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Pr4 add analyte cat remove omics type migration #1616

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brynnz22
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@brynnz22 brynnz22 commented Jan 6, 2024

Addresses PR: microbiomedata#4

This migration moves the values from omics_type to a new slot called analyte_category and removes the omics_type slot. It changes the values to match the AnalyteCategoryEnum permissible values.

brynnz22 and others added 30 commits December 13, 2023 13:54
Change WorkflowChain to a subclass of PlannedProcess
- make it a PlannedProcess
- update description
- acc comment
Fix indentation for resolution_category slot
Make exact_mappings for class MassSpectrometry a list.
Update slot name from mass_spectrum_mode to mass_spectrum_collection_mode
Updating MassSpectrumCollectionMode enumeration name to MassSpectrumCollectionModeEnum
…ClassLibraryPrep

1540, 1541, 1543 add slots to LibraryPreparation
ues:
was_informed_by
analyte_category
use existing AnalyteCategoryEnum
…rocessing-classes-that-were-on-OmicsProcessing

1525 add slots to material processing classes that were on omics processing
Adding class Instrument
Add instrument_used slot.
fix typo in multivalued
make workflowexecutionactivity a PlannedProcess
turbomam and others added 27 commits December 18, 2023 11:02
test for reiterated inherited slots, and related cleanup
- Update model to remove incorrect, non-monotonic `multivalued: false` usage directive for the slot `part_of`
- update valid models to have WorkflowExecution -- part_of --> WorkflowChain to have array data'
- add 2 invalid data examples
…lowExecution_multivalued_true

Update WorkflowExecution model to remove multivalued: false slot_usage on part_of
remove slots from Biosample & DataGeneration & update examples
…s_identifiers_to_WorkflowChain

Add external analysis project identifiers slots to WorkflowChain
readding omprc as a valid prefix for DataGeneration so we don't have to change the IDs of existing OmicsProcessing records just because we are changing the class name.
Add example data with 'omprc' prefix.
1581 keep omprc typecode for class Data Generation
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