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nadeemlab / SPT

Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images
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Too many null values in computed metrics #348

Closed jimmymathews closed 1 month ago

jimmymathews commented 3 months ago

In recent testing, repeated warnings were observed:

api       ║ 08-13 20:18:41 [WARNING]  71 ondemand.providers.pending_provider            ┃ Feature 187 has too many values, 52 / 50.
api       ║ INFO:     10.6.176.85:42602 - "GET /request-spatial-metrics-computation-custom-phenotypes/?negative_marker=&positive_marker=TCF7&negative_marker2=&positive_marker2=PD1&study=Urothelial+ICI&feature_class=neighborhood+enrichment&radius=100 HTTP/1.1" 200 OK

This was due to multiple inserts of null values in case of a single value computation failure. We should check the error handling and make sure this can be explained by and fixed with a review of the null inserts logic. Hopefully this is not due to a higher-level networking issue (e.g. multiple containers taking the same job from the queue, or some kind of automatic restart).

jimmymathews commented 1 month ago

The handling of these inserts has changed since this issue was opened, and the bug has not appeared again as far as I can tell. Considering this fixed.