Fix IRI references in tests after MyPy changes

Author: bencap

src/mavedb/lib/annotation/document.py

@@ -30,7 +30,7 @@ def experiment_to_document(experiment: Experiment) -> Document:
         id=experiment.urn,
         label="MaveDB experiment",
         title=experiment.title,
-        urls=[experiment_as_iri(experiment)],
+        urls=[experiment_as_iri(experiment).root],
     )
 
 
@@ -51,7 +51,7 @@ def score_set_to_document(score_set: ScoreSet) -> Document:
         id=score_set.urn,
         label="MaveDB score set",
         title=score_set.title,
-        urls=[score_set_as_iri(score_set)],
+        urls=[score_set_as_iri(score_set).root],
     )
 
 
@@ -62,7 +62,7 @@ def variant_as_iri(variant: Variant) -> IRI:
     """
     # TODO: We should decide if this should instead link to the variant measurement page.
     # TODO(#372): nullable URN.
-    return f"https://mavedb.org/score-sets/{variant.score_set.urn}?variant={urllib.parse.quote_plus(variant.urn)}"  # type: ignore
+    return IRI(f"https://mavedb.org/score-sets/{variant.score_set.urn}?variant={urllib.parse.quote_plus(variant.urn)}")  # type: ignore
 
 
 def variant_to_document(variant: Variant) -> Document:
@@ -73,5 +73,5 @@ def variant_to_document(variant: Variant) -> Document:
     return Document(
         id=variant.urn,
         label="MaveDB variant",
-        urls=[variant_as_iri(variant)],
+        urls=[variant_as_iri(variant).root],
     )

tests/lib/annotation/test_document.py

@@ -13,8 +13,8 @@
 
 
 def test_experiment_as_iri(mock_experiment):
-    expected_iri = f"{BASE_URL}/experiments/{mock_experiment.urn}"
-    assert experiment_as_iri(mock_experiment) == expected_iri
+    expected_iri_root = f"{BASE_URL}/experiments/{mock_experiment.urn}"
+    assert experiment_as_iri(mock_experiment).root == expected_iri_root
 
 
 def test_experiment_to_document(mock_experiment):
@@ -24,12 +24,12 @@ def test_experiment_to_document(mock_experiment):
     assert document.label == "MaveDB experiment"
     assert document.title == mock_experiment.title
     assert len(document.urls) > 0
-    assert experiment_as_iri(mock_experiment) in document.urls
+    assert experiment_as_iri(mock_experiment).root in document.urls
 
 
 def test_score_set_as_iri(mock_score_set):
-    expected_iri = f"{BASE_URL}/score-sets/{mock_score_set.urn}"
-    assert score_set_as_iri(mock_score_set) == expected_iri
+    expected_iri_root = f"{BASE_URL}/score-sets/{mock_score_set.urn}"
+    assert score_set_as_iri(mock_score_set).root == expected_iri_root
 
 
 def test_score_set_to_document(mock_score_set):
@@ -39,12 +39,12 @@ def test_score_set_to_document(mock_score_set):
     assert document.label == "MaveDB score set"
     assert document.title == mock_score_set.title
     assert len(document.urls) > 0
-    assert score_set_as_iri(mock_score_set) in document.urls
+    assert score_set_as_iri(mock_score_set).root in document.urls
 
 
 def test_variant_as_iri(mock_variant):
-    expected_iri = f"https://mavedb.org/score-sets/{mock_variant.score_set.urn}?variant={urllib.parse.quote_plus(mock_variant.urn)}"
-    assert variant_as_iri(mock_variant) == expected_iri
+    expected_iri_root = f"https://mavedb.org/score-sets/{mock_variant.score_set.urn}?variant={urllib.parse.quote_plus(mock_variant.urn)}"
+    assert variant_as_iri(mock_variant).root == expected_iri_root
 
 
 def test_variant_to_document(mock_variant):
@@ -53,4 +53,4 @@ def test_variant_to_document(mock_variant):
     assert document.id == mock_variant.urn
     assert document.label == "MaveDB variant"
     assert len(document.urls) > 0
-    assert variant_as_iri(mock_variant) in document.urls
+    assert variant_as_iri(mock_variant).root in document.urls

tests/lib/annotation/test_method.py

@@ -25,7 +25,7 @@
 
 
 def test_publication_as_iri(mock_publication):
-    assert publication_as_iri(mock_publication) == mock_publication.url
+    assert publication_as_iri(mock_publication).root == mock_publication.url
 
 
 def test_publication_as_iri_no_url(mock_publication):
@@ -74,7 +74,7 @@ def test_nonexistent_primary_publication_identifiers_to_method(mock_publication)
 
 
 def test_mavedb_api_releases_as_iri():
-    assert mavedb_api_releases_as_iri() == MAVEDB_API_RELEASES_URL
+    assert mavedb_api_releases_as_iri().root == MAVEDB_API_RELEASES_URL
 
 
 def test_mavedb_api_as_method():
@@ -85,7 +85,7 @@ def test_mavedb_api_as_method():
 
