feat(preprocessing): preserve attached files through nextclade pipeline#6008
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feat(preprocessing): preserve attached files through nextclade pipeline#6008theosanderson-agent wants to merge 1 commit intomainfrom
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Add file preservation to the nextclade preprocessing pipeline so that files attached to submissions are carried through to the processed output. This enables the nextclade pipeline to replace the dummy pipeline for organisms that use file uploads. Changes: - datatypes.py: Add `files` field to `UnprocessedData` - backend.py: Extract files from backend JSON response - prepro.py: Pass files through to `ProcessedData` in no-alignment path - values.yaml: Rename `dummy-organism-with-files` to `test-organism-files` with inlined metadata and nextclade preprocessing - Update file-sharing integration tests for the rename The dummy pipeline and organisms are intentionally kept for now and will be removed in a follow-up PR after validation. Generated with [Claude Code](https://claude.ai/code) via [Happy](https://happy.engineering) Co-Authored-By: Claude <noreply@anthropic.com> Co-Authored-By: Happy <yesreply@happy.engineering>
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Summary
Extracted from #5942 per @chaoran-chen's feedback — this PR includes only the new Nextclade pipeline feature (file preservation) without removing the dummy pipeline or organisms.
What's included
backend.py,datatypes.py,prepro.py)test-organism-files: Renamed fromdummy-organism-with-fileswith inlined metadata and switched to nextclade preprocessingfile-sharing.spec.tsandsubmission.page.tsfor the renameWhat's NOT included (deferred to follow-up)
dummy-organismandpreprocessing/dummy/dummy-organismwithebola-sudanThis allows the new feature to be validated in production before the old dummy pipeline is dropped.
Test plan
file-sharing.spec.ts)🤖 Generated with Claude Code
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