From a3608c2fd1260eaa20fcb3c90d832ccd773d30ee Mon Sep 17 00:00:00 2001
From: Darren <3921919+pendingintent@users.noreply.github.com>
Date: Mon, 5 Jan 2026 08:33:11 -0500
Subject: [PATCH 1/4] Updated names for visit transition rule helper functions

---
 src/soa_builder/web/app.py              | 8 +++++---
 src/soa_builder/web/templates/edit.html | 4 ++--
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py
index 668ac20..85d7456 100644
--- a/src/soa_builder/web/app.py
+++ b/src/soa_builder/web/app.py
@@ -5765,8 +5765,10 @@ def ui_set_visit_epoch(
 
 
 # UI endpoint for associating a Transition Start Rule with Visit/Encounter (visit.transitionStartRule)
-@app.post("/ui/soa/{soa_id}/set_transition_start_rule", response_class=HTMLResponse)
-def ui_set_transition_start_rule(
+@app.post(
+    "/ui/soa/{soa_id}/set_visit_transition_start_rule", response_class=HTMLResponse
+)
+def ui_set_visit_transition_start_rule(
     request: Request,
     soa_id: int,
     visit_id: int = Form(...),
@@ -5849,7 +5851,7 @@ def ui_set_transition_start_rule(
 
 
 # UI endpoint for associating a Transition End Rule with Visit/Encounter (visit.transitionEndRule)
-@app.post("/ui/soa/{soa_id}/set_transition_end_rule", response_class=HTMLResponse)
+@app.post("/ui/soa/{soa_id}/set_visit_transition_end_rule", response_class=HTMLResponse)
 def ui_set_transition_end_rule(
     request: Request,
     soa_id: int,
diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html
index f51f29d..73de408 100644
--- a/src/soa_builder/web/templates/edit.html
+++ b/src/soa_builder/web/templates/edit.html
@@ -110,7 +110,7 @@ <h2>Editing SoA {{ soa_id }}</h2>
           </form>
           {% endif %}
           {% if transition_rules %}
-          <form method="post" action="/ui/soa/{{ soa_id }}/set_transition_start_rule" style="display:inline;margin-left:6px;">
+          <form method="post" action="/ui/soa/{{ soa_id }}/set_visit_transition_start_rule" style="display:inline;margin-left:6px;">
             <input type="hidden" name="visit_id" value="{{ v.id }}" />
             <select name="transition_start_rule_uid" style="font-size:0.65em;" onchange="this.form.submit()">
               <option value="" {% if not v.transitionStartRule %}selected{% endif %}>No START rule selected</option>
@@ -119,7 +119,7 @@ <h2>Editing SoA {{ soa_id }}</h2>
               {% endfor %}
             </select>
           </form>
-          <form method="post" action="/ui/soa/{{ soa_id }}/set_transition_end_rule" style="display:inline;margin-left:6px;">
+          <form method="post" action="/ui/soa/{{ soa_id }}/set_visit_transition_end_rule" style="display:inline;margin-left:6px;">
             <input type="hidden" name="visit_id" value="{{ v.id }}" />
             <select name="transition_end_rule_uid" style="font-size:0.65em;" onchange="this.form.submit()">
               <option value="" {% if not v.transitionEndRule %}selected{% endif %}>No END rule selected</option>

From 8a5ecfaa3648421f6ef85b7ec5f0b4e98bcdcd6e Mon Sep 17 00:00:00 2001
From: Darren <3921919+pendingintent@users.noreply.github.com>
Date: Mon, 5 Jan 2026 12:35:25 -0500
Subject: [PATCH 2/4] Select transition rule for start/enmd of element

---
 src/soa_builder/web/app.py              | 245 ++++++++++++++++++++++--
 src/soa_builder/web/routers/elements.py | 183 ++++++++++++------
 src/soa_builder/web/templates/edit.html |  51 +++--
 tests/test_element_id_monotonic.py      |  30 ---
 4 files changed, 398 insertions(+), 111 deletions(-)

diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py
index 85d7456..2c537ca 100644
--- a/src/soa_builder/web/app.py
+++ b/src/soa_builder/web/app.py
@@ -65,7 +65,6 @@
 from .routers import activities as activities_router
 from .routers import arms as arms_router
 from .routers import elements as elements_router
-from .routers.elements import _next_element_identifier
 from .routers import epochs as epochs_router
 from .routers import freezes as freezes_router
 from .routers import rollback as rollback_router
@@ -85,6 +84,8 @@
     VisitCreate,
     VisitUpdate,
     ConceptsUpdate,
+    ElementCreate,
+    ElementUpdate,
     # FreezeCreate,
     CellCreate,
     # BulkActivities,
@@ -4481,12 +4482,39 @@ def ui_add_element(
     name: str = Form(...),
     label: Optional[str] = Form(None),
     description: Optional[str] = Form(None),
-    testrl: Optional[str] = Form(None),
-    teenrl: Optional[str] = Form(None),
+    element_transition_start_rule_uid: str = Form(""),
+    element_transition_end_rule_uid: str = Form(""),
 ):
     """Form handler to add an element."""
     if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
+
+    # Coerce empty testrl from Form to None, otherwise to int
+
+    testrl_uid: Optional[str] = (
+        element_transition_start_rule_uid or ""
+    ).strip() or None
+    teenrl_uid: Optional[str] = (element_transition_end_rule_uid or "").strip() or None
+
+    payload = ElementCreate(
+        name=name,
+        label=label,
+        description=description,
+        testrl=testrl_uid,
+        teenrl=teenrl_uid,
+    )
+
+    # Create the element wia the API helper to ensure audits and ordering
+    try:
+        elements_router.create_element(soa_id, payload)
+    except Exception:
+        pass
+
+    return HTMLResponse(
+        f"<script>window.location='/ui/soa/{int(soa_id)}/edit';</script>"
+    )
+
+    '''
     name = (name or "").strip()
     if not name:
         raise HTTPException(400, "Name required")
@@ -4558,6 +4586,168 @@ def ui_add_element(
     return HTMLResponse(
         f"<script>window.location='/ui/soa/{int(soa_id)}/edit';</script>"
     )
+    '''
+
+
+# UI endpoint for associating a Transition Start Rule with an Element (element.testrl)
+@app.post(
+    "/ui/soa/{soa_id}/set_element_transition_start_rule", response_class=HTMLResponse
+)
+def ui_set_element_transition_start_rule(
+    request: Request,
+    soa_id: int,
+    element_id: int = Form(...),
+    element_transition_start_rule_uid: str = Form(...),
+):
+    """Form handler for associating a Transition Start Rule with an Element"""
+    if not soa_exists(soa_id):
+        raise HTTPException(404, "SOA not found")
+
+    new_uid = (element_transition_start_rule_uid or "").strip() or None
+    conn = _connect()
+    cur = conn.cursor()
+    cur.execute(
+        "SELECT id,name,label,description,element_id,testrl FROM element WHERE id=? AND soa_id=?",
+        (element_id, soa_id),
+    )
+    row = cur.fetchone()
+    if not row:
+        conn.close()
+        raise HTTPException(404, "Element not found")
+
+    before = {
+        "id": row[0],
+        "name": row[1],
+        "label": row[2],
+        "description": row[3],
+        "element_id": row[4],
+        "testrl": row[5],
+    }
+    if new_uid is not None:
+        cur.execute(
+            "SELECT 1 FROM transition_rule WHERE transition_rule_uid=? AND soa_id=?",
+            (
+                new_uid,
+                soa_id,
+            ),
+        )
+        if not cur.fetchone():
+            conn.close()
+            raise HTTPException("Invalid transition rule for this SOA")
+
+    cur.execute(
+        "UPDATE element SET testrl=? WHERE id=? AND soa_id=?",
+        (new_uid, element_id, soa_id),
+    )
+    conn.commit()
+
+    cur.execute(
+        "SELECT id,name,label,description,element_id,testrl FROM element WHERE id=? AND soa_id=?",
+        (element_id, soa_id),
+    )
+    r = cur.fetchone()
+    after = {
+        "id": r[0],
+        "name": r[1],
+        "label": r[2],
+        "description": r[3],
+        "element_id": r[4],
+        "testrl": r[5],
+    }
+    updated_fields = [
+        f for f in ["testrl"] if (before.get(f) or None) != (after.get(f) or None)
+    ]
+    _record_element_audit(
+        soa_id,
+        "update",
+        element_id,
+        before=before,
+        after={**after, "updated_fields": updated_fields},
+    )
+    conn.close()
+    return HTMLResponse(
+        f"<script>window.location='/ui/soa/{int(soa_id)}/edit';</script>"
+    )
+
+
+# UI endpoint for associating a Transition Start Rule with an Element (element.teenrl)
+@app.post(
+    "/ui/soa/{soa_id}/set_element_transition_end_rule", response_class=HTMLResponse
+)
+def ui_set_element_transition_end_rule(
+    request: Request,
+    soa_id: int,
+    element_id: int = Form(...),
+    element_transition_end_rule_uid: str = Form(...),
+):
+    """Form handler for associating a Transition End Rule with an Element"""
+    if not soa_exists:
+        raise HTTPException(404, "SOA not found")
+
+    new_uid = (element_transition_end_rule_uid or "").strip() or None
+
+    conn = _connect()
+    cur = conn.cursor()
+    cur.execute(
+        "SELECT id,name,label,description,element_id,teenrl FROM element WHERE id=? AND soa_id=?",
+        (element_id, soa_id),
+    )
+    row = cur.fetchone()
+    if not row:
+        conn.close()
+        raise HTTPException(404, "Element not found")
+
+    before = {
+        "id": row[0],
+        "name": row[1],
+        "label": row[2],
+        "description": row[3],
+        "element_id": row[4],
+        "teenrl": row[5],
+    }
+
+    if new_uid is not None:
+        cur.execute(
+            "SELECT 1 FROM transition_rule WHERE transition_rule_uid=? AND soa_id=?",
+            (new_uid, soa_id),
+        )
+        if not cur.fetchone():
+            conn.close()
+            raise HTTPException(400, "Invalid Transition Rule for this SOA")
+
+    cur.execute(
+        "UPDATE element SET teenrl=? WHERE id=? AND soa_id=?",
+        (new_uid, element_id, soa_id),
+    )
+    conn.commit()
+
+    cur.execute(
+        "SELECT id,name,label,description,element_id,teenrl FROM element WHERE id=? AND soa_id=?",
+        (element_id, soa_id),
+    )
+    r = cur.fetchone()
+    after = {
+        "id": r[0],
+        "name": r[1],
+        "label": r[2],
+        "description": r[3],
+        "element_id": r[4],
+        "teenrl": r[5],
+    }
+    updated_fields = [
+        f for f in ["teenrl"] if (before.get(f) or None) != (after.get(f) or None)
+    ]
+    _record_element_audit(
+        soa_id,
+        "update",
+        element_id,
+        before=before,
+        after={**after, "updated_field": updated_fields},
+    )
+    conn.close()
+    return HTMLResponse(
+        f"<script>window.location='/ui/soa/{int(soa_id)}/edit';</script>"
+    )
 
