Comments (5)
Here are links to the schema documentation pages for the classes I think will be involved here.
PlannedProcess has these child classes:
- CollectingBiosamplesFromSite - has no child classes
- ProtocolExecution - has no child classes
- StorageProcess - has no child classes
- MaterialProcessing
- DataGeneration
- WorkflowChain - has no child classes
- WorkflowExecution
MaterialProcessing has these child classes:
- Pooling
- Extraction
- LibraryPreparation
- SubSamplingProcess
- MixingProcess
- FiltrationProcess
- ChromatographicSeparationProcess
- DissolvingProcess
- ChemicalConversionProcess
DataGeneration has these child classes:
WorkflowExecution has these child classes:
- MetagenomeAnnotation
- MetagenomeAssembly
- MetatranscriptomeAssembly
- MetatranscriptomeAnnotation
- MetatranscriptomeAnalysis
- MagsAnalysis
- MetagenomeSequencing
- ReadQcAnalysis
- ReadBasedTaxonomyAnalysis
- MetabolomicsAnalysis
- MetaproteomicsAnalysis
- NomAnalysis
from nmdc-schema.
In terms of existing adapter methods, here's what I expect this migrator to do for each of those child classes (written here in pseudocode):
# Move all documents from the "pooling_set" collection into the "material_processing_set" collection,
# then delete the "pooling_set" collection.
self.adapter.do_for_each_document(
collection_name="pooling_set",
action=lambda document: self.adapter.insert_document(collection="material_processing_set", document=document)
)
self.adapter.delete_collection(collection_name="pooling_set")
from nmdc-schema.
DataGeneration subclasses are already in a combined collection so there no action there. All existing collections from children of MaterialProcessing should combined to a new collection called material_processing_set, same for WorkflowExecution. Im assuming you want to put this migrator at the end in which case you use commit id microbiomedata@ca304e4 to determine what the starting Database slot names are. If this is running earlier you may need to use nmdc-schema Database slot names. Note that some of these subclasses never had a collection in mongo so the code should be able to handle that.
from nmdc-schema.
Thanks! That was very helpful to me. I'm operating under the assumption that this will run after all migrators that have been implemented so far, so I'll refer to that commit you linked to.
P.S. I'll be out until about 9:45pm PT.
from nmdc-schema.
I implemented this migrator. It's in this PR: microbiomedata#196
from nmdc-schema.
Related Issues (20)
- backmerge issue with ID mention pattern constraints on WorkflowExecution HOT 3
- `berkeley-schema-fy24`: Implement migrator that adds `replaces` field to `WorkflowChain` documents HOT 1
- `berkeley-schema-fy24`: Delete obsolete code, including code obsoleted by Berkeley schema changes
- write a notebook report class.slot paths that take a ControlledTermValue* range
- Remodel class that aggregates steps of `WorkflowExecution` for easier schema traversal HOT 1
- `has_input`, `has_output`, and `has_process_parts` slots on `ProtocolExecution` need pattern constraints
- `berkeley-schema-fy24`: Facilitate access to `nmdc_materialized_patterns` schema via PyPI package HOT 2
- Delete Class WorkflowChain in Berkeley schema HOT 2
- `berkeley-schema-fy24`: Implement super migrator that runs all partial migrators in correct order HOT 1
- Find a home for these comments taken from `src/scripts/report_biosamples_per_study.py`
- check if classes associated with `alternative_identifiers` can use ANY `alternative_identifiers` HOT 5
- Migrations: Make it easier to test migrators against a Mongo database
- `berkeley-schema-fy24`: Update migrators to account for `WorkflowChain` class being removed
- Publish schema to PyPI via GitHub Release `v10.5.4` HOT 1
- Migrations: Implement "no op" migrator from `v10.4.0` to `v10.5.4`
- `berkeley-schema-fy24`: Some migrators use incorrect collection name (instead of `mags_set`)
- Rename branches to eliminate Berkeley commits from `main` HOT 6
- 2024-06-18 `id` pattern validation summaries and SPARQL-based referential integrity checks on MongoDB contents with and without migration HOT 6
- Facilitate access to `nmdc_materialized_patterns` schema variant via PyPI package HOT 1
- produce a nmdc-schema YAML artifact with deprecated elements included
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