monotonically increasing for this SOA
+ transition_rule_identifier = _next_transition_rule_uid(soa_id)
+ cur.execute(
+ """INSERT INTO transition_rule (soa_id,transition_rule_uid,name,label,description,text,order_index,created_at) VALUES (?,?,?,?,?,?,?,?)""",
+ (
+ soa_id,
+ transition_rule_identifier,
+ name,
+ (label or "").strip() or None,
+ (description or "").strip() or None,
+ text,
+ next_ord,
+ now,
+ ),
+ )
+ eid = cur.lastrowid
+ conn.commit()
+ conn.close()
+ _record_transition_rule_audit(
+ soa_id,
+ "create",
+ eid,
+ before=None,
+ after={
+ "id": eid,
+ "transition_rule_uid": transition_rule_identifier,
+ "name": name,
+ "label": (label or "").strip() or None,
+ "description": (description or "").strip() or None,
+ "text": text,
+ "order_index": next_ord,
+ },
+ )
+ return HTMLResponse(
+ f""
+ )
+
+
+@app.post("/ui/soa/{soa_id}/update_transition_rule", response_class=HTMLResponse)
+def ui_transition_rule_update(
+ request: Request,
+ soa_id: int,
+ transition_rule_uid: str = Form(...),
+ name: Optional[str] = Form(None),
+ label: Optional[str] = Form(None),
+ description: Optional[str] = Form(None),
+ text: Optional[str] = Form(None),
+):
+ """Form handler to update an existing Transition Rule."""
+ if not soa_exists(soa_id):
+ raise HTTPException(404, "SOA not found")
+ conn = _connect()
+ cur = conn.cursor()
+ # Verify exists and get id
+ cur.execute(
+ "SELECT id,transition_rule_uid,name,label,description,text,order_index,created_at FROM transition_rule WHERE soa_id=? AND transition_rule_uid=?",
+ (soa_id, transition_rule_uid),
+ )
+ b = cur.fetchone()
+ if not b:
+ conn.close()
+ raise HTTPException(404, "Transition Rule not found")
+ before = {
+ "id": b[0],
+ "transition_rule_uid": b[1],
+ "name": b[2],
+ "label": b[3],
+ "description": b[4],
+ "text": b[5],
+ "order_index": b[6],
+ "created_at": b[7],
+ }
+ sets = []
+ vals: list[Any] = []
+ if name is not None:
+ sets.append("name=?")
+ vals.append((name or "").strip() or None)
+ if label is not None:
+ sets.append("label=?")
+ vals.append((label or "").strip() or None)
+ if description is not None:
+ sets.append("description=?")
+ vals.append((description or "").strip() or None)
+ if text is not None:
+ sets.append("text=?")
+ vals.append((text or "").strip() or None)
+ if sets:
+ vals.append(before["id"])
+ cur.execute(f"UPDATE transition_rule SET {', '.join(sets)} WHERE id=?", vals)
+ conn.commit()
+ # Fetch after
+ cur.execute(
+ "SELECT id,name,label,description,text,order_index,created_at FROM transition_rule WHERE id=?",
+ (before["id"],),
+ )
+ a = cur.fetchone()
+ conn.close()
+ after = {
+ "id": a[0],
+ "name": a[1],
+ "label": a[2],
+ "description": a[3],
+ "text": a[4],
+ "order_index": a[5],
+ "created_at": a[6],
+ }
+ mutable_fields = ["name", "label", "description", "text"]
+ updated_fields = [
+ f for f in mutable_fields if before and before.get(f) != after.get(f)
+ ]
+ _record_transition_rule_audit(
+ soa_id,
+ "update",
+ before["id"],
+ before=before,
+ after={**after, "updated_fields": updated_fields},
+ )
+ # HTMX inline update: return refreshed list markup when requested
+ if request.headers.get("HX-Request") == "true":
+ conn_tr = _connect()
+ cur_tr = conn_tr.cursor()
+ cur_tr.execute(
+ "SELECT transition_rule_uid,name,label,description,text,order_index,created_at FROM transition_rule WHERE soa_id=? ORDER BY order_index",
+ (soa_id,),
+ )
+ transition_rules = [
+ dict(
+ transition_rule_uid=r[0],
+ name=r[1],
+ label=r[2],
+ description=r[3],
+ text=r[4],
+ order_index=r[5],
+ created_at=r[6],
+ )
+ for r in cur_tr.fetchall()
+ ]
+ conn_tr.close()
+ html = templates.get_template("transition_rules_list.html").render(
+ transition_rules=transition_rules, soa_id=soa_id
+ )
+ return HTMLResponse(html)
+ return HTMLResponse(
+ f""
+ )
+
+
+@app.post("/ui/soa/{soa_id}/delete_transition_rule")
+def ui_delete_transition_rule(
+ request: Request, soa_id: int, transition_rule_uid: str = Form(...)