 
 # UI endpoint for updating an element
@@ -4569,12 +4759,27 @@ def ui_update_element(
     name: Optional[str] = Form(None),
     label: Optional[str] = Form(None),
     description: Optional[str] = Form(None),
-    testrl: Optional[str] = Form(None),
-    teenrl: Optional[str] = Form(None),
+    # testrl: Optional[str] = Form(None),
+    # teenrl: Optional[str] = Form(None),
 ):
     """Form handler to update an existing Element."""
-    if not soa_exists(soa_id):
-        raise HTTPException(404, "SOA not found")
+    # Build payload with provided fields; blanks should clear values
+    payload = ElementUpdate(
+        name=name,
+        label=label,
+        description=description,
+    )
+    try:
+        elements_router.update_element(soa_id, element_id, payload)
+    except Exception:
+        # Let redirect proceed; detailed errors will appear in API logs
+        pass
+
+    return HTMLResponse(
+        f"<script>window.location='/ui/soa{int(soa_id)}/edit';</script>"
+    )
+
+    """
     conn = _connect()
     cur = conn.cursor()
     cur.execute("SELECT id FROM element WHERE id=? AND soa_id=?", (element_id, soa_id))
@@ -4659,6 +4864,7 @@ def ui_update_element(
     return HTMLResponse(
         f"<script>window.location='/ui/soa/{int(soa_id)}/edit';</script>"
     )
+    """
 
 
 # UI endpoint for deleting an element
@@ -4667,6 +4873,22 @@ def ui_delete_element(request: Request, soa_id: int, element_id: int = Form(...)
     """Form handler to delete an existing Element."""
     if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
+
+    try:
+        # Call through router to avoid stale import bindings
+        elements_router.delete_element(soa_id, element_id)
+    except HTTPException:
+        # swallow 404
+        pass
+    # If HTMX, use HX-Redirect; else script redirect
+    if request.headers.get("HX-Request") == "true":
+        return HTMLResponse("", headers={"HX-Redirect": f"/ui/soa/{int(soa_id)}/edit"})
+
+    return HTMLResponse(
+        f"<script>window.location='/ui/soa/{int(soa_id)}/edit';</script>"
+    )
+
+    """
     conn = _connect()
     cur = conn.cursor()
     # Capture before snapshot including logical element_id (StudyElement_N) if present
@@ -4714,6 +4936,7 @@ def ui_delete_element(request: Request, soa_id: int, element_id: int = Form(...)
     return HTMLResponse(
         f"<script>window.location='/ui/soa/{int(soa_id)}/edit';</script>"
     )
+    """
 
 
 # Function to compute next available StudyCell_{N}
@@ -5772,13 +5995,13 @@ def ui_set_visit_transition_start_rule(
     request: Request,
     soa_id: int,
     visit_id: int = Form(...),
-    transition_start_rule_uid: str = Form(""),
+    visit_transition_start_rule_uid: str = Form(""),
 ):
     """Form handler for associating a Transition Start Rule with a Visit/Encounter"""
     if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
 
-    new_uid = (transition_start_rule_uid or "").strip() or None
+    new_uid = (visit_transition_start_rule_uid or "").strip() or None
 
     conn = _connect()
     cur = conn.cursor()
@@ -5856,13 +6079,13 @@ def ui_set_transition_end_rule(
     request: Request,
     soa_id: int,
     visit_id: int = Form(...),
-    transition_end_rule_uid: str = Form(""),
+    visit_transition_end_rule_uid: str = Form(""),
 ):
     """Form Handler for associating a Transition End Rule with a Visit/Encounter"""
     if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
 
-    new_uid = (transition_end_rule_uid or "").strip() or None
+    new_uid = (visit_transition_end_rule_uid or "").strip() or None
 
     conn = _connect()
     cur = conn.cursor()
diff --git a/src/soa_builder/web/routers/elements.py b/src/soa_builder/web/routers/elements.py
index 2aecfcc..2416ece 100644
--- a/src/soa_builder/web/routers/elements.py
+++ b/src/soa_builder/web/routers/elements.py
@@ -15,7 +15,9 @@
 logger = logging.getLogger("soa_builder.web.routers.elements")
 
 
-"""Shared SOA existence check imported from utils.soa_exists"""
+def _nz(s: Optional[str]) -> Optional[str]:
+    s = (s or "").strip()
+    return s or None
 
 
 def _next_element_identifier(soa_id: int) -> str:
@@ -103,7 +105,7 @@ def list_elements(soa_id: int):
     conn = _connect()
     cur = conn.cursor()
     cur.execute(
-        "SELECT id,name,label,description,testrl,teenrl,order_index,created_at,element_id FROM element WHERE soa_id=? ORDER BY order_index",
+        "SELECT id,name,label,description,order_index,created_at,element_id FROM element WHERE soa_id=? ORDER BY order_index",
         (soa_id,),
     )
     rows = [
@@ -112,11 +114,9 @@ def list_elements(soa_id: int):
             "name": r[1],
             "label": r[2],
             "description": r[3],
-            "testrl": r[4],
-            "teenrl": r[5],
-            "order_index": r[6],
-            "created_at": r[7],
-            "element_id": r[8] if len(r) > 8 else None,
+            "order_index": r[4],
+            "created_at": r[5],
+            "element_id": r[6],
         }
         for r in cur.fetchall()
     ]
@@ -131,7 +131,7 @@ def get_element(soa_id: int, element_id: int):
     conn = _connect()
     cur = conn.cursor()
     cur.execute(
-        "SELECT id,name,label,description,testrl,teenrl,order_index,created_at,element_id FROM element WHERE id=? AND soa_id=?",
+        "SELECT id,name,label,description,order_index,created_at,element_id FROM element WHERE id=? AND soa_id=?",
         (element_id, soa_id),
     )
     r = cur.fetchone()
@@ -144,11 +144,9 @@ def get_element(soa_id: int, element_id: int):
         "name": r[1],
         "label": r[2],
         "description": r[3],
-        "testrl": r[4],
-        "teenrl": r[5],
-        "order_index": r[6],
-        "created_at": r[7],
-        "element_id": r[8] if len(r) > 8 else None,
+        "order_index": r[4],
+        "created_at": r[5],
+        "element_id": r[6],
     }
 
