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Performance improvement for SOMA collection-mapper UDF #596

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Performance improvement for SOMA collection-mapper UDF #596

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Performance improvement for SOMA collection-mapper UDF
johnkerl Jul 10, 2024
ca5e384
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johnkerl Jul 10, 2024
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16 changes: 14 additions & 2 deletions src/tiledb/cloud/soma/mapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
from typing import Any, Callable, Dict, Optional, Sequence, Tuple

import anndata as ad
import tiledb
import tiledbsoma

from tiledb.cloud import dag
Expand Down Expand Up @@ -233,8 +234,19 @@ def build_collection_mapper_workflow_graph(
"Retrieving SOMA Experiment URIs from SOMACollection %s"
% soma_collection_uri
)
with tiledbsoma.Collection.open(soma_collection_uri) as soco:
soma_experiment_uris = {k: v.uri for k, v in soco.items()}

# Alternative:
#
# with tiledbsoma.Collection.open(soma_collection_uri) as soco:
# soma_experiment_uris = {k: v.uri for k, v in soco.items()}
#
# -- however, that opens all the members sequentially, and we don't need
# that overhead here in the launcher node.
#
# See also
# https://github.com/single-cell-data/TileDB-SOMA/issues/2787
with tiledb.Group(soma_collection_uri) as grp:
soma_experiment_uris = {mbr.name: mbr.uri for mbr in grp}

if experiment_names is not None:
logger.info("Filtering SOMA Experiment URIs for specified names")
Expand Down
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