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Fix well naming case mismatch bug #254

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merged 7 commits into from
Oct 2, 2024
Merged

Fix well naming case mismatch bug #254

merged 7 commits into from
Oct 2, 2024

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ieivanov
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@ieivanov ieivanov commented Oct 1, 2024 •
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Skips test_combine_fovs_to_hcs, see #255

talonchandler
talonchandler approved these changes Oct 2, 2024
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LGTM. Added a couple simple tests for case insensitivity.

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talonchandler commented Oct 2, 2024 •
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Hmmm, this might be a genuine error.

    def test_create_position_case_sensitivity():
        """Test `iohub.ngff.Plate.create_position()`"""
        with TemporaryDirectory() as temp_dir:
            store_path = os.path.join(temp_dir, "hcs.zarr")
            dataset = open_ome_zarr(
                store_path, layout="hcs", mode="a", channel_names=["GFP"]
            )
            dataset.create_position("S", "0", "1")
>           dataset.create_position("s", "1", "0")

tests/ngff/test_ngff.py:680: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
iohub/ngff/nodes.py:1614: in create_position
    well = self.create_well(
iohub/ngff/nodes.py:1565: in create_well
    row_grp = self[row_name].zgroup
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <iohub.ngff.nodes.Plate object at 0x7fc8cf0ed1b0>, key = 's'

    def __getitem__(self, key):
        key = normalize_storage_path(key)
        znode = self.zgroup.get(key)
        if not znode:
>           raise KeyError(key)
E           KeyError: 's'

Looking closer...passes on the HPC FWIW.

Edt: passing on mac, but not HPC

talonchandler
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Fix linux tests

@ieivanov ieivanov linked an issue Oct 2, 2024 that may be closed by this pull request
create_position fails when inconsistent row/column capitalization is used #253
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talonchandler
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Reverted my tests, so that tests are not blocking. Approving, and we'll leave the issue open.

@ieivanov ieivanov merged commit 88623ea into main Oct 2, 2024
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@ieivanov ieivanov deleted the fix_well_naming_case branch October 2, 2024 21:50
@ziw-liu ziw-liu mentioned this pull request Oct 7, 2024
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ziw-liu
ziw-liu reviewed Oct 7, 2024
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iohub/ngff/nodes.py
@@ -193,7 +193,7 @@ def __delitem__(self, key):

def __contains__(self, key):
key = normalize_storage_path(key)
return key in self._member_names
return key.lower() in [name.lower() for name in self._member_names]
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I consider this a bug if a key in node is True does not guarantee that node[key] succeeds on all platforms.

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ziw-liu commented Oct 7, 2024

Is this PR intended to just modify test or also to modify library behavior?

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create_position fails when inconsistent row/column capitalization is used
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@ieivanov @talonchandler @ziw-liu