Stage partner changes against an annotatR project

Compute, without applying, the changes a partner patch would make to an annotatR project: ROIs are joined by id and classified as create, update, unchanged, delete (only with delete_missing = TRUE) or conflict. Reviewed or locked ROIs, and ROIs in locked layers, are never changed automatically; such changes become conflicts. When expected_revision is given and the project has moved on, staging aborts with an at_conflict_error (REVISION_CONFLICT).

Usage

at_stage_qupflowr(
  x,
  patch,
  expected_revision = NULL,
  delete_missing = FALSE,
  call = rlang::caller_env()
)

Arguments

x

An annot_project, or the path of a saved project .rds (then the commit re-reads and re-checks that file).

patch

An import report from at_import_qupflowr(), a handoff directory, or one or more annot_layer objects.

expected_revision

Optional revision of x the partner based its patch on (see at_annotation_revision()).

delete_missing

Logical; treat ROIs absent from the patch's layers as deletions. Default FALSE.

call

The calling environment, for error reporting.

Value

An at_staged_patch: a list with patch_id, state = "staged", created, base_revision, proposed_revision, operations (tibble of op, roi_id, layer, label, reason), summary (counts by op), base, proposed (the would-be project), target_path and patch_digest.

See also

at_commit_qupflowr()

Other interop: at_annotation_revision(), at_commit_qupflowr(), at_export_qupflowr(), at_import_qupflowr(), at_interop_capabilities(), at_interop_manifest()

Examples

proj <- at_example_project()
partner <- at_layer_add(at_layer("regions"), at_roi_rect(10, 10, 40, 40, label = "tumour",
                                                         id = "partner-1"))
st <- at_stage_qupflowr(proj, partner, expected_revision = at_annotation_revision(proj))
st$summary
#> $create
#> [1] 1
#> 
#> $update
#> [1] 0
#> 
#> $unchanged
#> [1] 0
#> 
#> $delete
#> [1] 0
#> 
#> $conflict
#> [1] 0
#>