[BUG]: Junifer log files formatting #128

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opened 2022-11-15 08:00:36 +00:00 by LeSasse · 1 comment

LeSasse commented

2022-11-15 08:00:36 +00:00

(Migrated from github.com)

Is there an existing issue for this?

I have searched the existing issues

Current Behavior

The names of junifer log files put a comma between elements of elements:

Expected Behavior

I think something like an underscore might be nicer instead of a comma which is not so nice in a file name.

Steps To Reproduce

yaml file:

workdir: /tmp

datagrabber:
    kind: DataladAOMICPIOP1
    tasks: ["restingstate"]

markers:
  - name: Schaefer100x17_FC
    kind: FunctionalConnectivityParcels
    parcellation: Schaefer100x17
    cor_method: correlation
  - name: Schaefer200x17_FC
    kind: FunctionalConnectivityParcels
    parcellation: Schaefer200x17
    cor_method: correlation
  - name: Schaefer400x17_FC
    kind: FunctionalConnectivityParcels
    parcellation: Schaefer400x17
    cor_method: correlation

preprocess:
    kind: fMRIPrepConfoundRemover
    strategy:
        motion: full
        wm_csf: full
        global_signal: full
    low_pass: 0.08
    high_pass: 0.008

storage: 
  kind: SQLiteFeatureStorage
  uri: /data/project/identification_prediction/data/junifer_aomic/storage/PIOP1

queue:
  jobname: PREPROCESS_PIOP1
  kind: HTCondor
  env:
    kind: conda
    name: junifer
  mem: 8G

I just run junifer queue on this yaml file.

Environment

junifer:
  version: 0.0.1.dev909
python:
  version: 3.10.6
  implementation: CPython
dependencies:
  click: 8.1.3
  numpy: 1.22.4
  datalad: 0.17.9
  pandas: 1.4.4
  nibabel: 4.0.2
  nilearn: 0.9.2
  sqlalchemy: 1.4.44
  yaml: '6.0'
system:
  platform: Linux-4.19.0-21-amd64-x86_64-with-glibc2.28
environment:
  LC_CTYPE: en_US.UTF-8
  PATH: /home/lsasse/miniconda3/envs/junifer/bin:/home/lsasse/miniconda3/condabin:/home/lsasse/.dotfiles/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/local/games:/usr/games



### Relevant log output

_No response_

### Anything else?

_No response_

### Is there an existing issue for this? - [X] I have searched the existing issues ### Current Behavior The names of junifer log files put a comma between elements of elements: ![Selection_015](https://user-images.githubusercontent.com/73998642/201862081-d68f2aef-d758-4162-87b9-80671b9c8940.png) ### Expected Behavior I think something like an underscore might be nicer instead of a comma which is not so nice in a file name. ### Steps To Reproduce yaml file: ``` workdir: /tmp datagrabber: kind: DataladAOMICPIOP1 tasks: ["restingstate"] markers: - name: Schaefer100x17_FC kind: FunctionalConnectivityParcels parcellation: Schaefer100x17 cor_method: correlation - name: Schaefer200x17_FC kind: FunctionalConnectivityParcels parcellation: Schaefer200x17 cor_method: correlation - name: Schaefer400x17_FC kind: FunctionalConnectivityParcels parcellation: Schaefer400x17 cor_method: correlation preprocess: kind: fMRIPrepConfoundRemover strategy: motion: full wm_csf: full global_signal: full low_pass: 0.08 high_pass: 0.008 storage: kind: SQLiteFeatureStorage uri: /data/project/identification_prediction/data/junifer_aomic/storage/PIOP1 queue: jobname: PREPROCESS_PIOP1 kind: HTCondor env: kind: conda name: junifer mem: 8G ``` I just run `junifer queue` on this yaml file. ### Environment ```markdown junifer: version: 0.0.1.dev909 python: version: 3.10.6 implementation: CPython dependencies: click: 8.1.3 numpy: 1.22.4 datalad: 0.17.9 pandas: 1.4.4 nibabel: 4.0.2 nilearn: 0.9.2 sqlalchemy: 1.4.44 yaml: '6.0' system: platform: Linux-4.19.0-21-amd64-x86_64-with-glibc2.28 environment: LC_CTYPE: en_US.UTF-8 PATH: /home/lsasse/miniconda3/envs/junifer/bin:/home/lsasse/miniconda3/condabin:/home/lsasse/.dotfiles/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/local/games:/usr/games ``` ``` ### Relevant log output _No response_ ### Anything else? _No response_

fraimondo commented

2022-11-15 08:53:55 +00:00

(Migrated from github.com)

@LeSasse can you try running from PR #129 ?

We don't have tests yet, but the issue should be solved there.

@LeSasse can you try running from PR #129 ? We don't have tests yet, but the issue should be solved there.