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

lamindb/_query_set.py

@@ -1,362 +1,362 @@
-from __future__ import annotations
-
-from collections import UserList
-from typing import TYPE_CHECKING, Iterable, NamedTuple
-
-import pandas as pd
-from django.db import models
-from django.db.models import F
-from lamin_utils import logger
-from lamindb_setup.core._docs import doc_args
-from lnschema_core.models import (
-    Artifact,
-    CanValidate,
-    Collection,
-    IsVersioned,
-    Record,
-    Registry,
-    Run,
-    Transform,
-    VisibilityChoice,
-)
-
-from lamindb.core.exceptions import DoesNotExist
-
-if TYPE_CHECKING:
-    from lnschema_core.types import ListLike, StrField
-
-
-class MultipleResultsFound(Exception):
-    pass
-
-
-# def format_and_convert_to_local_time(series: pd.Series):
-#     tzinfo = datetime.now().astimezone().tzinfo
-#     timedelta = tzinfo.utcoffset(datetime.now())  # type: ignore
-#     return (series + timedelta).dt.strftime("%Y-%m-%d %H:%M:%S %Z")
-
-
-def get_keys_from_df(data: list, registry: Record) -> list[str]:
-    if len(data) > 0:
-        if isinstance(data[0], dict):
-            keys = list(data[0].keys())
-        else:
-            keys = list(data[0].__dict__.keys())
-            if "_state" in keys:
-                keys.remove("_state")
-    else:
-        keys = [
-            field.name
-            for field in registry._meta.fields
-            if not isinstance(field, models.ForeignKey)
-        ]
-        keys += [
-            f"{field.name}_id"
-            for field in registry._meta.fields
-            if isinstance(field, models.ForeignKey)
-        ]
-    return keys
-
-
-def one_helper(self):
-    if len(self) == 0:
-        raise DoesNotExist
-    elif len(self) > 1:
-        raise MultipleResultsFound(self)
-    else:
-        return self[0]
-
-
-def process_expressions(registry: Registry, expressions: dict) -> dict:
-    if registry in {Artifact, Collection}:
-        # visibility is set to 0 unless expressions contains id or uid equality
-        if not (
-            "id" in expressions
-            or "uid" in expressions
-            or "uid__startswith" in expressions
-        ):
-            visibility = "visibility"
-            if not any(e.startswith(visibility) for e in expressions):
-                expressions[visibility] = (
-                    VisibilityChoice.default.value
-                )  # default visibility
-            # if visibility is None, do not apply a filter
-            # otherwise, it would mean filtering for NULL values, which doesn't make
-            # sense for a non-NULLABLE column
-            elif visibility in expressions and expressions[visibility] is None:
-                expressions.pop(visibility)
-    return expressions
-
-
-def get(
-    registry_or_queryset: type[Record] | QuerySet,
-    idlike: int | str | None = None,
-    **expressions,
-) -> Record:
-    if isinstance(registry_or_queryset, QuerySet):
-        qs = registry_or_queryset
-        registry = qs.model
-    else:
-        qs = QuerySet(model=registry_or_queryset)
-        registry = registry_or_queryset
-    if isinstance(idlike, int):
-        return super(QuerySet, qs).get(id=idlike)
-    elif isinstance(idlike, str):
-        qs = qs.filter(uid__startswith=idlike)
-        if issubclass(registry, IsVersioned):
-            if len(idlike) <= registry._len_stem_uid:
-                return qs.latest_version().one()
-            else:
-                return qs.one()
-        else:
-            return qs.one()
-    else:
-        assert idlike is None  # noqa: S101
-        expressions = process_expressions(registry, expressions)
-        return registry.objects.get(**expressions)
-
-
-class RecordsList(UserList):
-    """Is ordered, can't be queried, but has `.df()`."""
-
-    def __init__(self, records: Iterable[Record]):
-        super().__init__(record for record in records)
-
-    def df(self) -> pd.DataFrame:
-        keys = get_keys_from_df(self.data, self.data[0].__class__)
-        values = [record.__dict__ for record in self.data]
-        return pd.DataFrame(values, columns=keys)
-
-    def one(self) -> Record:
-        """Exactly one result. Throws error if there are more or none."""
