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looper isn't working with sample_table_index #458
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I believe this is a Peppy issue: pepkit/peppy#459 |
I don't think it's a peppy issue -- it's looper code that is referring to are you suggesting that peppy make available a |
Yes. I thought that was the original functionality. Some digging, for reference to this issue: |
I added a commit here where I made a test to help troubleshoot this issue further: 8fde43a Using a sample_table_index in the project config, I also replaced However, I now see an Eido validation error during the test where I simply attempt to use
Related test data: project config:
annotation sheet
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Future discussion to happen in: pepkit/peppy#459 However, will keep this open to track for Looper. |
Ok, I believe this PR in Peppy (pepkit/peppy#484) will solve this issue and the corresponding issue: pepkit/peppy#459
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Using a basic project with a sample table index fails, due to this line:
looper/looper/looper.py
Line 458 in 1468956
it's expecting there to be a
sample_name
column, which there is not, since I'm usingsample_table_index
.This makes looper not fully compliant with PEP.
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