Add study cell

src/soa_builder/web/audit.py

@@ -45,6 +45,18 @@ def _record_element_audit(
     try:
         conn = _connect()
         cur = conn.cursor()
+        # Ensure table exists (defensive for migrated databases)
+        cur.execute(
+            """CREATE TABLE IF NOT EXISTS element_audit (
+                id INTEGER PRIMARY KEY AUTOINCREMENT,
+                soa_id INTEGER NOT NULL,
+                element_id INTEGER,
+                action TEXT NOT NULL,
+                before_json TEXT,
+                after_json TEXT,
+                performed_at TEXT NOT NULL
+            )"""
+        )
         cur.execute(
             "INSERT INTO element_audit (soa_id, element_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)",
             (
@@ -139,3 +151,42 @@ def _record_activity_audit(
         conn.close()
     except Exception as e:
         logger.warning("Failed recording activity audit: %s", e)
+
+
+def _record_study_cell_audit(
+    soa_id: int,
+    action: str,
+    study_cell_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 study_cell_audit (
+                id INTEGER PRIMARY KEY AUTOINCREMENT,
+                soa_id INTEGER NOT NULL,
+                study_cell_id INTEGER,
+                action TEXT NOT NULL,
+                before_json TEXT,
+                after_json TEXT,
+                performed_at TEXT NOT NULL
+            )"""
+        )
+        cur.execute(
+            "INSERT INTO study_cell_audit (soa_id, study_cell_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)",
+            (
+                soa_id,
+                study_cell_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 study_cell audit: %s", e)

src/soa_builder/web/initialize_database.py

@@ -101,6 +101,30 @@ def _init_db():
             performed_at TEXT NOT NULL
         )"""
     )
+    # Study Cell audit table
+    cur.execute(
+        """CREATE TABLE IF NOT EXISTS study_cell_audit (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            soa_id INTEGER NOT NULL,
+            study_cell_id INTEGER,
+            action TEXT NOT NULL, -- create|update|delete
+            before_json TEXT,
+            after_json TEXT,
+            performed_at TEXT NOT NULL
+        )"""
+    )
+    # Transition rule audit table
+    cur.execute(
+        """CREATE TABLE IF NOT EXISTS transition_rule_audit (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            soa_id INTEGER NOT NULL,
+            transition_rule_id INTEGER,
+            action TEXT NOT NULL, -- create|update|delete
+            before_json TEXT,
+            after_json TEXT,
+            performed_at TEXT NOT NULL
+        )"""
+    )
     # Epochs: high-level study phase grouping (optional). Behaves like visits/activities list ordering.
     cur.execute(
         """CREATE TABLE IF NOT EXISTS epoch (id INTEGER PRIMARY KEY AUTOINCREMENT, soa_id INTEGER, name TEXT, order_index INTEGER)"""
@@ -160,5 +184,33 @@ def _init_db():
         )"""
     )
 
+    # create the study_cell table to store the relationship between Epoch, Arm and related elements
+    cur.execute(
+        """CREATE TABLE IF NOT EXISTS study_cell (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            soa_id INTEGER NOT NULL,
+            study_cell_uid TEXT NOT NULL, --immutable StudyCell_N identifier unique within SOA
+            arm_uid TEXT NOT NULL,
+            epoch_uid TEXT NOT NULL,
+            element_uid TEXT NOT NULL
+        )"""
+    )
+
+    # create the transition_rule table to store the transition rules for elements, encounters
+    cur.execute(
+        """CREATE TABLE IF NOT EXISTS transition_rule (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            soa_id INTEGER NOT NULL,
+            transition_rule_uid TEXT NOT NULL,  --immutable TransitionRule_N identifier unique within SOA
+            name TEXT NOT NULL,
+            label TEXT,
+            description TEXT,
+            text TEXT NOT NULL,
+            order_index INTEGER,
+            created_at TEXT,
+            UNIQUE(soa_id, transition_rule_uid)
+        )"""
+    )
+
     conn.commit()
     conn.close()

src/soa_builder/web/migrate_database.py

@@ -655,6 +655,62 @@ def _migrate_arm_add_type_fields():
         logger.warning("Arm type/data_origin_type migration failed: %s", e)
 