+):
+ """Form handler to delete a transition rule"""
+ if not soa_exists(soa_id):
+ raise HTTPException(404, "SOA not found")
+ conn = _connect()
+ cur = conn.cursor()
+ # Capture before for audit
+ cur.execute(
+ "SELECT id,transition_rule_uid,name,label,description,text,order_index,created_at FROM transition_rule WHERE soa_id=? AND transition_rule_uid=?",
+ (soa_id, transition_rule_uid),
+ )
+ b = cur.fetchone()
+ before = None
+ if b:
+ before = {
+ "id": b[0],
+ "transition_rule_uid": b[1],
+ "name": b[2],
+ "label": b[3],
+ "description": b[4],
+ "text": b[5],
+ "order_index": b[6],
+ "created_at": b[7],
+ }
+ cur.execute(
+ "DELETE FROM transition_rule WHERE transition_rule_uid=? AND soa_id=?",
+ (transition_rule_uid, soa_id),
+ )
+ conn.commit()
+ conn.close()
+ _record_transition_rule_audit(
+ soa_id,
+ "delete",
+ before["id"] if before else None,
+ before=before,
+ after=None,
+ )
+ # HTMX inline update: return refreshed list markup when requested
+ if request.headers.get("HX-Request") == "true":
+ conn_tr = _connect()
+ cur_tr = conn_tr.cursor()
+ cur_tr.execute(
+ "SELECT transition_rule_uid,name,label,description,text,order_index,created_at FROM transition_rule WHERE soa_id=? ORDER BY order_index",
+ (soa_id,),
+ )
+ transition_rules = [
+ dict(
+ transition_rule_uid=r[0],
+ name=r[1],
+ label=r[2],
+ description=r[3],
+ text=r[4],
+ order_index=r[5],
+ created_at=r[6],
+ )
+ for r in cur_tr.fetchall()
+ ]
+ conn_tr.close()
+ html = templates.get_template("transition_rules_list.html").render(
+ transition_rules=transition_rules, soa_id=soa_id
+ )
+ return HTMLResponse(html)
+ return HTMLResponse(
+ f""
+ )
+
+
+# -------------------------- Biomedical Concepts --------------------#
@app.post(
"/ui/soa/{soa_id}/activity/{activity_id}/concepts", response_class=HTMLResponse
)
@@ -4592,7 +5301,7 @@ def ui_activity_concepts_cell(
# surface a clear 400 error rather than proceeding and causing confusing downstream behavior.
if not activity_id:
raise HTTPException(status_code=400, detail="Missing activity_id")
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
concepts = fetch_biomedical_concepts()
conn = _connect()
@@ -4640,7 +5349,7 @@ def ui_toggle_cell(
):
"""Toggle logic: blank -> X, X -> blank (delete row). Returns updated snippet with next action encoded.
This avoids stale hx-vals attributes after a partial swap."""
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
# Determine current status
conn = _connect()
@@ -4707,7 +5416,7 @@ def ui_set_visit_epoch(
epoch_id: str = Form(""), # legacy field name used by template select
):
"""Form handler to associate an Epoch with a Visit/Encounter."""
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
# Determine provided raw value (prefer epoch_id_raw if non-blank)
raw_val = (epoch_id_raw or "").strip() or (epoch_id or "").strip()
@@ -4767,7 +5476,7 @@ def ui_delete_epoch(request: Request, soa_id: int, epoch_id: int = Form(...)):
@app.post("/ui/soa/{soa_id}/reorder_visits", response_class=HTMLResponse)
def ui_reorder_visits(request: Request, soa_id: int, order: str = Form("")):
"""Persist new visit ordering. 'order' is a comma-separated list of visit IDs in desired order."""
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
ids = [int(x) for x in order.split(",") if x.strip().isdigit()]
if not ids:
@@ -4795,7 +5504,7 @@ def ui_reorder_visits(request: Request, soa_id: int, order: str = Form("")):
@app.post("/ui/soa/{soa_id}/reorder_activities", response_class=HTMLResponse)
def ui_reorder_activities(request: Request, soa_id: int, order: str = Form("")):
"""Persist new activity ordering. 'order' is a comma-separated list of activity IDs in desired order."""
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
ids = [int(x) for x in order.split(",") if x.strip().isdigit()]
if not ids:
@@ -4823,7 +5532,7 @@ def ui_reorder_activities(request: Request, soa_id: int, order: str = Form("")):
@app.post("/ui/soa/{soa_id}/reorder_epochs", response_class=HTMLResponse)
def ui_reorder_epochs(request: Request, soa_id: int, order: str = Form("")):
"""Form handler to persist new epoch ordering."""
