🚚 Rename CanValidate to CanCurate

laminlabs · Nov 15, 2024 · 469189e · 469189e
1 parent f3cc457
commit 469189e
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Showing 18 changed files with 43 additions and 42 deletions.
diff --git a/docs/bio-registries.ipynb b/docs/bio-registries.ipynb
@@ -304,7 +304,7 @@
    "source": [
     "We'd like to load the corresponding records in our in-house registry to annotate a dataset.\n",
     "\n",
-    "To this end, you'll typically use {class}`~lamindb.core.CanValidate.from_values`, which will both validate & retrieve records that match the values."
+    "To this end, you'll typically use {class}`~lamindb.core.CanCurate.from_values`, which will both validate & retrieve records that match the values."
    ]
   },
   {

diff --git a/docs/curate-any.ipynb b/docs/curate-any.ipynb
@@ -20,11 +20,11 @@
    "source": [
     ":::{dropdown} How do I validate based on a public ontology?\n",
     "\n",
-    "LaminDB makes it easy to validate categorical variables based on registries that inherit from {class}`~lamindb.core.CanValidate`.\n",
+    "LaminDB makes it easy to validate categorical variables based on registries that inherit from {class}`~lamindb.core.CanCurate`.\n",
     "\n",
-    "{class}`~lamindb.core.CanValidate` methods validate against the registries in your LaminDB instance.\n",
+    "{class}`~lamindb.core.CanCurate` methods validate against the registries in your LaminDB instance.\n",
     "In {doc}`./bio-registries`, you'll see how to extend standard validation to validation against _public references_ using a `ReferenceTable` ontology object: `public = Record.public()`.\n",
-    "By default, {meth}`~lamindb.core.CanValidate.from_values` considers a match in a public reference a validated value for any {mod}`bionty` entity.\n",
+    "By default, {meth}`~lamindb.core.CanCurate.from_values` considers a match in a public reference a validated value for any {mod}`bionty` entity.\n",
     "\n",
     ":::"
    ]
@@ -92,7 +92,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "{meth}`~lamindb.core.CanValidate.validate` validates passed values against reference values in a registry.\n",
+    "{meth}`~lamindb.core.CanCurate.validate` validates passed values against reference values in a registry.\n",
     "It returns a boolean vector indicating whether a value has an exact match in the reference values."
    ]
   },
@@ -109,11 +109,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "When validation fails, you can call {meth}`~lamindb.core.CanValidate.inspect` to figure out what to do.\n",
+    "When validation fails, you can call {meth}`~lamindb.core.CanCurate.inspect` to figure out what to do.\n",
     "\n",
-    "{meth}`~lamindb.core.CanValidate.inspect` applies the same definition of validation as {meth}`~lamindb.core.CanValidate.validate`, but returns a rich return value {class}`~lamindb.core.InspectResult`. Most importantly, it logs recommended curation steps that would render the data validated.\n",
+    "{meth}`~lamindb.core.CanCurate.inspect` applies the same definition of validation as {meth}`~lamindb.core.CanCurate.validate`, but returns a rich return value {class}`~lamindb.core.InspectResult`. Most importantly, it logs recommended curation steps that would render the data validated.\n",
     "\n",
-    "Note: you can use {meth}`~lamindb.core.CanValidate.standardize` to standardize synonyms."
+    "Note: you can use {meth}`~lamindb.core.CanCurate.standardize` to standardize synonyms."
    ]
   },
   {
@@ -131,7 +131,7 @@
    "source": [
     "Following the suggestions to register new labels:\n",
     "\n",
-    "Bulk creating records using {meth}`~lamindb.core.CanValidate.from_values` only returns validated records:\n",
+    "Bulk creating records using {meth}`~lamindb.core.CanCurate.from_values` only returns validated records:\n",
     "\n",
     "Note: Terms validated with public reference are also created with `.from_values`, see {doc}`/bio-registries` for details."
    ]