 
 def test_mavedb_vrs_releases_as_iri():
-    assert mavedb_vrs_releases_as_iri() == MAVEDB_MAPPER_RELEASES_URL
+    assert mavedb_vrs_releases_as_iri().root == MAVEDB_MAPPER_RELEASES_URL
 
 
 def test_mavedb_vrs_as_method():
@@ -96,7 +96,7 @@ def test_mavedb_vrs_as_method():
 
 
 def test_pillar_project_calibrations_as_iri():
-    assert pillar_project_calibrations_as_iri() == MAVEDB_CALIBRATION_URL
+    assert pillar_project_calibrations_as_iri().root == MAVEDB_CALIBRATION_URL
 
 
 def test_pillar_project_calibration_method():
@@ -107,7 +107,7 @@ def test_pillar_project_calibration_method():
 
 
 def test_variant_interpretation_functional_guideline_as_iri():
-    assert variant_interpretation_functional_guideline_as_iri() == FUNCITONAL_GUIDELINES_URL
+    assert variant_interpretation_functional_guideline_as_iri().root == FUNCITONAL_GUIDELINES_URL
 
 
 def test_variant_interpretation_functional_guideline_method():
@@ -118,7 +118,7 @@ def test_variant_interpretation_functional_guideline_method():
 
 
 def test_variant_interpretation_clinical_guideline_as_iri():
-    assert variant_interpretation_clinical_guideline_as_iri() == CLINICAL_GUIDELINES_URL
+    assert variant_interpretation_clinical_guideline_as_iri().root == CLINICAL_GUIDELINES_URL
 
 
 def test_variant_interpretation_clinical_guideline_method():

tests/lib/annotation/test_variant.py

@@ -48,7 +48,7 @@ def test_mapped_variant_to_functional_classification_statement(mock_mapped_varia
     assert isinstance(result, AssayVariantEffectFunctionalClassificationStatement)
     assert result.classification == classification
     assert result.subjectVariant == MolecularVariation(**TEST_VALID_POST_MAPPED_VRS_ALLELE)
-    assert experiment_as_iri(mock_mapped_variant.variant.score_set.experiment) == result.objectAssay.root
+    assert experiment_as_iri(mock_mapped_variant.variant.score_set.experiment) == result.objectAssay
     assert len(result.reportedIn) > 0
     assert variant_to_document(mock_mapped_variant.variant) in result.reportedIn
     assert score_set_to_document(mock_mapped_variant.variant.score_set) in result.reportedIn
@@ -90,7 +90,7 @@ def test_mapped_variant_to_clinical_classification_statement(mock_mapped_variant
     assert isinstance(result, AssayVariantEffectClinicalClassificationStatement)
     assert result.classification == classification
     assert result.subjectVariant == MolecularVariation(**TEST_VALID_POST_MAPPED_VRS_ALLELE)
-    assert experiment_as_iri(mock_mapped_variant.variant.score_set.experiment) == result.objectAssay.root
+    assert experiment_as_iri(mock_mapped_variant.variant.score_set.experiment) == result.objectAssay
     assert len(result.reportedIn) > 0
     assert variant_to_document(mock_mapped_variant.variant) in result.reportedIn
     assert score_set_to_document(mock_mapped_variant.variant.score_set) in result.reportedIn
@@ -136,15 +136,13 @@ def test_annotation_for_variant(mock_mapped_variant):
     ):
         result = annotation_for_variant(mock_mapped_variant)
         assert isinstance(result, dict)
-        assert result[mock_mapped_variant.variant.urn]["AssayVariantEffectMeasurementStudyResult"].score == 1.0
+        assert result[mock_mapped_variant.variant.urn].AssayVariantEffectMeasurementStudyResult.score == 1.0
         assert (
-            result[mock_mapped_variant.variant.urn][
-                "AssayVariantEffectFunctionalClassificationStatement"
-            ].classification
+            result[mock_mapped_variant.variant.urn].AssayVariantEffectFunctionalClassificationStatement.classification
             == functional_classification
         )
         assert (
-            result[mock_mapped_variant.variant.urn]["AssayVariantEffectClinicalClassificationStatement"].classification
+            result[mock_mapped_variant.variant.urn].AssayVariantEffectClinicalClassificationStatement.classification
             == clinical_classification
         )
 
@@ -162,6 +160,6 @@ def test_annotation_for_variant_with_no_classifications(mock_mapped_variant):
     ):
         result = annotation_for_variant(mock_mapped_variant)
         assert isinstance(result, dict)
-        assert result[mock_mapped_variant.variant.urn]["AssayVariantEffectMeasurementStudyResult"].score == 1.0
-        assert result[mock_mapped_variant.variant.urn]["AssayVariantEffectFunctionalClassificationStatement"] is None
-        assert result[mock_mapped_variant.variant.urn]["AssayVariantEffectClinicalClassificationStatement"] is None
+        assert result[mock_mapped_variant.variant.urn].AssayVariantEffectMeasurementStudyResult.score == 1.0
+        assert result[mock_mapped_variant.variant.urn].AssayVariantEffectFunctionalClassificationStatement is None
+        assert result[mock_mapped_variant.variant.urn].AssayVariantEffectClinicalClassificationStatement is None