 
+# Migration: Ensure element_audit has before_json/after_json columns
+def _migrate_element_audit_columns():
+    """Add missing columns before_json and after_json to element_audit.
+
+    Handles legacy schemas that only had id, soa_id, element_id, action, performed_at.
+    Safe to run multiple times; idempotent via schema inspection.
+    """
+    try:
+        conn = _connect()
+        cur = conn.cursor()
+        # Ensure table exists; if not present, create with full schema
+        cur.execute(
+            "SELECT name FROM sqlite_master WHERE type='table' AND name='element_audit'"
+        )
+        exists = cur.fetchone() is not None
+        if not exists:
+            cur.execute(
+                """CREATE TABLE IF NOT EXISTS element_audit (
+                    id INTEGER PRIMARY KEY AUTOINCREMENT,
+                    soa_id INTEGER NOT NULL,
+                    element_id INTEGER,
+                    action TEXT NOT NULL,
+                    before_json TEXT,
+                    after_json TEXT,
+                    performed_at TEXT NOT NULL
+                )"""
+            )
+            conn.commit()
+            logger.info("Created element_audit table with full schema")
+            conn.close()
+            return
+        # Add columns if missing
+        cur.execute("PRAGMA table_info(element_audit)")
+        cols = {r[1] for r in cur.fetchall()}
+        alters = []
+        if "before_json" not in cols:
+            alters.append("ALTER TABLE element_audit ADD COLUMN before_json TEXT")
+        if "after_json" not in cols:
+            alters.append("ALTER TABLE element_audit ADD COLUMN after_json TEXT")
+        for stmt in alters:
+            try:
+                cur.execute(stmt)
+            except Exception as e:  # pragma: no cover
+                logger.warning(
+                    "Failed element_audit column migration '%s': %s", stmt, e
+                )
+        if alters:
+            conn.commit()
+            logger.info(
+                "Applied element_audit column migrations: %s", ", ".join(alters)
+            )
+        conn.close()
+    except Exception as e:  # pragma: no cover
+        logger.warning("element_audit column migration failed: %s", e)
+
+
 # Backfill dataset_date for existing terminology tables
 def _backfill_dataset_date(table: str, audit_table: str):
     """If terminology table exists and has dataset_date (or sheet_dataset_date) column with blank values,

src/soa_builder/web/routers/activities.py

@@ -1,4 +1,5 @@
 import json
+import logging
 
 # Lightweight concept fetcher to avoid circular import with app.py
 import os
@@ -11,10 +12,14 @@
 from ..audit import _record_activity_audit, _record_reorder_audit
 from ..db import _connect
 from ..schemas import ActivityCreate, ActivityUpdate, BulkActivities
+from ..utils import soa_exists
 
 _ACT_CONCEPT_CACHE = {"data": None, "fetched_at": 0}
 _ACT_CONCEPT_TTL = 60 * 60
 
+router = APIRouter(prefix="/soa/{soa_id}")
+logger = logging.getLogger("soa_builder.web.routers.activities")
+
 
 def fetch_biomedical_concepts(force: bool = False):
     override_json = os.environ.get("CDISC_CONCEPTS_JSON")
@@ -53,7 +58,8 @@ def fetch_biomedical_concepts(force: bool = False):
                 if code:
                     concepts.append({"code": code, "title": title})
             return concepts
-        except Exception:
+        except Exception as e:
+            logger.debug("fetch_biomedical_concepts override JSON parse failed: %s", e)
             return []
     now = time.time()
     if (
@@ -68,21 +74,12 @@ def fetch_biomedical_concepts(force: bool = False):
     return []
 
 
-router = APIRouter(prefix="/soa/{soa_id}")
-
-
-def _soa_exists(soa_id: int) -> bool:
-    conn = _connect()
-    cur = conn.cursor()
-    cur.execute("SELECT 1 FROM soa WHERE id=?", (soa_id,))
-    ok = cur.fetchone() is not None
-    conn.close()
-    return ok
+# Removed local _soa_exists; using shared utils.soa_exists
 
 
 @router.get("/activities", response_class=JSONResponse)
 def list_activities(soa_id: int):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     conn = _connect()
     cur = conn.cursor()
@@ -100,7 +97,7 @@ def list_activities(soa_id: int):
 
