lamindb 0.55.0__tar.gz → 0.55.1__tar.gz

{lamindb-0.55.0 → lamindb-0.55.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.55.0
+Version: 0.55.1
 Summary: Open-source data platform for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -8,9 +8,9 @@ Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
-Requires-Dist: lnschema_core==0.49.2
-Requires-Dist: lamindb_setup==0.54.2
-Requires-Dist: lamin_utils==0.11.3
+Requires-Dist: lnschema_core==0.50.0
+Requires-Dist: lamindb_setup==0.54.3
+Requires-Dist: lamin_utils==0.11.4
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -35,7 +35,7 @@ Requires-Dist: pytest-cov ; extra == "dev"
 Requires-Dist: nbproject_test>=0.3.0 ; extra == "dev"
 Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
-Requires-Dist: readfcs>=1.1.5 ; extra == "fcs"
+Requires-Dist: readfcs>=1.1.7 ; extra == "fcs"
 Requires-Dist: fsspec[gs]==2023.9.0 ; extra == "gcp"
 Requires-Dist: nbproject==0.9.2 ; extra == "jupyter"
 Requires-Dist: nbstripout ; extra == "jupyter"

{lamindb-0.55.0 → lamindb-0.55.1}/docs/changelog.md

@@ -6,13 +6,20 @@
 
 ## 0.55
 
+### 0.55.1 {small}`2023-10-4`
+
+- ✨ Dataset from paths aka storage [PR1222](https://github.com/laminlabs/lamindb/pull/1222) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Do not search for alternative names if id is passed [PR1225](https://github.com/laminlabs/lamindb/pull/1225) [@falexwolf](https://github.com/falexwolf)
+- 📝 Added lamindata badge [PR1223](https://github.com/laminlabs/lamindb/pull/1223) [@sunnyosun](https://github.com/sunnyosun)
+- ♻️ Refactor data flow tracking for Dataset [PR1224](https://github.com/laminlabs/lamindb/pull/1224) [@falexwolf](https://github.com/falexwolf)
+
 ### 0.55.0 {small}`2023-10-03`
 
 - ✨ Enable to transfer data between instances [PR1216](https://github.com/laminlabs/lamindb/pull/1216) [@falexwolf](https://github.com/falexwolf)
-- ✨ Save notebook files [PR1213](https://github.com/laminlabs/lamindb/pull/1213) [@falexwolf](https://github.com/falexwolf)
-- ♻️ Track dataset as run input also for dataset.files [PR1219](https://github.com/laminlabs/lamindb/pull/1219) [@falexwolf](https://github.com/falexwolf)
+- ✨ Enable saving notebook files [PR1213](https://github.com/laminlabs/lamindb/pull/1213) [@falexwolf](https://github.com/falexwolf)
 - 💄 Display id in view_parents [PR1215](https://github.com/laminlabs/lamindb/pull/1215) [@sunnyosun](https://github.com/sunnyosun)
-- ♻️ Move lamin-vault dependency to postgres extra [PR1214](https://github.com/laminlabs/lamindb/pull/1214) [@falexwolf](https://github.com/falexwolf)
+
+## 0.54
 
 ### 0.54.4 {small}`2023-09-29`
 

{lamindb-0.55.0 → lamindb-0.55.1}/docs/features-lamindb.md

@@ -1,4 +1,4 @@
-[Influenced](docs:influences) by a number of data tools, LaminDB's features address [key data management problem](https://lamin.ai/blog/2022/problems).
+[Influenced](docs:influences) by a number of data tools, LaminDB's features address [key data management problems](https://lamin.ai/blog/2022/problems).
 
