lamindb 1.10.1__py3-none-any.whl → 1.11.0__py3-none-any.whl

lamindb/models/save.py

@@ -47,11 +47,10 @@ def save(
 
     Args:
         records: Multiple :class:`~lamindb.models.SQLRecord` objects.
-        ignore_conflicts: If ``True``, do not error if some records violate a
-            unique or another constraint. However, it won't inplace update the id
-            fields of records. If you need records with ids, you need to query
-            them from the database.
-        batch_size: Number of records to process in each batch. Defaults to 10000.
+        ignore_conflicts: If `True`, do not error if some records violate a unique or another constraint.
+            However, it won't inplace update the id fields of records.
+            If you need records with ids, you need to query them from the database.
+        batch_size: Number of records to process in each batch.
             Large batch sizes can improve performance but may lead to memory issues.
 
     Examples:
@@ -130,7 +129,7 @@ def bulk_create(
     Args:
         records: Iterable of SQLRecord objects to create
         ignore_conflicts: Whether to ignore conflicts during creation
-        batch_size: Number of records to process in each batch. Defaults to 10000.
+        batch_size: Number of records to process in each batch.
     """
     records_by_orm = defaultdict(list)
     for record in records:
@@ -332,8 +331,7 @@ def store_artifacts(
     from .artifact import Artifact
 
     exception: Exception | None = None
-    # because uploads might fail, we need to maintain a new list
-    # of the succeeded uploads
+    # because uploads might fail, we need to maintain a new list of the succeeded uploads
     stored_artifacts = []
 
     # upload new local artifacts

lamindb/models/schema.py

@@ -6,6 +6,7 @@ import numpy as np
 from django.db import models
 from django.db.models import CASCADE, PROTECT, ManyToManyField
 from lamin_utils import logger
+from lamindb_setup.core import deprecated
 from lamindb_setup.core.hashing import HASH_LENGTH, hash_string
 from rich.table import Table
 from rich.text import Text
@@ -348,11 +349,12 @@ class Schema(SQLRecord, CanCurate, TracksRun):
 
             # from a dataframe
             df = pd.DataFrame({"feat1": [1, 2], "feat2": [3.1, 4.2], "feat3": ["cond1", "cond2"]})
-            schema = ln.Schema.from_df(df)
+            schema = ln.Schema.from_dataframe(df)
     """
 
     class Meta(SQLRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
         abstract = False
+        app_label = "lamindb"
 
     _name_field: str = "name"
     _aux_fields: dict[str, tuple[str, type]] = {
@@ -576,19 +578,22 @@ class Schema(SQLRecord, CanCurate, TracksRun):
                 self.optionals.set(optional_features)
                 return None
         self._slots: dict[str, Schema] = {}
+
         if features:
             self._features = (get_related_name(features_registry), features)  # type: ignore
-        elif slots:
+        if slots:
             for slot_key, component in slots.items():
                 if component._state.adding:
                     raise InvalidArgument(
                         f"schema for {slot_key} {component} must be saved before use"
                     )
             self._slots = slots
+
         if validated_kwargs["hash"] in KNOWN_SCHEMAS:
             validated_kwargs["uid"] = KNOWN_SCHEMAS[validated_kwargs["hash"]]
         else:
             validated_kwargs["uid"] = ids.base62_16()
+
         super().__init__(**validated_kwargs)
 
     def _validate_kwargs_calculate_hash(
@@ -623,14 +628,20 @@ class Schema(SQLRecord, CanCurate, TracksRun):
                 raise TypeError("index must be a Feature")
             features.insert(0, index)
 
+        if slots:
+            itype = "Composite"
+            if otype is None:
+                raise InvalidArgument("Please pass otype != None for composite schemas")
+
         if features:
             features, configs = get_features_config(features)
             features_registry = validate_features(features)
-            itype_compare = features_registry.__get_name_with_module__()
-            if itype is not None:
-                assert itype.startswith(itype_compare), str(itype_compare)  # noqa: S101
-            else:
-                itype = itype_compare
+            if itype != "Composite":
+                itype_compare = features_registry.__get_name_with_module__()
+                if itype is not None:
+                    assert itype.startswith(itype_compare), str(itype_compare)  # noqa: S101
+                else:
+                    itype = itype_compare
             if n_features is not None:
                 if n_features != len(features):
                     logger.important(f"updating to n {len(features)} features")
@@ -654,11 +665,6 @@ class Schema(SQLRecord, CanCurate, TracksRun):
         if flexible is None:
             flexible = flexible_default
 
