
 
 export interface GeocodeLocation {
     country: string;
+    countryISO3: string;
     administrativeAreaLevel1: string;
     administrativeAreaLevel2: string;
     administrativeAreaLevel3: string;

diff --git a/verification/curator-service/ui/src/components/CaseForm.tsx b/verification/curator-service/ui/src/components/CaseForm.tsx
@@ -169,6 +169,7 @@ const initialValuesFromCase = (
             ...c.location,
             geocodeLocation: {
                 country: c.location.countryISO3,
+                countryISO3: c.location.countryISO3,
                 administrativeAreaLevel1: '',
                 administrativeAreaLevel2: '',
                 administrativeAreaLevel3: '',
@@ -596,7 +597,7 @@ export default function CaseForm(props: Props): JSX.Element {
                                             isChecked: isChecked({
                                                 requiredValues: [
                                                     values.caseReference
-                                                        .sourceUrl,
+                                                        ?.sourceUrl,
                                                 ],
                                             }),
                                             hasError: hasErrors(

diff --git a/verification/curator-service/ui/src/components/new-case-form-fields/Location.tsx b/verification/curator-service/ui/src/components/new-case-form-fields/Location.tsx
@@ -5,7 +5,7 @@ import { FastField, useFormikContext } from 'formik';
 import makeStyles from '@mui/styles/makeStyles';
 import { Day0CaseFormValues } from '../../api/models/Day0Case';
 import { useEffect } from 'react';
-import { getAlpha3Codes, getName } from 'i18n-iso-countries';
+import { getAlpha3Codes, getName, alpha2ToAlpha3 } from 'i18n-iso-countries';
 
 const styles = makeStyles(() => ({
     root: {
@@ -40,7 +40,8 @@ export default function Location(): JSX.Element {
 
         setFieldValue(
             'location.countryISO3',
-            values.location.geocodeLocation.country,
+            values.location.geocodeLocation.countryISO3 ||
+                alpha2ToAlpha3(values.location.geocodeLocation.country),
         );
         setFieldValue('location.country', countryName);
         setFieldValue(