lamindb 0.74.2__py3-none-any.whl → 0.74.3__py3-none-any.whl

lamindb/__init__.py

@@ -42,7 +42,7 @@ Modules & settings:
 """
 
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "0.74.2"
+__version__ = "0.74.3"
 
 import os as _os
 

lamindb/_record.py

@@ -529,12 +529,7 @@ def save(self, *args, **kwargs) -> Record:
     if result is not None:
         init_self_from_db(self, result)
     else:
-        # here, we can't use the parents argument
-        # parents are not saved for the self record
-        save_kwargs = kwargs.copy()
-        if "parents" in save_kwargs:
-            save_kwargs.pop("parents")
-        super(Record, self).save(*args, **save_kwargs)
+        super(Record, self).save(*args, **kwargs)
     # perform transfer of many-to-many fields
     # only supported for Artifact and Collection records
     if db is not None and db != "default" and using_key is None:
@@ -554,16 +549,8 @@ def save(self, *args, **kwargs) -> Record:
             self_on_db._state.db = db
             self_on_db.pk = pk_on_db  # manually set the primary key
             self_on_db.features = FeatureManager(self_on_db)
-            # by default, transfer parents of the labels to maintain ontological hierarchy
-            try:
-                import bionty as bt
-
-                parents = kwargs.get("parents", bt.settings.auto_save_parents)
-            except ImportError:
-                parents = kwargs.get("parents", True)
-            add_from_kwargs = {"parents": parents}
-            self.features._add_from(self_on_db, **add_from_kwargs)
-            self.labels.add_from(self_on_db, **add_from_kwargs)
+            self.features._add_from(self_on_db)
+            self.labels.add_from(self_on_db)
     return self
 
 

lamindb/_save.py

@@ -27,9 +27,7 @@ if TYPE_CHECKING:
     from lamindb_setup.core.upath import UPath
 
 
-def save(
-    records: Iterable[Record], ignore_conflicts: bool | None = False, **kwargs
-) -> None:
+def save(records: Iterable[Record], ignore_conflicts: bool | None = False) -> None:
     """Bulk save to registries & storage.
 
     Note:
@@ -47,7 +45,6 @@ def save(
            unique or another constraint. However, it won't inplace update the id
            fields of records. If you need records with ids, you need to query
            them from the database.
-        **kwargs: Get kwargs related to parents.
 
     Examples:
 
@@ -87,27 +84,12 @@ def save(
         non_artifacts_with_parents = [
             r for r in non_artifacts_new if hasattr(r, "_parents")
         ]
-        if len(non_artifacts_with_parents) > 0 and kwargs.get("parents") is not False:
+        if len(non_artifacts_with_parents) > 0:
             # this can only happen within lnschema_bionty right now!!
             # we might extend to core lamindb later
-            import bionty as bt
-
-            if kwargs.get("parents") or (
-                kwargs.get("parents") is None and bt.settings.auto_save_parents
-            ):
-                mute = False if kwargs.get("mute") is None else kwargs.get("mute")
-                if not mute:
-                    # save the record with parents one by one
-                    logger.warning(
-                        "now recursing through parents: "
-                        "this only happens once, but is much slower than bulk saving"
-                    )
-                    logger.hint(
-                        "you can switch this off via: bt.settings.auto_save_parents ="
-                        " False"
-                    )
-                for record in non_artifacts_with_parents:
-                    record._save_ontology_parents(mute=True)
+            from lnschema_bionty.core import add_ontology
+
+            add_ontology(non_artifacts_with_parents)
 
     if artifacts:
         with transaction.atomic():

lamindb/core/_feature_manager.py

@@ -770,7 +770,7 @@ def _add_set_from_mudata(
     self._host.save()
 
