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delete_epoch(soa_id, epoch_id) return HTMLResponse(f"") @@ -3998,7 +4032,7 @@ 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("")): - """Persist new epoch ordering.""" + """Form handler to persist new epoch ordering.""" if not _soa_exists(soa_id): raise HTTPException(404, "SOA not found") ids = [int(x) for x in order.split(",") if x.strip().isdigit()] @@ -4333,6 +4367,7 @@ def ui_ddf_terminology( uploaded: Optional[str] = None, error: Optional[str] = None, ): + """Detail page to display loaded DDF terminology from the SQLite table""" data = get_ddf_terminology( search=search, code=code, @@ -4498,6 +4533,7 @@ def _get_ddf_sources() -> List[str]: def get_ddf_audit( source: Optional[str] = None, start: Optional[str] = None, end: Optional[str] = None ): + """Return audit report of DDF Terminology loads.""" conn = _connect() cur = conn.cursor() cur.execute( @@ -4556,6 +4592,7 @@ def _valid_date(d: str) -> bool: def export_ddf_audit_csv( source: Optional[str] = None, start: Optional[str] = None, end: Optional[str] = None ): + """Export DDF terminology audit report in CSV format.""" rows = get_ddf_audit(source=source, start=start, end=end) import csv import io @@ -4603,6 +4640,7 @@ def export_ddf_audit_csv( def export_ddf_audit_json( source: Optional[str] = None, start: Optional[str] = None, end: Optional[str] = None ): + """Export DDF terminology audit report in JSON format.""" return get_ddf_audit(source=source, start=start, end=end) @@ -4613,6 +4651,7 @@ def ui_ddf_audit( start: Optional[str] = None, end: Optional[str] = None, ): + """Display audit report of DDF Terminology loads""" rows = get_ddf_audit(source=source, start=start, end=end) sources = _get_ddf_sources() return templates.TemplateResponse( @@ -4756,6 +4795,7 @@ def load_protocol_terminology( def admin_load_protocol( file_path: Optional[str] = None, sheet_name: str = "Protocol Terminology 2025-09-26" ): + """Load new Protocol Terminology XLS.""" project_root = os.path.dirname( os.path.dirname(os.path.dirname(os.path.dirname(__file__))) ) @@ -4802,6 +4842,7 @@ def get_protocol_terminology( limit: int = 50, offset: int = 0, ): + """Return latest rotocol Terminology loaded into SQLite database.""" limit = max(1, min(limit, 200)) offset = max(0, offset) conn = _connect() @@ -4893,6 +4934,7 @@ def ui_protocol_terminology( uploaded: Optional[str] = None, error: Optional[str] = None, ): + """Form handler to display the latest loaded Protocol Terminology from the SQLite database.""" data = get_protocol_terminology( search=search, code=code, @@ -4922,6 +4964,7 @@ def ui_protocol_upload( sheet_name: str = Form("Protocol Terminology 2025-09-26"), file: UploadFile = File(...), ): + """Form handler for the upload of Protocol Terminology XLS.""" filename = file.filename or "uploaded.xls" if not (filename.lower().endswith(".xls") or filename.lower().endswith(".xlsx")): return HTMLResponse( @@ -5051,6 +5094,7 @@ def _get_protocol_sources() -> List[str]: def get_protocol_audit( source: Optional[str] = None, start: Optional[str] = None, end: Optional[str] = None ): + """Return the Protocol Terminology audit report.""" conn = _connect() cur = conn.cursor() cur.execute( @@ -5108,6 +5152,7 @@ def _valid_date(d: str) -> bool: def export_protocol_audit_csv( source: Optional[str] = None, start: Optional[str] = None, end: Optional[str] = None ): + """Export the latest Protocol Terminology from the SQLite database in CSV format.""" rows = get_protocol_audit(source=source, start=start, end=end) import csv import io @@ -5155,6 +5200,7 @@ def export_protocol_audit_csv( def export_protocol_audit_json( source: Optional[str] = None, start: Optional[str] = None, end: Optional[str] = None ): + """Export the latest Protocol Terminology from the SQLite database in JSON format.""" return get_protocol_audit(source=source, start=start, end=end) @@ -5165,6 +5211,7 @@ def ui_protocol_audit( start: Optional[str] = None, end: Optional[str] = None, ): + """Form handler for display of the Protocol Terminology audit report.""" rows = get_protocol_audit(source=source, start=start, end=end) sources = _get_protocol_sources() return templates.TemplateResponse( From ca7e46d6f3c00bb995943b1c26b9ad9cd09001fc Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Tue, 2 Dec 2025 14:06:51 -0500 Subject: [PATCH 02/20] Reordered object lists --- src/soa_builder/web/static/style.css | 2 +- src/soa_builder/web/templates/edit.html | 64 ++++++++++++------------- 2 files changed, 33 insertions(+), 33 deletions(-) diff --git a/src/soa_builder/web/static/style.css b/src/soa_builder/web/static/style.css index 04ae631..6c3d410 100644 --- a/src/soa_builder/web/static/style.css +++ b/src/soa_builder/web/static/style.css @@ -1,4 +1,4 @@ -body { font-family: system-ui, Arial, sans-serif; margin: 1.5rem; } +body { font-family: Arial, Helvetica, sans-serif; margin: 1.5rem; } header h1 { margin: 0; } nav a { margin-right: 1rem; } .table, table { border-collapse: collapse; } diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html index d670aa0..2b03dbb 100644 --- a/src/soa_builder/web/templates/edit.html +++ b/src/soa_builder/web/templates/edit.html @@ -82,34 +82,6 @@

Editing SoA {{ soa_id }}

-
- Epochs ({{ epochs|length }}) (drag to reorder) -
    - {% for e in epochs %} -
  • - {{ e.order_index }}. E{{ e.epoch_seq }} {{ e.name }} - {% if e.epoch_label %}[{{ e.epoch_label }}]{% endif %} -
    - - -
    -
    - - - - - -
    -
    • - {% endfor %} -
-
- - - - -
-
Visits ({{ visits|length }}) (drag to reorder)
    @@ -145,8 +117,6 @@

    Editing SoA {{ soa_id }}

-
-
Activities ({{ activities|length }}) (drag to reorder)
    @@ -164,7 +134,37 @@

    Editing SoA {{ soa_id }}

-
+
+
+
+ Epochs ({{ epochs|length }}) (drag to reorder) +
    + {% for e in epochs %} +
  • + {{ e.order_index }}. E{{ e.epoch_seq }} {{ e.name }} + {% if e.epoch_label %}[{{ e.epoch_label }}]{% endif %} +
    + + +
    +
    + + + + + +
    +
    • + {% endfor %} +
+
+ + + + +
+
+
Elements ({{ elements|length }}) (drag to reorder)
    {% for el in elements %} @@ -197,7 +197,7 @@

    Editing SoA {{ soa_id }}

-
+
Arms ({{ arms|length }}) (drag to reorder)
    {% for arm in arms %} From 672df4a0f52f8a8a4f644bbeb20205ea2f670001 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Tue, 2 Dec 2025 14:11:52 -0500 Subject: [PATCH 03/20] Added docs for 2 new endpoints for viewing categories --- docs/api_endpoints.xlsx | Bin 14635 -> 14693 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/docs/api_endpoints.xlsx b/docs/api_endpoints.xlsx index f4df9493743e82c08a9c82d458e2459cc1199dc6..f49a3326db24d7e4e11e27dee63df6e3422634cb 100644 GIT binary patch delta 8037 zcmY*ebx<6<(>~nY${{W8E{C z-#7EgP9}fknb~YM*1jn8U+AY!vp{b004lmBae@ZJH*1p1;Xv? zQW*?8f0ewjIz5S^n(L6Jy8bWROYQ)mhF98K^ZBh$w73HbEq2uqX6Clk};IaQO^BMYulfS^o zC0O*~cji17Mbd4qBoHujlVYT@68Y-ZZydN#q?bem`1a-=$9rDM6) z9JoGHEuW)fOTTXm*YrXiJ#2EG(Wl8f=#FO<<9fR;z&ve`t z&jF}Tn=jd7GV=gj-z56Bj0L^BzhEI3ylElfq;Xu-?bv?1HAWIL!f=f892<#sPZ+iV z#!ZxUZ!&+MKC#2Wu>(y_e~vro3nltlF^j3B3So-a4kG>TTai<311j;vTlF%t 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<3921919+pendingintent@users.noreply.github.com> Date: Tue, 2 Dec 2025 14:33:24 -0500 Subject: [PATCH 04/20] Added concept category cache and corresponding tests --- src/soa_builder/web/app.py | 41 +++++- .../web/templates/concept_categories.html | 9 +- .../templates/concept_category_detail.html | 5 + tests/test_categories_cache.py | 118 ++++++++++++++++++ tests/test_categories_ui_force.py | 89 +++++++++++++ tests/test_concept_categories.py | 16 ++- tests/test_concept_category_force_refresh.py | 66 ++++++++++ tests/test_concepts_by_category_ui_force.py | 88 +++++++++++++ 8 files changed, 418 insertions(+), 14 deletions(-) create mode 100644 tests/test_categories_cache.py create mode 100644 tests/test_categories_ui_force.py create mode 100644 tests/test_concept_category_force_refresh.py create mode 100644 tests/test_concepts_by_category_ui_force.py diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index 7cf95e8..db8c493 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -78,6 +78,12 @@ # SDTM dataset specializations cache (similar TTL) _sdtm_specializations_cache = {"data": None, "fetched_at": 0} _SDTM_SPECIALIZATIONS_CACHE_TTL = 60 * 60 +# Category-specific biomedical concepts cache (per category key) +_category_concepts_cache: dict[str, dict] = {} +_CATEGORY_CONCEPTS_CACHE_TTL = 60 * 60 # 1 hour +# Biomedical concept categories cache (whole list) +_bc_categories_cache = {"data": None, "fetched_at": 0} +_BC_CATEGORIES_CACHE_TTL = 60 * 60 # 1 hour app = FastAPI(title="SoA Builder API", version="0.1.0") logger = logging.getLogger("soa_builder.concepts") if not logger.handlers: @@ -1000,7 +1006,7 @@ def _fetch_matrix(soa_id: int): return visits, activities, cells -def fetch_biomedical_concept_categories() -> list[dict]: +def fetch_biomedical_concept_categories(force: bool = False) -> list[dict]: """Return list of Biomedical Concept Categories from CDISC Library. Normalized shape: @@ -1027,6 +1033,15 @@ def _normalize_href(h: Optional[str]) -> Optional[str]: return base_prefix + h return base_prefix + "/" + h + # Cache lookup + now = time.time() + if ( + not force + and _bc_categories_cache.get("data") + and now - _bc_categories_cache.get("fetched_at", 0) < _BC_CATEGORIES_CACHE_TTL + ): + return _bc_categories_cache.get("data") or [] + try: resp = requests.get(url, headers=headers, timeout=15) if resp.status_code != 200: @@ -1069,13 +1084,15 @@ def _normalize_href(h: Optional[str]) -> Optional[str]: ) categories.sort(key=lambda c: (c["title"] or "").lower()) logger.info("Fetched %d BC categories from remote API", len(categories)) + _bc_categories_cache["data"] = categories + _bc_categories_cache["fetched_at"] = now return categories except Exception as e: # pragma: no cover logger.error("BC categories fetch error: %s", e) return [] -def fetch_biomedical_concepts_by_category(name: str) -> list[dict]: +def fetch_biomedical_concepts_by_category(name: str, force: bool = False) -> list[dict]: """Return biomedical concepts for a given category name. Uses category-specific endpoint: /mdr/bc/biomedicalconcepts?category= @@ -1108,6 +1125,14 @@ def _normalize_href(h: Optional[str]) -> Optional[str]: return base_prefix + h return base_prefix + "/" + h + # Cache lookup + now = time.time() + ckey = category.lower() + if not force: + cached = _category_concepts_cache.get(ckey) + if cached and now - cached.get("fetched_at", 0) < _CATEGORY_CONCEPTS_CACHE_TTL: + return cached.get("data", []) or [] + concepts: list[dict] = [] try: resp = requests.get(url, headers=headers, timeout=20) @@ -1205,6 +1230,8 @@ def _normalize_href(h: Optional[str]) -> Optional[str]: logger.info( "Fetched %d biomedical concepts for category '%s'", len(concepts), category ) + # Populate cache + _category_concepts_cache[ckey] = {"data": concepts, "fetched_at": now} return concepts except Exception as e: # pragma: no cover logger.error("BC concepts by category fetch error for '%s': %s", category, e) @@ -3061,9 +3088,9 @@ def ui_concepts_list(request: Request): @app.get("/ui/concept_categories", response_class=HTMLResponse) -def ui_categories_list(request: Request): +def ui_categories_list(request: Request, force: bool = False): """Render table listing biomedical concept categories (name + title + href).""" - categories = fetch_biomedical_concept_categories() or [] + categories = fetch_biomedical_concept_categories(force=force) or [] rows = [ { "name": c.get("name"), @@ -3077,6 +3104,7 @@ def ui_categories_list(request: Request): request, "concept_categories.html", { + "force": force, "rows": rows, "count": len(rows), "missing_key": subscription_key is None, @@ -3085,7 +3113,7 @@ def ui_categories_list(request: Request): @app.get("/ui/concept_categories/view", response_class=HTMLResponse) -def ui_category_detail(request: Request, name: str = ""): +def ui_category_detail(request: Request, name: str = "", force: bool = False): """Render list of biomedical concepts within a given category name. Query params: @@ -3096,7 +3124,7 @@ def ui_category_detail(request: Request, name: str = ""): return HTMLResponse( "

    Category name required.

