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1995 split cases collection #2003

Merged
merged 21 commits into from
Jul 19, 2021
Merged

1995 split cases collection #2003

merged 21 commits into from
Jul 19, 2021

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iamleeg
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@iamleeg iamleeg commented Jul 16, 2021

This does all the stuff to make sure that GISAID/other excluded sources don't get into the cases collection, and reverts to using find() queries instead of aggregations for looking up cases which is sometimes hundreds of times faster.

What is doesn't do is migrate any of the existing data: AFAICT the only impact is that there's GISAID data in dev so we can delete and re-import if needed. No impact on prod.

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codecov-commenter commented Jul 16, 2021

Codecov Report

Merging #2003 (3a4b10a) into main (999e0a1) will decrease coverage by 15.72%.
The diff coverage is 89.90%.

Impacted file tree graph

@@             Coverage Diff             @@
##             main    #2003       +/-   ##
===========================================
- Coverage   81.40%   65.67%   -15.73%     
===========================================
  Files          56      105       +49     
  Lines        1845     3511     +1666     
  Branches      337     1033      +696     
===========================================
+ Hits         1502     2306      +804     
- Misses        343     1205      +862     
Impacted Files Coverage Δ
...tion/curator-service/ui/src/components/App/App.tsx 79.60% <ø> (ø)
data-serving/data-service/src/controllers/case.ts 82.28% <89.52%> (+1.81%) ⬆️
data-serving/data-service/src/model/case.ts 100.00% <100.00%> (ø)
data-serving/data-service/src/model/source.ts 100.00% <100.00%> (ø)
verification/curator-service/api/src/model/user.ts
...ion/curator-service/api/src/model/regex-parsing.ts
...rification/curator-service/api/src/model/source.ts
...ation/curator-service/api/src/controllers/users.ts
...ation/curator-service/api/src/util/validate-env.ts
...urator-service/api/src/clients/aws-batch-client.ts
... and 92 more

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@iamleeg
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iamleeg commented Jul 16, 2021

@abhidg @jim-sheldon fixed the date filtering now, this should be ready to go.

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Not sure about the package-lock.json diff (lockfileVersion changed, maybe due to different npm version?) other than that, looks good.

data-serving/data-service/src/controllers/case.ts Outdated Show resolved Hide resolved
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@abhidg abhidg self-requested a review July 19, 2021 13:28
@iamleeg iamleeg merged commit 1c1e2b9 into main Jul 19, 2021
@iamleeg iamleeg deleted the 1995_split_cases_collection branch July 19, 2021 14:24
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4 participants