[105] na fields (#158)

* Update UI YesNo enums to remove Na * Update Curator.spec.ts * Update data service * Update openapi.yaml * Update dockerfile * Update configuration for CI tests * Update make_superuser.sh
globaldothealth · Jan 13, 2025 · 4fb80a3 · 4fb80a3
1 parent 8db28d3
commit 4fb80a3
Show file tree

Hide file tree

Showing 20 changed files with 129 additions and 129 deletions.
diff --git a/data-serving/data-service/api/openapi.yaml b/data-serving/data-service/api/openapi.yaml
@@ -656,6 +656,9 @@ paths:
                     $ref: '#/components/responses/500'
 components:
     schemas:
+        YesNo:
+            type: string
+            enum: ['Y', 'N', '']
         BatchUpdateResponse:
             description: Response to batch update cases API requests
             properties:
@@ -766,8 +769,7 @@ components:
                         occupation:
                             type: string
                         healthcareWorker:
-                            type: string
-                            enum: ['Y', 'N', 'NA']
+                            $ref: '#/components/schemas/YesNo'
                 location:
                     $ref: '#/components/schemas/Location'
                 events:
@@ -788,8 +790,7 @@ components:
                         dateOfFirstConsult:
                             $ref: '#/components/schemas/Date'
                         hospitalized:
-                            type: string
-                            enum: ['Y', 'N', 'NA']
+                            $ref: '#/components/schemas/YesNo'
                         reasonForHospitalization:
                             type: string
                             enum: [monitoring, treatment, unknown]
@@ -798,18 +799,15 @@ components:
                         dateDischargeHospital:
                             $ref: '#/components/schemas/Date'
                         intensiveCare:
-                            type: string
-                            enum: ['Y', 'N', 'NA']
+                            $ref: '#/components/schemas/YesNo'
                         dateAdmissionICU:
                             $ref: '#/components/schemas/Date'
                         dateDischargeICU:
                             $ref: '#/components/schemas/Date'
                         homeMonitoring:
-                            type: string
-                            enum: ['Y', 'N', 'NA']
+                            $ref: '#/components/schemas/YesNo'
                         isolated:
-                            type: string
-                            enum: ['Y', 'N', 'NA']
+                            $ref: '#/components/schemas/YesNo'
                         dateIsolation:
                             $ref: '#/components/schemas/Date'
                         outcome:
@@ -825,21 +823,18 @@ components:
                     type: object
                     properties:
                         previousInfection:
-                            type: string
-                            enum: ['Y', 'N', 'NA']
+                            $ref: '#/components/schemas/YesNo'
                         coInfection:
                             type: string
                         preexistingCondition:
                             type: string
                         pregnancyStatus:
-                            type: string
-                            enum: ['Y', 'N', 'NA']
+                            $ref: '#/components/schemas/YesNo'
                 transmission:
                     type: object
                     properties:
                         contactWithCase:
-                            type: string
-                            enum: ['Y', 'N', 'NA']
+                            $ref: '#/components/schemas/YesNo'
                         contactId:
                             type: string
                         contactSetting:
@@ -854,8 +849,7 @@ components:
                     type: object
                     properties:
                         travelHistory:
-                            type: string
-                            enum: ['Y', 'N', 'NA']
+                            $ref: '#/components/schemas/YesNo'
                         travelHistoryEntry:
                             $ref: '#/components/schemas/Date'
                         travelHistoryStart:
@@ -875,8 +869,7 @@ components:
                     type: object
                     properties:
                         vaccination:
-                            type: string
-                            enum: ['Y', 'N', 'NA']
+                            $ref: '#/components/schemas/YesNo'
                         vaccineName:
                             type: string
                         vaccineDate:

diff --git a/data-serving/data-service/src/types/enums.ts b/data-serving/data-service/src/types/enums.ts
@@ -8,7 +8,7 @@ export enum CaseStatus {
 export enum YesNo {
     Y = 'Y',
     N = 'N',
-    NA = 'NA',
+    None = '',
 }
 
 export enum Role {

diff --git a/data-serving/data-service/test/util/case.test.ts b/data-serving/data-service/test/util/case.test.ts
@@ -22,6 +22,7 @@ import mongoose from 'mongoose';
 import { MongoMemoryServer } from 'mongodb-memory-server';
 import { GenomeSequenceDocument } from '../../src/model/genome-sequence';
 import { EventsDocument } from '../../src/model/events';
+import { YesNo } from '../../src/types/enums';
 
 let mongoServer: MongoMemoryServer;
 
