lamindb 0.74.3__py3-none-any.whl → 0.75.0__py3-none-any.whl

lamindb/core/_label_manager.py

@@ -4,13 +4,13 @@ from collections import defaultdict
 from typing import TYPE_CHECKING, Dict
 
 import numpy as np
-from lamin_utils import colors, logger
+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_default_str_field,
+    get_name_field,
     transfer_fk_to_default_db_bulk,
     transfer_to_default_db,
 )
@@ -28,17 +28,19 @@ if TYPE_CHECKING:
 def get_labels_as_dict(self: HasFeatures, links: bool = False):
     exclude_set = {
         "feature_sets",
-        "unordered_artifacts",
-        "input_of",
+        "artifacts",
+        "input_of_runs",
         "collections",
-        "source_code_of",
+        "_source_code_artifact_of",
         "report_of",
         "environment_of",
-        "collection_links",
-        "artifact_links",
-        "feature_set_links",
+        "links_collection",
+        "links_artifact",
+        "links_feature_set",
         "previous_runs",
-        "feature_values",
+        "_feature_values",
+        "_lnschema_core_collection__actions_+",
+        "_actions",
     }
     labels = {}  # type: ignore
     if self.id is None:
@@ -62,7 +64,7 @@ def print_labels(self: HasFeatures, field: str = "name", print_types: bool = Fal
         try:
             labels_list = list(labels.values_list(field, flat=True))
             if len(labels_list) > 0:
-                get_default_str_field(labels)
+                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"
@@ -84,18 +86,14 @@ def validate_labels(labels: QuerySet | list | dict):
             return [], []
         registry = labels[0].__class__
         field = REGISTRY_UNIQUE_FIELD.get(registry.__name__.lower(), "uid")
-        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 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 field == "ontology_id" and len(label_uids) > 0:
+        if hasattr(registry, "_ontology_id_field") and len(label_uids) > 0:
             try:
                 save(registry.from_values(label_uids, field=field))
             except Exception:  # noqa S110
@@ -201,10 +199,10 @@ class LabelManager:
                     transfer_fk_to_default_db_bulk(new_labels, using_key)
                 for label in labels:
                     # if the link table doesn't follow this convention, we'll ignore it
-                    if not hasattr(label, f"{data_name_lower}_links"):
+                    if not hasattr(label, f"links_{data_name_lower}"):
                         key = None
                     else:
-                        link = getattr(label, f"{data_name_lower}_links").get(
+                        link = getattr(label, f"links_{data_name_lower}").get(
                             **{f"{data_name_lower}_id": data.id}
                         )
                         if link.feature is not None:

lamindb/core/_mapped_collection.py

@@ -10,7 +10,7 @@ import pandas as pd
 from lamin_utils import logger
 from lamindb_setup.core.upath import UPath
 
-from .storage._backed_access import (
+from .storage._anndata_accessor import (
     ArrayType,
     ArrayTypes,
     GroupType,

lamindb/core/_run_context.py

@@ -11,7 +11,6 @@ from lamin_utils import logger
 from lamindb_setup.core.hashing import hash_file
 from lnschema_core import Run, Transform, ids
 from lnschema_core.models import Param, ParamValue, RunParamValue
-from lnschema_core.types import TransformType
 from lnschema_core.users import current_user_id
 
 from ._settings import settings
@@ -27,6 +26,7 @@ from .versioning import bump_version as bump_version_function
 
 if TYPE_CHECKING:
     from lamindb_setup.core.types import UPathStr
+    from lnschema_core.types import TransformType
 
 is_run_from_ipython = getattr(builtins, "__IPYTHON__", False)
 
@@ -279,14 +279,14 @@ class run_context:
                 ).one_or_none()
                 if is_run_from_ipython:
                     key, name = cls._track_notebook(path=path)
-                    transform_type = TransformType.notebook
+                    transform_type = "notebook"
                     transform_ref = None
                     transform_ref_type = None
                 else:
                     (name, key, transform_ref, transform_ref_type) = cls._track_script(
                         path=path
                     )
-                    transform_type = TransformType.script
+                    transform_type = "script"
                 # overwrite whatever is auto-detected in the notebook or script
                 if transform_settings.name is not None:
                     name = transform_settings.name
@@ -323,9 +323,7 @@ class run_context:
             cls.transform = transform_exists
 
         if new_run is None:  # for notebooks, default to loading latest runs
-            new_run = (
-                False if cls.transform.type == TransformType.notebook.value else True
-            )  # type: ignore
+            new_run = False if cls.transform.type == "notebook" else True  # type: ignore
 
