lamindb 0.76.8__py3-none-any.whl → 0.76.9__py3-none-any.whl

lamindb/_record.py

@@ -1,649 +1,649 @@
-from __future__ import annotations
-
-import builtins
-from typing import TYPE_CHECKING, List, NamedTuple
-
-import dj_database_url
-import lamindb_setup as ln_setup
-from django.db import connections, transaction
-from django.db.models import IntegerField, Manager, Q, QuerySet, Value
-from lamin_utils import logger
-from lamin_utils._lookup import Lookup
-from lamindb_setup._connect_instance import get_owner_name_from_identifier
-from lamindb_setup.core._docs import doc_args
-from lamindb_setup.core._hub_core import connect_instance
-from lnschema_core.models import IsVersioned, Record
-
-from lamindb._utils import attach_func_to_class_method
-from lamindb.core._settings import settings
-
-from ._from_values import get_or_create_records
-
-if TYPE_CHECKING:
-    import pandas as pd
-    from lnschema_core.types import ListLike, StrField
-
-
-IPYTHON = getattr(builtins, "__IPYTHON__", False)
-
-
-def init_self_from_db(self: Record, existing_record: Record):
-    new_args = [
-        getattr(existing_record, field.attname) for field in self._meta.concrete_fields
-    ]
-    super(self.__class__, self).__init__(*new_args)
-    self._state.adding = False  # mimic from_db
-    self._state.db = "default"
-
-
-def update_attributes(record: Record, attributes: dict[str, str]):
-    for key, value in attributes.items():
-        if getattr(record, key) != value:
-            logger.warning(f"updated {key} from {getattr(record, key)} to {value}")
-            setattr(record, key, value)
-
-
-def validate_required_fields(record: Record, kwargs):
-    required_fields = {
-        k.name for k in record._meta.fields if not k.null and k.default is None
-    }
-    required_fields_not_passed = {k: None for k in required_fields if k not in kwargs}
-    kwargs.update(required_fields_not_passed)
-    missing_fields = [
-        k for k, v in kwargs.items() if v is None and k in required_fields
-    ]
-    if missing_fields:
-        raise TypeError(f"{missing_fields} are required.")
-
-
-def suggest_records_with_similar_names(record: Record, kwargs) -> bool:
-    """Returns True if found exact match, otherwise False.
-
-    Logs similar matches if found.
-    """
-    if kwargs.get("name") is None:
-        return False
-    queryset = _search(
-        record.__class__, kwargs["name"], field="name", truncate_words=True, limit=3
-    )
-    if not queryset.exists():  # empty queryset
-        return False
-    for alternative_record in queryset:
-        if alternative_record.name == kwargs["name"]:
-            return True
-    s, it, nots = ("", "it", "s") if len(queryset) == 1 else ("s", "one of them", "")
-    msg = f"record{s} with similar name{s} exist{nots}! did you mean to load {it}?"
-    if IPYTHON:
-        from IPython.display import display
-
-        logger.warning(f"{msg}")
-        if settings._verbosity_int >= 1:
-            display(queryset.df())
-    else:
-        logger.warning(f"{msg}\n{queryset}")
-    return False
-
-
-def __init__(record: Record, *args, **kwargs):
-    if not args:
-        validate_required_fields(record, kwargs)
-
-        # do not search for names if an id is passed; this is important
-        # e.g. when synching ids from the notebook store to lamindb
-        has_consciously_provided_uid = False
-        if "_has_consciously_provided_uid" in kwargs:
-            has_consciously_provided_uid = kwargs.pop("_has_consciously_provided_uid")
-        if settings.creation.search_names and not has_consciously_provided_uid:
-            match = suggest_records_with_similar_names(record, kwargs)
-            if match:
-                if "version" in kwargs:
-                    if kwargs["version"] is not None:
-                        version_comment = " and version"
-                        existing_record = record.__class__.filter(
-                            name=kwargs["name"], version=kwargs["version"]
-                        ).one_or_none()
-                    else:
-                        # for a versioned record, an exact name match is not a
-                        # criterion for retrieving a record in case `version`
-                        # isn't passed - we'd always pull out many records with exactly the
-                        # same name
-                        existing_record = None
-                else:
-                    version_comment = ""
-                    existing_record = record.__class__.filter(
-                        name=kwargs["name"]
-                    ).one_or_none()
-                if existing_record is not None:
-                    logger.important(
-                        f"returning existing {record.__class__.__name__} record with same"
-                        f" name{version_comment}: '{kwargs['name']}'"
-                    )
-                    init_self_from_db(record, existing_record)
-                    return None
-        super(Record, record).__init__(**kwargs)
-    elif len(args) != len(record._meta.concrete_fields):
-        raise ValueError("please provide keyword arguments, not plain arguments")
-    else:
-        # object is loaded from DB (**kwargs could be omitted below, I believe)
-        super(Record, record).__init__(*args, **kwargs)
-
-
-@classmethod  # type:ignore
-@doc_args(Record.filter.__doc__)
-def filter(cls, *queries, **expressions) -> QuerySet:
-    """{}"""  # noqa: D415
-    from lamindb._filter import filter
-
-    return filter(cls, *queries, **expressions)
-
-
-@classmethod  # type:ignore
-@doc_args(Record.get.__doc__)
-def get(
-    cls,
-    idlike: int | str | None = None,
-    **expressions,
-) -> Record:
-    """{}"""  # noqa: D415