 **For data users**
 

{lamindb-0.55.0 → lamindb-0.55.1}/docs/introduction.ipynb

@@ -25,7 +25,7 @@
     "```\n",
     ":::\n",
     "\n",
-    "LaminHub is free for public data. Enterprise features, support, integration tests & wetlab plug-ins hosted in your or our infrastructure are available on a paid plan: please [reach out](https://lamin.ai/contact)!"
+    "LaminHub is free for public data. Enterprise features, support, integration tests & wetlab plug-ins hosted in your or our infrastructure are available on a [paid plan](https://lamin.ai/pricing): please [reach out](https://lamin.ai/contact)!"
    ]
   },
   {
@@ -578,6 +578,20 @@
     "dataset_v2.files.df()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Explore data in LaminHub"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You may explore [this notebook](https://lamin.ai/laminlabs/lamindata/record/core/Transform?id=Hc5AXzibjGg1z8) with [datasets & files](https://lamin.ai/laminlabs/lamindata/record/core/Dataset?id=PuCck2ARUd3rUrmdWYiI&tab=files&offset=0&limit=50) in `laminlabs/lamindata`."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

{lamindb-0.55.0 → lamindb-0.55.1}/docs/transfer.ipynb

@@ -75,7 +75,8 @@
    "outputs": [],
    "source": [
     "dataset = ln.Dataset.filter(\n",
-    "    using=\"laminlabs/cellxgene-census\", reference=\"c888b684-6c51-431f-972a-6c963044cef0\"\n",
+    "    using=\"laminlabs/cellxgene-census\",\n",
+    "    reference=\"c888b684-6c51-431f-972a-6c963044cef0\",\n",
     ").one()\n",
     "dataset"
    ]

{lamindb-0.55.0 → lamindb-0.55.1}/docs/tutorial.ipynb

@@ -4,8 +4,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "![tutorial1/2](https://img.shields.io/badge/tutorial1/2-lightgrey)\n",
-    "[![Jupyter Notebook](https://img.shields.io/badge/Jupyter%20Notebook-orange)](https://github.com/laminlabs/lamindb/blob/main/docs/tutorial.ipynb)"
+    "![](https://img.shields.io/badge/tutorial1/2-lightgrey)\n",
+    "[![](https://img.shields.io/badge/Jupyter%20Notebook-orange)](https://github.com/laminlabs/lamindb/blob/main/docs/tutorial.ipynb)\n",
+    "[![](https://img.shields.io/badge/laminlabs/lamindata-mediumseagreen)](https://lamin.ai/laminlabs/lamindata/record/core/Transform?id=NJvdsWWbJlZSz8)"
    ]
   },
   {
@@ -596,7 +597,7 @@
    "outputs": [],
    "source": [
     "transform = ln.Transform.filter(\n",
-    "    name__contains=\"files & datasets\"\n",
+    "    name__icontains=\"files & datasets\"\n",
     ").one()  # get exactly one result\n",
     "transform"
    ]

{lamindb-0.55.0 → lamindb-0.55.1}/docs/tutorial2.ipynb

@@ -4,8 +4,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "![tutorial2/2](https://img.shields.io/badge/tutorial2/2-lightgrey)\n",
-    "[![Jupyter Notebook](https://img.shields.io/badge/Jupyter%20Notebook-orange)](https://github.com/laminlabs/lamindb/blob/main/docs/tutorial1.ipynb)"
+    "![](https://img.shields.io/badge/tutorial2/2-lightgrey)\n",
+    "[![](https://img.shields.io/badge/Jupyter%20Notebook-orange)](https://github.com/laminlabs/lamindb/blob/main/docs/tutorial1.ipynb)\n",
+    "[![](https://img.shields.io/badge/laminlabs/lamindata-mediumseagreen)](https://lamin.ai/laminlabs/lamindata/record/core/Transform?id=dMtrt8YMSdl6z8)"
    ]
   },
   {
@@ -490,7 +491,7 @@
     "\n",
     "```python\n",
     "for feature in features:\n",
-    "    if feature.type == \"float\":\n",
+    "    if feature.type == \"number\":\n",
     "        feature.unit = \"m\"  # SI unit for meters\n",
     "        feature.save()\n",
     "```\n",

{lamindb-0.55.0 → lamindb-0.55.1}/lamindb/__init__.py

@@ -54,7 +54,7 @@ Static classes & modules:
 
 """
 
-__version__ = "0.55.0"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.55.1"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

