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Fix registered result paths broken by file attachment - #42
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Attaching workflow results could rename an already registered Zarr directory, fail with
IsADirectoryError, and leave OMERO pointing at a missing store. Regular files could also leave in-place attachments pointing at a temporary filename.Skip directory-backed stores before matching file attachments to their source images, and report the skipped count. Attach regular files from their permanent path; keep the workflow-qualified attachment name in OMERO's OriginalFile metadata. Neither upload nor link failures move result data.
Closes #37.
Validation: 12 focused regression cases (8 failed against unchanged master), plus the complete separate scripts harness: 263 passed, 4 skipped. Script compilation and
git diff --checkpassed. Tests cover Image/Plate Zarr directories, tracked/legacy attachment selection, permanent file paths, failures, mixed results, and filename collisions. Live OMERO attachment/download verification remains a deployment acceptance check.The regression tests are on
test/stable-result-attachment-paths, targeting the separatetest-suitebranch; production branches remain test-file-free. The companion test PR must merge after this production change. CI on this PR runs the currently published canonical harness.