Ensure incompletely extracted bin files get re-extracted #392
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…json creation time
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@ngreenwald with this PR, your STANFORD cohort stitched images don't show the corrupted artifacts on the bottom of images anymore. |
camisowers
requested changes
Jul 24, 2023
srivarra
requested changes
Jul 24, 2023
camisowers
approved these changes
Jul 24, 2023
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What is the purpose of this PR?
Closes #389. In some cases, even if the
.jsonfile is written for a FOV during a MIBI run, the.binfile will not have been fully copied over. The watcher needs to account for these cases because otherwise, the data extracted from the.binfile will be incomplete, leading to the artifacts highlighted in the issue.How did you implement your changes
When the control statement in
check_completeruns, one final pass of all the FOVs needs to be conducted. Offending.binfiles will have their created timestamp be later than their modified timestamp, in which case, the.binfile is once again thrown into the extraction pipeline.Remaining issues
Full testing needs to be conducted on @ngreenwald's cohort.