Import implementation of ExperimentAxisQuery.
#78
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thetorpedodog
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bkmartinjr
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Jan 13, 2023
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| # Internals | ||
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| def read( |
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Recommend prefixing this method with an underscore as it is internals. I originally omitted the underscore, as I wasn't sure if it was internal or public API
I am already confident that I need to significantly restructure read() and how it is used by to_anndata() for performance reasons.
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Prefixed both this and AxisQueryResult with _s.
bkmartinjr
reviewed
Jan 13, 2023
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| """ | ||
| column_names = column_names or AxisColumnNames(obs=None, var=None) | ||
| x_collection = self.experiment.ms[self.measurement_name].X |
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why not use self._ms property?
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Oops, I missed this one. Thanks!
bkmartinjr
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Jan 13, 2023
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| @attrs.define(frozen=True) | ||
| class AxisQueryResult: |
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This is (I believe) a private class and should probably have a underscore-prefixed name
bkmartinjr
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Jan 13, 2023
bkmartinjr
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Jan 13, 2023
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Two changes suggested:
- everything implementing the
to_anndatacode path (eg,read,AxisQueryResult, etc should have an under-score prefixed name as it is currently just private implementation, and very likely to change for performance reasons. - suggest pasting the lifecycle maturity tags on the public methods (eg,
lifecycle: experimental)
thetorpedodog
commented
Jan 13, 2023
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| # Internals | ||
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| def read( |
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Prefixed both this and AxisQueryResult with _s.
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| """ | ||
| column_names = column_names or AxisColumnNames(obs=None, var=None) | ||
| x_collection = self.experiment.ms[self.measurement_name].X |
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Oops, I missed this one. Thanks!
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| @attrs.define(frozen=True) | ||
| class AxisQueryResult: |
bkmartinjr
approved these changes
Jan 13, 2023
As discussed in #76, the full implementation of `ExperientAxisQuery` should be provided by the base SOMA implementation since it does not vary from storage engine to storage engine. This copies most of the implementation from the existing TileDB version, with some reorganization to make the main query class a little smaller: - Pulls more of the caching-specific behavior of join IDs into the `_JoinIDCache` class. - Pulls more indexing-related work into the `_AxisIndexer` class. - Makes formerly-public `AxisIndexer` private. (If this should be public this can be easily reverted.) - Renames methods to `by_[axis]`. - Separates out index caching logic from main methods. - Uses an `_Axis` enum internally for axis selection. - Shortens `AxisQueryResult` name.
- Removes defaults from `_read` so there is only one place where optional parameters are set. - Fix up last use of `self.experiment.ms[self.measurement_name]`.
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`contextlib.ContextManager` does not annotate its return type, so callers of `with ExperimentAxisQuery(...) as q:` will see it as an Any in type-checking. Instead we just write the `__enter__ return self` ourselves.
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As discussed in #76, the full implementation of
ExperientAxisQueryshould be provided by the base SOMA implementation since it does not vary from storage engine to storage engine. This copies most of the implementation from the existing TileDB version, with some reorganization to make the main query class a little smaller:_JoinIDCacheclass._AxisIndexerclass.AxisIndexerprivate. (If this should be public this can be easily reverted.)by_[axis]._Axisenum internally for axis selection.AxisQueryResultname.