pepkit / pepkit/pephub

derived sample_names cannot be modified

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bug server-side
Dominant language
TypeScript
Stars
22
Forks
2
PR merge metrics
No merged PRs in 30d

Description

The sample_name in PEPhub can be derived and modified in the config file.

Unfortunately, because of this, if sample_name does not exist in the sample table, modifying of the project becomes impossible.
An exception occurs when trying to retrieve the sample name from a sample table that was not initialized by peppy. The error is happening in pepdbagent.

Image

Example pep:

pep_version: 2.1.0
sample_table: samples.csv
name: cm4ai_images
description: ''
sample_modifiers:
  append:
    sample_name: key
  derive:
    attributes:
    - sample_name
    sources:
      key: '{Gene_Name}_{Treatment}'

csv file:

AntibodyID ENSEMBLID Gene_Name Treatment PlateID Well
CAB005042 ens123 EIF5A Paclitaxel 3 C2
CAB005042 ens124 EIF5A Vorinostat 3 C2
CAB005042 ens125 EIF5A untreated 3 C2

Contributor guide

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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 by reproducing the issue with the example PEP and trace sample_name retrieval through pepdbagent when the sample table was not initialized by peppy. Check the project modification path and confirm that a derived sample_name can be changed even when it is absent from the sample table, with modification completing without an exception.

Written by the indexing model from the issue text.

Assessment

Tech stack
typescript
Domain
backend, databases
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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