feat: Update chemometec_nc_view to use custom_information_aggregate_do…#1134
Open
joshua-benchling wants to merge 3 commits intomainfrom
Open
feat: Update chemometec_nc_view to use custom_information_aggregate_do…#1134joshua-benchling wants to merge 3 commits intomainfrom
joshua-benchling wants to merge 3 commits intomainfrom
Conversation
…ation_aggregate_document This PR migrates the cell_counting rec/_2024/_09 schema mapper from the legacy custom_information_document to the new custom_information_aggregate_document format. Changes: - Add add_custom_information_aggregate_document function to converter.py - Update _validate_structuring to handle dict types - Add structure/unstructure hooks for custom_information_aggregate_document - Update cell_counting rec/_2024/_09 schema mapper to use new function - Update test expectations for all parsers using this schema mapper: - beckman_vi_cell_blu (4 files) - beckman_vi_cell_xr (10 files) - chemometec_nc_view (1 file) - chemometec_nucleoview (8 files) - revvity_matrix (4 files) - roche_cedex_hires (4 files) The new format uses the ASM standard structure: - custom_information_aggregate_document contains custom_information_document array - Each item has datum_label, scalar type (scalar_double_datum, scalar_string_datum, etc.), and optional unit
joshua-benchling
force-pushed
the
jherna/poc_custom_information_aggregate_document_chemometec_nc_view
branch
from
819bad4 to
7c304e9
Compare
nathan-stender
requested changes
Jan 28, 2026
Collaborator
nathan-stender
left a comment
nathan-stender
left a comment
There was a problem hiding this comment.
Code LGTM - however title and description need update, as this change affects not just chemometec, but all cell counters.
Also - want to make sure we merge support for custom_information_aggregate_document in CSV parser library before merging this. That PR is currently waiting on some tests - perhaps some test outputs from this PR can be used to implement
…ment_chemometec_nc_view
…ment_chemometec_nc_view
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
3 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.
This PR demonstrates the migration from the legacy custom_information_document to the new custom_information_aggregate_document format for a single parser
Changes: