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

Use Ensembl v112 to temporarily address the missing exons issue #75

Merged
merged 4 commits into from
Dec 13, 2024
Merged

Use Ensembl v112 to temporarily address the missing exons issue #75

merged 4 commits into from
Dec 13, 2024

Conversation

northwestwitch
Copy link
Member

@northwestwitch northwestwitch commented Dec 13, 2024 •
edited
Loading

Description

Fixed

How to test

  • Launch the server -> schug serve --reload
  • In another terminal window, download exons in build 38 -> curl -X 'GET' 'http://0.0.0.0:8000/exons/ensembl_exons/?build=38' > exons_GRCh38_test.txt

Expected test outcome

  • Make sure missing exons are present in the downloaded data -> grep ENST00000414620 exons_GRCh38_test.txt

Review

  • Tests executed by CR, Jakob37
  • "Merge and deploy" approved by
    Thanks for filling in who performed the code review and the test!

This version is a

  • MAJOR - when you make incompatible API changes
  • MINOR - when you add functionality in a backwards compatible manner
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

@sonarqubecloud SonarQubeCloud
Copy link

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@northwestwitch
Copy link
Member Author

northwestwitch commented Dec 13, 2024 •
edited
Loading

@Jakob37 This is deployed to our stage server now. To test it:

curl -X 'GET' 'https://schug-stage.scilifelab.se/exons/ensembl_exons/?build=38' > exons_GRCh38_test.txt

@northwestwitch northwestwitch added Effort S Effort small Gain L Gain large labels Dec 13, 2024
@Jakob37
Copy link

Jakob37 commented Dec 13, 2024

@Jakob37 This is deployed to our stage server now. To test it:

curl -X 'GET' 'https://schug-stage.scilifelab.se/exons/ensembl_exons/?build=38' > exons_GRCh38_test.txt

$ curl -X 'GET' 'https://schug-stage.scilifelab.se/exons/ensembl_exons/?build=38'
<html>
<head><title>403 Forbidden</title></head>
<body>
<center><h1>403 Forbidden</h1></center>
<hr><center>nginx</center>
</body>
</html>

I'll try it out through my local Schug version ..

@northwestwitch
Copy link
Member Author

$ curl -X 'GET' 'https://schug-stage.scilifelab.se/exons/ensembl_exons/?build=38'

<title>403 Forbidden</title>

403 Forbidden

nginx

Ah sorry!

@Jakob37
Copy link

Jakob37 commented Dec 13, 2024

Repost from issue - I can see exons now!

241127_schug_ensembl$ grep ENST00000414620 *
ensembl_transcripts.tsv:7       ENSG00000075624 ENST00000414620 5529282 5562790
exons_GRCh38_test_new.txt:7       ENSG00000075624 ENST00000414620 ENSE00003542066 5529535 5529663 5529658 5529663                 -1      3
exons_GRCh38_test_new.txt:7       ENSG00000075624 ENST00000414620 ENSE00001784252 5562574 5562790 5562574 5562790                 -1      1
exons_GRCh38_test_new.txt:7       ENSG00000075624 ENST00000414620 ENSE00001775033 5540676 5540771 5540676 5540771                 -1      2
exons_GRCh38_test_new.txt:7       ENSG00000075624 ENST00000414620 ENSE00001688018 5529282 5529400

@northwestwitch northwestwitch merged commit 4dc2aa3 into main Dec 13, 2024
6 checks passed
@northwestwitch northwestwitch deleted the fix_missing_exons branch December 13, 2024 10:36
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
Effort S Effort small Gain L Gain large
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@northwestwitch @Jakob37