-    # this is the only place in which we need the lamindb queryset
-    # in this file; everywhere else it should be Django's
-    from lamindb._query_set import QuerySet
-
-    return QuerySet(model=cls).get(idlike, **expressions)
-
-
-@classmethod  # type:ignore
-@doc_args(Record.df.__doc__)
-def df(
-    cls,
-    include: str | list[str] | None = None,
-    join: str = "inner",
-    limit: int = 100,
-) -> pd.DataFrame:
-    """{}"""  # noqa: D415
-    from lamindb._filter import filter
-
-    query_set = filter(cls)
-    if hasattr(cls, "updated_at"):
-        query_set = query_set.order_by("-updated_at")
-    return query_set[:limit].df(include=include, join=join)
-
-
-# from_values doesn't apply for QuerySet or Manager
-@classmethod  # type:ignore
-@doc_args(Record.from_values.__doc__)
-def from_values(
-    cls,
-    values: ListLike,
-    field: StrField | None = None,
-    create: bool = False,
-    organism: Record | str | None = None,
-    source: Record | None = None,
-    mute: bool = False,
-) -> list[Record]:
-    """{}"""  # noqa: D415
-    from_source = True if cls.__module__.startswith("bionty.") else False
-
-    field_str = get_name_field(cls, field=field)
-    return get_or_create_records(
-        iterable=values,
-        field=getattr(cls, field_str),
-        create=create,
-        from_source=from_source,
-        organism=organism,
-        source=source,
-        mute=mute,
-    )
-
-
-def _search(
-    cls,
-    string: str,
-    *,
-    field: StrField | list[StrField] | None = None,
-    limit: int | None = 20,
-    case_sensitive: bool = False,
-    using_key: str | None = None,
-    truncate_words: bool = False,
-) -> QuerySet:
-    input_queryset = _queryset(cls, using_key=using_key)
-    registry = input_queryset.model
-    if field is None:
-        fields = [
-            field.name
-            for field in registry._meta.fields
-            if field.get_internal_type() in {"CharField", "TextField"}
-        ]
-    else:
-        if not isinstance(field, list):
-            fields_input = [field]
-        else:
-            fields_input = field
-        fields = []
-        for field in fields_input:
-            if not isinstance(field, str):
-                try:
-                    fields.append(field.field.name)
-                except AttributeError as error:
-                    raise TypeError(
-                        "Please pass a Record string field, e.g., `CellType.name`!"
-                    ) from error
-            else:
-                fields.append(field)
-
-    # decompose search string
-    def truncate_word(word) -> str:
-        if len(word) > 5:
-            n_80_pct = int(len(word) * 0.8)
-            return word[:n_80_pct]
-        elif len(word) > 3:
-            return word[:3]
-        else:
-            return word
-
-    decomposed_string = str(string).split()
-    # add the entire string back
-    decomposed_string += [string]
-    for word in decomposed_string:
-        # will not search against words with 3 or fewer characters
-        if len(word) <= 3:
-            decomposed_string.remove(word)
-    if truncate_words:
-        decomposed_string = [truncate_word(word) for word in decomposed_string]
-    # construct the query
-    expression = Q()
-    case_sensitive_i = "" if case_sensitive else "i"
-    for field in fields:
-        for word in decomposed_string:
-            query = {f"{field}__{case_sensitive_i}contains": word}
-            expression |= Q(**query)
-    output_queryset = input_queryset.filter(expression)
-    # ensure exact matches are at the top
-    narrow_expression = Q()
-    for field in fields:
-        query = {f"{field}__{case_sensitive_i}contains": string}
-        narrow_expression |= Q(**query)
-    refined_output_queryset = output_queryset.filter(narrow_expression).annotate(
-        ordering=Value(1, output_field=IntegerField())
-    )
-    remaining_output_queryset = output_queryset.exclude(narrow_expression).annotate(
-        ordering=Value(2, output_field=IntegerField())
-    )
-    combined_queryset = refined_output_queryset.union(
-        remaining_output_queryset
-    ).order_by("ordering")[:limit]
-    return combined_queryset
-
-
-@classmethod  # type: ignore
-@doc_args(Record.search.__doc__)
-def search(
-    cls,
-    string: str,
-    *,
-    field: StrField | None = None,
-    limit: int | None = 20,
-    case_sensitive: bool = False,
-) -> QuerySet:
-    """{}"""  # noqa: D415
-    return _search(
-        cls=cls,
-        string=string,
-        field=field,
-        limit=limit,
-        case_sensitive=case_sensitive,
-    )
-
-
-def _lookup(
-    cls,
-    field: StrField | None = None,
-    return_field: StrField | None = None,
-    using_key: str | None = None,
-) -> NamedTuple:
-    """{}"""  # noqa: D415
-    queryset = _queryset(cls, using_key=using_key)
-    field = get_name_field(registry=queryset.model, field=field)
-
-    return Lookup(
-        records=queryset,
-        values=[i.get(field) for i in queryset.values()],
-        tuple_name=cls.__class__.__name__,
-        prefix="ln",
-    ).lookup(
-        return_field=(
-            get_name_field(registry=queryset.model, field=return_field)
-            if return_field is not None
-            else None
-        )
-    )
-
-
-@classmethod  # type: ignore
-@doc_args(Record.lookup.__doc__)
-def lookup(
-    cls,
-    field: StrField | None = None,
-    return_field: StrField | None = None,
-) -> NamedTuple:
-    """{}"""  # noqa: D415
-    return _lookup(cls=cls, field=field, return_field=return_field)
-
-
-def get_name_field(
-    registry: type[Record] | QuerySet | Manager,
-    *,
-    field: str | StrField | None = None,
-) -> str:
-    """Get the 1st char or text field from the registry."""
