gramene-search 2.1.10 → 2.2.0

package/src/components/styles.css

@@ -14,8 +14,7 @@
     flex: 0 0 250px;
     position: sticky;
     top: 0;
-    max-height: 100vh;
-    overflow-y: auto;
+    align-self: flex-start;
     padding-left: 8px;
     padding-right: 8px;
     padding-bottom: 8px;
@@ -38,8 +37,6 @@
         flex: 0 0 auto;
         position: static;
         width: 100%;
-        max-height: none;
-        overflow-y: visible;
     }
     .search-views-content {
         width: 100%;

package/src/demo.js

@@ -21,16 +21,21 @@ import {
 } from "react-router-dom";
 import Feedback from './components/Feedback';
 import MDView from 'gramene-mdview';
+import bootViewFromUrl from './utils/bootView';
 
-const cache = getConfiguredCache({
-  maxAge: 24 * 60 * 60 * 1000,
-  version: 1
-});
 // const subsite = 'main';
 const subsite = process.env.SUBSITE;
 // const subsite = 'grapevine';
 // const subsite = 'sorghum';
 // const subsite = 'rice';
+// Scope the IndexedDB store to the subsite so caches from `npm run start-main`
+// don't leak into `npm run start-sorghum` (and vice versa). money-clip uses
+// the default keyval store when `name` is unset, which is shared across sites.
+const cache = getConfiguredCache({
+  maxAge: 24 * 60 * 60 * 1000,
+  version: 1,
+  name: `gramene_cache_${subsite || 'default'}`
+});
 
 const subsitelut = {
   main: 0,
@@ -141,20 +146,12 @@ const panSites = [
     ensemblURL: 'https://ensembl.sorghumbase.org',
     ensemblSite: 'https://ensembl.sorghumbase.org',
     ensemblRest: 'https://data.gramene.org/pansite-ensembl-108',
-    grameneData: 'https://data.sorghumbase.org/auth_testing',
+    grameneData: 'https://data.sorghumbase.org/sorghum_v10',
     ga: 'G-L5KXDCCZ16',
     targetTaxonId: 4558001,
     alertText: 'Click the search icon in the menu bar or type /',
     showViews: true,
     partialCompara: true,
-    firebaseConfig: {
-      apiKey: "AIzaSyCyTJmxfWgfuhI6-8uqocSiE9KOWUlkgkk",
-      authDomain: "gramene-auth.firebaseapp.com",
-      projectId: "gramene-auth",
-      storageBucket: "gramene-auth.appspot.com",
-      messagingSenderId: "590873346270",
-      appId: "1:590873346270:web:f76a31a93619e69439824f"
-    },
     details: {
       sequences: true,
       VEP: true,
@@ -273,6 +270,23 @@ const panSites = [
     }
   }
 ];
+
+// Firebase web config is loaded from FIREBASE_CONFIG_JSON in the build-time
+// env (.env, never committed). If unset, the Auth panel mounts but stays
+// inert. Attached to the sites that use gramene-auth.
+const firebaseConfig = (() => {
+  const raw = process.env.FIREBASE_CONFIG_JSON;
+  if (!raw) return null;
+  try { return JSON.parse(raw); }
+  catch (e) { console.warn('FIREBASE_CONFIG_JSON is not valid JSON; Auth disabled.', e); return null; }
+})();
+if (firebaseConfig) {
+  ['main', 'sorghum'].forEach(id => {
+    const site = panSites[subsitelut[id]];
+    if (site) site.firebaseConfig = firebaseConfig;
+  });
+}
+
 const initialState = Object.assign({helpIsOn:false}, panSites[subsitelut[subsite]]);
 
 const config = {
@@ -534,6 +548,9 @@ cache.getAll().then(initialData => {
   window.store = store;
   const config = store.selectConfiguration();
   ReactGA.initialize(config.ga);
+  // If the URL has ?view=<hash>, hydrate the snapshot before the user
+  // interacts. Errors are non-fatal (see utils/bootView.js).
+  bootViewFromUrl(store);
   if (initialData.hasOwnProperty('grameneMaps')) {
     // check for hidden genomes
     let notHidden = {};

package/src/index.js

@@ -3,5 +3,6 @@ import resultList from './components/resultList';
 import resultSummary from './components/resultSummary';
 import suggestions from './components/suggestions';
 import {Status, Filters, Results, Views, Auth} from './components/geneSearchUI';
+import bootViewFromUrl from './utils/bootView';
 
-export { bundles, resultList, resultSummary, suggestions, Status, Filters, Results, Views, Auth };
+export { bundles, resultList, resultSummary, suggestions, Status, Filters, Results, Views, Auth, bootViewFromUrl };

package/src/suppressDevWarnings.js

@@ -12,6 +12,19 @@ if (typeof console !== 'undefined' && typeof console.error === 'function') {
     'uses the legacy childContextTypes API',
     'uses the legacy contextTypes API',
     'findDOMNode is deprecated',
+    // Third-party libs (gramene-search-vis, gramene-mdview, Pathways, etc.)
+    // still use the pre-16.3 lifecycle methods. We can't fix them from here.
+    'componentWillReceiveProps has been renamed',
+    'componentWillMount has been renamed',
+    'componentWillUpdate has been renamed',
+    // Kept as a guard — react warns on any kebab-case inline-style property
+    // and Parcel's overlay turns that into a fatal runtime error. The known
+    // offender (BAR's max-width) was fixed when the component was absorbed
+    // from gramene-efp-browser, but the suppressor protects against any
+    // future regression in third-party libs.
+    'Unsupported style property',
+    // Stale-state setState after unmount in legacy class components.
+    "Can't perform a React state update on an unmounted component",
   ];
   console.error = function (...args) {
     const msg = typeof args[0] === 'string' ? args[0] : '';

package/src/utils/bootView.js

@@ -0,0 +1,38 @@
+// Boot-time hydration of a shared view link.
+//
+// Entry points call `bootViewFromUrl(store)` once the store is created.
+// Public views resolve anonymously. For private views, the initial call
+// will 401; the Auth panel then re-invokes with `{user}` once Firebase has
+// emitted its first signed-in state, and the fetch retries with a Bearer
+// token. On success we apply the snapshot and strip `?view=` from the URL
+// so subsequent user actions don't sit under a stale shared-state URL.
+//
+// All errors are non-fatal — they surface in state.savedViews.fetchError
+// for any UI that wants to show them.
+
+const PARAM = 'view';
+
+export default function bootViewFromUrl(store, opts = {}) {
+  if (typeof window === 'undefined') return Promise.resolve(null);
+  const url = new URL(window.location.href);
+  const hash = url.searchParams.get(PARAM);
+  if (!hash) return Promise.resolve(null);
+
+  const { user = null } = opts;
+
+  return store.doFetchView({ hash, user })
+    .then(({ snapshot }) => {
+      store.doApplyViewSnapshot(snapshot);
+      url.searchParams.delete(PARAM);
+      window.history.replaceState({}, '', url.toString());
+      return { hash, applied: true };
+    })
+    .catch((err) => {
+      // 401 here on the anonymous pass is expected for private views — the
+      // Auth panel will retry once it has a user. Other errors (404, 5xx,
+      // network) are reported and leave the param so a manual refresh can
+      // retry too.
+      console.warn('bootViewFromUrl:', err.message || err);
+      return { hash, applied: false, error: err.message || String(err) };
+    });
+}