-        return one_helper(self)
-
-
-class QuerySet(models.QuerySet):
-    """Sets of records returned by queries.
-
-    See Also:
-
-        `django QuerySet <https://docs.djangoproject.com/en/4.2/ref/models/querysets/>`__ # noqa
-
-    Examples:
-
-        >>> ln.ULabel(name="my label").save()
-        >>> queryset = ln.ULabel.filter(name="my label")
-        >>> queryset
-    """
-
-    @doc_args(Record.df.__doc__)
-    def df(
-        self, include: str | list[str] | None = None, join: str = "inner"
-    ) -> pd.DataFrame:
-        """{}"""  # noqa: D415
-        # re-order the columns
-        exclude_field_names = ["created_at"]
-        field_names = [
-            field.name
-            for field in self.model._meta.fields
-            if (
-                not isinstance(field, models.ForeignKey)
-                and field.name not in exclude_field_names
-            )
-        ]
-        field_names += [
-            f"{field.name}_id"
-            for field in self.model._meta.fields
-            if isinstance(field, models.ForeignKey)
-        ]
-        for field_name in ["run_id", "created_at", "created_by_id", "updated_at"]:
-            if field_name in field_names:
-                field_names.remove(field_name)
-                field_names.append(field_name)
-        if field_names[0] != "uid" and "uid" in field_names:
-            field_names.remove("uid")
-            field_names.insert(0, "uid")
-        # create the dataframe
-        df = pd.DataFrame(self.values(), columns=field_names)
-        # if len(df) > 0 and "updated_at" in df:
-        #     df.updated_at = format_and_convert_to_local_time(df.updated_at)
-        # if len(df) > 0 and "started_at" in df:
-        #     df.started_at = format_and_convert_to_local_time(df.started_at)
-        pk_name = self.model._meta.pk.name
-        pk_column_name = pk_name if pk_name in df.columns else f"{pk_name}_id"
-        if pk_column_name in df.columns:
-            df = df.set_index(pk_column_name)
-        if len(df) == 0:
-            return df
-        if include is not None:
-            if isinstance(include, str):
-                include = [include]
-            # fix ordering
-            include = include[::-1]
-            for expression in include:
-                split = expression.split("__")
-                field_name = split[0]
-                if len(split) > 1:
-                    lookup_str = "__".join(split[1:])
-                else:
-                    lookup_str = "id"
-                Record = self.model
-                field = getattr(Record, field_name)
-                if isinstance(field.field, models.ManyToManyField):
-                    related_ORM = (
-                        field.field.model
-                        if field.field.model != Record
-                        else field.field.related_model
-                    )
-                    if Record == related_ORM:
-                        left_side_link_model = f"from_{Record.__name__.lower()}"
-                        values_expression = (
-                            f"to_{Record.__name__.lower()}__{lookup_str}"
-                        )
-                    else:
-                        left_side_link_model = f"{Record.__name__.lower()}"
-                        values_expression = (
-                            f"{related_ORM.__name__.lower()}__{lookup_str}"
-                        )
-                    link_df = pd.DataFrame(
-                        field.through.objects.values(
-                            left_side_link_model, values_expression
-                        )
-                    )
-                    if link_df.shape[0] == 0:
-                        return df
-                    link_groupby = link_df.groupby(left_side_link_model)[
-                        values_expression
-                    ].apply(list)
-                    df = pd.concat((link_groupby, df), axis=1, join=join)
-                    df.rename(columns={values_expression: expression}, inplace=True)
-                else:
-                    # the F() based implementation could also work for many-to-many,
-                    # would need to test what is faster
-                    df_anno = pd.DataFrame(
-                        self.annotate(expression=F(expression)).values(
-                            pk_column_name, "expression"
-                        )
-                    )
-                    df_anno = df_anno.set_index(pk_column_name)
-                    df_anno.rename(columns={"expression": expression}, inplace=True)
-                    df = pd.concat((df_anno, df), axis=1, join=join)
-        return df
-
-    def delete(self, *args, **kwargs):
-        """Delete all records in the query set."""
