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Retry missing fov_group zip files in case of DeepCell response error #628

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alex-l-kong opened this issue Jun 29, 2022 · 2 comments · Fixed by #1023
Closed

Retry missing fov_group zip files in case of DeepCell response error #628

alex-l-kong opened this issue Jun 29, 2022 · 2 comments · Fixed by #1023
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enhancement New feature or request

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@alex-l-kong
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Is your feature request related to a problem? Please describe.

The currently-open PR to address retrying in case of a bad DeepCell response assumes that this operation can be completed in n tries, printing an error if it doesn't. In the long term, what we want happening is to identify the fov_groups that don't have an associated .zip file, then re-run the call to Deepcell on those.

Describe the solution you'd like

This requires a few steps to complete:

  1. Standardized naming conventions for .zip files. Currently, it's hard to associate which FOVs were placed in which .zip files without unzipping them. A more indicative name would be the easier solution.
  2. Enclose the call to the Deepcell runner function in a loop, with a check to see if all the .zip files have been created (number will depend on the batch size). If not, then identify which fov_groups need to be resent, and remain in the loop. Otherwise, break.
@alex-l-kong alex-l-kong added the enhancement New feature or request label Jun 29, 2022
@alex-l-kong
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Addressed by #605.

@ngreenwald
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@alex-l-kong it says in the description that the currently open PR (#605) doesn't address this issue. In addition, that PR has a detailed discussion of what a future PR would look like to address this. I appreciate you helping to clean up stale issues, but please make sure they're actually stale before closing them.

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3 participants