Update h5ad datatype #17574
Update h5ad datatype #17574
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Can you show me where this is used in the linked PR. Could not find it...
Metadata is just used in very few tools. |
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Some tests from the preprocessing tool (planemo/galaxy) are failing currently to set the metadata. If the same Python code is run outside Galaxy, they are working fine. For a quick test, try to upload this h5ad file to a Galaxy server. The upload will fail, despite the fact that it is a valid file h5ad file. Reading the same file using |
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Maybe my previous comment was not clear. I edited it. |
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How about adding a unit test over here: https://github.com/galaxyproject/galaxy/tree/dev/test/unit/data/datatypes? Seems that you already have a test case (or is it a large file)?
Should not be to complicated with inspiration from other data types, e.g. here.
| @@ -1565,7 +1565,7 @@ def _layercountsize(tmp, lennames=0): | |||
| # Shape we determine here due to the non-standard representation of 'X' dimensions | |||
| shape = anndata_file["X"].attrs.get("shape") | |||
| if shape is not None: | |||
| dataset.metadata.shape = tuple(shape) | |||
| dataset.metadata.shape = (int(shape[0]), int(shape[1])) | |||
| elif hasattr(anndata_file["X"], "shape"): | |||
| dataset.metadata.shape = tuple(anndata_file["X"].shape) | |||
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Guess an analogous change should be applied here, or?
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Bumped to 24.2 for now. We can merge it into 24.1 though since this is a bug and/or a datatype fix. |
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@pavanvidem do you still want to get this in ? Can you address the comments ? |
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I will try to write tests in coming days. If it cannot wait, it is fine to remove from the next release. |
A small fix to the h5ad shape metadata. Recently, found an issue setting the metadata of an anndata object as part of this PR tests: galaxyproject/tools-iuc#5740
Surprisingly, in all these years, we did not encounter a dataset with this particular case of setting metadata.
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