lamindb 0.76.12__py3-none-any.whl → 0.76.14__py3-none-any.whl

lamindb/core/_label_manager.py

@@ -26,32 +26,19 @@ if TYPE_CHECKING:
 
     from lamindb._query_set import QuerySet
 
+LABELS_EXCLUDE_SET = {"feature_sets"}
 
-def get_labels_as_dict(self: Artifact | Collection, links: bool = False):
-    exclude_set = {
-        "feature_sets",
-        "artifacts",
-        "input_of_runs",
-        "collections",
-        "_source_code_artifact_of",
-        "_report_of",
-        "_environment_of",
-        "links_collection",
-        "links_artifact",
-        "links_feature_set",
-        "previous_runs",
-        "_feature_values",
-        "_action_targets",
-        "_lnschema_core_collection__actions_+",  # something seems off with this one
-        "_actions",
-    }
+
+def get_labels_as_dict(
+    self: Artifact | Collection, links: bool = False, instance: str | None = None
+) -> dict:
     labels = {}  # type: ignore
     if self.id is None:
         return labels
     for related_model_name, related_name in dict_related_model_to_related_name(
-        self.__class__, links=links
+        self.__class__, links=links, instance=instance
     ).items():
-        if related_name not in exclude_set:
+        if related_name not in LABELS_EXCLUDE_SET and not related_name.startswith("_"):
             labels[related_name] = (
                 related_model_name,
                 getattr(self, related_name).all(),
@@ -86,18 +73,15 @@ def print_labels(
         labels_msg = _print_labels_postgres(self, m2m_data, print_types)
     else:
         labels_msg = ""
-        for related_name, (related_model, labels) in get_labels_as_dict(self).items():
-            # there is a try except block here to deal with schema inconsistencies
-            # during transfer between instances
-            try:
-                field = get_name_field(labels)
-                labels_list = list(labels.values_list(field, flat=True))
-                if len(labels_list) > 0:
-                    print_values = _print_values(labels_list, n=10)
-                    type_str = f": {related_model}" if print_types else ""
-                    labels_msg += f"    .{related_name}{type_str} = {print_values}\n"
-            except Exception:  # noqa: S112
-                continue
+        for related_name, (related_model, labels) in get_labels_as_dict(
+            self, instance=self._state.db
+        ).items():
+            field = get_name_field(labels)
+            labels_list = list(labels.values_list(field, flat=True))
+            if len(labels_list) > 0:
+                print_values = _print_values(labels_list, n=10)
+                type_str = f": {related_model}" if print_types else ""
+                labels_msg += f"    .{related_name}{type_str} = {print_values}\n"
 
     msg = ""
     if labels_msg:
@@ -214,75 +198,89 @@ class LabelManager:
             >>> artifact1.ulabels.set(labels)
             >>> artifact2.labels.add_from(artifact1)
         """
-        from django.db.utils import ProgrammingError
-
         if transfer_logs is None:
             transfer_logs = {"mapped": [], "transferred": [], "run": None}
         using_key = settings._using_key
-        for related_name, (_, labels) in get_labels_as_dict(data).items():
+        for related_name, (_, labels) in get_labels_as_dict(
+            data, instance=self._host._state.db
+        ).items():
             labels = labels.all()
-            try:
-                if not labels.exists():
-                    continue
-                # look for features
-                data_name_lower = data.__class__.__name__.lower()
-                labels_by_features = defaultdict(list)
-                features = set()
-                _, new_labels = validate_labels(labels)
-                if len(new_labels) > 0:
-                    transfer_fk_to_default_db_bulk(
-                        new_labels, using_key, transfer_logs=transfer_logs
+            if not labels.exists():
+                continue
+            # look for features
+            data_name_lower = data.__class__.__name__.lower()
+            labels_by_features = defaultdict(list)
+            features = set()
+            _, new_labels = validate_labels(labels)
+            if len(new_labels) > 0:
+                transfer_fk_to_default_db_bulk(
+                    new_labels, using_key, transfer_logs=transfer_logs
+                )
+            for label in labels:
+                # if the link table doesn't follow this convention, we'll ignore it
+                if not hasattr(label, f"links_{data_name_lower}"):
+                    key = None
+                else:
+                    link = getattr(label, f"links_{data_name_lower}").get(
+                        **{f"{data_name_lower}_id": data.id}
                     )
-                for label in labels:
-                    # if the link table doesn't follow this convention, we'll ignore it
-                    if not hasattr(label, f"links_{data_name_lower}"):
-                        key = None
+                    if link.feature is not None:
+                        features.add(link.feature)
+                        key = link.feature.name
                     else:
-                        link = getattr(label, f"links_{data_name_lower}").get(
-                            **{f"{data_name_lower}_id": data.id}
-                        )
-                        if link.feature is not None:
-                            features.add(link.feature)
-                            key = link.feature.name
-                        else:
-                            key = None
-                    label_returned = transfer_to_default_db(
-                        label,
+                        key = None
+                label_returned = transfer_to_default_db(
+                    label,
+                    using_key,
+                    transfer_logs=transfer_logs,
+                    transfer_fk=False,
+                    save=True,
+                )
+                # TODO: refactor return value of transfer to default db
+                if label_returned is not None:
+                    label = label_returned
+                labels_by_features[key].append(label)
+            # treat features
+            _, new_features = validate_labels(list(features))
+            if len(new_features) > 0:
+                transfer_fk_to_default_db_bulk(
+                    new_features, using_key, transfer_logs=transfer_logs
+                )
+                for feature in new_features:
+                    transfer_to_default_db(
+                        feature,
                         using_key,
                         transfer_logs=transfer_logs,
                         transfer_fk=False,
-                        save=True,
                     )
-                    # TODO: refactor return value of transfer to default db
-                    if label_returned is not None:
-                        label = label_returned
-                    labels_by_features[key].append(label)
-                # treat features
-                _, new_features = validate_labels(list(features))
-                if len(new_features) > 0:
-                    transfer_fk_to_default_db_bulk(
-                        new_features, using_key, transfer_logs=transfer_logs
+                save(new_features)
+            if hasattr(self._host, related_name):
+                for feature_name, labels in labels_by_features.items():
+                    if feature_name is not None:
+                        feature_id = Feature.get(name=feature_name).id
+                    else:
+                        feature_id = None
+                    getattr(self._host, related_name).add(
+                        *labels, through_defaults={"feature_id": feature_id}
                     )
-                    for feature in new_features:
-                        transfer_to_default_db(
-                            feature,
-                            using_key,
-                            transfer_logs=transfer_logs,
-                            transfer_fk=False,
-                        )
-                    save(new_features)
-                if hasattr(self._host, related_name):
-                    for feature_name, labels in labels_by_features.items():
-                        if feature_name is not None:
-                            feature_id = Feature.get(name=feature_name).id
-                        else:
-                            feature_id = None
-                        getattr(self._host, related_name).add(
-                            *labels, through_defaults={"feature_id": feature_id}
-                        )
-            # ProgrammingError is raised when schemas don't match between source and target instances
-            except ProgrammingError:
-                logger.warning(
-                    f"{related_name} labels cannot be transferred because schema module does not exist in target instance: {labels}"
-                )
-                continue
+
+    def make_external(self, label: Record):
+        """Make a label external, aka dissociate label from internal features.
+
+        Args:
+            label: Label record to make external.
+        """
+        d = dict_related_model_to_related_name(self._host)
+        registry = label.__class__
+        related_name = d.get(registry.__get_name_with_schema__())
+        link_model = getattr(self._host, related_name).through
+        link_records = link_model.filter(
+            artifact_id=self._host.id, **{f"{registry.__name__.lower()}_id": label.id}
+        )
+        features = link_records.values_list("feature__name", flat=True).distinct()
+        s = "s" if len(features) > 1 else ""
+        link_records.update(feature_id=None, feature_ref_is_name=None)
+        logger.warning(
+            f'{registry.__name__} "{getattr(label, label._name_field)}" is no longer associated with the following feature{s}:\n'
+            f"{list(features)}"
+        )

lamindb/core/exceptions.py

@@ -11,6 +11,7 @@
    MissingContextUID
    UpdateContext
    IntegrityError
+   RecordNameChangeIntegrityError
 
 """
 
@@ -57,6 +58,12 @@ class InconsistentKey(Exception):
     pass
 
 
+class RecordNameChangeIntegrityError(SystemExit):
+    """Custom exception for name change errors."""
+
+    pass
+
+
 # -------------------------------------------------------------------------------------
 # run context
 # -------------------------------------------------------------------------------------

lamindb/core/schema.py

@@ -1,31 +1,66 @@
 from __future__ import annotations
 
+import lamindb_setup as ln_setup
 from django.db.models import ManyToManyField
+from lamindb_setup._connect_instance import (
+    get_owner_name_from_identifier,
+    load_instance_settings,
+)
+from lamindb_setup.core._settings_store import instance_settings_file
 from lnschema_core.models import Feature, FeatureSet, LinkORM, Record
 
