refactor: Consolidate calculated data documents into shared mapping#1223
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nathan-stender wants to merge 4 commits into
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refactor: Consolidate calculated data documents into shared mapping#1223nathan-stender wants to merge 4 commits into
nathan-stender wants to merge 4 commits into
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Replace 12 independent _get_calculated_data_aggregate_document() implementations and 7 local CalculatedDataItem/DataSource type definitions with a single shared mapping function and the universal CalculatedDocument intermediate type. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…node lists Introduce a flat, config-based API (CalcDoc, Measurement, build_calc_docs) for defining calculated data dependency graphs. This replaces 50+ nested helper functions across parsers with readable node list constants, making it clear how to add/edit calc docs without understanding the internal resolution engine. - New: calcdocs/builder.py (Measurement, CalcDoc, build_calc_docs) - New: calcdocs/views.py (shared FieldView, UuidView, SampleView, TargetView, etc.) - Migrated: appbio_quantstudio, designandanalysis, unchained_labs, msd_workbench, cytiva_biacore, bmg_labtech parsers - Removed: 7 redundant parser-specific view/config files - Moved CalculatedDataConfigWithOptional to core config.py - Net reduction: ~400 lines Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- CalcDoc.sources now takes list[Measurement | CalcDoc] instead of list[str] - Removes output_name field — node identity is the Python object, not the name - Removes _find_node linear scan — direct references eliminate name lookup - Adds _validate_graph() for eager error checking at build time - Adds describe_graph() utility for debugging node lists - Removes internal config exports from __init__.py (public API only) - Updates example to use new FieldView + build_calc_docs pattern - Each experiment type's nodes defined in a function for clear object scoping Benefits: typos in source names are now impossible (caught by Python itself), duplicate name disambiguation is explicit (separate objects), and IDE support (jump-to-definition, autocomplete) works on source references. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
map_calculated_data_documents()function inparsers/utils/calculated_data_documents/mapping.pythat replaces 12 independent_get_calculated_data_aggregate_document()implementations across schema mappersCalculatedDataItem/DataSourcetype definitions from schema mappers, standardizing onCalculatedDocumentfromdefinition.pyas the universal intermediate typeCalculatedDocument→CalculatedDataItemand back)Details
New file:
src/allotropy/parsers/utils/calculated_data_documents/mapping.pymap_calculated_data_documents()— generic mapping for all schema versionsmap_calculated_data_documents_for_dpcr()— thin wrapper for dPCR'scalculated_datumfieldSchema mappers updated (12):
Parsers updated (7):
Test plan
🤖 Generated with Claude Code