lamindb 0.74.3__py3-none-any.whl → 0.75.1__py3-none-any.whl

lamindb/core/storage/_valid_suffixes.py

@@ -1,5 +1,19 @@
-from lamindb_setup.core.upath import VALID_COMPOSITE_SUFFIXES, VALID_SUFFIXES
+from lamindb_setup.core.upath import VALID_COMPOSITE_SUFFIXES, VALID_SIMPLE_SUFFIXES
 
 # add new composite suffixes like so
-VALID_COMPOSITE_SUFFIXES.update({".vitessce.json"})
+VALID_COMPOSITE_SUFFIXES.update(
+    {
+        ".vitessce.json",
+        ".ome.zarr",
+    }
+)
 # can do the same for simple valid suffixes
+
+
+class VALID_SUFFIXES:
+    """Valid suffixes."""
+
+    SIMPLE: set[str] = VALID_SIMPLE_SUFFIXES
+    """Simple suffixes."""
+    COMPOSITE: set[str] = VALID_COMPOSITE_SUFFIXES
+    """Composite suffixes."""

lamindb/core/storage/paths.py

@@ -39,7 +39,7 @@ is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
 
 # add type annotations back asap when re-organizing the module
 def auto_storage_key_from_artifact(artifact: Artifact):
-    if artifact.key is None or artifact.key_is_virtual:
+    if artifact.key is None or artifact._key_is_virtual:
         is_dir = artifact.n_objects is not None
         return auto_storage_key_from_artifact_uid(artifact.uid, artifact.suffix, is_dir)
     else:
@@ -56,6 +56,14 @@ def auto_storage_key_from_artifact_uid(uid: str, suffix: str, is_dir: bool) -> s
     return storage_key
 
 
+def check_path_is_child_of_root(path: Path | UPath, root: Path | UPath | None) -> bool:
+    # str is needed to eliminate UPath storage_options
+    # from the equality checks below
+    path = UPath(str(path))
+    root = UPath(str(root))
+    return root.resolve() in path.resolve().parents
+
+
 def attempt_accessing_path(
     artifact: Artifact,
     storage_key: str,
@@ -141,19 +149,6 @@ def delete_storage(
     storagepath: Path, raise_file_not_found_error: bool = True
 ) -> None | str:
     """Delete arbitrary artifact."""
-    # TODO is_relative_to is not available in 3.8 and deprecated since 3.12
-    # replace with check_path_is_child_of_root but this needs to first be debugged
-    # if not check_path_is_child_of_root(storagepath, settings.storage.root):
-    if not storagepath.is_relative_to(settings.storage.root):  # type: ignore
-        allow_delete = False
-        if setup_settings.instance.keep_artifacts_local:
-            allow_delete = storagepath.is_relative_to(  # type: ignore
-                setup_settings.instance.storage_local.root
-            )
-        if not allow_delete:
-            logger.warning("couldn't delete files outside of default storage")
-            return "did-not-delete"
-    # only delete files in the default storage
     if storagepath.is_file():
         storagepath.unlink()
     elif storagepath.is_dir():

lamindb/core/types.py

@@ -7,9 +7,12 @@
    StrField
    ListLike
    TransformType
+   ArtifactType
 """
+
 from lamindb_setup.core.types import UPathStr
 from lnschema_core.types import (
+    ArtifactType,
     ListLike,
     StrField,
     TransformType,

lamindb/core/versioning.py

@@ -136,7 +136,7 @@ def process_is_new_version_of(
     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}")
+        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:

lamindb/integrations/__init__.py

@@ -5,4 +5,5 @@
 
    save_vitessce_config
 """
+
 from ._vitessce import save_vitessce_config

lamindb/integrations/_vitessce.py

@@ -15,61 +15,98 @@ if TYPE_CHECKING:
     from vitessce import VitessceConfig
 
 
-# tested & context in https://github.com/laminlabs/lamin-spatial
-def save_vitessce_config(vitessce_config: VitessceConfig, description: str) -> Artifact:
+# "unit test": https://github.com/laminlabs/lamindb/blob/main/docs/storage/vitessce.ipynb
+# integration test & context: https://github.com/laminlabs/lamin-spatial/blob/main/docs/vitessce.ipynb
+def save_vitessce_config(
+    vitessce_config: VitessceConfig, description: str | None = None
+) -> Artifact:
     """Validates and saves a ``VitessceConfig`` object.
 
-    Example: :doc:`docs:vitessce`.
+    Guide: :doc:`docs:vitessce`.
 
     Args:
-        vitessce_config (``VitessceConfig``): A VitessceConfig object.
-        description: A description for the artifact.
+        vitessce_config (``VitessceConfig``): A `VitessceConfig` object.
+        description: A description for the `VitessceConfig` artifact.
 
