checksum-directory, publish-xenium-results: Introduce checksums folder mode - #568
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checksum-directory, publish-xenium-results: Introduce checksums folder mode#568ce10-sanger wants to merge 6 commits into
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Test failure accounting
Test symbolic links skipped
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ce10-sanger
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Jun 23, 2026
| Supports two modes of specifying checksum locations: | ||
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| - Explicitly specifying a file to write checksums to (`--md5sums-path`) | ||
| - Specifying a directory (`--checksums-directory`). Checksums are written to a |
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md5sums-directory?
ce10-sanger
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Jun 23, 2026
| - Explicitly specifying a file to write checksums to (`--md5sums-path`) | ||
| - Specifying a directory (`--checksums-directory`). Checksums are written to a | ||
| file within the directory that can be uniquely retrieved by other | ||
| npg-irods-python utilities. |
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explain structure of dir of files with one file per dir
ce10-sanger
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Jun 23, 2026
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| The output follows GNU coreutils md5sum format. Checksum files (*.md5) are | ||
| ignored. Files with existing checksums are skipped. | ||
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simpler just to have one file?
ce10-sanger
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Jun 23, 2026
| continue | ||
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| with open(path, "rb") as f: | ||
| if file_path.is_symlink(): |
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fix problem at source rather than filtering out?
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decided to add as flag
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label up as a workaround
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June 23, 2026 11:32
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moved back to draft - will return to decisions when learnt more from building xenium automation |
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Docs unclear whether directory of files per file or files per directory
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Introduces a new checksumming mode - checksums folder - where instead of specifying a checksums file you specify a directory and the tools calculate location of the checksums file within the checksums folder.
Motivated by adopting checksumming in Xenium publishing and not wanting to change the interface of
publish-xenium-resultsfrom accepting directories to publish one per line.