lamindb 0.76.7__py3-none-any.whl → 0.76.8__py3-none-any.whl

lamindb/_from_values.py

@@ -1,382 +1,382 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING, Iterable
-
-import pandas as pd
-from django.core.exceptions import FieldDoesNotExist
-from lamin_utils import colors, logger
-from lnschema_core.models import Feature, Record, ULabel
-
-from .core._settings import settings
-
-if TYPE_CHECKING:
-    from lnschema_core.types import ListLike, StrField
-
-
-# The base function for `from_values`
-def get_or_create_records(
-    iterable: ListLike,
-    field: StrField,
-    *,
-    create: bool = False,
-    from_source: bool = False,
-    organism: Record | str | None = None,
-    source: Record | None = None,
-    mute: bool = False,
-) -> list[Record]:
-    """Get or create records from iterables."""
-    registry = field.field.model
-    if create:
-        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)
-    kwargs: dict = {}
-    if organism is not None:
-        kwargs["organism"] = organism
-    if source is not None:
-        kwargs["source"] = source
-    settings.creation.search_names = False
-    try:
-        iterable_idx = index_iterable(iterable)
-
-        # returns existing records & non-existing values
-        records, nonexist_values, msg = get_existing_records(
-            iterable_idx=iterable_idx, field=field, mute=mute, **kwargs
-        )
-
-        # new records to be created based on new values
-        if len(nonexist_values) > 0:
-            source_record = None
-            if from_source:
-                if isinstance(source, Record):
-                    source_record = source
-                elif (
-                    len(records) > 0
-                    and hasattr(records[0], "source_id")
-                    and records[0].source_id
-                ):
-                    source_record = records[0].source
-            if not source_record and hasattr(registry, "public"):
-                from bionty._bionty import get_source_record
-
-                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=registry,
-                    source=source_record,
-                    update=True,
-                )
-
-                from_source = not source_record.in_db
-            elif hasattr(registry, "source_id"):
-                from_source = True
-            else:
-                from_source = False
-
-            if from_source:
-                records_bionty, unmapped_values = create_records_from_source(
-                    iterable_idx=nonexist_values,
-                    field=field,
-                    msg=msg,
-                    mute=mute,
-                    **kwargs,
-                )
-                if len(records_bionty) > 0:
-                    msg = ""
-                for record in records_bionty:
-                    record._from_source = True
-                records += records_bionty
-            else:
-                unmapped_values = nonexist_values
-            # unmapped new_ids will NOT create records
-            if len(unmapped_values) > 0:
-                if len(msg) > 0 and not mute:
-                    logger.success(msg)
-                s = "" if len(unmapped_values) == 1 else "s"
-                print_values = colors.yellow(_print_values(unmapped_values))
-                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 registry.__get_schema_name__() == "bionty" or registry == ULabel:
-            if isinstance(iterable, pd.Series):
-                feature = iterable.name
-            feature_name = None
-            if isinstance(feature, str):
-                feature_name = feature
-            if feature_name is not None:
-                if feature_name is not None:
-                    for record in records:
-                        record._feature = feature_name
-                logger.debug(f"added default feature '{feature_name}'")
-        return records
-    finally:
-        settings.creation.search_names = creation_search_names
-
-
-def get_existing_records(
-    iterable_idx: pd.Index,
-    field: StrField,
-    mute: bool = False,
-    **kwargs,
-):
-    model = field.field.model
-    condition: dict = {} if len(kwargs) == 0 else kwargs.copy()
-    # existing records matching is agnostic to the bionty source
-    if "source" in condition:
-        condition.pop("source")
-
-    # standardize based on the DB reference
-    # log synonyms mapped terms
-    result = model.inspect(
-        iterable_idx,
-        field=field,
-        organism=kwargs.get("organism"),