    Back

    " ) - concepts = fetch_biomedical_concepts_by_category(category_name) or [] + concepts = fetch_biomedical_concepts_by_category(category_name, force=force) or [] rows = [ { "code": c.get("code"), @@ -3110,6 +3138,7 @@ def ui_category_detail(request: Request, name: str = ""): "concept_category_detail.html", { "category": category_name, + "force": force, "rows": rows, "count": len(rows), }, diff --git a/src/soa_builder/web/templates/concept_categories.html b/src/soa_builder/web/templates/concept_categories.html index b59342f..83852ba 100644 --- a/src/soa_builder/web/templates/concept_categories.html +++ b/src/soa_builder/web/templates/concept_categories.html @@ -5,6 +5,10 @@

    Biomedical Concept Categories ({{ count }}) +

    + Refresh Categories (bypass cache) + {% if force %}Cache refreshed{% endif %} +

    @@ -14,7 +18,7 @@

    Biomedical Concept Categories ({{ count }}) - + Concepts Name Title @@ -25,11 +29,12 @@

    Biomedical Concept Categories ({{ count }}) {% if r.name %} - {{ r.name }} + View Concepts {% else %} n/a {% endif %} + {{ r.name }} {{ r.title }} {% endfor %} diff --git a/src/soa_builder/web/templates/concept_category_detail.html b/src/soa_builder/web/templates/concept_category_detail.html index 16f63b5..df02857 100644 --- a/src/soa_builder/web/templates/concept_category_detail.html +++ b/src/soa_builder/web/templates/concept_category_detail.html @@ -1,6 +1,11 @@ {% extends 'base.html' %} {% block content %}

    Biomedical Concepts in Category: {{ category }}

    +

    + Refresh (bypass cache) + {% if force %}Cache bypassed{% endif %} + | Back to Categories +

