data,curator: remove notes #2673

data-serving/data-service/api/openapi.yaml

@@ -816,10 +816,6 @@ components:
                                 type: integer
                                 format: int32
                                 minimum: 0
-                notes:
-                    type: string
-                restrictedNotes:
-                    type: string
                 revisionMetadata:
                     type: object
                     properties:

data-serving/data-service/src/controllers/case.ts

@@ -78,6 +78,7 @@ const dtoFromCase = async (storedCase: LeanDocument<CaseDocument>) => {
         delete (dto as unknown as { demographics: { ageBuckets?: [ObjectId] }}).demographics.ageBuckets;
     }
     delete dto.restrictedNotes;
+    delete dto.notes;
 
     return dto;
 }
@@ -117,9 +118,10 @@ export class CasesController {
             return;
         }
 
-        // don't export restricted notes
+        // don't export any note
         c.forEach((aCase: LeanDocument<CaseDocument>) => {
             delete aCase.restrictedNotes;
+            delete aCase.notes;
         });
 
         res.json(await Promise.all(c.map(aCase => dtoFromCase(aCase))));
@@ -242,10 +244,8 @@ export class CasesController {
                 doc = await cursor.next();
                 while (doc != null) {
                     delete doc.restrictedNotes;
+                    delete doc.notes;
                     const normalizedDoc = denormalizeFields(doc);
-                    if (!doc.hasOwnProperty('notes')) {
-                        normalizedDoc.notes = '';
-                    }
                     if (!doc.hasOwnProperty('SGTF')) {
                         normalizedDoc.SGTF = 'NA';
                     }
@@ -340,7 +340,6 @@ export class CasesController {
             ]);
 
             const dtos = await Promise.all(docs.map(dtoFromCase));
-
             logger.info('got results');
             // total is actually stored in a count index in mongo, so the query is fast.
             // however to maintain existing behaviour, only return the count limit

data-serving/data-service/src/model/case.ts

@@ -120,8 +120,6 @@ caseSchema.methods.equalsJSON = function (jsonCase: any): boolean {
         _.isEqual(thisJson.exclusionData, other.exclusionData) &&
         _.isEqual(thisJson.genomeSequences, other.genomeSequences) &&
         _.isEqual(thisJson.location, other.location) &&
-        _.isEqual(thisJson.notes, other.notes) &&
-        _.isEqual(thisJson.restrictedNotes, other.restrictedNotes) &&
         _.isEqual(thisJson.pathogens, other.pathogens) &&
         _.isEqual(
             thisJson.preexistingConditions,
@@ -145,7 +143,7 @@ export type ICase = {
     importedCase: unknown;
     location: LocationDocument;
     revisionMetadata: RevisionMetadataDocument;
-    notes: string;
+    notes?: string;
     restrictedNotes?: string;
     pathogens: [PathogenDocument];
     list: boolean;