-    if isinstance(registry, (QuerySet, Manager)):
-        registry = registry.model
-    model_field_names = [i.name for i in registry._meta.fields]
-
-    # set to default name field
-    if field is None:
-        if hasattr(registry, "_name_field"):
-            field = registry._meta.get_field(registry._name_field)
-        elif "name" in model_field_names:
-            field = registry._meta.get_field("name")
-        else:
-            # first char or text field that doesn't contain "id"
-            for i in registry._meta.fields:
-                if "id" in i.name:
-                    continue
-                if i.get_internal_type() in {"CharField", "TextField"}:
-                    field = i
-                    break
-
-        # no default name field can be found
-        if field is None:
-            raise ValueError(
-                "please pass a Record string field, e.g., `CellType.name`!"
-            )
-        else:
-            field = field.name  # type:ignore
-    if not isinstance(field, str):
-        try:
-            field = field.field.name
-        except AttributeError:
-            raise TypeError(
-                "please pass a Record string field, e.g., `CellType.name`!"
-            ) from None
-
-    return field
-
-
-def _queryset(cls: Record | QuerySet | Manager, using_key: str) -> QuerySet:
-    if isinstance(cls, (QuerySet, Manager)):
-        return cls.all()
-    elif using_key is None or using_key == "default":
-        return cls.objects.all()
-    else:
-        # using must be called on cls, otherwise the connection isn't found
-        return cls.using(using_key).all()
-
-
-def add_db_connection(db: str, using: str):
-    db_config = dj_database_url.config(
-        default=db, conn_max_age=600, conn_health_checks=True
-    )
-    db_config["TIME_ZONE"] = "UTC"
-    db_config["OPTIONS"] = {}
-    db_config["AUTOCOMMIT"] = True
-    connections.settings[using] = db_config
-
-
-@classmethod  # type: ignore
-@doc_args(Record.using.__doc__)
-def using(
-    cls,
-    instance: str | None,
-) -> QuerySet:
-    """{}"""  # noqa: D415
-    if instance is None:
-        return QuerySet(model=cls, using=None)
-    from lamindb_setup._connect_instance import (
-        load_instance_settings,
-        update_db_using_local,
-    )
-    from lamindb_setup.core._settings_store import instance_settings_file
-
-    owner, name = get_owner_name_from_identifier(instance)
-    settings_file = instance_settings_file(name, owner)
-    if not settings_file.exists():
-        load_result = connect_instance(owner=owner, name=name)
-        if isinstance(load_result, str):
-            raise RuntimeError(
-                f"Failed to load instance {instance}, please check your permission!"
-            )
-        instance_result, _ = load_result
-        settings_file = instance_settings_file(name, owner)
-        db = update_db_using_local(instance_result, settings_file)
-    else:
-        isettings = load_instance_settings(settings_file)
-        db = isettings.db
-    add_db_connection(db, instance)
-    return QuerySet(model=cls, using=instance)
-
-
-REGISTRY_UNIQUE_FIELD = {
-    "storage": "root",
-    "feature": "name",
-    "ulabel": "name",
-}
-
-
-def update_fk_to_default_db(
-    records: Record | list[Record] | QuerySet,
-    fk: str,
-    using_key: str | None,
-    transfer_logs: dict,
-):
-    record = records[0] if isinstance(records, (List, QuerySet)) else records
-    if hasattr(record, f"{fk}_id") and getattr(record, f"{fk}_id") is not None:
-        fk_record = getattr(record, fk)
-        field = REGISTRY_UNIQUE_FIELD.get(fk, "uid")
-        fk_record_default = fk_record.__class__.filter(
-            **{field: getattr(fk_record, field)}
-        ).one_or_none()
-        if fk_record_default is None:
-            from copy import copy
-
-            fk_record_default = copy(fk_record)
-            transfer_to_default_db(
-                fk_record_default, using_key, save=True, transfer_logs=transfer_logs
-            )
-        if isinstance(records, (List, QuerySet)):
-            for r in records:
-                setattr(r, f"{fk}", None)
-                setattr(r, f"{fk}_id", fk_record_default.id)
-        else:
-            setattr(records, f"{fk}", None)
-            setattr(records, f"{fk}_id", fk_record_default.id)
-
-
-FKBULK = [
-    "organism",
-    "source",
-    "_source_code_artifact",  # Transform
-    "report",  # Run
-]
-
-
-def transfer_fk_to_default_db_bulk(
-    records: list | QuerySet, using_key: str | None, transfer_logs: dict
-):
-    for fk in FKBULK:
-        update_fk_to_default_db(records, fk, using_key, transfer_logs=transfer_logs)
-
-
-def transfer_to_default_db(
-    record: Record,
-    using_key: str | None,
-    *,
-    transfer_logs: dict,
-    save: bool = False,
-    transfer_fk: bool = True,
