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Fix chunking bug with compound dtypes #1146

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9e53812
initial fix
pauladkisson Nov 22, 2024
3bb63c4
Merge branch 'main' into fix_dev_tests
pauladkisson Nov 22, 2024
ff479cb
add inputs to dev tests workflow dispatch
pauladkisson Nov 22, 2024
9fb42ee
removed unused get_spec fn
pauladkisson Nov 22, 2024
5298401
implemented builder-based fix
pauladkisson Dec 4, 2024
6e05f7d
implemented builder-based compound dtype check
pauladkisson Dec 5, 2024
9890484
added docstrings
pauladkisson Dec 5, 2024
73e4c39
Merge branch 'main' into fix_dev_tests
pauladkisson Dec 5, 2024
330dd22
added fix for top-level datasets like electrodes
pauladkisson Dec 5, 2024
541eafb
added fix for stimulus
pauladkisson Dec 6, 2024
cd7670b
switched to breadth-first search
pauladkisson Dec 6, 2024
d296d7f
added support for missing top-level categories like lab_meta_data
pauladkisson Dec 6, 2024
8f2d1d2
added support for links
pauladkisson Dec 6, 2024
64c00ba
added builder to the tests
pauladkisson Dec 13, 2024
06615cb
Merge branch 'main' into fix_dev_tests
pauladkisson Dec 13, 2024
72f49c0
Merge branch 'main' into fix_dev_tests
pauladkisson Jan 24, 2025
8a772b4
updated changelog
pauladkisson Jan 27, 2025
ea5f99d
Merge branch 'main' into fix_dev_tests
pauladkisson Jan 30, 2025
57fdd7e
updated pyproject.toml
pauladkisson Feb 6, 2025
872ad6c
updated pyproject.toml
pauladkisson Feb 6, 2025
fd82b29
added tests
pauladkisson Feb 6, 2025
f668ad3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Feb 6, 2025
50b88a8
Merge branch 'main' into fix_dev_tests
pauladkisson Feb 6, 2025
23c0c89
Merge branch 'main' into fix_dev_tests
pauladkisson Feb 7, 2025
7c17005
Merge branch 'main' into fix_dev_tests
pauladkisson Feb 12, 2025
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added support for links
pauladkisson committed Dec 6, 2024
commit 8f2d1d24518b0220481edf335ff722a0879831db
Original file line number Diff line number Diff line change
@@ -11,6 +11,7 @@
from hdmf import Container
from hdmf.build.builders import (
BaseBuilder,
LinkBuilder,
)
from hdmf.utils import get_data_shape
from pydantic import (
@@ -387,15 +388,17 @@ def get_dataset_builder(builder, location_in_file):
if _find_sub_builder(builder, name) is None:
name = next(split_location)

while name not in builder.datasets:
while name not in builder.datasets and name not in builder.links:
builder = _find_sub_builder(builder, name)
if builder is None:
raise ValueError(f"Could not find location '{location_in_file}' in builder.")
raise ValueError(f"Could not find location '{location_in_file}' in builder ({name} is missing).")
try:
name = next(split_location)
except StopIteration:
raise ValueError(f"Could not find location '{location_in_file}' in builder.")
builder = builder.datasets[name]
raise ValueError(f"Could not find location '{location_in_file}' in builder ({name} is not a dataset).")
builder = builder[name]
if isinstance(builder, LinkBuilder):
builder = builder.builder
return builder