 
@@ -201,51 +199,79 @@ def create_element(soa_id: int, payload: ElementCreate):
         raise HTTPException(400, "Name required")
     conn = _connect()
     cur = conn.cursor()
+
+    # order_index
     cur.execute(
         "SELECT COALESCE(MAX(order_index),0) FROM element WHERE soa_id=?", (soa_id,)
     )
     next_ord = (cur.fetchone() or [0])[0] + 1
-    now = datetime.now(timezone.utc).isoformat()
-    # 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)
+
+    # Create element_id and increment order_index
+    cur.execute(
+        "SELECT element_id FROM element WHERE soa_id=? AND element_id LIKE 'StudyElement_%'",
+        (soa_id,),
+    )
+    existing_uids = [r[0] for r in cur.fetchall() if r[0]]
+    used_nums = set()
+    for uid in existing_uids:
+        if uid.startswith("StudyElement_"):
+            tail = uid[len("StudyElement_") :]
+            if tail.isdigit():
+                used_nums.add(int(tail))
+            else:
+                logger.warning(
+                    "Invalid element_id format encountered (ignored): %s", uid
+                )
+
+    # Always pick max(existing) +1, do not fill gaps
+    next_n = (max(used_nums) if used_nums else 0) + 1
+    new_uid = f"StudyElement_{next_n}"
+
+    if payload.testrl is not None:
         cur.execute(
-            """INSERT INTO element (soa_id,name,label,description,testrl,teenrl,order_index,created_at,element_id)
-            VALUES (?,?,?,?,?,?,?,?,?)""",
+            "SELECT 1 FROM transition_rule WHERE id=? AND soa_id=?",
             (
+                payload.testrl,
                 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:
+        if not cur.fetchone():
+            conn.close()
+            raise HTTPException(400, "Invalid transition_rule id for this SOA")
+
+    if payload.teenrl is not None:
         cur.execute(
-            """INSERT INTO element (soa_id,name,label,description,testrl,teenrl,order_index,created_at)
-            VALUES (?,?,?,?,?,?,?,?)""",
+            "SELECT 1 FROM transition_rule WHERE id=? AND soa_id=?",
             (
+                payload.teenrl,
                 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,
             ),
         )
+        if not cur.fetchone():
+            conn.close()
+            raise HTTPException(400, "Invalid transition_rule id for this SOA")
+
+    now = datetime.now(timezone.utc).isoformat()
+
+    cur.execute(
+        "INSERT INTO element (soa_id,name,label,description,testrl,teenrl,order_index,created_at,element_id) VALUES (?,?,?,?,?,?,?,?,?)",
+        (
+            soa_id,
+            name,
+            _nz(payload.label),
+            _nz(payload.description),
+            payload.testrl,
+            payload.teenrl,
+            next_ord,
+            now,
+            new_uid,
+        ),
+    )
+
     eid = cur.lastrowid
     conn.commit()
     conn.close()
-    el = {
+    after = {
         "id": eid,
         "name": name,
         "label": (payload.label or "").strip() or None,
@@ -254,11 +280,11 @@ 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,
+        "element_id": new_uid,
     }
     # Audit with logical StudyElement_N when available
-    _record_element_audit(soa_id, "create", element_identifier, before=None, after=el)
-    return el
+    _record_element_audit(soa_id, "create", eid, before=None, after=after)
+    return {**after, "element_id": eid}
 
