NickAkhmetov/Update Say & See to udi-yac 0.9.0, fix chart field changes

CHANGELOG-udi-yac-0.9.md

@@ -0,0 +1,4 @@
+- Upgrade `udi-yac` (Say & See chat) from 0.5.0 to 0.10.0 and `udiagent` from 0.6.0 to 0.10.0. The chat now sends its active filters with each message, and the agent takes them into account, so it can answer "which filters are on?" and build on the current filters.
+- Fix changing a field on a Say & See chart: the chat calls `/v1/yac/vis_instantiate` to rebuild the chart from its template, and the portal had no such route.
+- Link Say & See table rows and chart points to their donor, sample or dataset page.
+- Let Say & See users save sessions in the browser and load them later from the Session menu, kept separately for the public and consortium data, and for each signed-in user.

context/app/routes_udi.py

@@ -8,6 +8,7 @@
 from flask import current_app, jsonify, make_response, request, session
 
 from udiagent import Orchestrator, UDIAgent
+from udiagent.api import EndpointError, vis_instantiate
 
 from .routes_api import (
     _first_fields,
@@ -450,6 +451,8 @@ def yac_completions():
                 data_schema=data_schema,
                 data_domains=data_domains,
                 openai_api_key=openai_api_key,
+                # The chat's active filters; udiagent drops malformed entries.
+                filters=body.get('filters'),
             )
     except Exception as e:
         current_app.logger.exception('UDIAgent orchestrator failed')
@@ -458,6 +461,21 @@ def yac_completions():
     return jsonify(result.tool_calls)
 
 
+# The chat calls this when the user swaps a field on a template-generated chart.
+# No LLM call, so no OpenAI key is needed.
+@blueprint.route('/v1/yac/vis_instantiate', methods=['POST'])
+def yac_vis_instantiate():
+    try:
+        return jsonify(vis_instantiate(request.get_json(silent=True) or {}))
+    except EndpointError as e:
+        if e.status >= 500:
+            # udiagent logs only the message; keep the traceback of a template bug.
+            current_app.logger.exception('vis_instantiate failed: %s', e.code)
+        # udiagent's {code, error, errors} shape: the chat reads `code`, and drops a
+        # chart's tweak controls on `unknown_template`.
+        return jsonify(e.body()), e.status
+
+
 @blueprint.route('/v1/yac/examples', methods=['GET'])
 def yac_examples():
     examples_path = os.path.join(os.path.dirname(__file__), 'udi_example_prompts.json')

context/app/static/js/components/search/SaySeePanel/SaySeePanel.spec.tsx

@@ -26,14 +26,21 @@ vi.mock('udi-yac', () => ({
     dataPackagePath,
     onEvent,
     palette,
+    recordUrl,
+    savedSessionsKey,
   }: {
     dataPackagePath: string;
+    savedSessionsKey?: string;
     onEvent?: (name: string, properties?: Record<string, unknown>) => void;
     palette?: { category?: unknown[]; mark?: string };
+    recordUrl?: (record: Record<string, unknown>, source: string) => string | null | undefined;
   }) => (
     <div
       data-testid="udi-chat"
       data-path={dataPackagePath}
+      data-saved-sessions-key={savedSessionsKey}
+      data-record-url={recordUrl?.({ uuid: 'abc' }, 'datasets') ?? undefined}
+      data-aggregate-record-url={String(recordUrl?.({ count: 3 }, 'datasets'))}
       data-palette-count={palette?.category?.length}
       data-palette-mark={palette?.mark}
     >
@@ -67,6 +74,7 @@ interface AppContextOverrides {
   isAuthenticated?: boolean;
   isHubmapUser?: boolean;
   isWorkspacesUser?: boolean;
+  userEmail?: string;
 }
 