-) -> Record | None:
-    from lamindb.core._context import context
-    from lamindb.core._data import WARNING_RUN_TRANSFORM
-
-    registry = record.__class__
-    record_on_default = registry.objects.filter(uid=record.uid).one_or_none()
-    record_str = f"{record.__class__.__name__}(uid='{record.uid}')"
-    if record_on_default is not None:
-        transfer_logs["mapped"].append(record_str)
-        return record_on_default
-    else:
-        transfer_logs["transferred"].append(record_str)
-
-    if hasattr(record, "created_by_id"):
-        record.created_by = None
-        record.created_by_id = ln_setup.settings.user.id
-    if hasattr(record, "run_id"):
-        record.run = None
-        if context.run is not None:
-            record.run_id = context.run.id
-        else:
-            if not settings.creation.artifact_silence_missing_run_warning:
-                logger.warning(WARNING_RUN_TRANSFORM)
-            record.run_id = None
-    if hasattr(record, "transform_id") and record._meta.model_name != "run":
-        record.transform = None
-        if context.run is not None:
-            record.transform_id = context.run.transform_id
-        else:
-            record.transform_id = None
-    # transfer other foreign key fields
-    fk_fields = [
-        i.name
-        for i in record._meta.fields
-        if i.get_internal_type() == "ForeignKey"
-        if i.name not in {"created_by", "run", "transform"}
-    ]
-    if not transfer_fk:
-        # don't transfer fk fields that are already bulk transferred
-        fk_fields = [fk for fk in fk_fields if fk not in FKBULK]
-    for fk in fk_fields:
-        update_fk_to_default_db(record, fk, using_key, transfer_logs=transfer_logs)
-    record.id = None
-    record._state.db = "default"
-    if save:
-        record.save()
-    return None
-
-
-# docstring handled through attach_func_to_class_method
-def save(self, *args, **kwargs) -> Record:
-    using_key = None
-    if "using" in kwargs:
-        using_key = kwargs["using"]
-    db = self._state.db
-    pk_on_db = self.pk
-    artifacts: list = []
-    if self.__class__.__name__ == "Collection" and self.id is not None:
-        # when creating a new collection without being able to access artifacts
-        artifacts = self.ordered_artifacts.list()
-    pre_existing_record = None
-    # consider records that are being transferred from other databases
-    transfer_logs: dict[str, list[str]] = {"mapped": [], "transferred": []}
-    if db is not None and db != "default" and using_key is None:
-        if isinstance(self, IsVersioned):
-            if not self.is_latest:
-                raise NotImplementedError(
-                    "You are attempting to transfer a record that's not the latest in its version history. This is currently not supported."
-                )
-        pre_existing_record = transfer_to_default_db(
-            self, using_key, transfer_logs=transfer_logs
-        )
-    if pre_existing_record is not None:
-        init_self_from_db(self, pre_existing_record)
-    else:
-        # save versioned record
-        if isinstance(self, IsVersioned) and self._revises is not None:
-            assert self._revises.is_latest  # noqa: S101
-            revises = self._revises
-            revises.is_latest = False
-            with transaction.atomic():
-                revises._revises = None  # ensure we don't start a recursion
-                revises.save()
-                super(Record, self).save(*args, **kwargs)
-            self._revises = None
-        # save unversioned record
-        else:
-            super(Record, self).save(*args, **kwargs)
-    # perform transfer of many-to-many fields
-    # only supported for Artifact and Collection records
-    if db is not None and db != "default" and using_key is None:
-        if self.__class__.__name__ == "Collection":
-            if len(artifacts) > 0:
-                logger.info("transfer artifacts")
-                for artifact in artifacts:
-                    artifact.save()
-                self.artifacts.add(*artifacts)
-        if hasattr(self, "labels"):
-            from copy import copy
-
-            from lnschema_core.models import FeatureManager
-
-            # here we go back to original record on the source database
-            self_on_db = copy(self)
-            self_on_db._state.db = db
-            self_on_db.pk = pk_on_db  # manually set the primary key
-            self_on_db.features = FeatureManager(self_on_db)
-            self.features._add_from(self_on_db, transfer_logs=transfer_logs)
-            self.labels.add_from(self_on_db, transfer_logs=transfer_logs)
-        for k, v in transfer_logs.items():
-            logger.important(f"{k} records: {', '.join(v)}")
-    return self
-
-
-def delete(self) -> None:
-    """Delete the record."""