 
-def _add_from(self, data: HasFeatures, parents: bool = True):
+def _add_from(self, data: HasFeatures):
     """Transfer features from a artifact or collection."""
     # This only covers feature sets, though.
     using_key = settings._using_key
@@ -782,23 +782,18 @@ def _add_from(self, data: HasFeatures, parents: bool = True):
         # note here the features are transferred based on an unique field
         field = REGISTRY_UNIQUE_FIELD.get(registry.__name__.lower(), "uid")
         # TODO: get a default ID field for the registry
-        if hasattr(registry, "ontology_id") and parents:
+        if hasattr(registry, "ontology_id"):
             field = "ontology_id"
         elif hasattr(registry, "ensembl_gene_id"):
             field = "ensembl_gene_id"
         elif hasattr(registry, "uniprotkb_id"):
             field = "uniprotkb_id"
-
-        if registry.__get_name_with_schema__() == "bionty.Organism":
-            parents = False
         # this will be e.g. be a list of ontology_ids or uids
         member_uids = list(members.values_list(field, flat=True))
-        # create records from ontology_id in order to populate parents
-        if field == "ontology_id" and len(member_uids) > 0 and parents:
+        # create records from ontology_id
+        if field == "ontology_id" and len(member_uids) > 0:
             # create from bionty
-            records = registry.from_values(member_uids, field=field)
-            if len(records) > 0:
-                save(records, parents=parents)
+            save(registry.from_values(member_uids, field=field))
         validated = registry.validate(member_uids, field=field, mute=True)
         new_members_uids = list(compress(member_uids, ~validated))
         new_members = members.filter(**{f"{field}__in": new_members_uids}).all()
@@ -814,7 +809,7 @@ def _add_from(self, data: HasFeatures, parents: bool = True):
                 # in the previous step transfer_fk_to_default_db_bulk
                 transfer_to_default_db(feature, using_key, mute=mute, transfer_fk=False)
             logger.info(f"saving {n_new_members} new {registry.__name__} records")
-            save(new_members, parents=parents)
+            save(new_members)
 
         # create a new feature set from feature values using the same uid
         feature_set_self = FeatureSet.from_values(

lamindb/core/_label_manager.py

@@ -76,32 +76,28 @@ def print_labels(self: HasFeatures, field: str = "name", print_types: bool = Fal
 
 
 # Alex: is this a label transfer function?
-def validate_labels(labels: QuerySet | list | dict, parents: bool = True):
+def validate_labels(labels: QuerySet | list | dict):
     def validate_labels_registry(
-        labels: QuerySet | list | dict, parents: bool = True
+        labels: QuerySet | list | dict,
     ) -> tuple[list[str], list[str]]:
         if len(labels) == 0:
             return [], []
         registry = labels[0].__class__
         field = REGISTRY_UNIQUE_FIELD.get(registry.__name__.lower(), "uid")
-        if hasattr(registry, "ontology_id") and parents:
+        if hasattr(registry, "ontology_id"):
             field = "ontology_id"
         elif hasattr(registry, "ensembl_gene_id"):
             field = "ensembl_gene_id"
         elif hasattr(registry, "uniprotkb_id"):
             field = "uniprotkb_id"
-        if registry.__get_name_with_schema__() == "bionty.Organism":
-            parents = False
         # if the field value is None, use uid field
         label_uids = np.array(
             [getattr(label, field) for label in labels if label is not None]
         )
-        # save labels from ontology_ids so that parents are populated
+        # save labels from ontology_ids
         if field == "ontology_id" and len(label_uids) > 0:
             try:
-                records = registry.from_values(label_uids, field=field)
-                if len(records) > 0:
-                    save(records, parents=parents)
+                save(registry.from_values(label_uids, field=field))
             except Exception:  # noqa S110
                 pass
             field = "uid"
@@ -117,11 +113,9 @@ def validate_labels(labels: QuerySet | list | dict, parents: bool = True):
     if isinstance(labels, Dict):
         result = {}
         for registry, labels_registry in labels.items():
-            result[registry] = validate_labels_registry(
-                labels_registry, parents=parents
-            )
+            result[registry] = validate_labels_registry(labels_registry)
     else:
-        return validate_labels_registry(labels, parents=parents)
+        return validate_labels_registry(labels)
 
 
 class LabelManager:
@@ -176,7 +170,7 @@ class LabelManager:
 
         return get_labels(self._host, feature=feature, mute=mute, flat_names=flat_names)
 
-    def add_from(self, data: HasFeatures, parents: bool = True) -> None:
+    def add_from(self, data: HasFeatures) -> None:
         """Add labels from an artifact or collection to another artifact or collection.
 
