Fix: exit non-zero when all slides fail in aggregate_slide_features_batch#132
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raylim wants to merge 1 commit into
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Fix: exit non-zero when all slides fail in aggregate_slide_features_batch#132raylim wants to merge 1 commit into
raylim wants to merge 1 commit into
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…atch Previously, when TITAN slide aggregation failed for every slide in a batch (e.g. CUDA OOM), extract_features would exit 0 with no output files. Nextflow then showed confusing 'exit:0 Failed Tasks' and spuriously retried the tasks using the cluster-profile retry policy. Fix (two locations): 1. feature_extract.py aggregate_slide_features_batch: raise RuntimeError when len(failed_slides) == num_slides, for both model and non-model paths. 2. extract_features.py _main_batch: defense-in-depth check after aggregate_slide_features_batch — raise if all output .pt files are missing. With errorStrategy='ignore' in nextflow.config, exit:1 is properly ignored; WDS coverage check resets the slides to PENDING for retry in the next batch. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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Duplicate of #131, which has been merged. |
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Summary
When TITAN slide aggregation fails for every slide in a batch (e.g. CUDA OOM),
extract_featureswas silently exiting 0 with no output files. Nextflow showed confusingexit:0 Failed Tasksand spuriously retried tasks.Changes
feature_extract.py aggregate_slide_features_batch: raiseRuntimeErrorwhen all slides fail (both model and non-model paths).extract_features.py _main_batch: defense-in-depth — raise if all output.ptfiles are missing after aggregation.With
errorStrategy='ignore'in nextflow.config, exit:1 is cleanly ignored; WDS coverage check resets slides to PENDING.Testing
pytest tests/mussel/utils/test_feature_extract.py tests/mussel/cli/test_extract_features.py