-        source=kwargs.get("source"),
-        mute=True,
-    )
-    syn_mapper = result.synonyms_mapper
-
-    syn_msg = ""
-    if len(syn_mapper) > 0:
-        s = "" if len(syn_mapper) == 1 else "s"
-        names = list(syn_mapper.keys())
-        print_values = colors.green(_print_values(names))
-        syn_msg = (
-            "loaded"
-            f" {colors.green(f'{len(syn_mapper)} {model.__name__} record{s}')}"
-            f" matching {colors.italic('synonyms')}: {print_values}"
-        )
-        iterable_idx = iterable_idx.to_frame().rename(index=syn_mapper).index
-
-    # get all existing records in the db
-    # if necessary, create records for the values in kwargs
-    # k:v -> k:v_record
-    # kwargs is used to deal with organism
-    condition.update({f"{field.field.name}__in": iterable_idx.values})
-
-    query_set = model.filter(**condition)
-    records = query_set.list()
-
-    # now we have to sort the list of queried records
-    # preserved = Case(
-    #     *[
-    #         When(**{field.field.name: value}, then=pos)
-    #         for pos, value in enumerate(iterable_idx)
-    #     ]
-    # )
-    # order by causes a factor 10 in runtime
-    # records = query_set.order_by(preserved).list()
-
-    # log validated terms
-    validated = result.validated
-    msg = ""
-    if len(validated) > 0:
-        s = "" if len(validated) == 1 else "s"
-        print_values = colors.green(_print_values(validated))
-        msg = (
-            "loaded"
-            f" {colors.green(f'{len(validated)} {model.__name__} record{s}')}"
-            f" matching {colors.italic(f'{field.field.name}')}: {print_values}"
-        )
-
-    # no logging if all values are validated
-    # logs if there are synonyms
-    if len(syn_msg) > 0:
-        if len(msg) > 0 and not mute:
-            logger.success(msg)
-        if not mute:
-            logger.success(syn_msg)
-        msg = ""
-
-    existing_values = iterable_idx.intersection(
-        query_set.values_list(field.field.name, flat=True)
-    )
-    nonexist_values = iterable_idx.difference(existing_values)
-
-    return records, nonexist_values, msg
-
-
-def create_records_from_source(
-    iterable_idx: pd.Index,
-    field: StrField,
-    msg: str = "",
-    mute: bool = False,
-    **kwargs,
-):
-    model = field.field.model
-    records: list = []
-    # populate additional fields from bionty
-    from bionty._bionty import get_source_record
-    from bionty.core._bionty import filter_bionty_df_columns
-
-    # create the corresponding bionty object from model
-    try:
-        # TODO: more generic
-        organism = kwargs.get("organism")
-        if field.field.name == "ensembl_gene_id":
-            if iterable_idx[0].startswith("ENSG"):
-                organism = "human"
-            elif iterable_idx[0].startswith("ENSMUSG"):
-                organism = "mouse"
-        public_ontology = model.public(organism=organism, source=kwargs.get("source"))
-    except Exception:
-        # 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, model)
-    kwargs.update({"source": source_record})
-
-    # filter the columns in bionty df based on fields
-    bionty_df = filter_bionty_df_columns(model=model, public_ontology=public_ontology)
-
-    # standardize in the bionty reference
-    result = public_ontology.inspect(iterable_idx, field=field.field.name, mute=True)
-    syn_mapper = result.synonyms_mapper
-
-    msg_syn: str = ""
-    if len(syn_mapper) > 0:
-        s = "" if len(syn_mapper) == 1 else "s"
-        names = list(syn_mapper.keys())
-        print_values = colors.purple(_print_values(names))
-        msg_syn = (
-            "created"
-            f" {colors.purple(f'{len(syn_mapper)} {model.__name__} record{s} from Bionty')}"
-            f" matching {colors.italic('synonyms')}: {print_values}"
-        )
-
-        iterable_idx = iterable_idx.to_frame().rename(index=syn_mapper).index
-
-    # create records for values that are found in the bionty reference
-    # matching either field or synonyms
-    mapped_values = iterable_idx.intersection(bionty_df[field.field.name])
-
-    multi_msg = ""
-    if len(mapped_values) > 0:
-        bionty_kwargs, multi_msg = _bulk_create_dicts_from_df(
-            keys=mapped_values, column_name=field.field.name, df=bionty_df
-        )
-        organism_kwargs = {}
-        if "organism" not in kwargs:
-            organism_record = _get_organism_record(
-                field, public_ontology.organism, force=True
-            )
-            if organism_record is not None:
-                organism_kwargs["organism"] = organism_record
-        for bk in bionty_kwargs:
-            records.append(model(**bk, **kwargs, **organism_kwargs))
-
-        # number of records that matches field (not synonyms)
-        validated = result.validated
-        if len(validated) > 0:
-            s = "" if len(validated) == 1 else "s"
-            print_values = colors.purple(_print_values(validated))
-            # this is the success msg for existing records in the DB
-            if len(msg) > 0 and not mute:
-                logger.success(msg)
-            if not mute:
-                logger.success(
-                    "created"
-                    f" {colors.purple(f'{len(validated)} {model.__name__} record{s} from Bionty')}"
-                    f" matching {colors.italic(f'{field.field.name}')}: {print_values}"
-                )
-
-    # make sure that synonyms logging appears after the field logging
-    if len(msg_syn) > 0 and not mute:
-        logger.success(msg_syn)
-    # warning about multi matches
-    if len(multi_msg) > 0 and not mute:
-        logger.warning(multi_msg)
-
-    # return the values that are not found in the bionty reference
-    unmapped_values = iterable_idx.difference(mapped_values)
-    return records, unmapped_values
-
-
-def index_iterable(iterable: Iterable) -> pd.Index:
-    idx = pd.Index(iterable).unique()
-    # No entries are made for NAs, '', None
-    # returns an ordered unique not null list
-    return idx[(idx != "") & (~idx.isnull())]
-
-
-def _print_values(names: Iterable, n: int = 20, quotes: bool = True) -> str:
-    if isinstance(names, dict):
-        items = {
-            f"{key}: {value}": None
-            for key, value in names.items()
-            if key != "None" and value != "None"
-        }
-    else:
-        # Use a dictionary instead of a list to have unique values and preserve order
-        items = {str(name): None for name in names if name != "None"}
-
-    unique_items = list(items.keys())
-
-    if quotes:
-        unique_items = [f"'{item}'" for item in unique_items]
-
-    print_values = ", ".join(unique_items[:n])
-
-    if len(unique_items) > n:
-        print_values += ", ..."
-
-    return print_values
-
-
-def _bulk_create_dicts_from_df(
-    keys: set | list, column_name: str, df: pd.DataFrame
-) -> tuple[dict, str]:
-    """Get fields from a DataFrame for many rows."""
-    multi_msg = ""
-    if df.index.name != column_name:
-        df = df.set_index(column_name).loc[list(keys)]
-    if not df.index.is_unique:
-        # return all records for multi-matches with a warning
-        dup = df.index[df.index.duplicated()].unique().tolist()
-        if len(dup) > 0:
-            s = "" if len(dup) == 1 else "s"
-            print_values = _print_values(dup)
-            multi_msg = (
-                f"ambiguous validation in Bionty for {len(dup)} record{s}:"
-                f" {print_values}"
-            )
-
-    return df.reset_index().to_dict(orient="records"), multi_msg
-
-
-def _has_organism_field(registry: type[Record]) -> bool:
-    try:
-        registry._meta.get_field("organism")
-        return True
-    except FieldDoesNotExist:
-        return False
-
-
-def _get_organism_record(
-    field: StrField, organism: str | Record, force: bool = False
-) -> Record:
-    registry = field.field.model
-    check = True
-    if not force and hasattr(registry, "_ontology_id_field"):
-        check = field.field.name != registry._ontology_id_field
-        # e.g. bionty.CellMarker has "name" as _ontology_id_field
-        if not registry._ontology_id_field.endswith("id"):
-            check = True
-
-    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, registry=registry
-        )
-        if organism_record is not None:
-            return organism_record
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Iterable
+
+import pandas as pd
+from django.core.exceptions import FieldDoesNotExist
+from lamin_utils import colors, logger
+from lnschema_core.models import Feature, Record, ULabel
+
+from .core._settings import settings
+
+if TYPE_CHECKING:
+    from lnschema_core.types import ListLike, StrField
+
+
+# The base function for `from_values`
+def get_or_create_records(
+    iterable: ListLike,
+    field: StrField,
+    *,
+    create: bool = False,
+    from_source: bool = False,
+    organism: Record | str | None = None,
+    source: Record | None = None,
+    mute: bool = False,
+) -> list[Record]:
+    """Get or create records from iterables."""