         Examples:
@@ -202,7 +196,7 @@ class LabelManager:
                 data_name_lower = data.__class__.__name__.lower()
                 labels_by_features = defaultdict(list)
                 features = set()
-                _, new_labels = validate_labels(labels, parents=parents)
+                _, new_labels = validate_labels(labels)
                 if len(new_labels) > 0:
                     transfer_fk_to_default_db_bulk(new_labels, using_key)
                 for label in labels:
@@ -237,7 +231,7 @@ class LabelManager:
                         transfer_to_default_db(
                             feature, using_key, mute=True, transfer_fk=False
                         )
-                    save(new_features, parents=parents)
+                    save(new_features)
                 if hasattr(self._host, related_name):
                     for feature_name, labels in labels_by_features.items():
                         if feature_name is not None:

lamindb/core/datasets/_core.py

@@ -185,8 +185,6 @@ def anndata_mouse_sc_lymph_node(
 
         verbosity = ln.settings.verbosity
         ln.settings.verbosity = "error"
-        auto_save_parents = bt.settings.auto_save_parents
-        bt.settings.auto_save_parents = False
         # strain
         bt.ExperimentalFactor.from_public(ontology_id="EFO:0004472").save()
         # developmental stage
@@ -215,7 +213,6 @@ def anndata_mouse_sc_lymph_node(
             labels += [ln.ULabel(name=name) for name in adata.obs[col]]
         ln.save(labels)
         ln.settings.verbosity = verbosity
-        bt.settings.auto_save_parents = auto_save_parents
 
     return adata
 
@@ -313,8 +310,6 @@ def anndata_human_immune_cells(
 
         verbosity = ln.settings.verbosity
         ln.settings.verbosity = "error"
-        auto_save_parents = bt.settings.auto_save_parents
-        bt.settings.auto_save_parents = False
         ln.save(
             bt.Gene.from_values(
                 adata.var.index, field="ensembl_gene_id", organism="human"
@@ -331,7 +326,6 @@ def anndata_human_immune_cells(
         bt.ExperimentalFactor.from_public(ontology_id="EFO:0008913").save()
         ln.save([ln.ULabel(name=name) for name in adata.obs.donor.unique()])
         ln.settings.verbosity = verbosity
-        bt.settings.auto_save_parents = auto_save_parents
     return adata
 
 

{lamindb-0.74.2.dist-info → lamindb-0.74.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.74.2
+Version: 0.74.3
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -10,7 +10,7 @@ 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==0.74.1
+Requires-Dist: lamindb_setup==0.74.2
 Requires-Dist: lamin_utils==0.13.2
 Requires-Dist: lamin_cli==0.15.0
 Requires-Dist: rapidfuzz
@@ -24,7 +24,7 @@ Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.44.2 ; extra == "bionty"
+Requires-Dist: bionty==0.44.3 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"
@@ -37,7 +37,7 @@ Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.8 ; extra == "fcs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
-Requires-Dist: nbproject==0.10.3 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.4 ; extra == "jupyter"
 Requires-Dist: nbstripout==0.6.1 ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"