 interface PrefsOverrides {
@@ -167,4 +175,22 @@ describe('SaySeePanel', () => {
     expect(chat).toHaveAttribute('data-palette-count', '18');
     expect(chat).toHaveAttribute('data-palette-mark', theme.palette.primary.main);
   });
+
+  it('keeps saved sessions per user', async () => {
+    setup({ isAuthenticated: true, isHubmapUser: true, userEmail: 'a@example.org' }, { scope: 'authenticated' });
+    render(<SaySeePanel />, { wrapper: Wrapper });
+    const chat = await screen.findByTestId('udi-chat');
+    expect(chat).toHaveAttribute(
+      'data-saved-sessions-key',
+      '/metadata/v0/udi/consortium/datapackage.json:a@example.org',
+    );
+  });
+
+  it('links records to their detail page, and aggregated rows to nothing', async () => {
+    setup({ isAuthenticated: true, isHubmapUser: true });
+    render(<SaySeePanel />, { wrapper: Wrapper });
+    const chat = await screen.findByTestId('udi-chat');
+    expect(chat).toHaveAttribute('data-record-url', '/browse/dataset/abc');
+    expect(chat).toHaveAttribute('data-aggregate-record-url', 'null');
+  });
 });

context/app/static/js/components/search/SaySeePanel/SaySeePanel.tsx

@@ -49,6 +49,19 @@ const ENTITY_ICONS = {
   donors: DonorIcon,
 };
 
+const ENTITY_TYPES: Record<string, string> = {
+  datasets: 'dataset',
+  samples: 'sample',
+  donors: 'donor',
+};
+
+// Links a chart point or table row to its detail page. Aggregated rows carry no
+// `uuid`, so they get no link.
+function recordUrl(record: Record<string, unknown>, source: string) {
+  const type = ENTITY_TYPES[source];
+  return type && typeof record.uuid === 'string' ? `/browse/${type}/${record.uuid}` : null;
+}
+
 function visualizationSelector(store: VisualizationStore) {
   return {
     fullscreenVizId: store.fullscreenVizId,
@@ -63,7 +76,7 @@ function ChatFallback() {
 }
 
 function SaySeePanel() {
-  const { isHubmapUser, isWorkspacesUser } = useAppContext();
+  const { isHubmapUser, isWorkspacesUser, userEmail } = useAppContext();
   const { fullscreenVizId, theme, expandViz, collapseViz } = useVisualizationStore(useShallow(visualizationSelector));
   const isFullscreen = fullscreenVizId === SAY_SEE_VIZ_ID;
   // Subscribe to the shared Escape-collapses-fullscreen listener; the
@@ -154,6 +167,10 @@ function SaySeePanel() {
                 palette={palette}
                 downloadActions={downloadActions}
                 downloadButtonLabel="Download Metadata"
+                recordUrl={recordUrl}
+                // One saved-session store per data package, as udi-yac requires, and per
+                // user, so people sharing a browser don't see each other's sessions.
+                savedSessionsKey={userEmail ? `${dataPackagePath}:${userEmail}` : dataPackagePath}
               />
             )}
           </Suspense>

context/app/static/js/components/search/SaySeePanel/SeeSayPanelDescription.tsx

@@ -102,8 +102,8 @@ export default function SaySeePanelDescription() {
         <Typography variant="body1">
           Explore HuBMAP&apos;s public data through a natural language chat interface. Ask questions about donor,
           sample, and dataset metadata and get visualizations back. Results are independent from the Filter &amp; Browse
-          Mode and do not link to individual dataset, sample, or donor pages. <ContactUsLink capitalize /> to report an
-          issue or share feedback.
+          Mode. Table rows and chart points link to their dataset, sample, or donor pages. <ContactUsLink capitalize />{' '}
+          to report an issue or share feedback.
         </Typography>
         <div>
           <Typography variant="subtitle1">How to get access?</Typography>

