✨ Allow add source to entity (#1824)

lamindb/_can_validate.py

@@ -332,7 +332,9 @@ def _standardize(
         # here, we can safely import bionty
         from bionty._bionty import create_or_get_organism_record
 
-        organism_record = create_or_get_organism_record(organism=organism, orm=registry)
+        organism_record = create_or_get_organism_record(
+            organism=organism, registry=registry
+        )
         organism = (
             organism_record.name if organism_record is not None else organism_record
         )
@@ -514,7 +516,9 @@ def _filter_query_based_on_organism(
         # here, we can safely import bionty
         from bionty._bionty import create_or_get_organism_record
 
-        organism_record = create_or_get_organism_record(organism=organism, orm=registry)
+        organism_record = create_or_get_organism_record(
+            organism=organism, registry=registry
+        )
         if organism_record is not None:
             queryset = queryset.filter(organism__name=organism_record.name)
 

lamindb/_from_values.py

@@ -25,9 +25,9 @@ def get_or_create_records(
     mute: bool = False,
 ) -> list[Record]:
     """Get or create records from iterables."""
-    Record = field.field.model
+    registry = field.field.model
     if create:
-        return [Record(**{field.field.name: value}) for value in iterable]
+        return [registry(**{field.field.name: value}) for value in iterable]
     creation_search_names = settings.creation.search_names
     feature: Feature = None
     organism = _get_organism_record(field, organism)
@@ -57,21 +57,23 @@ def get_or_create_records(
                     and records[0].source_id
                 ):
                     source_record = records[0].source
-            if not source_record and hasattr(Record, "public"):
+            if not source_record and hasattr(registry, "public"):
                 from bionty._bionty import get_source_record
 
-                source_record = get_source_record(Record.public(organism=organism))
+                source_record = get_source_record(
+                    registry.public(organism=organism), registry
+                )
             if source_record:
                 from bionty.core._add_ontology import check_source_in_db
 
                 check_source_in_db(
-                    registry=Record,
+                    registry=registry,
                     source=source_record,
                     update=True,
                 )
 
                 from_source = not source_record.in_db
-            elif hasattr(Record, "source_id"):
+            elif hasattr(registry, "source_id"):
                 from_source = True
             else:
                 from_source = False
@@ -97,14 +99,14 @@ def get_or_create_records(
                     logger.success(msg)
                 s = "" if len(unmapped_values) == 1 else "s"
                 print_values = colors.yellow(_print_values(unmapped_values))
-                name = Record.__name__
+                name = registry.__name__
                 n_nonval = colors.yellow(f"{len(unmapped_values)} non-validated")
                 if not mute:
                     logger.warning(
                         f"{colors.red('did not create')} {name} record{s} for "
                         f"{n_nonval} {colors.italic(f'{field.field.name}{s}')}: {print_values}"
                     )
-        if Record.__module__.startswith("bionty.") or Record == ULabel:
+        if registry.__get_schema_name__() == "bionty" or registry == ULabel:
             if isinstance(iterable, pd.Series):
                 feature = iterable.name
             feature_name = None
@@ -230,7 +232,7 @@ def create_records_from_source(
         # for custom records that are not created from public sources
         return records, iterable_idx
     # add source record to the kwargs
-    source_record = get_source_record(public_ontology)
+    source_record = get_source_record(public_ontology, model)
     kwargs.update({"source": source_record})
 
     # filter the columns in bionty df based on fields
@@ -373,6 +375,8 @@ def _get_organism_record(
     if _has_organism_field(registry) and check:
         from bionty._bionty import create_or_get_organism_record
 
-        organism_record = create_or_get_organism_record(organism=organism, orm=registry)
+        organism_record = create_or_get_organism_record(
+            organism=organism, registry=registry
+        )
         if organism_record is not None:
             return organism_record

tests/test_uid.py

@@ -1,18 +1,14 @@
 import bionty as bt
-import lamindb as ln
-import pytest
 from bionty._bionty import encode_uid
 
 
-def test_lb_encode_uid():
+def test_bionty_encode_uid():
     assert (
         encode_uid(bt.Gene, {"ensembl_gene_id": "ENSG00000081059", "symbol": "TCF7"})[
             "uid"
         ]
         == "7IkHKPl0ScQR"
     )
-    with pytest.raises(AssertionError):
-        encode_uid(bt.Organism, {"ensembl_gene_id": "ENSG00000081059"})
     assert encode_uid(bt.CellType, {"ontology_id": "CL:0000084"})["uid"] == "22LvKd01"
     assert (
         encode_uid(bt.Organism, {"ontology_id": "NCBITaxon:9606", "name": "human"})[
@@ -21,3 +17,23 @@ def test_lb_encode_uid():
         == "1dpCL6Td"
     )
     assert encode_uid(bt.Organism, {"name": "human"})["uid"] == "4gQdjtxb"
+    assert (
+        encode_uid(
+            bt.Source,
+            {
+                "entity": "Source",
+                "name": "ensembl",
+                "version": "release-112",
+                "organism": "vertebrates",
+            },
+        )["uid"]
+        == "5MUN"
+    )
+    bt.settings.organism = "human"
+    assert (
+        encode_uid(bt.CellMarker, {"name": "test", "organism": bt.settings.organism})[
+            "uid"
+        ]
+        == "2dZ52W9noUDK"
+    )
+    bt.settings.organism.delete()