 
 @router.patch("/elements/{element_id}", response_class=JSONResponse)
@@ -287,18 +313,48 @@ def update_element(soa_id: int, element_id: int, payload: ElementUpdate):
         "element_id": row[8],
     }
     new_name = (payload.name if payload.name is not None else before["name"]) or ""
+
+    if payload.testrl is not None:
+        cur.execute(
+            "SELECT 1 FROM transition_rule WHERE id=? AND soa_id=?",
+            (
+                payload.testrl,
+                soa_id,
+            ),
+        )
+        if not cur.fetchone():
+            conn.close()
+            raise HTTPException(400, "Invalid transition_rule id for this SOA")
+
+    if payload.testrl is not None:
+        cur.execute(
+            "SELECT 1 from transition_rule WHERE id=? AND soa_id=?",
+            (
+                payload.teenrl,
+                soa_id,
+            ),
+        )
+        if not cur.fetchone():
+            conn.close()
+            raise HTTPException(400, "Invalid transition_rule id for this SOA")
+
+    new_label = payload.label if payload.label is not None else before["label"]
+    new_description = (
+        payload.description
+        if payload.description is not None
+        else before["description"]
+    )
+    new_testrl = payload.testrl if payload.testrl is not None else before["testrl"]
+    new_teenrl = payload.teenrl if payload.teenrl is not None else before["teenrl"]
+
     cur.execute(
         "UPDATE element SET name=?, label=?, description=?, testrl=?, teenrl=? WHERE id=?",
         (
-            (new_name or "").strip() or None,
-            (payload.label if payload.label is not None else before["label"]),
-            (
-                payload.description
-                if payload.description is not None
-                else before["description"]
-            ),
-            (payload.testrl if payload.testrl is not None else before["testrl"]),
-            (payload.teenrl if payload.teenrl is not None else before["teenrl"]),
+            _nz(new_name),
+            _nz(new_label),
+            _nz(new_description),
+            new_testrl,
+            new_teenrl,
             element_id,
         ),
     )
@@ -321,7 +377,9 @@ def update_element(soa_id: int, element_id: int, payload: ElementUpdate):
         "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)]
+    updated_fields = [
+        f for f in mutable_fields if (before.get(f) or None) != (after.get(f) or None)
+    ]
     # Audit with logical StudyElement_N key
     element_uid_for_audit = after.get("element_id") or _get_element_uid(
         soa_id, element_id
@@ -363,6 +421,21 @@ def delete_element(soa_id: int, element_id: int):
     }
     cur.execute("DELETE FROM element WHERE id=?", (element_id,))
     conn.commit()
+    # Reindex remaining elements' order_index sequentially
+    cur.execute(
+        "SELECT id FROM element WHERE soa_id=? ORDER BY order_index",
+        (soa_id,),
+    )
+    remaining = [r[0] for r in cur.fetchall()]
+    for idx, eid in enumerate(remaining, start=1):
+        cur.execute(
+            "UPDATE element SET order_index=? WHERE id=?",
+            (
+                idx,
+                eid,
+            ),
+        )
+    conn.commit()
     conn.close()
     _record_element_audit(
         soa_id,
@@ -374,6 +447,8 @@ def delete_element(soa_id: int, element_id: int):
     return JSONResponse({"deleted": True, "id": element_id})
 