context/app/test_routes_udi.py

@@ -1,4 +1,5 @@
 import pytest
+from udiagent.api import EndpointError
 
 from . import routes_udi
 from .main import create_app
@@ -290,6 +291,28 @@ def test_yac_completions_anon_with_header(client, mocker):
     assert response.get_json() == [{'name': 'CreateVisualization', 'arguments': {'title': 'test'}}]
     assert captured['self'] is routes_udi._get_byok_orchestrator()
     assert captured['openai_api_key'] == 'sk-anon'
+    # udi-yac < 0.9 sends no filters; udiagent treats None as "no active filters".
+    assert captured['filters'] is None
+
+
+def test_yac_completions_forwards_filters(client, mocker):
+    captured = _capture_run(mocker)
+    filters = [
+        {
+            'id': 'f1',
+            'entity': 'datasets',
+            'field': 'organ',
+            'filterType': 'point',
+            'pointValues': ['Kidney'],
+        }
+    ]
+    response = client.post(
+        '/v1/yac/completions',
+        json={**_sample_completion_body, 'filters': filters},
+        headers={'X-OpenAI-Key': 'sk-anon'},
+    )
+    assert response.status == '200 OK'
+    assert captured['filters'] == filters
 
 
 def test_yac_completions_hubmap_user_uses_config_key(client, mocker):
@@ -836,3 +859,47 @@ def test_build_resource_survives_a_nested_field(client, mocker):
     entities = [{'hubmap_id': 'HBM1', 'nested': {'entity_type': ['Dataset']}}]
     with pytest.raises(TypeError):
         build_resource('datasets', entities, {}, {}, ['hubmap_id'])
+
+
+@pytest.mark.parametrize(
+    'body, status, code',
+    [
+        ({'toolArgs': {}}, 404, 'unknown_template'),
+        ({'toolArgs': None}, 422, 'bad_request'),
+    ],
+)
+def test_yac_vis_instantiate_answers_like_udiagent(client, body, status, code):
+    """A real udiagent call, so an upstream rename or contract change fails here.
+    An unknown template is answered before the schema is read, so no real
+    template name (which udiagent renumbers) is needed."""
+    response = client.post(
+        '/v1/yac/vis_instantiate',
+        json={'tool': 'vis_999_no_such_template', 'dataSchema': '{}', **body},
+    )
+    assert response.status_code == status
+    # udi-yac reads the top-level `code`; `unknown_template` drops the tweak UI.
+    assert response.get_json()['code'] == code
+
+
+def test_yac_vis_instantiate_returns_the_spec(client, mocker):
+    payload = {'spec': {'source': []}, 'toolArgs': {'field': 'organ'}, 'params': []}
+    instantiate = mocker.patch('app.routes_udi.vis_instantiate', return_value=payload)
+    body = {'tool': 'vis_001', 'toolArgs': {'field': 'organ'}, 'dataSchema': '{}'}
+    response = client.post('/v1/yac/vis_instantiate', json=body)
+    assert response.status_code == 200
+    assert response.get_json() == payload
+    instantiate.assert_called_once_with(body)
+
+
+def test_yac_vis_instantiate_logs_server_errors(client, mocker, caplog):
+    mocker.patch(
+        'app.routes_udi.vis_instantiate',
+        side_effect=EndpointError(500, 'instantiate_failed', 'Could not build a spec.'),
+    )
+    response = client.post('/v1/yac/vis_instantiate', json={})
+    assert response.status_code == 500
+    assert response.get_json() == {
+        'code': 'instantiate_failed',
+        'error': 'Could not build a spec.',
+    }
+    assert any(r.exc_info for r in caplog.records)

context/package.json

@@ -58,7 +58,7 @@
     "rehype-raw": "^7.0.0",
     "scellop": "^0.3.0",
     "swr": "^2.4.1",
-    "udi-yac": "^0.5.0",
+    "udi-yac": "^0.10.0",
     "universal-cookie": "^7.1.2",
     "use-resize-observer": "^9.1.0",
     "uuid": "^14.0.0",

pyproject.toml

@@ -26,8 +26,8 @@ dependencies = [
     "python-frontmatter>=1.1.0",
     "hubmap-commons>=2.1.20",
     "portal-visualization[full]>=0.5.13",
-    "udiagent>=0.6.0",
-    "udiagent[langfuse]>=0.6.0",
+    "udiagent>=0.10.0",
+    "udiagent[langfuse]>=0.10.0",
     "gunicorn>=23.0.0",
     "whitenoise[brotli]>=6.9.0",
 ]