From adc9870737545fab652eb4c03d2cda67d024863f Mon Sep 17 00:00:00 2001
From: jkobject <jkobject@gmail.com>
Date: Wed, 20 May 2026 07:50:43 +0000
Subject: [PATCH] fix(translate): handle comma-concatenated and missing
 ontology ids (#49)

CELLxGENE allows comma-concatenated ontology terms in single-cell
metadata (e.g. self_reported_ethnicity_ontology_term_id='HANCESTRO:0005,
HANCESTRO:0008'). These concatenated strings are not individual entries
in lamindb, so the old translate() call hit
'.filter(ontology_id=...).one()' on a non-existent record and crashed
the whole Embedder.log_adata() step.

This patch:
- splits comma-concatenated ontology ids and resolves each part
  separately, joining the resolved names with the same separator,
- falls back to the raw id (instead of raising) when an ontology id is
  not present in the current lamindb instance, so a single missing /
  custom term no longer kills the entire embedding run.

Refs jkobject/scPRINT#49.
---
 scprint/model/utils.py | 29 ++++++++++++++++++++++++-----
 1 file changed, 24 insertions(+), 5 deletions(-)

diff --git a/scprint/model/utils.py b/scprint/model/utils.py
index 22855c16..5e42aa02 100644
--- a/scprint/model/utils.py
+++ b/scprint/model/utils.py
@@ -458,14 +458,33 @@ def translate(
         obj = bt.Ethnicity.df().set_index("ontology_id")
     else:
         return None
+    def _lookup(ontology_id: str) -> str:
+        """Look up a single ontology id, falling back to the raw id on miss.
+
+        CELLxGENE allows comma-concatenated ontology terms (e.g.
+        self_reported_ethnicity_ontology_term_id='HANCESTRO:0005,HANCESTRO:0008')
+        which are not themselves entries in lamindb. Split, resolve each part,
+        and rejoin the names so translation no longer crashes on such cells.
+        See https://github.com/cantinilab/scPRINT/issues/49
+        """
+        if ontology_id == "unknown":
+            return ontology_id
+        if "," in ontology_id:
+            parts = [p.strip() for p in ontology_id.split(",") if p.strip()]
+            return ",".join(_lookup(p) for p in parts)
+        try:
+            return obj.loc[ontology_id]["name"]
+        except KeyError:
+            # Unknown ontology id (not in the current lamindb instance):
+            # fall back to the raw id rather than crashing the whole call.
+            return ontology_id
+
     if type(val) is str:
-        if val == "unknown":
-            return {val: val}
-        return {val: obj.loc[val]["name"]}
+        return {val: _lookup(val)}
     elif type(val) is list or type(val) is set:
-        return {i: obj.loc[i]["name"] if i != "unknown" else i for i in set(val)}
+        return {i: _lookup(i) for i in set(val)}
     elif type(val) is dict or type(val) is Counter:
-        return {obj.loc[k]["name"] if k != "unknown" else k: v for k, v in val.items()}
+        return {_lookup(k): v for k, v in val.items()}
 
 
 class Attention: