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ENH: organize - show files with conflicts requiring adding _obj- #1490

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@yarikoptic yarikoptic commented Aug 20, 2024

Logging check is currently not really functioning since IIRC we do enable logging into a file at higher level than INFO. So we might need to tune decision making here

Should provide UX side to partially address:

example:

❯ dandi organize --dandiset-path /tmp/outds /home/yoh/proj/dandi/dandisets/000004/sub-P53CS/*nwb /home/yoh/proj/dandi/dandisets/000004/sub-P54CS/*nwb
...
2024-08-19 20:03:17,448 [    INFO] Symlink support autodetected; setting files_mode='symlink'
2024-08-19 20:03:17,452 [    INFO] 2 out of 5 paths are not unique.
 2 paths 'compete' for the path 'sub-P53CS/sub-P53CS_ses-20171101_ecephys+image.nwb':
  /home/yoh/proj/dandi/dandisets/000004/sub-P53CS/sub-P53CS_ses-20171101_obj-108aqix_ecephys+image.nwb
  /home/yoh/proj/dandi/dandisets/000004/sub-P53CS/sub-P53CS_ses-20171101_obj-lj04dr_ecephys+image.nwb
 3 paths 'compete' for the path 'sub-P54CS/sub-P54CS_ses-20180101_ecephys+image.nwb':
  /home/yoh/proj/dandi/dandisets/000004/sub-P54CS/sub-P54CS_ses-20180101_obj-1ru98u8_ecephys+image.nwb
  /home/yoh/proj/dandi/dandisets/000004/sub-P54CS/sub-P54CS_ses-20180101_obj-1ukzk61_ecephys+image.nwb
  /home/yoh/proj/dandi/dandisets/000004/sub-P54CS/sub-P54CS_ses-20180101_obj-1vx1a5w_ecephys+image.nwb
 We will try adding _obj- based on crc32 of object_id

TODOs

  • check what leads to tests failing ATM
  • extend test covering this code to have multiple groups requiring _obj

dandi/organize.py Outdated Show resolved Hide resolved
Logging check is currently not really functioning since IIRC we
do enable logging into a file at higher level than INFO. So we
might need to tune decision making here
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codecov bot commented Aug 20, 2024

Codecov Report

Attention: Patch coverage is 66.66667% with 5 lines in your changes missing coverage. Please review.

Project coverage is 88.60%. Comparing base (44e097f) to head (e456ebb).

Files Patch % Lines
dandi/organize.py 66.66% 5 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master    #1490      +/-   ##
==========================================
+ Coverage   88.55%   88.60%   +0.04%     
==========================================
  Files          77       77              
  Lines       10568    10581      +13     
==========================================
+ Hits         9359     9375      +16     
+ Misses       1209     1206       -3     
Flag Coverage Δ
unittests 88.60% <66.66%> (+0.04%) ⬆️

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dandi/organize.py Outdated Show resolved Hide resolved
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yarikoptic and others added 2 commits August 20, 2024 10:00
Co-authored-by: John T. Wodder II <[email protected]>
…s at DEBUG

With this change logging looks like

    2024-08-21 09:42:39,718 [    INFO] 2 out of 5 paths are not unique.
     2 paths 'compete' for the path 'sub-P53CS/sub-P53CS_ses-20171101_ecephys+image.nwb':
      /home/yoh/proj/dandi/dandisets/000004/sub-P53CS/sub-P53CS_ses-20171101_obj-108aqix_ecephys+image.nwb
      /home/yoh/proj/dandi/dandisets/000004/sub-P53CS/sub-P53CS_ses-20171101_obj-lj04dr_ecephys+image.nwb
     1 more case(s) are listed at DEBUG level.
    2024-08-21 09:42:39,718 [   DEBUG] Additional non-unique paths:
     3 paths 'compete' for the path 'sub-P54CS/sub-P54CS_ses-20180101_ecephys+image.nwb':
      /home/yoh/proj/dandi/dandisets/000004/sub-P54CS/sub-P54CS_ses-20180101_obj-1ru98u8_ecephys+image.nwb
      /home/yoh/proj/dandi/dandisets/000004/sub-P54CS/sub-P54CS_ses-20180101_obj-1ukzk61_ecephys+image.nwb
      /home/yoh/proj/dandi/dandisets/000004/sub-P54CS/sub-P54CS_ses-20180101_obj-1vx1a5w_ecephys+image.nwb
    2024-08-21 09:42:39,718 [    INFO] We will try adding _obj- based on crc32 of object_id
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2 participants