{lamindb-0.55.0 → lamindb-0.55.1}/lamindb/_dataset.py

@@ -1,10 +1,15 @@
 from collections import defaultdict
+from pathlib import Path
 from typing import Dict, Iterable, Literal, Optional, Tuple, Union
 
 import anndata as ad
 import pandas as pd
 from lamin_utils import logger
+from lamindb_setup._init_instance import register_storage
+from lamindb_setup.dev import StorageSettings
 from lamindb_setup.dev._docs import doc_args
+from lamindb_setup.dev._hub_utils import get_storage_region
+from lamindb_setup.dev.upath import UPath
 from lnschema_core import Modality
 from lnschema_core.models import Dataset, Feature, FeatureSet
 from lnschema_core.types import AnnDataLike, DataLike, FieldAttr
@@ -84,11 +89,12 @@ def __init__(
             )
 
     run = get_run(run)
-    # there are exactly two ways of creating a Dataset object right now
+    # there are exactly 3 ways of creating a Dataset object right now
     # using exactly one file or using more than one file
     # init file
     if isinstance(data, (pd.DataFrame, ad.AnnData, File)):
         files = None
+        storage = None
         if isinstance(data, File):
             file = data
             if file._state.adding:
@@ -116,9 +122,23 @@ def __init__(
         if file.description is None or file.description == "tmp":
             file.description = f"See dataset {provisional_id}"  # type: ignore
         file._feature_sets = feature_sets
+        storage = None
+    # init from directory or bucket
+    elif isinstance(data, (str, Path, UPath)):
+        file = None
+        files = None
+        upath = UPath(data)
+        if not upath.is_dir:
+            raise ValueError(f"Can only pass buckets or directories, not {data}")
+        upath_str = upath.as_posix().rstrip("/")
+        region = get_storage_region(upath_str)
+        storage_settings = StorageSettings(upath_str, region)
+        storage = register_storage(storage_settings)
+        hash = None
     # init files
     else:
         file = None
+        storage = None
         if hasattr(data, "__getitem__"):
             assert isinstance(data[0], File)  # type: ignore
             files = data
@@ -144,6 +164,7 @@ def __init__(
             reference=reference,
             reference_type=reference_type,
             file=file,
+            storage=storage,
             hash=hash,
             run=run,
             version=version,
@@ -276,8 +297,9 @@ def load(
     is_run_input: Optional[bool] = None,
     **kwargs,
 ) -> DataLike:
-    _track_run_input(self, is_run_input)
+    # cannot call _track_run_input here, see comment further down
     if self.file is not None:
+        _track_run_input(self, is_run_input)
         return self.file.load()
     else:
         all_files = self.files.all()
@@ -291,9 +313,14 @@ def load(
         objects = [file.load(is_run_input=False) for file in all_files]
         file_ids = [file.id for file in all_files]
         if isinstance(objects[0], pd.DataFrame):
-            return pd.concat(objects, join=join)
+            concat_object = pd.concat(objects, join=join)
         elif isinstance(objects[0], ad.AnnData):
-            return ad.concat(objects, join=join, label="file_id", keys=file_ids)
+            concat_object = ad.concat(
+                objects, join=join, label="file_id", keys=file_ids
+            )
+        # only call it here because there might be errors during concat
+        _track_run_input(self, is_run_input)
+        return concat_object
 
 
 # docstring handled through attach_func_to_class_method
@@ -316,6 +343,14 @@ def save(self, *args, **kwargs) -> None:
     save_feature_set_links(self)
 
 
+@property  # type: ignore
+@doc_args(Dataset.path.__doc__)
+def path(self) -> Union[Path, UPath]:
+    """{}"""
+    _track_run_input(self)
+    return self.storage.path
+
+
 METHOD_NAMES = [
     "__init__",
     "from_anndata",
@@ -337,3 +372,5 @@ if _TESTING:
 
 for name in METHOD_NAMES:
     attach_func_to_class_method(name, Dataset, globals())
+
+setattr(Dataset, "path", path)

