Pr4 add analyte cat remove omics type migration #1616
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Change WorkflowChain to a subclass of PlannedProcess
- make it a PlannedProcess - update description - acc comment
…crobiomedata/berkeley-schema-fy24 into 1536_add_workflow_chain_class
Fix indentation for resolution_category slot
Make exact_mappings for class MassSpectrometry a list.
Make Class:ProtocolExecution
1552 deprecate activity
Update slot name from mass_spectrum_mode to mass_spectrum_collection_mode
Updating MassSpectrumCollectionMode enumeration name to MassSpectrumCollectionModeEnum
…-that-were-on-OmicsProcessing
…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.
Removed slot used
fix typo in multivalued
make workflowexecutionactivity a PlannedProcess
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
and autoformatting it
…efinition in external_identifiers
…n' of https://github.com/microbiomedata/berkeley-schema-fy24 into 11232_add_external_analysis_identifiers_to_WorkflowChain
…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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Addresses PR: microbiomedata#4
This migration moves the values from
omics_typeto a new slot calledanalyte_categoryand removes theomics_typeslot. It changes the values to match theAnalyteCategoryEnumpermissible values.