Split HPO phenotypes and diseases and use as fixtures.

tests/conftest.py

@@ -1,4 +1,5 @@
 import os
+import typing
 
 import hpotk
 import pytest
@@ -45,17 +46,19 @@ def toy_validation_runner(toy_hpo: hpotk.MinimalOntology) -> hpotk.validate.Vali
 def make_region(contig: str, start: int, end: int) -> GenomicRegion:
     return GenomicRegion(GRCh38.contig_by_name(contig), start, end, Strand.POSITIVE)
 
+
 @pytest.fixture(scope='session')
 def protein_test_service() -> ProteinTestMetadataService:
     return ProteinTestMetadataService()
 
-@pytest.fixture
-def toy_cohort() -> Cohort:
 
+@pytest.fixture(scope='session')
+def toy_cohort(
+        test_phenotypes: typing.Mapping[str, Phenotype],
+        test_diseases: typing.Mapping[str, Disease],
+) -> Cohort:
     prot_id = 'NP_037407.4'
 
-    phenos = get_test_phenotypes()
-
     dup = Variant(VariantCoordinates(make_region("16", 89279849, 89279850), ref='G', alt='GC', change_length=1),
                   [
                       TranscriptAnnotation('ANKRD11', 'NM_013275.6', 'NM_013275.6:c.6691dup', False, [VariantEffect.FRAMESHIFT_VARIANT], [9],
@@ -102,27 +105,38 @@ def toy_cohort() -> Cohort:
 
     patients = (
         Patient(SampleLabels('HetSingleVar'),
-                phenotypes=(phenos['arachnodactyly_T'], phenos['spasticity_F'], phenos['focal_clonic_seizure_T']),
+                phenotypes=(
+                    test_phenotypes['arachnodactyly_T'],
+                    test_phenotypes['spasticity_F'],
+                    test_phenotypes['focal_clonic_seizure_T']),
                 variants=(dup,),
-                diseases=(phenos['KBG_T'],)
+                diseases=(test_diseases['KBG_T'],)
                 ),
         Patient(SampleLabels('HetDoubleVar1'),
-                phenotypes=(phenos['arachnodactyly_T'], phenos['seizure_T'], phenos['spasticity_T']),
+                phenotypes=(
+                    test_phenotypes['arachnodactyly_T'], test_phenotypes['seizure_T'], test_phenotypes['spasticity_T'],
+                ),
                 variants=(indel, snv_stop_gain),
-                diseases=(phenos['KBG_T'],)
+                diseases=(test_diseases['KBG_T'],)
                 ),
         Patient(SampleLabels('HetDoubleVar2'),
-                phenotypes=(phenos['arachnodactyly_F'], phenos['spasticity_T'], phenos['seizure_T']),
+                phenotypes=(
+                    test_phenotypes['arachnodactyly_F'], test_phenotypes['spasticity_T'], test_phenotypes['seizure_T'],
+                ),
                 variants=(snv_missense, del_frameshift),
-                diseases=(phenos['KBG_T'],)
+                diseases=(test_diseases['KBG_T'],)
                 ),
         Patient(SampleLabels('HomoVar'),
-                phenotypes=(phenos['arachnodactyly_T'], phenos['spasticity_T'], phenos['seizure_T']),
+                phenotypes=(
+                    test_phenotypes['arachnodactyly_T'], test_phenotypes['spasticity_T'], test_phenotypes['seizure_T'],
+                ),
                 variants=(del_small,),
                 diseases=()
                 ),
         Patient(SampleLabels('LargeCNV'),
-                phenotypes=(phenos['arachnodactyly_T'], phenos['spasticity_T'], phenos['seizure_F']),
+                phenotypes=(
+                    test_phenotypes['arachnodactyly_T'], test_phenotypes['spasticity_T'], test_phenotypes['seizure_F'],
+                ),
                 variants=(del_large,),
                 diseases=()
                 ),
@@ -131,19 +145,28 @@ def toy_cohort() -> Cohort:
     return Cohort.from_patients(patients)
 
 
-def get_test_phenotypes():
-    phenotypes = {}
-
-    phenotypes['arachnodactyly_T'] = Phenotype(hpotk.TermId.from_curie('HP:0001166'), "Arachnodactyly", True)
-    phenotypes['seizure_T'] = Phenotype(hpotk.TermId.from_curie('HP:0001250'), "Seizure", True)
-    phenotypes['focal_clonic_seizure_T'] = Phenotype(hpotk.TermId.from_curie('HP:0002266'), "Focal clonic seizure", True)
-    phenotypes['spasticity_T'] = Phenotype(hpotk.TermId.from_curie('HP:0001257'), "Spasticity", True)
-    phenotypes['arachnodactyly_F'] = Phenotype(hpotk.TermId.from_curie('HP:0001166'), "Arachnodactyly", False)
-    phenotypes['seizure_F'] = Phenotype(hpotk.TermId.from_curie('HP:0001250'), "Seizure", False)
-    phenotypes['spasticity_F'] = Phenotype(hpotk.TermId.from_curie('HP:0001257'), "Spasticity", False)
-    phenotypes['focal_clonic_seizure_F'] = Phenotype(hpotk.TermId.from_curie('HP:0002266'), "Focal clonic seizure", False)
-    phenotypes['KBG_T'] = Disease(hpotk.TermId.from_curie("OMIM:148050"), "KBG syndrome", True)
-    phenotypes['KBG_F'] = Disease(hpotk.TermId.from_curie("OMIM:148050"), "KBG syndrome", False)
+@pytest.fixture(scope='session')
+def test_phenotypes() -> typing.Mapping[str, Phenotype]:
+    return {
+        'arachnodactyly_T': Phenotype(hpotk.TermId.from_curie('HP:0001166'), "Arachnodactyly", True),
+        'seizure_T': Phenotype(hpotk.TermId.from_curie('HP:0001250'), "Seizure", True),
+        'focal_clonic_seizure_T': Phenotype(
+            hpotk.TermId.from_curie('HP:0002266'), "Focal clonic seizure", True,
+        ),
+        'spasticity_T': Phenotype(hpotk.TermId.from_curie('HP:0001257'), "Spasticity", True),
+
+        'arachnodactyly_F': Phenotype(hpotk.TermId.from_curie('HP:0001166'), "Arachnodactyly", False),
+        'seizure_F': Phenotype(hpotk.TermId.from_curie('HP:0001250'), "Seizure", False),
+        'spasticity_F': Phenotype(hpotk.TermId.from_curie('HP:0001257'), "Spasticity", False),
+        'focal_clonic_seizure_F': Phenotype(
+            hpotk.TermId.from_curie('HP:0002266'), "Focal clonic seizure", False,
+        ),
+    }
 
-    return phenotypes
 
+@pytest.fixture(scope='session')
+def test_diseases() -> typing.Mapping[str, Disease]:
+    return {
+        'KBG_T': Disease(hpotk.TermId.from_curie("OMIM:148050"), "KBG syndrome", True),
+        'KBG_F': Disease(hpotk.TermId.from_curie("OMIM:148050"), "KBG syndrome", False),
+    }