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Have VectorData expandable by default #1064

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Have VectorData expandable by default #1064

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2f3a01a
import
mavaylon1 Mar 4, 2024
a66914f
initial changes
mavaylon1 Mar 4, 2024
b9fc2a6
checkpoint
mavaylon1 Mar 4, 2024
0d2229c
most tests
mavaylon1 Mar 17, 2024
321a0a2
update
mavaylon1 Mar 17, 2024
b9771b5
update
mavaylon1 Mar 17, 2024
c0ce73b
Merge branch 'dev' into expand
mavaylon1 Apr 6, 2024
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2 changes: 2 additions & 0 deletions src/hdmf/common/table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
from ..data_utils import DataIO, AbstractDataChunkIterator
from ..utils import docval, getargs, ExtenderMeta, popargs, pystr, AllowPositional, check_type
from ..term_set import TermSetWrapper
from ..backends.hdf5.h5_utils import H5DataIO


@register_class('VectorData')
Expand All @@ -41,6 +42,7 @@ class VectorData(Data):
'doc': 'a dataset where the first dimension is a concatenation of multiple vectors', 'default': list()},
allow_positional=AllowPositional.WARNING)
def __init__(self, **kwargs):
kwargs['data'] = H5DataIO(data=kwargs['data'], maxshape=(None,))
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Hardcoding H5DataIO will probably create issues with ZarrIO. In the best case, ZarrIO ignores the wrapper and worst case it would fail.... I'm not sure which. For ZarrIO we should not need to wrap for datasets to be expandable, but the problem is, we won't know which backend will be used until we call write to know which wrapper to use.

Not sure what the best solution is for this. I could imagine a few approaches:

  1. Have "expandable" as an option on the base DataIO class and wrap with DataIO as a generic wrapper that the specific backend (HD5FIO, ZarrIO etc.) would then need to know how to translate. ---> I think this should be feasible, but would require changes in both HDF5IO and ZarrIO
  2. Maybe we would need to wrap in the build process ---> I think this could work, but may be tricky
  3. Wrap with H5DataIO and require that the other backends know how to translate it ---> I don't like this one, because it hard-codes backend-specific wrappers in the Container

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This is what was going through my mind as well. I made a note documenting that. I had a expandable field idea.

description = popargs('description', kwargs)
super().__init__(**kwargs)
self.description = description
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5 changes: 4 additions & 1 deletion src/hdmf/container.py
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Expand Up @@ -799,7 +799,10 @@ def __init__(self, **kwargs):

@property
def data(self):
return self.__data
if isinstance(self.__data, DataIO):
return self.__data.data
else:
return self.__data

@property
def shape(self):
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2 changes: 2 additions & 0 deletions tests/unit/common/test_table.py
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Expand Up @@ -389,6 +389,7 @@ def test_add_column_auto_index_bool(self):
description='qux column',
data=expected,
index=True)

self.assertListEqual(table['qux'][:], expected)
self.assertListEqual(table.qux_index.data, [3, 7])
# Add more rows after we created the column
Expand Down Expand Up @@ -1805,6 +1806,7 @@ def test_get_2d(self):
elements=['a', 'b', 'c'],
data=np.array([[0, 0], [1, 1], [2, 2]]))
dat = ed[0]
breakpoint()
np.testing.assert_array_equal(dat, ['a', 'a'])

def test_get_2d_w_2d(self):
Expand Down
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