lamindb 1.6.2__py3-none-any.whl → 1.7.0__py3-none-any.whl

lamindb/models/storage.py

@@ -0,0 +1,278 @@
+from __future__ import annotations
+
+from typing import (
+    TYPE_CHECKING,
+    overload,
+)
+
+from django.db import models
+from lamin_utils import logger
+from lamindb_setup import settings as setup_settings
+from lamindb_setup.core._hub_core import (
+    delete_storage_record,
+    get_storage_records_for_instance,
+)
+from lamindb_setup.core._settings_storage import StorageSettings, init_storage
+from lamindb_setup.core.upath import check_storage_is_empty, create_path
+
+from lamindb.base.fields import (
+    CharField,
+)
+
+from ..base.ids import base62_12
+from .run import TracksRun, TracksUpdates
+from .sqlrecord import SQLRecord
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+    from lamindb_setup.types import StorageType
+    from upath import UPath
+
+    from .artifact import Artifact
+
+
+class Storage(SQLRecord, TracksRun, TracksUpdates):
+    """Storage locations of artifacts such as folders and S3 buckets.
+
+    A storage location is either a folder (local or in the cloud) or
+    an entire S3/GCP bucket.
+
+    A LaminDB instance can manage and reference multiple storage locations. But any
+    storage location is managed by *at most one* LaminDB instance.
+
+    .. dropdown:: Managed vs. referenced storage locations
+
+        A LaminDB instance can only write artifacts to its managed storage
+        locations and merely reads artifacts from its referenced storage locations.
+
+        The :attr:`~lamindb.Storage.instance_uid` field defines the managing LaminDB instance of a
+        storage location. Some storage locations may not be managed by any LaminDB
+        instance, in which case the `instance_uid` is `None`. If it matches the
+        :attr:`~lamindb.core.Settings.instance_uid` of the current instance, the storage location
+        is managed by the current instance.
+
+        Here is an example based (`source <https://lamin.ai/laminlabs/lamindata/transform/dPco79GYgzag0000>`__):
+
+        .. image:: https://lamin-site-assets.s3.amazonaws.com/.lamindb/eHDmIOAxLEoqZ2oK0000.png
+           :width: 400px
+
+    .. dropdown:: Managing access to storage locations across instances
+
+        You can low-level manage access through AWS policies that you attach to your S3 bucket
+        or leverage LaminHub's fine-grained access management.
+
+        Head over to `https://lamin.ai/{account}/infrastructure` and you'll see a UI as in the screenshot below.
+        By clicking the green button that says "Connect S3 bucket", you enable LaminHub to issue federated S3 tokens
+        for a new S3 bucket so that your collaborators can access data in this bucket based on their permissions in LaminHub.
+        :doc:`docs:access` has more details.
+
+        .. image:: https://lamin-site-assets.s3.amazonaws.com/.lamindb/ze8hkgVxVptSSZEU0000.png
+           :width: 800px
+
+    Args:
+        root: `str` The root path of the storage location, e.g., `"./myfolder"`, `"s3://my-bucket/myfolder"`, or `"gs://my-bucket/myfolder"`.
+        type: :class:`~lamindb.setup.types.StorageType` The type of storage.
+        description: `str | None = None` A description.
+        region: `str | None = None` Cloud storage region, if applicable. Auto-populated for AWS S3.
+
+    See Also:
+        :attr:`lamindb.core.Settings.storage`
+            Current default storage location of your compute session for writing artifacts.
+        :attr:`~lamindb.setup.core.StorageSettings`
+            Storage settings.
+
+    Examples:
+
+        When you create a LaminDB instance, you configure its default storage location via `--storage`::
+
+            lamin init --storage ./myfolder  # or "s3://my-bucket/myfolder" or "gs://my-bucket/myfolder"
+
+        View the current default storage location in your compute session for writing artifacts::
+
+            import lamindb as ln
+
+            ln.settings.storage
+
+        Switch to another default storage location for writing artifacts::
+
+            ln.settings.storage = "./myfolder2"  # or "s3://my-bucket/my-folder2" or "gs://my-bucket/my-folder2"
+
+        View all storage locations used in your LaminDB instance::
+
+            ln.Storage.df()
+
+        Create a new storage location::
+
+            ln.Storage(root="./myfolder3").save()
+
+    Notes:
+
+        .. dropdown:: What is the `.lamindb/` directory inside a storage location?
+
+            It stores all artifacts that are ingested through `lamindb`, indexed by the artifact `uid`.
+            This means you don't have to worry about renaming or moving files, as this all happens on the database level.
+
+            Existing artifacts are typically stored in hierarchical structures with semantic folder names.
+            Instead of copying such artifacts into `.lamindb/` upon calls of `Artifact("legacy_path").save()`,
+            LaminDB registers them with the semantic `key` representing the relative path within the storage location.
+            These artifacts are marked with `artifact._key_is_virtual = False` and treated correspondingly.
+
+            There is only a single `.lamindb/` directory per storage location.
+
+        .. dropdown:: What should I do if I want to bulk migrate all artifacts to another storage?
+
+            Currently, you can only achieve this manually and you should be careful with it.
+
+            1. Copy or move artifacts into the desired new storage location
+            2. Adapt the corresponding record in the {class}`~lamindb.Storage` registry by setting the `root` field to the new location
+            3. If your LaminDB storage location is managed through the hub, you also need to update the storage record on the hub -- contact support
+
+    """
+
+    class Meta(SQLRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