data-serving/data-service/src/model/fields.json

@@ -1 +1 @@
-["_id","caseReference.additionalSources","caseReference.sourceEntryId","caseReference.sourceId","caseReference.sourceUrl","caseReference.uploadIds","caseReference.verificationStatus","demographics.ageRange.end","demographics.ageRange.start","demographics.ethnicity","demographics.gender","demographics.nationalities","demographics.occupation","events","location.administrativeAreaLevel1","location.administrativeAreaLevel2","location.administrativeAreaLevel3","location.country","location.geoResolution","location.geometry.latitude","location.geometry.longitude","location.name","location.place","location.query","notes","pathogens","preexistingConditions.hasPreexistingConditions","preexistingConditions.values","revisionMetadata.creationMetadata.curator","revisionMetadata.creationMetadata.date","revisionMetadata.creationMetadata.notes","revisionMetadata.editMetadata.curator","revisionMetadata.editMetadata.date","revisionMetadata.editMetadata.notes","revisionMetadata.revisionNumber", "SGTF", "symptoms.status","symptoms.values","transmission.linkedCaseIds","transmission.places","transmission.routes","travelHistory.travel.dateRange.end","travelHistory.travel.dateRange.start","travelHistory.travel.location.name","travelHistory.travel.methods","travelHistory.travel.purpose","travelHistory.traveledPrior30Days","vaccines.0.name","vaccines.0.batch","vaccines.0.date","vaccines.0.sideEffects","vaccines.1.name","vaccines.1.batch","vaccines.1.date","vaccines.1.sideEffects","vaccines.2.name","vaccines.2.batch","vaccines.2.date","vaccines.2.sideEffects","vaccines.3.name","vaccines.3.batch","vaccines.3.date","vaccines.3.sideEffects",""]
+["_id","caseReference.additionalSources","caseReference.sourceEntryId","caseReference.sourceId","caseReference.sourceUrl","caseReference.uploadIds","caseReference.verificationStatus","demographics.ageRange.end","demographics.ageRange.start","demographics.ethnicity","demographics.gender","demographics.nationalities","demographics.occupation","events","location.administrativeAreaLevel1","location.administrativeAreaLevel2","location.administrativeAreaLevel3","location.country","location.geoResolution","location.geometry.latitude","location.geometry.longitude","location.name","location.place","location.query","pathogens","preexistingConditions.hasPreexistingConditions","preexistingConditions.values","revisionMetadata.creationMetadata.curator","revisionMetadata.creationMetadata.date","revisionMetadata.creationMetadata.notes","revisionMetadata.editMetadata.curator","revisionMetadata.editMetadata.date","revisionMetadata.editMetadata.notes","revisionMetadata.revisionNumber", "SGTF", "symptoms.status","symptoms.values","transmission.linkedCaseIds","transmission.places","transmission.routes","travelHistory.travel.dateRange.end","travelHistory.travel.dateRange.start","travelHistory.travel.location.name","travelHistory.travel.methods","travelHistory.travel.purpose","travelHistory.traveledPrior30Days","vaccines.0.name","vaccines.0.batch","vaccines.0.date","vaccines.0.sideEffects","vaccines.1.name","vaccines.1.batch","vaccines.1.date","vaccines.1.sideEffects","vaccines.2.name","vaccines.2.batch","vaccines.2.date","vaccines.2.sideEffects","vaccines.3.name","vaccines.3.batch","vaccines.3.date","vaccines.3.sideEffects",""]

