fix: improve data handling in initializers and transferer, streamline constructor in radionuclides#480
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fix: improve data handling in initializers and transferer, streamline constructor in radionuclides#480
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… constructor in radionuclides
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Pull request overview
Improves transfer/import robustness by centralizing CSV reading, tightening sample-info filtering, and extending minor-trace chemistry lineage with additional legacy sample point identifiers.
Changes:
- Normalize CSV ingestion and filtering behavior across transferers (including cleanup in radionuclides).
- Add
SamplePtID/SamplePointIDlineage fields to MinorTraceChemistry (model, transfer logic, tests, and migration). - Prevent duplicate term-category associations during lexicon initialization.
Reviewed changes
Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| transfers/transferer.py | Switches to internal CSV reader and improves orphan-record logging/details. |
| transfers/radionuclides.py | Removes custom dataframe-loading path and streamlines constructor. |
| transfers/minor_trace_chemistry_transfer.py | Persists additional sample-point lineage fields and upserts them. |
| db/nma_legacy.py | Adds new mapped columns for sample-point lineage on NMA_MinorTraceChemistry. |
| alembic/versions/e71807682f57_add_sample_point_fields_to_minor_trace.py | Introduces schema changes to store new lineage fields. |
| core/initializers.py | Avoids inserting duplicate lexicon links within a single init run. |
| tests/test_nma_chemistry_lineage.py | Adjusts expectations and persistence tests for new columns. |
| tests/test_minor_trace_chemistry_transfer.py | Ensures transfer dict includes new lineage keys. |
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alembic/versions/e71807682f57_add_sample_point_fields_to_minor_trace.py
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…ters_transfer and minor_trace_chemistry_transfer
…_trace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
alembic/versions/e71807682f57_add_sample_point_fields_to_minor_trace.py
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…_trace.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…TraceChemistryTransferer ```
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