lamindb 1.11.0__tar.gz → 1.11.1__tar.gz

{lamindb-1.11.0 → lamindb-1.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: lamindb
-Version: 1.11.0
+Version: 1.11.1
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.10,<3.14
@@ -129,7 +129,7 @@ Conversely, you can query artifacts by the script that created them.
 ln.Artifact.get(transform__key="create-fasta.py")  # query artifact by transform key
 ```
 
-Data lineage is just one type of metadata to help analysis and model training through queries, validation, and annotation. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/fgKBV8qdSnbIga0i).
+Data lineage is just one type of metadata to help analysis and model training through queries, validation, and annotation. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/9K1dteZ6Qx0EXK8g).
 
 <img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/6sofuDVvTANB0f480001.png" width="850">
 

{lamindb-1.11.0 → lamindb-1.11.1}/README.md

@@ -76,7 +76,7 @@ Conversely, you can query artifacts by the script that created them.
 ln.Artifact.get(transform__key="create-fasta.py")  # query artifact by transform key
 ```
 
-Data lineage is just one type of metadata to help analysis and model training through queries, validation, and annotation. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/fgKBV8qdSnbIga0i).
+Data lineage is just one type of metadata to help analysis and model training through queries, validation, and annotation. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/9K1dteZ6Qx0EXK8g).
 
 <img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/6sofuDVvTANB0f480001.png" width="850">
 

{lamindb-1.11.0 → lamindb-1.11.1}/lamindb/__init__.py

@@ -114,7 +114,7 @@ Backwards compatibility.
 
 # ruff: noqa: I001
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "1.11.0"
+__version__ = "1.11.1"
 
 import warnings as _warnings
 

{lamindb-1.11.0 → lamindb-1.11.1}/lamindb/core/_context.py

@@ -600,9 +600,11 @@ class Context:
         if pypackages is None:
             pypackages = True
         description = None
+        if path.suffix == ".ipynb" and path.stem.startswith("Untitled"):
+            raise RuntimeError(
+                "Your notebook is untitled, please rename it before tracking"
+            )
         path_str = path.as_posix()
-        if path_str.endswith("Untitled.ipynb"):
-            raise RuntimeError("Please rename your notebook before tracking it")
         if path_str.startswith("/fileId="):
             logger.warning("tracking on Google Colab is experimental")
             path_str = get_notebook_key_colab()

{lamindb-1.11.0 → lamindb-1.11.1}/lamindb/models/artifact.py

@@ -10,7 +10,7 @@ import fsspec
 import lamindb_setup as ln_setup
 import pandas as pd
 from anndata import AnnData
-from django.db import connections, models
+from django.db import ProgrammingError, connections, models
 from django.db.models import CASCADE, PROTECT, Q
 from django.db.models.functions import Length
 from lamin_utils import colors, logger
@@ -32,7 +32,7 @@ from lamindb.base.fields import (
     CharField,
     ForeignKey,
 )
-from lamindb.errors import FieldValidationError, UnknownStorageLocation
+from lamindb.errors import FieldValidationError, NoWriteAccess, UnknownStorageLocation
 from lamindb.models.query_set import QuerySet
 
 from ..base.users import current_user_id
@@ -294,6 +294,7 @@ def process_data(
 
 def get_stat_or_artifact(
     path: UPath,
+    storage: Record,
     key: str | None = None,
     check_hash: bool = True,
     is_replace: bool = False,
@@ -331,14 +332,14 @@ def get_stat_or_artifact(
     else:
         result = (
             Artifact.objects.using(instance)
-            .filter(Q(hash=hash) | Q(key=key, storage=settings.storage.record))
+            .filter(Q(hash=hash) | Q(key=key, storage=storage))
             .order_by("-created_at")
             .all()
         )
         artifact_with_same_hash_exists = result.filter(hash=hash).count() > 0
         if not artifact_with_same_hash_exists and len(result) > 0:
             logger.important(
-                f"creating new artifact version for key='{key}' (storage: '{settings.storage.root_as_str}')"
+                f"creating new artifact version for key='{key}' (storage: '{storage.root}')"
             )
             previous_artifact_version = result[0]
     if artifact_with_same_hash_exists:
@@ -438,6 +439,7 @@ def get_artifact_kwargs_from_data(
 