-        # both Transform & Run might reference artifacts
-        if self.model in {Artifact, Collection, Transform, Run}:
-            for record in self:
-                logger.important(f"deleting {record}")
-                record.delete(*args, **kwargs)
-        else:
-            self._delete_base_class(*args, **kwargs)
-
-    def list(self, field: str | None = None) -> list[Record]:
-        """Populate a list with the results.
-
-        Examples:
-            >>> queryset.list()  # list of records
-            >>> queryset.list("name")  # list of values
-        """
-        if field is None:
-            return list(self)
-        else:
-            return list(self.values_list(field, flat=True))
-
-    def first(self) -> Record | None:
-        """If non-empty, the first result in the query set, otherwise ``None``.
-
-        Examples:
-            >>> queryset.first()
-        """
-        if len(self) == 0:
-            return None
-        return self[0]
-
-    def get(self, idlike: int | str | None = None, **expressions) -> Record:
-        """Query a single record. Raises error if there are more or none."""
-        return get(self, idlike, **expressions)
-
-    def one(self) -> Record:
-        """Exactly one result. Raises error if there are more or none."""
-        return one_helper(self)
-
-    def one_or_none(self) -> Record | None:
-        """At most one result. Returns it if there is one, otherwise returns ``None``.
-
-        Examples:
-            >>> ln.ULabel.filter(name="benchmark").one_or_none()
-            >>> ln.ULabel.filter(name="non existing label").one_or_none()
-        """
-        if len(self) == 0:
-            return None
-        elif len(self) == 1:
-            return self[0]
-        else:
-            raise MultipleResultsFound(self.all())
-
-    def latest_version(self) -> QuerySet:
-        """Filter every version family by latest version."""
-        if issubclass(self.model, IsVersioned):
-            return self.filter(is_latest=True)
-        else:
-            raise ValueError("Record isn't subclass of `lamindb.core.IsVersioned`")
-
-
-# -------------------------------------------------------------------------------------
-# CanValidate
-# -------------------------------------------------------------------------------------
-
-
-@doc_args(Record.search.__doc__)
-def search(self, string: str, **kwargs):
-    """{}"""  # noqa: D415
-    from ._record import _search
-
-    return _search(cls=self, string=string, **kwargs)
-
-
-@doc_args(Record.lookup.__doc__)
-def lookup(self, field: StrField | None = None, **kwargs) -> NamedTuple:
-    """{}"""  # noqa: D415
-    from ._record import _lookup
-
-    return _lookup(cls=self, field=field, **kwargs)
-
-
-@doc_args(CanValidate.validate.__doc__)
-def validate(self, values: ListLike, field: str | StrField | None = None, **kwargs):
-    """{}"""  # noqa: D415
-    from ._can_validate import _validate
-
-    return _validate(cls=self, values=values, field=field, **kwargs)
-
-
-@doc_args(CanValidate.inspect.__doc__)
-def inspect(self, values: ListLike, field: str | StrField | None = None, **kwargs):
-    """{}"""  # noqa: D415
-    from ._can_validate import _inspect
-
-    return _inspect(cls=self, values=values, field=field, **kwargs)
-
-
-@doc_args(CanValidate.standardize.__doc__)
-def standardize(self, values: Iterable, field: str | StrField | None = None, **kwargs):
-    """{}"""  # noqa: D415
-    from ._can_validate import _standardize
-
-    return _standardize(cls=self, values=values, field=field, **kwargs)
-
-
-models.QuerySet.df = QuerySet.df
-models.QuerySet.list = QuerySet.list
-models.QuerySet.first = QuerySet.first
-models.QuerySet.one = QuerySet.one
-models.QuerySet.one_or_none = QuerySet.one_or_none
-models.QuerySet.latest_version = QuerySet.latest_version
-models.QuerySet.search = search
-models.QuerySet.lookup = lookup
-models.QuerySet.validate = validate
-models.QuerySet.inspect = inspect
-models.QuerySet.standardize = standardize
-models.QuerySet._delete_base_class = models.QuerySet.delete
-models.QuerySet.delete = QuerySet.delete
+from __future__ import annotations