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
ids = [int(x) for x in order.split(",") if x.strip().isdigit()]
if not ids:
diff --git a/src/soa_builder/web/audit.py b/src/soa_builder/web/audit.py
index 6c2b685..b2847ef 100644
--- a/src/soa_builder/web/audit.py
+++ b/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)
diff --git a/src/soa_builder/web/initialize_database.py b/src/soa_builder/web/initialize_database.py
index 8ccd3ac..c4c06d4 100644
--- a/src/soa_builder/web/initialize_database.py
+++ b/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()
diff --git a/src/soa_builder/web/migrate_database.py b/src/soa_builder/web/migrate_database.py
index 16fc06e..03b8ef0 100644
--- a/src/soa_builder/web/migrate_database.py
+++ b/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,
diff --git a/src/soa_builder/web/routers/activities.py b/src/soa_builder/web/routers/activities.py
index b29b2e6..afd795f 100644
--- a/src/soa_builder/web/routers/activities.py
+++ b/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()
diff --git a/src/soa_builder/web/routers/arms.py b/src/soa_builder/web/routers/arms.py
index b3eccbc..53f2a7c 100644
--- a/src/soa_builder/web/routers/arms.py
+++ b/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")
diff --git a/src/soa_builder/web/routers/elements.py b/src/soa_builder/web/routers/elements.py
index 245b623..2aecfcc 100644
--- a/src/soa_builder/web/routers/elements.py
+++ b/src/soa_builder/web/routers/elements.py
@@ -1,34 +1,109 @@
import json
+import logging
from datetime import datetime, timezone
-from typing import List
+from typing import List, Optional
from fastapi import APIRouter, HTTPException
from fastapi.responses import JSONResponse
from ..audit import _record_element_audit
from ..db import _connect
+from ..utils import soa_exists
from ..schemas import ElementCreate, ElementUpdate
router = APIRouter(prefix="/soa/{soa_id}")
+logger = logging.getLogger("soa_builder.web.routers.elements")
-def _soa_exists(soa_id: int) -> bool:
+"""Shared SOA existence check imported from utils.soa_exists"""
+
+
+def _next_element_identifier(soa_id: int) -> str:
+ """Compute next monotonically increasing StudyElement_N for an SoA.
+ Scans current element rows and element_audit snapshots to avoid reusing numbers after deletes.
+ """
conn = _connect()
cur = conn.cursor()
- cur.execute("SELECT 1 FROM soa WHERE id=?", (soa_id,))
- ok = cur.fetchone() is not None
+ max_n = 0
+ try:
+ cur.execute("SELECT element_id FROM element WHERE soa_id=?", (soa_id,))
+ for (eid,) in cur.fetchall():
+ if isinstance(eid, str) and eid.startswith("StudyElement_"):
+ tail = eid.split("StudyElement_")[-1]
+ if tail.isdigit():
+ max_n = max(max_n, int(tail))
+ except Exception as e:
+ logger.exception(
+ "_next_element_identifier scan elements failed for soa_id=%s: %s",
+ soa_id,
+ e,
+ )
+ try:
+ cur.execute(
+ "SELECT before_json, after_json FROM element_audit WHERE soa_id=?",
+ (soa_id,),
+ )
+ for bjson, ajson in cur.fetchall():
+ for js in (bjson, ajson):
+ if not js:
+ continue
+ try:
+ obj = json.loads(js)
+ except Exception as e:
+ logger.debug(
+ "_next_element_identifier JSON parse failed soa_id=%s: %s",
+ soa_id,
+ e,
+ )
+ obj = None
+ if isinstance(obj, dict):
+ val = obj.get("element_id")
+ if isinstance(val, str) and val.startswith("StudyElement_"):
+ tail = val.split("StudyElement_")[-1]
+ if tail.isdigit():
+ max_n = max(max_n, int(tail))
+ except Exception as e:
+ logger.exception(
+ "_next_element_identifier scan element_audit failed for soa_id=%s: %s",
+ soa_id,
+ e,
+ )
conn.close()
- return ok
+ return f"StudyElement_{max_n + 1}"
+
+
+def _get_element_uid(soa_id: int, row_id: int) -> Optional[str]:
+ """Return element.element_id (StudyElement_N) for row id if column exists, else None."""
+ try:
+ conn = _connect()
+ cur = conn.cursor()
+ cur.execute("PRAGMA table_info(element)")
+ cols = {r[1] for r in cur.fetchall()}
+ if "element_id" not in cols:
+ conn.close()
+ return None
+ cur.execute(
+ "SELECT element_id FROM element WHERE id=? AND soa_id=?",
+ (row_id, soa_id),
+ )
+ r = cur.fetchone()
+ conn.close()
+ return r[0] if r else None
+ except Exception as e:
+ logger.exception(
+ "_get_element_uid failed for soa_id=%s row_id=%s: %s", soa_id, row_id, e
+ )
+ return None
@router.get("/elements", response_class=JSONResponse)
def list_elements(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()
cur.execute(
- "SELECT id,name,label,description,testrl,teenrl,order_index,created_at FROM element WHERE soa_id=? ORDER BY order_index",
+ "SELECT id,name,label,description,testrl,teenrl,order_index,created_at,element_id FROM element WHERE soa_id=? ORDER BY order_index",
(soa_id,),
)
rows = [
@@ -41,6 +116,7 @@ def list_elements(soa_id: int):
"teenrl": r[5],
"order_index": r[6],
"created_at": r[7],
+ "element_id": r[8] if len(r) > 8 else None,
}
for r in cur.fetchall()
]
@@ -50,12 +126,12 @@ def list_elements(soa_id: int):
@router.get("/elements/{element_id}", response_class=JSONResponse)
def get_element(soa_id: int, element_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()
cur.execute(
- "SELECT id,name,label,description,testrl,teenrl,order_index,created_at FROM element WHERE id=? AND soa_id=?",
+ "SELECT id,name,label,description,testrl,teenrl,order_index,created_at,element_id FROM element WHERE id=? AND soa_id=?",
(element_id, soa_id),
)
r = cur.fetchone()
@@ -72,12 +148,13 @@ def get_element(soa_id: int, element_id: int):
"teenrl": r[5],
"order_index": r[6],
"created_at": r[7],
+ "element_id": r[8] if len(r) > 8 else None,
}
@router.get("/element_audit", response_class=JSONResponse)
def list_element_audit(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()
@@ -89,11 +166,17 @@ def list_element_audit(soa_id: int):
for r in cur.fetchall():
try:
before = json.loads(r[3]) if r[3] else None
- except Exception:
+ except Exception as e:
+ logger.debug(
+ "list_element_audit before JSON parse failed soa_id=%s: %s", soa_id, e
+ )
before = None
try:
after = json.loads(r[4]) if r[4] else None
- except Exception:
+ except Exception as e:
+ logger.debug(
+ "list_element_audit after JSON parse failed soa_id=%s: %s", soa_id, e
+ )
after = None
rows.append(
{
@@ -111,7 +194,7 @@ def list_element_audit(soa_id: int):
@router.post("/elements", response_class=JSONResponse, status_code=201)
def create_element(soa_id: int, payload: ElementCreate):
- 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:
@@ -123,20 +206,42 @@ def create_element(soa_id: int, payload: ElementCreate):
)
next_ord = (cur.fetchone() or [0])[0] + 1
now = datetime.now(timezone.utc).isoformat()
- cur.execute(
- """INSERT INTO element (soa_id,name,label,description,testrl,teenrl,order_index,created_at)
- VALUES (?,?,?,?,?,?,?,?)""",
- (
- soa_id,
- name,
- (payload.label or "").strip() or None,
- (payload.description or "").strip() or None,
- (payload.testrl or "").strip() or None,
- (payload.teenrl or "").strip() or None,
- next_ord,
- now,
- ),
- )
+ # Insert, setting element_id if column exists
+ cur.execute("PRAGMA table_info(element)")
+ element_cols = {r[1] for r in cur.fetchall()}
+ element_identifier: Optional[str] = None
+ if "element_id" in element_cols:
+ element_identifier = _next_element_identifier(soa_id)
+ cur.execute(
+ """INSERT INTO element (soa_id,name,label,description,testrl,teenrl,order_index,created_at,element_id)
+ VALUES (?,?,?,?,?,?,?,?,?)""",
+ (
+ soa_id,
+ name,
+ (payload.label or "").strip() or None,
+ (payload.description or "").strip() or None,
+ (payload.testrl or "").strip() or None,
