AlexsLemonade / AlexsLemonade/refinebio

Could not discover organism type for run.

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backlog metadata zf crunch
Dominant language
Python
Stars
135
Forks
21
PR merge metrics
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Description

This pertains to this accession: https://www.ebi.ac.uk/ena/data/view/SRA059568

There are a couple things that strike me as atypical about it:
* Multiple runs map to the same _sample_ accession
* The [sample metadata](https://www.ebi.ac.uk/ena/data/view/SRS369361&display=xml) contains a taxonomy id `` but no ``

In any case, I don't think this is high priority due to the low frequency but is probably worth examining eventually.

https://sentry.io/greenelab/staging-refinebio/issues/647990148/

```
Could not discover organism type for run.
```

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reviewing the Sentry report and the ENA accession SRA059568, including sample SRS369361 and its metadata. Determine why organism discovery fails when TAXON_ID is present without SCIENTIFIC_NAME, then verify the behavior for this run and related runs before considering the issue resolved.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-engineering
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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