lamindb 0.76.1__py3-none-any.whl → 0.76.3__py3-none-any.whl

lamindb/core/storage/_tiledbsoma.py

@@ -0,0 +1,192 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Literal
+
+from anndata import AnnData
+from lamin_utils import logger
+from lamindb_setup import settings as setup_settings
+from lamindb_setup.core._settings_storage import get_storage_region
+from lamindb_setup.core.upath import create_path
+from lnschema_core import Artifact, Run
+
+if TYPE_CHECKING:
+    from lamindb_setup.core.types import UPathStr
+    from tiledbsoma import Collection as SOMACollection
+    from tiledbsoma import Experiment as SOMAExperiment
+    from tiledbsoma.io import ExperimentAmbientLabelMapping
+    from upath import UPath
+
+
+def _read_adata_h5ad_zarr(objpath: UPath):
+    from lamindb.core.storage.paths import read_adata_h5ad, read_adata_zarr
+
+    if objpath.is_dir():
+        adata = read_adata_zarr(objpath)
+    else:
+        adata = read_adata_h5ad(objpath)
+    return adata
+
+
+def _tiledb_config_s3(storepath: UPath) -> dict:
+    region = get_storage_region(storepath)
+    tiledb_config = {"vfs.s3.region": region}
+    storage_options = storepath.storage_options
+    if "key" in storage_options:
+        tiledb_config["vfs.s3.aws_access_key_id"] = storage_options["key"]
+    if "secret" in storage_options:
+        tiledb_config["vfs.s3.aws_secret_access_key"] = storage_options["secret"]
+    if "token" in storage_options:
+        tiledb_config["vfs.s3.aws_session_token"] = storage_options["token"]
+
+    return tiledb_config
+
+
+def _open_tiledbsoma(
+    storepath: UPath, mode: Literal["r", "w"] = "r"
+) -> SOMACollection | SOMAExperiment:
+    try:
+        import tiledbsoma as soma
+    except ImportError as e:
+        raise ImportError("Please install tiledbsoma: pip install tiledbsoma") from e
+
+    storepath_str = storepath.as_posix()
+    if storepath.protocol == "s3":
+        ctx = soma.SOMATileDBContext(tiledb_config=_tiledb_config_s3(storepath))
+        # this is a strange bug
+        # for some reason iterdir futher gives incorrect results
+        # if cache is not invalidated
+        # instead of obs and ms it gives ms and ms in the list of names
+        storepath.fs.invalidate_cache()
+    else:
+        ctx = None
+
+    soma_objects = [obj.name for obj in storepath.iterdir()]
+    if "obs" in soma_objects and "ms" in soma_objects:
+        SOMAType = soma.Experiment
+    else:
+        SOMAType = soma.Collection
+    return SOMAType.open(storepath_str, mode=mode, context=ctx)
+
+
+def save_tiledbsoma_experiment(
+    # Artifact args
+    adatas: list[AnnData | UPathStr],
+    key: str | None = None,
+    description: str | None = None,
+    run: Run | None = None,
+    revises: Artifact | None = None,
+    # tiledbsoma.io.from_anndata args
+    measurement_name: str = "RNA",
+    obs_id_name: str = "obs_id",
+    var_id_name: str = "var_id",
+    append_obsm_varm: bool = False,
+    # additional keyword args for tiledbsoma.io.from_anndata
+    **kwargs,
+) -> Artifact:
+    """Write `AnnData` to `tiledbsoma.Experiment`.
+
+    Reads `AnnData` objects, writes them to `tiledbsoma.Experiment`, creates `lamindb.Artifact`
+    and saves the artifact.
+    Note that this function adds `lamin_run_uid` column to `obs` of in-memory `AnnData` objects
+    when it writes to a new store or appends to a store that has this column in `obs`.
+
+    See also `tiledbsoma.io.from_anndata
+    <https://tiledbsoma.readthedocs.io/en/latest/_autosummary/tiledbsoma.io.from_anndata.html>`__.
+
+    Args:
+        adatas: `AnnData` objects to write, in-memory or on-disk.
+        key: A relative path within default storage.
+        description: A description.
+        run: The run that creates the artifact.
+        revises: `lamindb.Artifact` with `tiledbsoma.Experiment` to append to.
+            Triggers a revision (a new untagged version).
+        measurement_name: The name of the measurement to store data in `tiledbsoma.Experiment`.
+        obs_id_name: Which `AnnData` `obs` column to use for append mode.
+        var_id_name: Which `AnnData` `var` column to use for append mode.
+        append_obsm_varm: Whether to append `obsm` and `varm` in append mode .
+        **kwargs: Additional keyword arguments passed to `tiledbsoma.io.from_anndata` that
+            writes `adatas`.
+    """
+    try:
+        import tiledbsoma as soma
+        import tiledbsoma.io as soma_io
+    except ImportError as e:
+        raise ImportError("Please install tiledbsoma: pip install tiledbsoma") from e
+
+    from lamindb.core._data import get_run
+    from lamindb.core.storage.paths import auto_storage_key_from_artifact_uid
+    from lamindb.core.versioning import create_uid
+
+    run = get_run(run)
+
+    appending = revises is not None
+
+    if appending:
+        _uid = None
+        storepath = revises.path
+    else:
+        _uid, _ = create_uid(n_full_id=20)
+        storage_key = auto_storage_key_from_artifact_uid(
+            _uid, ".tiledbsoma", is_dir=True
+        )
+        storepath = setup_settings.storage.root / storage_key
+
+    if storepath.protocol == "s3":
+        ctx = soma.SOMATileDBContext(tiledb_config=_tiledb_config_s3(storepath))
+    else:
+        ctx = None
+
+    storepath = storepath.as_posix()
+
+    add_run_uid = True
+    if appending:
+        with soma.Experiment.open(storepath, mode="r", context=ctx) as store:
+            add_run_uid = "lamin_run_uid" in store["obs"].schema.names
+
+    if add_run_uid and run is None:
+        raise ValueError("Pass `run`")
+
+    adata_objects = []
+    for adata in adatas:
+        if isinstance(adata, AnnData):
+            if add_run_uid:
+                if adata.is_view:
+                    raise ValueError(
+                        "Can not write an `AnnData` view, please do `adata.copy()` before passing."
+                    )
+                else:
+                    adata.obs["lamin_run_uid"] = run.uid
+        else:
+            adata = _read_adata_h5ad_zarr(create_path(adata))
+            if add_run_uid:
+                adata.obs["lamin_run_uid"] = run.uid
+        adata_objects.append(adata)
+
+    if appending or len(adata_objects) > 1:
+        registration_mapping = soma_io.register_anndatas(
+            experiment_uri=storepath if appending else None,
+            adatas=adata_objects,
+            measurement_name=measurement_name,
+            obs_field_name=obs_id_name,
+            var_field_name=var_id_name,
+            append_obsm_varm=append_obsm_varm,
+            context=ctx,
+        )
+    else:
+        registration_mapping = None
+
+    for adata_obj in adata_objects:
+        soma_io.from_anndata(
+            storepath,
+            adata_obj,
+            measurement_name,
+            context=ctx,
+            obs_id_name=obs_id_name,
+            var_id_name=var_id_name,
+            registration_mapping=registration_mapping,
+            **kwargs,
+        )
+
+    return Artifact(
+        storepath, key=key, description=description, run=run, revises=revises, _uid=_uid
+    ).save()