+ (payload.teenrl or "").strip() or None,
+ next_ord,
+ now,
+ element_identifier,
+ ),
+ )
+ else:
+ cur.execute(
+ """INSERT INTO element (soa_id,name,label,description,testrl,teenrl,order_index,created_at)
+ VALUES (?,?,?,?,?,?,?,?)""",
+ (
+ soa_id,
+ name,
+ (payload.label or "").strip() or None,
+ (payload.description or "").strip() or None,
+ (payload.testrl or "").strip() or None,
+ (payload.teenrl or "").strip() or None,
+ next_ord,
+ now,
+ ),
+ )
eid = cur.lastrowid
conn.commit()
conn.close()
@@ -149,19 +254,21 @@ def create_element(soa_id: int, payload: ElementCreate):
"teenrl": (payload.teenrl or "").strip() or None,
"order_index": next_ord,
"created_at": now,
+ "element_id": element_identifier,
}
- _record_element_audit(soa_id, "create", eid, before=None, after=el)
+ # Audit with logical StudyElement_N when available
+ _record_element_audit(soa_id, "create", element_identifier, before=None, after=el)
return el
@router.patch("/elements/{element_id}", response_class=JSONResponse)
def update_element(soa_id: int, element_id: int, payload: ElementUpdate):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
conn = _connect()
cur = conn.cursor()
cur.execute(
- "SELECT id,name,label,description,testrl,teenrl,order_index,created_at FROM element WHERE id=? AND soa_id=?",
+ "SELECT id,name,label,description,testrl,teenrl,order_index,created_at,element_id FROM element WHERE id=? AND soa_id=?",
(element_id, soa_id),
)
row = cur.fetchone()
@@ -177,6 +284,7 @@ def update_element(soa_id: int, element_id: int, payload: ElementUpdate):
"teenrl": row[5],
"order_index": row[6],
"created_at": row[7],
+ "element_id": row[8],
}
new_name = (payload.name if payload.name is not None else before["name"]) or ""
cur.execute(
@@ -196,7 +304,7 @@ def update_element(soa_id: int, element_id: int, payload: ElementUpdate):
)
conn.commit()
cur.execute(
- "SELECT id,name,label,description,testrl,teenrl,order_index,created_at FROM element WHERE id=?",
+ "SELECT id,name,label,description,testrl,teenrl,order_index,created_at,element_id FROM element WHERE id=?",
(element_id,),
)
r = cur.fetchone()
@@ -210,13 +318,18 @@ def update_element(soa_id: int, element_id: int, payload: ElementUpdate):
"teenrl": r[5],
"order_index": r[6],
"created_at": r[7],
+ "element_id": r[8],
}
mutable_fields = ["name", "label", "description", "testrl", "teenrl"]
updated_fields = [f for f in mutable_fields if before.get(f) != after.get(f)]
+ # Audit with logical StudyElement_N key
+ element_uid_for_audit = after.get("element_id") or _get_element_uid(
+ soa_id, element_id
+ )
_record_element_audit(
soa_id,
"update",
- element_id,
+ element_uid_for_audit,
before=before,
after={**after, "updated_fields": updated_fields},
)
@@ -225,12 +338,12 @@ def update_element(soa_id: int, element_id: int, payload: ElementUpdate):
@router.delete("/elements/{element_id}", response_class=JSONResponse)
def delete_element(soa_id: int, element_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()
cur.execute(
- "SELECT id,name,label,description,testrl,teenrl,order_index,created_at FROM element WHERE id=? AND soa_id=?",
+ "SELECT id,name,label,description,testrl,teenrl,order_index,created_at,element_id FROM element WHERE id=? AND soa_id=?",
(element_id, soa_id),
)
row = cur.fetchone()
@@ -246,17 +359,24 @@ def delete_element(soa_id: int, element_id: int):
"teenrl": row[5],
"order_index": row[6],
"created_at": row[7],
+ "element_id": row[8],
}
cur.execute("DELETE FROM element WHERE id=?", (element_id,))
conn.commit()
conn.close()
- _record_element_audit(soa_id, "delete", element_id, before=before, after=None)
+ _record_element_audit(
+ soa_id,
+ "delete",
+ before.get("element_id"),
+ before=before,
+ after=None,
+ )
return JSONResponse({"deleted": True, "id": element_id})
