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

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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
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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

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@TimothyStiles
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TimothyStiles commented Oct 6, 2023 •
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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
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adding @Koeng101 to the issue.

@abondrn abondrn mentioned this issue Oct 30, 2023
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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
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Working on this now!

@carreter carreter removed the stale label Dec 12, 2023
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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
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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
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