fix: use safe ancestors() wrapper in CellGuide tree_builder (#7686)

Author: kaloster

backend/cellguide/pipeline/ontology_tree/tree_builder.py

@@ -10,7 +10,13 @@
 from backend.cellguide.pipeline.constants import CELLGUIDE_PIPELINE_NUM_CPUS
 from backend.cellguide.pipeline.ontology_tree.types import OntologyTree, OntologyTreeState
 from backend.common.census_cube.data.ontology_labels import ontology_term_label
-from backend.common.census_cube.utils import ontology_parser, rollup_across_cell_type_descendants, to_dict
+from backend.common.census_cube.utils import (
+    ancestors,
+    descendants,
+    ontology_parser,
+    rollup_across_cell_type_descendants,
+    to_dict,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -88,7 +94,7 @@ def __init__(self, cell_counts_df, root_node="CL:0000000"):
 
         logger.info("Initializing cell type data structures from the input cell counts dataframe...")
 
-        self.all_cell_type_ids = self.ontology.get_term_descendants(root_node, include_self=True)
+        self.all_cell_type_ids = descendants(root_node)
 
         self.cell_counts_df, self.cell_counts_df_rollup = self._initialize_cell_counts_df_rollup(cell_counts_df)
         self.all_cell_type_ids_in_corpus = self.cell_counts_df_rollup.index.values[
@@ -392,15 +398,13 @@ def _process_tissue__parallel(self, tissueId: str) -> OntologyTreeState:
         """
         end_nodes = self.uberon_by_celltype[tissueId]
         tissue_label = ontology_term_label(tissueId)
-        uberon_ancestors = self.ontology.get_term_ancestors(tissueId, include_self=True)
+        uberon_ancestors = ancestors(tissueId)
 
         # filter out hemaotoietic cell types from non-whitelisted tissues
         uberon_ancestors_in_whitelist = list(set(TISSUES_IMMUNE_CELL_WHITELIST).intersection(uberon_ancestors))
         if len(uberon_ancestors_in_whitelist) == 0:
             end_nodes_that_are_not_hematopoietic = [
-                e
-                for e in end_nodes
-                if HEMATOPOIETIC_CELL_TYPE_ID not in self.ontology.get_term_ancestors(e, include_self=True)
+                e for e in end_nodes if HEMATOPOIETIC_CELL_TYPE_ID not in ancestors(e)
             ]
             if len(end_nodes_that_are_not_hematopoietic) == 0:
                 logger.info(f"Not filtering out immune cell for {tissue_label}")

backend/common/census_cube/utils.py

@@ -190,7 +190,7 @@ def get_all_cell_type_ids_in_corpus(snapshot: CensusCubeSnapshot, root_node="CL:
         list[str]: A list of cell type ontology term IDs that have at least one cell in the corpus.
     """
 
-    all_cell_type_ids = ontology_parser.get_term_descendants(root_node, include_self=True)
+    all_cell_type_ids = descendants(root_node)
     cell_counts_df = snapshot.cell_counts_df
 
     cell_counts_df = (