-        if slots:
-            itype = "Composite"
-            if otype is None:
-                raise InvalidArgument("Please pass otype != None for composite schemas")
-
         if itype is not None and not isinstance(itype, str):
             itype_str = serialize_dtype(itype, is_itype=True)
         else:
@@ -771,7 +777,7 @@ class Schema(SQLRecord, CanCurate, TracksRun):
         cls,
         values: ListLike,
         field: FieldAttr = Feature.name,
-        type: str | None = None,
+        dtype: str | None = None,
         name: str | None = None,
         mute: bool = False,
         organism: SQLRecord | str | None = None,
@@ -783,7 +789,7 @@ class Schema(SQLRecord, CanCurate, TracksRun):
         Args:
             values: A list of values, like feature names or ids.
             field: The field of a reference registry to map values.
-            type: The simple type.
+            dtype: The simple dtype.
                 Defaults to `None` if reference registry is :class:`~lamindb.Feature`,
                 defaults to `"float"` otherwise.
             name: A name.
@@ -816,8 +822,8 @@ class Schema(SQLRecord, CanCurate, TracksRun):
         if isinstance(values, DICT_KEYS_TYPE):
             values = list(values)
         registry = field.field.model
-        if registry != Feature and type is None:
-            type = NUMBER_TYPE
+        if registry != Feature and dtype is None:
+            dtype = NUMBER_TYPE
             logger.debug("setting feature set to 'number'")
         validated = registry.validate(values, field=field, mute=mute, organism=organism)
         values_array = np.array(values)
@@ -841,12 +847,12 @@ class Schema(SQLRecord, CanCurate, TracksRun):
         schema = Schema(
             features=validated_features,
             name=name,
-            dtype=get_type_str(type),
+            dtype=get_type_str(dtype),
         )
         return schema
 
     @classmethod
-    def from_df(
+    def from_dataframe(
         cls,
         df: pd.DataFrame,
         field: FieldAttr = Feature.name,
@@ -889,15 +895,28 @@ class Schema(SQLRecord, CanCurate, TracksRun):
             )
         return schema
 
+    @classmethod
+    @deprecated("from_dataframe")
+    def from_df(
+        cls,
+        df: pd.DataFrame,
+        field: FieldAttr = Feature.name,
+        name: str | None = None,
+        mute: bool = False,
+        organism: SQLRecord | str | None = None,
+        source: SQLRecord | None = None,
+    ) -> Schema | None:
+        return cls.from_dataframe(df, field, name, mute, organism, source)
+
     def save(self, *args, **kwargs) -> Schema:
-        """Save."""
+        """Save schema."""
         from .save import bulk_create
 
         if self.pk is not None:
             features = (
                 self._features[1]
                 if hasattr(self, "_features")
-                else (self.members.list() if self.members.exists() else [])
+                else (self.members.to_list() if self.members.exists() else [])
             )
             index_feature = self.index
             _, validated_kwargs, _, _, _ = self._validate_kwargs_calculate_hash(
@@ -925,7 +944,7 @@ class Schema(SQLRecord, CanCurate, TracksRun):
                 datasets = Artifact.filter(schema=self).all()
                 if datasets.exists():
                     logger.warning(
-                        f"you updated the schema hash and might invalidate datasets that were previously validated with this schema: {datasets.list('uid')}"
+                        f"you updated the schema hash and might invalidate datasets that were previously validated with this schema: {datasets.to_list('uid')}"
                     )
                 self.hash = validated_kwargs["hash"]
                 self.n = validated_kwargs["n"]
@@ -947,13 +966,16 @@ class Schema(SQLRecord, CanCurate, TracksRun):
             assert self.n > 0  # noqa: S101
             using: bool | None = kwargs.pop("using", None)
             related_name, records = self._features
+
+            # .set() does not preserve the order but orders by the feature primary key
             # only the following method preserves the order
-            # .set() does not preserve the order but orders by
-            # the feature primary key
             through_model = getattr(self, related_name).through
-            related_model_split = parse_cat_dtype(self.itype, is_itype=True)[
-                "registry_str"
-            ].split(".")
+            if self.itype == "Composite":
+                related_model_split = ["Feature"]
+            else:
+                related_model_split = parse_cat_dtype(self.itype, is_itype=True)[
+                    "registry_str"
+                ].split(".")
             if len(related_model_split) == 1:
                 related_field = related_model_split[0].lower()
             else:
@@ -965,6 +987,7 @@ class Schema(SQLRecord, CanCurate, TracksRun):
             ]
             through_model.objects.using(using).bulk_create(links, ignore_conflicts=True)
             delattr(self, "_features")
+
         return self
 
