lamindb 0.76.6__py3-none-any.whl → 0.76.8__py3-none-any.whl

lamindb/core/_label_manager.py

@@ -1,252 +1,253 @@
-from __future__ import annotations
-
-from collections import defaultdict
-from typing import TYPE_CHECKING, Dict
-
-import numpy as np
-from lamin_utils import colors
-from lnschema_core.models import Feature
-
-from lamindb._from_values import _print_values
-from lamindb._record import (
-    REGISTRY_UNIQUE_FIELD,
-    get_name_field,
-    transfer_fk_to_default_db_bulk,
-    transfer_to_default_db,
-)
-from lamindb._save import save
-
-from ._settings import settings
-from .schema import dict_related_model_to_related_name
-
-if TYPE_CHECKING:
-    from lnschema_core.models import Artifact, Collection, Record
-
-    from lamindb._query_set import QuerySet
-
-
-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",
-    }
-    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
-    ).items():
-        if related_name not in exclude_set:
-            labels[related_name] = (
-                related_model_name,
-                getattr(self, related_name).all(),
-            )
-    return labels
-
-
-def print_labels(
-    self: Artifact | Collection, field: str = "name", print_types: bool = False
-):
-    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:
-            labels_list = list(labels.values_list(field, flat=True))
-            if len(labels_list) > 0:
-                get_name_field(labels)
-                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
-    msg = ""
-    if labels_msg:
-        msg += f"  {colors.italic('Labels')}\n"
-        msg += labels_msg
-    return msg
-
-
-# Alex: is this a label transfer function?
-def validate_labels(labels: QuerySet | list | dict):
-    def validate_labels_registry(
-        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_field"):
-            field = registry._ontology_id_field
-        # 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
-        if hasattr(registry, "_ontology_id_field") and len(label_uids) > 0:
-            try:
-                save(registry.from_values(label_uids, field=field))
-            except Exception:  # noqa S110
-                pass
-            field = "uid"
-            label_uids = np.array(
-                [getattr(label, field) for label in labels if label is not None]
-            )
-        validated = registry.validate(label_uids, field=field, mute=True)
-        validated_uids = label_uids[validated]
-        validated_labels = registry.filter(**{f"{field}__in": validated_uids}).list()
-        new_labels = [labels[int(i)] for i in np.argwhere(~validated).flatten()]
-        return validated_labels, new_labels
-
-    if isinstance(labels, Dict):
-        result = {}
-        for registry, labels_registry in labels.items():
-            result[registry] = validate_labels_registry(labels_registry)
-    else:
-        return validate_labels_registry(labels)
-
-
-class LabelManager:
-    """Label manager.
-
-    This allows to manage untyped labels :class:`~lamindb.ULabel` and arbitrary
-    typed labels (e.g., :class:`~bionty.CellLine`) and associate labels
-    with features.
-    """
-
-    def __init__(self, host: Artifact | Collection):
-        self._host = host
-
-    def __repr__(self) -> str:
-        msg = print_labels(self._host)
-        if len(msg) > 0:
-            return msg
-        else:
-            return "no linked labels"
-
-    def add(
-        self,
-        records: Record | list[Record] | QuerySet,
-        feature: Feature | None = None,
-    ) -> None:
-        """Add one or several labels and associate them with a feature.
-
-        Args:
-            records: Label records to add.
-            feature: Feature under which to group the labels.
-        """
-        from ._data import add_labels
-
-        return add_labels(self._host, records=records, feature=feature)
-
-    def get(
-        self,
-        feature: Feature,
-        mute: bool = False,
-        flat_names: bool = False,
-    ) -> QuerySet | dict[str, QuerySet] | list:
-        """Get labels given a feature.
-
-        Args:
-            feature: Feature under which labels are grouped.
-            mute: Show no logging.
-            flat_names: Flatten list to names rather than returning records.
-        """
-        from ._data import get_labels
-
-        return get_labels(self._host, feature=feature, mute=mute, flat_names=flat_names)
-
-    def add_from(self, data: Artifact | Collection, transfer_logs: dict = None) -> None:
-        """Add labels from an artifact or collection to another artifact or collection.
