feat: Migrate cell_counting parsers to REC 2026/03 schema#1180
Open
nathan-stender wants to merge 2 commits into
Open
feat: Migrate cell_counting parsers to REC 2026/03 schema#1180nathan-stender wants to merge 2 commits into
nathan-stender wants to merge 2 commits into
Conversation
Migrate all 6 cell_counting parsers from REC 2024/09 to REC 2026/03. Includes downloading the schema, generating model code, creating the 2026/03 schema mapper, and updating all parser imports. Parsers migrated: - beckman_vi_cell_blu - beckman_vi_cell_xr - chemometec_nc_view - chemometec_nucleoview - revvity_matrix - roche_cedex_hires Structural changes in the migration: - Field renamed: average_live_cell_diameter__cell_counter_ → average_viable_cell_diameter__cell_counter_ (JSON: "average live cell diameter (cell counter)" → "average viable cell diameter (cell counter)") - group_identifier promoted from SampleDocument custom info to native field on ProcessedDataDocumentItem - experimental_data_identifier now also set on MeasurementDocumentItem (in addition to ImageDocumentItem) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
ajcariaga16
approved these changes
Apr 30, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Migrates all 6 cell_counting parsers from REC 2024/09 to REC 2026/03:
Changes
New files
src/allotropy/allotrope/schema_mappers/adm/cell_counting/rec/_2026/_03/cell_counting.pyschemas/adm/cell-counting/REC/2026/03/+ core/qudt dependenciesmodels/adm/cell_counting/rec/_2026/_03/+ core dependenciesImport path updates (12 parser source files)
All parser
*_parser.pyand*_structure.pyfiles updated fromrec._2024._09torec._2026._03.Mapper changes from 2024/09
average_live_cell_diameter__cell_counter_→average_viable_cell_diameter__cell_counter_(model field renamed in 2026/03 schema)SampleDocumentcustom info to nativeProcessedDataDocumentItem.group_identifierfieldMeasurementDocumentItem(in addition toImageDocumentItem)JSON test data audit (31 files)
REC/2024/09→REC/2026/030.1.118data system documentanddevice system documentnow appear beforecell counting documentarray. Fields within objects sorted per schema order."average live cell diameter (cell counter)"→"average viable cell diameter (cell counter)""group identifier"moved fromsample document > custom information documenttoprocessed data documentas a native fieldNo changes to measurement values, cell counts, densities, diameters, viabilities, or any other numeric data.
Test plan
hatch run test:test tests/parsers/{all 6 parsers}/— 35 passedhatch run lint— cleanhatch run lint:typing— clean🤖 Generated with Claude Code