pepkit / pepkit/pephub

PEPhub wont save my PEP

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bug help wanted
Dominant language
TypeScript
Stars
22
Forks
2
PR merge metrics
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Description

I can't get PEPhub to save my PEP. I have tried two ways:

  1. File upload interface
  2. 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:
  1. Log in to PEPhub
  2. Navigate to your profile
  3. Click "Add" at the top right
  4. Navigate to the "upload PEP" form
  5. Select the attached files in the file selector
  6. Click, submit
  7. 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

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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