    Total concepts: {{ count }}

    {% if rows %} diff --git a/tests/test_categories_cache.py b/tests/test_categories_cache.py new file mode 100644 index 0000000..c5864ff --- /dev/null +++ b/tests/test_categories_cache.py @@ -0,0 +1,118 @@ +from types import SimpleNamespace + +import pytest + +from soa_builder.web.app import ( + fetch_biomedical_concept_categories, + _bc_categories_cache, +) + + +class DummyResponse: + def __init__(self, payload, status_code=200): + self._payload = payload + self.status_code = status_code + + def json(self): + return self._payload + + +@pytest.fixture(autouse=True) +def clear_categories_cache(): + _bc_categories_cache.clear() + + +def test_categories_cache_hit(monkeypatch): + call_count = SimpleNamespace(n=0) + + payload = { + "_links": { + "categories": [ + { + "name": "CategoryA", + "_links": { + "self": {"href": "/mdr/bc/categories/A", "title": "TitleA"} + }, + }, + { + "name": "CategoryB", + "_links": { + "self": {"href": "/mdr/bc/categories/B", "title": "TitleB"} + }, + }, + ] + } + } + + def fake_get(url, headers=None, timeout=None): + call_count.n += 1 + return DummyResponse(payload) + + monkeypatch.setattr("requests.get", fake_get) + + # First call populates cache + cats1 = fetch_biomedical_concept_categories(force=False) + assert call_count.n == 1 + assert len(cats1) == 2 + + # Second call within TTL should hit cache, no new HTTP call + cats2 = fetch_biomedical_concept_categories(force=False) + assert call_count.n == 1 + assert cats2 == cats1 + + +def test_categories_cache_force_bypass(monkeypatch): + call_count = SimpleNamespace(n=0) + + payload1 = { + "_links": { + "categories": [ + { + "name": "CategoryA", + "_links": { + "self": {"href": "/mdr/bc/categories/A", "title": "TitleA"} + }, + } + ] + } + } + payload2 = { + "_links": { + "categories": [ + { + "name": "CategoryA", + "_links": { + "self": {"href": "/mdr/bc/categories/A2", "title": "TitleA2"} + }, + }, + { + "name": "CategoryC", + "_links": { + "self": {"href": "/mdr/bc/categories/C", "title": "TitleC"} + }, + }, + ] + } + } + + def fake_get(url, headers=None, timeout=None): + call_count.n += 1 + # Return payload1 first, payload2 thereafter + return DummyResponse(payload1 if call_count.n == 1 else payload2) + + monkeypatch.setattr("requests.get", fake_get) + + # Populate cache + cats1 = fetch_biomedical_concept_categories(force=False) + assert call_count.n == 1 + assert [c["name"] for c in cats1] == ["CategoryA"] + + # Force bypass should trigger a new HTTP call and new content + cats2 = fetch_biomedical_concept_categories(force=True) + assert call_count.n == 2 + assert [c["name"] for c in cats2] == ["CategoryA", "CategoryC"] + + # Regular call after force should use cached latest content (no extra HTTP) + cats3 = fetch_biomedical_concept_categories(force=False) + assert call_count.n == 2 + assert cats3 == cats2 diff --git a/tests/test_categories_ui_force.py b/tests/test_categories_ui_force.py new file mode 100644 index 0000000..194cfb1 --- /dev/null +++ b/tests/test_categories_ui_force.py @@ -0,0 +1,89 @@ +from types import SimpleNamespace + +import pytest +from fastapi.testclient import TestClient + +from soa_builder.web.app import app, _bc_categories_cache + +client = TestClient(app) + + +class DummyResponse: + def __init__(self, payload, status_code=200, text=""): + self._payload = payload + self.status_code = status_code + self.text = text or "" + + def json(self): + return self._payload + + +@pytest.fixture(autouse=True) +def clear_categories_cache(): + _bc_categories_cache.clear() + + +def test_ui_categories_force_bypass(monkeypatch): + call_count = SimpleNamespace(n=0) + + payload1 = { + "_links": { + "categories": [ + { + "name": "CategoryA", + "_links": { + "self": {"href": "/mdr/bc/categories/A", "title": "TitleA"} + }, + }, + ] + } + } + payload2 = { + "_links": { + "categories": [ + { + "name": "CategoryA", + "_links": { + "self": {"href": "/mdr/bc/categories/A2", "title": "TitleA2"} + }, + }, + { + "name": "CategoryC", + "_links": { + "self": {"href": "/mdr/bc/categories/C", "title": "TitleC"} + }, + }, + ] + } + } + + def fake_get(url, headers=None, timeout=None): + call_count.n += 1 + return DummyResponse(payload1 if call_count.n == 1 else payload2, text="ok") + + monkeypatch.setattr("requests.get", fake_get) + + # Initial request populates cache, shows TitleA only + r1 = client.get("/ui/concept_categories") + assert r1.status_code == 200 + html1 = r1.text + assert "TitleA" in html1 + assert "TitleA2" not in html1 + assert "TitleC" not in html1 + assert call_count.n == 1 + + # Force bypass should fetch again and render updated titles + r2 = client.get("/ui/concept_categories?force=1") + assert r2.status_code == 200 + html2 = r2.text + assert "TitleA2" in html2 + assert "TitleC" in html2 + assert call_count.n == 2 + + # Subsequent non-force call should serve cached updated content (no new HTTP) + r3 = client.get("/ui/concept_categories") + assert r3.status_code == 200 + html3 = r3.text + assert "TitleA2" in html3 + assert "TitleC" in html3 + assert call_count.n == 2 diff --git a/tests/test_concept_categories.py b/tests/test_concept_categories.py index 4c07769..13b90a7 100644 --- a/tests/test_concept_categories.py +++ b/tests/test_concept_categories.py @@ -42,7 +42,7 @@ def fake_get(url, headers=None, timeout=0): return DummyResp(200, {"items": []}) monkeypatch.setattr("requests.get", fake_get) - fetch_biomedical_concepts_by_category(raw_category) + fetch_biomedical_concepts_by_category(raw_category, force=True) assert len(captured_urls) == 1 assert expected_url_fragment in captured_urls[0] @@ -68,7 +68,7 @@ def fake_get(url, headers=None, timeout=0): return DummyResp(200, payload) monkeypatch.setattr("requests.get", fake_get) - concepts = fetch_biomedical_concepts_by_category("Liver Findings") + concepts = fetch_biomedical_concepts_by_category("Liver Findings", force=True) assert {c["code"] for c in concepts} == {"ALT", "AST"} assert all( c["href"].startswith( @@ -100,7 +100,7 @@ def fake_get(url, headers=None, timeout=0): return DummyResp(200, payload) monkeypatch.setattr("requests.get", fake_get) - concepts = fetch_biomedical_concepts_by_category("Liver Findings") + concepts = fetch_biomedical_concepts_by_category("Liver Findings", force=True) codes = {c["code"] for c in concepts} assert codes == {"ALT", "AST"} # Titles preserved @@ -114,7 +114,7 @@ def fake_get(url, headers=None, timeout=0): return DummyResp(404, {}, text="Not Found") monkeypatch.setattr("requests.get", fake_get) - concepts = fetch_biomedical_concepts_by_category("Liver Findings") + concepts = fetch_biomedical_concepts_by_category("Liver Findings", force=True) assert concepts == [] @@ -139,7 +139,9 @@ def fake_get(url, headers=None, timeout=0): return DummyResp(200, payload) monkeypatch.setattr("requests.get", fake_get) - resp = client.get("/ui/concept_categories/view", params={"name": "Liver Findings"}) + resp = client.get( + "/ui/concept_categories/view", params={"name": "Liver Findings", "force": True} + ) assert resp.status_code == 200 text = resp.text # Internal links to concept detail page @@ -156,6 +158,8 @@ def fake_get(url, headers=None, timeout=0): return DummyResp(200, {"items": []}) monkeypatch.setattr("requests.get", fake_get) - resp = client.get("/ui/concept_categories/view", params={"name": "Liver Findings"}) + resp = client.get( + "/ui/concept_categories/view", params={"name": "Liver Findings", "force": True} + ) assert resp.status_code == 200 assert "No concepts found for this category." in resp.text diff --git a/tests/test_concept_category_force_refresh.py b/tests/test_concept_category_force_refresh.py new file mode 100644 index 0000000..c0c512f --- /dev/null +++ b/tests/test_concept_category_force_refresh.py @@ -0,0 +1,66 @@ +import json +from typing import List +from fastapi.testclient import TestClient + +from soa_builder.web.app import app, _category_concepts_cache + +client = TestClient(app) + + +class DummyResp: + def __init__(self, status_code: int, json_data=None, text: str = ""): + self.status_code = status_code + self._json = json_data + self.text = text or json.dumps(json_data or {}) + + def json(self): + if self._json is None: + raise ValueError("No JSON") + return self._json + + +def test_ui_category_force_refresh(monkeypatch): + _category_concepts_cache.clear() + calls: List[str] = [] + payload1 = { + "items": [ + { + "code": "ALT", + "title": "Alanine", + "href": "/mdr/bc/biomedicalconcepts/ALT", + } + ] + } + payload2 = { + "items": [ + { + "code": "AST", + "title": "Aspartate", + "href": "/mdr/bc/biomedicalconcepts/AST", + } + ] + } + + def fake_get(url, headers=None, timeout=0): + # First call returns ALT, subsequent calls return AST + if not calls: + calls.append(url) + return DummyResp(200, payload1) + calls.append(url) + return DummyResp(200, payload2) + + monkeypatch.setattr("requests.get", fake_get) + # Initial request populates cache with ALT + r1 = client.get("/ui/concept_categories/view", params={"name": "Force Test"}) + assert r1.status_code == 200 + assert "/ui/concepts/ALT" in r1.text + # Second request without force still uses cache (ALT) + r2 = client.get("/ui/concept_categories/view", params={"name": "Force Test"}) + assert r2.status_code == 200 + assert "/ui/concepts/ALT" in r2.text + # Third request with force bypasses cache and shows AST + r3 = client.get( + "/ui/concept_categories/view", params={"name": "Force Test", "force": True} + ) + assert r3.status_code == 200 + assert "/ui/concepts/AST" in r3.text diff --git a/tests/test_concepts_by_category_ui_force.py b/tests/test_concepts_by_category_ui_force.py new file mode 100644 index 0000000..c036973 --- /dev/null +++ b/tests/test_concepts_by_category_ui_force.py @@ -0,0 +1,88 @@ +from types import SimpleNamespace + +import pytest +from fastapi.testclient import TestClient + +from soa_builder.web.app import app, _category_concepts_cache + +client = TestClient(app) + + +class DummyResponse: + def __init__(self, payload, status_code=200, text=""): + self._payload = payload + self.status_code = status_code + self.text = text or "" + + def json(self): + return self._payload + + +@pytest.fixture(autouse=True) +def clear_concepts_cache(): + _category_concepts_cache.clear() + + +def