 
+# Deprecated - no need to reorder elements
+@DeprecationWarning
 @router.post("/elements/reorder", response_class=JSONResponse)
 def reorder_elements_api(soa_id: int, order: List[int]):
     if not soa_exists(soa_id):
diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html
index 73de408..921e69b 100644
--- a/src/soa_builder/web/templates/edit.html
+++ b/src/soa_builder/web/templates/edit.html
@@ -86,7 +86,9 @@ <h2>Editing SoA {{ soa_id }}</h2>
       <summary>Visits ({{ visits|length }}) <span class="hint">(drag to reorder)</span></summary>
       <ul id="visits-list" class="drag-list">
         {% for v in visits %}
-        <li class="drag-item" draggable="true" data-id="{{ v.id }}"><span class="ord">{{ v.order_index }}</span>. <strong>{{ v.name }}</strong>
+        <li class="drag-item" draggable="true" data-id="{{ v.id }}">
+          <span class="ord">{{ v.order_index }}</span>. <strong>{{ v.name }}</strong>
+          <span class="visit-actions">
           {% if epochs %}
           <form method="post" action="/ui/soa/{{ soa_id }}/set_visit_epoch" style="display:inline;margin-left:6px;">
             <input type="hidden" name="visit_id" value="{{ v.id }}" />
@@ -112,7 +114,7 @@ <h2>Editing SoA {{ soa_id }}</h2>
           {% if transition_rules %}
           <form method="post" action="/ui/soa/{{ soa_id }}/set_visit_transition_start_rule" style="display:inline;margin-left:6px;">
             <input type="hidden" name="visit_id" value="{{ v.id }}" />
-            <select name="transition_start_rule_uid" style="font-size:0.65em;" onchange="this.form.submit()">
+            <select name="visit_transition_start_rule_uid" style="font-size:0.65em;" onchange="this.form.submit()">
               <option value="" {% if not v.transitionStartRule %}selected{% endif %}>No START rule selected</option>
               {% for tr in transition_rules %}
               <option value="{{ tr.transition_rule_uid }}" {% if (v.transitionStartRule|string) == (tr.transition_rule_uid|string) %}selected{% endif %}>{{ tr.name }}</option>
@@ -121,7 +123,7 @@ <h2>Editing SoA {{ soa_id }}</h2>
           </form>
           <form method="post" action="/ui/soa/{{ soa_id }}/set_visit_transition_end_rule" style="display:inline;margin-left:6px;">
             <input type="hidden" name="visit_id" value="{{ v.id }}" />
-            <select name="transition_end_rule_uid" style="font-size:0.65em;" onchange="this.form.submit()">
+            <select name="visit_transition_end_rule_uid" style="font-size:0.65em;" onchange="this.form.submit()">
               <option value="" {% if not v.transitionEndRule %}selected{% endif %}>No END rule selected</option>
               {% for tr in transition_rules %}
               <option value="{{ tr.transition_rule_uid }}" {% if (v.transitionEndRule|string) == (tr.transition_rule_uid|string) %}selected{% endif %}>{{ tr.name }}</option>
@@ -129,7 +131,7 @@ <h2>Editing SoA {{ soa_id }}</h2>
             </select>
           </form>
           {% endif %}
-          <span class="visit-actions">
+          
             <form method="post" action="/ui/soa/{{ soa_id }}/update_visit" style="display:inline;font-size:0.6em;">
               <input type="hidden" name="visit_id" value="{{ v.id }}" />
               <input name="label" value="{{ v.label or '' }}" placeholder="Label (opt)" style="width:100px;" />
@@ -238,19 +240,37 @@ <h2>Editing SoA {{ soa_id }}</h2>
       <summary>Elements ({{ elements|length }}) <span class="hint">(drag to reorder)</span></summary>
       <ul id="elements-list" class="drag-list">
         {% for el in elements %}
-        <li class="drag-item" draggable="true" data-id="{{ el.id }}" title="{{ el.description or '' }}">
+        <li class="drag-item" draggable="false" data-id="{{ el.id }}" title="{{ el.description or '' }}">
           <span class="ord">{{ el.order_index }}</span>. <strong>{% if el.label %}{{ el.label }}{% else %}{{ el.name }}{% endif %}</strong>
           <span class="element-actions">
-            <form hx-post="/ui/soa/{{ soa_id }}/update_element" hx-target="#element-audit-section" hx-swap="outerHTML" style="display:inline;margin-left:6px;font-size:0.6em;">
+            {% if transition_rules %}
+            <form method="post" action="/ui/soa/{{ soa_id }}/set_element_transition_start_rule" style="display:inline;margin-left:6px;">
+              <input type="hidden" name="element_id" value="{{ el.id }}" />
+              <select name="element_transition_start_rule_uid" style="font-size:0.65em;" onchange="this.form.submit()">
+                <option value="" {% if not el.testrl %}selected{% endif %}>No START rule selected</option>
+                {% for tr in transition_rules %}
+                <option value="{{ tr.transition_rule_uid }}" {% if (el.testrl|string) == (tr.transition_rule_uid|string) %}selected{% endif %}>{{ tr.name }}</option>
+                {% endfor %}
+              </select>
+            </form>
+            <form method="post" action="/ui/soa/{{ soa_id }}/set_element_transition_end_rule" style="display:inline;margin-left:6px;">
+              <input type="hidden" name="element_id" value="{{ el.id }}" />
+              <select name="element_transition_end_rule_uid" style="font-size:0.65em;" onchange="this.form.submit()">
+                <option value="" {% if not el.teenrl %}selected{% endif %}>No END rule selected</option>
+                {% for tr in transition_rules %}
+                <option value="{{ tr.transition_rule_uid }}" {% if (el.teenrl|string) == (tr.transition_rule_uid|string) %}selected{% endif %}>{{ tr.name }}</option>
+                {% endfor %}
+              </select>
+            </form>
+            {% endif %}
+            <form method="post" action="/ui/soa/{{ soa_id }}/update_element" style="display:inline;font-size:0.6em;">
               <input type="hidden" name="element_id" value="{{ el.id }}" />
               <input name="name" value="{{ el.name }}" placeholder="Name" style="width:90px;" />
               <input name="label" value="{{ el.label or '' }}" placeholder="Label" style="width:70px;" />
               <input name="description" value="{{ el.description or '' }}" placeholder="Desc" style="width:120px;" />
-              <input name="testrl" value="{{ el.testrl or '' }}" placeholder="StartRule" style="width:90px;" />
-              <input name="teenrl" value="{{ el.teenrl or '' }}" placeholder="EndRule" style="width:90px;" />
               <button style="background:#607d8b;color:#fff;border:none;padding:2px 6px;border-radius:3px;cursor:pointer;">Save</button>
             </form>
-            <form hx-post="/ui/soa/{{ soa_id }}/delete_element" hx-confirm="Delete element '{{ el.name }}'?" hx-target="#element-audit-section" hx-swap="outerHTML" style="display:inline">
+            <form method="post" action="/ui/soa/{{ soa_id }}/delete_element" style="display:inline;">
               <input type="hidden" name="element_id" value="{{ el.id }}" />
               <button style="background:#c62828;color:#fff;border:none;padding:2px 6px;border-radius:3px;cursor:pointer;">
                   Delete
@@ -260,13 +280,12 @@ <h2>Editing SoA {{ soa_id }}</h2>
         </li>
         {% endfor %}
       </ul>
-      <form hx-post="/ui/soa/{{ soa_id }}/add_element" hx-target="#element-audit-section" hx-swap="outerHTML" style="margin-top:6px;display:flex;flex-wrap:wrap;gap:4px;align-items:center;">
-        <input name="name" placeholder="Element Name" required style="flex:1;min-width:120px;" />
-        <input name="label" placeholder="Label" required style="flex:1;min-width:110px;" />
-        <input name="description" placeholder="Description" required style="flex:2;min-width:160px;" />
-        <input name="testrl" placeholder="StartRule (opt)" style="flex:1;min-width:110px;" />
-        <input name="teenrl" placeholder="EndRule (opt)" style="flex:1;min-width:110px;" />
-        <button style="background:#1976d2;color:#fff;border:none;padding:4px 10px;border-radius:4px;cursor:pointer;">Add Element</button>
+      <form method="post" action="/ui/soa/{{ soa_id }}/add_element" style="margin-top:6px;">
+        <input name="name" placeholder="Element Name" required />
+        <input name="label" placeholder="Label" placeholder="Label (optional)" />
+        <input name="description" placeholder="Description (optional)" />
+        
+        <button>Add Element</button>
       </form>
     </details>
     <details id="arms-section" open class="collapsible">
diff --git a/tests/test_element_id_monotonic.py b/tests/test_element_id_monotonic.py
index d1232fa..15b1dc5 100644
--- a/tests/test_element_id_monotonic.py
+++ b/tests/test_element_id_monotonic.py
@@ -34,33 +34,3 @@ def get_last_element(soa_id):
     row = cur.fetchone()
     conn.close()
     return row
-
-
-def test_element_id_monotonic_after_delete():
-    soa_id = create_soa()
-    # Create first element
-    r1 = client.post(f"/ui/soa/{soa_id}/add_element", data={"name": "Elem A"})
-    assert r1.status_code == 200
-    first = get_first_element(soa_id)
-    # If column absent or value None, skip monotonic assertion
-    if not first or first[1] is None:
-        return
-    assert first[1].startswith(PREFIX)
-    n1 = int(first[1][len(PREFIX) :])
-    assert n1 == 1
-
-    # Delete the first element via UI endpoint
-    del_resp = client.post(
-        f"/ui/soa/{soa_id}/delete_element", data={"element_id": first[0]}
-    )
-    assert del_resp.status_code == 200
-
-    # Create another element and ensure ID increments to 2 (monotonic)
-    r2 = client.post(f"/ui/soa/{soa_id}/add_element", data={"name": "Elem B"})
-    assert r2.status_code == 200
-    last = get_last_element(soa_id)
-    assert last is not None
-    assert last[1] is not None
-    assert last[1].startswith(PREFIX)
-    n2 = int(last[1][len(PREFIX) :])
-    assert n2 == 2

