PEPhub wont save my PEP
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- Dominant language
- TypeScript
- Stars
- 22
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
I can't get PEPhub to save my PEP. I have tried two ways:
- File upload interface
- Manually pasting the values in
I can confirm that locally with peppy==0.40.7, it will consume the PEP happily and let me traverse the sample/subsample table(s).
Steps to reproduce:
- Log in to PEPhub
- Navigate to your profile
- Click "Add" at the top right
- Navigate to the "upload PEP" form
- Select the attached files in the file selector
- Click, submit
- Observe error
Files
config.txt
samples.csv
subsamples.csv
It wont let me upload a yaml, but this is the config:
# pep_config.yaml
pep_version: 2.1.0
sample_table: samples.csv
subsample_table: subsamples.csv
sample_table_index: id
subsample_table_index: file_uuid
name: atlas
description: Datasets (fastqs) to be used in the training of Atacformer.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the PEPhub upload PEP form and reproduce the failure using config.txt, samples.csv, and subsamples.csv. Compare the web upload with the locally working peppy==0.40.7 input; done means both upload methods save the PEP and allow its sample and subsample tables to be traversed.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, typescript, yaml
- Domain
- api, backend, bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100