BDMS-501: Implement read-only admin view for NMAMinorTraceChemistry

admin/views/minor_trace_chemistry.py

@@ -33,8 +33,8 @@ class MinorTraceChemistryAdmin(OcotilloModelView):
     # ========== Basic Configuration ==========
 
     identity = "n-m-a_-minor-trace-chemistry"
-    name = "Minor Trace Chemistry"
-    label = "Minor Trace Chemistry"
+    name = "NMA Minor Trace Chemistry"
+    label = "NMA Minor Trace Chemistry"
     icon = "fa fa-flask"
     pk_attr = "global_id"
     pk_type = uuid.UUID
@@ -53,33 +53,45 @@ def can_delete(self, request: Request) -> bool:
     list_fields = [
         "global_id",
         HasOne("chemistry_sample_info", identity="n-m-a_-chemistry_-sample-info"),
+        "sample_pt_id",
+        "sample_point_id",
         "analyte",
         "sample_value",
         "units",
         "symbol",
         "analysis_date",
         "analyses_agency",
+        "wclab_id",
+        "object_id",
     ]
 
     sortable_fields = [
         "global_id",
+        "sample_pt_id",
+        "sample_point_id",
         "analyte",
         "sample_value",
         "units",
         "symbol",
         "analysis_date",
         "analyses_agency",
+        "wclab_id",
+        "object_id",
     ]
 
     fields_default_sort = [("analysis_date", True)]
 
     searchable_fields = [
         "global_id",
+        "sample_pt_id",
+        "sample_point_id",
         "analyte",
         "symbol",
         "analysis_method",
+        "analysis_date",
         "notes",
         "analyses_agency",
+        "wclab_id",
     ]
 
     page_size = 50
@@ -90,6 +102,8 @@ def can_delete(self, request: Request) -> bool:
     fields = [
         "global_id",
         HasOne("chemistry_sample_info", identity="n-m-a_-chemistry_-sample-info"),
+        "sample_pt_id",
+        "sample_point_id",
         "analyte",
         "symbol",
         "sample_value",
@@ -100,23 +114,29 @@ def can_delete(self, request: Request) -> bool:
         "notes",
         "volume",
         "volume_unit",
+        "object_id",
         "analyses_agency",
+        "wclab_id",
     ]
 
     field_labels = {
         "global_id": "GlobalID",
         "chemistry_sample_info": "Chemistry Sample Info",
+        "sample_pt_id": "SamplePtID",
+        "sample_point_id": "SamplePointID",
         "analyte": "Analyte",
         "symbol": "Symbol",
-        "sample_value": "Sample Value",
+        "sample_value": "SampleValue",
         "units": "Units",
         "uncertainty": "Uncertainty",
-        "analysis_method": "Analysis Method",
-        "analysis_date": "Analysis Date",
+        "analysis_method": "AnalysisMethod",
+        "analysis_date": "AnalysisDate",
         "notes": "Notes",
         "volume": "Volume",
-        "volume_unit": "Volume Unit",
-        "analyses_agency": "Analyses Agency",
+        "volume_unit": "VolumeUnit",
+        "object_id": "OBJECTID",
+        "analyses_agency": "AnalysesAgency",
+        "wclab_id": "WCLab_ID",
     }
 
 

