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feat(catalog): add tissue/disease facet-hierarchy columns to schema #69

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Merged
timtreis merged 1 commit into from
Nov 5, 2026
Merged

feat(catalog): add tissue/disease facet-hierarchy columns to schema #69

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11 changes: 11 additions & 0 deletions src/sddb/_catalog_schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,17 @@
"disease": "string",
"disease_id": "string",
"development_stage": "string",
# Facet hierarchy, computed at the cut from the pinned UBERON/MONDO node graphs + the hub's ordered
# anchor tables (first anchor by id over the term + its ancestors wins; self-anchor is its own organ).
# Unmapped tissue -> system "other tissues"; unmapped disease -> "other conditions"; unknown stays null.
"tissue_system": "string",
"tissue_system_id": "string",
"tissue_organ": "string",
"tissue_organ_id": "string",
"disease_class": "string",
"disease_class_id": "string",
"disease_group": "string",
"disease_group_id": "string",
# technology
"technology": "string",
"assay": "string",
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19 changes: 19 additions & 0 deletions tests/test_catalog_schema.py
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Expand Up @@ -226,6 +226,25 @@ def test_obs_unit_and_segmentation_columns_present():
assert col not in schema.REQUIRED_COLUMNS


def test_facet_hierarchy_columns_present():
# tissue_system/organ + disease_class/group (+ UBERON/MONDO ids) the cut computes from the pinned
# ontology node graphs + anchor tables; nullable strings, not required.
from sddb import _catalog_schema as schema

for col in (
"tissue_system",
"tissue_system_id",
"tissue_organ",
"tissue_organ_id",
"disease_class",
"disease_class_id",
"disease_group",
"disease_group_id",
):
assert schema.CATALOG_COLUMNS[col] == "string"
assert col not in schema.REQUIRED_COLUMNS


_NEW_DATASET_COLUMNS = {
"sample_title": "string",
"timepoint": "string",
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