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fix: pull the rebuilt tool images from vjaganat90 - #28
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bbbcdownload has failed since 2026-10-14: polusai/bbbc-download-plugin:0.1.0-dev1 (Ubuntu 20.04, a 2022 CA bundle) does not trust the certificate chain data.broadinstitute.org now serves. The seven images are rebuilt from their PolusAI/image-tools sources (precompute-slide-tool from NovagenResearch/image-tools#571) on the newest base images with fresh CA certificates, under the tools' own image names and dev-bumped versions, so they can be re-tagged to polusai/ unchanged. The file-renaming, montage and basic-flatfield plugin images give way to the image-tools tools. precompute-slide-tool 1.7.3-dev1 drops preadator, whose worker initializer reads its name with a zero-timeout queue get and breaks the process pool under load: 11/300 runs of 1.7.3-dev0 failed with 12 runs at once on the BBBC001 data, 0/300 of 1.7.3-dev1.
file-renaming-tool takes --mapDirectory as a boolean flag where file-renaming-plugin took raw, map or nothing, so any string value is now an unexpected extra argument. The bbbc workflows leave it unset.
This was referenced Oct 14, 2026
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What
The seven adapters pull images rebuilt from PolusAI/image-tools fa9f73c (precompute-slide-tool from Precompute-update-docker-python NovagenResearch/image-tools#571) with one commit per tool, tagged
vjaganat90/<tool>:<version>:Every image has a current CA bundle. precompute-slide-tool runs its slides on the stdlib
ProcessPoolExecutorinstead of preadator. ome-converter and image-assembler ship the JRE that bfio's Bio-Formats reader needs, so they no longer download it at run time.file-renaming's
mapDirectoryis a boolean flag in file-renaming-tool; no workflow here sets it.Why
data.broadinstitute.org's certificate chain does not verify against the 2022 CA bundle in bbbc-download-plugin:0.1.0-dev1, so every bbbc workflow fails at the download. preadator 0.4.0.dev2 also races when its pool starts (
queue.EmptyinProcessManager.__init__), which is the intermittent precompute_slide failure.Two output changes come with the newer tools and match polusai's own builds of the same sources: ome-converter writes
PhysicalSizefrom the TIFFs' resolution into the OME-XML, and basic-flatfield 2.1.6 (BaSiCPy 1.2) gives slightly different fields and rejects groups of a single image. No workflow here uses basic-flatfield. The images are amd64 only, because polusai/bfio and the TensorFlow GPU base are amd64 only.