lamindb 0.66.1__tar.gz → 0.67.1__tar.gz

{lamindb-0.66.1 → lamindb-0.67.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.66.1
+Version: 0.67.1
 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==0.61.0
-Requires-Dist: lamindb_setup==0.64.1
+Requires-Dist: lnschema_core==0.61.1
+Requires-Dist: lamindb_setup==0.64.2
 Requires-Dist: lamin_utils==0.13.0
-Requires-Dist: lamin_cli==0.6.0
+Requires-Dist: lamin_cli==0.6.1
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -28,7 +28,7 @@ Requires-Dist: boto3==1.28.17 ; extra == "aws"
 Requires-Dist: aiobotocore==2.5.4 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.9.0 ; extra == "aws"
 Requires-Dist: s3fs>=2023.9.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.37.2 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.39.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
@@ -42,7 +42,7 @@ Requires-Dist: lamin_vault ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 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: nbproject==0.10.0 ; extra == "jupyter"
 Requires-Dist: nbstripout ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"

{lamindb-0.66.1 → lamindb-0.67.1}/docs/annotate.ipynb

@@ -311,7 +311,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "organism = lb.Organism.from_bionty(name=external_meta[\"organism\"])\n",
+    "organism = lb.Organism.from_public(name=external_meta[\"organism\"])\n",
     "organism.save()\n",
     "organism"
    ]
@@ -322,7 +322,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assay = lb.ExperimentalFactor.from_bionty(name=external_meta[\"assay\"])\n",
+    "assay = lb.ExperimentalFactor.from_public(name=external_meta[\"assay\"])\n",
     "assay.save()\n",
     "assay"
    ]

{lamindb-0.66.1 → lamindb-0.67.1}/docs/bio-registries.ipynb

@@ -24,7 +24,7 @@
     "\n",
     "In LaminDB, registries are standard SQL tables, equipped with [mechanisms that avoid typos & duplicated data](/faq/idempotency).\n",
     "\n",
-    "In addition, LaminDB makes it easy to import records from public ontologies, based on plug-in {mod}`lnschema_bionty`.\n",
+    "In addition, LaminDB makes it easy to import records from public biological ontologies, based on plug-in {mod}`lnschema_bionty`.\n",
     "\n",
     "In this notebook, you'll see how to manage an in-house ontology anchored in public knowledge.\n",
     "\n",
@@ -43,7 +43,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Let us create an instance that has {mod}`lnschema_bionty` mounted:"
+    "Let us create an instance that has {mod}`lnschema_bionty` mounted, which extends to include biological registries:"
    ]
   },
   {
@@ -95,8 +95,8 @@
    },
    "outputs": [],
    "source": [
-    "lb.Organism.from_bionty(name=\"human\").save()\n",
-    "lb.CellType.from_bionty(name=\"T cell\").save()\n",
+    "lb.Organism.from_public(name=\"human\").save()\n",
+    "lb.CellType.from_public(name=\"T cell\").save()\n",
     "lb.CellType(name=\"my T cell subtype\").save()"
    ]
   },
@@ -115,13 +115,11 @@
    "source": [
     "We start with a public ontology for cell types.\n",
     "\n",
-    "[Bionty](https://lamin.ai/docs/bionty/bionty.bionty) - short for \"biological entity\" - is a class for accessing public ontologies.\n",
+    "`.public()` gives you access to the `ReferenceTable`, a class for accessing public ontologies.\n",
     "\n",
-    "Bionty provides simple access to curated public ontologies that Lamin hosts for reliable and performant access. For most Bionty objects, you can access the underlying ontology through [Pronto](https://github.com/althonos/pronto).\n",
+    "`ReferenceTable` provides simple access to curated public ontologies that Lamin hosts for reliable and performant access. For most `ReferenceTable` objects, you can access the underlying ontology through [Pronto](https://github.com/althonos/pronto).\n",
     "\n",
-    "(If you don't need to manage in-house registries, you can also use the [bionty](https://lamin.ai/docs/bionty) package standalone.)\n",
-    "\n",
-    "Let's create a `Bionty` object:"
+    "Let's create a `ReferenceTable` object:"
    ]
   },
   {
@@ -134,7 +132,7 @@
    },
    "outputs": [],
    "source": [
-    "bionty = lb.CellType.bionty()"
+    "public = lb.CellType.public()"
    ]
   },
   {
@@ -143,7 +141,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "bionty"
+    "public"
    ]
   },
   {
@@ -160,7 +158,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "bionty.search(\"gamma delta T cell\").head(3)"
+    "public.search(\"gamma delta T cell\").head(3)"
    ]
   },
   {
@@ -177,7 +175,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lookup = bionty.lookup()\n",
+    "lookup = public.lookup()\n",
     "lookup.gamma_delta_t_cell"
    ]
   },
@@ -206,11 +204,20 @@
     "gdt_cell = lb.CellType(lookup.gamma_delta_t_cell)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "gdt_cell"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "(Alternatively, we could construct the gamma delta T cell via {meth}`~lnschema_bionty.dev.BioRegistry.from_bionty`, which is synonyms-aware.)"