test_ui_concepts_by_category_force_bypass(monkeypatch): + call_count = SimpleNamespace(n=0) + + # The app queries: /mdr/bc/biomedicalconcepts?category=CategoryA (encoded) + # Provide payloads representing concepts in direct 'items' list form. + payload1 = { + "items": [ + { + "code": "C100", + "title": "Alpha", + "href": "/mdr/bc/biomedicalconcepts/C100", + }, + ] + } + payload2 = { + "items": [ + { + "code": "C100", + "title": "Alpha v2", + "href": "/mdr/bc/biomedicalconcepts/C100", + }, + { + "code": "C200", + "title": "Beta", + "href": "/mdr/bc/biomedicalconcepts/C200", + }, + ] + } + + def fake_get(url, headers=None, timeout=None): + # Ensure we are mocking the concepts-by-category endpoint + assert "/mdr/bc/biomedicalconcepts?category=" in url + call_count.n += 1 + return DummyResponse(payload1 if call_count.n == 1 else payload2, text="ok") + + monkeypatch.setattr("requests.get", fake_get) + + # Initial request populates cache, shows Alpha only + r1 = client.get("/ui/concept_categories/view", params={"name": "CategoryA"}) + assert r1.status_code == 200 + html1 = r1.text + assert "Alpha" in html1 + assert "Alpha v2" not in html1 + assert "Beta" not in html1 + assert call_count.n == 1 + + # Force bypass should fetch again and render updated concept titles + r2 = client.get( + "/ui/concept_categories/view", params={"name": "CategoryA", "force": 1} + ) + assert r2.status_code == 200 + html2 = r2.text + assert "Alpha v2" in html2 + assert "Beta" in html2 + assert call_count.n == 2 + + # Subsequent non-force call should serve cached updated content (no new HTTP) + r3 = client.get("/ui/concept_categories/view", params={"name": "CategoryA"}) + assert r3.status_code == 200 + html3 = r3.text + assert "Alpha v2" in html3 + assert "Beta" in html3 + assert call_count.n == 2 From ab410d24db6c7344cadff467b0f2a7b096b0c1e1 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Tue, 2 Dec 2025 17:14:34 -0500 Subject: [PATCH 05/20] Arm type now chosen from dropdown from codelist C174222 --- src/soa_builder/web/app.py | 164 +++++++++++++++++++-- src/soa_builder/web/initialize_database.py | 13 ++ src/soa_builder/web/templates/edit.html | 16 ++ 3 files changed, 184 insertions(+), 9 deletions(-) diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index db8c493..49aafdc 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -65,8 +65,8 @@ from .routers import rollback as rollback_router from .routers import visits as visits_router from .routers.arms import create_arm # re-export for backward compatibility -from .routers.arms import delete_arm, update_arm -from .schemas import ArmCreate, ArmUpdate, SOACreate, SOAMetadataUpdate +from .routers.arms import delete_arm +from .schemas import ArmCreate, SOACreate, SOAMetadataUpdate load_dotenv() # must come BEFORE reading env-based configuration so values are populated DB_PATH = os.environ.get("SOA_BUILDER_DB", "soa_builder_web.db") @@ -881,7 +881,7 @@ def _fetch_arms_for_edit(soa_id: int) -> list[dict]: conn = _connect() cur = conn.cursor() cur.execute( - "SELECT id,name,label,description,order_index FROM arm WHERE soa_id=? ORDER BY order_index", + "SELECT id,name,label,description,order_index,COALESCE(type,'') FROM arm WHERE soa_id=? ORDER BY order_index", (soa_id,), ) rows = [ @@ -891,6 +891,7 @@ def _fetch_arms_for_edit(soa_id: int) -> list[dict]: "label": r[2], "description": r[3], "order_index": r[4], + "type": r[5] or None, } for r in cur.fetchall() ] @@ -3036,6 +3037,16 @@ def ui_edit(request: Request, soa_id: int): "study_label": meta_row[1] if meta_row else None, "study_description": meta_row[2] if meta_row else None, } + # Protocol terminology options for Arm Type (C174222) + conn_pt = _connect() + cur_pt = conn_pt.cursor() + cur_pt.execute( + "SELECT cdisc_submission_value FROM protocol_terminology WHERE codelist_code='C174222' ORDER BY cdisc_submission_value" + ) + protocol_terminology_C174222 = [ + {"cdisc_submission_value": r[0] or ""} for r in cur_pt.fetchall() + ] + conn_pt.close() return templates.TemplateResponse( request, "edit.html", @@ -3045,7 +3056,64 @@ def ui_edit(request: Request, soa_id: int): "visits": visits, "activities": activities_page, "elements": elements, - "arms": _fetch_arms_for_edit(soa_id), + # Enrich arms with current type display (map Code_N -> cdisc_submission_value via protocol code) + "arms": ( + lambda _arms: ( + ( + lambda mapping, submission_values: [ + ( + lambda _type: ( + { + **a, + "type_display": ( + mapping.get(_type) + if mapping.get(_type) is not None + else ( + _type + if (_type in submission_values) + else None + ) + ), + } + ) + )(a.get("type")) + for a in _arms + ] + )( + ( + lambda: ( + ( + lambda conn: ( + ( + lambda cur, rows: ( + (lambda m: (conn.close(), m)[1])( + {row[0]: row[2] for row in rows} + ) + ) + )( + conn.cursor(), + conn.cursor() + .execute( + "SELECT c.code_uid, c.code, pt.cdisc_submission_value " + "FROM code c JOIN protocol_terminology pt ON pt.code = c.code " + "WHERE c.soa_id=? AND c.codelist_code='C174222'", + (soa_id,), + ) + .fetchall(), + ) + ) + )(_connect()) + ) + )(), + set( + [ + opt.get("cdisc_submission_value") or "" + for opt in protocol_terminology_C174222 + ] + ), + ) + ) + )(_fetch_arms_for_edit(soa_id)), "cell_map": cell_map, "concepts": concepts, "activity_concepts": activity_concepts, @@ -3057,6 +3125,7 @@ def ui_edit(request: Request, soa_id: int): "freeze_count": len(freeze_list), "last_frozen_at": last_frozen_at, **study_meta, + "protocol_terminology_C174222": protocol_terminology_C174222, }, ) @@ -3413,7 +3482,7 @@ def ui_add_arm( @app.post("/ui/soa/{soa_id}/update_arm", response_class=HTMLResponse) -def ui_update_arm( +async def ui_update_arm( request: Request, soa_id: int, arm_id: int = Form(...), @@ -3425,10 +3494,87 @@ def ui_update_arm( """Form handler to update an existing Arm.""" if not _soa_exists(soa_id): raise HTTPException(404, "SOA not found") - # Coerce possible blank element selection to None; avoid 422 validation error from string "" into Optional[int]. - eid = int(element_id) if element_id and element_id.strip().isdigit() else None - payload = ArmUpdate(name=name, label=label, description=description, element_id=eid) - update_arm(soa_id, arm_id, payload) + + # Read raw form to capture field name with hyphen: 'arm-type' + try: + form_data = await request.form() + arm_type_submission = (form_data.get("arm-type") or "").strip() + except Exception: + arm_type_submission = "" + + # Fetch current arm (including existing type code_uid if any) + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id, name, label, description, COALESCE(type,''), COALESCE(data_origin_type,'') FROM arm WHERE id=? AND soa_id=?", + (arm_id, soa_id), + ) + row = cur.fetchone() + if not row: + conn.close() + raise HTTPException(404, "Arm not found") + current_code_uid = row[4] or None + + # Resolve submission value to protocol terminology code (C174222) + resolved_code: Optional[str] = None + if arm_type_submission: + cur.execute( + "SELECT code FROM protocol_terminology WHERE codelist_code='C174222' AND (cdisc_submission_value=? OR LOWER(TRIM(cdisc_submission_value))=LOWER(TRIM(?)))", + (arm_type_submission, arm_type_submission), + ) + r = cur.fetchone() + resolved_code = r[0] if r else None + if resolved_code is None: + conn.close() + return HTMLResponse( + f"", + status_code=400, + ) + + # Maintain code table row with immutable code_uid (Code_N unique per SoA) + new_code_uid = current_code_uid + if resolved_code is not None: + if current_code_uid: + # Update existing junction row for this code_uid + cur.execute( + "UPDATE code SET code=?, codelist_code='C174222', codelist_table='protocol_terminology' WHERE soa_id=? AND code_uid=?", + (resolved_code, soa_id, current_code_uid), + ) + else: + # Create new Code_N within this SoA + cur.execute( + "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", + (soa_id,), + ) + existing = [x[0] for x in cur.fetchall() if x[0]] + n = 1 + if existing: + try: + n = max(int(x.split("_")[1]) for x in existing) + 1 + except Exception: + n = len(existing) + 1 + new_code_uid = f"Code_{n}" + cur.execute( + "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", + ( + soa_id, + new_code_uid, + "protocol_terminology", + "C174222", + resolved_code, + ), + ) + + # Apply arm field updates (including setting type to code_uid if resolved) + new_name = name if name is not None else row[1] + new_label = label if label is not None else row[2] + new_desc = description if description is not None else row[3] + cur.execute( + "UPDATE arm SET name=?, label=?, description=?, type=? WHERE id=? AND soa_id=?", + (new_name, new_label, new_desc, new_code_uid, arm_id, soa_id), + ) + conn.commit() + conn.close() return HTMLResponse(f"") diff --git a/src/soa_builder/web/initialize_database.py b/src/soa_builder/web/initialize_database.py index fde39eb..d4c0366 100644 --- a/src/soa_builder/web/initialize_database.py +++ b/src/soa_builder/web/initialize_database.py @@ -146,5 +146,18 @@ def _init_db(): performed_at TEXT NOT NULL )""" ) + + # create the code table to store unique Code_uid values associated with study objects + cur.execute( + """CREATE TABLE IF NOT EXISTS code ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + soa_id INTEGER NOT NULL, + code_uid TEXT, -- immutable Code_N identifier unique within an SOA + codelist_table TEXT, + codelist_code TEXT NOT NULL, + code TEXT NOT NULL + )""" + ) + conn.commit() conn.close() diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html index 2b03dbb..579df09 100644 --- a/src/soa_builder/web/templates/edit.html +++ b/src/soa_builder/web/templates/edit.html @@ -213,6 +213,22 @@

    Editing SoA {{ soa_id }}

    + {# Type selection from protocol terminology C174222 #} + {% if protocol_terminology_C174222 %} + + {% if arm.type_display %} + [type: {{ arm.type_display }}] + {% else %} + [type: n/a] + {% endif %} + {% endif %} From 7ecf23f3294ab4b6cbb801e7cf4f1456bc65f114 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 08:39:08 -0500 Subject: [PATCH 06/20] Commented out arm.type debug --- src/soa_builder/web/templates/edit.html | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html index 579df09..87baba8 100644 --- a/src/soa_builder/web/templates/edit.html +++ b/src/soa_builder/web/templates/edit.html @@ -223,11 +223,13 @@

