fix: Use deepcopy instead of model_dump to copy view#163
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pkerpedjiev merged 1 commit intomainfrom Jan 27, 2025
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nvictus
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src/higlass/_utils.py
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| def copy_unique(model: ModelT) -> ModelT: | ||
| """Creates a deep copy of a pydantic BaseModel with new UID.""" | ||
| copy = model.__class__(**model.model_dump()) | ||
| copy = deepcopy(model) |
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Not familiar enough to know the consequences of deepcopy on a pydantic model, but pydantic appears to have this API:
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| copy = deepcopy(model) | |
| copy = model.copy(deep=True) |
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So that works too. I don't know what the difference is either but I switched over to model.model_copy (deep=True) (model.copy is deprecated).
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manzt
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Looks good to me! I'm surprised by the hack I had there before (rather than using .copy(deep=True). This is certainly an improvement.
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| def test_plugin_track(): | ||
| """Test that plugin track attributes are maintained after a copy.""" | ||
| some_url = "https://some_url" | ||
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| # Here we'll create a custom plugin track. | ||
| class PileupTrack(hg.PluginTrack): | ||
| type: Literal["pileup"] = "pileup" | ||
| plugin_url: ClassVar[str] = some_url | ||
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| # Specify the track-specific data | ||
| pileup_data = { | ||
| "type": "bam", | ||
| "url": "https://some_url/sorted.bam", | ||
| "chromSizesUrl": "https://some_url/sorted.chromsizes.bam", | ||
| "options": {"maxTileWidth": 30000}, | ||
| } | ||
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| # Create and use the custom track | ||
| pileup_track = PileupTrack(data=pileup_data) | ||
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| view = hg.view((pileup_track, "top")) | ||
| uid1 = view.uid | ||
| assert view.tracks.top[0].plugin_url == some_url | ||
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| # The .domain() function creates a copy of the view. We want to make sure | ||
| # that the plugin_url attribute of the PluginTrack is maintained | ||
| view = view.domain(x=[0, 10]) | ||
| uid2 = view.uid | ||
| assert view.tracks.top[0].plugin_url == some_url | ||
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| # Check to make sure the copy behavior changed the uid as expected | ||
| assert uid1 != uid2 |
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Description
Calling the
.domain()function on a view creates a copy of the view. The current copy method dumps the view model and creates a new one from the view. Because views expect PluginTrack types instead of specific subclasses, the dumped model does not contain the class vars of the subclasses (e.g. PileupTrack). Switching todeepcopypreserves the class vars of the subclasses.Here's the error that occurs in the added test without this change:
Fixes #___
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