fix: remove legacy SamplePtID references and update schema to use SamplePointID

Author: jirhiker

alembic/versions/e71807682f57_add_sample_point_fields_to_minor_trace.py

@@ -10,7 +10,6 @@
 
 import sqlalchemy as sa
 from alembic import op
-from sqlalchemy.dialects import postgresql
 
 # revision identifiers, used by Alembic.
 revision: str = "e71807682f57"
@@ -21,10 +20,6 @@
 
 def upgrade() -> None:
     """Upgrade schema."""
-    op.add_column(
-        "NMA_MinorTraceChemistry",
-        sa.Column("nma_SamplePtID", postgresql.UUID(as_uuid=True), nullable=False),
-    )
     op.add_column(
         "NMA_MinorTraceChemistry",
         sa.Column("nma_SamplePointID", sa.String(length=10), nullable=False),
@@ -34,4 +29,3 @@ def upgrade() -> None:
 def downgrade() -> None:
     """Downgrade schema."""
     op.drop_column("NMA_MinorTraceChemistry", "nma_SamplePointID")
-    op.drop_column("NMA_MinorTraceChemistry", "nma_SamplePtID")

db/nma_legacy.py

@@ -774,7 +774,6 @@ class NMA_MinorTraceChemistry(Base):
     - nma_global_id: Original UUID PK, now UNIQUE for audit
     - chemistry_sample_info_id: Integer FK to NMA_Chemistry_SampleInfo.id
     - nma_chemistry_sample_info_uuid: Legacy UUID FK for audit
-    - nma_sample_pt_id: Legacy UUID FK (SamplePtID) for audit
     - nma_sample_point_id: Legacy SamplePointID string
     - nma_wclab_id: Legacy WCLab_ID string (audit)
     """
@@ -809,9 +808,6 @@ class NMA_MinorTraceChemistry(Base):
     )
 
     # Additional columns
-    nma_sample_pt_id: Mapped[Optional[uuid.UUID]] = mapped_column(
-        "nma_SamplePtID", UUID(as_uuid=True), nullable=False
-    )
     nma_sample_point_id: Mapped[Optional[str]] = mapped_column(
         "nma_SamplePointID", String(10), nullable=False
     )

tests/test_minor_trace_chemistry_transfer.py

@@ -36,5 +36,4 @@ def test_row_to_dict_includes_wclab_id():
 
     row_dict = transfer._row_to_dict(row)
     assert row_dict["nma_WCLab_ID"] == "LAB-123"
-    assert row_dict["nma_SamplePtID"] == sample_pt_id
     assert row_dict["nma_SamplePointID"] == "POINT-1"

tests/test_nma_chemistry_lineage.py

@@ -134,7 +134,6 @@ def test_nma_minor_trace_chemistry_columns():
         "id",  # Integer PK
         "nma_global_id",  # Legacy UUID
         "chemistry_sample_info_id",  # Integer FK
-        "nma_sample_pt_id",  # Legacy UUID FK
         "nma_sample_point_id",  # Legacy sample point id
         # from legacy
         "analyte",
@@ -175,7 +174,6 @@ def test_nma_minor_trace_chemistry_save_all_columns(shared_thing):
         mtc = NMA_MinorTraceChemistry(
             nma_global_id=_next_global_id(),
             chemistry_sample_info=sample_info,
-            nma_sample_pt_id=sample_info.nma_sample_pt_id,
             nma_sample_point_id=sample_info.nma_sample_point_id,
             analyte="As",
             sample_value=0.015,
@@ -197,7 +195,6 @@ def test_nma_minor_trace_chemistry_save_all_columns(shared_thing):
         assert mtc.id is not None  # Integer PK
         assert mtc.nma_global_id is not None  # Legacy UUID
         assert mtc.chemistry_sample_info_id == sample_info.id  # Integer FK
-        assert mtc.nma_sample_pt_id == sample_info.nma_sample_pt_id
         assert mtc.nma_sample_point_id == sample_info.nma_sample_point_id
         assert mtc.analyte == "As"
         assert mtc.sample_value == 0.015

transfers/minor_trace_chemistry_transfer.py

@@ -25,7 +25,6 @@
 - nma_global_id: Legacy UUID PK (GlobalID), UNIQUE for audit
 - chemistry_sample_info_id: Integer FK to NMA_Chemistry_SampleInfo.id
 - nma_chemistry_sample_info_uuid: Legacy UUID FK for audit
-- nma_sample_pt_id: Legacy UUID FK (SamplePtID) for audit
 - nma_sample_point_id: Legacy SamplePointID string
 """
 
@@ -149,7 +148,6 @@ def _transfer_hook(self, session: Session) -> None:
                 set_={
                     "chemistry_sample_info_id": excluded.chemistry_sample_info_id,
                     "nma_chemistry_sample_info_uuid": excluded.nma_chemistry_sample_info_uuid,
-                    "nma_SamplePtID": excluded.nma_SamplePtID,
                     "nma_SamplePointID": excluded.nma_SamplePointID,
                     "sample_value": excluded.sample_value,
                     "units": excluded.units,
@@ -216,7 +214,6 @@ def _row_to_dict(self, row) -> Optional[dict[str, Any]]:
             "chemistry_sample_info_id": chemistry_sample_info_id,
             # Legacy UUID FK for audit
             "nma_chemistry_sample_info_uuid": legacy_sample_pt_id,
-            "nma_SamplePtID": legacy_sample_pt_id,
             "nma_SamplePointID": sample_point_id,
             # Data columns
             "analyte": self._safe_str(row, "Analyte"),