[tests] - test adapter + results

nwb_linkml/pyproject.toml

@@ -5,11 +5,15 @@ description = "Translating NWB schema language to LinkML"
 authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]
 license = "GPL-3.0"
 readme = "README.md"
+homepage = "https://nwb-linkml.readthedocs.io"
+repository = "https://github.com/p2p-ld/nwb-linkml/"
+documentation = "https://nwb-linkml.readthedocs.io"
 packages = [
     {include = "nwb_linkml", from="src"},
     #{include = "nwb_schema_language", from="../nwb_schema_language/src"}
 ]
 
+
 [tool.poetry.dependencies]
 python = ">=3.11,<3.13"
 pyyaml = "^6.0"

nwb_linkml/src/nwb_linkml/adapters/adapter.py

@@ -8,6 +8,7 @@ from dataclasses import dataclass, field
 from typing import List, Dict, Type, Generator, Any, Tuple, Optional, TypeVar, TypeVarTuple, Unpack, Literal
 from pydantic import BaseModel, Field, validator
 from linkml_runtime.linkml_model import Element, SchemaDefinition, ClassDefinition, SlotDefinition, TypeDefinition
+from nwb_schema_language import Dataset, Attribute, Schema, Group
 
 # SchemaDefClass = dataclass(SchemaDefinition).__pydantic_model__
 
@@ -60,7 +61,7 @@ class BuildResult:
 
         return out_str
 
-T = TypeVar
+T = TypeVar('T', Dataset, Attribute, Schema, Group)
 Ts = TypeVarTuple('Ts')
 
 class Adapter(BaseModel):
@@ -148,7 +149,7 @@ class Adapter(BaseModel):
 
 
 
-    def walk_types(self, input: BaseModel | list | dict, get_type: T | List[Unpack[Ts]] | Tuple[Unpack[T]]) -> Generator[T, None, None]:
+    def walk_types(self, input: BaseModel | list | dict, get_type: Type[T] | Tuple[Type[T], Type[Unpack[Ts]]]) -> Generator[T | Ts, None, None]:
         if not isinstance(get_type, (list, tuple)):
             get_type = [get_type]
 

nwb_linkml/tests/test_adapters/test_adapter.py

@@ -1,10 +1,11 @@
 import pdb
 
+import numpy as np
 import pytest
 from ..fixtures import nwb_core_fixture
 
 from linkml_runtime.linkml_model import SchemaDefinition, ClassDefinition, SlotDefinition, TypeDefinition
-from nwb_schema_language import Dataset, Group, Schema, CompoundDtype
+from nwb_schema_language import Dataset, Group, Schema, CompoundDtype, Attribute
 
 from nwb_linkml.adapters import BuildResult
 
@@ -32,13 +33,22 @@ def test_walk_types(nwb_core_fixture, walk_class, known_number):
     assert len(class_list) == known_number
 
 def test_walk_fields(nwb_core_fixture):
-    dtype = nwb_core_fixture.walk_fields(nwb_core_fixture, 'dtype')
+    # should get same number of dtype fields as there are datasets and attributes + compound dtypes
+    dtype = list(nwb_core_fixture.walk_fields(nwb_core_fixture, 'dtype'))
+
+    dtype_havers = list(nwb_core_fixture.walk_types(nwb_core_fixture, (Dataset, Attribute)))
+    compound_dtypes = [len(d.dtype) for d in dtype_havers if isinstance(d.dtype, list)]
+    expected_dtypes = np.sum(compound_dtypes) + len(dtype_havers)
+    assert expected_dtypes == len(dtype)
 
 
 def test_walk_field_values(nwb_core_fixture):
     dtype_models = list(nwb_core_fixture.walk_field_values(nwb_core_fixture, 'dtype', value=None))
-
-    compounds = [d for d in dtype_models if isinstance(d.dtype, list) and len(d.dtype) > 0 and isinstance(d.dtype[0], CompoundDtype)]
+    assert all([hasattr(d, 'dtype') for d in dtype_models])
+    text_models = list(nwb_core_fixture.walk_field_values(nwb_core_fixture, 'dtype', value='text'))
+    assert all([d.dtype == 'text' for d in text_models])
+    # 135 known value from regex search
+    assert len(text_models) == len([d for d in dtype_models if d.dtype == 'text']) == 135
 
 
 def test_build_result(linkml_schema_bare):