+        abstract = False
+
+    _name_field: str = "root"
+
+    id: int = models.AutoField(primary_key=True)
+    """Internal id, valid only in one DB instance."""
+    uid: str = CharField(
+        editable=False, unique=True, max_length=12, default=base62_12, db_index=True
+    )
+    """Universal id, valid across DB instances."""
+    root: str = CharField(db_index=True, unique=True)
+    """Root path of storage (cloud or local path)."""
+    description: str | None = CharField(db_index=True, null=True)
+    """A description of what the storage location is used for (optional)."""
+    type: StorageType = CharField(max_length=30, db_index=True)
+    """Can be "local" vs. "s3" vs. "gs"."""
+    region: str | None = CharField(max_length=64, db_index=True, null=True)
+    """Cloud storage region, if applicable."""
+    instance_uid: str | None = CharField(max_length=12, db_index=True, null=True)
+    """Instance that manages this storage location."""
+    artifacts: Artifact
+    """Artifacts contained in this storage location."""
+
+    @overload
+    def __init__(
+        self,
+        root: str,
+        type: str,
+        description: str | None = None,
+        region: str | None = None,
+    ): ...
+
+    @overload
+    def __init__(
+        self,
+        *db_args,
+    ): ...
+
+    def __init__(
+        self,
+        *args,
+        **kwargs,
+    ):
+        if len(args) == len(self._meta.concrete_fields):
+            super().__init__(*args)
+            return None
+        storage_record = Storage.filter(root=kwargs["root"]).one_or_none()
+        if storage_record is not None:
+            from .sqlrecord import init_self_from_db
+
+            init_self_from_db(self, storage_record)
+            return None
+
+        skip_preparation = kwargs.pop("_skip_preparation", False)
+        if skip_preparation:
+            super().__init__(*args, **kwargs)
+            return None
+
+        # instance_id won't take effect if
+        # - there is no write access
+        # - the storage location is already managed by another instance
+        ssettings, _ = init_storage(
+            kwargs["root"],
+            instance_id=setup_settings.instance._id,
+            instance_slug=setup_settings.instance.slug,
+            prevent_register_hub=not setup_settings.instance.is_on_hub,
+        )
+        # ssettings performed validation and normalization of the root path
+        kwargs["root"] = ssettings.root_as_str  # noqa: S101
+        if "instance_uid" in kwargs:
+            assert kwargs["instance_uid"] == ssettings.instance_uid  # noqa: S101
+        else:
+            kwargs["instance_uid"] = ssettings.instance_uid
+        if ssettings._uid is not None:  # need private attribute here
+            kwargs["uid"] = ssettings._uid
+        if "type" not in kwargs:
+            kwargs["type"] = ssettings.type
+        else:
+            assert kwargs["type"] == ssettings.type  # noqa: S101
+        if "region" in kwargs:
+            assert kwargs["region"] == ssettings.region  # noqa: S101
+        else:
+            kwargs["region"] = ssettings.region
+
+        is_managed_by_current_instance = (
+            ssettings.instance_uid == setup_settings.instance.uid
+        )
+        if ssettings.instance_uid is not None and not is_managed_by_current_instance:
+            is_managed_by_instance = (
+                f", is managed by instance with uid {ssettings.instance_uid}"
+            )
+        else:
+            is_managed_by_instance = ""
+        hub_message = ""
+        if setup_settings.instance.is_on_hub and is_managed_by_current_instance:
+            instance_owner = setup_settings.instance.owner
+            hub_message = f", see: https://lamin.ai/{instance_owner}/infrastructure"
+        managed_message = (
+            "created managed"
+            if is_managed_by_current_instance
+            else "referenced read-only"
+        )
+        logger.important(
+            f"{managed_message} storage location at {kwargs['root']}{is_managed_by_instance}{hub_message}"
+        )
+        super().__init__(**kwargs)
+
+    @property
+    def path(self) -> Path | UPath:
+        """Path.
+
+        Uses the `.root` field and converts it into a `Path` or `UPath`.
+        """
+        access_token = self._access_token if hasattr(self, "_access_token") else None
+        return create_path(self.root, access_token=access_token)
+
+    def delete(self) -> None:
+        """Delete the storage location.
+
+        This errors in case the storage location is not empty.
+        """
+        from .. import settings
+
+        assert not self.artifacts.exists(), "Cannot delete storage holding artifacts."  # noqa: S101
+        check_storage_is_empty(self.path)
+        assert settings.storage.root_as_str != self.root, (  # noqa: S101
+            "Cannot delete the current storage location, switch to another."
+        )
+        if setup_settings.user.handle != "anonymous":  # only attempt if authenticated
+            storage_records = get_storage_records_for_instance(
+                # only query those storage records on the hub that are managed by the current instance
+                setup_settings.instance._id
+            )
+            for storage_record in storage_records:
+                if storage_record["lnid"] == self.uid:
+                    assert storage_record["is_default"] in {False, None}, (  # noqa: S101
+                        "Cannot delete default storage of instance."
+                    )
+                    delete_storage_record(storage_record)
+        ssettings = StorageSettings(self.root)
+        if ssettings._mark_storage_root.exists():
+            ssettings._mark_storage_root.unlink(
+                missing_ok=True  # this is totally weird, but needed on Py3.11
+            )
+        super().delete()