alembic/versions/3a9c1f5b7d2e_align_nma_minor_trace_columns.py

@@ -0,0 +1,134 @@
+"""Align NMA_MinorTraceChemistry columns with legacy schema.
+
+Revision ID: 3a9c1f5b7d2e
+Revises: c1d2e3f4a5b6
+Create Date: 2026-01-31 12:00:00.000000
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy import inspect
+
+# revision identifiers, used by Alembic.
+revision: str = "3a9c1f5b7d2e"
+down_revision: Union[str, Sequence[str], None] = "c1d2e3f4a5b6"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def _column_names(inspector, table_name: str) -> set[str]:
+    return {col["name"] for col in inspector.get_columns(table_name)}
+
+
+def upgrade() -> None:
+    """Rename legacy columns and add missing fields."""
+    bind = op.get_bind()
+    inspector = inspect(bind)
+    if not inspector.has_table("NMA_MinorTraceChemistry"):
+        return
+
+    table_name = "NMA_MinorTraceChemistry"
+    columns = _column_names(inspector, table_name)
+
+    rename_map = {
+        "chemistry_sample_info_id": "SamplePtID",
+        "sample_point_id": "SamplePointID",
+        "analyte": "Analyte",
+        "sample_value": "SampleValue",
+        "units": "Units",
+        "symbol": "Symbol",
+        "analysis_method": "AnalysisMethod",
+        "analysis_date": "AnalysisDate",
+        "notes": "Notes",
+        "analyses_agency": "AnalysesAgency",
+        "uncertainty": "Uncertainty",
+        "volume": "Volume",
+        "volume_unit": "VolumeUnit",
+    }
+
+    for old_name, new_name in rename_map.items():
+        if old_name in columns and new_name not in columns:
+            op.alter_column(table_name, old_name, new_column_name=new_name)
+            columns.remove(old_name)
+            columns.add(new_name)
+
+    if "SamplePointID" not in columns:
+        op.add_column(
+            table_name, sa.Column("SamplePointID", sa.String(length=10), nullable=True)
+        )
+    if "OBJECTID" not in columns:
+        op.add_column(table_name, sa.Column("OBJECTID", sa.Integer(), nullable=True))
+    if "WCLab_ID" not in columns:
+        op.add_column(
+            table_name, sa.Column("WCLab_ID", sa.String(length=25), nullable=True)
+        )
+
+    unique_constraints = inspector.get_unique_constraints(table_name)
+    unique_columns = {tuple(uc.get("column_names") or []) for uc in unique_constraints}
+    unique_names = {uc.get("name") for uc in unique_constraints}
+
+    if (
+        ("OBJECTID",) not in unique_columns
+        and "uq_nma_minor_trace_chemistry_objectid" not in unique_names
+    ):
+        op.create_unique_constraint(
+            "uq_nma_minor_trace_chemistry_objectid",
+            table_name,
+            ["OBJECTID"],
+        )
+
+    if "uq_minor_trace_chemistry_sample_analyte" not in unique_names:
+        op.create_unique_constraint(
+            "uq_minor_trace_chemistry_sample_analyte",
+            table_name,
+            ["SamplePtID", "Analyte"],
+        )
+
+
+def downgrade() -> None:
+    """Revert column names and remove added fields."""
+    bind = op.get_bind()
+    inspector = inspect(bind)
+    if not inspector.has_table("NMA_MinorTraceChemistry"):
+        return
+
+    table_name = "NMA_MinorTraceChemistry"
+    columns = _column_names(inspector, table_name)
+
+    unique_constraints = inspector.get_unique_constraints(table_name)
+    unique_names = {uc.get("name") for uc in unique_constraints}
+
+    if "uq_nma_minor_trace_chemistry_objectid" in unique_names:
+        op.drop_constraint(
+            "uq_nma_minor_trace_chemistry_objectid",
+            table_name,
+            type_="unique",
+        )
+
+    for column_name in ("WCLab_ID", "OBJECTID", "SamplePointID"):
+        if column_name in columns:
+            op.drop_column(table_name, column_name)
+
+    rename_map = {
+        "SamplePtID": "chemistry_sample_info_id",
+        "Analyte": "analyte",
+        "SampleValue": "sample_value",
+        "Units": "units",
+        "Symbol": "symbol",
+        "AnalysisMethod": "analysis_method",
+        "AnalysisDate": "analysis_date",
+        "Notes": "notes",
+        "AnalysesAgency": "analyses_agency",
+        "Uncertainty": "uncertainty",
+        "Volume": "volume",
+        "VolumeUnit": "volume_unit",
+    }
+
+    columns = _column_names(inspector, table_name)
+    for old_name, new_name in rename_map.items():
+        if old_name in columns and new_name not in columns:
+            op.alter_column(table_name, old_name, new_column_name=new_name)
+            columns.remove(old_name)
+            columns.add(new_name)

