Remove 'name' field and add 'notes' field to score calibrations

Author: bencap

alembic/versions/8886f0453125_remove_name_add_notes_to_calibrations.py

@@ -0,0 +1,31 @@
+"""remove name add notes to calibrations
+
+Revision ID: 8886f0453125
+Revises: f5a72192fafd
+Create Date: 2025-10-19 13:21:14.338094
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "8886f0453125"
+down_revision = "f5a72192fafd"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column("score_calibrations", sa.Column("notes", sa.String(), nullable=True))
+    op.drop_column("score_calibrations", "name")
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column("score_calibrations", sa.Column("name", sa.VARCHAR(), autoincrement=False, nullable=False))
+    op.drop_column("score_calibrations", "notes")
+    # ### end Alembic commands ###

src/mavedb/models/score_calibration.py

@@ -31,11 +31,11 @@ class ScoreCalibration(Base):
     score_set: Mapped["ScoreSet"] = relationship("ScoreSet", back_populates="score_calibrations")
 
     title = Column(String, nullable=False)
-    name = Column(String, nullable=False)
     research_use_only = Column(Boolean, nullable=False, default=False)
     primary = Column(Boolean, nullable=False, default=False)
     investigator_provided = Column(Boolean, nullable=False, default=False)
     private = Column(Boolean, nullable=False, default=True)
+    notes = Column(String, nullable=True)
 
     baseline_score = Column(Float, nullable=True)
     baseline_score_description = Column(String, nullable=True)

src/mavedb/view_models/score_calibration.py

@@ -178,12 +178,12 @@ class ScoreCalibrationBase(BaseModel):
     """
 
     title: str
-    name: str
     investigator_provided: bool
     research_use_only: bool = False
 
     baseline_score: Optional[float] = None
     baseline_score_description: Optional[str] = None
+    notes: Optional[str] = None
 
     functional_ranges: Optional[Sequence[FunctionalRangeBase]] = None
     threshold_sources: Optional[Sequence[PublicationIdentifierBase]] = None

tests/helpers/constants.py

@@ -1485,7 +1485,6 @@
 
 TEST_BRNICH_SCORE_CALIBRATION = {
     "title": "Test BRNICH Score Calibration",
-    "name": "brnich_style",
     "research_use_only": False,
     "investigator_provided": False,
     "baseline_score": TEST_BASELINE_SCORE,
@@ -1542,19 +1541,16 @@
 
 TEST_INVESTIGATOR_PROVIDED_SCORE_CALIBRATION = {
     **TEST_BRNICH_SCORE_CALIBRATION,
-    "name": "investigator_provided",
     "investigator_provided": True,
 }
 
 TEST_SAVED_INVESTIGATOR_PROVIDED_SCORE_CALIBRATION = {
     **TEST_SAVED_BRNICH_SCORE_CALIBRATION,
-    "name": "investigator_provided",
     "investigatorProvided": True,
 }
 
 TEST_PATHOGENICITY_SCORE_CALIBRATION = {
     "title": "Test Pathogenicity Score Calibration",
-    "name": "pathogenicity",
     "research_use_only": False,
     "investigator_provided": False,
     "baseline_score": TEST_BASELINE_SCORE,

tests/view_models/test_score_calibration.py

@@ -173,7 +173,6 @@ def test_can_create_valid_score_calibration(valid_calibration):
     sc = ScoreCalibrationCreate.model_validate(valid_calibration)
 
     assert sc.title == valid_calibration["title"]
-    assert sc.name == valid_calibration["name"]
     assert sc.research_use_only == valid_calibration.get("research_use_only", False)
     assert sc.investigator_provided == valid_calibration.get("investigator_provided", False)
     assert sc.baseline_score == valid_calibration.get("baseline_score")
@@ -225,7 +224,6 @@ def test_can_create_valid_score_calibration_without_functional_ranges(valid_cali
     sc = ScoreCalibrationCreate.model_validate(valid_calibration)
 
     assert sc.title == valid_calibration["title"]
-    assert sc.name == valid_calibration["name"]
     assert sc.research_use_only == valid_calibration.get("research_use_only", False)
     assert sc.investigator_provided == valid_calibration.get("investigator_provided", False)
     assert sc.baseline_score == valid_calibration.get("baseline_score")
@@ -336,7 +334,6 @@ def test_can_create_valid_score_calibration_from_attributed_object(valid_calibra
     sc = ScoreCalibration.model_validate(dummy_attributed_object_from_dict(valid_calibration))
 
     assert sc.title == valid_calibration["title"]
-    assert sc.name == valid_calibration["name"]
     assert sc.research_use_only == valid_calibration.get("researchUseOnly", False)
     assert sc.primary == valid_calibration.get("primary", True)
     assert sc.investigator_provided == valid_calibration.get("investigatorProvided", False)
@@ -411,7 +408,6 @@ def test_can_create_score_calibration_from_association_style_publication_identif
     sc = ScoreCalibration.model_validate(dummy_attributed_object_from_dict(data))
 
     assert sc.title == orig_data["title"]
-    assert sc.name == orig_data["name"]
     assert sc.research_use_only == orig_data.get("research_use_only", False)
     assert sc.primary == orig_data.get("primary", False)
     assert sc.investigator_provided == orig_data.get("investigator_provided", False)
@@ -474,7 +470,6 @@ def test_score_calibration_with_score_set_urn_can_be_created_from_attributed_obj
     sc = ScoreCalibrationWithScoreSetUrn.model_validate(dummy_attributed_object_from_dict(data))
 
     assert sc.title == data["title"]
-    assert sc.name == data["name"]
     assert sc.score_set_urn == data["score_set"].urn