cytomining / cytomining/profiling-recipe

feature_select not parsing batches correctly

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#43 0 comments 0 reactions 0 assignees View on GitHub
bug
Dominant language
Python
Stars
11
Forks
34
PR merge metrics
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Description

Needs to be confirmed/replicated, but I had a config with two batches set up just like example in config:
```
---
batch:
plates:
- name:
process: true
- name:
process: true
process: true
---
batch:
plates:
- name:
process: true
- name:
process: true
process: true
```
and had all steps set to `perform: false` other than `feature_select`.

When I triggered it printed `Now processing...batch: Batch1` but went immediately to `Now processing...batch: Batch2` without performing the feature selection on Batch1. (Batch2 feature selected appropriately)

I then set Batch2 `process: false` and it errored:
```
File "/Users/eweisbar/Desktop/github/PROJECT/profiling-recipe/profiles/utils.py", line 15, in load_pipeline
if "pipeline" in data.keys():
AttributeError: 'NoneType' object has no attribute 'keys'
```
I then deleted Batch2 from the config and Batch1 ran fine.

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Research direction

Reproduce the two-batch configuration with only feature_select enabled, then inspect profiles/utils.py at load_pipeline and the batch-processing path. Confirm that feature selection runs for each process-enabled batch and that disabling a batch does not produce the reported NoneType error.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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