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fix: move image_assembler and precompute_slide to the image-tools images - #27
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…age-tools images The image-assembler-plugin 1.4.0-dev0 and precompute-slide-plugin 1.7.0-dev0 images pin preadator 0.3.0.dev1. Its worker initializer reads each worker's name with a zero-timeout get on a shared queue, so a worker that loses the queue's lock to a sibling gets queue.Empty and the process pool breaks. Under load this failed 10/30 assembler and 12/30 precompute runs on the BBBC001 data. image-assembler-tool 1.4.3 uses the stdlib ProcessPoolExecutor and no preadator: 0/150 under the same load. precompute-slide-tool 1.7.3-dev0 uses preadator 0.4.0.dev2, which still has the zero-timeout get in a nested ProcessManager, so it fails far less often (2/90) but not never. 1.7.2 cannot be used: it fails on the deflate-compressed TIFF the new assembler writes (ADOBE_DEFLATE needs imagecodecs). The new precompute-slide's imageType values are Intensity and Segmentation instead of image and segmentation, so the bbbc workflows pass Intensity. The doc and manifest links point at the image-tools repository the tools moved to.
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Fixes #26.
What
image_assembler.cwl:polusai/image-assembler-plugin:1.4.0-dev0→polusai/image-assembler-tool:1.4.3. The new image uses the stdlib process pool and no preadator. Its options and output are unchanged.precompute_slide.cwl:polusai/precompute-slide-plugin:1.7.0-dev0→polusai/precompute-slide-tool:1.7.3-dev0. ItsimageTypevalues are nowIntensity/Segmentation, sobbbc.wicandbbbc.pypassIntensity, and the input's label says so.Why
Both old images install preadator 0.3.0.dev1, whose worker start-up races on a zero-timeout queue read and breaks the process pool intermittently (Nicholas-Schaub/preadator#12). Under load that failed 10/30 assembler and 12/30 precompute runs.
Choices a reviewer should know
ADOBE_DEFLATEneedsimagecodecs). 1.7.3-dev0 reads it.ProcessManager, so it can still fail, at a much lower rate. That ends when preadator releases a fix and precompute-slide-tool is rebuilt on it.Measured (CI cannot show a failure rate)
Each tool on the BBBC001 intermediates, 3 runs in parallel:
image-assembler-tool:1.4.3precompute-slide-tool:1.7.3-dev0The whole workflow through Sophios with cwltool, 6 runs each, 3 at a time:
bbbc.wic: 6/6.bbbc.py: 5/6. The one failure was the remaining precompute race.