aedes_add_neurons enrichment + aedes_set_meta / aedes_set_group - #10
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aedes_add_neurons enrichment + aedes_set_meta / aedes_set_group#10jefferis wants to merge 6 commits into
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…equire curation fields
Auto-fills soma_xyz + nucleus_id (via aedes_soma_position) and side (via
aedes_point_side on the soma nm coords, falling back to aedes_key_point
with a warning when the soma cascade returns nothing). Callers' `...`
values always win, and existing non-NA cells on update rows are never
clobbered.
Also introduces:
- `status` shortlist in signature (tab-completion); values outside the
shortlist are live-checked against unique(aedes_main$status) and
rejected with a helpful message.
- `required = c("superclass","status","initials")` — missing fields
error, pointing users at options(aedes.initials="XY").
Factor the timestamp-pinned "update existing aedes_main rows by root_id" core out of aedes_add_neurons into internal helpers in flytable.R: - .aedes_pin_meta(): pin one timestamp, return latest ids + a timestamp-consistent aedes_main (shared read). - .aedes_update_existing(): resolve root_id -> _id in that snapshot and write exactly the supplied columns (verbatim; no no-clobber). Update-only -- absent ids are returned in `missing` rather than appended. Errors on duplicated root_id; accepts a pre-pinned am/ts to avoid a second read. - .aedes_reject_dry_run(): guard for `...`-carrying entry points so a mistyped `dry_run` errors clearly instead of being written as a column. aedes_add_neurons now pins via .aedes_pin_meta and routes its update branch through .aedes_update_existing, keeping its auto-col no-clobber policy local and its append logic and list(up, new) return shape unchanged. Verified the dry-run update frame is identical() to the pre-refactor version.
Port aedes_set_meta into the package (previously a project-local helper). Bulk-updates existing rows from a per-row data.frame of metadata, resolving ids via aedes_ids() and writing through the shared .aedes_update_existing() engine so the join is timestamp-consistent. Update-only: rows with status bad_nucleus/duplicate/not_a_neuron are dropped first, and any remaining id absent from aedes_main is an error (all-or-nothing, nothing is written). Uses the standard `dryrun` argument with the alias guard.
New aedes_set_group() assigns a shared `group` id to a set of neurons, building on aedes_set_meta()'s update engine (writing directly to it, reusing the pinned snapshot so the returned preview matches what is written). Improvements over the old project-local helper: - `group=` now works: integer forces an id; 0/NA ungroups; a query/ids joins the group of those neurons (join-by-example). - join_existing controls conflicts when selected neurons are already grouped: NA (default) refuses to guess -- warns on dry run, errors on a live write, and prints the exact re-run call; TRUE joins the existing group (keeping its id, merging several with a warning); FALSE mints a fresh group from min(serial_id). - Warns when a reassignment would split an existing group (orphan guard). - Dry run returns a per-neuron preview (root_id, serial_id, group_old, group_new, changed) instead of a bare number; live writes only changed rows. Both aedes_set_meta and aedes_set_group added to the _pkgdown reference index.
Exposes fafbseg::cam_meta()'s new translate_ids argument through aedes_meta (and thus aedes_ids). The stale-id translation itself now lives in cam_meta, so aedes_meta simply forwards the argument rather than reimplementing the flywire_latestid() step locally (removing the .aedes_explicit_ids helper).
…ect support
Add generic multi-select column merge across the three writers so curator
initials land in the aedes_main annotator/proofreader columns without
overwriting existing tokens.
- .aedes_append_multiselect(): shared engine that merges a named list of
values into the update frame, per column, sorted-unique. Comma-string
output (fafbseg's flytable_listify_multiselect_col handles the JSON).
wipe = FALSE (default) appends; wipe = TRUE replaces.
- .aedes_resolve_initials(): shared TRUE/FALSE/vector -> tokens resolver
that looks up getOption("aedes.initials") when TRUE.
- Wire annotator = TRUE, proofreader = FALSE, wipe = FALSE through
aedes_add_neurons(), aedes_set_meta(), aedes_set_group().
- Empty-cell handling: drop actual NA and empty/whitespace tokens only;
literal "NA" / "NaN" strings are treated as data so real curator
initials survive round-trips.
- aedes_add_neurons(): improved missing-required-columns error message
pointing at options(aedes.initials = "XY") for initials specifically.
- aedes-package.R: document aedes.version and aedes.initials options.
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Summary
aedes_add_neuronsnow auto-fillssoma_xyz,nucleus_id,sideandpoint_xyz(never overwriting non-NA values on existing rows), validatesstatusagainst a liveaedes_mainvocabulary, and requiressuperclass/status/initialsby default (viarequired=). Initials default togetOption("aedes.initials")..aedes_update_existingand shared with two new helpers:aedes_set_meta()— bulk update columns on existingaedes_mainrows.aedes_set_group()— convenient grouping / add-to-group onaedes_main.Test plan
devtools::check()clean on macOSaedes_add_neurons(ids, superclass=..., status=..., cell_class=...)on a known KC + a not-yet-added id: verifysoma_xyz,nucleus_id,sideandpoint_xyzare populated for the new row; existing row's non-NA cells are preservedstatus = "not_a_status"errors with the live vocabulary listedsuperclass/initialserrors with the pointer tooptions(aedes.initials=...)aedes_set_meta()updates the intended cells and leaves others aloneaedes_set_group()creates a new group and appends to an existing one as expected🤖 Generated with Claude Code