Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Create QC to limit rare disease to the human disease branch #6416

Open
sabrinatoro opened this issue Jun 30, 2023 · 7 comments · May be fixed by #6421
Open

Create QC to limit rare disease to the human disease branch #6416

sabrinatoro opened this issue Jun 30, 2023 · 7 comments · May be fixed by #6421
Assignees
@matentzn @sabrinatoro
Labels
blocked Something needs to be done before work can proceed
Projects
Sabrina's tickets

Comments

@sabrinatoro
Copy link
Collaborator

rare diseases should be limited to the human disease branch.

This Sparql query can be used: https://api.triplydb.com/s/CQyBQn-dk
@sabrinatoro
Copy link
Collaborator Author

There are 20 diseases that are 'rare' and are in the susceptibility branch. I will update them.
(@matentzn : should I wait and keep these as a test for the QC?)

@sabrinatoro sabrinatoro added this to to do in Sabrina's tickets via automation Jun 30, 2023
@matentzn
Copy link
Member

You should be able to do this yourself! Just add the query as

src/sparql/qc/mondo/qc-susceptibility-rare.sparql

open a PR like https://github.com/monarch-initiative/mondo/pull/6248/files

and ask me for a review!

@sabrinatoro
Copy link
Collaborator Author

sabrinatoro commented Jun 30, 2023 •
edited

Let me ask the question differently:
If I leave these errors (the 20 susceptibility terms that are in the rare subset), will it be caught in the PR adding the QC test?
Or will it be caught only after the PR is merged (and therefore through off a failure for everything as soon as the PR is merge)?
(I think number 2, but I am hoping for number 1)

Just wondering about order of operations and if I will possibly "break" everyone's PR.

@sabrinatoro
Copy link
Collaborator Author

(and yes :-) I was planning of doing it myself :-) )

@matentzn
Copy link
Member

I rcommend to write the failing check first, then fix. Two Different PRs!

So:

  1. Make PR (PR1) that fails.
  2. Fix everything on another PR. Nothing will fail (because the test is still on PR1).
  3. Merge master into PR1
  4. If passes, merge.

@sabrinatoro
Copy link
Collaborator Author

Makes sense. Thank you!

@sabrinatoro sabrinatoro mentioned this issue Jun 30, 2023
Closed
sabrinatoro added a commit that referenced this issue Jun 30, 2023
@sabrinatoro
remove susceptibility terms from "rare" subset
eca82b4 
Addresses #6416
@sabrinatoro sabrinatoro mentioned this issue Jun 30, 2023
Open
@sabrinatoro
Copy link
Collaborator Author

Issue blocked by #6419

sabrinatoro added a commit that referenced this issue Jun 30, 2023
@sabrinatoro
create QC for susceptibility
3b44318 
Closes #6416

DO NOT MERGE until #6419 is closed.
@sabrinatoro sabrinatoro linked a pull request Jun 30, 2023 that will close this issue
Open
@sabrinatoro sabrinatoro added this to the September release milestone Jun 30, 2023
@sabrinatoro sabrinatoro added the blocked Something needs to be done before work can proceed label Jun 30, 2023
@sabrinatoro sabrinatoro mentioned this issue Oct 25, 2023
Closed
@nicolevasilevsky nicolevasilevsky removed this from the December release milestone Nov 27, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@matentzn matentzn

@sabrinatoro sabrinatoro

Labels
blocked Something needs to be done before work can proceed
Projects
Sabrina's tickets
to do
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

DO NOT MERGE until... create QC for susceptibility monarch-initiative/mondo
3 participants
@nicolevasilevsky @matentzn @sabrinatoro