-    # note that the logic below does not fire if a record is moved to the trash
-    # the idea is that moving a record to the trash should move its entire version family
-    # to the trash, whereas permanently deleting should default to only deleting a single record
-    # of a version family
-    # we can consider making it easy to permanently delete entire version families as well,
-    # but that's for another time
-    if isinstance(self, IsVersioned) and self.is_latest:
-        new_latest = (
-            self.__class__.objects.using(self._state.db)
-            .filter(is_latest=False, uid__startswith=self.stem_uid)
-            .order_by("-created_at")
-            .first()
-        )
-        if new_latest is not None:
-            new_latest.is_latest = True
-            with transaction.atomic():
-                new_latest.save()
-                super(Record, self).delete()
-            logger.warning(f"new latest version is {new_latest}")
-            return None
-    super(Record, self).delete()
-
-
-METHOD_NAMES = [
-    "__init__",
-    "filter",
-    "get",
-    "df",
-    "search",
-    "lookup",
-    "save",
-    "delete",
-    "from_values",
-    "using",
-]
-
-if ln_setup._TESTING:  # type: ignore
-    from inspect import signature
-
-    SIGS = {
-        name: signature(getattr(Record, name))
-        for name in METHOD_NAMES
-        if not name.startswith("__")
-    }
-
-for name in METHOD_NAMES:
-    attach_func_to_class_method(name, Record, globals())
+from __future__ import annotations
+
+import builtins
+from typing import TYPE_CHECKING, List, NamedTuple
+
+import dj_database_url
+import lamindb_setup as ln_setup
+from django.db import connections, transaction
+from django.db.models import IntegerField, Manager, Q, QuerySet, Value
+from lamin_utils import logger
+from lamin_utils._lookup import Lookup
+from lamindb_setup._connect_instance import get_owner_name_from_identifier
+from lamindb_setup.core._docs import doc_args
+from lamindb_setup.core._hub_core import connect_instance
+from lnschema_core.models import IsVersioned, Record
+
+from lamindb._utils import attach_func_to_class_method
+from lamindb.core._settings import settings
+
+from ._from_values import get_or_create_records
+
+if TYPE_CHECKING:
+    import pandas as pd
+    from lnschema_core.types import ListLike, StrField
+
+
+IPYTHON = getattr(builtins, "__IPYTHON__", False)
+
+
+def init_self_from_db(self: Record, existing_record: Record):
+    new_args = [
+        getattr(existing_record, field.attname) for field in self._meta.concrete_fields
+    ]
+    super(self.__class__, self).__init__(*new_args)
+    self._state.adding = False  # mimic from_db
+    self._state.db = "default"
+
+
+def update_attributes(record: Record, attributes: dict[str, str]):
+    for key, value in attributes.items():
+        if getattr(record, key) != value:
+            logger.warning(f"updated {key} from {getattr(record, key)} to {value}")
+            setattr(record, key, value)
+
+
+def validate_required_fields(record: Record, kwargs):
+    required_fields = {
+        k.name for k in record._meta.fields if not k.null and k.default is None
+    }
+    required_fields_not_passed = {k: None for k in required_fields if k not in kwargs}
+    kwargs.update(required_fields_not_passed)
+    missing_fields = [
+        k for k, v in kwargs.items() if v is None and k in required_fields
+    ]
+    if missing_fields:
+        raise TypeError(f"{missing_fields} are required.")
+
+
+def suggest_records_with_similar_names(record: Record, kwargs) -> bool:
+    """Returns True if found exact match, otherwise False.
+
+    Logs similar matches if found.
+    """
+    if kwargs.get("name") is None:
+        return False
+    queryset = _search(
+        record.__class__, kwargs["name"], field="name", truncate_words=True, limit=3
+    )
+    if not queryset.exists():  # empty queryset
+        return False
+    for alternative_record in queryset:
+        if alternative_record.name == kwargs["name"]:
+            return True
+    s, it, nots = ("", "it", "s") if len(queryset) == 1 else ("s", "one of them", "")
+    msg = f"record{s} with similar name{s} exist{nots}! did you mean to load {it}?"
+    if IPYTHON:
+        from IPython.display import display
+
+        logger.warning(f"{msg}")
+        if settings._verbosity_int >= 1:
+            display(queryset.df())
+    else:
+        logger.warning(f"{msg}\n{queryset}")
+    return False
+
+
+def __init__(record: Record, *args, **kwargs):
+    if not args:
+        validate_required_fields(record, kwargs)
+
+        # do not search for names if an id is passed; this is important
+        # e.g. when synching ids from the notebook store to lamindb
+        has_consciously_provided_uid = False
+        if "_has_consciously_provided_uid" in kwargs:
+            has_consciously_provided_uid = kwargs.pop("_has_consciously_provided_uid")
+        if settings.creation.search_names and not has_consciously_provided_uid:
+            match = suggest_records_with_similar_names(record, kwargs)
+            if match:
+                if "version" in kwargs:
+                    if kwargs["version"] is not None:
+                        version_comment = " and version"
+                        existing_record = record.__class__.filter(
+                            name=kwargs["name"], version=kwargs["version"]
+                        ).one_or_none()
+                    else:
+                        # for a versioned record, an exact name match is not a
+                        # criterion for retrieving a record in case `version`
+                        # isn't passed - we'd always pull out many records with exactly the
+                        # same name
+                        existing_record = None
+                else:
+                    version_comment = ""
+                    existing_record = record.__class__.filter(
+                        name=kwargs["name"]
+                    ).one_or_none()
+                if existing_record is not None:
+                    logger.important(
+                        f"returning existing {record.__class__.__name__} record with same"
+                        f" name{version_comment}: '{kwargs['name']}'"
+                    )
+                    init_self_from_db(record, existing_record)
+                    return None
+        super(Record, record).__init__(**kwargs)
+    elif len(args) != len(record._meta.concrete_fields):