     @property
@@ -978,6 +1001,8 @@ class Schema(SQLRecord, CanCurate, TracksRun):
             # this should return a queryset and not a list...
             # need to fix this
             return self._features[1]
+        if len(self.features.all()) > 0:
+            return self.features.order_by("links_schema__id")
         if self.itype == "Composite" or self.is_type:
             return Feature.objects.none()
         related_name = self._get_related_name()
@@ -1200,6 +1225,7 @@ class SchemaFeature(BaseSQLRecord, IsLink):
     feature: Feature = ForeignKey(Feature, PROTECT, related_name="links_schema")
 
     class Meta:
+        app_label = "lamindb"
         unique_together = ("schema", "feature")
 
 
@@ -1211,6 +1237,7 @@ class ArtifactSchema(BaseSQLRecord, IsLink, TracksRun):
     feature_ref_is_semantic: bool | None = BooleanField(null=True)
 
     class Meta:
+        app_label = "lamindb"
         unique_together = (("artifact", "schema"), ("artifact", "slot"))
 
 
@@ -1221,6 +1248,7 @@ class SchemaComponent(BaseSQLRecord, IsLink, TracksRun):
     slot: str | None = CharField(null=True)
 
     class Meta:
+        app_label = "lamindb"
         unique_together = (("composite", "slot", "component"), ("composite", "slot"))
 
 

lamindb/models/sqlrecord.py

@@ -319,6 +319,43 @@ def suggest_records_with_similar_names(
     return None
 
 
+def delete_record(record: BaseSQLRecord, is_soft: bool = True):
+    def delete():
+        if is_soft:
+            record.branch_id = -1
+            record.save()
+        else:
+            super(BaseSQLRecord, record).delete()
+
+    # deal with versioned records
+    # if _ovewrite_version = True, there is only a single version and
+    # no need to set the new latest version because all versions are deleted
+    # when deleting the latest version
+    if (
+        isinstance(record, IsVersioned)
+        and record.is_latest
+        and not getattr(record, "_overwrite_versions", False)
+    ):
+        new_latest = (
+            record.__class__.objects.using(record._state.db)
+            .filter(is_latest=False, uid__startswith=record.stem_uid)
+            .exclude(branch_id=-1)  # exclude candidates in the trash
+            .order_by("-created_at")
+            .first()
+        )
+        if new_latest is not None:
+            new_latest.is_latest = True
+            if is_soft:
+                record.is_latest = False
+            with transaction.atomic():
+                new_latest.save()
+                delete()
+            logger.warning(f"new latest version is: {new_latest}")
+            return None
+    # deal with all other cases of the nested if condition now
+    delete()
+
+
 RECORD_REGISTRY_EXAMPLE = """Example::
 
         from lamindb import SQLRecord, fields
@@ -334,7 +371,7 @@ RECORD_REGISTRY_EXAMPLE = """Example::
         experiment.save()
 
         # `Experiment` refers to the registry, which you can query
-        df = Experiment.filter(name__startswith="my ").df()
+        df = Experiment.filter(name__startswith="my ").to_dataframe()
 """
 
 
@@ -425,7 +462,7 @@ class Registry(ModelBase):
 
         Examples:
             >>> ln.ULabel(name="my label").save()
-            >>> ln.ULabel.filter(name__startswith="my").df()
+            >>> ln.ULabel.filter(name__startswith="my").to_dataframe()
         """
         from .query_set import QuerySet
 
@@ -464,7 +501,7 @@ class Registry(ModelBase):
 
         return QuerySet(model=cls).get(idlike, **expressions)
 
-    def df(
+    def to_dataframe(
         cls,
         include: str | list[str] | None = None,
         features: bool | list[str] | str = False,
@@ -492,21 +529,30 @@ class Registry(ModelBase):
 
             Include the name of the creator in the `DataFrame`:
 