@@ -368,7 +369,7 @@ describe('Case', () => {
             ageBuckets: [anAgeBucket._id],
             gender: 'male',
             occupation: 'Anesthesiologist',
-            healthcareWorker: 'Y',
+            healthcareWorker: YesNo.Y,
         } as DemographicsDocument;
 
         const caseDoc = {
@@ -395,7 +396,7 @@ describe('Case', () => {
         expect(denormalizedCase['demographics.occupation']).toEqual(
             'Anesthesiologist',
         );
-        expect(denormalizedCase['demographics.healthcareWorker']).toEqual('Y');
+        expect(denormalizedCase['demographics.healthcareWorker']).toEqual(YesNo.Y);
     });
     it('denormalizes events fields', async () => {
         const eventsDoc = {
@@ -507,10 +508,10 @@ describe('Case', () => {
     });
     it('denormalizes preexisting conditions fields', async () => {
         const conditionsDoc = {
-            previousInfection: 'Y',
+            previousInfection: YesNo.Y,
             coInfection: 'Flu',
             preexistingCondition: '',
-            pregnancyStatus: 'NA',
+            pregnancyStatus: YesNo.None,
         } as PreexistingConditionsDocument;
 
         const caseDoc = {
@@ -533,7 +534,7 @@ describe('Case', () => {
         const denormalizedCase = await denormalizeFields(caseDoc);
         expect(
             denormalizedCase['preexistingConditions.previousInfection'],
-        ).toEqual('Y');
+        ).toEqual(YesNo.Y);
         expect(denormalizedCase['preexistingConditions.coInfection']).toEqual(
             'Flu',
         );
@@ -542,11 +543,11 @@ describe('Case', () => {
         ).toEqual('');
         expect(
             denormalizedCase['preexistingConditions.pregnancyStatus'],
-        ).toEqual('NA');
+        ).toEqual(YesNo.None);
     });
     it('denormalizes transmission fields', async () => {
         const transmissionDoc = {
-            contactWithCase: 'Y',
+            contactWithCase: YesNo.Y,
             contactId: 'abc123',
             contactSetting: 'setting',
             contactAnimal: 'animal',
@@ -572,7 +573,7 @@ describe('Case', () => {
 
         const denormalizedCase = await denormalizeFields(caseDoc);
 
-        expect(denormalizedCase['transmission.contactWithCase']).toEqual('Y');
+        expect(denormalizedCase['transmission.contactWithCase']).toEqual(YesNo.Y);
         expect(denormalizedCase['transmission.contactId']).toEqual('abc123');
         expect(denormalizedCase['transmission.contactSetting']).toEqual(
             'setting',
@@ -589,7 +590,7 @@ describe('Case', () => {
     });
     it('denormalizes travel history fields', async () => {
         const travelHistoryDoc = {
-            travelHistory: 'Y',
+            travelHistory: YesNo.Y,
             travelHistoryEntry: new Date('2020-11-01'),
             travelHistoryStart: 'start',
             travelHistoryLocation: 'London',
@@ -614,7 +615,7 @@ describe('Case', () => {
 
         const denormalizedCase = await denormalizeFields(caseDoc);
 
-        expect(denormalizedCase['travelHistory.travelHistory']).toEqual('Y');
+        expect(denormalizedCase['travelHistory.travelHistory']).toEqual(YesNo.Y);
         expect(denormalizedCase['travelHistory.travelHistoryEntry']).toEqual(
             formatDateWithoutTime(travelHistoryDoc.travelHistoryEntry),
         );
@@ -630,7 +631,7 @@ describe('Case', () => {
     });
     it('denormalizes vaccine fields', async () => {
         const vaccinationDoc = {
-            vaccination: 'Y',
+            vaccination: YesNo.Y,
             vaccineName: 'Pfizer',
             vaccineDate: new Date('2020-11-01'),
             vaccineSideEffects: 'cough',
@@ -653,7 +654,7 @@ describe('Case', () => {
         } as CaseDocument;
 
         const denormalizedCase = await denormalizeFields(caseDoc);
-        expect(denormalizedCase['vaccination.vaccination']).toEqual('Y');
+        expect(denormalizedCase['vaccination.vaccination']).toEqual(YesNo.Y);
         expect(denormalizedCase['vaccination.vaccineName']).toEqual('Pfizer');
         expect(denormalizedCase['vaccination.vaccineDate']).toEqual(
             formatDateWithoutTime(vaccinationDoc.vaccineDate),

diff --git a/dev/make_superuser.sh b/dev/make_superuser.sh
@@ -10,6 +10,6 @@ cd `dirname "$0"`
 # Pass database name as the first parameter
 DB="${GDH_DATABASE:-$1}"
 # Pass email of user to grant an admin role as second parameter
-docker-compose -f docker-compose.yml -f docker-compose.dev.yml exec mongo mongosh "${DB}" --eval "var email='$2'; var roles=['admin', 'curator'];" /verification/scripts/roles.js
+docker compose -f docker-compose.yml -f docker-compose.dev.yml exec mongo mongosh "${DB}" --eval "var email='$2'; var roles=['admin', 'curator'];" /verification/scripts/roles.js
 # Restore directory.
 popd
diff --git a/geocoding/location-service/Dockerfile b/geocoding/location-service/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.10-slim
+FROM python:3.10-bullseye
 
