derived sample_names cannot be modified
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- 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.
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
- 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 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