{lamindb-0.55.0 → lamindb-0.55.1}/lamindb/_file.py

@@ -85,9 +85,9 @@ def process_pathlike(
                 new_root_str = new_root.as_posix().rstrip("/")
                 region = get_storage_region(new_root_str)
                 storage_settings = StorageSettings(new_root_str, region)
-                register_storage(storage_settings)
+                storage_record = register_storage(storage_settings)
                 use_existing_storage_key = True
-                return storage_settings.record, use_existing_storage_key
+                return storage_record, use_existing_storage_key
             # if the filepath is local
             else:
                 use_existing_storage_key = False

{lamindb-0.55.0 → lamindb-0.55.1}/lamindb/_filter.py

@@ -3,10 +3,6 @@ from uuid import UUID
 
 import dj_database_url
 from django.db import connections
-from django.db.backends.postgresql.base import (
-    DatabaseWrapper as DatabaseWrapperPostgres,
-)
-from django.db.backends.sqlite3.base import DatabaseWrapper as DatabaseWrapperSQLite
 from lamindb_setup._init_instance import InstanceSettings
 from lamindb_setup._load_instance import get_owner_name_from_identifier
 from lamindb_setup.dev._hub_core import load_instance
@@ -22,11 +18,8 @@ def add_db_connection(isettings: InstanceSettings, using: str):
     db_config["TIME_ZONE"] = "UTC"
     db_config["OPTIONS"] = {}
     db_config["AUTOCOMMIT"] = True
-    if isettings.dialect == "sqlite":
-        db_wrapper = DatabaseWrapperSQLite(db_config, alias=using)
-    else:
-        db_wrapper = DatabaseWrapperPostgres(db_config, alias=using)
-    connections[using] = db_wrapper
+
+    connections.settings[using] = db_config
 
 
 def filter(Registry: Type[Registry], using: str = None, **expressions) -> QuerySet:

{lamindb-0.55.0 → lamindb-0.55.1}/lamindb/_query_manager.py

@@ -25,6 +25,16 @@ class QueryManager(models.Manager):
         >>> manager.df()
     """
 
+    def _track_run_input_manager(self):
+        if hasattr(self, "source_field_name") and hasattr(self, "target_field_name"):
+            if self.source_field_name == "dataset" and self.target_field_name == "file":
+                from lamindb.dev._data import WARNING_RUN_TRANSFORM, _track_run_input
+                from lamindb.dev._run_context import run_context
+
+                if run_context.run is None:
+                    logger.warning(WARNING_RUN_TRANSFORM)
+                _track_run_input(self.instance)
+
     def list(self, field: Optional[str] = None):
         """Populate a list with the results.
 
@@ -41,6 +51,7 @@ class QueryManager(models.Manager):
             >>> label.parents.list("name")
             ['ULabel1', 'ULabel2', 'ULabel3']
         """
+        self._track_run_input_manager()
         if field is None:
             return [item for item in self.all()]
         else:
@@ -58,15 +69,8 @@ class QueryManager(models.Manager):
 
         For `**kwargs`, see :meth:`lamindb.dev.QuerySet.df`.
         """
-        if hasattr(self, "source_field_name") and hasattr(self, "target_field_name"):
-            if self.source_field_name == "dataset" and self.target_field_name == "file":
-                from lamindb.dev._data import WARNING_RUN_TRANSFORM, _track_run_input
-                from lamindb.dev._run_context import run_context
-
-                if run_context.run is None:
-                    logger.warning(WARNING_RUN_TRANSFORM)
-                _track_run_input(self.instance)
-        return self.all()
+        self._track_run_input_manager()
+        return self.all_base_class()
 
     def __getitem__(self, item: str):
         try:
@@ -86,3 +90,10 @@ class QueryManager(models.Manager):
 setattr(models.Manager, "list", QueryManager.list)
 setattr(models.Manager, "df", QueryManager.df)
 setattr(models.Manager, "__getitem__", QueryManager.__getitem__)
+setattr(
+    models.Manager, "_track_run_input_manager", QueryManager._track_run_input_manager
+)
+# the two lines below would be easy if we could actually inherit; like this,
+# they're suboptimal
+setattr(models.Manager, "all_base_class", models.Manager.all)
+setattr(models.Manager, "all", QueryManager.all)