+
+from collections import UserList
+from typing import TYPE_CHECKING, Iterable, NamedTuple
+
+import pandas as pd
+from django.db import models
+from django.db.models import F
+from lamin_utils import logger
+from lamindb_setup.core._docs import doc_args
+from lnschema_core.models import (
+    Artifact,
+    CanValidate,
+    Collection,
+    IsVersioned,
+    Record,
+    Registry,
+    Run,
+    Transform,
+    VisibilityChoice,
+)
+
+from lamindb.core.exceptions import DoesNotExist
+
+if TYPE_CHECKING:
+    from lnschema_core.types import ListLike, StrField
+
+
+class MultipleResultsFound(Exception):
+    pass
+
+
+# def format_and_convert_to_local_time(series: pd.Series):
+#     tzinfo = datetime.now().astimezone().tzinfo
+#     timedelta = tzinfo.utcoffset(datetime.now())  # type: ignore
+#     return (series + timedelta).dt.strftime("%Y-%m-%d %H:%M:%S %Z")
+
+
+def get_keys_from_df(data: list, registry: Record) -> list[str]:
+    if len(data) > 0:
+        if isinstance(data[0], dict):
+            keys = list(data[0].keys())
+        else:
+            keys = list(data[0].__dict__.keys())
+            if "_state" in keys:
+                keys.remove("_state")
+    else:
+        keys = [
+            field.name
+            for field in registry._meta.fields
+            if not isinstance(field, models.ForeignKey)
+        ]
+        keys += [
+            f"{field.name}_id"
+            for field in registry._meta.fields
+            if isinstance(field, models.ForeignKey)
+        ]
+    return keys
+
+
+def one_helper(self):
+    if len(self) == 0:
+        raise DoesNotExist
+    elif len(self) > 1:
+        raise MultipleResultsFound(self)
+    else:
+        return self[0]
+
+
+def process_expressions(registry: Registry, expressions: dict) -> dict:
+    if registry in {Artifact, Collection}:
+        # visibility is set to 0 unless expressions contains id or uid equality
+        if not (
+            "id" in expressions
+            or "uid" in expressions
+            or "uid__startswith" in expressions
+        ):
+            visibility = "visibility"
+            if not any(e.startswith(visibility) for e in expressions):
+                expressions[visibility] = (
+                    VisibilityChoice.default.value
+                )  # default visibility
+            # if visibility is None, do not apply a filter
+            # otherwise, it would mean filtering for NULL values, which doesn't make
+            # sense for a non-NULLABLE column
+            elif visibility in expressions and expressions[visibility] is None:
+                expressions.pop(visibility)
+    return expressions
+
+
+def get(
+    registry_or_queryset: type[Record] | QuerySet,
+    idlike: int | str | None = None,
+    **expressions,
+) -> Record:
+    if isinstance(registry_or_queryset, QuerySet):
+        qs = registry_or_queryset
+        registry = qs.model
+    else:
+        qs = QuerySet(model=registry_or_queryset)
+        registry = registry_or_queryset
+    if isinstance(idlike, int):
+        return super(QuerySet, qs).get(id=idlike)
+    elif isinstance(idlike, str):
+        qs = qs.filter(uid__startswith=idlike)
+        if issubclass(registry, IsVersioned):
+            if len(idlike) <= registry._len_stem_uid:
+                return qs.latest_version().one()
+            else:
+                return qs.one()
+        else:
+            return qs.one()
+    else:
+        assert idlike is None  # noqa: S101
+        expressions = process_expressions(registry, expressions)
+        return registry.objects.get(**expressions)
+
+
+class RecordsList(UserList):
+    """Is ordered, can't be queried, but has `.df()`."""
+
+    def __init__(self, records: Iterable[Record]):
+        super().__init__(record for record in records)
+
+    def df(self) -> pd.DataFrame:
+        keys = get_keys_from_df(self.data, self.data[0].__class__)
+        values = [record.__dict__ for record in self.data]
+        return pd.DataFrame(values, columns=keys)
+
+    def one(self) -> Record:
+        """Exactly one result. Throws error if there are more or none."""