+        raise ValueError("please provide keyword arguments, not plain arguments")
+    else:
+        # object is loaded from DB (**kwargs could be omitted below, I believe)
+        super(Record, record).__init__(*args, **kwargs)
+
+
+@classmethod  # type:ignore
+@doc_args(Record.filter.__doc__)
+def filter(cls, *queries, **expressions) -> QuerySet:
+    """{}"""  # noqa: D415
+    from lamindb._filter import filter
+
+    return filter(cls, *queries, **expressions)
+
+
+@classmethod  # type:ignore
+@doc_args(Record.get.__doc__)
+def get(
+    cls,
+    idlike: int | str | None = None,
+    **expressions,
+) -> Record:
+    """{}"""  # noqa: D415
+    # this is the only place in which we need the lamindb queryset
+    # in this file; everywhere else it should be Django's
+    from lamindb._query_set import QuerySet
+
+    return QuerySet(model=cls).get(idlike, **expressions)
+
+
+@classmethod  # type:ignore
+@doc_args(Record.df.__doc__)
+def df(
+    cls,
+    include: str | list[str] | None = None,
+    join: str = "inner",
+    limit: int = 100,
+) -> pd.DataFrame:
+    """{}"""  # noqa: D415
+    from lamindb._filter import filter
+
+    query_set = filter(cls)
+    if hasattr(cls, "updated_at"):
+        query_set = query_set.order_by("-updated_at")
+    return query_set[:limit].df(include=include, join=join)
+
+
+# from_values doesn't apply for QuerySet or Manager
+@classmethod  # type:ignore
+@doc_args(Record.from_values.__doc__)
+def from_values(
+    cls,
+    values: ListLike,
+    field: StrField | None = None,
+    create: bool = False,
+    organism: Record | str | None = None,
+    source: Record | None = None,
+    mute: bool = False,
+) -> list[Record]:
+    """{}"""  # noqa: D415
+    from_source = True if cls.__module__.startswith("bionty.") else False
+
+    field_str = get_name_field(cls, field=field)
+    return get_or_create_records(
+        iterable=values,
+        field=getattr(cls, field_str),
+        create=create,
+        from_source=from_source,
+        organism=organism,
+        source=source,
+        mute=mute,
+    )
+
+
+def _search(
+    cls,
+    string: str,
+    *,
+    field: StrField | list[StrField] | None = None,
+    limit: int | None = 20,
+    case_sensitive: bool = False,
+    using_key: str | None = None,
+    truncate_words: bool = False,
+) -> QuerySet:
+    input_queryset = _queryset(cls, using_key=using_key)
+    registry = input_queryset.model
+    if field is None:
+        fields = [
+            field.name
+            for field in registry._meta.fields
+            if field.get_internal_type() in {"CharField", "TextField"}
+        ]
+    else:
+        if not isinstance(field, list):
+            fields_input = [field]
+        else:
+            fields_input = field
+        fields = []
+        for field in fields_input:
+            if not isinstance(field, str):
+                try:
+                    fields.append(field.field.name)
+                except AttributeError as error:
+                    raise TypeError(
+                        "Please pass a Record string field, e.g., `CellType.name`!"
+                    ) from error
+            else:
+                fields.append(field)
+
+    # decompose search string
+    def truncate_word(word) -> str:
+        if len(word) > 5:
+            n_80_pct = int(len(word) * 0.8)
+            return word[:n_80_pct]
+        elif len(word) > 3:
+            return word[:3]
+        else:
+            return word
+
+    decomposed_string = str(string).split()
+    # add the entire string back
+    decomposed_string += [string]
+    for word in decomposed_string:
+        # will not search against words with 3 or fewer characters
+        if len(word) <= 3:
+            decomposed_string.remove(word)
+    if truncate_words:
+        decomposed_string = [truncate_word(word) for word in decomposed_string]
+    # construct the query
+    expression = Q()
+    case_sensitive_i = "" if case_sensitive else "i"
+    for field in fields:
+        for word in decomposed_string:
+            query = {f"{field}__{case_sensitive_i}contains": word}
+            expression |= Q(**query)
+    output_queryset = input_queryset.filter(expression)
+    # ensure exact matches are at the top
+    narrow_expression = Q()
+    for field in fields:
+        query = {f"{field}__{case_sensitive_i}contains": string}
+        narrow_expression |= Q(**query)
+    refined_output_queryset = output_queryset.filter(narrow_expression).annotate(
+        ordering=Value(1, output_field=IntegerField())
+    )
+    remaining_output_queryset = output_queryset.exclude(narrow_expression).annotate(
+        ordering=Value(2, output_field=IntegerField())
+    )
+    combined_queryset = refined_output_queryset.union(
+        remaining_output_queryset
+    ).order_by("ordering")[:limit]
+    return combined_queryset
+
+
+@classmethod  # type: ignore
+@doc_args(Record.search.__doc__)
+def search(
+    cls,
+    string: str,
+    *,
+    field: StrField | None = None,
+    limit: int | None = 20,
+    case_sensitive: bool = False,
+) -> QuerySet:
+    """{}"""  # noqa: D415
+    return _search(
+        cls=cls,
+        string=string,
+        field=field,
+        limit=limit,
+        case_sensitive=case_sensitive,
+    )
+
+
+def _lookup(
+    cls,
+    field: StrField | None = None,
+    return_field: StrField | None = None,
+    using_key: str | None = None,
+) -> NamedTuple:
+    """{}"""  # noqa: D415
+    queryset = _queryset(cls, using_key=using_key)
+    field = get_name_field(registry=queryset.model, field=field)
+
+    return Lookup(
+        records=queryset,
+        values=[i.get(field) for i in queryset.values()],
+        tuple_name=cls.__class__.__name__,
+        prefix="ln",
+    ).lookup(
+        return_field=(
+            get_name_field(registry=queryset.model, field=return_field)
+            if return_field is not None
+            else None
+        )
+    )
+
+
+@classmethod  # type: ignore
+@doc_args(Record.lookup.__doc__)
+def lookup(
+    cls,
+    field: StrField | None = None,
+    return_field: StrField | None = None,
+) -> NamedTuple:
+    """{}"""  # noqa: D415
+    return _lookup(cls=cls, field=field, return_field=return_field)
+
+
+def get_name_field(
+    registry: type[Record] | QuerySet | Manager,
+    *,
+    field: str | StrField | None = None,
+) -> str:
+    """Get the 1st char or text field from the registry."""