{lamindb-0.55.0 → lamindb-0.55.1}/lamindb/_registry.py

@@ -82,7 +82,12 @@ def __init__(orm: Registry, *args, **kwargs):
         validate_required_fields(orm, kwargs)
         from .dev._settings import settings
 
-        if settings.upon_create_search_names:
+        # do not search for names if an id is passed; this is important
+        # e.g. when synching ids from the notebook store to lamindb
+        has_consciously_provided_id = False
+        if "_has_consciously_provided_id" in kwargs:
+            has_consciously_provided_id = kwargs.pop("_has_consciously_provided_id")
+        if settings.upon_create_search_names and not has_consciously_provided_id:
             result = suggest_objects_with_same_name(orm, kwargs)
             if result == "object-with-same-name-exists":
                 if "version" in kwargs:
@@ -341,7 +346,7 @@ def transfer_to_default_db(record: Registry, save: bool = False):
                 record.transform_id = run_context.transform.id
             else:
                 record.transform_id = None
-        if hasattr(record, "storage_id"):
+        if hasattr(record, "storage_id") and record.storage_id is not None:
             record.storage.save()
         record._state.db = "default"
         if save:

lamindb-0.55.1/lamindb/_storage.py

@@ -0,0 +1,18 @@
+from lamindb_setup.dev._docs import doc_args
+from lamindb_setup.dev.upath import UPath, create_path
+from lnschema_core import Storage
+
+
+def root_as_path(self) -> UPath:
+    return create_path(self.root)
+
+
+@property  # type: ignore
+@doc_args(Storage.path.__doc__)
+def path(self) -> UPath:
+    """{}"""
+    return create_path(self.root)
+
+
+setattr(Storage, "root_as_path", root_as_path)
+setattr(Storage, "path", path)

{lamindb-0.55.0 → lamindb-0.55.1}/lamindb/_transform.py

@@ -44,8 +44,14 @@ def __init__(transform: Transform, *args, **kwargs):
         )
         if name is None:
             name = is_new_version_of.name
+
+    # this is only because the user-facing constructor allows passing an id
+    # most others don't
     if id is None:
+        has_consciously_provided_id = False
         id = new_id
+    else:
+        has_consciously_provided_id = True
     super(Transform, transform).__init__(
         id=id,
         name=name,
@@ -54,6 +60,7 @@ def __init__(transform: Transform, *args, **kwargs):
         version=version,
         initial_version_id=initial_version_id,
         reference=reference,
+        _has_consciously_provided_id=has_consciously_provided_id,
     )
 
 

{lamindb-0.55.0 → lamindb-0.55.1}/lamindb/dev/_label_manager.py

@@ -127,4 +127,7 @@ class LabelManager:
             labels_list = labels.list()
             for label in labels_list:
                 transfer_to_default_db(label, save=True)
-            getattr(self._host, related_name).add(*labels_list)
+            # this should not occur as file and dataset should have the same attributes
+            # but this might not be true for custom schema
+            if hasattr(self._host, related_name):
+                getattr(self._host, related_name).add(*labels_list)

{lamindb-0.55.0 → lamindb-0.55.1}/pyproject.toml

@@ -15,9 +15,9 @@ classifiers = [
 ]
 dependencies = [
     # Lamin PINNED packages
-    "lnschema_core==0.49.2",
-    "lamindb_setup==0.54.2",
-    "lamin_utils==0.11.3",
+    "lnschema_core==0.50.0",
+    "lamindb_setup==0.54.3",
+    "lamin_utils==0.11.4",
     # others
     "rapidfuzz",
     "pyarrow",
@@ -59,7 +59,7 @@ zarr = [
     "zarr>=2.16.0",
 ]
 fcs = [
-    "readfcs>=1.1.5",
+    "readfcs>=1.1.7",
 ]
 erdiagram = [
     "django-schema-graph",