+    "(Alternatively, we could construct the gamma delta T cell via {meth}`~lnschema_bionty.dev.BioRegistry.from_public`, which is synonyms-aware.)"
    ]
   },
   {
@@ -219,7 +226,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "gdt_cell"
+    "lb.CellType.from_public(ontology_id=\"CL:0000798\")"
    ]
   },
   {
@@ -405,7 +412,7 @@
     "\n",
     "1. If registry records match the values, load these records\n",
     "2. If values match synonyms of registry records, load these records\n",
-    "3. (`lnschema_bionty`-only) If no record in the registry matches, attempt to load records from a public reference through Bionty\n",
+    "3. (`lnschema_bionty`-only) If no record in the registry matches, attempt to load records from a public reference\n",
     "4. (`lnschema_bionty`-only) Same as 3. but based on synonyms\n",
     "\n",
     "No records will be returned if input field values aren't mappable.\n",
@@ -416,9 +423,9 @@
     "celltype_names = [\n",
     "    \"gamma-delta T cell\",  # existing record with the same name\n",
     "    \"T lymphocyte\",  # existing record with synonym\n",
-    "    \"hepatocyte\",  # Bionty record with the same name\n",
-    "    \"HSC\",  # Bionty record with synonym\n",
-    "    \"my new cell type\",  # Not exist in DB, not exist in Bionty\n",
+    "    \"hepatocyte\",  # public record with the same name\n",
+    "    \"HSC\",  # public record with synonym\n",
+    "    \"my new cell type\",  # Not exist in in-house registry, not exist in public reference\n",
     "]\n",
     "lb.CellType.from_values(celltype_names)\n",
     "```\n",
@@ -699,7 +706,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lb.Gene.from_bionty(symbol=\"TCF7\", organism=\"human\")"
+    "lb.Gene.from_public(symbol=\"TCF7\", organism=\"human\")"
    ]
   },
   {
@@ -751,7 +758,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lb.Gene.from_bionty(symbol=\"Ap5b1\")"
+    "lb.Gene.from_public(symbol=\"Ap5b1\")"
    ]
   },
   {
@@ -780,7 +787,7 @@
    },
    "outputs": [],
    "source": [
-    "lb.BiontySource.filter(currently_used=True).df()"
+    "lb.PublicSource.filter(currently_used=True).df()"
    ]
   },
   {
@@ -788,7 +795,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Each record is linked to a versioned bionty source (if it was created from bionty):"
+    "Each record is linked to a versioned public source (if it was created from public):"
    ]
   },
   {
@@ -798,7 +805,7 @@
    "outputs": [],
    "source": [
     "hepatocyte = lb.CellType.filter(name=\"hepatocyte\").one()\n",
-    "hepatocyte.bionty_source"
+    "hepatocyte.public_source"
    ]
   },
   {
@@ -807,7 +814,7 @@
    "source": [
     "## Create records from specific public ontologies\n",
     "\n",
-    "By default, records are created from the `\"currently_used\"` Bionty sources which are configured during the instance initialization, e.g.:"
+    "By default, records are created from the `\"currently_used\"` public sources which are configured during the instance initialization, e.g.:"
    ]
   },
   {
@@ -816,7 +823,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lb.Phenotype.bionty()"
+    "lb.Phenotype.public()"
    ]
   },
   {
@@ -838,8 +845,8 @@
    },
    "outputs": [],
    "source": [
-    "bionty_source = lb.BiontySource.filter(entity=\"Organism\", source=\"ncbitaxon\").one()\n",
-    "iris_setosa = lb.Organism.from_bionty(name=\"iris setosa\", bionty_source=bionty_source)\n",
+    "public_source = lb.PublicSource.filter(entity=\"Organism\", source=\"ncbitaxon\").one()\n",
+    "iris_setosa = lb.Organism.from_public(name=\"iris setosa\", public_source=public_source)\n",
     "iris_setosa.save()"
    ]
   },
@@ -858,7 +865,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "iris_setosa.bionty_source"
+    "iris_setosa.public_source"
    ]
   },
   {
@@ -874,7 +881,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Analogously, you can pass `bionty_source` to bulk-create records from a non-default source:"