-            >>> ln.ULabel.df(include="created_by__name"])
+            >>> ln.ULabel.to_dataframe(include="created_by__name"])
 
             Include display of features for `Artifact`:
 
-            >>> df = ln.Artifact.df(features=True)
+            >>> df = ln.Artifact.to_dataframe(features=True)
             >>> ln.view(df)  # visualize with type annotations
 
             Only include select features:
 
-            >>> df = ln.Artifact.df(features=["cell_type_by_expert", "cell_type_by_model"])
+            >>> df = ln.Artifact.to_dataframe(features=["cell_type_by_expert", "cell_type_by_model"])
         """
         query_set = cls.filter()
         if hasattr(cls, "updated_at"):
             query_set = query_set.order_by("-updated_at")
-        return query_set[:limit].df(include=include, features=features)
+        return query_set[:limit].to_dataframe(include=include, features=features)
+
+    @deprecated(new_name="to_dataframe")
+    def df(
+        cls,
+        include: str | list[str] | None = None,
+        features: bool | list[str] | str = False,
+        limit: int = 100,
+    ) -> pd.DataFrame:
+        return cls.to_dataframe(include, features, limit)
 
     @doc_args(_search.__doc__)
     def search(
@@ -580,7 +626,7 @@ class Registry(ModelBase):
             # this just retrives the full connection string from iresult
             db = update_db_using_local(iresult, settings_file)
             cache_using_filepath.write_text(
-                f"{iresult['lnid']}\n{iresult['schema_str']}"
+                f"{iresult['lnid']}\n{iresult['schema_str']}", encoding="utf-8"
             )
             # need to set the token if it is a fine_grained_access and the user is jwt (not public)
             is_fine_grained_access = (
@@ -593,7 +639,7 @@ class Registry(ModelBase):
             source_modules = isettings.modules
             db = isettings.db
             cache_using_filepath.write_text(
-                f"{isettings.uid}\n{','.join(source_modules)}"
+                f"{isettings.uid}\n{','.join(source_modules)}", encoding="utf-8"
             )
             # need to set the token if it is a fine_grained_access and the user is jwt (not public)
             is_fine_grained_access = (
@@ -795,7 +841,7 @@ class BaseSQLRecord(models.Model, metaclass=Registry):
         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()
+            artifacts = self.ordered_artifacts.to_list()
         pre_existing_record = None
         # consider records that are being transferred from other databases
         transfer_logs: dict[str, list[str]] = {
@@ -920,27 +966,7 @@ class BaseSQLRecord(models.Model, metaclass=Registry):
 
     def delete(self) -> None:
         """Delete."""
-        # 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().delete()  # type: ignore
-                logger.warning(f"new latest version is {new_latest}")
-                return None
-        super().delete()
+        delete_record(self, is_soft=False)
 
 
 class Space(BaseSQLRecord):
@@ -952,6 +978,7 @@ class Space(BaseSQLRecord):
     """
 
     class Meta:
+        app_label = "lamindb"
         constraints = [
             models.UniqueConstraint(Lower("name"), name="unique_space_name_lower")
         ]
@@ -964,8 +991,7 @@ class Space(BaseSQLRecord):
         editable=False,
         unique=True,
         max_length=12,
-        default="aaaaaaaaaaaaa",
-        db_default="aaaaaaaaaaaa",
+        default=base62_12,
         db_index=True,
     )
     """Universal id."""
@@ -998,6 +1024,21 @@ class Space(BaseSQLRecord):
         *args,
         **kwargs,
     ):
+        if not args and "uid" not in kwargs:
+            warn = False
+            msg = ""
+            isettings = setup_settings.instance
+            if (dialect := isettings.dialect) != "postgresql":
+                warn = True
+                msg = f"on {dialect} databases"
+            elif not isettings.is_on_hub:
+                warn = True
+                msg = "on local instances"
+            if warn:
+                logger.warning(
+                    f"creating spaces manually {msg} is possible for demo purposes, "
+                    "but does *not* affect access permissions"
+                )
         super().__init__(*args, **kwargs)
 
 
@@ -1007,6 +1048,12 @@ class Branch(BaseSQLRecord):
     Every `SQLRecord` has a `branch` field, which dictates where a record appears in queries & searches.
     """
 
+    class Meta:
+        app_label = "lamindb"
+        constraints = [
+            models.UniqueConstraint(Lower("name"), name="unique_branch_name_lower")
+        ]
+
     # below isn't fully implemented but a roadmap
     # - 3: template (hidden in queries & searches)
     # - 2: locked (same as default, but locked for edits except for space admins)
@@ -1018,11 +1065,6 @@ class Branch(BaseSQLRecord):
     # that can be merged onto the main branch in an experience akin to a Pull Request. The mapping
     # onto a semantic branch name is handled through LaminHub.
 