data-serving/data-service/test/controllers/case.test.ts

@@ -114,6 +114,13 @@ describe('GET', () => {
         const res = await request(app).get(`/api/cases/${c._id}`).expect(200);
         expect(res.body[0].restrictedNotes).toBeUndefined();
     });
+    it('should not show the notes for a case', async () => {
+        const c = new Case(minimalCase);
+        c.notes = 'I want to tell you a secret';
+        await c.save();
+        const res = await request(app).get(`/api/cases/${c._id}`).expect(200);
+        expect(res.body[0].notes).toBeUndefined();
+    });
     it('should convert age bucket to age range', async () => {
         const c = new Case(minimalCase);
         const bucket = await AgeBucket.findOne({});
@@ -200,41 +207,21 @@ describe('GET', () => {
                 .expect(200);
             expect(res.body.cases).toHaveLength(1);
         });
-        it('should query results', async () => {
-            // Simulate index creation used in unit tests, in production they are
-            // setup by the migrations and such indexes are not present by
-            // default in the in memory mongo spawned by unit tests.
-            await mongoose.connection.collection('cases').createIndex({
-                notes: 'text',
-            });
-
-            const c = new Case(minimalCase);
-            c.notes = 'got it at work';
-            await c.save();
-            // Search for non-matching notes.
-            const res = await request(app)
-                .get('/api/cases?page=1&limit=10&q=home')
-                .expect(200)
-                .expect('Content-Type', /json/);
-            expect(res.body.cases).toHaveLength(0);
-            expect(res.body.total).toEqual(0);
-            // Search for matching notes.
-            await request(app)
-                .get(`/api/cases?page=1&limit=10&q=${encodeURI('at work')}`)
-                .expect(200, /got it at work/)
-                .expect('Content-Type', /json/);
-        });
         it('should use age buckets in results', async () => {
             const c = new Case(minimalCase);
             const aBucket = await AgeBucket.findOne({});
             c.demographics.ageBuckets = [aBucket!._id];
             await c.save();
             const res = await request(app)
-                .get(`/api/cases?page=1&limit=10`)
+                .get('/api/cases?page=1&limit=10')
                 .expect(200)
                 .expect('Content-Type', /json/);
-            expect(res.body.cases[0].demographics.ageRange.start).toEqual(aBucket!.start);
-            expect(res.body.cases[0].demographics.ageRange.end).toEqual(aBucket!.end);
+            expect(res.body.cases[0].demographics.ageRange.start).toEqual(
+                aBucket!.start,
+            );
+            expect(res.body.cases[0].demographics.ageRange.end).toEqual(
+                aBucket!.end,
+            );
         });
         it('should ignore the restricted collection', async () => {
             const r = new RestrictedCase(minimalCase);
@@ -265,6 +252,14 @@ describe('GET', () => {
             expect(res.body.cases).toHaveLength(1);
             expect(res.body.cases[0].restrictedNotes).toBeUndefined();
         });
+        it('should strip out notes', async () => {
+            const c = new Case(minimalCase);
+            c.notes = 'Can you keep a secret?';
+            await c.save();
+            const res = await request(app).get('/api/cases').expect(200);
+            expect(res.body.cases).toHaveLength(1);
+            expect(res.body.cases[0].notes).toBeUndefined();
+        });
         describe('keywords', () => {
             beforeEach(async () => {
                 const c = new Case(minimalCase);
@@ -504,7 +499,7 @@ describe('POST', () => {
         const theCase = await Case.findOne({});
         // case has range 40-50, should be bucketed into 36-40, 41-45, 46-50
         expect(theCase!.demographics.ageBuckets).toHaveLength(3);
-    })
+    });
     it('GETting the POSTed case should return an age range', async () => {
         const theCase = await request(app)
             .post('/api/cases')
@@ -1596,11 +1591,11 @@ describe('PUT', () => {
             .send({
                 ...curatorMetadata,
                 cases: [
-                    { 
+                    {
                         _id: c._id,
                         demographics: {
                             ageRange,
-                        }
+                        },
                     },
                 ],
             })

data-serving/data-service/test/util/case.test.ts

@@ -90,7 +90,7 @@ describe('Case', () => {
             'demographics.gender','demographics.nationalities','demographics.occupation','events','genomeSequences',
             'location.administrativeAreaLevel1','location.administrativeAreaLevel2','location.administrativeAreaLevel3',
             'location.country','location.geoResolution','location.geometry.latitude','location.geometry.longitude',
-            'location.name','location.place','location.query','notes','pathogens',
+            'location.name','location.place','location.query','pathogens',
             'preexistingConditions.hasPreexistingConditions','preexistingConditions.values',
             'revisionMetadata.creationMetadata.curator','revisionMetadata.creationMetadata.date',
             'revisionMetadata.creationMetadata.notes','revisionMetadata.editMetadata.curator',
@@ -114,7 +114,7 @@ describe('Case', () => {
             'events.outcome.value','events.icuAdmission.value', 'genomeSequences','location.administrativeAreaLevel1',
             'location.administrativeAreaLevel2','location.administrativeAreaLevel3',
             'location.country','location.geoResolution','location.geometry.latitude','location.geometry.longitude',
-            'location.name','location.place','location.query','notes','pathogens',
+            'location.name','location.place','location.query','pathogens',
             'preexistingConditions.hasPreexistingConditions','preexistingConditions.values',
             'revisionMetadata.creationMetadata.curator','revisionMetadata.creationMetadata.date',
             'revisionMetadata.creationMetadata.notes','revisionMetadata.editMetadata.curator',
@@ -139,7 +139,7 @@ describe('Case', () => {
             'events.selfIsolation.value', 'genomeSequences','location.administrativeAreaLevel1',
             'location.administrativeAreaLevel2','location.administrativeAreaLevel3',
             'location.country','location.geoResolution','location.geometry.latitude','location.geometry.longitude',
-            'location.name','location.place','location.query','notes','pathogens',
+            'location.name','location.place','location.query','pathogens',
             'preexistingConditions.hasPreexistingConditions','preexistingConditions.values',
             'revisionMetadata.creationMetadata.curator','revisionMetadata.creationMetadata.date',
             'revisionMetadata.creationMetadata.notes','revisionMetadata.editMetadata.curator',
@@ -163,7 +163,7 @@ describe('Case', () => {
             'events.selfIsolation.value', 'genomeSequences','location.administrativeAreaLevel1',
             'location.administrativeAreaLevel2','location.administrativeAreaLevel3',
             'location.country','location.geoResolution','location.geometry.latitude','location.geometry.longitude',
-            'location.name','location.place','location.query','notes','pathogens',
+            'location.name','location.place','location.query','pathogens',
             'preexistingConditions.hasPreexistingConditions','preexistingConditions.values',
             'revisionMetadata.creationMetadata.curator','revisionMetadata.creationMetadata.date',
             'revisionMetadata.creationMetadata.notes','revisionMetadata.editMetadata.curator',