+    "Analogously, you can pass `public_source` to bulk-create records from a non-default source:"
    ]
   },
   {
@@ -888,7 +895,7 @@
    "outputs": [],
    "source": [
     "records = lb.Organism.from_values(\n",
-    "    [\"iris setosa\", \"iris versicolor\", \"iris virginica\"], bionty_source=bionty_source\n",
+    "    [\"iris setosa\", \"iris versicolor\", \"iris virginica\"], public_source=public_source\n",
     ")\n",
     "ln.save(records)"
    ]

{lamindb-0.66.1 → lamindb-0.67.1}/docs/changelog.md

@@ -5,6 +5,20 @@
 .. role:: small
 ```
 
+## 0.67
+
+### 0.67.1 {small}`2024-01-12`
+
+- 🐛 Fix idempotency of `collection.save()` [PR](https://github.com/laminlabs/lamindb/pull/1401) [@falexwolf](https://github.com/falexwolf)
+- 🩹 Also amend run [PR](https://github.com/laminlabs/lamindb/pull/1399) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Disallow bulk-delete for Artifact, Transform & Collection [PR](https://github.com/laminlabs/lamindb/pull/1398) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Init transform versions at 1 [PR](https://github.com/laminlabs/lamindb/pull/1397) [@falexwolf](https://github.com/falexwolf)
+- ✨ Load json and html files [PR](https://github.com/laminlabs/lamindb/pull/1396) [@falexwolf](https://github.com/falexwolf)
+
+### 0.67.0 {small}`2024-01-11`
+
+- 🚚 Rename `.bionty` to `.public`, `.from_bionty` to `.from_public` [PR](https://github.com/laminlabs/lamindb/pull/1394) [@sunnyosun](https://github.com/sunnyosun)
+
 ## 0.66
 
 ### 0.66.1 {small}`2024-01-09`

{lamindb-0.66.1 → lamindb-0.67.1}/docs/introduction.ipynb

@@ -751,7 +751,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lb.Tissue.bionty().search(\"umbilical blood\").head(2)"
+    "lb.Tissue.public().search(\"umbilical blood\").head(2)"
    ]
   },
   {
@@ -769,7 +769,7 @@
    },
    "outputs": [],
    "source": [
-    "tissue = lb.Tissue.from_bionty(name=\"umbilical cord blood\")\n",
+    "tissue = lb.Tissue.from_public(name=\"umbilical cord blood\")\n",
     "tissue.save()\n",
     "tissue.view_parents(distance=2)"
    ]
@@ -897,7 +897,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lb.Gene.from_bionty(symbol=\"CD38\", organism=\"human\").save()\n",
+    "lb.Gene.from_public(symbol=\"CD38\", organism=\"human\").save()\n",
     "artifact2 = ln.Artifact.from_anndata(\n",
     "    adata, description=\"my RNA-seq batch 2\", field=lb.Gene.symbol, organism=\"human\"\n",
     ")\n",
@@ -1038,7 +1038,7 @@
     "import lnschema_bionty as lb\n",
     "\n",
     "# create an ontology-coupled cell type record and save it\n",
-    "lb.CellType.from_bionty(name=\"neuron\").save()\n",
+    "lb.CellType.from_public(name=\"neuron\").save()\n",
     "\n",
     "# create a record to track a new cell state\n",
     "new_cell_state = lb.CellType(name=\"my neuron cell state\", description=\"explains X\")\n",

{lamindb-0.66.1 → lamindb-0.67.1}/docs/transfer.ipynb

@@ -167,11 +167,11 @@
    "name": "python3"
   },
   "language_info": {
-   "artifact_extension": ".py",
    "codemirror_mode": {
     "name": "ipython",
     "version": 3
    },
+   "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",

{lamindb-0.66.1 → lamindb-0.67.1}/docs/validate.ipynb

@@ -38,7 +38,7 @@
     "\n",
     "{class}`~lamindb.dev.CanValidate` methods validate against the registries in your LaminDB instance.\n",
     "\n",
-    "In {doc}`./bio-registries`, you'll see how to extend standard validation to validation against _public references_ using a {meth}`~lnschema_bionty.dev.BioRegistry.bionty` ontology object: `bionty_object = Registry.bionty()`.\n",
+    "In {doc}`./bio-registries`, you'll see how to extend standard validation to validation against _public references_ using a `ReferenceTable` ontology object: `public = Registry.public()`.\n",
     "\n",
     "By default, {meth}`~lamindb.dev.Registry.from_values` considers a match in a public reference a validated value for any {mod}`lnschema_bionty` entity.\n",