 
-def dict_schema_name_to_model_name(registry: type[Record]) -> dict[str, Record]:
+def get_schemas_modules(instance: str | None) -> set[str]:
+    if instance is None or instance == "default":
+        schema_modules = set(ln_setup.settings.instance.schema)
+        schema_modules.add("core")
+        return schema_modules
+    owner, name = get_owner_name_from_identifier(instance)
+    settings_file = instance_settings_file(name, owner)
+    if settings_file.exists():
+        schema = set(load_instance_settings(settings_file).schema)
+    else:
+        cache_filepath = (
+            ln_setup.settings.cache_dir / f"instance--{owner}--{name}--uid.txt"
+        )
+        if cache_filepath.exists():
+            schema = set(cache_filepath.read_text().split("\n")[1].split(","))
+        else:
+            raise ValueError(f"Instance {instance} not found")
+    shared_schema_modules = set(ln_setup.settings.instance.schema).intersection(schema)
+    shared_schema_modules.add("core")
+    return shared_schema_modules
+
+
+def dict_schema_name_to_model_name(
+    registry: type[Record], instance: str | None = None
+) -> dict[str, Record]:
+    schema_modules = get_schemas_modules(instance)
     d: dict = {
         i.related_model.__get_name_with_schema__(): i.related_model
         for i in registry._meta.related_objects
         if i.related_name is not None
+        and i.related_model.__get_schema_name__() in schema_modules
     }
     d.update(
         {
             i.related_model.__get_name_with_schema__(): i.related_model
             for i in registry._meta.many_to_many
             if i.name is not None
+            and i.related_model.__get_schema_name__() in schema_modules
         }
     )
     return d
 
 
 def dict_related_model_to_related_name(
-    registry: type[Record], links: bool = False
+    registry: type[Record], links: bool = False, instance: str | None = None
 ) -> dict[str, str]:
     def include(model: Record):
         return not links != issubclass(model, LinkORM)
 
+    schema_modules = get_schemas_modules(instance)
+
     related_objects = registry._meta.related_objects + registry._meta.many_to_many
     d: dict = {
         record.related_model.__get_name_with_schema__(): (
@@ -34,7 +69,11 @@ def dict_related_model_to_related_name(
             else record.name
         )
         for record in related_objects
-        if (record.name is not None and include(record.related_model))
+        if (
+            record.name is not None
+            and include(record.related_model)
+            and record.related_model.__get_schema_name__() in schema_modules
+        )
     }
     return d
 

lamindb/core/types.py

@@ -13,6 +13,7 @@
 from lamindb_setup.core.types import UPathStr
 from lnschema_core.types import (
     ArtifactType,
+    FieldAttr,
     ListLike,
     StrField,
     TransformType,

{lamindb-0.76.12.dist-info → lamindb-0.76.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.12
+Version: 0.76.14
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.9
@@ -8,9 +8,9 @@ Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.75.0
-Requires-Dist: lamin_utils==0.13.6
-Requires-Dist: lamin_cli==0.18.0
+Requires-Dist: lnschema_core==0.76.0
+Requires-Dist: lamin_utils==0.13.7
+Requires-Dist: lamin_cli==0.20.1
 Requires-Dist: lamindb_setup
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
@@ -23,7 +23,7 @@ Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.51.2 ; extra == "bionty"
+Requires-Dist: bionty==0.52.0 ; extra == "bionty"
 Requires-Dist: line_profiler ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; 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==0.10.4 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.5 ; extra == "jupyter"
 Requires-Dist: jupytext ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"

