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Import lifecycle

ImportOptionsEnvelope is the versioned request that accompanies an import order. It keeps optional preprocessing/postprocessing operations separate from OMERO registration settings.

Schema 2 envelope

{
  "schema": 2,
  "registration": {
    "schema": 1,
    "platePixelSource": "source",
    "plateLabelName": null
  },
  "operations": []
}

No operations means the established importer behavior. Legacy empty options and flat schema-1 ZarrImportOptions are upcast to this shape, so deployments that do not enable shallow storage remain unaffected.

Shallow-Zarr operation

The biomero.shallow-zarr postprocess operation asks the importer to:

  1. use the supplied ordered CanonicalInputManifest as the authoritative workflow-input snapshot;
  2. compute identities for returned image nodes;
  3. retain a full result whenever matching is missing, ambiguous, changed, or fails;
  4. otherwise normalize the result into a managed shallow collection before registering it with OMERO.

Identity worker parallelism is deployment configuration, not a client field. This lets facilities balance import latency against CPU and storage costs.

{
  "kind": "biomero.shallow-zarr",
  "phase": "postprocess",
  "schema": 1,
  "canonicalInputs": {
    "schema": 1,
    "workflowId": "00000000-0000-0000-0000-000000000000",
    "exportTaskId": "00000000-0000-0000-0000-000000000001",
    "inputs": []
  },
  "failurePolicy": "keep-full",
  "importImageLabelViews": true,
  "importPlateLabelPreview": false,
  "plateLabelName": null
}

Registration controls

For a derived Plate, platePixelSource: source registers the source pixels as the normal OMERO view while preserving the shallow collection as authority. When an operator explicitly requests a Plate label preview, platePixelSource: label and plateLabelName select one label node per Plate image for the registered preview. No label array needs to be copied for that view.

These controls are specific to the current OMERO Zarr registration workaround. They can be retired or adapted when native OMERO label/collection support makes them unnecessary.