db/nma_legacy.py

@@ -475,8 +475,8 @@ class NMA_MinorTraceChemistry(Base):
     __tablename__ = "NMA_MinorTraceChemistry"
     __table_args__ = (
         UniqueConstraint(
-            "chemistry_sample_info_id",
-            "analyte",
+            "SamplePtID",
+            "Analyte",
             name="uq_minor_trace_chemistry_sample_analyte",
         ),
     )
@@ -486,32 +486,42 @@ class NMA_MinorTraceChemistry(Base):
     )
 
     # FK to ChemistrySampleInfo - required (no orphans)
-    chemistry_sample_info_id: Mapped[uuid.UUID] = mapped_column(
+    sample_pt_id: Mapped[uuid.UUID] = mapped_column(
+        "SamplePtID",
         UUID(as_uuid=True),
         ForeignKey("NMA_Chemistry_SampleInfo.SamplePtID", ondelete="CASCADE"),
         nullable=False,
     )
 
     # Legacy columns
-    analyte: Mapped[Optional[str]] = mapped_column(String(50))
-    sample_value: Mapped[Optional[float]] = mapped_column(Float)
-    units: Mapped[Optional[str]] = mapped_column(String(20))
-    symbol: Mapped[Optional[str]] = mapped_column(String(10))
-    analysis_method: Mapped[Optional[str]] = mapped_column(String(100))
-    analysis_date: Mapped[Optional[date]] = mapped_column(Date)
-    notes: Mapped[Optional[str]] = mapped_column(Text)
-    analyses_agency: Mapped[Optional[str]] = mapped_column(String(100))
-    uncertainty: Mapped[Optional[float]] = mapped_column(Float)
-    volume: Mapped[Optional[int]] = mapped_column(Integer)
-    volume_unit: Mapped[Optional[str]] = mapped_column(String(20))
+    sample_point_id: Mapped[Optional[str]] = mapped_column("SamplePointID", String(10))
+    analyte: Mapped[Optional[str]] = mapped_column("Analyte", String(50))
+    symbol: Mapped[Optional[str]] = mapped_column("Symbol", String(50))
+    sample_value: Mapped[Optional[float]] = mapped_column(
+        "SampleValue", Float, server_default=text("0")
+    )
+    units: Mapped[Optional[str]] = mapped_column("Units", String(50))
+    uncertainty: Mapped[Optional[float]] = mapped_column("Uncertainty", Float)
+    analysis_method: Mapped[Optional[str]] = mapped_column(
+        "AnalysisMethod", String(255)
+    )
+    analysis_date: Mapped[Optional[datetime]] = mapped_column("AnalysisDate", DateTime)
+    notes: Mapped[Optional[str]] = mapped_column("Notes", String(255))
+    volume: Mapped[Optional[int]] = mapped_column(
+        "Volume", Integer, server_default=text("0")
+    )
+    volume_unit: Mapped[Optional[str]] = mapped_column("VolumeUnit", String(50))
+    object_id: Mapped[Optional[int]] = mapped_column("OBJECTID", Integer, unique=True)
+    analyses_agency: Mapped[Optional[str]] = mapped_column("AnalysesAgency", String(50))
+    wclab_id: Mapped[Optional[str]] = mapped_column("WCLab_ID", String(25))
 
     # --- Relationships ---
     chemistry_sample_info: Mapped["NMA_Chemistry_SampleInfo"] = relationship(
         "NMA_Chemistry_SampleInfo", back_populates="minor_trace_chemistries"
     )
 