    Editing SoA {{ soa_id }}

    {% endfor %} + {# --DEBUG {% if arm.type_display %} [type: {{ arm.type_display }}] {% else %} [type: n/a] {% endif %} + --END_DEBUG #} {% endif %} From 9b5c8ec7bb0cdeff43aa43b5541c9bf5df49d9dd Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 11:05:23 -0500 Subject: [PATCH 07/20] Added arm type and dataTypeOrigin properties and auditing --- soa_builder_web.db-shm | Bin 0 -> 32768 bytes soa_builder_web.db-wal | Bin 0 -> 300792 bytes src/soa_builder/web/app.py | 265 ++++++++++++++++++------ src/soa_builder/web/db.py | 10 +- src/soa_builder/web/templates/edit.html | 16 +- 5 files changed, 222 insertions(+), 69 deletions(-) create mode 100644 soa_builder_web.db-shm create mode 100644 soa_builder_web.db-wal diff --git a/soa_builder_web.db-shm b/soa_builder_web.db-shm new file mode 100644 index 0000000000000000000000000000000000000000..a44f49a673708edcdfd5b1a239507569b96a65da GIT binary patch literal 32768 zcmeI)M@oc25J2H)&N}8X=N!hIbM_h@M8uVsaO>U+xbPb81eb2SfOd<&h>U`uAj2yt zI#5)1e+TIF{RA<3Lgqp0IE=R;PcqjB_nFh9%ZL8KtMj&tyR(k-k*Bf8^bhMptJjEq zpFhOg_WQ6HW-B2JLdNssm~AiC+=NVOlXa}mHvg_i?2}}2Zd@nxukMiC@8fyN-goCE zeY4eM+xy%p*>h5`yG@OJ_Q6j4e!)zs2J3vJ;Kq<#h&VT=i;m|;HrK(xXJTkNvW(cfLg z&I%}?fC36Apnw7jD4>7>3Mim}0tzUgfC36Apnw7j??hk0tzUg zfC36A5C!rnp@J%EsH2fI?F=)?980XT!+}T&D4>7>3Mim}0t)1WKqV>aX`+Kpy6C2l V49gtm#M^v?0tzUgfCB$f;05+oN(TS{ literal 0 HcmV?d00001 diff --git a/soa_builder_web.db-wal b/soa_builder_web.db-wal new file mode 100644 index 0000000000000000000000000000000000000000..0bf8247151b13ba8c17468a993d65db00ecd3794 GIT binary patch literal 300792 zcmeI5511R}edlL1T4|+SY5a$+D+_~G{AVRG|3|9?$i~>`Jn=Tbu6;fTR=|P_Iv^EVT$&sVvj-xzW9twmjCAlLlP1EC& za>uZd%@RQ!$Krl>WPxjp>mrI$ZC z9X|4}JwH3~0rtcHN=#~_{p#>*UtIscM;`SPqlZ04vG1_2vCp$7+2ian_Fgk5HV^;- z5C8!X009sH0T2KI5C8!X0D;aESmUPq>G+6I$xRKFCeo6x$sl@~3_@3vfp=R5#;!wT znhb)AC9U{oa`2=dDe`){e!t-RV@Ge;@crGN2m}?%6QpSN1@;hoS&#}|8+<14qt5pl zHG%*LfB*=900@8p2!H?xfB*<|gn;VxOFlnEZ`!np?hjG%QLSu5GNp;;cej1bC~ekr zT3V6Zq*OS3iLXBth~HSqWVJEf`4$BQJ>HX z`JxutuJ4cBpqI54rlG8n-={^&m9essDQ2}uf#l7Rye_*9!D>SwT&|`s=_W0N*7wo< z6csnjP6_5;@~@#MyFDb6EDw?02*exO+?F5T+q@sPt+pd0_Kxf|bDMiIbJZ+bdm<)x zGTpTXn2uII;v)50{2J?BAiWq(Dz!$GaSmkdlXE-?WyYL=_4@+s1M&a%!Oy;aDiHiz z>bHWo^s+x@|Al>veVl!OeTuz{eTB`iA7V#Yo;BD_!6U(m;GYNI4L%h7``|6?db1vE zAOHd&00JNY0w4eaAOHd&00JOTC9pQaT;`g{7^VDybXF@A%G76h35<@069{SWqHQoA;(XZKdqdM?<+47i&1#Pyf#Hz<#9Uw1##N1LTQ>(($=(HZkj zM&79H=s+OITuhTYF4c-+>v~9*l3pl`WwLivZLXePCQNGuZ9*#=Th{uSE9xJr>7!nj zS#MV1Bd@hyl3ddCQcf#XlQ;HtF>#mOYE~zAPbLlO3HD{m@3Z>gb2EJ|6Djpz(8Ki8 zWj&MLQ_{3MwUC!4Rg=#NG6rs6H?yJIYkx1pY_fZ@)8`@y7VH6%?`iW@zc29F2bEuZ z{pv5j6(B}eaFk+W+KLg=S+;D`!jjNh7Zpo0E*GNvjU)fxcqa zkjogEv|h@O=ZooDYOzu%kd*2*cfOd@4v=ajVlgl4E7tx*?Ntg=^pL;_a-0|9oH)u$ zDM3w1a)KX}WodAL<5C=V_@)7?U)1z4=~uR-WfrSnwLR}}pTv|Xq+~I{%e)|S)jpA7 zb*vW%U&U+x@5%S?zjfOT zga77=jlX>FSmGU1chF0O2BACHVrs(#0w4eaAOHd&00JNY0w4eaAOHd#C(tA!DEXTV z=SFw%cRwxt-viMT-#2v!y-m7g-uS|&U*G<227UycIWSQR2!H?xfB*=900@8p z2!H?xtX=}E!jB-n5Z%Eg;z!`n9sD03Xa4Hw?|$TSrtTmUIBMw*k~eH100JNY0w4ea zAOHd&00JNY0*g=J@YZ-u)=nLc`yH}&JV(^>>Uw?V({hJaU)|88(^oe;RrorrWhbR1 zJ|!v%RpkXqsp<1UchHOx=@_F?GH7*U(>OIIE$UdEj_zRm)|)@E`4dN;!FqwkKj6^< z2!H?xfB*=900@8p2!H?xtZV|yf4zXWeVoFTuwEc#&ck|~!jX*^{P~q1yzl;&`T}2C z*)tZs0|5{K0T2KI5C8!X009sHfn`kK9P0}ZQeIjVZ|x$^|Dt$3-5;XjyD~+6LM!Bp zT4cMvKXQX!)>@c`vPOQN7AaTe@sPKI4+>Y>$^xWvbL~U@<(`QxXysIQd&q9c@(|gL zK;v#~%a8AE-VfVW+mR7_NA{Yzb7Zd>yMEECUrg>~x@!$E4PCOUYGpgE>PK9pUW;F2 zy$hsw#`*%M$Y?%Yzb|m?t-t)6w_jNEzUfEc4L(A#&$AD)x3fvs6MT_;#0CN&00JNY z0w4eaAOHd&00JNY0_T_j=k-!_NDhbN)w=+bCEd`odLeCSrHOn|FX-b_n|W0d1i^Y! zInLuKp|mTZB)Kj}3AtSfLE+qv5>mSoWUm-U39(%XMde(M62fVepdBUnwk48eFwOM> z_I-gPyB~P#y7AY)RlP3|qS+VNL+oY2Q1IH|GeN8uILC7z&4B<2fB*=900@8p2!H?x zfWT=J==^$tsGB^54+jE1^CA3=g-li()9nZ8ymg7rW4*w_mLn{U^#Y7J%j)X|ZvDso z-#K#4sZG!qIPGH(89@L9KmY_l00ck)1V8`;KmY_<5?KEF0^O@nU*H4ZzHra`k>eYx z>jl==*9)x2dV!Xc97YfT0T2KI5C8!X009sH0T5U!1Uk81;L4em0-?E93Rvp}l2|XW z64nbi^aa)z_lUPlTzS;IFVG#VH0cWv12zx<0T2KI5C8!X009sH0T2KI5LhUIfo{_c zexNQHkj&-wIMo7@NmWoc^NO4lIp_=2lob|BU%=r<@bk}a_*^&rgB|cASm-22c@O{r z5C8!X009sH0T2KI5LoR5mcJi?Zx#9xe2e|XQ#*!>V}ancls9m~_9FHycdY@YRaLEQr&axki_|NM*VFxt^)ApQBu0}; 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ORDER BY order_index", + "SELECT id,name,label,description,order_index,COALESCE(type,''),COALESCE(data_origin_type,'') FROM arm WHERE soa_id=? ORDER BY order_index", (soa_id,), ) rows = [ @@ -892,6 +892,7 @@ def _fetch_arms_for_edit(soa_id: int) -> list[dict]: "description": r[3], "order_index": r[4], "type": r[5] or None, + "data_origin_type": r[6] or None, } for r in cur.fetchall() ] @@ -3047,6 +3048,71 @@ def ui_edit(request: Request, soa_id: int): {"cdisc_submission_value": r[0] or ""} for r in cur_pt.fetchall() ] conn_pt.close() + # Build mapping code_uid -> submission value (Arm Type C174222) + conn_map = _connect() + cur_map = conn_map.cursor() + cur_map.execute( + "SELECT c.code_uid, pt.cdisc_submission_value " + "FROM code c JOIN protocol_terminology pt ON pt.code = c.code " + "WHERE c.soa_id=? AND c.codelist_code='C174222'", + (soa_id,), + ) + code_to_submission = {row[0]: row[1] for row in cur_map.fetchall()} + conn_map.close() + submission_values = { + opt.get("cdisc_submission_value") or "" for opt in protocol_terminology_C174222 + } + + # DDF Terminology options for Arm type (C188727) + conn_ddft = _connect() + cur_ddft = conn_ddft.cursor() + cur_ddft.execute( + "SELECT cdisc_submission_value FROM ddf_terminology WHERE codelist_code = 'C188727' ORDER BY cdisc_submission_value" + ) + ddf_terminology_C188727 = [ + {"cdisc_submission_value": r[0] or ""} for r in cur_ddft.fetchall() + ] + conn_ddft.close() + # logger.info("DDF Terminology values: ", ddf_terminology_C188727) + + # Build mapping code_uid -> submission value (Arm dataOriginType C188727) + conn_ddf_map = _connect() + cur_ddf_map = conn_ddf_map.cursor() + cur_ddf_map.execute( + "SELECT c.code_uid, dt.cdisc_submission_value " + "FROM code c JOIN ddf_terminology dt ON dt.code = c.code " + "WHERE c.soa_id=? AND c.codelist_code='C188727'", + (soa_id,), + ) + ddf_code_to_submission = {row[0]: row[1] for row in cur_ddf_map.fetchall()} + conn_ddf_map.close() + ddf_submission_values = { + ddf_opt.get("cdisc_submission_value") or "" + for ddf_opt in ddf_terminology_C188727 + } + # logger.info("DDF Data Origin Type submission values", ddf_submission_values) + + base_arms = _fetch_arms_for_edit(soa_id) + arms_enriched = [] + for a in base_arms: + type = a.get("type") + type_display = code_to_submission.get(type) + data_origin_type = a.get("data_origin_type") + data_origin_type_display = ddf_code_to_submission.get(data_origin_type) + if type_display is None and type: + type_display = type if type in submission_values else None + if data_origin_type_display is None and data_origin_type: + data_origin_type_display = ( + data_origin_type if data_origin_type in ddf_submission_values else None + ) + arms_enriched.append( + { + **a, + "type_display": type_display, + "data_origin_type_display": data_origin_type_display, + } + ) + return templates.TemplateResponse( request, "edit.html", @@ -3056,64 +3122,7 @@ def ui_edit(request: Request, soa_id: int): "visits": visits, "activities": activities_page, "elements": elements, - # Enrich arms with current type display (map Code_N -> cdisc_submission_value via protocol code) - "arms": ( - lambda _arms: ( - ( - lambda mapping, submission_values: [ - ( - lambda _type: ( - { - **a, - "type_display": ( - mapping.get(_type) - if mapping.get(_type) is not None - else ( - _type - if (_type in submission_values) - else None - ) - ), - } - ) - )(a.get("type")) - for a in _arms - ] - )( - ( - lambda: ( - ( - lambda conn: ( - ( - lambda cur, rows: ( - (lambda m: (conn.close(), m)[1])( - {row[0]: row[2] for row in rows} - ) - ) - )( - conn.cursor(), - conn.cursor() - .execute( - "SELECT c.code_uid, c.code, pt.cdisc_submission_value " - "FROM code c JOIN protocol_terminology pt ON pt.code = c.code " - "WHERE c.soa_id=? AND c.codelist_code='C174222'", - (soa_id,), - ) - .fetchall(), - ) - ) - )(_connect()) - ) - )(), - set( - [ - opt.get("cdisc_submission_value") or "" - for opt in protocol_terminology_C174222 - ] - ), - ) - ) - )(_fetch_arms_for_edit(soa_id)), + "arms": arms_enriched, "cell_map": cell_map, "concepts": concepts, "activity_concepts": activity_concepts, @@ -3126,6 +3135,7 @@ def ui_edit(request: Request, soa_id: int): "last_frozen_at": last_frozen_at, **study_meta, "protocol_terminology_C174222": protocol_terminology_C174222, + "ddf_terminology_C188727": ddf_terminology_C188727, }, ) @@ -3495,12 +3505,14 @@ async def ui_update_arm( if not _soa_exists(soa_id): raise HTTPException(404, "SOA not found") - # Read raw form to capture field name with hyphen: 'arm-type' + # Read raw form to capture field names with hyphens: 'arm-type' and 'data-origin-type' try: form_data = await request.form() arm_type_submission = (form_data.get("arm-type") or "").strip() + data_origin_type_submission = (form_data.get("data-origin-type") or "").strip() except Exception: arm_type_submission = "" + data_origin_type_submission = "" # Fetch current arm (including existing type code_uid if any) conn = _connect() @@ -3514,6 +3526,32 @@ async def ui_update_arm( conn.close() raise HTTPException(404, "Arm not found") current_code_uid = row[4] or None + current_data_origin_uid = row[5] or None + # Capture prior code values for audits when code mapping changes without uid change + prior_arm_type_code_value: Optional[str] = None + prior_data_origin_code_value: Optional[str] = None + if current_code_uid: + cur.execute( + "SELECT code FROM code WHERE soa_id=? AND code_uid=?", + (soa_id, current_code_uid), + ) + rcv = cur.fetchone() + prior_arm_type_code_value = rcv[0] if rcv else None + if current_data_origin_uid: + cur.execute( + "SELECT code FROM code WHERE soa_id=? AND code_uid=?", + (soa_id, current_data_origin_uid), + ) + rdv = cur.fetchone() + prior_data_origin_code_value = rdv[0] if rdv else None + before_state = { + "id": row[0], + "name": row[1], + "label": row[2], + "description": row[3], + "type": current_code_uid, + "data_origin_type": current_data_origin_uid, + } # Resolve submission value to protocol terminology code (C174222) resolved_code: Optional[str] = None @@ -3565,15 +3603,118 @@ async def ui_update_arm( ), ) + # Resolve Data Origin Type submission value to DDF terminology code (C188727) + resolved_ddf_code: Optional[str] = None + new_data_origin_uid = current_data_origin_uid + if data_origin_type_submission: + cur.execute( + "SELECT code FROM ddf_terminology WHERE codelist_code='C188727' AND (cdisc_submission_value=? OR LOWER(TRIM(cdisc_submission_value))=LOWER(TRIM(?)))", + (data_origin_type_submission, data_origin_type_submission), + ) + r2 = cur.fetchone() + resolved_ddf_code = r2[0] if r2 else None + if resolved_ddf_code is None: + conn.close() + return HTMLResponse( + f"", + status_code=400, + ) + # Maintain/Upsert immutable Code_N for DDF mapping + if current_data_origin_uid: + cur.execute( + "UPDATE code SET code=?, codelist_code='C188727', codelist_table='ddf_terminology' WHERE soa_id=? AND code_uid=?", + (resolved_ddf_code, soa_id, current_data_origin_uid), + ) + new_data_origin_uid = current_data_origin_uid + else: + # Create new Code_N, ensuring unique across this SoA + cur.execute( + "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", + (soa_id,), + ) + existing = [x[0] for x in cur.fetchall() if x[0]] + n = 1 + if existing: + try: + n = max(int(x.split("_")[1]) for x in existing) + 1 + except Exception: + n = len(existing) + 1 + new_data_origin_uid = f"Code_{n}" + cur.execute( + "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", + ( + soa_id, + new_data_origin_uid, + "ddf_terminology", + "C188727", + resolved_ddf_code, + ), + ) + # Apply arm field updates (including setting type to code_uid if resolved) new_name = name if name is not None else row[1] new_label = label if label is not None else row[2] new_desc = description if description is not None else row[3] cur.execute( - "UPDATE arm SET name=?, label=?, description=?, type=? WHERE id=? AND soa_id=?", - (new_name, new_label, new_desc, new_code_uid, arm_id, soa_id), + "UPDATE arm SET name=?, label=?, description=?, type=?, data_origin_type=? WHERE id=? AND soa_id=?", + ( + new_name, + new_label, + new_desc, + new_code_uid, + new_data_origin_uid, + arm_id, + soa_id, + ), ) conn.commit() + # Capture post-update code values + post_arm_type_code_value: Optional[str] = None + post_data_origin_code_value: Optional[str] = None + if new_code_uid: + cur.execute( + "SELECT code FROM code WHERE soa_id=? AND code_uid=?", + (soa_id, new_code_uid), + ) + rav = cur.fetchone() + post_arm_type_code_value = rav[0] if rav else None + if new_data_origin_uid: + cur.execute( + "SELECT code FROM code WHERE soa_id=? AND code_uid=?", + (soa_id, new_data_origin_uid), + ) + rdv2 = cur.fetchone() + post_data_origin_code_value = rdv2[0] if rdv2 else None + after_state = { + "id": arm_id, + "name": new_name, + "label": new_label, + "description": new_desc, + "type": new_code_uid, + "data_origin_type": new_data_origin_uid, + "type_code": post_arm_type_code_value, + "data_origin_type_code": post_data_origin_code_value, + } + # Record audit if any relevant fields or underlying code mappings changed + if ( + before_state["type"] != after_state["type"] + or before_state["data_origin_type"] != after_state["data_origin_type"] + or prior_arm_type_code_value != post_arm_type_code_value + or prior_data_origin_code_value != post_data_origin_code_value + or before_state["name"] != after_state["name"] + or before_state["label"] != after_state["label"] + or before_state["description"] != after_state["description"] + ): + try: + _record_arm_audit( + soa_id, + "update", + arm_id=arm_id, + before=before_state, + after=after_state, + ) + except Exception: + pass conn.close() return HTMLResponse(f"") diff --git a/src/soa_builder/web/db.py b/src/soa_builder/web/db.py index 2b3e336..681a2b5 100644 --- a/src/soa_builder/web/db.py +++ b/src/soa_builder/web/db.py @@ -8,4 +8,12 @@ def _connect(): - return sqlite3.connect(DB_PATH) + conn = sqlite3.connect(DB_PATH, timeout=5.0, check_same_thread=False) + try: + # Improve concurrency and reduce lock errors + conn.execute("PRAGMA journal_mode=WAL") + conn.execute("PRAGMA synchronous=NORMAL") + conn.execute("PRAGMA busy_timeout=3000") + except Exception: + pass + return conn diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html index 87baba8..a243423 100644 --- a/src/soa_builder/web/templates/edit.html +++ b/src/soa_builder/web/templates/edit.html @@ -223,13 +223,17 @@