+    registry = field.field.model
+    if create:
+        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)
+    kwargs: dict = {}
+    if organism is not None:
+        kwargs["organism"] = organism
+    if source is not None:
+        kwargs["source"] = source
+    settings.creation.search_names = False
+    try:
+        iterable_idx = index_iterable(iterable)
+
+        # returns existing records & non-existing values
+        records, nonexist_values, msg = get_existing_records(
+            iterable_idx=iterable_idx, field=field, mute=mute, **kwargs
+        )
+
+        # new records to be created based on new values
+        if len(nonexist_values) > 0:
+            source_record = None
+            if from_source:
+                if isinstance(source, Record):
+                    source_record = source
+                elif (
+                    len(records) > 0
+                    and hasattr(records[0], "source_id")
+                    and records[0].source_id
+                ):
+                    source_record = records[0].source
+            if not source_record and hasattr(registry, "public"):
+                from bionty._bionty import get_source_record
+
+                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=registry,
+                    source=source_record,
+                    update=True,
+                )
+
+                from_source = not source_record.in_db
+            elif hasattr(registry, "source_id"):
+                from_source = True
+            else:
+                from_source = False
+
+            if from_source:
+                records_bionty, unmapped_values = create_records_from_source(
+                    iterable_idx=nonexist_values,
+                    field=field,
+                    msg=msg,
+                    mute=mute,
+                    **kwargs,
+                )
+                if len(records_bionty) > 0:
+                    msg = ""
+                for record in records_bionty:
+                    record._from_source = True
+                records += records_bionty
+            else:
+                unmapped_values = nonexist_values
+            # unmapped new_ids will NOT create records
+            if len(unmapped_values) > 0:
+                if len(msg) > 0 and not mute:
+                    logger.success(msg)
+                s = "" if len(unmapped_values) == 1 else "s"
+                print_values = colors.yellow(_print_values(unmapped_values))
+                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 registry.__get_schema_name__() == "bionty" or registry == ULabel:
+            if isinstance(iterable, pd.Series):
+                feature = iterable.name
+            feature_name = None
+            if isinstance(feature, str):
+                feature_name = feature
+            if feature_name is not None:
+                if feature_name is not None:
+                    for record in records:
+                        record._feature = feature_name
+                logger.debug(f"added default feature '{feature_name}'")
+        return records
+    finally:
+        settings.creation.search_names = creation_search_names
+
+
+def get_existing_records(
+    iterable_idx: pd.Index,
+    field: StrField,
+    mute: bool = False,
+    **kwargs,
+):
+    model = field.field.model
+    condition: dict = {} if len(kwargs) == 0 else kwargs.copy()
+    # existing records matching is agnostic to the bionty source
+    if "source" in condition:
+        condition.pop("source")
+
+    # standardize based on the DB reference
+    # log synonyms mapped terms
+    result = model.inspect(
+        iterable_idx,
+        field=field,
+        organism=kwargs.get("organism"),
+        source=kwargs.get("source"),
+        mute=True,
+    )
+    syn_mapper = result.synonyms_mapper
+
+    syn_msg = ""
+    if len(syn_mapper) > 0:
+        s = "" if len(syn_mapper) == 1 else "s"
+        names = list(syn_mapper.keys())
+        print_values = colors.green(_print_values(names))