+    .. versionchanged:: 0.75.1
+        Now displays the "Vitessce button" on the hub next to the dataset. It additionally keeps displaying it next to the configuration file.
     .. versionchanged:: 0.70.2
-        This function no longer saves the dataset. It only saves the VitessceConfig object.
+        No longer saves the dataset. It only saves the `VitessceConfig` object.
     """
+    # can only import here because vitessce is not a dependency
+    from vitessce import VitessceConfig
+
+    from lamindb.core.storage import VALID_SUFFIXES
+
+    assert isinstance(vitessce_config, VitessceConfig)  # noqa: S101
     vc_dict = vitessce_config.to_dict()
+    valid_composite_zarr_suffixes = [
+        suffix for suffix in VALID_SUFFIXES.COMPOSITE if suffix.endswith(".zarr")
+    ]
     # validate
-    datasets = vc_dict["datasets"]
-    input_artifacts = []
-    for dataset in datasets:
-        if "files" not in dataset:
-            raise ValueError("Each dataset must have a 'files' key.")
-        for file in dataset["files"]:
+    dataset_artifacts = []
+    assert vc_dict["datasets"]  # noqa: S101
+    for vitessce_dataset in vc_dict["datasets"]:
+        # didn't find good ways to violate the below, hence using plain asserts
+        # without user feedback
+        assert "files" in vitessce_dataset  # noqa: S101
+        assert vitessce_dataset["files"]  # noqa: S101
+        for file in vitessce_dataset["files"]:
             if "url" not in file:
                 raise ValueError("Each file must have a 'url' key.")
-            filename = file["url"].split("/")[-1]
-            if not filename.endswith((".anndata.zarr", ".zarr", ".ome.zarr")):
-                logger.warning(
-                    "filename should end with '.anndata.zarr', '.zarr', or '.ome.zarr'."
+            s3_path = file["url"]
+            s3_path_last_element = s3_path.split("/")[-1]
+            # note 1: the following parses the stem uid of the artifact from the S3 path
+            # there might be a better way of doing this in case the vitessce config
+            # gets updated in the future; but given these paths are set in stone
+            # this should be more robust than it looks
+            #
+            # note 2: what's not great is the fact that people might use composite suffixes we don't recognize
+            # I don't know what to do about it other than documenting it clearly
+            # https://github.com/laminlabs/lamindb/blob/main/lamindb/core/storage/_valid_suffixes.py
+            # https://docs.lamin.ai/lamindb.core.storage.valid_suffixes
+            #
+            # now start with attempting to strip the composite suffix candidates
+            for suffix in valid_composite_zarr_suffixes:
+                s3_path_last_element = s3_path_last_element.replace(suffix, "")
+            # in case there was no hit, strip plain ".zarr"
+            artifact_stem_uid = s3_path_last_element.replace(".zarr", "")
+            # if there is still a "." in string, we
+            if "." in artifact_stem_uid:
+                raise ValueError(
+                    f"Suffix should be '.zarr' or one of {valid_composite_zarr_suffixes}. Inspect your path {s3_path}"
                 )
-            filestem = (
-                filename.replace(".anndata.zarr", "")
-                .replace(".spatialdata.zarr", "")
-                .replace(".ome.zarr", "")
-            )
-            artifact = Artifact.filter(uid__startswith=filestem).one_or_none()
+            artifact = Artifact.filter(uid__startswith=artifact_stem_uid).one_or_none()
             if artifact is None:
-                logger.warning(
-                    f"could not find dataset '{filestem}' in lamindb: {dataset}"
+                raise ValueError(
+                    f"Could not find dataset with stem uid '{artifact_stem_uid}' in lamindb: {vitessce_dataset}. Did you follow https://docs.lamin.ai/vitessce? It appears the AWS S3 path doesn't encode a lamindb uid."
                 )
             else:
-                input_artifacts.append(artifact)
+                dataset_artifacts.append(artifact)
     # link inputs
     with logger.mute():
-        transform = Transform(name="save_vitessce_config", type="function", version="1")
+        transform = Transform(name="save_vitessce_config", type="function", version="2")
         transform.save()
     run = Run(transform=transform)
     run.save()
-    run.input_artifacts.set(input_artifacts)
+    if len(dataset_artifacts) > 1:
+        # if we have more datasets, we should create a collection
+        # and attach an action to the collection
+        raise NotImplementedError
+    run.input_artifacts.set(dataset_artifacts)
     # create a JSON export
     config_file_local_path = (
         ln_setup.settings.storage.cache_dir / "config.vitessce.json"
     )
     with open(config_file_local_path, "w") as file:
         json.dump(vc_dict, file)
-    artifact = Artifact(config_file_local_path, description=description, run=run)
-    artifact.save()
+    vitessce_config_artifact = Artifact(
+        config_file_local_path, description=description, run=run
+    ).save()
+    # we have one and only one dataset artifact, hence the following line is OK
+    dataset_artifacts[0]._actions.add(vitessce_config_artifact)
     slug = ln_setup.settings.instance.slug
-    logger.important(f"go to: https://lamin.ai/{slug}/artifact/{artifact.uid}")
-    return artifact
+    logger.important(
+        f"go to: https://lamin.ai/{slug}/artifact/{vitessce_config_artifact.uid}"
+    )
+    return vitessce_config_artifact

{lamindb-0.74.3.dist-info → lamindb-0.75.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.74.3
+Version: 0.75.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,10 +9,10 @@ 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==0.70.5
-Requires-Dist: lamindb_setup==0.74.2
+Requires-Dist: lnschema_core==0.72.2
+Requires-Dist: lamindb_setup==0.76.3
 Requires-Dist: lamin_utils==0.13.2
-Requires-Dist: lamin_cli==0.15.0
+Requires-Dist: lamin_cli==0.16.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -24,7 +24,7 @@ Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.44.3 ; extra == "bionty"
+Requires-Dist: bionty==0.48.0 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"

lamindb-0.75.1.dist-info/RECORD

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lamindb-0.74.3.dist-info/RECORD

@@ -1,57 +0,0 @@
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