lamindb/core/storage/paths.py

@@ -84,13 +84,9 @@ def attempt_accessing_path(
             )
     else:
         if artifact._state.db not in ("default", None) and using_key is None:
-            storage = (
-                Storage.using(artifact._state.db).filter(id=artifact.storage_id).one()
-            )
+            storage = Storage.using(artifact._state.db).get(id=artifact.storage_id)
         else:
-            storage = (
-                Storage.objects.using(using_key).filter(id=artifact.storage_id).one()
-            )
+            storage = Storage.objects.using(using_key).get(id=artifact.storage_id)
         # find a better way than passing None to instance_settings in the future!
         storage_settings = StorageSettings(storage.root, access_token=access_token)
     path = storage_settings.key_to_filepath(storage_key)

lamindb/core/versioning.py

@@ -11,6 +11,16 @@ if TYPE_CHECKING:
     from lnschema_core.models import IsVersioned
 
 
+def message_update_key_in_version_family(
+    *,
+    suid: str,
+    existing_key: str,
+    registry: str,
+    new_key: str,
+) -> str:
+    return f'Or update key "{existing_key}" in your existing family:\n\nln.{registry}.filter(uid__startswith="{suid}").update(key="{new_key}")'
+
+
 def increment_base62(s: str) -> str:
     # we don't need to throw an error for zzzz because uids are enforced to be unique
     # on the db level and have an enforced maximum length
@@ -78,57 +88,43 @@ def set_version(version: str | None = None, previous_version: str | None = None)
         version: Version string.
         previous_version: Previous version string.
     """
-    if version == previous_version:
-        raise ValueError(f"Please increment the previous version: '{previous_version}'")
     if version is None and previous_version is not None:
         version = bump_version(previous_version, bump_type="major")
     return version
 