+        syn_msg = (
+            "loaded"
+            f" {colors.green(f'{len(syn_mapper)} {model.__name__} record{s}')}"
+            f" matching {colors.italic('synonyms')}: {print_values}"
+        )
+        iterable_idx = iterable_idx.to_frame().rename(index=syn_mapper).index
+
+    # get all existing records in the db
+    # if necessary, create records for the values in kwargs
+    # k:v -> k:v_record
+    # kwargs is used to deal with organism
+    condition.update({f"{field.field.name}__in": iterable_idx.values})
+
+    query_set = model.filter(**condition)
+    records = query_set.list()
+
+    # now we have to sort the list of queried records
+    # preserved = Case(
+    #     *[
+    #         When(**{field.field.name: value}, then=pos)
+    #         for pos, value in enumerate(iterable_idx)
+    #     ]
+    # )
+    # order by causes a factor 10 in runtime
+    # records = query_set.order_by(preserved).list()
+
+    # log validated terms
+    validated = result.validated
+    msg = ""
+    if len(validated) > 0:
+        s = "" if len(validated) == 1 else "s"
+        print_values = colors.green(_print_values(validated))
+        msg = (
+            "loaded"
+            f" {colors.green(f'{len(validated)} {model.__name__} record{s}')}"
+            f" matching {colors.italic(f'{field.field.name}')}: {print_values}"
+        )
+
+    # no logging if all values are validated
+    # logs if there are synonyms
+    if len(syn_msg) > 0:
+        if len(msg) > 0 and not mute:
+            logger.success(msg)
+        if not mute:
+            logger.success(syn_msg)
+        msg = ""
+
+    existing_values = iterable_idx.intersection(
+        query_set.values_list(field.field.name, flat=True)
+    )
+    nonexist_values = iterable_idx.difference(existing_values)
+
+    return records, nonexist_values, msg
+
+
+def create_records_from_source(
+    iterable_idx: pd.Index,
+    field: StrField,
+    msg: str = "",
+    mute: bool = False,
+    **kwargs,
+):
+    model = field.field.model
+    records: list = []
+    # populate additional fields from bionty
+    from bionty._bionty import get_source_record
+    from bionty.core._bionty import filter_bionty_df_columns
+
+    # create the corresponding bionty object from model
+    try:
+        # TODO: more generic
+        organism = kwargs.get("organism")
+        if field.field.name == "ensembl_gene_id":
+            if iterable_idx[0].startswith("ENSG"):
+                organism = "human"
+            elif iterable_idx[0].startswith("ENSMUSG"):
+                organism = "mouse"
+        public_ontology = model.public(organism=organism, source=kwargs.get("source"))
+    except Exception:
+        # 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, model)
+    kwargs.update({"source": source_record})
+
+    # filter the columns in bionty df based on fields
+    bionty_df = filter_bionty_df_columns(model=model, public_ontology=public_ontology)
+
+    # standardize in the bionty reference
+    result = public_ontology.inspect(iterable_idx, field=field.field.name, mute=True)
+    syn_mapper = result.synonyms_mapper
+
+    msg_syn: str = ""
+    if len(syn_mapper) > 0:
+        s = "" if len(syn_mapper) == 1 else "s"
+        names = list(syn_mapper.keys())
+        print_values = colors.purple(_print_values(names))
+        msg_syn = (
+            "created"
+            f" {colors.purple(f'{len(syn_mapper)} {model.__name__} record{s} from Bionty')}"
+            f" matching {colors.italic('synonyms')}: {print_values}"
+        )
+
+        iterable_idx = iterable_idx.to_frame().rename(index=syn_mapper).index
+
+    # create records for values that are found in the bionty reference
+    # matching either field or synonyms
+    mapped_values = iterable_idx.intersection(bionty_df[field.field.name])
+
+    multi_msg = ""
+    if len(mapped_values) > 0:
+        bionty_kwargs, multi_msg = _bulk_create_dicts_from_df(
+            keys=mapped_values, column_name=field.field.name, df=bionty_df
+        )
+        organism_kwargs = {}