+        return one_helper(self)
+
+
+class QuerySet(models.QuerySet):
+    """Sets of records returned by queries.
+
+    See Also:
+
+        `django QuerySet <https://docs.djangoproject.com/en/4.2/ref/models/querysets/>`__ # noqa
+
+    Examples:
+
+        >>> ln.ULabel(name="my label").save()
+        >>> queryset = ln.ULabel.filter(name="my label")
+        >>> queryset
+    """
+
+    @doc_args(Record.df.__doc__)
+    def df(
+        self, include: str | list[str] | None = None, join: str = "inner"
+    ) -> pd.DataFrame:
+        """{}"""  # noqa: D415
+        # re-order the columns
+        exclude_field_names = ["created_at"]
+        field_names = [
+            field.name
+            for field in self.model._meta.fields
+            if (
+                not isinstance(field, models.ForeignKey)
+                and field.name not in exclude_field_names
+            )
+        ]
+        field_names += [
+            f"{field.name}_id"
+            for field in self.model._meta.fields
+            if isinstance(field, models.ForeignKey)
+        ]
+        for field_name in ["run_id", "created_at", "created_by_id", "updated_at"]:
+            if field_name in field_names:
+                field_names.remove(field_name)
+                field_names.append(field_name)
+        if field_names[0] != "uid" and "uid" in field_names:
+            field_names.remove("uid")
+            field_names.insert(0, "uid")
+        # create the dataframe
+        df = pd.DataFrame(self.values(), columns=field_names)
+        # if len(df) > 0 and "updated_at" in df:
+        #     df.updated_at = format_and_convert_to_local_time(df.updated_at)
+        # if len(df) > 0 and "started_at" in df:
+        #     df.started_at = format_and_convert_to_local_time(df.started_at)
+        pk_name = self.model._meta.pk.name
+        pk_column_name = pk_name if pk_name in df.columns else f"{pk_name}_id"
+        if pk_column_name in df.columns:
+            df = df.set_index(pk_column_name)
+        if len(df) == 0:
+            return df
+        if include is not None:
+            if isinstance(include, str):
+                include = [include]
+            # fix ordering
+            include = include[::-1]
+            for expression in include:
+                split = expression.split("__")
+                field_name = split[0]
+                if len(split) > 1:
+                    lookup_str = "__".join(split[1:])
+                else:
+                    lookup_str = "id"
+                Record = self.model
+                field = getattr(Record, field_name)
+                if isinstance(field.field, models.ManyToManyField):
+                    related_ORM = (
+                        field.field.model
+                        if field.field.model != Record
+                        else field.field.related_model
+                    )
+                    if Record == related_ORM:
+                        left_side_link_model = f"from_{Record.__name__.lower()}"
+                        values_expression = (
+                            f"to_{Record.__name__.lower()}__{lookup_str}"
+                        )
+                    else:
+                        left_side_link_model = f"{Record.__name__.lower()}"
+                        values_expression = (
+                            f"{related_ORM.__name__.lower()}__{lookup_str}"
+                        )
+                    link_df = pd.DataFrame(
+                        field.through.objects.values(
+                            left_side_link_model, values_expression
+                        )
+                    )
+                    if link_df.shape[0] == 0:
+                        return df
+                    link_groupby = link_df.groupby(left_side_link_model)[
+                        values_expression
+                    ].apply(list)
+                    df = pd.concat((link_groupby, df), axis=1, join=join)
+                    df.rename(columns={values_expression: expression}, inplace=True)
+                else:
+                    # the F() based implementation could also work for many-to-many,
+                    # would need to test what is faster
+                    df_anno = pd.DataFrame(
+                        self.annotate(expression=F(expression)).values(
+                            pk_column_name, "expression"
+                        )
+                    )
+                    df_anno = df_anno.set_index(pk_column_name)
+                    df_anno.rename(columns={"expression": expression}, inplace=True)
+                    df = pd.concat((df_anno, df), axis=1, join=join)
+        return df
+
+    def delete(self, *args, **kwargs):
+        """Delete all records in the query set."""