{lamindb-0.76.12.dist-info → lamindb-0.76.14.dist-info}/RECORD

@@ -1,18 +1,18 @@
-lamindb/__init__.py,sha256=IriWYyrDC6JejjCZBDmycpYNGj9hiGgJZ7vAFBCcq9w,2278
-lamindb/_artifact.py,sha256=Q0fCuD2nDQdqtQIxA9I4dTOY6R-12fv4ImeoNYEgL5I,44800
+lamindb/__init__.py,sha256=PelFCbUaNuz_1rnpOqj-mDCMqCfT2hJ27M3C-VkGJl0,2278
+lamindb/_artifact.py,sha256=9soXXT3g9tG1BTwX4DCRPurbFFcpHKOT8W7SsoLiNbo,44847
 lamindb/_can_validate.py,sha256=1pUavLwZ_yPAtbVYKOGYUHaPxlJGZ246qZ0e-4ZUDSc,19552
-lamindb/_collection.py,sha256=TSkJ3z0axRAFrV2PvZf1YMz7NXWLX3hYoNQ48l4NoyM,14129
-lamindb/_curate.py,sha256=KpEP0-9nQUmiRn6z7fiGs6BmQdpqSg3QPlAgV-S9_wA,58839
+lamindb/_collection.py,sha256=vt604fUjkmOYCGR4Sq_NTwnPywATfjUAdkQjuJJ17y0,14613
+lamindb/_curate.py,sha256=rFbPEoD-E-5s3QPIcUuedUO6a2c8QfpTrBfVX9gUVpE,63120
 lamindb/_feature.py,sha256=nZhtrH0ssoNls-hV-dkwfK9sKypg2El59R9qfarxfUE,5340
-lamindb/_feature_set.py,sha256=lHKATvs8NagaaHwsWqi4XMTPTNKsGdM-6ZRctTHHSNc,8130
+lamindb/_feature_set.py,sha256=JQSP-YLam1KW-rDzly5Dm4IYVL2A6ec7ufIf6iCc2W8,8169
 lamindb/_filter.py,sha256=Pf9NHV4gm7NOC0Frtvx4W7nvwt2EowOP74DwppyXAZs,635
 lamindb/_finish.py,sha256=VMAmxCUFmTKIMSCx7LEh4QAnWDeue6MeUAAzkMVEYMU,9546
-lamindb/_from_values.py,sha256=iqcR8T8i9VZpnn09W441zW-djhWMh8EZj7XFJq9jP2k,14211
+lamindb/_from_values.py,sha256=uRtZLaMWKoANMMXm1hrADHfckRCTiK8_d02Yp07nLkw,14119
 lamindb/_is_versioned.py,sha256=5lAnhTboltFkZCKVRV1uxkm0OCjJz_HKi3yQq_vEuMs,1306
-lamindb/_parents.py,sha256=eMavdd6IO6STOVJSlR2TzdRtx6sKYDKsMOtlR3DZlgQ,15599
-lamindb/_query_manager.py,sha256=Ipe85HL31DDwMbC8CN_1Svbwk48a_DUh_INGQdZL08I,4222
-lamindb/_query_set.py,sha256=jPW7vUm_lMtL3qhLJ16nJxZkf184mM0Ny1OM1uaztto,12717
-lamindb/_record.py,sha256=OUW0xr2s7I2iML2GoFjdZ3nNc0q9RKMLUXnTU5cwBs8,23260
+lamindb/_parents.py,sha256=KMBUfCLNqjmFzOdZIXaUFqDPeEpWP28MCkHHPq887h8,16341
+lamindb/_query_manager.py,sha256=pmPhJQ85-7XeAU9TFv6LPGi9F7dBgztZgZcXz33HYJM,3710
+lamindb/_query_set.py,sha256=AyWvFZ-Vnd_1dhbDLkiyEh2-2XiIR_OpEk72xoQ2JVg,12980
+lamindb/_record.py,sha256=FkU7G1OUl0HPQO6wh8EkPh4T_ogxcy6QGkrVz_I4WUw,26840
 lamindb/_run.py,sha256=K_5drpLn3D7y3XtZ3vtAw35rG5RCSvB4bXQZx4ESSI0,1964
 lamindb/_save.py,sha256=BCaSFnANYPxTqL5gw7Hrh_9kz7SDyOxrJV2KW6rXqts,11366
 lamindb/_storage.py,sha256=GBVChv-DHVMNEBJL5l_JT6B4RDhZ6NnwgzmUICphYKk,413
@@ -20,21 +20,21 @@ lamindb/_transform.py,sha256=wZDkY8lp4d_OsO5a7rLs1RamkDzBXZSLaWJU34zRnmA,4728
 lamindb/_ulabel.py,sha256=XDSdZBXX_ki5s1vOths3MjF2x5DPggBR_PV_KF4SGyg,1611
 lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
 lamindb/_view.py,sha256=4Ln2ItTb3857PAI-70O8eJYqoTJ_NNFc7E_wds6OGns,2412
