Comments (2)
@mbthornton-lbl will be continuing to work on this in the next sprint per Slack message. Moving over.
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Upon review I am planning on re-implementing the blocks of logic for Metabolomics and NOM in the re_id_tool.py
tool in nmdc-automation
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Related Issues (20)
- Flush out `SubstanceRoleEnum` HOT 1
- Add `sample_portion` to `SubsamplingProcess`
- Add `StorageProcess` class (a subclass of `MaterialProcessing` with slots like `substances_used` (already exists) and `contained_in` slot (already exists), `duration` (already exists), and `temperature` (already exists). With `input` and 'output` HOT 3
- Expand `StationaryPhaseEnum` to include values needed for GC-MS and LC-MS metab data HOT 1
- Accommodate multiple detection configurations for single `MassSpectrometry` instance HOT 1
- Add `workflow_version` slot to `WorkflowExecution` classes HOT 1
- Add slot `workflow_configuration_object` should be multivalued with a range of `DataObject` with the config files captured as `DataObject`s HOT 3
- Create `MassSpectrometryConfiguration` class and modify existing `MassSpectrometry` class to accommodate
- Rename `has_metabolite_quantification` and associated class to `has_metabolite_identification` HOT 5
- support slot for when document was added HOT 12
- Refactor `principal_investigator` slot on `Study`
- Refactor `has_calibration` to use a class HOT 5
- Create `ChromatographicSeparationConfiguration` class and modify existing `ChromatographicSeparation` to accommodate HOT 1
- Add sets to `Database` for the `MaterialProcess` subclasses HOT 5
- generate prefixmap for nmdc HOT 2
- Migrations: Add example doctests for functions that use adapter methods
- Use PyPI trusted publisher settings in release publishing workflow
- GitHub Actions workflow is failing due to inability to install `bioregistry` HOT 1
- Add slots to Biosample class to disambiguate standard MG metadata vs long-read MG metadata HOT 2
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