-
-        Examples:
-            >>> artifact1 = ln.Artifact(pd.DataFrame(index=[0, 1])).save()
-            >>> artifact2 = ln.Artifact(pd.DataFrame(index=[2, 3])).save()
-            >>> ulabels = ln.ULabel.from_values(["Label1", "Label2"], field="name")
-            >>> ln.save(ulabels)
-            >>> labels = ln.ULabel.filter(name__icontains = "label").all()
-            >>> artifact1.ulabels.set(labels)
-            >>> artifact2.labels.add_from(artifact1)
-        """
-        from django.db.utils import ProgrammingError
-
-        if transfer_logs is None:
-            transfer_logs = {"mapped": [], "transferred": []}
-        using_key = settings._using_key
-        for related_name, (_, labels) in get_labels_as_dict(data).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
-                    )
-                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}
-                        )
-                        if link.feature is not None:
-                            features.add(link.feature)
-                            key = link.feature.name
-                        else:
-                            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(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:
-                continue
+from __future__ import annotations
+
+from collections import defaultdict
+from typing import TYPE_CHECKING, Dict
+
+import numpy as np
+from lamin_utils import colors
+from lnschema_core.models import Feature
+
+from lamindb._from_values import _print_values
+from lamindb._record import (
+    REGISTRY_UNIQUE_FIELD,
+    get_name_field,
+    transfer_fk_to_default_db_bulk,
+    transfer_to_default_db,
+)
+from lamindb._save import save
+
+from ._settings import settings
+from .schema import dict_related_model_to_related_name
+
+if TYPE_CHECKING:
+    from lnschema_core.models import Artifact, Collection, Record
+
+    from lamindb._query_set import QuerySet
+
+
+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",
+    }
+    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
+    ).items():
+        if related_name not in exclude_set:
+            labels[related_name] = (
+                related_model_name,
+                getattr(self, related_name).all(),
+            )
+    return labels
+
+
+def print_labels(
+    self: Artifact | Collection, field: str = "name", print_types: bool = False
+):
+    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:
+            labels_list = list(labels.values_list(field, flat=True))
+            if len(labels_list) > 0:
+                get_name_field(labels)
+                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
+    msg = ""
+    if labels_msg:
+        msg += f"  {colors.italic('Labels')}\n"
+        msg += labels_msg
+    return msg
+
+
+# Alex: is this a label transfer function?
+def validate_labels(labels: QuerySet | list | dict):
+    def validate_labels_registry(
+        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_field"):
+            field = registry._ontology_id_field
+        # 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
+        if hasattr(registry, "_ontology_id_field") and len(label_uids) > 0:
+            try:
+                labels_records = registry.from_values(label_uids, field=field)
+                save([r for r in labels_records if r._state.adding])
+            except Exception:  # noqa S110
+                pass
+            field = "uid"
+            label_uids = np.array(
+                [getattr(label, field) for label in labels if label is not None]
+            )
+        validated = registry.validate(label_uids, field=field, mute=True)
+        validated_uids = label_uids[validated]
+        validated_labels = registry.filter(**{f"{field}__in": validated_uids}).list()
+        new_labels = [labels[int(i)] for i in np.argwhere(~validated).flatten()]
+        return validated_labels, new_labels
+
+    if isinstance(labels, Dict):
+        result = {}
+        for registry, labels_registry in labels.items():
+            result[registry] = validate_labels_registry(labels_registry)
+    else:
+        return validate_labels_registry(labels)
+
+
+class LabelManager:
+    """Label manager.
+
+    This allows to manage untyped labels :class:`~lamindb.ULabel` and arbitrary
+    typed labels (e.g., :class:`~bionty.CellLine`) and associate labels
+    with features.
+    """
+
+    def __init__(self, host: Artifact | Collection):
+        self._host = host
+
+    def __repr__(self) -> str:
+        msg = print_labels(self._host)
+        if len(msg) > 0:
+            return msg
+        else:
+            return "no linked labels"
+
+    def add(
+        self,
+        records: Record | list[Record] | QuerySet,
+        feature: Feature | None = None,
+    ) -> None:
+        """Add one or several labels and associate them with a feature.
+
+        Args:
+            records: Label records to add.
+            feature: Feature under which to group the labels.
+        """
+        from ._data import add_labels
+
+        return add_labels(self._host, records=records, feature=feature)
+
+    def get(
+        self,
+        feature: Feature,
+        mute: bool = False,
+        flat_names: bool = False,
+    ) -> QuerySet | dict[str, QuerySet] | list:
+        """Get labels given a feature.
+
+        Args:
+            feature: Feature under which labels are grouped.
+            mute: Show no logging.
+            flat_names: Flatten list to names rather than returning records.
+        """
+        from ._data import get_labels
+
+        return get_labels(self._host, feature=feature, mute=mute, flat_names=flat_names)
+
+    def add_from(self, data: Artifact | Collection, transfer_logs: dict = None) -> None:
+        """Add labels from an artifact or collection to another artifact or collection.
+
+        Examples:
+            >>> artifact1 = ln.Artifact(pd.DataFrame(index=[0, 1])).save()
+            >>> artifact2 = ln.Artifact(pd.DataFrame(index=[2, 3])).save()
+            >>> ulabels = ln.ULabel.from_values(["Label1", "Label2"], field="name")
+            >>> ln.save(ulabels)
+            >>> labels = ln.ULabel.filter(name__icontains = "label").all()
+            >>> artifact1.ulabels.set(labels)
+            >>> artifact2.labels.add_from(artifact1)
+        """
+        from django.db.utils import ProgrammingError
+
+        if transfer_logs is None:
+            transfer_logs = {"mapped": [], "transferred": []}
+        using_key = settings._using_key
+        for related_name, (_, labels) in get_labels_as_dict(data).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
+                    )
+                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}
+                        )
+                        if link.feature is not None:
+                            features.add(link.feature)
+                            key = link.feature.name
+                        else:
+                            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(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:
+                continue