AlexsLemonade / AlexsLemonade/refinebio
Encountered error in R code while running gene_convert_illumina.R pipeline during processing of /...
- Dominant language
- Python
- Stars
- 135
- Forks
- 21
- PR merge metrics
- No merged PRs in 30d
Description
Pretty sure the line with the error message should be using result.returncode and result.stderr. Not e. Assigned myself but if anyone else wants to tackle it before I get to things today, feel free. Should be a quick fix.
https://sentry.io/greenelab/staging-refinebio/issues/667326691/
```
Encountered error in R code while running gene_convert_illumina.R pipeline during processing of /home/user/data_store/GSE98897/raw/GSM2627179-tbl-1.txt.fixed: Can't convert 'NoneType' object to str implicitly
```
Contributor guide
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Research direction
Locate the error-handling code for the gene_convert_illumina.R pipeline and inspect the line that produces the shown message. Verify the available result fields and run the relevant pipeline or tests with a failing R conversion; done means the error reports the command return code and stderr instead of the missing value.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, r
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100