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April 8, 2026 21:23
…blic models New response models to support returning file metadata inline with samples: - SampleFilePublic: compact file with uri and flat-dict tags - SampleWithFilesPublic(SamplePublic): extends SamplePublic with files list - SamplesWithFilesPublic: paginated wrapper for the files-enriched response Needed by backend workers to construct samplesheets from sample file data.
- Add include query parameter (list of strings) to get_project_samples route - When include contains 'files', use selectinload to eagerly load Sample -> FileSample -> File -> FileTag in a single query - Build SampleFilePublic objects with flattened tags dict per sample - Return SamplesWithFilesPublic when files requested, SamplesPublic otherwise - Avoids N+1 API calls for backend workers that need file URIs and tags
- Assert existing test_get_samples_for_a_project_with_samples verifies no 'files' key present without ?include=files - test_get_samples_include_files_with_tagged_files: R1/R2 FASTQs, flat tags - test_get_samples_include_files_sample_with_no_files: files is null - test_get_samples_include_files_with_untagged_files: tags is null - test_get_samples_include_files_pagination_works: pagination correctness - test_get_samples_include_files_mixed_samples: with and without files
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the backend worker needs files for each sample to construct samplesheets. however, the GET samples endpoint only returned attributes, not associated files.
this PR modifies the route to include an optional ?includes=files querystring param which keeps the existing return format by default, but optionally returns a new public model with the full files + tags included to enable samplesheet generation.