-    class Meta:
-        constraints = [
-            models.UniqueConstraint(Lower("name"), name="unique_branch_name_lower")
-        ]
-
     id: int = models.AutoField(primary_key=True)
     """An integer id that's synchronized for a family of coupled database instances.
 
@@ -1119,6 +1161,75 @@ class SQLRecord(BaseSQLRecord, metaclass=Registry):
     def _branch_code(self, value: int):
         self.branch_id = value
 
+    def delete(self, permanent: bool | None = None, **kwargs) -> None:
+        """Delete record.
+
+        Args:
+            permanent: Whether to permanently delete the record (skips trash).
+
+        Examples:
+
+            For any `SQLRecord` object `record`, call:
+
+            >>> record.delete()
+        """
+        if self._state.adding:
+            logger.warning("record is not yet saved, delete has no effect")
+            return
+        name_with_module = self.__class__.__get_name_with_module__()
+
+        if name_with_module == "Artifact":
+            # this first check means an invalid delete fails fast rather than cascading through
+            # database and storage permission errors
+            isettings = setup_settings.instance
+            if self.storage.instance_uid != isettings.uid and (
+                kwargs["storage"] or kwargs["storage"] is None
+            ):
+                from ..errors import IntegrityError
+                from .storage import Storage
+
+                raise IntegrityError(
+                    "Cannot simply delete artifacts outside of this instance's managed storage locations."
+                    "\n(1) If you only want to delete the metadata record in this instance, pass `storage=False`"
+                    f"\n(2) If you want to delete the artifact in storage, please load the managing lamindb instance (uid={self.storage.instance_uid})."
+                    f"\nThese are all managed storage locations of this instance:\n{Storage.filter(instance_uid=isettings.uid).to_dataframe()}"
+                )
+
+        # change branch_id to trash
+        trash_branch_id = -1
+        if self.branch_id > trash_branch_id and permanent is not True:
+            delete_record(self, is_soft=True)
+            logger.warning(f"moved record to trash (branch_id = -1): {self}")
+            return
+
+        # permanent delete
+        if permanent is None:
+            response = input(
+                f"Record {self.uid} is already in trash! Are you sure you want to delete it from your"
+                " database? You can't undo this action. (y/n) "
+            )
+            confirm_delete = response == "y"
+        else:
+            confirm_delete = permanent
+
+        if confirm_delete:
+            if name_with_module == "Run":
+                from .run import delete_run_artifacts
+
+                delete_run_artifacts(self)
+            elif name_with_module == "Transform":
+                from .transform import delete_transform_relations
+
+                delete_transform_relations(self)
+            elif name_with_module == "Artifact":
+                from .artifact import delete_permanently
+
+                delete_permanently(
+                    self, storage=kwargs["storage"], using_key=kwargs["using_key"]
+                )
+            if name_with_module != "Artifact":
+                super().delete()
+
 
 def _format_django_validation_error(record: SQLRecord, e: DjangoValidationError):
     """Pretty print Django validation errors."""
@@ -1464,7 +1575,7 @@ def check_name_change(record: SQLRecord):
                 .exclude(feature_id=None)  # must have a feature
                 .distinct()
             )
-            artifact_ids = linked_records.list("artifact__uid")
+            artifact_ids = linked_records.to_list("artifact__uid")
             n = len(artifact_ids)
             if n > 0:
                 s = "s" if n > 1 else ""
@@ -1482,7 +1593,7 @@ def check_name_change(record: SQLRecord):
         # when a feature is renamed
         elif isinstance(record, Feature):
             # only internal features are associated with schemas
-            linked_artifacts = Artifact.filter(feature_sets__features=record).list(
+            linked_artifacts = Artifact.filter(feature_sets__features=record).to_list(
                 "uid"
             )
             n = len(linked_artifacts)
@@ -1806,6 +1917,7 @@ class Migration(BaseSQLRecord):
 
     class Meta:
         db_table = "django_migrations"
+        app_label = "lamindb"
         managed = False