+        # both Transform & Run might reference artifacts
+        if self.model in {Artifact, Collection, Transform, Run}:
+            for record in self:
+                logger.important(f"deleting {record}")
+                record.delete(*args, **kwargs)
+        else:
+            self._delete_base_class(*args, **kwargs)
+
+    def list(self, field: str | None = None) -> list[Record]:
+        """Populate a list with the results.
+
+        Examples:
+            >>> queryset.list()  # list of records
+            >>> queryset.list("name")  # list of values
+        """
+        if field is None:
+            return list(self)
+        else:
+            return list(self.values_list(field, flat=True))
+
+    def first(self) -> Record | None:
+        """If non-empty, the first result in the query set, otherwise ``None``.
+
+        Examples:
+            >>> queryset.first()
+        """
+        if len(self) == 0:
+            return None
+        return self[0]
+
+    def get(self, idlike: int | str | None = None, **expressions) -> Record:
+        """Query a single record. Raises error if there are more or none."""
+        return get(self, idlike, **expressions)
+
+    def one(self) -> Record:
+        """Exactly one result. Raises error if there are more or none."""
+        return one_helper(self)
+
+    def one_or_none(self) -> Record | None:
+        """At most one result. Returns it if there is one, otherwise returns ``None``.
+
+        Examples:
+            >>> ln.ULabel.filter(name="benchmark").one_or_none()
+            >>> ln.ULabel.filter(name="non existing label").one_or_none()
+        """
+        if len(self) == 0:
+            return None
+        elif len(self) == 1:
+            return self[0]
+        else:
+            raise MultipleResultsFound(self.all())
+
+    def latest_version(self) -> QuerySet:
+        """Filter every version family by latest version."""
+        if issubclass(self.model, IsVersioned):
+            return self.filter(is_latest=True)
+        else:
+            raise ValueError("Record isn't subclass of `lamindb.core.IsVersioned`")
+
+
+# -------------------------------------------------------------------------------------
+# CanValidate
+# -------------------------------------------------------------------------------------
+
+
+@doc_args(Record.search.__doc__)
+def search(self, string: str, **kwargs):
+    """{}"""  # noqa: D415
+    from ._record import _search
+
+    return _search(cls=self, string=string, **kwargs)
+
+
+@doc_args(Record.lookup.__doc__)
+def lookup(self, field: StrField | None = None, **kwargs) -> NamedTuple:
+    """{}"""  # noqa: D415
+    from ._record import _lookup
+
+    return _lookup(cls=self, field=field, **kwargs)
+
+
+@doc_args(CanValidate.validate.__doc__)
+def validate(self, values: ListLike, field: str | StrField | None = None, **kwargs):
+    """{}"""  # noqa: D415
+    from ._can_validate import _validate
+
+    return _validate(cls=self, values=values, field=field, **kwargs)
+
+
+@doc_args(CanValidate.inspect.__doc__)
+def inspect(self, values: ListLike, field: str | StrField | None = None, **kwargs):
+    """{}"""  # noqa: D415
+    from ._can_validate import _inspect
+
+    return _inspect(cls=self, values=values, field=field, **kwargs)
+
+
+@doc_args(CanValidate.standardize.__doc__)
+def standardize(self, values: Iterable, field: str | StrField | None = None, **kwargs):
+    """{}"""  # noqa: D415
+    from ._can_validate import _standardize
+
+    return _standardize(cls=self, values=values, field=field, **kwargs)
+
+
+models.QuerySet.df = QuerySet.df
+models.QuerySet.list = QuerySet.list
+models.QuerySet.first = QuerySet.first
+models.QuerySet.one = QuerySet.one
+models.QuerySet.one_or_none = QuerySet.one_or_none
+models.QuerySet.latest_version = QuerySet.latest_version
+models.QuerySet.search = search
+models.QuerySet.lookup = lookup
+models.QuerySet.validate = validate
+models.QuerySet.inspect = inspect
+models.QuerySet.standardize = standardize
+models.QuerySet._delete_base_class = models.QuerySet.delete
+models.QuerySet.delete = QuerySet.delete