     "\n",
@@ -114,7 +114,7 @@
     "ln.Artifact(df, description=\"test data\").save()\n",
     "ln.ULabel(name=\"Project A\").save()\n",
     "ln.ULabel(name=\"Project B\").save()\n",
-    "lb.Disease.from_bionty(ontology_id=\"MONDO:0004975\").save()"
+    "lb.Disease.from_public(ontology_id=\"MONDO:0004975\").save()"
    ]
   },
   {
@@ -153,7 +153,7 @@
    "source": [
     "Bulk creating records using {meth}`~lamindb.dev.Registry.from_values` only returns validated records:\n",
     "\n",
-    "Note: Bionty-validated terms are also created with `.from_values`, see {doc}`/bio-registries` for details."
+    "Note: Terms validated with public reference are also created with `.from_values`, see {doc}`/bio-registries` for details."
    ]
   },
   {

{lamindb-0.66.1 → lamindb-0.67.1}/lamindb/__init__.py

@@ -54,7 +54,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.66.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.67.1"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 
@@ -102,20 +102,20 @@ if _INSTANCE_SETUP:
         User,
     )
 
-    File = Artifact  # backward compat
-    from . import _artifact  # noqa
-    from . import _collection
-    from . import _feature
-    from . import _feature_set
-    from . import _parents
-    from . import _registry
-    from . import _run
-    from . import _storage
-    from . import _transform
-    from . import _ulabel
-    from . import _validate
-    from . import dev
-    from ._delete import delete
+    from . import (
+        _artifact,
+        _collection,
+        _feature,
+        _feature_set,
+        _parents,
+        _registry,
+        _run,
+        _storage,
+        _transform,
+        _ulabel,
+        _validate,
+        dev,
+    )
     from ._save import save
     from ._view import view
     from .dev._run_context import run_context

{lamindb-0.66.1 → lamindb-0.67.1}/lamindb/_artifact.py

@@ -911,13 +911,13 @@ def delete(
     self, permanent: Optional[bool] = None, storage: Optional[bool] = None
 ) -> None:
     # by default, we only move artifacts into the trash
-    if self.visibility > VisibilityChoice.trash.value and permanent is not True:
+    if self.visibility > -1 and permanent is not True:
         if storage is not None:
             logger.warning("moving artifact to trash, storage arg is ignored")
         # move to trash
-        self.visibility = VisibilityChoice.trash.value
+        self.visibility = -1
         self.save()
-        logger.warning("moved artifact to trash")
+        logger.warning("moved artifact to trash (visibility = -1)")
         return
 
     # if the artifact is already in the trash
@@ -929,6 +929,7 @@ def delete(
         )
         delete_record = response == "y"
     else:
+        # this second option doesn't feel very intuitive
         delete_record = permanent
 
     if delete_record:

{lamindb-0.66.1 → lamindb-0.67.1}/lamindb/_collection.py

@@ -424,8 +424,12 @@ def save(self, *args, **kwargs) -> None:
         self.artifact.save()
     # we don't need to save feature sets again
     save_feature_sets(self)
+    state_was_adding = self._state.adding
     super(Collection, self).save()
-    if hasattr(self, "_artifacts"):
+    # we don't allow updating the collection of artifacts
+    # if users want to update the set of artifacts, they
+    # have to create a new collection
+    if state_was_adding and hasattr(self, "_artifacts"):
         if self._artifacts is not None and len(self._artifacts) > 0:
             links = [
                 CollectionArtifact(collection_id=self.id, artifact_id=artifact.id)

{lamindb-0.66.1 → lamindb-0.67.1}/lamindb/_from_values.py

@@ -14,7 +14,7 @@ def get_or_create_records(
     iterable: ListLike,
     field: StrField,
     *,
-    from_bionty: bool = False,
+    from_public: bool = False,
     **kwargs,
 ) -> List[Registry]:
     """Get or create records from iterables."""