diff --git a/lamindb/__init__.py b/lamindb/__init__.py
@@ -79,7 +79,7 @@ def __getattr__(name):
     from . import core  # isort: split
     from . import (
         _artifact,
-        _can_validate,
+        _can_curate,
         _collection,
         _curate,
         _feature,

diff --git a/lamindb/_can_validate.py → lamindb/_can_curate.py b/lamindb/_can_validate.py → lamindb/_can_curate.py
@@ -8,7 +8,7 @@
 from django.core.exceptions import FieldDoesNotExist
 from lamin_utils import colors, logger
 from lamindb_setup.core._docs import doc_args
-from lnschema_core import CanValidate, Record
+from lnschema_core import CanCurate, Record
 
 from ._from_values import _has_organism_field, _print_values, get_or_create_records
 from ._record import _queryset, get_name_field
@@ -23,7 +23,7 @@
 
 # from_values doesn't apply for QuerySet or Manager
 @classmethod  # type:ignore
-@doc_args(CanValidate.from_values.__doc__)
+@doc_args(CanCurate.from_values.__doc__)
 def from_values(
     cls,
     values: ListLike,
@@ -49,7 +49,7 @@ def from_values(
 
 
 @classmethod  # type: ignore
-@doc_args(CanValidate.inspect.__doc__)
+@doc_args(CanCurate.inspect.__doc__)
 def inspect(
     cls,
     values: ListLike,
@@ -71,7 +71,7 @@ def inspect(
 
 
 @classmethod  # type: ignore
-@doc_args(CanValidate.validate.__doc__)
+@doc_args(CanCurate.validate.__doc__)
 def validate(
     cls,
     values: ListLike,
@@ -268,7 +268,7 @@ def _validate(
 
 
 @classmethod  # type: ignore
-@doc_args(CanValidate.standardize.__doc__)
+@doc_args(CanCurate.standardize.__doc__)
 def standardize(
     cls,
     values: ListLike,
@@ -621,10 +621,10 @@ def _field_is_id(field: str, registry: type[Record]) -> bool:
     from inspect import signature
 
     SIGS = {
-        name: signature(getattr(CanValidate, name))
+        name: signature(getattr(CanCurate, name))
         for name in METHOD_NAMES
         if not name.startswith("__")
     }
 
 for name in METHOD_NAMES:
-    attach_func_to_class_method(name, CanValidate, globals())
+    attach_func_to_class_method(name, CanCurate, globals())
diff --git a/lamindb/_curate.py b/lamindb/_curate.py
@@ -1731,7 +1731,7 @@ def _save_organism(name: str):  # pragma: no cover
 
 def _ref_is_name(field: FieldAttr) -> bool | None:
     """Check if the reference field is a name field."""
-    from ._can_validate import get_name_field
+    from ._can_curate import get_name_field
 
     name_field = get_name_field(field.field.model)
     return field.field.name == name_field

diff --git a/lamindb/_query_set.py b/lamindb/_query_set.py
@@ -12,7 +12,7 @@
 from lamindb_setup.core._docs import doc_args
 from lnschema_core.models import (
     Artifact,
-    CanValidate,
+    CanCurate,
     Collection,
     IsVersioned,
     Record,
@@ -354,7 +354,7 @@ def latest_version(self) -> QuerySet:
 
 
 # -------------------------------------------------------------------------------------
-# CanValidate
+# CanCurate
 # -------------------------------------------------------------------------------------
 
 
@@ -374,26 +374,26 @@ def lookup(self, field: StrField | None = None, **kwargs) -> NamedTuple:
     return _lookup(cls=self, field=field, **kwargs)
 
 
-@doc_args(CanValidate.validate.__doc__)
+@doc_args(CanCurate.validate.__doc__)
 def validate(self, values: ListLike, field: str | StrField | None = None, **kwargs):
     """{}"""  # noqa: D415
-    from ._can_validate import _validate
+    from ._can_curate import _validate
 
     return _validate(cls=self, values=values, field=field, **kwargs)
 
