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

Genbank parser doesn't handle feature attributes with colliding names. #383

Open
TimothyStiles opened this issue Oct 6, 2023 · 5 comments
Open

Genbank parser doesn't handle feature attributes with colliding names. #383

TimothyStiles opened this issue Oct 6, 2023 · 5 comments
Labels
bug Something isn't working hard A major or complex undertaking help wanted Extra attention is needed high priority High priority - something is broken or missing that is critical for users or developers. stale

Comments

@TimothyStiles
Copy link
Collaborator

TimothyStiles commented Oct 6, 2023 •
edited

Describe the bug

The genbank parser cannot handle repeating attribute keys like with /db_xref below:

Screen Shot 2023-10-06 at 2 01 30 PM

Severity of the bug

This is blocking Ark's ability to cross reference other databases. (priority)

Steps to reproduce

You can debug this by debugging BenchmarkRead(b *testing.B){} in genbank_test.go within a couple of feature extraction loops you'll see that db_xref only keeps the last reference.

Expected behavior

We need to be able to track attributes with the same key name. List of tuples?

Screenshots

Screen Shot 2023-10-06 at 3 39 43 PM

Client information

  • OS: Mac OSX 0.15.7
  • Golang version: 1.21
  • poly version v0.27.1
@TimothyStiles TimothyStiles added bug Something isn't working needs-triage An issue that needs to be triaged labels Oct 6, 2023
@TimothyStiles TimothyStiles changed the title Genbank doesn't handle feature attributes with colliding names. Genbank parser doesn't handle feature attributes with colliding names. Oct 6, 2023
@TimothyStiles TimothyStiles added help wanted Extra attention is needed high priority High priority - something is broken or missing that is critical for users or developers. hard A major or complex undertaking and removed needs-triage An issue that needs to be triaged labels Oct 6, 2023
@TimothyStiles
Copy link
Collaborator Author

adding @Koeng101 to the issue.

@abondrn abondrn mentioned this issue Oct 30, 2023
Closed
6 tasks
@github-actions GitHub Actions
Copy link

github-actions bot commented Dec 6, 2023

This issue has had no activity in the past 2 months. Marking as stale.

@github-actions github-actions bot added the stale label Dec 6, 2023
@carreter
Copy link
Collaborator

Working on this now!

@carreter carreter removed the stale label Dec 12, 2023
@carreter
Copy link
Collaborator

This should be an easy fix, but the entire genbank parser needs to be reworked, and it seems like it won't be trivial. I'll open a separate issue.

@carreter carreter added help wanted Extra attention is needed and removed help wanted Extra attention is needed labels Dec 12, 2023
@carreter carreter mentioned this issue Dec 20, 2023
Open
@github-actions GitHub Actions
Copy link

This issue has had no activity in the past 2 months. Marking as stale.

@github-actions github-actions bot added the stale label Feb 10, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working hard A major or complex undertaking help wanted Extra attention is needed high priority High priority - something is broken or missing that is critical for users or developers. stale
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@carreter @TimothyStiles