    Editing SoA {{ soa_id }}

    {% endfor %} - {# --DEBUG - {% if arm.type_display %} - [type: {{ arm.type_display }}] - {% else %} - [type: n/a] {% endif %} - --END_DEBUG #} + {# Type selection from ddf terminology C188727 #} + {% if ddf_terminology_C188727 %} + {% endif %} From 6240e8edc502cc374ad97f0a211f579289df6352 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 11:10:33 -0500 Subject: [PATCH 08/20] Removed temp shared memory and write-ahead logging database files from git --- .gitignore | 2 ++ soa_builder_web.db-shm | Bin 32768 -> 0 bytes soa_builder_web.db-wal | Bin 300792 -> 0 bytes 3 files changed, 2 insertions(+) delete mode 100644 soa_builder_web.db-shm delete mode 100644 soa_builder_web.db-wal diff --git a/.gitignore b/.gitignore index b6ae2a7..19300fd 100644 --- a/.gitignore +++ b/.gitignore @@ -48,6 +48,8 @@ Thumbs.db # SQLite / local DBs *.db +*.db-shm +*.db-wal *.sqlite # Environment variables / secrets (add if created) diff --git a/soa_builder_web.db-shm b/soa_builder_web.db-shm deleted file mode 100644 index a44f49a673708edcdfd5b1a239507569b96a65da..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 32768 zcmeI)M@oc25J2H)&N}8X=N!hIbM_h@M8uVsaO>U+xbPb81eb2SfOd<&h>U`uAj2yt zI#5)1e+TIF{RA<3Lgqp0IE=R;PcqjB_nFh9%ZL8KtMj&tyR(k-k*Bf8^bhMptJjEq zpFhOg_WQ6HW-B2JLdNssm~AiC+=NVOlXa}mHvg_i?2}}2Zd@nxukMiC@8fyN-goCE zeY4eM+xy%p*>h5`yG@OJ_Q6j4e!)zs2J3vJ;Kq<#h&VT=i;m|;HrK(xXJTkNvW(cfLg z&I%}?fC36Apnw7jD4>7>3Mim}0tzUgfC36Apnw7j??hk0tzUg zfC36A5C!rnp@J%EsH2fI?F=)?980XT!+}T&D4>7>3Mim}0t)1WKqV>aX`+Kpy6C2l V49gtm#M^v?0tzUgfCB$f;05+oN(TS{ diff --git a/soa_builder_web.db-wal b/soa_builder_web.db-wal deleted file mode 100644 index 0bf8247151b13ba8c17468a993d65db00ecd3794..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 300792 zcmeI5511R}edlL1T4|+SY5a$+D+_~G{AVRG|3|9?$i~>`Jn=Tbu6;fTR=|P_Iv^EVT$&sVvj-xzW9twmjCAlLlP1EC& za>uZd%@RQ!$Krl>WPxjp>mrI$ZC z9X|4}JwH3~0rtcHN=#~_{p#>*UtIscM;`SPqlZ04vG1_2vCp$7+2ian_Fgk5HV^;- z5C8!X009sH0T2KI5C8!X0D;aESmUPq>G+6I$xRKFCeo6x$sl@~3_@3vfp=R5#;!wT znhb)AC9U{oa`2=dDe`){e!t-RV@Ge;@crGN2m}?%6QpSN1@;hoS&#}|8+<14qt5pl zHG%*LfB*=900@8p2!H?xfB*<|gn;VxOFlnEZ`!np?hjG%QLSu5GNp;;cej1bC~ekr zT3V6Zq*OS3iLXBth~HSqWVJEf`4$BQJ>HX z`JxutuJ4cBpqI54rlG8n-={^&m9essDQ2}uf#l7Rye_*9!D>SwT&|`s=_W0N*7wo< z6csnjP6_5;@~@#MyFDb6EDw?02*exO+?F5T+q@sPt+pd0_Kxf|bDMiIbJZ+bdm<)x zGTpTXn2uII;v)50{2J?BAiWq(Dz!$GaSmkdlXE-?WyYL=_4@+s1M&a%!Oy;aDiHiz z>bHWo^s+x@|Al>veVl!OeTuz{eTB`iA7V#Yo;BD_!6U(m;GYNI4L%h7``|6?db1vE zAOHd&00JNY0w4eaAOHd&00JOTC9pQaT;`g{7^VDybXF@A%G76h35<@069{SWqHQoA;(XZKdqdM?<+47i&1#Pyf#Hz<#9Uw1##N1LTQ>(($=(HZkj zM&79H=s+OITuhTYF4c-+>v~9*l3pl`WwLivZLXePCQNGuZ9*#=Th{uSE9xJr>7!nj zS#MV1Bd@hyl3ddCQcf#XlQ;HtF>#mOYE~zAPbLlO3HD{m@3Z>gb2EJ|6Djpz(8Ki8 zWj&MLQ_{3MwUC!4Rg=#NG6rs6H?yJIYkx1pY_fZ@)8`@y7VH6%?`iW@zc29F2bEuZ z{pv5j6(B}eaFk+W+KLg=S+;D`!jjNh7Zpo0E*GNvjU)fxcqa zkjogEv|h@O=ZooDYOzu%kd*2*cfOd@4v=ajVlgl4E7tx*?Ntg=^pL;_a-0|9oH)u$ zDM3w1a)KX}WodAL<5C=V_@)7?U)1z4=~uR-WfrSnwLR}}pTv|Xq+~I{%e)|S)jpA7 zb*vW%U&U+x@5%S?zjfOT zga77=jlX>FSmGU1chF0O2BACHVrs(#0w4eaAOHd&00JNY0w4eaAOHd#C(tA!DEXTV z=SFw%cRwxt-viMT-#2v!y-m7g-uS|&U*G<227UycIWSQR2!H?xfB*=900@8p z2!H?xtX=}E!jB-n5Z%Eg;z!`n9sD03Xa4Hw?|$TSrtTmUIBMw*k~eH100JNY0w4ea zAOHd&00JNY0*g=J@YZ-u)=nLc`yH}&JV(^>>Uw?V({hJaU)|88(^oe;RrorrWhbR1 zJ|!v%RpkXqsp<1UchHOx=@_F?GH7*U(>OIIE$UdEj_zRm)|)@E`4dN;!FqwkKj6^< z2!H?xfB*=900@8p2!H?xtZV|yf4zXWeVoFTuwEc#&ck|~!jX*^{P~q1yzl;&`T}2C z*)tZs0|5{K0T2KI5C8!X009sHfn`kK9P0}ZQeIjVZ|x$^|Dt$3-5;XjyD~+6LM!Bp zT4cMvKXQX!)>@c`vPOQN7AaTe@sPKI4+>Y>$^xWvbL~U@<(`QxXysIQd&q9c@(|gL zK;v#~%a8AE-VfVW+mR7_NA{Yzb7Zd>yMEECUrg>~x@!$E4PCOUYGpgE>PK9pUW;F2 zy$hsw#`*%M$Y?%Yzb|m?t-t)6w_jNEzUfEc4L(A#&$AD)x3fvs6MT_;#0CN&00JNY z0w4eaAOHd&00JNY0_T_j=k-!_NDhbN)w=+bCEd`odLeCSrHOn|FX-b_n|W0d1i^Y! zInLuKp|mTZB)Kj}3AtSfLE+qv5>mSoWUm-U39(%XMde(M62fVepdBUnwk48eFwOM> z_I-gPyB~P#y7AY)RlP3|qS+VNL+oY2Q1IH|GeN8uILC7z&4B<2fB*=900@8p2!H?x zfWT=J==^$tsGB^54+jE1^CA3=g-li()9nZ8ymg7rW4*w_mLn{U^#Y7J%j)X|ZvDso z-#K#4sZG!qIPGH(89@L9KmY_l00ck)1V8`;KmY_<5?KEF0^O@nU*H4ZzHra`k>eYx z>jl==*9)x2dV!Xc97YfT0T2KI5C8!X009sH0T5U!1Uk81;L4em0-?E93Rvp}l2|XW z64nbi^aa)z_lUPlTzS;IFVG#VH0cWv12zx<0T2KI5C8!X009sH0T2KI5LhUIfo{_c zexNQHkj&-wIMo7@NmWoc^NO4lIp_=2lob|BU%=r<@bk}a_*^&rgB|cASm-22c@O{r z5C8!X009sH0T2KI5LoR5mcJi?Zx#9xe2e|XQ#*!>V}ancls9m~_9FHycdY@YRaLEQr&axki_|NM*VFxt^)ApQBu0}; 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z)-YGuYJFAFz=1%Jx!4p9tbSYx>jhHg%z60DOD}(PI(+1!H!gVf2jA;GS=ARfK(jBf zhuF)4>jNi(Cxat_150g|VShjX1V8`;KmY_l00ck)1VCW95>RX>`fzxDC;I9FJEi)j zu55h)0r~=3WV^mUa)Vyhc4dnCgjUEGXG}w8lmabMu8ft942e?^>4d((DRK_*3pNk{ z0T2KI5C8!X009sH0T5Uk1Y&Ew6dfKQSJ|~I=v;13+R#c9`J!IX$EP;)$)qZ%=37#c z_%&v3+0Ly@mUKhU>IG*JRT2bYGjF~rG1l3DJXZsXoD?}e=xji0*MOqN0?r1+xf-bU zpx4=e(5?ZMi}g4g;OA>ViTRzmxp{LB_(<-Mjel_d%-xR6$$2w#UNf^jRBF3^Dk|r3 zlxRD)N|Nhxl#tuCAt;>NQKIeesvO5SN{H>+ApLMTO0*qeQi67r;M=yLkb{>o58(QG zfsOz0*uG=yUcU%_1WV(zhP?m*5C8!X009sH0T2KI5CDPYOJG&_5hPcd?%>w%Tr;-q zlh?dqt``WpJ~@x>AW6gq0*gXmdRMY4s5LP?Mbz;slSIKzI~cWO>G*S`j%Q1+b*#Ob zw%S~BD79ouVr{ncn$WUXlfY4vxRxc<#|sISSCfOus#Y0v2epE!b7zX^S&~t+B^2x0 zcQbN$RVBYBVY8WJ(JXORGB#v{_!O@slANl_YE4aUm)tP*DvN})jZdJbtw zd-8Xzz1r-C?qKswk;y2u65W)W#mb;NXdP#>PmL;P9mq|G=lrKe=nj_B`C?8xK+a;) z95b-#+r&b~$%#Q#Rm7T9BXkE(=W7|dgO(a`^((;A7o2?%E6^Q;?jUprOZiD7uNTeV dmM!!Y=l{`mwm(9}lqi^z#=Oi6a_z+a{{i4Ps~`XX From b59752327059a67428e574bee6651b0722f1a400 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 11:28:57 -0500 Subject: [PATCH 09/20] Added temp shared memory and write-ahead logging to sqlite db --- src/soa_builder/web/db.py | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/src/soa_builder/web/db.py b/src/soa_builder/web/db.py index 681a2b5..2b3e336 100644 --- a/src/soa_builder/web/db.py +++ b/src/soa_builder/web/db.py @@ -8,12 +8,4 @@ def _connect(): - conn = sqlite3.connect(DB_PATH, timeout=5.0, check_same_thread=False) - try: - # Improve concurrency and reduce lock errors - conn.execute("PRAGMA journal_mode=WAL") - conn.execute("PRAGMA synchronous=NORMAL") - conn.execute("PRAGMA busy_timeout=3000") - except Exception: - pass - return conn + return sqlite3.connect(DB_PATH) From 31582eb0cebb7e3a95ece894761acb8ec91544f2 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 12:11:59 -0500 Subject: [PATCH 10/20] Arm audit added to edit.html --- src/soa_builder/web/app.py | 21 +++++++++++++++++ src/soa_builder/web/templates/edit.html | 30 +++++++++++++++++++++++++ 2 files changed, 51 insertions(+) diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index 1221362..fde0b73 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -3113,6 +3113,26 @@ def ui_edit(request: Request, soa_id: int): } ) + # Admin audit view: recent arm audits for this SOA + conn_audit = _connect() + cur_audit = conn_audit.cursor() + cur_audit.execute( + "SELECT id, arm_id, action, before_json, after_json, performed_at FROM arm_audit WHERE soa_id=? ORDER BY id DESC LIMIT 50", + (soa_id,), + ) + arm_audits = [ + { + "id": r[0], + "arm_id": r[1], + "action": r[2], + "before_json": r[3], + "after_json": r[4], + "performed_at": r[5], + } + for r in cur_audit.fetchall() + ] + conn_audit.close() + return templates.TemplateResponse( request, "edit.html", @@ -3136,6 +3156,7 @@ def ui_edit(request: Request, soa_id: int): **study_meta, "protocol_terminology_C174222": protocol_terminology_C174222, "ddf_terminology_C188727": ddf_terminology_C188727, + "arm_audits": arm_audits, }, ) diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html index a243423..e408716 100644 --- a/src/soa_builder/web/templates/edit.html +++ b/src/soa_builder/web/templates/edit.html @@ -247,6 +247,36 @@