 @router.get("/activities/{activity_id}", response_class=JSONResponse)
 def get_activity(soa_id: int, activity_id: int):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     conn = _connect()
     cur = conn.cursor()
@@ -123,7 +120,7 @@ def get_activity(soa_id: int, activity_id: int):
 
 @router.post("/activities", response_class=JSONResponse)
 def add_activity(soa_id: int, payload: ActivityCreate):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     conn = _connect()
     cur = conn.cursor()
@@ -152,7 +149,7 @@ def add_activity(soa_id: int, payload: ActivityCreate):
 
 @router.patch("/activities/{activity_id}", response_class=JSONResponse)
 def update_activity(soa_id: int, activity_id: int, payload: ActivityUpdate):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     conn = _connect()
     cur = conn.cursor()
@@ -196,7 +193,7 @@ def update_activity(soa_id: int, activity_id: int, payload: ActivityUpdate):
 
 @router.post("/activities/reorder", response_class=JSONResponse)
 def reorder_activities_api(soa_id: int, order: List[int]):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     if not order:
         raise HTTPException(400, "Order list required")
@@ -256,7 +253,7 @@ def reorder_activities_api(soa_id: int, order: List[int]):
 
 @router.post("/activities/bulk", response_class=JSONResponse)
 def add_activities_bulk(soa_id: int, payload: BulkActivities):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     names = [n.strip() for n in payload.names if n and n.strip()]
     if not names:
@@ -293,7 +290,7 @@ def add_activities_bulk(soa_id: int, payload: BulkActivities):
 
 @router.post("/activities/{activity_id}/concepts", response_class=JSONResponse)
 def set_activity_concepts(soa_id: int, activity_id: int, concept_codes: List[str]):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     conn = _connect()
     cur = conn.cursor()

src/soa_builder/web/routers/arms.py

@@ -7,22 +7,18 @@
 from ..audit import _record_arm_audit, _record_reorder_audit
 from ..db import _connect
 from ..schemas import ArmCreate, ArmUpdate
+from ..utils import soa_exists
 
 router = APIRouter(prefix="/soa/{soa_id}")
+logger = logging.getLogger("soa_builder.web.routers.arms")
 
 
-def _soa_exists(soa_id: int) -> bool:
-    conn = _connect()
-    cur = conn.cursor()
-    cur.execute("SELECT 1 FROM soa WHERE id=?", (soa_id,))
-    ok = cur.fetchone() is not None
-    conn.close()
-    return ok
+# Removed local _soa_exists; using shared utils.soa_exists
 
 
 @router.get("/arms", response_class=JSONResponse)
 def list_arms(soa_id: int):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     conn = _connect()
     cur = conn.cursor()
@@ -49,7 +45,7 @@ def list_arms(soa_id: int):
 
 @router.post("/arms", response_class=JSONResponse, status_code=201)
 def create_arm(soa_id: int, payload: ArmCreate):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     name = (payload.name or "").strip()
     if not name:
@@ -72,7 +68,7 @@ def create_arm(soa_id: int, payload: ArmCreate):
             if tail.isdigit():
                 used_nums.add(int(tail))
             else:
-                logging.getLogger("soa_builder.concepts").warning(
+                logger.warning(
                     "Invalid arm_uid format encountered (ignored for numbering): %s",
                     uid,
                 )
@@ -113,7 +109,7 @@ def create_arm(soa_id: int, payload: ArmCreate):
 
 @router.patch("/arms/{arm_id}", response_class=JSONResponse)
 def update_arm(soa_id: int, arm_id: int, payload: ArmUpdate):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     conn = _connect()
     cur = conn.cursor()
@@ -190,7 +186,7 @@ def update_arm(soa_id: int, arm_id: int, payload: ArmUpdate):
 
 @router.delete("/arms/{arm_id}", response_class=JSONResponse)
 def delete_arm(soa_id: int, arm_id: int):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     conn = _connect()
     cur = conn.cursor()
@@ -221,7 +217,7 @@ def delete_arm(soa_id: int, arm_id: int):
 
 @router.post("/arms/reorder", response_class=JSONResponse)
 def reorder_arms_api(soa_id: int, order: List[int]):
-    if not _soa_exists(soa_id):
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
     if not order:
         raise HTTPException(400, "Order list required")