         run = None
         from lamindb._run import Run
@@ -479,7 +477,7 @@ class run_context:
                     transform.save()
                     logger.important(f"updated: {transform}")
             # check whether transform source code was already saved
-            if transform.source_code_id is not None:
+            if transform._source_code_artifact_id is not None:
                 response = None
                 if is_run_from_ipython:
                     if os.getenv("LAMIN_TESTING") is None:
@@ -491,7 +489,7 @@ class run_context:
                         response = "y"
                 else:
                     hash, _ = hash_file(cls.path)  # ignore hash_type for now
-                    if hash != transform.source_code.hash:
+                    if hash != transform._source_code_artifact.hash:
                         # only if hashes don't match, we need user input
                         if os.getenv("LAMIN_TESTING") is None:
                             response = input(

lamindb/core/datasets/_core.py

@@ -83,7 +83,7 @@ def file_tsv_rnaseq_nfcore_salmon_merged_gene_counts(
         ln.settings.verbosity = "error"
         ln.Feature(name="assay", dtype=[bt.ExperimentalFactor]).save()
         ln.Feature(name="organism", dtype=[bt.Organism]).save()
-        bt.ExperimentalFactor.from_public(ontology_id="EFO:0008896").save()
+        bt.ExperimentalFactor.from_source(ontology_id="EFO:0008896").save()
         ln.settings.verbosity = verbosity
 
     return Path(filepath)
@@ -186,16 +186,16 @@ def anndata_mouse_sc_lymph_node(
         verbosity = ln.settings.verbosity
         ln.settings.verbosity = "error"
         # strain
-        bt.ExperimentalFactor.from_public(ontology_id="EFO:0004472").save()
+        bt.ExperimentalFactor.from_source(ontology_id="EFO:0004472").save()
         # developmental stage
-        bt.ExperimentalFactor.from_public(ontology_id="EFO:0001272").save()
+        bt.ExperimentalFactor.from_source(ontology_id="EFO:0001272").save()
         # tissue
-        bt.Tissue.from_public(ontology_id="UBERON:0001542").save()
+        bt.Tissue.from_source(ontology_id="UBERON:0001542").save()
         # cell types
         ln.save(bt.CellType.from_values(["CL:0000115", "CL:0000738"], "ontology_id"))
         # assays
         ln.Feature(name="assay", dtype=[bt.ExperimentalFactor]).save()
-        bt.ExperimentalFactor.from_public(ontology_id="EFO:0008913").save()
+        bt.ExperimentalFactor.from_source(ontology_id="EFO:0008913").save()
         # genes
         validated = bt.Gene.public(organism="mouse").validate(
             adata.var.index, field="ensembl_gene_id"
@@ -323,7 +323,7 @@ def anndata_human_immune_cells(
         ln.Feature(name="tissue", dtype=[bt.Tissue]).save()
         ln.Feature(name="organism", dtype=[bt.Organism]).save()
         ln.Feature(name="donor", dtype=[ln.ULabel]).save()
-        bt.ExperimentalFactor.from_public(ontology_id="EFO:0008913").save()
+        bt.ExperimentalFactor.from_source(ontology_id="EFO:0008913").save()
         ln.save([ln.ULabel(name=name) for name in adata.obs.donor.unique()])
         ln.settings.verbosity = verbosity
     return adata
@@ -332,7 +332,7 @@ def anndata_human_immune_cells(
 def anndata_with_obs() -> ad.AnnData:
     """Create a mini anndata with cell_type, disease and tissue."""
     import anndata as ad
-    import bionty_base
+    import bionty.base as bionty_base
 
     celltypes = ["T cell", "hematopoietic stem cell", "hepatocyte", "my new cell type"]
     celltype_ids = ["CL:0000084", "CL:0000037", "CL:0000182", ""]

lamindb/core/exceptions.py

@@ -10,6 +10,7 @@ The registry base class:
    NoTitleError
    MissingTransformSettings
    UpdateTransformSettings
+   IntegrityError
 
 """
 
@@ -25,6 +26,16 @@ class ValidationError(SystemExit):
 # -------------------------------------------------------------------------------------
 
 
+class IntegrityError(Exception):
+    """Integrity error.
+
+    For instance, it's not allowed to delete artifacts outside managed storage
+    locations.
+    """
+
+    pass
+
+
 class NotebookNotSavedError(Exception):
     """Notebook wasn't saved."""
 

lamindb/core/storage/__init__.py

@@ -6,6 +6,7 @@
    AnnDataAccessor
    BackedAccessor
 """
+
 from lamindb_setup.core.upath import LocalPathClasses, UPath, infer_filesystem
 
 from ._anndata_sizes import size_adata