    Editing SoA {{ soa_id }}

+ +
+
+
+ Arm Audit (latest {{ arm_audits|length }}) + {% if arm_audits %} + + + + + + + + + + {% for au in arm_audits %} + + + + + + + + + {% endfor %} +
IDArmActionPerformedBeforeAfter
{{ au.id }}{{ au.arm_id }}{{ au.action }}{{ au.performed_at }}{{ au.before_json or '' }}{{ au.after_json or '' }}
+ {% else %} +
No arm audit entries yet.
+ {% endif %} +
From e66ad609404063106771ddba1393b7dcdb10fe0e Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 12:33:18 -0500 Subject: [PATCH 11/20] Arm create includes type & data_origin_type --- src/soa_builder/web/app.py | 225 +++++++++++++++++++++++- src/soa_builder/web/templates/edit.html | 18 ++ 2 files changed, 241 insertions(+), 2 deletions(-) diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index fde0b73..0d87a4d 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -3494,7 +3494,7 @@ def ui_add_visit( @app.post("/ui/soa/{soa_id}/add_arm", response_class=HTMLResponse) -def ui_add_arm( +async def ui_add_arm( request: Request, soa_id: int, name: str = Form(...), @@ -3508,7 +3508,168 @@ def ui_add_arm( # Accept blank/empty element selection gracefully. The form may submit "" which would 422 with Optional[int]. eid = int(element_id) if element_id and element_id.strip().isdigit() else None payload = ArmCreate(name=name, label=label, description=description, element_id=eid) - create_arm(soa_id, payload) + # Create base arm (function may not return id; fetch if needed) + created = create_arm(soa_id, payload) + # routers.arms.create_arm returns a row dict; extract id + new_arm_id = None + try: + if isinstance(created, dict): + new_arm_id = created.get("id") + elif isinstance(created, int): + new_arm_id = created + except Exception: + new_arm_id = None + if not new_arm_id: + try: + conn_tmp = _connect() + cur_tmp = conn_tmp.cursor() + cur_tmp.execute( + "SELECT id FROM arm WHERE soa_id=? ORDER BY id DESC LIMIT 1", + (soa_id,), + ) + rtmp = cur_tmp.fetchone() + new_arm_id = rtmp[0] if rtmp else None + conn_tmp.close() + except Exception: + new_arm_id = None + if not new_arm_id: + return HTMLResponse( + f"", + status_code=500, + ) + # Read optional type fields with hyphenated names + try: + form_data = await request.form() + arm_type_submission = (form_data.get("arm-type") or "").strip() + data_origin_type_submission = (form_data.get("data-origin-type") or "").strip() + except Exception: + arm_type_submission = "" + data_origin_type_submission = "" + + # If type selections provided, resolve to terminology codes and persist via junction table + if arm_type_submission or data_origin_type_submission: + conn = _connect() + cur = conn.cursor() + logger.info( + "ui_add_arm: received type selections arm-type='%s', data-origin-type='%s' for soa_id=%s arm_id=%s", + arm_type_submission, + data_origin_type_submission, + soa_id, + new_arm_id, + ) + new_type_uid: Optional[str] = None + new_data_origin_uid: Optional[str] = None + if arm_type_submission: + cur.execute( + "SELECT code FROM protocol_terminology WHERE codelist_code='C174222' AND (cdisc_submission_value=? OR LOWER(TRIM(cdisc_submission_value))=LOWER(TRIM(?)))", + (arm_type_submission, arm_type_submission), + ) + r = cur.fetchone() + resolved_code = r[0] if r else None + if resolved_code is None: + logger.warning( + "ui_add_arm: unknown arm type submission '%s' for soa_id=%s", + arm_type_submission, + soa_id, + ) + conn.close() + return HTMLResponse( + f"", + status_code=400, + ) + # Create Code_N + cur.execute( + "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", + (soa_id,), + ) + existing = [x[0] for x in cur.fetchall() if x[0]] + n = 1 + if existing: + try: + n = max(int(x.split("_")[1]) for x in existing) + 1 + except Exception: + n = len(existing) + 1 + new_type_uid = f"Code_{n}" + cur.execute( + "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", + ( + soa_id, + new_type_uid, + "protocol_terminology", + "C174222", + resolved_code, + ), + ) + logger.info( + "ui_add_arm: created code junction %s -> table=%s list=%s code=%s", + new_type_uid, + "protocol_terminology", + "C174222", + resolved_code, + ) + if data_origin_type_submission: + cur.execute( + "SELECT code FROM ddf_terminology WHERE codelist_code='C188727' AND (cdisc_submission_value=? OR LOWER(TRIM(cdisc_submission_value))=LOWER(TRIM(?)))", + (data_origin_type_submission, data_origin_type_submission), + ) + r2 = cur.fetchone() + resolved_ddf_code = r2[0] if r2 else None + if resolved_ddf_code is None: + logger.warning( + "ui_add_arm: unknown data origin type submission '%s' for soa_id=%s", + data_origin_type_submission, + soa_id, + ) + conn.close() + return HTMLResponse( + f"", + status_code=400, + ) + # Create Code_N (continue numbering) + cur.execute( + "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", + (soa_id,), + ) + existing = [x[0] for x in cur.fetchall() if x[0]] + n = 1 + if existing: + try: + n = max(int(x.split("_")[1]) for x in existing) + 1 + except Exception: + n = len(existing) + 1 + new_data_origin_uid = f"Code_{n}" + cur.execute( + "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", + ( + soa_id, + new_data_origin_uid, + "ddf_terminology", + "C188727", + resolved_ddf_code, + ), + ) + logger.info( + "ui_add_arm: created code junction %s -> table=%s list=%s code=%s", + new_data_origin_uid, + "ddf_terminology", + "C188727", + resolved_ddf_code, + ) + # Update arm row with new code_uids + if new_type_uid or new_data_origin_uid: + cur.execute( + "UPDATE arm SET type=COALESCE(?, type), data_origin_type=COALESCE(?, data_origin_type) WHERE id=? AND soa_id=?", + (new_type_uid, new_data_origin_uid, new_arm_id, soa_id), + ) + logger.info( + "ui_add_arm: updated arm id=%s set type=%s data_origin_type=%s", + new_arm_id, + new_type_uid, + new_data_origin_uid, + ) + conn.commit() + # routers.arms.create_arm already records a create audit; avoid duplicating here + conn.close() return HTMLResponse(f"") @@ -3534,6 +3695,13 @@ async def ui_update_arm( except Exception: arm_type_submission = "" data_origin_type_submission = "" + logger.info( + "ui_update_arm: arm_id=%s soa_id=%s incoming arm-type='%s' data-origin-type='%s'", + arm_id, + soa_id, + arm_type_submission, + data_origin_type_submission, + ) # Fetch current arm (including existing type code_uid if any) conn = _connect() @@ -3584,6 +3752,12 @@ async def ui_update_arm( r = cur.fetchone() resolved_code = r[0] if r else None if resolved_code is None: + logger.warning( + "ui_update_arm: unknown arm type submission '%s' for soa_id=%s arm_id=%s", + arm_type_submission, + soa_id, + arm_id, + ) conn.close() return HTMLResponse( f"", @@ -3599,6 +3773,13 @@ async def ui_update_arm( "UPDATE code SET code=?, codelist_code='C174222', codelist_table='protocol_terminology' WHERE soa_id=? AND code_uid=?", (resolved_code, soa_id, current_code_uid), ) + logger.info( + "ui_update_arm: updated junction code_uid=%s -> table=%s list=%s code=%s", + current_code_uid, + "protocol_terminology", + "C174222", + resolved_code, + ) else: # Create new Code_N within this SoA cur.execute( @@ -3623,6 +3804,13 @@ async def ui_update_arm( resolved_code, ), ) + logger.info( + "ui_update_arm: created junction code_uid=%s -> table=%s list=%s code=%s", + new_code_uid, + "protocol_terminology", + "C174222", + resolved_code, + ) # Resolve Data Origin Type submission value to DDF terminology code (C188727) resolved_ddf_code: Optional[str] = None @@ -3635,6 +3823,12 @@ async def ui_update_arm( r2 = cur.fetchone() resolved_ddf_code = r2[0] if r2 else None if resolved_ddf_code is None: + logger.warning( + "ui_update_arm: unknown data origin type submission '%s' for soa_id=%s arm_id=%s", + data_origin_type_submission, + soa_id, + arm_id, + ) conn.close() return HTMLResponse( f"", @@ -3647,6 +3841,13 @@ async def ui_update_arm( (resolved_ddf_code, soa_id, current_data_origin_uid), ) new_data_origin_uid = current_data_origin_uid + logger.info( + "ui_update_arm: updated junction code_uid=%s -> table=%s list=%s code=%s", + current_data_origin_uid, + "ddf_terminology", + "C188727", + resolved_ddf_code, + ) else: # Create new Code_N, ensuring unique across this SoA cur.execute( @@ -3671,6 +3872,13 @@ async def ui_update_arm( resolved_ddf_code, ), ) + logger.info( + "ui_update_arm: created junction code_uid=%s -> table=%s list=%s code=%s", + new_data_origin_uid, + "ddf_terminology", + "C188727", + resolved_ddf_code, + ) # Apply arm field updates (including setting type to code_uid if resolved) new_name = name if name is not None else row[1] @@ -3688,6 +3896,14 @@ async def ui_update_arm( soa_id, ), ) + logger.info( + "ui_update_arm: applied UPDATE arm id=%s set name='%s' label='%s' type=%s data_origin_type=%s", + arm_id, + new_name, + new_label, + new_code_uid, + new_data_origin_uid, + ) conn.commit() # Capture post-update code values post_arm_type_code_value: Optional[str] = None @@ -3736,6 +3952,11 @@ async def ui_update_arm( ) except Exception: pass + else: + logger.info( + "ui_update_arm: no-op update detected for arm_id=%s (no field or code changes)", + arm_id, + ) conn.close() return HTMLResponse(f"") diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html index e408716..31ec5eb 100644 --- a/src/soa_builder/web/templates/edit.html +++ b/src/soa_builder/web/templates/edit.html @@ -244,6 +244,24 @@