@@ -32,14 +32,14 @@ def get_or_create_records(
 
         # new records to be created based on new values
         if len(nonexist_values) > 0:
-            if from_bionty:
-                records_bionty, unmapped_values = create_records_from_bionty(
+            if from_public:
+                records_bionty, unmapped_values = create_records_from_public(
                     iterable_idx=nonexist_values, field=field, msg=msg, **kwargs
                 )
                 if len(records_bionty) > 0:
                     msg = ""
                 for record in records_bionty:
-                    record._from_bionty = True
+                    record._from_public = True
                 records += records_bionty
             else:
                 unmapped_values = nonexist_values
@@ -81,8 +81,8 @@ def get_existing_records(
     model = field.field.model
     condition: Dict = {} if len(kwargs) == 0 else kwargs.copy()
     # existing records matching is agnostic to the bionty source
-    if "bionty_source" in condition:
-        condition.pop("bionty_source")
+    if "public_source" in condition:
+        condition.pop("public_source")
 
     if _has_organism_field(model):
         from lnschema_bionty._bionty import create_or_get_organism_record
@@ -160,7 +160,7 @@ def get_existing_records(
     return records, nonexist_values, msg
 
 
-def create_records_from_bionty(
+def create_records_from_public(
     iterable_idx: pd.Index,
     field: StrField,
     msg: str = "",
@@ -169,24 +169,24 @@ def create_records_from_bionty(
     model = field.field.model
     records: List = []
     # populate additional fields from bionty
-    from lnschema_bionty._bionty import get_bionty_source_record
+    from lnschema_bionty._bionty import get_public_source_record
 
     # create the corresponding bionty object from model
     try:
-        bionty_object = model.bionty(
-            organism=kwargs.get("organism"), bionty_source=kwargs.get("bionty_source")
+        public_ontology = model.public(
+            organism=kwargs.get("organism"), public_source=kwargs.get("public_source")
         )
     except Exception:
         # for custom records that are not created from bionty sources
         return records, iterable_idx
-    # add bionty_source record to the kwargs
-    kwargs.update({"bionty_source": get_bionty_source_record(bionty_object)})
+    # add public_source record to the kwargs
+    kwargs.update({"public_source": get_public_source_record(public_ontology)})
 
     # filter the columns in bionty df based on fields
-    bionty_df = _filter_bionty_df_columns(model=model, bionty_object=bionty_object)
+    bionty_df = _filter_bionty_df_columns(model=model, public_ontology=public_ontology)
 
     # standardize in the bionty reference
-    result = bionty_object.inspect(iterable_idx, field=field.field.name, mute=True)
+    result = public_ontology.inspect(iterable_idx, field=field.field.name, mute=True)
     syn_mapper = result.synonyms_mapper
 
     msg_syn: str = ""
@@ -254,13 +254,13 @@ def _print_values(names: List, n: int = 20) -> str:
     return print_values
 
 
-def _filter_bionty_df_columns(model: Registry, bionty_object: Any) -> pd.DataFrame:
+def _filter_bionty_df_columns(model: Registry, public_ontology: Any) -> pd.DataFrame:
     bionty_df = pd.DataFrame()
-    if bionty_object is not None:
+    if public_ontology is not None:
         model_field_names = {i.name for i in model._meta.fields}
         # parents needs to be added here as relationships aren't in fields
         model_field_names.add("parents")
-        bionty_df = bionty_object.df().reset_index()
+        bionty_df = public_ontology.df().reset_index()
         if model.__name__ == "Gene":
             # groupby ensembl_gene_id and concat ncbi_gene_ids
             groupby_id_col = (

{lamindb-0.66.1 → lamindb-0.67.1}/lamindb/_query_manager.py