+        if "organism" not in kwargs:
+            organism_record = _get_organism_record(
+                field, public_ontology.organism, force=True
+            )
+            if organism_record is not None:
+                organism_kwargs["organism"] = organism_record
+        for bk in bionty_kwargs:
+            records.append(model(**bk, **kwargs, **organism_kwargs))
+
+        # number of records that matches field (not synonyms)
+        validated = result.validated
+        if len(validated) > 0:
+            s = "" if len(validated) == 1 else "s"
+            print_values = colors.purple(_print_values(validated))
+            # this is the success msg for existing records in the DB
+            if len(msg) > 0 and not mute:
+                logger.success(msg)
+            if not mute:
+                logger.success(
+                    "created"
+                    f" {colors.purple(f'{len(validated)} {model.__name__} record{s} from Bionty')}"
+                    f" matching {colors.italic(f'{field.field.name}')}: {print_values}"
+                )
+
+    # make sure that synonyms logging appears after the field logging
+    if len(msg_syn) > 0 and not mute:
+        logger.success(msg_syn)
+    # warning about multi matches
+    if len(multi_msg) > 0 and not mute:
+        logger.warning(multi_msg)
+
+    # return the values that are not found in the bionty reference
+    unmapped_values = iterable_idx.difference(mapped_values)
+    return records, unmapped_values
+
+
+def index_iterable(iterable: Iterable) -> pd.Index:
+    idx = pd.Index(iterable).unique()
+    # No entries are made for NAs, '', None
+    # returns an ordered unique not null list
+    return idx[(idx != "") & (~idx.isnull())]
+
+
+def _print_values(names: Iterable, n: int = 20, quotes: bool = True) -> str:
+    if isinstance(names, dict):
+        items = {
+            f"{key}: {value}": None
+            for key, value in names.items()
+            if key != "None" and value != "None"
+        }
+    else:
+        # Use a dictionary instead of a list to have unique values and preserve order
+        items = {str(name): None for name in names if name != "None"}
+
+    unique_items = list(items.keys())
+
+    if quotes:
+        unique_items = [f"'{item}'" for item in unique_items]
+
+    print_values = ", ".join(unique_items[:n])
+
+    if len(unique_items) > n:
+        print_values += ", ..."
+
+    return print_values
+
+
+def _bulk_create_dicts_from_df(
+    keys: set | list, column_name: str, df: pd.DataFrame
+) -> tuple[dict, str]:
+    """Get fields from a DataFrame for many rows."""
+    multi_msg = ""
+    if df.index.name != column_name:
+        df = df.set_index(column_name).loc[list(keys)]
+    if not df.index.is_unique:
+        # return all records for multi-matches with a warning
+        dup = df.index[df.index.duplicated()].unique().tolist()
+        if len(dup) > 0:
+            s = "" if len(dup) == 1 else "s"
+            print_values = _print_values(dup)
+            multi_msg = (
+                f"ambiguous validation in Bionty for {len(dup)} record{s}:"
+                f" {print_values}"
+            )
+
+    return df.reset_index().to_dict(orient="records"), multi_msg
+
+
+def _has_organism_field(registry: type[Record]) -> bool:
+    try:
+        registry._meta.get_field("organism")
+        return True
+    except FieldDoesNotExist:
+        return False
+
+
+def _get_organism_record(
+    field: StrField, organism: str | Record, force: bool = False
+) -> Record:
+    registry = field.field.model
+    check = True
+    if not force and hasattr(registry, "_ontology_id_field"):
+        check = field.field.name != registry._ontology_id_field
+        # e.g. bionty.CellMarker has "name" as _ontology_id_field
+        if not registry._ontology_id_field.endswith("id"):
+            check = True
+
+    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, registry=registry
+        )
+        if organism_record is not None:
+            return organism_record