{lamindb-0.55.0 → lamindb-0.55.1}/sub/lamindb-setup/docs/changelog.md

@@ -3,6 +3,9 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🚸 Allow saving notebooks of other users | [547](https://github.com/laminlabs/lamindb-setup/pull/547) | [falexwolf](https://github.com/falexwolf) | 2023-10-04 | 0.54.3
+🔊 Add more logging | [546](https://github.com/laminlabs/lamindb-setup/pull/546) | [falexwolf](https://github.com/falexwolf) | 2023-10-04 |
+🔒 Enforce compatibility with lamin-vault 0.0.7 | [545](https://github.com/laminlabs/lamindb-setup/pull/545) | [fredericenard](https://github.com/fredericenard) | 2023-10-03 |
 🐛 Prevent using vault by default when loading an instance | [544](https://github.com/laminlabs/lamindb-setup/pull/544) | [fredericenard](https://github.com/fredericenard) | 2023-10-03 | 0.54.2
 🚸 Do not use vault for SQLite instances | [543](https://github.com/laminlabs/lamindb-setup/pull/543) | [falexwolf](https://github.com/falexwolf) | 2023-10-02 | 0.54.2
 ✅ Complete notebook tests | [542](https://github.com/laminlabs/lamindb-setup/pull/542) | [falexwolf](https://github.com/falexwolf) | 2023-10-02 | 0.54.1

{lamindb-0.55.0 → lamindb-0.55.1}/sub/lamindb-setup/lamindb_setup/__init__.py

@@ -41,7 +41,7 @@ Developer API.
 """
 
 
-__version__ = "0.54.2"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.54.3"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import sys
 from os import name as _os_name

{lamindb-0.55.0 → lamindb-0.55.1}/sub/lamindb-setup/lamindb_setup/_init_instance.py

@@ -37,6 +37,7 @@ def register_storage(ssettings: StorageSettings):
     )
     if created:
         logger.save(f"saved: {storage}")
+    return storage
 
 
 def register_user(usettings):

{lamindb-0.55.0 → lamindb-0.55.1}/sub/lamindb-setup/lamindb_setup/_load_instance.py

@@ -3,8 +3,8 @@ from typing import Optional, Union
 from uuid import UUID
 
 from lamin_utils import logger
-
 from lamindb_setup.dev.upath import UPath
+
 from ._close import close as close_instance
 from ._init_instance import load_from_isettings
 from ._settings import InstanceSettings, settings
@@ -12,10 +12,7 @@ from ._silence_loggers import silence_loggers
 from .dev._settings_load import load_instance_settings
 from .dev._settings_storage import StorageSettings
 from .dev._settings_store import instance_settings_file
-from .dev.cloud_sqlite_locker import (
-    unlock_cloud_sqlite_upon_exception,
-)
-
+from .dev.cloud_sqlite_locker import unlock_cloud_sqlite_upon_exception
 
 # this is for testing purposes only
 # set to True only to test failed load
@@ -144,25 +141,19 @@ def get_db_from_vault(instance_result):
         from lamin_vault.client.postgres._get_db_from_vault import (
             get_db_from_vault as get_db_from_vault_base,
         )
-        from lamin_vault.client.postgres._connection_config_db_exists import (
-            connection_config_db_exists,
-        )
 
         vault_client = create_vault_authenticated_client(
-            access_token=settings.user.access_token,
+            access_token=settings.user.access_token, instance_id=instance_result["id"]
         )
-        config_db_exists = connection_config_db_exists(
-            vault_client, instance_result["id"]
+        return get_db_from_vault_base(
+            vault_client=vault_client,
+            scheme=instance_result["db_scheme"],
+            host=instance_result["db_host"],
+            port=instance_result["db_port"],
+            name=instance_result["db_database"],
+            role=f'{instance_result["id"]}-{settings.user.uuid}-db',
         )
-        if config_db_exists:
-            return get_db_from_vault_base(
-                vault_client=vault_client,
-                scheme=instance_result["db_scheme"],
-                host=instance_result["db_host"],
-                port=instance_result["db_port"],
-                name=instance_result["db_database"],
-                role=f'{instance_result["id"]}-{settings.user.uuid}-db',
-            )
+
     except Exception:
         logger.warning("Failed to connect to vault!")
     return None