-lamindb/core/__init__.py,sha256=57AXQ286eOX2_o5HUeqIFJrfqN-OZ_E7FVHd3Xm5oOk,1483
-lamindb/core/_context.py,sha256=6N8SlTRJyVwhm0kLmd_ToHvT4BhQI977PUhUv8e8KN4,22900
-lamindb/core/_data.py,sha256=P0vlbw_UQp9UDNMmUo9YFxqurcWtMaKPWCT12IRA2C0,19672
-lamindb/core/_django.py,sha256=mqZ0WhTakLDrGVp3MVI6RNfu8kZ2L5BiEnMwXnkfsG0,6760
-lamindb/core/_feature_manager.py,sha256=f7pO3RQ0ojYvofLYqioE4CV2t8nXTkQcXvJDuMB_XaY,38941
-lamindb/core/_label_manager.py,sha256=GoluSFk_z1c1fZw8OGKkaIURWgognEsOHCo9mzigd-A,11108
+lamindb/core/__init__.py,sha256=y87MCP1BEC2qHNVDIOwqVteIP_2hPCdIoa9JXr0EG8U,1524
+lamindb/core/_context.py,sha256=dI3z7fCMRPC3IMb7-EIaQYhacSZBA4HfLVFyoJtVL7I,22900
+lamindb/core/_data.py,sha256=BVZkxK8aloSecH25LivbwnjcG1fz7Gs2UDceO5pWd3I,20049
+lamindb/core/_django.py,sha256=yeMPp1n9WrFmEjVRdavfpVqAolPLd24RseTQlvsK67w,7157
+lamindb/core/_feature_manager.py,sha256=q4WmzJvFLL_fAs-vNRgV2klanAoU6Wu8_g0O2dyIjVg,40027
+lamindb/core/_label_manager.py,sha256=yh-r4KbtOArMUKPJL75yOxJc8HUKqsik8pExBVKyDlA,10949
 lamindb/core/_mapped_collection.py,sha256=M50haewVAFONeF71QQbzD09L8lVZCL1hyf0W87jKE5U,24575
 lamindb/core/_settings.py,sha256=6jNadlQdimxCsKR2ZyUD0YJYzOdubTnKktki-MqEWqQ,6137
 lamindb/core/_sync_git.py,sha256=lIgl6YfpH4rCFT1WILAp7zlemZfxog1d0zp3cX0KIZw,4531
 lamindb/core/_track_environment.py,sha256=Ywzg_sJ7guI1dcsN7h5orce9VdYl8VGVE3OLITlHBXQ,820
-lamindb/core/exceptions.py,sha256=0B36kOVo-Dik5KbSKvy5GPuMjUfhVb99dJwXl_J0ldo,1636
+lamindb/core/exceptions.py,sha256=Y1XQGbv9MgNLVvoClpcwN4NugrLW3Xgy1up15wZK740,1783
 lamindb/core/fields.py,sha256=47Jmh3efUr5ZscgimR_yckY-I3cNf8ScLutbwKCK3j4,162
 lamindb/core/loaders.py,sha256=KMTkDa73jkRVvI9uc5Fgr0t6mq22cAxBwhSlUZKUaBg,4016
-lamindb/core/schema.py,sha256=KiYQn_8fokSMztTNDe6qUocZzKXWxU32H-YChNJv51A,1877
-lamindb/core/types.py,sha256=uVBqSVLoQaTkqP9nqsJhwU6yYnx8H5e6-ZxrB6vpOOw,265
+lamindb/core/schema.py,sha256=Y1tGn93B236PtnYZkpgTNFgTXBcVujPM1qh1kNG6Nbs,3441
+lamindb/core/types.py,sha256=cL4cmJFA1xfxAIFOQqoa_fvVzdUM3A5blHStVwRNtk4,280
 lamindb/core/versioning.py,sha256=KUpd94F5QpbDxx9eKgZwrpPyQpm9YeHVedrTEO2a_mI,4839
 lamindb/core/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0f-DI,1353
 lamindb/core/datasets/_core.py,sha256=JGP_q-OQibDCEaI54jZ2F6fSbSW9Yg6oYOqgOCXM0v4,20414
@@ -55,7 +55,7 @@ lamindb/integrations/__init__.py,sha256=RWGMYYIzr8zvmNPyVB4m-p4gMDhxdRbjES2Ed23O
 lamindb/integrations/_vitessce.py,sha256=uPl45_w4Uu9_BhpBDDVonC1nDOuAnB7DAnzi5w5bZAE,4032
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
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