+    if isinstance(registry, (QuerySet, Manager)):
+        registry = registry.model
+    model_field_names = [i.name for i in registry._meta.fields]
+
+    # set to default name field
+    if field is None:
+        if hasattr(registry, "_name_field"):
+            field = registry._meta.get_field(registry._name_field)
+        elif "name" in model_field_names:
+            field = registry._meta.get_field("name")
+        else:
+            # first char or text field that doesn't contain "id"
+            for i in registry._meta.fields:
+                if "id" in i.name:
+                    continue
+                if i.get_internal_type() in {"CharField", "TextField"}:
+                    field = i
+                    break
+
+        # no default name field can be found
+        if field is None:
+            raise ValueError(
+                "please pass a Record string field, e.g., `CellType.name`!"
+            )
+        else:
+            field = field.name  # type:ignore
+    if not isinstance(field, str):
+        try:
+            field = field.field.name
+        except AttributeError:
+            raise TypeError(
+                "please pass a Record string field, e.g., `CellType.name`!"
+            ) from None
+
+    return field
+
+
+def _queryset(cls: Record | QuerySet | Manager, using_key: str) -> QuerySet:
+    if isinstance(cls, (QuerySet, Manager)):
+        return cls.all()
+    elif using_key is None or using_key == "default":
+        return cls.objects.all()
+    else:
+        # using must be called on cls, otherwise the connection isn't found
+        return cls.using(using_key).all()
+
+
+def add_db_connection(db: str, using: str):
+    db_config = dj_database_url.config(
+        default=db, conn_max_age=600, conn_health_checks=True
+    )
+    db_config["TIME_ZONE"] = "UTC"
+    db_config["OPTIONS"] = {}
+    db_config["AUTOCOMMIT"] = True
+    connections.settings[using] = db_config
+
+
+@classmethod  # type: ignore
+@doc_args(Record.using.__doc__)
+def using(
+    cls,
+    instance: str | None,
+) -> QuerySet:
+    """{}"""  # noqa: D415
+    if instance is None:
+        return QuerySet(model=cls, using=None)
+    from lamindb_setup._connect_instance import (
+        load_instance_settings,
+        update_db_using_local,
+    )
+    from lamindb_setup.core._settings_store import instance_settings_file
+
+    owner, name = get_owner_name_from_identifier(instance)
+    settings_file = instance_settings_file(name, owner)
+    if not settings_file.exists():
+        load_result = connect_instance(owner=owner, name=name)
+        if isinstance(load_result, str):
+            raise RuntimeError(
+                f"Failed to load instance {instance}, please check your permission!"
+            )
+        instance_result, _ = load_result
+        settings_file = instance_settings_file(name, owner)
+        db = update_db_using_local(instance_result, settings_file)
+    else:
+        isettings = load_instance_settings(settings_file)
+        db = isettings.db
+    add_db_connection(db, instance)
+    return QuerySet(model=cls, using=instance)
+
+
+REGISTRY_UNIQUE_FIELD = {
+    "storage": "root",
+    "feature": "name",
+    "ulabel": "name",
+}
+
+
+def update_fk_to_default_db(
+    records: Record | list[Record] | QuerySet,
+    fk: str,
+    using_key: str | None,
+    transfer_logs: dict,
+):
+    record = records[0] if isinstance(records, (List, QuerySet)) else records
+    if hasattr(record, f"{fk}_id") and getattr(record, f"{fk}_id") is not None:
+        fk_record = getattr(record, fk)
+        field = REGISTRY_UNIQUE_FIELD.get(fk, "uid")
+        fk_record_default = fk_record.__class__.filter(
+            **{field: getattr(fk_record, field)}
+        ).one_or_none()
+        if fk_record_default is None:
+            from copy import copy
+
+            fk_record_default = copy(fk_record)
+            transfer_to_default_db(
+                fk_record_default, using_key, save=True, transfer_logs=transfer_logs
+            )
+        if isinstance(records, (List, QuerySet)):
+            for r in records:
+                setattr(r, f"{fk}", None)
+                setattr(r, f"{fk}_id", fk_record_default.id)
+        else:
+            setattr(records, f"{fk}", None)
+            setattr(records, f"{fk}_id", fk_record_default.id)
+
+
+FKBULK = [
+    "organism",
+    "source",
+    "_source_code_artifact",  # Transform
+    "report",  # Run
+]
+
+
+def transfer_fk_to_default_db_bulk(
+    records: list | QuerySet, using_key: str | None, transfer_logs: dict
+):
+    for fk in FKBULK:
+        update_fk_to_default_db(records, fk, using_key, transfer_logs=transfer_logs)
+
+
+def transfer_to_default_db(
+    record: Record,
+    using_key: str | None,
+    *,
+    transfer_logs: dict,
+    save: bool = False,
+    transfer_fk: bool = True,
+) -> Record | None:
+    from lamindb.core._context import context
+    from lamindb.core._data import WARNING_RUN_TRANSFORM
+
+    registry = record.__class__
+    record_on_default = registry.objects.filter(uid=record.uid).one_or_none()
+    record_str = f"{record.__class__.__name__}(uid='{record.uid}')"
+    if record_on_default is not None:
+        transfer_logs["mapped"].append(record_str)
+        return record_on_default
+    else:
+        transfer_logs["transferred"].append(record_str)
+
+    if hasattr(record, "created_by_id"):
+        record.created_by = None
+        record.created_by_id = ln_setup.settings.user.id
+    if hasattr(record, "run_id"):
+        record.run = None
+        if context.run is not None:
+            record.run_id = context.run.id
+        else:
+            if not settings.creation.artifact_silence_missing_run_warning:
+                logger.warning(WARNING_RUN_TRANSFORM)
+            record.run_id = None
+    if hasattr(record, "transform_id") and record._meta.model_name != "run":
+        record.transform = None
+        if context.run is not None:
+            record.transform_id = context.run.transform_id
+        else:
+            record.transform_id = None
+    # transfer other foreign key fields
+    fk_fields = [
+        i.name
+        for i in record._meta.fields
+        if i.get_internal_type() == "ForeignKey"
+        if i.name not in {"created_by", "run", "transform"}
+    ]
+    if not transfer_fk:
+        # don't transfer fk fields that are already bulk transferred
+        fk_fields = [fk for fk in fk_fields if fk not in FKBULK]
+    for fk in fk_fields:
+        update_fk_to_default_db(record, fk, using_key, transfer_logs=transfer_logs)
+    record.id = None
+    record._state.db = "default"
+    if save:
+        record.save()
+    return None
+
+
+# docstring handled through attach_func_to_class_method
+def save(self, *args, **kwargs) -> Record:
+    using_key = None
+    if "using" in kwargs:
+        using_key = kwargs["using"]
+    db = self._state.db
+    pk_on_db = self.pk
+    artifacts: list = []
+    if self.__class__.__name__ == "Collection" and self.id is not None:
+        # when creating a new collection without being able to access artifacts
+        artifacts = self.ordered_artifacts.list()
+    pre_existing_record = None
+    # consider records that are being transferred from other databases
+    transfer_logs: dict[str, list[str]] = {"mapped": [], "transferred": []}
+    if db is not None and db != "default" and using_key is None:
+        if isinstance(self, IsVersioned):
+            if not self.is_latest:
+                raise NotImplementedError(
+                    "You are attempting to transfer a record that's not the latest in its version history. This is currently not supported."
+                )
+        pre_existing_record = transfer_to_default_db(
+            self, using_key, transfer_logs=transfer_logs
+        )
+    if pre_existing_record is not None:
+        init_self_from_db(self, pre_existing_record)
+    else:
+        # save versioned record
+        if isinstance(self, IsVersioned) and self._revises is not None:
+            assert self._revises.is_latest  # noqa: S101
+            revises = self._revises
+            revises.is_latest = False
+            with transaction.atomic():
+                revises._revises = None  # ensure we don't start a recursion
+                revises.save()
+                super(Record, self).save(*args, **kwargs)
+            self._revises = None
+        # save unversioned record
+        else:
+            super(Record, self).save(*args, **kwargs)
+    # perform transfer of many-to-many fields
+    # only supported for Artifact and Collection records
+    if db is not None and db != "default" and using_key is None:
+        if self.__class__.__name__ == "Collection":
+            if len(artifacts) > 0:
+                logger.info("transfer artifacts")
+                for artifact in artifacts:
+                    artifact.save()
+                self.artifacts.add(*artifacts)
+        if hasattr(self, "labels"):
+            from copy import copy
+
+            from lnschema_core.models import FeatureManager
+
+            # here we go back to original record on the source database
+            self_on_db = copy(self)
+            self_on_db._state.db = db
+            self_on_db.pk = pk_on_db  # manually set the primary key
+            self_on_db.features = FeatureManager(self_on_db)
+            self.features._add_from(self_on_db, transfer_logs=transfer_logs)
+            self.labels.add_from(self_on_db, transfer_logs=transfer_logs)
+        for k, v in transfer_logs.items():
+            logger.important(f"{k} records: {', '.join(v)}")
+    return self
+
+
+def delete(self) -> None:
+    """Delete the record."""
+    # note that the logic below does not fire if a record is moved to the trash
+    # the idea is that moving a record to the trash should move its entire version family
+    # to the trash, whereas permanently deleting should default to only deleting a single record
+    # of a version family
+    # we can consider making it easy to permanently delete entire version families as well,
+    # but that's for another time
+    if isinstance(self, IsVersioned) and self.is_latest:
+        new_latest = (
+            self.__class__.objects.using(self._state.db)
+            .filter(is_latest=False, uid__startswith=self.stem_uid)
+            .order_by("-created_at")
+            .first()
+        )
+        if new_latest is not None:
+            new_latest.is_latest = True
+            with transaction.atomic():
+                new_latest.save()
+                super(Record, self).delete()
+            logger.warning(f"new latest version is {new_latest}")
+            return None
+    super(Record, self).delete()
+
+
+METHOD_NAMES = [
+    "__init__",
+    "filter",
+    "get",
+    "df",
+    "search",
+    "lookup",
+    "save",
+    "delete",
+    "from_values",
+    "using",
+]
+
+if ln_setup._TESTING:  # type: ignore
+    from inspect import signature
+
+    SIGS = {
+        name: signature(getattr(Record, name))
+        for name in METHOD_NAMES
+        if not name.startswith("__")
+    }
+
+for name in METHOD_NAMES:
+    attach_func_to_class_method(name, Record, globals())