verification/curator-service/api/openapi/openapi.yaml

@@ -1590,14 +1590,6 @@ components:
                                 type: integer
                                 format: int32
                                 minimum: 0
-                notes:
-                    type: string
-                    description: >
-                        Anything that does not fit in a schema but worth mentioning about
-                        the case
-                    example: >
-                        Case travelled to meet their family in their hometown, got infected
-                        at a party there.
                 revisionMetadata:
                     type: object
                     description: Various revisions of this case over time

verification/curator-service/ui/cypress/integration/components/ViewCase.spec.ts

@@ -56,7 +56,7 @@ describe('View case', function () {
             cy.visit('/');
             cy.visit(`cases/view/${resp.body.cases[0]._id}`);
             cy.contains('France');
-            cy.contains('some notes');
+            cy.should('not.contain', 'some notes');
             cy.contains('www.example.com');
             cy.contains('PCR test');
             cy.contains('French');

verification/curator-service/ui/src/components/Case.tsx

@@ -148,7 +148,6 @@ export interface Case {
     travelHistory: TravelHistory;
     genomeSequences: GenomeSequence[];
     pathogens: Pathogen[];
-    notes: string;
     revisionMetadata: RevisionMetadata;
     exclusionData?: ExclusionData;
     variant?: Variant;

verification/curator-service/ui/src/components/ViewCase.test.tsx

@@ -57,9 +57,6 @@ it('loads and displays case', async () => {
     expect(getByText('2020-01-20')).toBeInTheDocument();
     expect(getByText('xyz789')).toBeInTheDocument();
     expect(getByText('2020-04-13')).toBeInTheDocument();
-    expect(
-        getByText('Contact of a confirmed case at work.'),
-    ).toBeInTheDocument();
     // Demographics.
     expect(getByText('Non-binary/Third gender')).toBeInTheDocument();
     expect(getByText('50-59')).toBeInTheDocument();

verification/curator-service/ui/src/components/ViewCase.tsx

@@ -235,12 +235,6 @@ function CaseDetails(props: CaseDetailsProps): JSX.Element {
                     >
                         vaccines
                     </Button>
-                    <Button
-                        variant="text"
-                        onClick={(): void => scrollTo('notes')}
-                    >
-                        notes
-                    </Button>
                 </nav>
             )}
             <div
@@ -722,20 +716,6 @@ function CaseDetails(props: CaseDetailsProps): JSX.Element {
                         </Grid>
                     </Scroll.Element>
                 </Paper>
-                <Paper className={classes.paper} variant="outlined" square>
-                    <Scroll.Element name="notes" className={classes.casebox}>
-                        <Typography
-                            className={classes.sectionTitle}
-                            variant="overline"
-                        >
-                            Notes
-                        </Typography>
-                        <Grid container className={classes.grid}>
-                            <RowHeader title="Notes" />
-                            <RowContent content={props.c.notes} />
-                        </Grid>
-                    </Scroll.Element>
-                </Paper>
             </div>
         </>
     );