     stat_or_artifact = get_stat_or_artifact(
         path=path,
+        storage=storage,
         key=key,
         instance=using_key,
         is_replace=is_replace,
@@ -3072,8 +3074,12 @@ def _track_run_input(
                 )
                 data.save()
                 is_valid = True
+            data_run_id, run_id = data.run_id, run.id
+            different_runs = (data_run_id != run_id) or (
+                data_run_id is None and run_id is None
+            )
             return (
-                data.run_id != run.id
+                different_runs
                 and not data._state.adding  # this seems duplicated with data._state.db is None
                 and is_valid
             )
@@ -3118,8 +3124,9 @@ def _track_run_input(
     if track_run_input:
         if run is None:
             raise ValueError("No run context set. Call `ln.track()`.")
-        # avoid adding the same run twice
-        run.save()
+        if run._state.adding:
+            # avoid adding the same run twice
+            run.save()
         if data_class_name == "artifact":
             IsLink = run.input_artifacts.through
             links = [
@@ -3131,7 +3138,41 @@ def _track_run_input(
                 IsLink(run_id=run.id, collection_id=data_id)
                 for data_id in input_data_ids
             ]
-        IsLink.objects.bulk_create(links, ignore_conflicts=True)
+        try:
+            IsLink.objects.bulk_create(links, ignore_conflicts=True)
+        except ProgrammingError as e:
+            if "new row violates row-level security policy" in str(e):
+                instance = setup_settings.instance
+                available_spaces = instance.available_spaces
+                if available_spaces is None:
+                    raise NoWriteAccess(
+                        f"You’re not allowed to write to the instance {instance.slug}.\n"
+                        "Please contact administrators of the instance if you need write access."
+                    ) from None
+                write_access_spaces = (
+                    available_spaces["admin"] + available_spaces["write"]
+                )
+                no_write_access_spaces = {
+                    data_space
+                    for data in input_data
+                    if (data_space := data.space) not in write_access_spaces
+                }
+                if (run_space := run.space) not in write_access_spaces:
+                    no_write_access_spaces.add(run_space)
+                if len(no_write_access_spaces) > 1:
+                    name_msg = ", ".join(
+                        f"'{space.name}'" for space in no_write_access_spaces
+                    )
+                    space_msg = "spaces"
+                else:
+                    name_msg = f"'{no_write_access_spaces.pop().name}'"
+                    space_msg = "space"
+                raise NoWriteAccess(
+                    f"You’re not allowed to write to the {space_msg} {name_msg}.\n"
+                    f"Please contact administrators of the {space_msg} if you need write access."
+                ) from None
+            else:
+                raise e
 
 
 # privates currently dealt with separately

{lamindb-1.11.0 → lamindb-1.11.1}/lamindb/models/sqlrecord.py

@@ -918,7 +918,7 @@ class BaseSQLRecord(models.Model, metaclass=Registry):
                 ):
                     raise NoWriteAccess(
                         f"You’re not allowed to write to the space '{self.space.name}'.\n"
-                        "Please contact an administrator of the space if you need write access."
+                        "Please contact administrators of the space if you need write access."
                     ) from None
                 else:
                     raise

{lamindb-1.11.0 → lamindb-1.11.1}/tests/permissions/scripts/setup_access.py

@@ -100,6 +100,11 @@ feature = ln.Feature(name="team_access_feature", dtype=float)
 feature.space = team_access
 feature.save()
 
+# artifact for testing tracking error
+artifact = ln.Artifact("README.md", description="test tracking error")
+artifact.space = select_access
+artifact.save()
+
 print("Created models")
 
 # save jwt db connection

{lamindb-1.11.0 → lamindb-1.11.1}/tests/permissions/test_permissions.py

@@ -10,6 +10,7 @@ import pytest
 from django.db import connection, transaction
 from django.db.utils import IntegrityError, InternalError, ProgrammingError
 from jwt_utils import sign_jwt
+from lamindb.models.artifact import _track_run_input
 from lamindb_setup.core.django import DBToken, db_token_manager
 from psycopg2.extensions import adapt
 
@@ -294,6 +295,49 @@ def test_write_role():
 
     ln.ULabel(name="new label team default space").save()
 
+    with psycopg2.connect(pgurl) as conn, conn.cursor() as cur:
+        cur.execute(
+            "UPDATE hubmodule_team SET role = 'read' WHERE uid = 'teamuiduid11'",
+        )
+
+
+def test_tracking_error():
+    # switch user role to write to create the transform and run
+    with psycopg2.connect(pgurl) as conn, conn.cursor() as cur:
+        cur.execute(
+            "UPDATE hubmodule_account SET role = 'write' WHERE id = %s", (user_uuid,)
+        )
+
+    artifact = ln.Artifact.get(description="test tracking error")
+
+    transform = ln.Transform(key="My transform").save()
+    run = ln.Run(transform)  # unsaved, this is saved inside _track_run_input
+
+    # this error because ln.setup.settings.instance._db_permissions is not jwt
+    # it is None
+    with pytest.raises(ln.errors.NoWriteAccess) as e:
+        _track_run_input(artifact, run)
+    assert "You’re not allowed to write to the instance " in str(e)
+
+    # the instance is local so we set this manually
+    ln.setup.settings.instance._db_permissions = "jwt"
+    # artifact.space is not available for writes
+    with pytest.raises(ln.errors.NoWriteAccess) as e:
+        _track_run_input(artifact, run)
+    assert "You’re not allowed to write to the space " in str(e)
+
+    # switch user role back to read
+    with psycopg2.connect(pgurl) as conn, conn.cursor() as cur:
+        cur.execute(
+            "UPDATE hubmodule_account SET role = 'read' WHERE id = %s", (user_uuid,)
+        )
+    # as the user is read-only now, 2 spaces are unavailable for writes (artifact.space, run.space)
+    with pytest.raises(ln.errors.NoWriteAccess) as e:
+        _track_run_input(artifact, run)
+    assert "You’re not allowed to write to the spaces " in str(e)
+
+    ln.setup.settings.instance._db_permissions = None
+
 
 def test_token_reset():
     db_token_manager.reset()

{lamindb-1.11.0 → lamindb-1.11.1}/tests/storage/test_streaming.py

@@ -680,10 +680,18 @@ def test_compressed():
     _compress(adata_f, adata_gz)
 
     artifact = ln.Artifact.from_anndata(adata_gz, key="adata.h5ad.gz").save()
+
+    print("begin open adata.h5ad.gz")
+
     with artifact.open() as store:
         assert isinstance(store, AnnDataAccessor)
+
+    print("begin load adata.h5ad.gz")
+
     assert isinstance(artifact.load(), ad.AnnData)
 
+    print("begin open adata.h5ad.gz with compression=None")
+
     with pytest.raises(OSError):
         artifact.open(compression=None)