 
-@doc_args(CanValidate.inspect.__doc__)
+@doc_args(CanCurate.inspect.__doc__)
 def inspect(self, values: ListLike, field: str | StrField | None = None, **kwargs):
     """{}"""  # noqa: D415
-    from ._can_validate import _inspect
+    from ._can_curate import _inspect
 
     return _inspect(cls=self, values=values, field=field, **kwargs)
 
 
-@doc_args(CanValidate.standardize.__doc__)
+@doc_args(CanCurate.standardize.__doc__)
 def standardize(self, values: Iterable, field: str | StrField | None = None, **kwargs):
     """{}"""  # noqa: D415
-    from ._can_validate import _standardize
+    from ._can_curate import _standardize
 
     return _standardize(cls=self, values=values, field=field, **kwargs)
 

diff --git a/lamindb/core/__init__.py b/lamindb/core/__init__.py
@@ -14,7 +14,7 @@
    ParamManager
    LabelManager
    IsVersioned
-   CanValidate
+   CanCurate
    HasParents
    TracksRun
    TracksUpdates
@@ -68,7 +68,7 @@
 from lamin_utils import logger
 from lamin_utils._inspect import InspectResult
 from lnschema_core.models import (
-    CanValidate,
+    CanCurate,
     FeatureValue,
     HasParents,
     IsVersioned,

diff --git a/lamindb/core/_django.py b/lamindb/core/_django.py
@@ -33,7 +33,7 @@ def get_artifact_with_related(
     include_featureset: bool = False,
 ) -> dict:
     """Fetch an artifact with its related data."""
-    from lamindb._can_validate import get_name_field
+    from lamindb._can_curate import get_name_field
 
     from ._label_manager import LABELS_EXCLUDE_SET
 
@@ -163,7 +163,7 @@ def get_featureset_m2m_relations(
     artifact: Artifact, slot_featureset: dict, limit: int = 20
 ):
     """Fetch all many-to-many relationships for given feature sets."""
-    from lamindb._can_validate import get_name_field
+    from lamindb._can_curate import get_name_field
 
     m2m_relations = [
         v

diff --git a/lamindb/core/_label_manager.py b/lamindb/core/_label_manager.py
@@ -6,7 +6,7 @@
 import numpy as np
 from django.db import connections
 from lamin_utils import colors, logger
-from lnschema_core.models import CanValidate, Feature
+from lnschema_core.models import CanCurate, Feature
 
 from lamindb._from_values import _print_values
 from lamindb._record import (
@@ -116,7 +116,7 @@ def validate_labels_registry(
             label_uids = np.array(
                 [getattr(label, field) for label in labels if label is not None]
             )
-        if issubclass(registry, CanValidate):
+        if issubclass(registry, CanCurate):
             validated = registry.validate(label_uids, field=field, mute=True)
             validated_uids = label_uids[validated]
             validated_labels = registry.filter(

diff --git a/sub/bionty b/sub/bionty
diff --git a/sub/cellregistry b/sub/cellregistry
diff --git a/sub/clinicore b/sub/clinicore
diff --git a/sub/findrefs b/sub/findrefs
diff --git a/sub/lnschema-core b/sub/lnschema-core
diff --git a/sub/omop b/sub/omop
diff --git a/sub/ourprojects b/sub/ourprojects
diff --git a/sub/wetlab b/sub/wetlab
diff --git a/tests/core/test_parents.py b/tests/core/test_parents.py
@@ -1,7 +1,7 @@
 import lamindb as ln
 import pytest
-from django.core.exceptions import ValidationError
 from lamindb._parents import _add_emoji
+from lnschema_core.validation import FieldValidationError
 
 
 def test_view_parents():
@@ -38,7 +38,8 @@ def test_query_parents_children():
 def test_add_emoji():
     record = ln.Transform(type="upload")
     assert _add_emoji(record, label="transform") == "🖥️ transform"
-    with pytest.raises(ValidationError):
+    # validate literal
+    with pytest.raises(FieldValidationError):
         transform = ln.Transform(name="test", type="app")
     transform = ln.Transform(name="test", type="upload")
     transform.save()