@router.post("/elements/reorder", response_class=JSONResponse)
def reorder_elements_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")
diff --git a/src/soa_builder/web/routers/epochs.py b/src/soa_builder/web/routers/epochs.py
index 3e00146..f77c562 100644
--- a/src/soa_builder/web/routers/epochs.py
+++ b/src/soa_builder/web/routers/epochs.py
@@ -1,4 +1,5 @@
import json
+import logging
import os
import sqlite3
from datetime import datetime, timezone
@@ -8,25 +9,18 @@
from fastapi.responses import JSONResponse
from ..schemas import EpochCreate, EpochUpdate
+from ..utils import soa_exists
DB_PATH = os.environ.get("SOA_BUILDER_DB", "soa_builder_web.db")
router = APIRouter()
+logger = logging.getLogger("soa_builder.web.routers.epochs")
def _connect():
return sqlite3.connect(DB_PATH)
-def _soa_exists(soa_id: int) -> bool:
- conn = _connect()
- cur = conn.cursor()
- cur.execute("SELECT 1 FROM soa WHERE id=?", (soa_id,))
- row = cur.fetchone()
- conn.close()
- return row is not None
-
-
def _record_epoch_audit(
soa_id: int,
action: str,
@@ -50,13 +44,19 @@ def _record_epoch_audit(
)
conn.commit()
conn.close()
- except Exception:
- pass
+ except Exception as e:
+ logger.exception(
+ "_record_epoch_audit failed soa_id=%s epoch_id=%s action=%s: %s",
+ soa_id,
+ epoch_id,
+ action,
+ e,
+ )
@router.post("/soa/{soa_id}/epochs")
def add_epoch(soa_id: int, payload: EpochCreate):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
conn = _connect()
cur = conn.cursor()
@@ -99,7 +99,7 @@ def add_epoch(soa_id: int, payload: EpochCreate):
@router.get("/soa/{soa_id}/epochs")
def list_epochs(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()
@@ -124,7 +124,7 @@ def list_epochs(soa_id: int):
@router.get("/soa/{soa_id}/epochs/{epoch_id}")
def get_epoch(soa_id: int, epoch_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()
@@ -149,7 +149,7 @@ def get_epoch(soa_id: int, epoch_id: int):
@router.post("/soa/{soa_id}/epochs/{epoch_id}/metadata")
def update_epoch_metadata(soa_id: int, epoch_id: int, payload: EpochUpdate):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
conn = _connect()
cur = conn.cursor()
@@ -178,8 +178,13 @@ def update_epoch_metadata(soa_id: int, epoch_id: int, payload: EpochUpdate):
tr = cur.fetchone()
if before is not None:
before["type"] = tr[0] if tr else None
- except Exception:
- pass
+ except Exception as e:
+ logger.debug(
+ "update_epoch_metadata type fetch failed soa_id=%s epoch_id=%s: %s",
+ soa_id,
+ epoch_id,
+ e,
+ )
sets = []
vals = []
if payload.name is not None:
@@ -223,7 +228,7 @@ def update_epoch_metadata(soa_id: int, epoch_id: int, payload: EpochUpdate):
@router.post("/soa/{soa_id}/epochs/reorder", response_class=JSONResponse)
def reorder_epochs_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")
diff --git a/src/soa_builder/web/routers/freezes.py b/src/soa_builder/web/routers/freezes.py
index eba1c90..839738e 100644
--- a/src/soa_builder/web/routers/freezes.py
+++ b/src/soa_builder/web/routers/freezes.py
@@ -1,29 +1,26 @@
import json
+import logging
import os
import sqlite3
from fastapi import APIRouter, Form, HTTPException, Request
from fastapi.responses import HTMLResponse, JSONResponse
from fastapi.templating import Jinja2Templates
+from ..utils import soa_exists
DB_PATH = os.environ.get("SOA_BUILDER_DB", "soa_builder_web.db")
TEMPLATES_DIR = os.path.join(os.path.dirname(os.path.dirname(__file__)), "templates")
templates = Jinja2Templates(directory=TEMPLATES_DIR)
router = APIRouter()
+logger = logging.getLogger("soa_builder.web.routers.freezes")
def _connect():
return sqlite3.connect(DB_PATH)
-def _soa_exists(soa_id: int) -> bool:
- conn = _connect()
- cur = conn.cursor()
- cur.execute("SELECT 1 FROM soa WHERE id=?", (soa_id,))
- r = cur.fetchone()
- conn.close()