Editing SoA {{ soa_id }}

+ {% if protocol_terminology_C174222 %} + + {% endif %} + {% if ddf_terminology_C188727 %} + + {% endif %} From 211eaa720ddc5faaf5af8ed376e2984289444ff7 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 12:50:47 -0500 Subject: [PATCH 12/20] Update src/soa_builder/web/initialize_database.py code_uid column should be 'unique within an SOA' so added a uniqueness constraint on (soa_id, code_uid) Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- src/soa_builder/web/initialize_database.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/soa_builder/web/initialize_database.py b/src/soa_builder/web/initialize_database.py index d4c0366..8ccd3ac 100644 --- a/src/soa_builder/web/initialize_database.py +++ b/src/soa_builder/web/initialize_database.py @@ -155,7 +155,8 @@ def _init_db(): code_uid TEXT, -- immutable Code_N identifier unique within an SOA codelist_table TEXT, codelist_code TEXT NOT NULL, - code TEXT NOT NULL + code TEXT NOT NULL, + UNIQUE(soa_id, code_uid) )""" ) From 65309acbb63aa1404f23a228d14acad03164987b Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 12:51:08 -0500 Subject: [PATCH 13/20] Update src/soa_builder/web/app.py removed logger info statement Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- src/soa_builder/web/app.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index 0d87a4d..431a2d3 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -3073,8 +3073,6 @@ def ui_edit(request: Request, soa_id: int): {"cdisc_submission_value": r[0] or ""} for r in cur_ddft.fetchall() ] conn_ddft.close() - # logger.info("DDF Terminology values: ", ddf_terminology_C188727) - # Build mapping code_uid -> submission value (Arm dataOriginType C188727) conn_ddf_map = _connect() cur_ddf_map = conn_ddf_map.cursor() From 7f09a34361d77b60261d35fce8e9397ef235db17 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 12:51:27 -0500 Subject: [PATCH 14/20] Update src/soa_builder/web/app.py removed logger INFO statement Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- src/soa_builder/web/app.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index 431a2d3..74d113f 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -3088,7 +3088,6 @@ def ui_edit(request: Request, soa_id: int): ddf_opt.get("cdisc_submission_value") or "" for ddf_opt in ddf_terminology_C188727 } - # logger.info("DDF Data Origin Type submission values", ddf_submission_values) base_arms = _fetch_arms_for_edit(soa_id) arms_enriched = [] From 12dcc0e02bc0455cfca1d9d612c4b2909c0459e3 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 12:51:45 -0500 Subject: [PATCH 15/20] Update src/soa_builder/web/app.py corrected spelling Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- src/soa_builder/web/app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index 74d113f..2721b6a 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -5397,7 +5397,7 @@ def get_protocol_terminology( limit: int = 50, offset: int = 0, ): - """Return latest rotocol Terminology loaded into SQLite database.""" + """Return latest Protocol Terminology loaded into SQLite database.""" limit = max(1, min(limit, 200)) offset = max(0, offset) conn = _connect() From b7909b376927e6085ee0e4786397ed0c9249f6c5 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 13:20:10 -0500 Subject: [PATCH 16/20] Added helper _get_next_code_uid and refactor --- normalize_soa.py | 2 - src/soa_builder/web/app.py | 89 ++++++++++++++++++------------- src/soa_builder/web/db.py | 10 +++- tests/test_code_uid_generation.py | 80 +++++++++++++++++++++++++++ 4 files changed, 142 insertions(+), 39 deletions(-) create mode 100644 tests/test_code_uid_generation.py diff --git a/normalize_soa.py b/normalize_soa.py index e1ad818..11f7431 100644 --- a/normalize_soa.py +++ b/normalize_soa.py @@ -37,7 +37,6 @@ import csv import os import re -import sys from dataclasses import asdict, dataclass from typing import Any, Dict, List, Optional @@ -259,7 +258,6 @@ def build_visit_activities( vas: List[VisitActivity] = [] next_id = 1 for a_idx, r in enumerate(rows, start=1): - activity_name = r[0] for v_idx, visit in enumerate(visits, start=1): if v_idx >= len(r): continue diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index 2721b6a..cad5ce2 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -138,6 +138,24 @@ def _get_concepts_override(): return os.environ.get("CDISC_CONCEPTS_JSON") +def _get_next_code_uid(cur, soa_id: int) -> str: + """Compute next unique Code_N for the given SOA. + Assumes `cur` is a sqlite cursor within an open transaction. + """ + cur.execute( + "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", + (soa_id,), + ) + existing = [x[0] for x in cur.fetchall() if x[0]] + n = 1 + if existing: + try: + n = max(int(x.split("_")[1]) for x in existing) + 1 + except Exception: + n = len(existing) + 1 + return f"Code_{n}" + + # Audit functions def _record_element_audit( soa_id: int, @@ -2250,23 +2268,23 @@ def export_xlsx(soa_id: int, left: Optional[int] = None, right: Optional[int] = conn_info = _connect() cur_info = conn_info.cursor() cur_info.execute( - "SELECT name, created_at, study_id, study_label, study_description FROM soa WHERE id=?", + "SELECT name, study_id, study_label, study_description, created_at FROM soa WHERE id=?", (soa_id,), ) - info_row = cur_info.fetchone() - conn_info.close() - if info_row: - soa_name_val, created_at_val, study_id_val, study_label_val, study_desc_val = ( - info_row + row_info = cur_info.fetchone() + if row_info: + soa_name_val, study_id_val, study_label_val, study_desc_val, created_at_val = ( + row_info ) else: - soa_name_val, created_at_val, study_id_val, study_label_val, study_desc_val = ( + soa_name_val, study_id_val, study_label_val, study_desc_val, created_at_val = ( f"SOA {soa_id}", None, None, None, None, ) + conn_info.close() freezes = _list_freezes(soa_id) last_freeze_label = freezes[0]["version_label"] if freezes else None last_freeze_time = freezes[0]["created_at"] if freezes else None @@ -3029,16 +3047,37 @@ def ui_edit(request: Request, soa_id: int): conn_meta = _connect() cur_meta = conn_meta.cursor() cur_meta.execute( - "SELECT study_id, study_label, study_description FROM soa WHERE id=?", (soa_id,) + "SELECT study_id, study_label, study_description, name, created_at FROM soa WHERE id=?", + (soa_id,), ) meta_row = cur_meta.fetchone() conn_meta.close() + if meta_row: + study_id_val, study_label_val, study_desc_val, soa_name_val, created_at_val = ( + meta_row + ) + else: + study_id_val, study_label_val, study_desc_val, soa_name_val, created_at_val = ( + None, + None, + None, + f"SOA {soa_id}", + None, + ) study_meta = { - "study_id": meta_row[0] if meta_row else None, - "study_label": meta_row[1] if meta_row else None, - "study_description": meta_row[2] if meta_row else None, + "study_id": study_id_val, + "study_label": study_label_val, + "study_description": study_desc_val, + "soa_name": soa_name_val, + "created_at": created_at_val, } - # Protocol terminology options for Arm Type (C174222) + # Compute next Code_N using a fresh cursor + conn_codes = _connect() + cur_codes = conn_codes.cursor() + # Precompute next Code_N if needed for UI defaults (currently not displayed) + _ = _get_next_code_uid(cur_codes, soa_id) + conn_codes.close() + # Load Protocol Terminology (C174222) options conn_pt = _connect() cur_pt = conn_pt.cursor() cur_pt.execute( @@ -3779,18 +3818,7 @@ async def ui_update_arm( ) else: # Create new Code_N within this SoA - cur.execute( - "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", - (soa_id,), - ) - existing = [x[0] for x in cur.fetchall() if x[0]] - n = 1 - if existing: - try: - n = max(int(x.split("_")[1]) for x in existing) + 1 - except Exception: - n = len(existing) + 1 - new_code_uid = f"Code_{n}" + new_code_uid = _get_next_code_uid(cur, soa_id) cur.execute( "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", ( @@ -3847,18 +3875,7 @@ async def ui_update_arm( ) else: # Create new Code_N, ensuring unique across this SoA - cur.execute( - "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", - (soa_id,), - ) - existing = [x[0] for x in cur.fetchall() if x[0]] - n = 1 - if existing: - try: - n = max(int(x.split("_")[1]) for x in existing) + 1 - except Exception: - n = len(existing) + 1 - new_data_origin_uid = f"Code_{n}" + new_data_origin_uid = _get_next_code_uid(cur, soa_id) cur.execute( "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", ( diff --git a/src/soa_builder/web/db.py b/src/soa_builder/web/db.py index 2b3e336..681a2b5 100644 --- a/src/soa_builder/web/db.py +++ b/src/soa_builder/web/db.py @@ -8,4 +8,12 @@ def _connect(): - return sqlite3.connect(DB_PATH) + conn = sqlite3.connect(DB_PATH, timeout=5.0, check_same_thread=False) + try: + # Improve concurrency and reduce lock errors + conn.execute("PRAGMA journal_mode=WAL") + conn.execute("PRAGMA synchronous=NORMAL") + conn.execute("PRAGMA busy_timeout=3000") + except Exception: + pass + return conn diff --git a/tests/test_code_uid_generation.py b/tests/test_code_uid_generation.py new file mode 100644 index 0000000..6fda689 --- /dev/null +++ b/tests/test_code_uid_generation.py @@ -0,0 +1,80 @@ +from soa_builder.web.db import _connect +from soa_builder.web.initialize_database import _init_db +from soa_builder.web.app import _get_next_code_uid + + +def setup_module(module): + # Ensure test DB is initialized + _init_db() + + +def test_get_next_code_uid_empty_soA(): + conn = _connect() + cur = conn.cursor() + # create a dummy SOA + cur.execute( + "INSERT INTO soa (name, created_at) VALUES (?, datetime('now'))", ("TestStudy",) + ) + soa_id = cur.lastrowid + conn.commit() + # No existing codes -> should return Code_1 + code_uid = _get_next_code_uid(cur, soa_id) + assert code_uid == "Code_1" + conn.close() + + +def test_get_next_code_uid_mixed_existing(): + conn = _connect() + cur = conn.cursor() + # create a new SOA + cur.execute( + "INSERT INTO soa (name, created_at) VALUES (?, datetime('now'))", + ("TestStudy2",), + ) + soa_id = cur.lastrowid + conn.commit() + # Insert mixed existing code_uids + cur.execute( + "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", + (soa_id, "Code_1", "protocol_terminology", "C174222", "X"), + ) + cur.execute( + "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", + (soa_id, "Code_3", "ddf_terminology", "C188727", "Y"), + ) + # Malformed tail should be ignored in max() and trigger fallback only if parsing fails for all + cur.execute( + "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", + (soa_id, "Code_X", "protocol_terminology", "C174222", "Z"), + ) + conn.commit() + # Expect next to be max numeric + 1 -> Code_4 + next_uid = _get_next_code_uid(cur, soa_id) + assert next_uid == "Code_4" + conn.close() + + +def test_get_next_code_uid_all_invalid_tails(): + conn = _connect() + cur = conn.cursor() + # create a new SOA + cur.execute( + "INSERT INTO soa (name, created_at) VALUES (?, datetime('now'))", + ("TestStudy3",), + ) + soa_id = cur.lastrowid + conn.commit() + # Insert only invalid tails that cannot be parsed as integers + cur.execute( + "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", + (soa_id, "Code_A", "protocol_terminology", "C174222", "X"), + ) + cur.execute( + "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", + (soa_id, "Code_B", "ddf_terminology", "C188727", "Y"), + ) + conn.commit() + # Fallback should use len(existing)+1 -> 3 + next_uid = _get_next_code_uid(cur, soa_id) + assert next_uid == "Code_3" + conn.close() From cb79e60693ad456a8ba14b1a4946a66b7dc1a072 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 14:17:17 -0500 Subject: [PATCH 17/20] Moved _get_next_code_uid to utils.py and removed duplicate logic for Code_N --- src/soa_builder/web/app.py | 45 +++--------------------------------- src/soa_builder/web/utils.py | 20 ++++++++++++++++ 2 files changed, 23 insertions(+), 42 deletions(-) create mode 100644 src/soa_builder/web/utils.py diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index cad5ce2..97b78ab 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -67,6 +67,7 @@ from .routers.arms import create_arm # re-export for backward compatibility from .routers.arms import delete_arm from .schemas import ArmCreate, SOACreate, SOAMetadataUpdate +from .utils import get_next_code_uid as _get_next_code_uid load_dotenv() # must come BEFORE reading env-based configuration so values are populated DB_PATH = os.environ.get("SOA_BUILDER_DB", "soa_builder_web.db") @@ -138,24 +139,6 @@ def _get_concepts_override(): return os.environ.get("CDISC_CONCEPTS_JSON") -def _get_next_code_uid(cur, soa_id: int) -> str: - """Compute next unique Code_N for the given SOA. - Assumes `cur` is a sqlite cursor within an open transaction. - """ - cur.execute( - "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", - (soa_id,), - ) - existing = [x[0] for x in cur.fetchall() if x[0]] - n = 1 - if existing: - try: - n = max(int(x.split("_")[1]) for x in existing) + 1 - except Exception: - n = len(existing) + 1 - return f"Code_{n}" - - # Audit functions def _record_element_audit( soa_id: int, @@ -3614,18 +3597,7 @@ async def ui_add_arm( status_code=400, ) # Create Code_N - cur.execute( - "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", - (soa_id,), - ) - existing = [x[0] for x in cur.fetchall() if x[0]] - n = 1 - if existing: - try: - n = max(int(x.split("_")[1]) for x in existing) + 1 - except Exception: - n = len(existing) + 1 - new_type_uid = f"Code_{n}" + new_type_uid = _get_next_code_uid(cur, soa_id) cur.execute( "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", ( @@ -3662,18 +3634,7 @@ async def ui_add_arm( status_code=400, ) # Create Code_N (continue numbering) - cur.execute( - "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", - (soa_id,), - ) - existing = [x[0] for x in cur.fetchall() if x[0]] - n = 1 - if existing: - try: - n = max(int(x.split("_")[1]) for x in existing) + 1 - except Exception: - n = len(existing) + 1 - new_data_origin_uid = f"Code_{n}" + new_data_origin_uid = _get_next_code_uid(cur, soa_id) cur.execute( "INSERT INTO code (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", ( diff --git a/src/soa_builder/web/utils.py b/src/soa_builder/web/utils.py new file mode 100644 index 0000000..87e37f7 --- /dev/null +++ b/src/soa_builder/web/utils.py @@ -0,0 +1,20 @@ +from typing import Any + + +def get_next_code_uid(cur: Any, soa_id: int) -> str: + """Compute next unique Code_N for the given SOA. + + Assumes `cur` is a sqlite cursor within an open transaction. + """ + cur.execute( + "SELECT code_uid FROM code WHERE soa_id=? AND code_uid LIKE 'Code_%'", + (soa_id,), + ) + existing = [x[0] for x in cur.fetchall() if x[0]] + n = 1 + if existing: + try: + n = max(int(x.split("_")[1]) for x in existing) + 1 + except Exception: + n = len(existing) + 1 + return f"Code_{n}" From dd2aceb8c1c38092054c3135e8551453b548e2ce Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 14:39:47 -0500 Subject: [PATCH 18/20] Removed cross-site and scripting vulnerabilities --- src/soa_builder/web/app.py | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index 97b78ab..b76864a 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -27,6 +27,7 @@ from contextlib import asynccontextmanager from datetime import datetime, timezone from typing import Any, List, Optional +import html import pandas as pd import requests @@ -3553,7 +3554,7 @@ async def ui_add_arm( new_arm_id = None if not new_arm_id: return HTMLResponse( - f"", + f"", status_code=500, ) # Read optional type fields with hyphenated names @@ -3593,7 +3594,7 @@ async def ui_add_arm( ) conn.close() return HTMLResponse( - f"", + f"", status_code=400, ) # Create Code_N @@ -3629,8 +3630,14 @@ async def ui_add_arm( soa_id, ) conn.close() + # Properly escape the value for safety in HTML/JS context + escaped_selection = ( + html.escape(data_origin_type_submission, quote=True) + .replace("\\", "\\\\") + .replace("'", "\\'") + ) return HTMLResponse( - f"", + f"", status_code=400, ) # Create Code_N (continue numbering) @@ -3757,7 +3764,7 @@ async def ui_update_arm( ) conn.close() return HTMLResponse( - f"", + f"", status_code=400, ) @@ -3817,7 +3824,7 @@ async def ui_update_arm( ) conn.close() return HTMLResponse( - f"", + f"", status_code=400, ) # Maintain/Upsert immutable Code_N for DDF mapping From 7967c112f0fe788c21a67f2cbd52d9fa799358ed Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 14:51:35 -0500 Subject: [PATCH 19/20] Update tests/test_code_uid_generation.py Consistent capitalization Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- tests/test_code_uid_generation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_code_uid_generation.py b/tests/test_code_uid_generation.py index 6fda689..bfe7437 100644 --- a/tests/test_code_uid_generation.py +++ b/tests/test_code_uid_generation.py @@ -8,7 +8,7 @@ def setup_module(module): _init_db() -def test_get_next_code_uid_empty_soA(): +def test_get_next_code_uid_empty_soa(): conn = _connect() cur = conn.cursor() # create a dummy SOA From 76d8ee2507778a4056b249254ee4cc8dbbaa1b86 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 3 Dec 2025 14:54:23 -0500 Subject: [PATCH 20/20] Removed unused import --- src/soa_builder/web/app.py | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index b76864a..9c473a7 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -27,7 +27,6 @@ from contextlib import asynccontextmanager from datetime import datetime, timezone from typing import Any, List, Optional -import html import pandas as pd import requests @@ -3115,12 +3114,12 @@ def ui_edit(request: Request, soa_id: int): base_arms = _fetch_arms_for_edit(soa_id) arms_enriched = [] for a in base_arms: - type = a.get("type") - type_display = code_to_submission.get(type) + arm_type = a.get("type") + type_display = code_to_submission.get(arm_type) data_origin_type = a.get("data_origin_type") data_origin_type_display = ddf_code_to_submission.get(data_origin_type) - if type_display is None and type: - type_display = type if type in submission_values else None + if type_display is None and arm_type: + type_display = arm_type if arm_type in submission_values else None if data_origin_type_display is None and data_origin_type: data_origin_type_display = ( data_origin_type if data_origin_type in ddf_submission_values else None @@ -3594,7 +3593,7 @@ async def ui_add_arm( ) conn.close() return HTMLResponse( - f"", + f"", status_code=400, ) # Create Code_N @@ -3631,13 +3630,9 @@ async def ui_add_arm( ) conn.close() # Properly escape the value for safety in HTML/JS context - escaped_selection = ( - html.escape(data_origin_type_submission, quote=True) - .replace("\\", "\\\\") - .replace("'", "\\'") - ) + escaped_selection = json.dumps(data_origin_type_submission) return HTMLResponse( - f"", + f"", status_code=400, ) # Create Code_N (continue numbering)