{lamindb-0.74.2.dist-info → lamindb-0.74.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb/__init__.py,sha256=N8c6LCD-NLi9UTsmkOIvRcPOdu183747G8mdfsLfNJI,2249
+lamindb/__init__.py,sha256=VfwmNQfCefzn3jsRS2l3fnV7jub1RpMj4aVCFh09vxI,2249
 lamindb/_artifact.py,sha256=pdSMBuZnlr-Jfot8p90x7TEbto-viXyryax5p1FljEs,40133
 lamindb/_can_validate.py,sha256=CUu-lBY9XnSYGWiazYhLMW5H0LuuR86mVbU7UnIZTVU,15010
 lamindb/_collection.py,sha256=P4UjZxC2OcViTmqSeW3NIiXU3C0ZF5BF9P6YcchS2Zg,14617
@@ -12,9 +12,9 @@ lamindb/_is_versioned.py,sha256=8pXW2gkLTZsTxRERuWZLidiagNIC8evmCmnbztWkVQ4,1343
 lamindb/_parents.py,sha256=Zgi9Lmw9td18Y0QJ96rYaBrjSaZ8XGcseWdbJkpJhFU,15061
 lamindb/_query_manager.py,sha256=6_ZqQr0SKTYsbMtJd5BmaMoyASIVel5v2F1KMgacWlU,4252
 lamindb/_query_set.py,sha256=LM5NsAWy5FCZZSxX1VbE20RdA5nsyk4_5p4abuMjdcI,11662
-lamindb/_record.py,sha256=LPIUvJut4mFqk4231SaA7jpyKcN8K4RU2kpfNIo9I-4,19768
+lamindb/_record.py,sha256=5B0mMvEoZ0gZ6MALy6bsbDOVU47pkVEhRCBVwVJnNwg,19150
 lamindb/_run.py,sha256=xj3ER4F_yWvuNw1mr0XU-QuIPi5hBO7Ue0ygBgJQ6mc,1887
-lamindb/_save.py,sha256=FrtaW8uaw4YLMPixpW1T2o8SmNJqgNdpPF-xUf5tXJ8,11852
+lamindb/_save.py,sha256=xs1ZdTYGd78zA3XqXhiwZ_QKAogLdHCQv1EBVFDWCis,11020
 lamindb/_storage.py,sha256=GBVChv-DHVMNEBJL5l_JT6B4RDhZ6NnwgzmUICphYKk,413
 lamindb/_transform.py,sha256=E9C7psuOnsNrUQpWRuGgEUM8_pc7YhDn7n4ieHzB4X0,3169
 lamindb/_ulabel.py,sha256=XDSdZBXX_ki5s1vOths3MjF2x5DPggBR_PV_KF4SGyg,1611
@@ -22,8 +22,8 @@ lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
 lamindb/_view.py,sha256=_sAcSD06bC92R_LLDcHMhO0IfOqybBXXRYxOXvm1Juc,2322
 lamindb/core/__init__.py,sha256=HtyYVFrS6RclSk7gZty9vgXU0k2_oZiqFPfqghBc4Fc,1415
 lamindb/core/_data.py,sha256=yk2ozTt-mNIA8bWllmcC__WgFukj03fZU41rr_ultlM,16264
-lamindb/core/_feature_manager.py,sha256=dWrHtICaJpKdaSKtU9etg3SbUnWJ3fKZWkSM0ZKFJes,32184
-lamindb/core/_label_manager.py,sha256=51VzgF_TtdQDmKBjWmZcuE4OHVtsy-HdxdPHhUb5eJg,9659
+lamindb/core/_feature_manager.py,sha256=EvMoY9EAFGdbRkDR44YMJBMWBEt9IbtfZ0RHmiv0D58,31910
+lamindb/core/_label_manager.py,sha256=udG70H1FucAr4lmtFMgAcMJiAcYvoZIyT034NO93YF8,9265
 lamindb/core/_mapped_collection.py,sha256=SGUsR6RbjNzUOq6A6wTa4M4GkLMuP4Z70WOeF39WPCU,19618
 lamindb/core/_run_context.py,sha256=w_LdfwYTncCZmh4agNPey37UdKrzSglLfLUNBe5z1mw,18421
 lamindb/core/_settings.py,sha256=sDfIfq9H7H8nUE51FJF4EO_Zihlxh44S3GbaliHKJY4,6108
@@ -35,7 +35,7 @@ lamindb/core/schema.py,sha256=sNrzWnqeyh9Ppr7yImlSAXiHb_VJdB5DWuO-QERxQGY,1847
 lamindb/core/types.py,sha256=xeQF2x40p2pR9eIVQrXT74RrS810z2fbjmTRTSQUqPM,230
 lamindb/core/versioning.py,sha256=lz1JP3K-0npeSTZPY7kMVXqOOcB8IEGmdG0Si3kSdN8,4956
 lamindb/core/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0f-DI,1353
-lamindb/core/datasets/_core.py,sha256=11vsIRREU7TvjwkL2htJWAGoBNCmG2qz8ps4Bd4SNLQ,19873
+lamindb/core/datasets/_core.py,sha256=NhMELgF4aR9HAlU37BF3FkPLobxinRbMJ8s6XwgIqEM,19549
 lamindb/core/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh4,953
 lamindb/core/storage/__init__.py,sha256=5LUFQKRr2BX24d-yWBezhTXBV83sShcOvPj5Y5u6qIg,441
 lamindb/core/storage/_anndata_sizes.py,sha256=aXO3OB--tF5MChenSsigW6Q-RuE8YJJOUTVukkLrv9A,1029
@@ -51,7 +51,7 @@ lamindb/integrations/__init__.py,sha256=aH2PmO2m4-vwIifMYTB0Fyyr_gZWtVnV71jT0tVW
 lamindb/integrations/_vitessce.py,sha256=VC80NKuzZ0FdjFxaLvyD78kAUNwvwBnGblSPDqT_mGQ,2737
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
-lamindb-0.74.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.74.2.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.74.2.dist-info/METADATA,sha256=PjbRqnIXHyjshCFH9JlZR32KTSw_1i85gT3FWNj4MkI,2669
-lamindb-0.74.2.dist-info/RECORD,,
+lamindb-0.74.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.74.3.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.74.3.dist-info/METADATA,sha256=v0qwjHuybQfWzw2juEC3T31Ot74DQtbjlUR2Rhzg4Yg,2669
+lamindb-0.74.3.dist-info/RECORD,,