- return r is not None
+# Removed local _soa_exists; using shared utils.soa_exists
# Dynamic helper imports inside endpoint bodies avoid circular import at module load.
@@ -31,7 +28,7 @@ def _soa_exists(soa_id: int) -> bool:
@router.post("/ui/soa/{soa_id}/freeze", response_class=HTMLResponse)
def ui_freeze_soa(request: Request, soa_id: int, version_label: str = Form("")):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
try:
from ..app import _create_freeze # type: ignore
@@ -52,7 +49,7 @@ def ui_freeze_soa(request: Request, soa_id: int, version_label: str = Form("")):
@router.get("/soa/{soa_id}/freeze/{freeze_id}")
def get_freeze(soa_id: int, freeze_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()
@@ -66,7 +63,13 @@ def get_freeze(soa_id: int, freeze_id: int):
raise HTTPException(404, "Freeze not found")
try:
data = json.loads(row[0])
- except Exception:
+ except Exception as e:
+ logger.exception(
+ "get_freeze JSON decode failed soa_id=%s freeze_id=%s: %s",
+ soa_id,
+ freeze_id,
+ e,
+ )
data = {"error": "Corrupt snapshot"}
return JSONResponse(data)
diff --git a/src/soa_builder/web/routers/rollback.py b/src/soa_builder/web/routers/rollback.py
index b32d02f..01a3d50 100644
--- a/src/soa_builder/web/routers/rollback.py
+++ b/src/soa_builder/web/routers/rollback.py
@@ -1,32 +1,28 @@
import io
import os
+import logging
import pandas as pd
from fastapi import APIRouter, HTTPException, Request
from fastapi.responses import HTMLResponse, StreamingResponse
from fastapi.templating import Jinja2Templates
-from ..db import _connect
+from ..utils import soa_exists
DB_PATH = os.environ.get("SOA_BUILDER_DB", "soa_builder_web.db")
TEMPLATES_DIR = os.path.join(os.path.dirname(os.path.dirname(__file__)), "templates")
templates = Jinja2Templates(directory=TEMPLATES_DIR)
router = APIRouter()
+logger = logging.getLogger("soa_builder.web.routers.rollback")
-def _soa_exists(soa_id: int) -> bool:
- conn = _connect()
- cur = conn.cursor()
- cur.execute("SELECT 1 FROM soa WHERE id=?", (soa_id,))
- r = cur.fetchone()
- conn.close()
- return r is not None
+# Removed local _soa_exists; using shared utils.soa_exists
@router.get("/soa/{soa_id}/rollback_audit")
def get_rollback_audit_json(soa_id: int):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
from ..app import _list_rollback_audit # type: ignore
@@ -35,7 +31,7 @@ def get_rollback_audit_json(soa_id: int):
@router.get("/soa/{soa_id}/reorder_audit")
def get_reorder_audit_json(soa_id: int):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
from ..app import _list_reorder_audit # type: ignore
@@ -44,7 +40,7 @@ def get_reorder_audit_json(soa_id: int):
@router.get("/ui/soa/{soa_id}/rollback_audit", response_class=HTMLResponse)
def ui_rollback_audit(request: Request, soa_id: int):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
from ..app import _list_rollback_audit # type: ignore
@@ -57,7 +53,7 @@ def ui_rollback_audit(request: Request, soa_id: int):
@router.get("/ui/soa/{soa_id}/reorder_audit", response_class=HTMLResponse)
def ui_reorder_audit(request: Request, soa_id: int):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
from ..app import _list_reorder_audit # type: ignore
@@ -70,7 +66,7 @@ def ui_reorder_audit(request: Request, soa_id: int):
@router.get("/soa/{soa_id}/rollback_audit/export/xlsx")
def export_rollback_audit_xlsx(soa_id: int):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
from ..app import _list_rollback_audit # type: ignore
@@ -103,30 +99,38 @@ def export_rollback_audit_xlsx(soa_id: int):
@router.get("/soa/{soa_id}/reorder_audit/export/xlsx")
def export_reorder_audit_xlsx(soa_id: int):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
from ..app import _list_reorder_audit # type: ignore
rows = _list_reorder_audit(soa_id)
flat = []
for r in rows:
- moves = []
- old_pos = {vid: idx + 1 for idx, vid in enumerate(r.get("old_order", []))}
- new_order = r.get("new_order", [])
- for idx, vid in enumerate(new_order, start=1):
- op = old_pos.get(vid)
- if op and op != idx:
- moves.append(f"{vid}:{op}->{idx}")
- flat.append(
- {
- "id": r.get("id"),
- "entity_type": r.get("entity_type"),
- "performed_at": r.get("performed_at"),
- "old_order": ",".join(map(str, r.get("old_order", []))),
- "new_order": ",".join(map(str, new_order)),
- "moves": "; ".join(moves) if moves else "",
- }
- )
+ try:
+ moves = []
+ old_pos = {vid: idx + 1 for idx, vid in enumerate(r.get("old_order", []))}
+ new_order = r.get("new_order", [])
+ for idx, vid in enumerate(new_order, start=1):
+ op = old_pos.get(vid)
+ if op and op != idx:
+ moves.append(f"{vid}:{op}->{idx}")
+ flat.append(
+ {
+ "id": r.get("id"),
+ "entity_type": r.get("entity_type"),
+ "performed_at": r.get("performed_at"),
+ "old_order": ",".join(map(str, r.get("old_order", []))),
+ "new_order": ",".join(map(str, new_order)),
+ "moves": "; ".join(moves) if moves else "",
+ }
+ )
+ except Exception as e:
+ logger.debug(
+ "export_reorder_audit_xlsx flatten failure soa_id=%s row_id=%s: %s",
+ soa_id,
+ r.get("id"),
+ e,
+ )
df = pd.DataFrame(flat)
if df.empty:
df = pd.DataFrame(
diff --git a/src/soa_builder/web/routers/visits.py b/src/soa_builder/web/routers/visits.py
index 87296c5..dcfdf9d 100644
--- a/src/soa_builder/web/routers/visits.py
+++ b/src/soa_builder/web/routers/visits.py
@@ -1,27 +1,24 @@
from typing import List
from fastapi import APIRouter, HTTPException
+import logging
from fastapi.responses import JSONResponse
from ..audit import _record_reorder_audit, _record_visit_audit
from ..db import _connect
+from ..utils import soa_exists
from ..schemas import VisitCreate, VisitUpdate
router = APIRouter(prefix="/soa/{soa_id}")
+logger = logging.getLogger("soa_builder.web.routers.visits")
-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("/visits", response_class=JSONResponse)
def list_visits(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()
@@ -45,7 +42,7 @@ def list_visits(soa_id: int):
@router.get("/visits/{visit_id}", response_class=JSONResponse)
def get_visit(soa_id: int, visit_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()
@@ -69,7 +66,7 @@ def get_visit(soa_id: int, visit_id: int):
@router.post("/visits", response_class=JSONResponse)
def add_visit(soa_id: int, payload: VisitCreate):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
conn = _connect()
cur = conn.cursor()
@@ -108,7 +105,7 @@ def add_visit(soa_id: int, payload: VisitCreate):
@router.patch("/visits/{visit_id}", response_class=JSONResponse)
def update_visit(soa_id: int, visit_id: int, payload: VisitUpdate):
- if not _soa_exists(soa_id):
+ if not soa_exists(soa_id):
raise HTTPException(404, "SOA not found")
conn = _connect()
cur = conn.cursor()
@@ -178,7 +175,7 @@ def update_visit(soa_id: int, visit_id: int, payload: VisitUpdate):
@router.post("/visits/reorder", response_class=JSONResponse)
def reorder_visits_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")
diff --git a/src/soa_builder/web/templates/ddf_terminology.html b/src/soa_builder/web/templates/ddf_terminology.html
index 4a6bfd5..65b3277 100644
--- a/src/soa_builder/web/templates/ddf_terminology.html
+++ b/src/soa_builder/web/templates/ddf_terminology.html
@@ -4,10 +4,12 @@ DDF Terminology
{% if uploaded %}Upload successful: table reloaded. {% endif %}
{% if error %}Error: {{ error }} {% endif %}
-
+
+ Study Cells ({{ study_cells|length }})
+
+
+
+
+ | UID |
+ Arm |
+ Epoch |
+ Element |
+ Actions |
+
+ {% for sc in study_cells %}
+
+ | {{ sc.study_cell_uid }} |
+
+ {% set arm_match = arms | selectattr('arm_uid', 'equalto', sc.arm_uid) | list %}
+ {% if arm_match and arm_match[0] and arm_match[0].name %}
+ {{ arm_match[0].name }}
+ {% else %}
+ {{ sc.arm_uid }}
+ {% endif %}
+ |
+ {{ sc.epoch_name or sc.epoch_uid }} |
+ {{ sc.element_name or sc.element_uid }} |
+
+
+ |
+
+ {% else %}
+ | No study cells yet. |
+ {% endfor %}
+
+
+
+ Transition Rules ({{ transition_rules|length }})
+ {% include 'transition_rules_list.html' %}
+
+
@@ -360,6 +439,34 @@ Editing SoA {{ soa_id }}
No epoch audit entries yet.
{% endif %}
+
+ Study Cell Audit (latest {{ study_cell_audits|length }})
+ {% if study_cell_audits %}
+
+
+ | ID |
+ Study Cell |
+ Action |
+ Performed |
+ Before |
+ After |
+
+ {% for au in study_cell_audits %}
+
+ | {{ au.id }} |
+ {{ au.study_cell_id }} |
+ {{ au.action }} |
+ {{ au.performed_at }} |
+ {{ au.before_json or '' }} |
+ {{ au.after_json or '' }} |
+
+ {% endfor %}
+
+ {% else %}
+ No study cell audit entries yet.
+ {% endif %}
+
+ {% include 'element_audit_section.html' %}
@@ -370,8 +477,8 @@ Matrix
| Concepts |
{% for v in visits %}
- {{ v.name }}
- {{ v.raw_header or v.name }}
+ {{ v.raw_header or v.name }}
+ Encounter: {{ v.name }}
{% if v.epoch_id %}
{% set ep = (epochs | selectattr('id','equalto', v.epoch_id) | list) %}
{% if ep and ep[0] %}Epoch: {{ ep[0].name }} {% endif %}
@@ -398,7 +505,6 @@ Matrix
Generate Normalized Summary (JSON)
|