@@ -46,14 +46,11 @@ class QueryManager(models.Manager):
 
         Examples:
             >>> ln.save(ln.ULabel.from_values(["ULabel1", "ULabel2", "ULabel3"], field="name"))
-            >>> labels = ln.ULabel.filter(name__icontains = "label").all()
+            >>> labels = ln.ULabel.filter(name__icontains="label").all()
             >>> ln.ULabel(name="ULabel1").save()
             >>> label = ln.ULabel.filter(name="ULabel1").one()
             >>> label.parents.set(labels)
             >>> label.parents.list()
-            [ULabel(id=sFMcPepC, name=ULabel1, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
-            ULabel(id=2SscQvsM, name=ULabel2, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
-            ULabel(id=lecV87vi, name=ULabel3, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse)] # noqa
             >>> label.parents.list("name")
             ['ULabel1', 'ULabel2', 'ULabel3']
         """
@@ -76,7 +73,7 @@ class QueryManager(models.Manager):
         For `**kwargs`, see :meth:`lamindb.dev.QuerySet.df`.
         """
         self._track_run_input_manager()
-        return self.all_base_class()
+        return self._all_base_class()
 
     @doc_args(Registry.search.__doc__)
     def search(self, string: str, **kwargs):
@@ -115,5 +112,5 @@ models.Manager.__getitem__ = QueryManager.__getitem__
 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
-models.Manager.all_base_class = models.Manager.all
+models.Manager._all_base_class = models.Manager.all
 models.Manager.all = QueryManager.all

{lamindb-0.66.1 → lamindb-0.67.1}/lamindb/_query_set.py

@@ -4,7 +4,14 @@ from typing import Dict, Iterable, List, NamedTuple, Optional, Union
 import pandas as pd
 from django.db import models
 from lamindb_setup.dev._docs import doc_args
-from lnschema_core.models import CanValidate, IsTree, Registry
+from lnschema_core.models import (
+    Artifact,
+    CanValidate,
+    Collection,
+    IsTree,
+    Registry,
+    Transform,
+)
 from lnschema_core.types import ListLike, StrField
 
 
@@ -147,6 +154,13 @@ class QuerySet(models.QuerySet, CanValidate, IsTree):
                 df.rename(columns={values_expression: expression}, inplace=True)
         return df
 
+    def delete(self, *args, **kwargs):
+        if self.model in {Artifact, Collection, Transform}:
+            for record in self:
+                record.delete(*args, **kwargs)
+        else:
+            self._delete_base_class(*args, **kwargs)
+
     def list(self, field: Optional[str] = None) -> List[Registry]:
         """Populate a list with the results.
 
@@ -282,3 +296,5 @@ models.QuerySet.lookup = QuerySet.lookup
 models.QuerySet.validate = QuerySet.validate
 models.QuerySet.inspect = QuerySet.inspect
 models.QuerySet.standardize = QuerySet.standardize
+models.QuerySet._delete_base_class = models.QuerySet.delete
+models.QuerySet.delete = QuerySet.delete

{lamindb-0.66.1 → lamindb-0.67.1}/lamindb/_registry.py

@@ -129,12 +129,12 @@ def from_values(
     cls, values: ListLike, field: Optional[StrField] = None, **kwargs
 ) -> List["Registry"]:
     """{}."""
-    from_bionty = True if cls.__module__.startswith("lnschema_bionty.") else False
+    from_public = True if cls.__module__.startswith("lnschema_bionty.") else False
     field_str = get_default_str_field(cls, field=field)
     return get_or_create_records(
         iterable=values,
         field=getattr(cls, field_str),
-        from_bionty=from_bionty,
+        from_public=from_public,
         **kwargs,
     )
 
@@ -412,7 +412,7 @@ def update_fk_to_default_db(
 def transfer_fk_to_default_db_bulk(records: Union[List, QuerySet]):
     for fk in [
         "organism",
-        "bionty_source",
+        "public_source",
         "initial_version",
         "latest_report",  # Transform
         "source_code",  # Transform