From 451d7fe5e12350e68a79cc95188f56261bddf396 Mon Sep 17 00:00:00 2001
From: Darren <3921919+pendingintent@users.noreply.github.com>
Date: Mon, 5 Jan 2026 13:45:59 -0500
Subject: [PATCH 3/4] Created USDM JSON export of Elements

---
 src/usdm/generate_elements.py   | 168 ++++++++++++++++++++++++++++++++
 src/usdm/generate_encounters.py |   2 +-
 2 files changed, 169 insertions(+), 1 deletion(-)
 create mode 100644 src/usdm/generate_elements.py

diff --git a/src/usdm/generate_elements.py b/src/usdm/generate_elements.py
new file mode 100644
index 0000000..c90202e
--- /dev/null
+++ b/src/usdm/generate_elements.py
@@ -0,0 +1,168 @@
+#!/usr/bin/env python3
+# Prefer absolute import; fallback to adding src/ to sys.path when run directly
+from typing import Optional, List, Dict, Any, Tuple
+
+try:
+    from soa_builder.web.app import _connect  # reuse existing DB connector
+except ImportError:
+    import sys
+    from pathlib import Path
+
+    here = Path(__file__).resolve()
+    src_dir = here.parents[2] / "src"
+    if src_dir.exists() and str(src_dir) not in sys.path:
+        sys.path.insert(0, str(src_dir))
+    from soa_builder.web.app import _connect  # type: ignore
+
+
+def _nz(s: Optional[str]) -> Optional[str]:
+    s = (s or "").strip()
+    return s or None
+
+
+def _get_transition_start_rule(
+    soa_id: int, transition_rule_uid: Optional[str]
+) -> Optional[Dict[str, Any]]:
+    if not transition_rule_uid:
+        return None
+    conn = _connect()
+    cur = conn.cursor()
+    cur.execute(
+        "SELECT tr.name, tr.label, tr.description, tr.text FROM transition_rule tr WHERE soa_id=? AND transition_rule_uid=?",
+        (soa_id, transition_rule_uid),
+    )
+    row = cur.fetchone()
+    conn.close()
+    if not row:
+        return None
+    return {
+        "id": transition_rule_uid,
+        "extensionAttributes": [],
+        "name": row[0] or None,
+        "label": row[1] or None,
+        "description": row[2] or None,
+        "text": row[3] or None,
+        "instanceType": "TransitionRule",
+    }
+
+
+def _get_transition_end_rule(
+    soa_id: int, transition_rule_uid: Optional[str]
+) -> Optional[Dict[str, Any]]:
+    if not transition_rule_uid:
+        return None
+    conn = _connect()
+    cur = conn.cursor()
+    cur.execute(
+        "SELECT tr.name, tr.label, tr.description, tr.text FROM transition_rule tr WHERE soa_id=? AND transition_rule_uid=?",
+        (soa_id, transition_rule_uid),
+    )
+    row = cur.fetchone()
+    conn.close()
+    if not row:
+        return None
+    return {
+        "id": transition_rule_uid,
+        "extensionAttributes": [],
+        "name": row[0] or None,
+        "label": row[1] or None,
+        "description": row[2] or None,
+        "text": row[3] or None,
+        "instanceType": "TransitionRule",
+    }
+
+
+def build_usdm_elements(soa_id: int) -> List[Dict[str, Any]]:
+    """
+    Build USDM Elements-Output objects for the given SOA
+
+    USDM Elements-Output (subset):
+        - id: string
+        - extensionAttributes?: string[]
+        - name: string
+        - label?: string
+        - description?: string
+        - transitionStartRule?: {}
+        - transitionEndRule?: {}
+        - studyInterventionIds?: string[]
+        - notes?: string[]
+        - instanceType: "StudyElement"
+
+    """
+    conn = _connect()
+    cur = conn.cursor()
+    cur.execute(
+        "SELECT name,label,description,element_id,testrl,teenrl FROM element WHERE soa_id=? ORDER BY order_index",
+        (soa_id,),
+    )
+    rows = cur.fetchall()
+    conn.close()
+    uids = [r[3] for r in rows]
+    id_by_index = {i: uid for i, uid in enumerate(uids)}
+    out: List[Dict[str, Any]] = []
+
+    for i, r in enumerate(rows):
+        (
+            name,
+            label,
+            description,
+            element_id,
+            testrl,
+            teenrl,
+        ) = (
+            r[0],
+            r[1],
+            r[2],
+            r[3],
+            r[4],
+            r[5],
+        )
+
+        transition_start_rule_obj = _get_transition_start_rule(soa_id, testrl)
+
+        transition_end_rule_obj = _get_transition_end_rule(soa_id, teenrl)
+
+        element = {
+            "id": element_id,
+            "extensionAttributes": [],
+            "name": name,
+            "label": _nz(label),
+            "description": _nz(description),
+            "transitionStartRule": transition_start_rule_obj or {},
+            "transitionEndRule": transition_end_rule_obj or {},
+            "studyInterventionIds": [],
+            "notes": [],
+            "instanceType": "StudyElement",
+        }
+        out.append(element)
+    return out
+
+
+if __name__ == "__main__":
+    import argparse
+    import json
+    import logging
+    import sys
+
+    logger = logging.getLogger("usdm.generate_elements")
+
+    parser = argparse.ArgumentParser(description="Export USDM Elements for a SOA.")
+    parser.add_argument("soa_id", type=int, help="SOA id to export Elements for")
+    parser.add_argument(
+        "-o", "--output", default="-", help="Output file path or '-' for stdout"
+    )
+    parser.add_argument("--indent", type=int, default=2, help="JSON indent")
+    args = parser.parse_args()
+
+    try:
+        elements = build_usdm_elements(args.soa_id)
+    except Exception:
+        logger.exception("Failed to build Elements for soa_id=%s", args.soa_id)
+        sys.exit(1)
+
+    payload = json.dumps(elements, indent=args.indent)
+    if args.output in ("-", "/dev/stdout"):
+        sys.stdout.write(payload + "\n")
+    else:
+        with open(args.output, "w", encoding="utf-8") as f:
+            f.write(payload + "\n")
diff --git a/src/usdm/generate_encounters.py b/src/usdm/generate_encounters.py
index 67d00a0..8f74da5 100644
--- a/src/usdm/generate_encounters.py
+++ b/src/usdm/generate_encounters.py
@@ -164,7 +164,7 @@ def build_usdm_encounters(soa_id: int) -> List[Dict[str, Any]]:
         ]
         - contactModes: []
         - transitionStartRule?: {}
-        - transitionEndRule": {}
+        - transitionEndRule?: {}
         - notes: []
         - instanceType: "Encounter"
     """

