Add timing

src/soa_builder/web/app.py

@@ -68,6 +68,7 @@
 from .routers import freezes as freezes_router
 from .routers import rollback as rollback_router
 from .routers import visits as visits_router
+from .routers import timings as timings_router
 from .routers.arms import create_arm  # re-export for backward compatibility
 from .routers.arms import delete_arm
 from .schemas import ArmCreate, SOACreate, SOAMetadataUpdate
@@ -317,6 +318,7 @@ def _record_arm_audit(
 app.include_router(epochs_router.router)
 app.include_router(freezes_router.router)
 app.include_router(rollback_router.router)
+app.include_router(timings_router.router)
 
 
 @app.post("/soa/{soa_id}/visits/reorder", response_class=JSONResponse)
@@ -408,14 +410,6 @@ def reorder_activities_api(soa_id: int, order: List[int]):
     return JSONResponse({"ok": True, "old_order": old_order, "new_order": order})
 
 
-class ConceptsUpdate(BaseModel):
-    concept_codes: List[str]
-
-
-class FreezeCreate(BaseModel):
-    version_label: Optional[str] = None
-
-
 def _list_freezes(soa_id: int):
     conn = _connect()
     cur = conn.cursor()
@@ -1052,6 +1046,15 @@ def _rollback_preview(soa_id: int, freeze_id: int) -> dict:
     }
 
 
+# ------ Schemas -----#
+class ConceptsUpdate(BaseModel):
+    concept_codes: List[str]
+
+
+class FreezeCreate(BaseModel):
+    version_label: Optional[str] = None
+
+
 class CellCreate(BaseModel):
     visit_id: int
     activity_id: int
@@ -1078,12 +1081,6 @@ class MatrixImport(BaseModel):
     reset: bool = True
 
 
-# --------------------- Helpers ---------------------
-
-
-# Use shared utils.soa_exists instead of local helper
-
-
 def _fetch_matrix(soa_id: int):
     conn = _connect()
     cur = conn.cursor()
@@ -2151,23 +2148,11 @@ def update_soa_metadata(soa_id: int, payload: SOAMetadataUpdate):
 
 
 """Visit creation handled in routers/visits.py"""
-
-
 """Visit update handled in routers/visits.py"""
-
-
 """Visit detail handled in routers/visits.py"""
-
-
 """Activity creation handled in routers/activities.py"""
-
-
 """Activity update handled in routers/activities.py"""
-
-
 """Activity detail handled in routers/activities.py"""
-
-
 """Epoch CRUD and reorder endpoints refactored into epochs_router."""
 
 
@@ -5902,7 +5887,6 @@ def _epoch_types_snapshot(soa_id_int: int) -> list[dict]:
     return HTMLResponse("OK")
 
 
-# --------------------- DDF Terminology Load ---------------------
 def _sanitize_column(name: str) -> str:
     """Sanitize Excel column header to safe SQLite identifier: lowercase, replace spaces & non-alnum with underscore, collapse repeats."""
     import re
@@ -5915,6 +5899,7 @@ def _sanitize_column(name: str) -> str:
     return s
 
 
+# ------------------------- DDF Terminology ----------------------#
 def load_ddf_terminology(
     file_path: str,
     sheet_name: str = "DDF Terminology 2025-09-26",
@@ -6507,7 +6492,7 @@ def ui_ddf_audit(
     )
 
 
-# Protocol Terminology functions
+# ------------------------ Protocol Terminology ----------------------#
 def load_protocol_terminology(
     file_path: str,
     sheet_name: str = "Protocol Terminology 2025-09-26",

src/soa_builder/web/audit.py

@@ -190,3 +190,42 @@ def _record_study_cell_audit(
         conn.close()
     except Exception as e:
         logger.warning("Failed recording study_cell audit: %s", e)
+
+
+def _record_timing_audit(
+    soa_id: int,
+    action: str,
+    timing_id: int | None,
+    before: Optional[Dict[str, Any]] = None,
+    after: Optional[Dict[str, Any]] = None,
+):
+    try:
+        conn = _connect()
+        cur = conn.cursor()
+        # Ensure table exists (defensive for migrated databases)
+        cur.execute(
+            """CREATE TABLE IF NOT EXISTS timing_audit (
+                id INTEGER PRIMARY KEY AUTOINCREMENT,
+                soa_id INTEGER NOT NULL,
+                timing_id INTEGER,
+                action TEXT NOT NULL,
+                before_json TEXT,
+                after_json TEXT,
+                performed_at TEXT NOT NULL
+            )"""
+        )
+        cur.execute(
+            "INSERT INTO timing_audit (soa_id, timing_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)",
+            (
+                soa_id,
+                timing_id,
+                action,
+                json.dumps(before) if before else None,
+                json.dumps(after) if after else None,
+                datetime.now(timezone.utc).isoformat(),
+            ),
+        )
+        conn.commit()
+        conn.close()
+    except Exception as e:
+        logger.warning("Failed recording timing audit: %s", e)

src/soa_builder/web/initialize_database.py

@@ -255,5 +255,41 @@ def _init_db():
         )"""
     )
 
+    # create the timing table
+    cur.execute(
+        """CREATE TABLE IF NOT EXISTS timing (
+        id INTEGER PRIMARY KEY AUTOINCREMENT,
+        soa_id INTEGER NOT NULL,
+        timing_uid TEXT NOT NULL,   -- immutable Timing_N identifier unique within SOA
+        name TEXT NOT NULL,
+        label TEXT,
+        description TEXT,
+        type TEXT,  -- value chosen from submissionValue in codelist_code C201264
+        value TEXT,
+        value_label TEXT,
+        relative_to_from TEXT,  -- value chosen from submissionValue in codelist_code C201265
+        relative_from_schedule_instance TEXT,
+        relative_to_schedule_instance TEXT,
+        window_label TEXT,
+        window_upper TEXT,
+        window_lower TEXT,
+        order_index INTEGER,
+        UNIQUE(soa_id, timing_uid)
+        )"""
+    )
+
+    # create timing_audit table
+    cur.execute(
+        """CREATE TABLE IF NOT EXISTS timing_audit (
+        id INTEGER PRIMARY KEY AUTOINCREMENT,
+        soa_id INT NOT NULL,
+        timing_id INT NOT NULL,
+        action TEXT NOT NULL,   -- create|update|delete
+        before_json TEXT,
+        after_json TEXT,
+        performed_at TEXT
+        )"""
+    )
+
     conn.commit()
     conn.close()