 
-def init_uid(
+def create_uid(
     *,
     version: str | None = None,
     n_full_id: int = 20,
-    is_new_version_of: IsVersioned | None = None,
-) -> str:
-    if is_new_version_of is not None:
-        stem_uid = is_new_version_of.stem_uid
+    revises: IsVersioned | None = None,
+) -> tuple[str, IsVersioned | None]:
+    if revises is not None:
+        if not revises.is_latest:
+            # need one more request
+            revises = revises.__class__.objects.get(
+                is_latest=True, uid__startswith=revises.stem_uid
+            )
+            logger.warning(
+                f"didn't pass the latest version in `revises`, retrieved it: {revises}"
+            )
+        suid = revises.stem_uid
+        vuid = increment_base62(revises.uid[-4:])
     else:
-        stem_uid = ids.base62(n_full_id - 4)
+        suid = ids.base62(n_full_id - 4)
+        vuid = "0000"
     if version is not None:
         if not isinstance(version, str):
             raise ValueError(
                 "`version` parameter must be `None` or `str`, e.g., '0.1', '1', '2',"
                 " etc."
             )
-    return stem_uid + ids.base62_4()
-
-
-def get_uid_from_old_version(
-    is_new_version_of: IsVersioned,
-    version: str | None = None,
-    using_key: str | None = None,
-) -> tuple[str, str]:
-    """{}"""  # noqa: D415
-    msg = ""
-    if is_new_version_of.version is None:
-        previous_version = "1"
-        msg = f"setting previous version to '{previous_version}'"
-    else:
-        previous_version = is_new_version_of.version
-    version = set_version(version, previous_version)
-    new_uid = init_uid(
-        version=version,
-        n_full_id=is_new_version_of._len_full_uid,
-        is_new_version_of=is_new_version_of,
-    )
-    # the following covers the edge case where the old file was unversioned
-    if is_new_version_of.version is None:
-        is_new_version_of.version = previous_version
-        is_new_version_of.save(using=using_key)
-        if msg != "":
-            msg += f"& new version to '{version}'"
-    return new_uid, version
+        if revises is not None:
+            if version == revises.version:
+                raise ValueError(
+                    f"Please increment the previous version: '{revises.version}'"
+                )
+    return suid + vuid, revises
 
 
 def get_new_path_from_uid(old_path: UPath, old_uid: str, new_uid: str):
@@ -141,18 +137,18 @@ def get_new_path_from_uid(old_path: UPath, old_uid: str, new_uid: str):
     return new_path
 
 
-def process_is_new_version_of(
-    is_new_version_of: IsVersioned,
+def process_revises(
+    revises: IsVersioned | None,
     version: str | None,
     name: str | None,
     type: type[IsVersioned],
-) -> tuple[str, str, str]:
-    if is_new_version_of is not None and not isinstance(is_new_version_of, type):
-        raise TypeError(f"is_new_version_of has to be of type {type.__name__}")
-    if is_new_version_of is None:
-        uid = init_uid(version=version, n_full_id=type._len_full_uid)
-    else:
-        uid, version = get_uid_from_old_version(is_new_version_of, version)
+) -> tuple[str, str, str, IsVersioned | None]:
+    if revises is not None and not isinstance(revises, type):
+        raise TypeError(f"`revises` has to be of type `{type.__name__}`")
+    uid, revises = create_uid(
+        revises=revises, version=version, n_full_id=type._len_full_uid
+    )
+    if revises is not None:
         if name is None:
-            name = is_new_version_of.name
-    return uid, version, name
+            name = revises.name
+    return uid, version, name, revises

lamindb/integrations/__init__.py

@@ -4,6 +4,9 @@
    :toctree: .
 
    save_vitessce_config
+   save_tiledbsoma_experiment
 """
 
+from lamindb.core.storage import save_tiledbsoma_experiment
+
 from ._vitessce import save_vitessce_config

lamindb/integrations/_vitessce.py

@@ -109,4 +109,6 @@ def save_vitessce_config(
     logger.important(
         f"go to: https://lamin.ai/{slug}/artifact/{vitessce_config_artifact.uid}"
     )
+    run.finished_at = datetime.now(timezone.utc)
+    run.save()
     return vitessce_config_artifact

{lamindb-0.76.1.dist-info → lamindb-0.76.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.1
+Version: 0.76.3
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,9 +9,9 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.73.1
-Requires-Dist: lamindb_setup==0.76.5
-Requires-Dist: lamin_utils==0.13.2
+Requires-Dist: lnschema_core==0.73.3
+Requires-Dist: lamindb_setup==0.76.7
+Requires-Dist: lamin_utils==0.13.4
 Requires-Dist: lamin_cli==0.16.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
@@ -24,7 +24,7 @@ Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.48.2 ; extra == "bionty"
+Requires-Dist: bionty==0.49.0 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"
@@ -57,13 +57,5 @@ Provides-Extra: zarr
 
 # LaminDB - A data framework for biology
 
-- Manage data & metadata with a unified Python API ("lakehouse").
-- Track data lineage across notebooks & pipelines.
-- Integrate registries for experimental metadata & in-house ontologies.
-- Validate, standardize & annotate.
-- Collaborate across distributed databases.
-
-## Documentation
-
-Read the [docs](https://lamin.ai/docs).
+Read the [docs](https://docs.lamin.ai).
 

lamindb-0.76.3.dist-info/RECORD

@@ -0,0 +1,59 @@
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