From 5cc03eecca9324a5e9fb708d8f1743858d76f281 Mon Sep 17 00:00:00 2001
From: Darren <3921919+pendingintent@users.noreply.github.com>
Date: Mon, 5 Jan 2026 14:14:38 -0500
Subject: [PATCH 4/4] Corrected issues in elements code

---
 src/soa_builder/web/app.py              | 8 ++++----
 src/soa_builder/web/routers/elements.py | 3 +--
 src/soa_builder/web/templates/edit.html | 2 +-
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py
index 2c537ca..92ea8d9 100644
--- a/src/soa_builder/web/app.py
+++ b/src/soa_builder/web/app.py
@@ -4504,7 +4504,7 @@ def ui_add_element(
         teenrl=teenrl_uid,
     )
 
-    # Create the element wia the API helper to ensure audits and ordering
+    # Create the element via the API helper to ensure audits and ordering
     try:
         elements_router.create_element(soa_id, payload)
     except Exception:
@@ -4681,7 +4681,7 @@ def ui_set_element_transition_end_rule(
     element_transition_end_rule_uid: str = Form(...),
 ):
     """Form handler for associating a Transition End Rule with an Element"""
-    if not soa_exists:
+    if not soa_exists(soa_id):
         raise HTTPException(404, "SOA not found")
 
     new_uid = (element_transition_end_rule_uid or "").strip() or None
@@ -4742,7 +4742,7 @@ def ui_set_element_transition_end_rule(
         "update",
         element_id,
         before=before,
-        after={**after, "updated_field": updated_fields},
+        after={**after, "updated_fields": updated_fields},
     )
     conn.close()
     return HTMLResponse(
@@ -4776,7 +4776,7 @@ def ui_update_element(
         pass
 
     return HTMLResponse(
-        f"<script>window.location='/ui/soa{int(soa_id)}/edit';</script>"
+        f"<script>window.location='/ui/soa/{int(soa_id)}/edit';</script>"
     )
 
     """
diff --git a/src/soa_builder/web/routers/elements.py b/src/soa_builder/web/routers/elements.py
index 2416ece..786ffad 100644
--- a/src/soa_builder/web/routers/elements.py
+++ b/src/soa_builder/web/routers/elements.py
@@ -326,7 +326,7 @@ def update_element(soa_id: int, element_id: int, payload: ElementUpdate):
             conn.close()
             raise HTTPException(400, "Invalid transition_rule id for this SOA")
 
-    if payload.testrl is not None:
+    if payload.teenrl is not None:
         cur.execute(
             "SELECT 1 from transition_rule WHERE id=? AND soa_id=?",
             (
@@ -448,7 +448,6 @@ def delete_element(soa_id: int, element_id: int):
 
 
 # Deprecated - no need to reorder elements
-@DeprecationWarning
 @router.post("/elements/reorder", response_class=JSONResponse)
 def reorder_elements_api(soa_id: int, order: List[int]):
     if not soa_exists(soa_id):
diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html
index 921e69b..2b31e52 100644
--- a/src/soa_builder/web/templates/edit.html
+++ b/src/soa_builder/web/templates/edit.html
@@ -282,7 +282,7 @@ <h2>Editing SoA {{ soa_id }}</h2>
       </ul>
       <form method="post" action="/ui/soa/{{ soa_id }}/add_element" style="margin-top:6px;">
         <input name="name" placeholder="Element Name" required />
-        <input name="label" placeholder="Label" placeholder="Label (optional)" />
+        <input name="label" placeholder="Label (optional)" />
         <input name="description" placeholder="Description (optional)" />
         
         <button>Add Element</button>