 RUN apt-get update -y
 RUN apt-get install -y python3-pip
@@ -14,7 +14,7 @@ WORKDIR /usr/src/app/geocoding/location-service
 USER flask
 
 # install dependencies
-RUN pip install poetry
+RUN pip install poetry==1.8.5
 COPY geocoding/location-service/pyproject.toml .
 COPY geocoding/location-service/poetry.lock .
 RUN /home/flask/.local/bin/poetry install

diff --git a/geocoding/location-service/Dockerfile-test b/geocoding/location-service/Dockerfile-test
@@ -1,5 +1,5 @@
 # `python-base` sets up all our shared environment variables
-FROM python:3.10-slim as python-base
+FROM python:3.10-bullseye as python-base
 
 ENV PYTHONUNBUFFERED=1 \
     # prevents python creating .pyc files

diff --git a/verification/curator-service/api/openapi/openapi.yaml b/verification/curator-service/api/openapi/openapi.yaml
@@ -1283,6 +1283,9 @@ paths:
 
 components:
     schemas:
+        YesNo:
+            type: string
+            enum: [ 'Y', 'N', '' ]
         Parser:
             description: A parser for automated ingestion
             type: object
@@ -1593,8 +1596,7 @@ components:
                         occupation:
                             type: string
                         healthcareWorker:
-                            type: string
-                            enum: ['Y', 'N', 'NA', undefined]
+                            $ref: '#/components/schemas/YesNo'
                 location:
                     $ref: '#/components/schemas/Location'
                 events:
@@ -1615,8 +1617,7 @@ components:
                         dateOfFirstConsult:
                             $ref: '#/components/schemas/Date'
                         hospitalized:
-                            type: string
-                            enum: ['Y', 'N', 'NA', undefined]
+                            $ref: '#/components/schemas/YesNo'
                         reasonForHospitalization:
                             type: string
                             enum: [monitoring, treatment, unknown]
@@ -1625,18 +1626,15 @@ components:
                         dateDischargeHospital:
                             $ref: '#/components/schemas/Date'
                         intensiveCare:
-                            type: string
-                            enum: ['Y', 'N', 'NA', undefined]
+                            $ref: '#/components/schemas/YesNo'
                         dateAdmissionICU:
                             $ref: '#/components/schemas/Date'
                         dateDischargeICU:
                             $ref: '#/components/schemas/Date'
                         homeMonitoring:
-                            type: string
-                            enum: ['Y', 'N', 'NA', undefined]
+                            $ref: '#/components/schemas/YesNo'
                         isolated:
-                            type: string
-                            enum: ['Y', 'N', 'NA', undefined]
+                            $ref: '#/components/schemas/YesNo'
                         dateIsolation:
                             $ref: '#/components/schemas/Date'
                         outcome:
@@ -1653,22 +1651,19 @@ components:
                     type: object
                     properties:
                         previousInfection:
-                            type: string
-                            enum: ['Y', 'N', 'NA', undefined]
+                            $ref: '#/components/schemas/YesNo'
                         coInfection:
                             type: string
                         preexistingCondition:
                             type: string
                         pregnancyStatus:
-                            type: string
-                            enum: ['Y', 'N', 'NA', undefined]
+                            $ref: '#/components/schemas/YesNo'
                 transmission:
                     description: How this case got infected and by who if known
                     type: object
                     properties:
                         contactWithCase:
-                            type: string
-                            enum: ['Y', 'N', 'NA', undefined]
+                            $ref: '#/components/schemas/YesNo'
                         contactId:
                             type: string
                         contactSetting:
@@ -1684,8 +1679,7 @@ components:
                     description: Travel history of the patient if known
                     properties:
                         travelHistory:
-                            type: string
-                            enum: ['Y', 'N', 'NA', undefined]
+                            $ref: '#/components/schemas/YesNo'
                         travelHistoryEntry:
                             $ref: '#/components/schemas/Date'
                         travelHistoryStart:
@@ -1709,8 +1703,7 @@ components:
                     type: object
                     properties:
                         vaccination:
-                            type: string
-                            enum: ['Y', 'N', 'NA', undefined]
+                            $ref: '#/components/schemas/YesNo'
                         vaccineName:
                             type: string
                         vaccineDate: