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Fix data-service CI failures #2691

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merged 1 commit into from
May 4, 2022
Merged

Fix data-service CI failures #2691

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65 changes: 43 additions & 22 deletions data-serving/data-service/src/controllers/case.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -39,49 +39,66 @@ class InvalidParamError extends Error {}
type BatchValidationErrors = { index: number; message: string }[];

const caseFromDTO = async (receivedCase: CaseDTO) => {
const aCase = receivedCase as unknown as LeanDocument<CaseDocument>;
const aCase = (receivedCase as unknown) as LeanDocument<CaseDocument>;
if (receivedCase.demographics?.ageRange) {
// won't be many age buckets, so fetch all of them.
const allBuckets = await AgeBucket.find({});
const caseStart = receivedCase.demographics?.ageRange.start;
const caseEnd = receivedCase.demographics?.ageRange.end;
const matchingBucketIDs = allBuckets.filter(b => {
const bucketContainsStart = (b.start <= caseStart && b.end >= caseStart);
const bucketContainsEnd = (b.start <= caseEnd && b.end >= caseEnd);
const bucketWithinCaseRange = (b.start > caseStart && b.end < caseEnd);
return bucketContainsStart || bucketContainsEnd || bucketWithinCaseRange;
}).map((b) => (b._id));
const matchingBucketIDs = allBuckets
.filter((b) => {
const bucketContainsStart =
b.start <= caseStart && b.end >= caseStart;
const bucketContainsEnd =
b.start <= caseEnd && b.end >= caseEnd;
const bucketWithinCaseRange =
b.start > caseStart && b.end < caseEnd;
return (
bucketContainsStart ||
bucketContainsEnd ||
bucketWithinCaseRange
);
})
.map((b) => b._id);
aCase.demographics.ageBuckets = matchingBucketIDs;
}
return aCase;
}
};

const dtoFromCase = async (storedCase: LeanDocument<CaseDocument>) => {
let dto = storedCase as unknown as CaseDTO;
if (storedCase.demographics && storedCase.demographics.ageBuckets && storedCase.demographics.ageBuckets.length > 0) {
const ageBuckets = await Promise.all(storedCase.demographics.ageBuckets.map((bucketId) => {
return AgeBucket.findById(bucketId).lean()
}));
const minimumAge = Math.min(...(ageBuckets.map(b => b!.start)));
const maximumAge = Math.max(...(ageBuckets.map(b => b!.end)));
let dto = (storedCase as unknown) as CaseDTO;
if (
storedCase.demographics &&
storedCase.demographics.ageBuckets &&
storedCase.demographics.ageBuckets.length > 0
) {
const ageBuckets = await Promise.all(
storedCase.demographics.ageBuckets.map((bucketId) => {
return AgeBucket.findById(bucketId).lean();
}),
);
const minimumAge = Math.min(...ageBuckets.map((b) => b!.start));
const maximumAge = Math.max(...ageBuckets.map((b) => b!.end));
dto = {
...dto,
demographics: {
...dto.demographics!,
ageRange: {
start: minimumAge,
end: maximumAge,
}
}
}
},
},
};
// although the type system can't see it, there's an ageBuckets property on the demographics DTO now
delete (dto as unknown as { demographics: { ageBuckets?: [ObjectId] }}).demographics.ageBuckets;
delete ((dto as unknown) as {
demographics: { ageBuckets?: [ObjectId] };
}).demographics.ageBuckets;
}
delete dto.restrictedNotes;
delete dto.notes;

return dto;
}
};

export class CasesController {
private csvHeaders: string[];
Expand Down Expand Up @@ -124,7 +141,7 @@ export class CasesController {
delete aCase.notes;
});

res.json(await Promise.all(c.map(aCase => dtoFromCase(aCase))));
res.json(await Promise.all(c.map((aCase) => dtoFromCase(aCase))));
};