-    @validates("chemistry_sample_info_id")
-    def validate_chemistry_sample_info_id(self, key, value):
+    @validates("sample_pt_id")
+    def validate_sample_pt_id(self, key, value):
         """Prevent orphan NMA_MinorTraceChemistry - must have a parent ChemistrySampleInfo."""
         if value is None:
             raise ValueError(

tests/features/admin-minor-trace-chemistry.feature

@@ -31,7 +31,7 @@ Feature: Minor Trace Chemistry Admin View
     Then the Minor Trace Chemistry admin view should have these fields configured:
       | field                     |
       | global_id                 |
-      | chemistry_sample_info_id  |
+      | sample_pt_id              |
       | analyte                   |
       | symbol                    |
       | sample_value              |

tests/integration/test_admin_minor_trace_chemistry.py

@@ -84,7 +84,7 @@ def minor_trace_chemistry_record():
         # Create MinorTraceChemistry record
         chemistry = NMA_MinorTraceChemistry(
             global_id=uuid.uuid4(),
-            chemistry_sample_info_id=sample_info.sample_pt_id,
+            sample_pt_id=sample_info.sample_pt_id,
             analyte="Arsenic",
             symbol="As",
             sample_value=0.005,
@@ -120,7 +120,7 @@ def test_list_view_contains_view_name(self, admin_client):
         """List view should contain the view name."""
         response = admin_client.get(f"{ADMIN_BASE_URL}/list")
         assert response.status_code == 200
-        assert "Minor Trace Chemistry" in response.text
+        assert "NMA Minor Trace Chemistry" in response.text
 
     def test_no_create_button_in_list_view(self, admin_client):
         """List view should not have a Create button for read-only view."""

tests/test_admin_minor_trace_chemistry.py

@@ -37,15 +37,15 @@ def test_minor_trace_chemistry_view_is_registered(self):
         admin = create_admin(app)
         view_names = [v.name for v in admin._views]
 
-        assert "Minor Trace Chemistry" in view_names, (
-            f"Expected 'Minor Trace Chemistry' to be registered in admin views. "
+        assert "NMA Minor Trace Chemistry" in view_names, (
+            f"Expected 'NMA Minor Trace Chemistry' to be registered in admin views. "
             f"Found: {view_names}"
         )
 
     def test_view_has_correct_label(self):
         """View should have proper label for sidebar display."""
         view = MinorTraceChemistryAdmin(NMA_MinorTraceChemistry)
-        assert view.label == "Minor Trace Chemistry"
+        assert view.label == "NMA Minor Trace Chemistry"
 
     def test_class_has_flask_icon_configured(self):
         """View class should have flask icon configured for chemistry data."""
@@ -108,6 +108,8 @@ def test_list_fields_include_required_columns(self, view):
         required_columns = [
             "global_id",
             "chemistry_sample_info",  # HasOne relationship to parent
+            "sample_pt_id",
+            "sample_point_id",
             "analyte",
             "sample_value",
             "units",
@@ -146,6 +148,8 @@ def test_form_includes_all_chemistry_fields(self):
         # Note: chemistry_sample_info is a HasOne field, not a string
         expected_string_fields = [
             "global_id",
+            "sample_pt_id",
+            "sample_point_id",
             "analyte",
             "symbol",
             "sample_value",
@@ -156,7 +160,9 @@ def test_form_includes_all_chemistry_fields(self):
             "notes",
             "volume",
             "volume_unit",
+            "object_id",
             "analyses_agency",
+            "wclab_id",
         ]
         configured_fields = MinorTraceChemistryAdmin.fields
 
@@ -176,8 +182,8 @@ def test_form_includes_all_chemistry_fields(self):
     def test_field_labels_are_human_readable(self, view):
         """Field labels should be human-readable."""
         assert view.field_labels.get("global_id") == "GlobalID"
-        assert view.field_labels.get("sample_value") == "Sample Value"
-        assert view.field_labels.get("analysis_date") == "Analysis Date"
+        assert view.field_labels.get("sample_value") == "SampleValue"
+        assert view.field_labels.get("analysis_date") == "AnalysisDate"
 
     def test_searchable_fields_include_key_fields(self, view):
         """Searchable fields should include commonly searched columns."""