{lamindb-0.55.0 → lamindb-0.55.1}/sub/lamindb-setup/lamindb_setup/_notebook.py

@@ -12,17 +12,22 @@ def update_notebook_metadata(nb, notebook_path):
     from nbproject.dev import write_notebook
     from nbproject.dev._initialize import nbproject_id
 
+    stem_id = nb.metadata["nbproject"]["id"]
+    current_version = nb.metadata["nbproject"]["version"]
+    logger.info(
+        f"the notebook {notebook_path} is already tracked (stem_id='{stem_id}',"
+        f" version: '{current_version}')"
+    )
     updated = False
     # ask for generating new id
     if os.getenv("LAMIN_TESTING") is None:
-        response = input("Do you want to generate a new id? (y/n) ")
+        response = input("Do you want to generate a new id prefix? (y/n) ")
     else:
         response = "y"
     if response == "y":
         nb.metadata["nbproject"]["id"] = nbproject_id()
         updated = True
     else:
-        current_version = nb.metadata["nbproject"]["version"]
         response = input(
             f"The current version is '{current_version}' - do you want to set a new"
             " version? (y/n) "
@@ -52,7 +57,6 @@ def track(notebook_path: str, pypackage: Optional[str] = None) -> None:
         write_notebook(nb, notebook_path)
         logger.success("attached notebook id to ipynb file")
     else:
-        logger.info(f"the notebook {notebook_path} is already tracked")
         update_notebook_metadata(nb, notebook_path)
     return None
 
@@ -102,19 +106,21 @@ def save(notebook_path: str) -> Optional[str]:
     transform_family = ln.Transform.filter(id__startswith=meta_store.id).all()
     if len(transform_family) == 0:
         logger.error(
-            "didn't find notebook in transform registry, did you run ln.track() in it?"
+            f"Didn't find notebook with stem_id {meta_store.id} (12 initial characters)"
+            " in transform registry, did you run ln.track() in it?"
         )
         return "not-tracked-in-transform-registry"
     # the specific version
     transform = transform_family.filter(version=transform_version).one()
     # latest run of this transform by user
-    run = (
-        ln.Run.filter(
-            transform=transform, created_by__id=lamindb_setup.settings.user.id
+    run = ln.Run.filter(transform=transform).order_by("-run_at").first()
+    if run.created_by.id != lamindb_setup.settings.user.id:
+        response = input(
+            "You are trying to save a notebook created by another user: Source and"
+            " report files will be tagged with *your* user id. Proceed? (y/n)"
         )
-        .order_by("-run_at")
-        .first()
-    )
+        if response != "y":
+            return "aborted-save-notebook-created-by-different-user"
     # convert the notebook file to html
     notebook_path_html = notebook_path.replace(".ipynb", ".html")
     logger.info(f"exporting notebook as html {notebook_path_html}")

{lamindb-0.55.0 → lamindb-0.55.1}/sub/lamindb-setup/pyproject.toml

@@ -19,7 +19,7 @@ dependencies = [
     "universal_pathlib==0.1.1",  # is still experimental, need pinning
     "botocore<2.0.0",
     "supabase==1.0.3",
-    "lamin_vault",
+    "lamin_vault==0.0.7",
 ]
 
 [project.urls]

{lamindb-0.55.0 → lamindb-0.55.1}/sub/lamindb-setup/tests/notebooks/test.py

@@ -74,10 +74,7 @@ def test_save_consecutive():
         env=env,
     )
     assert result.returncode == 1
-    assert (
-        "didn't find notebook in transform registry, did you run ln.track() in it?"
-        in result.stdout.decode()
-    )
+    assert "Didn't find notebook with stem_id" in result.stdout.decode()
 
     # now, let's re-run this notebook so that ln.track() is actually run
     nbproject_test.execute_notebooks(notebook_path)