/**
Expand Down Expand Up @@ -538,7 +555,9 @@ export class CasesController {
// eslint-disable-next-line @typescript-eslint/no-explicit-any
const upsertLambda = async (c: any) => {
delete c.caseCount;
c = caseWithDenormalisedConfirmationDate(await caseFromDTO(c as CaseDTO));
c = caseWithDenormalisedConfirmationDate(
await caseFromDTO(c as CaseDTO),
);
if (
c.caseReference?.sourceId &&
c.caseReference?.sourceEntryId
Expand Down Expand Up @@ -1099,7 +1118,9 @@ export const casesMatchingSearchQuery = (opts: {
}): any => {
// set data limit to 10K by default
const countLimit = opts.limit ? opts.limit : 10000;
console.log(`Search query: ${opts.searchQuery}`);
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switch to logger.debug?

const parsedSearch = parseSearchQuery(opts.searchQuery);
console.log(`Parsed search (full text?): ${parsedSearch.fullTextSearch}`);
const queryOpts = parsedSearch.fullTextSearch
? {
$text: { $search: parsedSearch.fullTextSearch },
Expand Down
19 changes: 14 additions & 5 deletions data-serving/data-service/test/controllers/case.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ import { CaseRevision } from '../../src/model/case-revision';
import { Demographics } from '../../src/model/demographics';
import { MongoMemoryServer } from 'mongodb-memory-server';
import { Source } from '../../src/model/source';
import { PathogenDocument } from '../../src/model/pathogen';
import app from './../../src/index';
import fullCase from './../model/data/case.full.json';
import minimalCase from './../model/data/case.minimal.json';
Expand Down Expand Up @@ -310,7 +311,7 @@ describe('GET', () => {
it('Search for matching country and something else that does not match', async () => {
const res = await request(app)
.get(
'/api/cases?page=1&limit=1&q=country%3ADE%occupation%3Anope',
'/api/cases?page=1&limit=1&q=country%3ADE%20occupation%3Anope',
)
.expect(200)
.expect('Content-Type', /json/);
Expand Down Expand Up @@ -589,7 +590,9 @@ describe('POST', () => {

const changedCaseWithEntryId = new Case(fullCase);
await changedCaseWithEntryId.save();
changedCaseWithEntryId.notes = 'new notes';
changedCaseWithEntryId.pathogens = [
{ id: '304', name: 'Pneumonia' } as PathogenDocument,
];

const unchangedCaseWithEntryId = new Case(fullCase);
unchangedCaseWithEntryId.caseReference.sourceEntryId =
Expand Down Expand Up @@ -633,7 +636,9 @@ describe('POST', () => {
const changedCaseWithEntryId = new Case(fullCase);
await changedCaseWithEntryId.save();
changedCaseWithEntryId.caseReference.uploadIds = newUploadIds;
changedCaseWithEntryId.notes = 'new notes';
changedCaseWithEntryId.pathogens = [
{ id: '304', name: 'Pneumonia' } as PathogenDocument,
];

const unchangedCaseWithEntryId = new Case(fullCase);
unchangedCaseWithEntryId.caseReference.sourceEntryId =
Expand Down Expand Up @@ -767,7 +772,9 @@ describe('POST', () => {
it('batch upsert should result in create and update metadata', async () => {
const existingCase = new Case(fullCase);
await existingCase.save();
existingCase.notes = 'new notes';
existingCase.pathogens = [
{ id: '104', name: 'Pneumonia' } as PathogenDocument,
];

const res = await request(app)
.post('/api/cases/batchUpsert')
Expand Down Expand Up @@ -798,7 +805,9 @@ describe('POST', () => {
it('batch upsert should result in case revisions of existing cases', async () => {
const existingCase = new Case(fullCase);
await existingCase.save();
existingCase.notes = 'new notes';
existingCase.pathogens = [
{ id: '104', name: 'Pneumonia' } as PathogenDocument,
];

const res = await request(app)
.post('/api/cases/batchUpsert')
Expand Down
1 change: 0 additions & 1 deletion data-serving/data-service/test/model/data/case.full.json
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,6 @@
"id": 104
}
],
"notes": "Contact of a confirmed case at work.",
"revisionMetadata": {
"revisionNumber": 0,
"creationMetadata": {
Expand Down