Fix #204 and the remainder of the HPOA evaluation (#207)

Repair the test for HPOA evaluation, its fixtures, and the associated evaluation functions.

src/ontogpt/evaluation/hpoa/eval_hpoa.py

@@ -7,7 +7,7 @@
 from random import shuffle
 from typing import Dict, Iterable, Iterator, List, Tuple
 
-from oaklib import BasicOntologyInterface, get_implementation_from_shorthand
+from oaklib import BasicOntologyInterface, get_adapter
 from oaklib.datamodels.search import SearchConfiguration
 from oaklib.datamodels.search_datamodel import SearchProperty
 from oaklib.interfaces import SearchInterface
@@ -18,12 +18,10 @@
 from ontogpt.evaluation.evaluation_engine import SimilarityScore, SPIRESEvaluationEngine
 from ontogpt.templates.mendelian_disease import MendelianDisease
 
-THIS_DIR = Path(__file__).parent
 DATABASE_DIR = Path(__file__).parent / "database"
-TEST_CASES_DIR = THIS_DIR / "test_cases"
-EXEMPLARS_DIR = THIS_DIR / "exemplars"
-EXEMPLAR_CASES = EXEMPLARS_DIR / "drugmechdb-exemplars.yaml"
-
+TEST_CASES_DIR = Path("tests").joinpath("input")
+TEST_HPOA_FILE = "test_sample.hpoa.tsv"
+NUM_TESTS = 3 # Note: each test requires input text; see provided test cases
 
 DISEASE_ID = str
 TERM = str
@@ -72,18 +70,18 @@ class EvalHPOA(SPIRESEvaluationEngine):
 
     def __post_init__(self):
         self.extractor = SPIRESEngine("mendelian_disease.MendelianDisease")
-        self.mondo = get_implementation_from_shorthand("sqlite:obo:mondo")
+        self.mondo = get_adapter("sqlite:obo:mondo")
 
     def load_test_cases(self) -> List[MendelianDisease]:
         return []
 
     def disease_text(self, id: str):
-        id = id.replace("OMIM:", "omim-")
-        with open(TEST_CASES_DIR / f"{id}.txt") as f:
+        id = id.lower().replace(":", "-")
+        with open(TEST_CASES_DIR / "cases" / f"{id}.txt") as f:
             return f.read()
 
     def parse_hpoa(self) -> Iterator[HPOAnnotation]:
-        with open(TEST_CASES_DIR / "test.hpoa.tsv") as file:
+        with open(TEST_CASES_DIR / TEST_HPOA_FILE) as file:
             reader = csv.reader(file, delimiter="\t")
             for row in reader:
                 yield HPOAnnotation(
@@ -155,7 +153,7 @@ def enhance(self, obj: MendelianDisease):
         obj.name = mondo.label(entity)
         obj.label = obj.name
         obj.description = mondo.definition(entity)
-        obj.subclass_of = list(mondo.hierararchical_parents(entity))
+        obj.subclass_of = list(mondo.hierarchical_parents(entity))
         obj.synonyms = list(mondo.entity_aliases(entity))
         for _s, _p, gene in mondo.relationships([entity], ["RO:0004003"]):
             gene = (
@@ -176,15 +174,15 @@ def eval(self, task: str = None, **kwargs) -> EvaluationObjectSetHPOA:
         else:
             raise ValueError(f"Unknown task {task}")
 
-    def eval_against_pubs(self, num_tests=3) -> EvaluationObjectSetHPOA:
+    def eval_against_pubs(self, num_tests=NUM_TESTS) -> EvaluationObjectSetHPOA:
         ke = self.extractor
         pmc = PubmedClient()
         eos = EvaluationObjectSetHPOA()
         eos.test = list(self.diseases_by_publication().values())
         eos.training = []
         eos.predictions = []
         shuffle(eos.test)
-        for test_case in eos.test[0:num_tests]:
+        for test_case in eos.test[0:num_tests-1]:
             # text = self.disease_text(test_case.id)
             if len(test_case.publications) != 1:
                 raise ValueError(f"Expected 1 publication, got {len(test_case.publications)}")
@@ -204,7 +202,7 @@ def eval_against_omim_plus_pubs(self, **kwargs) -> EvaluationObjectSetHPOA:
         return self.eval_against_omim_or_pubs(use_publications=True)
 
     def eval_against_omim_or_pubs(
-        self, num_tests=3, use_publications=False
+        self, num_tests=NUM_TESTS, use_publications=False
     ) -> EvaluationObjectSetHPOA:
         ke = self.extractor
         eos = EvaluationObjectSetHPOA()

tests/input/cases/omim-608716.txt

@@ -0,0 +1 @@
+Autosomal recessive primary microcephaly-5 (MCPH5) is characterized by decreased occipitofrontal circumference (OFC), usually less than 3 standard deviations (SD) of the mean, present at birth and associated with mental retardation and speech delay. Other features may include short stature or mild seizures. MCPH5 is associated with a simplification of the cerebral cortical gyral pattern in some cases, which is considered within the phenotypic spectrum of primary microcephaly (review by Woods et al., 2005; Saadi et al., 2009; Passemard et al., 2009). 

tests/input/cases/omim-619428.txt

@@ -0,0 +1 @@
+Focal segmental glomerulosclerosis and neurodevelopmental syndrome (FSGSNEDS) is characterized by global developmental delay and renal dysfunction manifest as proteinuria and nephrotic syndrome apparent from infancy or early childhood. Some patients present with renal disease, whereas others present with developmental delay and develop renal disease later in childhood. Renal biopsy shows focal segmental glomerulosclerosis (FSGS), but the course of the disease is variable: some patients have transient proteinuria and others require renal transplant. Neurodevelopmental features are also variable, with some patients having only mildly impaired intellectual development, and others having a severe developmental disorder associated with early-onset refractory seizures or epileptic encephalopathy. Additional features, including feeding difficulties, poor overall growth, and nonspecific dysmorphic facial features, are commonly observed (summary by Assoum et al., 2018 and Weng et al., 2021). 

tests/input/cases/omim-620038.txt

@@ -0,0 +1 @@
+Neurodevelopmental disorder with microcephaly, hypotonia, and absent language (NEDMHAL) is a severe autosomal recessive disorder characterized by the constellation of these features. Behavioral problems and hearing loss are also present (Ansar et al., 2020).