lamindb/models/transform.py

@@ -66,8 +66,8 @@ class Transform(SQLRecord, IsVersioned):
         revises: `Transform | None = None` An old version of the transform.
 
     See Also:
-        :meth:`~lamindb.core.Context.track`
-            Globally track a script, notebook or pipeline run.
+        :func:`~lamindb.track`
+            Globally track a script or notebook run.
         :class:`~lamindb.Run`
             Executions of transforms.
 
@@ -201,6 +201,10 @@ class Transform(SQLRecord, IsVersioned):
         type: TransformType | None = kwargs.pop("type", "pipeline")
         reference: str | None = kwargs.pop("reference", None)
         reference_type: str | None = kwargs.pop("reference_type", None)
+        branch = kwargs.pop("branch", None)
+        branch_id = kwargs.pop("branch_id", 1)
+        space = kwargs.pop("space", None)
+        space_id = kwargs.pop("space_id", 1)
         using_key = kwargs.pop("using_key", None)
         if "name" in kwargs:
             if key is None:
@@ -292,6 +296,10 @@ class Transform(SQLRecord, IsVersioned):
             hash=hash,
             _has_consciously_provided_uid=has_consciously_provided_uid,
             revises=revises,
+            branch=branch,
+            branch_id=branch_id,
+            space=space,
+            space_id=space_id,
         )
 
     @property

lamindb/models/ulabel.py

@@ -35,7 +35,7 @@ class ULabel(SQLRecord, HasParents, CanCurate, TracksRun, TracksUpdates):
 
     Args:
         name: `str` A name.
-        description: `str` A description.
+        description: `str | None = None` A description.
         reference: `str | None = None` For instance, an external ID or a URL.
         reference_type: `str | None = None` For instance, `"url"`.
 
@@ -175,6 +175,10 @@ class ULabel(SQLRecord, HasParents, CanCurate, TracksRun, TracksUpdates):
         description: str | None = kwargs.pop("description", None)
         reference: str | None = kwargs.pop("reference", None)
         reference_type: str | None = kwargs.pop("reference_type", None)
+        branch = kwargs.pop("branch", None)
+        branch_id = kwargs.pop("branch_id", 1)
+        space = kwargs.pop("space", None)
+        space_id = kwargs.pop("space_id", 1)
         _skip_validation = kwargs.pop("_skip_validation", False)
         _aux = kwargs.pop("_aux", None)
         if len(kwargs) > 0:
@@ -189,6 +193,10 @@ class ULabel(SQLRecord, HasParents, CanCurate, TracksRun, TracksUpdates):
             description=description,
             reference=reference,
             reference_type=reference_type,
+            branch=branch,
+            branch_id=branch_id,
+            space=space,
+            space_id=space_id,
             _skip_validation=_skip_validation,
             _aux=_aux,
         )

lamindb/setup/__init__.py

@@ -7,7 +7,8 @@ from lamindb_setup import (
     settings,
 )
 
