Fix data-service CI failures

Data service CI was failing due to the notes removal change. After this, setting the 'notes' field of a case document doesn't actually result in a updated case, as the notes field is deleted by controllers, and it is not returned from the data service APIs. To simulate an updated document, this adds a pathogen key to a case.
globaldothealth · May 4, 2022 · 1f49d9b · 1f49d9b
1 parent c12dd70
commit 1f49d9b
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Showing 3 changed files with 59 additions and 28 deletions.
diff --git a/data-serving/data-service/src/controllers/case.ts b/data-serving/data-service/src/controllers/case.ts
@@ -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[];
@@ -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))));
  };
 
  /**
@@ -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
@@ -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}`);
  const parsedSearch = parseSearchQuery(opts.searchQuery);
+ console.log(`Parsed search (full text?): ${parsedSearch.fullTextSearch}`);
  const queryOpts = parsedSearch.fullTextSearch
  ? {
  $text: { $search: parsedSearch.fullTextSearch },

diff --git a/data-serving/data-service/test/controllers/case.test.ts b/data-serving/data-service/test/controllers/case.test.ts
@@ -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';
@@ -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/);
@@ -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 =
@@ -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 =
@@ -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')
@@ -779,13 +786,15 @@ describe('POST', () => {
  const newCaseInDb = await Case.findOne({
  'revisionMetadata.revisionNumber': 0,
  });
+ console.log(newCaseInDb);
  expect(newCaseInDb?.revisionMetadata.creationMetadata.curator).toEqual(
  curatorMetadata.curator.email,
  );
 
  const updatedCaseInDb = await Case.findOne({
  'revisionMetadata.revisionNumber': 1,
  });
+ console.log(updatedCaseInDb);
  expect(
  updatedCaseInDb?.revisionMetadata.updateMetadata?.curator,
  ).toEqual(curatorMetadata.curator.email);
@@ -798,7 +807,9 @@ 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')

diff --git a/data-serving/data-service/test/model/data/case.full.json b/data-serving/data-service/test/model/data/case.full.json
@@ -140,7 +140,6 @@
  "id": 104
  }
  ],
- "notes": "Contact of a confirmed case at work.",
  "revisionMetadata": {
  "revisionNumber": 0,
  "creationMetadata": {