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Disallow duplicates #199

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merged 2 commits into from
Jun 28, 2022
Merged

Disallow duplicates #199

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cd3c8f3
disallow duplicates
johnkerl Jun 26, 2022
c49fcaf
parameterize allows_duplicates within soma_options
johnkerl Jun 28, 2022
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2 changes: 1 addition & 1 deletion apis/python/src/tiledbsc/annotation_dataframe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,7 @@ def from_dataframe(self, dataframe: pd.DataFrame, extent: int = 2048) -> None:
dataframe=dataframe,
name=self.name,
sparse=True,
allows_duplicates=False,
allows_duplicates=self._soma_options.allows_duplicates,
offsets_filters=offsets_filters,
attr_filters=attr_filters,
dim_filters=dim_filters,
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2 changes: 1 addition & 1 deletion apis/python/src/tiledbsc/annotation_matrix.py
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Original file line number Diff line number Diff line change
Expand Up @@ -174,7 +174,7 @@ def _create_empty_array(self, matrix_dtypes, attr_names) -> None:
domain=dom,
attrs=attrs,
sparse=True,
allows_duplicates=True,
allows_duplicates=self._soma_options.allows_duplicates,
offsets_filters=[
tiledb.DoubleDeltaFilter(),
tiledb.BitWidthReductionFilter(),
Expand Down
2 changes: 1 addition & 1 deletion apis/python/src/tiledbsc/assay_matrix.py
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Original file line number Diff line number Diff line change
Expand Up @@ -212,7 +212,7 @@ def _create_empty_array(self, matrix_dtype: np.dtype) -> None:
domain=dom,
attrs=(att,),
sparse=True,
allows_duplicates=True,
allows_duplicates=self._soma_options.allows_duplicates,
offsets_filters=[
tiledb.DoubleDeltaFilter(),
tiledb.BitWidthReductionFilter(),
Expand Down
3 changes: 3 additions & 0 deletions apis/python/src/tiledbsc/soma_options.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ class SOMAOptions:
write_X_chunked: bool
goal_chunk_nnz: int
member_uris_are_relative: bool
allows_duplicates: bool

def __init__(
self,
Expand All @@ -27,6 +28,7 @@ def __init__(
write_X_chunked=True,
goal_chunk_nnz=20_000_000,
member_uris_are_relative=None, # Allows relocatability for local disk / S3, and correct behavior for TileDB Cloud
allows_duplicates=False,
):
self.obs_extent = obs_extent
self.var_extent = var_extent
Expand All @@ -37,3 +39,4 @@ def __init__(
self.write_X_chunked = write_X_chunked
self.goal_chunk_nnz = goal_chunk_nnz
self.member_uris_are_relative = member_uris_are_relative
self.allows_duplicates = allows_duplicates
4 changes: 2 additions & 2 deletions apis/python/src/tiledbsc/uns_array.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ def from_pandas_dataframe(self, df: pd.DataFrame) -> None:
uri=self.uri,
dataframe=df,
sparse=True,
allows_duplicates=False,
allows_duplicates=self._soma_options.allows_duplicates,
ctx=self._ctx,
)

Expand Down Expand Up @@ -169,7 +169,7 @@ def create_empty_array_for_csr(
domain=dom,
attrs=(att,),
sparse=True,
allows_duplicates=True,
allows_duplicates=self._soma_options.allows_duplicates,
offsets_filters=[
tiledb.DoubleDeltaFilter(),
tiledb.BitWidthReductionFilter(),
Expand Down