-from . import core
+from . import core, errors, types
+from ._switch import switch  # noqa: F401
 
 del connect  # we have this at the root level, hence, we don't want it here
 __doc__ = _lamindb_setup.__doc__.replace("lamindb_setup", "lamindb.setup")

lamindb/setup/_switch.py

@@ -0,0 +1,16 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from lamindb_setup import settings
+
+if TYPE_CHECKING:
+    from lamindb.models import Branch, Space
+
+
+def switch(*, branch: str | Branch | None = None, space: str | Space | None = None):
+    """Switch to a branch or space, create if not exists."""
+    if branch is not None:
+        settings.branch = branch
+    if space is not None:
+        settings.space = space

lamindb/setup/errors/__init__.py

@@ -0,0 +1,4 @@
+import lamindb_setup as _lamindb_setup
+from lamindb_setup.errors import *  # noqa: F403
+
+__doc__ = _lamindb_setup.errors.__doc__.replace("lamindb_setup", "lamindb.setup")

lamindb/setup/types/__init__.py

@@ -0,0 +1,4 @@
+import lamindb_setup as _lamindb_setup
+from lamindb_setup.types import *  # noqa: F403
+
+__doc__ = _lamindb_setup.types.__doc__.replace("lamindb_setup", "lamindb.setup")

{lamindb-1.6.2.dist-info → lamindb-1.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.6.2
+Version: 1.7.0
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.14
@@ -9,9 +9,9 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: lamin_utils==0.14.0
-Requires-Dist: lamin_cli==1.4.2
-Requires-Dist: lamindb_setup[aws]==1.6.1
+Requires-Dist: lamin_utils==0.15.0
+Requires-Dist: lamin_cli==1.5.3
+Requires-Dist: lamindb_setup[aws]==1.7.2
 Requires-Dist: pyyaml
 Requires-Dist: pyarrow
 Requires-Dist: pandera>=0.24.0
@@ -23,7 +23,7 @@ Requires-Dist: anndata>=0.8.0,<=0.11.4
 Requires-Dist: fsspec
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
-Requires-Dist: bionty>=1.5.0 ; extra == "bionty"
+Requires-Dist: bionty>=1.6.0 ; extra == "bionty"
 Requires-Dist: clinicore ; extra == "clinicore"
 Requires-Dist: tomlkit ; extra == "dev"
 Requires-Dist: line_profiler ; extra == "dev"

{lamindb-1.6.2.dist-info → lamindb-1.7.0.dist-info}/RECORD

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 lamindb/core/subsettings/__init__.py,sha256=f_vOqZOjVGez8pLmtrUuc_ayDGXl07t_ZY-P2Cedxbo,201
 lamindb/core/subsettings/_annotation_settings.py,sha256=o-yTYw-NmjFmtehbKU8qnf7tyaeDFkTRGan1pXAIVT0,370
 lamindb/core/subsettings/_creation_settings.py,sha256=NGHWKqCFSzVNBxAr2VnmdYguiFdW29XUK7T9wRsVshg,906
 lamindb/curators/__init__.py,sha256=rv5Xrhv0jS1NMpuRVUHEMAsu6pXhBdDP8PBlO4FXrsE,662
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 lamindb/curators/_cellxgene_schemas/__init__.py,sha256=iw6PrzhBQpAR7aQ4_MXopSAVX2hdderHH3LRWeQy7Hk,7511
 lamindb/curators/_cellxgene_schemas/schema_versions.csv,sha256=X9rmO88TW1Fht1f5mJs0JdW-VPvyKSajpf8lHNeECj4,1680
 lamindb/examples/__init__.py,sha256=DGImiuWYDvwxh78p5FCwQWClEwsE3ODLU49i_NqbW0c,533
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 lamindb/examples/schemas/__init__.py,sha256=NPDp7VjMOHStEIthx3xW9NSHtY7jnnMzrNPcSDgxT3M,241
 lamindb/examples/schemas/_anndata.py,sha256=Q0h7YWZ6lqAZtE0i1xxCvJ8JfSa_RhFj4RY1sE_9HZs,764
 lamindb/examples/schemas/_simple.py,sha256=JdavLLrJnxDLTKBKRk2Tb534AInlzX0jyEvU9LcH-NQ,568
@@ -82,38 +85,52 @@ lamindb/migrations/0099_alter_writelog_seqno.py,sha256=Sg4jbLO3dP69_A53EL2L3rwfM
 lamindb/migrations/0100_branch_alter_artifact__branch_code_and_more.py,sha256=dC1b1ntEVayNxBVEvJVVpVjqjV6qnzZxZ7Ez0qy_9j4,3158
 lamindb/migrations/0101_alter_artifact_hash_alter_feature_name_and_more.py,sha256=yxnVzVcoRxd-Xc2KIkR07EtlBxd3LyY4C7F8enBHBYY,14154
 lamindb/migrations/0102_remove_writelog_branch_code_and_more.py,sha256=LkedZIweHHQGytJbo3OhshLFZLMKAbp22EuW-YqoTp0,2222
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 lamindb/migrations/0104_alter_branch_uid.py,sha256=YHhQHblFoOG5jphqbtPg69gnkiBqw9wdVIFKVrzoRhk,12863
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 lamindb/migrations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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