tests: add importorskip for annotation tests

Author: bencap

tests/lib/annotation/test_agent.py

@@ -1,7 +1,11 @@
+# ruff: noqa: E402
+
 from unittest.mock import Mock
 
 import pytest
 
+pytest.importorskip("psycopg2")
+
 from mavedb import __version__
 from mavedb.lib.annotation.agent import mavedb_api_agent, mavedb_user_agent, mavedb_vrs_agent
 from mavedb.models.user import User

tests/lib/annotation/test_annotate.py

@@ -5,10 +5,14 @@
 for variants, focusing on object structure and validation.
 """
 
+# ruff: noqa: E402
+
 from copy import deepcopy
 
 import pytest
 
+pytest.importorskip("psycopg2")
+
 from mavedb.lib.annotation.annotate import (
     variant_functional_impact_statement,
     variant_pathogenicity_statement,
@@ -247,6 +251,7 @@ def test_variant_not_in_any_range_returns_uncertain_significance(
         from unittest.mock import patch
 
         from ga4gh.va_spec.acmg_2015 import VariantPathogenicityEvidenceLine
+
         from mavedb.lib.annotation.classification import ExperimentalVariantFunctionalImpactClassification
 
         mapped_variant = mock_mapped_variant_with_pathogenicity_calibration_score_set

tests/lib/annotation/test_classification.py

@@ -1,3 +1,5 @@
+# ruff: noqa: E402
+
 """
 Tests for mavedb.lib.annotation.classification module.
 
@@ -9,6 +11,9 @@
 from unittest.mock import MagicMock
 
 import pytest
+
+pytest.importorskip("psycopg2")
+
 from ga4gh.va_spec.acmg_2015 import VariantPathogenicityEvidenceLine
 from ga4gh.va_spec.base.enums import StrengthOfEvidenceProvided as GA4GHStrengthOfEvidenceProvided
 

tests/lib/annotation/test_condition.py

@@ -5,7 +5,12 @@
 specifically for generic disease conditions used in variant annotations.
 """
 
+# ruff: noqa: E402
+
 import pytest
+
+pytest.importorskip("psycopg2")
+
 from ga4gh.core.models import Coding, MappableConcept
 from ga4gh.core.models import iriReference as IRI
 from ga4gh.va_spec.base.domain_entities import Condition

tests/lib/annotation/test_constants.py

@@ -4,8 +4,12 @@
 This module tests constant values used throughout the annotation system.
 """
 
+# ruff: noqa: E402
+
 import pytest
 
+pytest.importorskip("psycopg2")
+
 from mavedb.lib.annotation.constants import (
     GENERIC_DISEASE_MEDGEN_CODE,
     MEDGEN_SYSTEM,

tests/lib/annotation/test_contribution.py

@@ -5,9 +5,14 @@
 including API, VRS mapping, score calibration, creator, and modifier contributions.
 """
 
+# ruff: noqa: E402
+
 from datetime import datetime
 
 import pytest
+
+pytest.importorskip("psycopg2")
+
 from ga4gh.core.models import Extension
 from ga4gh.va_spec.base import Contribution
 

tests/lib/annotation/test_dataset.py

@@ -1,3 +1,5 @@
+# ruff: noqa: E402
+
 """
 Tests for mavedb.lib.annotation.dataset module.
 
@@ -8,6 +10,9 @@
 from datetime import date
 
 import pytest
+
+pytest.importorskip("psycopg2")
+
 from ga4gh.core.models import Coding, MappableConcept
 from ga4gh.core.models import iriReference as IRI
 from ga4gh.va_spec.base import DataSet

tests/lib/annotation/test_direction.py

@@ -1,6 +1,11 @@
+# ruff: noqa: E402
+
 from unittest.mock import Mock
 
 import pytest
+
+pytest.importorskip("psycopg2")
+
 from ga4gh.va_spec.acmg_2015 import VariantPathogenicityEvidenceLine
 from ga4gh.va_spec.base.core import Direction, EvidenceLine
 

tests/lib/annotation/test_document.py

@@ -1,3 +1,5 @@
+# ruff: noqa: E402
+
 """
 Tests for mavedb.lib.annotation.document module.
 
@@ -9,6 +11,9 @@
 
 import pytest
 
+pytest.importorskip("psycopg2")
+
+
 from mavedb.lib.annotation.document import (
     experiment_as_iri,
     experiment_to_document,

tests/lib/annotation/test_evidence_line.py

@@ -1,3 +1,5 @@
+# ruff: noqa: E402
+
 """
 Tests for mavedb.lib.annotation.evidence_line module.
 
@@ -8,6 +10,9 @@
 from unittest.mock import MagicMock, patch
 
 import pytest
+
+pytest.importorskip("psycopg2")
+
 from ga4gh.va_spec.acmg_2015 import VariantPathogenicityEvidenceLine
 from ga4gh.va_spec.base.core import Direction, EvidenceLine
 from ga4gh.va_spec.base.enums import StrengthOfEvidenceProvided