Deploy d0d1a1b

AlphaFold failures now name their cause; drop the superseded mockups

Source: https://github.com/WINTER4000/turingDNA/commit/d0d1a1bee4bd36d3a803c847ba9065349794b20e

dee/static/app.js

@@ -4010,13 +4010,33 @@ function _afResize(viewer) {
 // Retry" affordance (the model DOES exist, EBI just blipped); a genuine
 // absence says so plainly. Never again claim "model doesn't exist" when the
 // truth is "EBI was momentarily down."
-function _afShowError(host, transient, retry) {
+function _afShowError(host, transient, retry, reason) {
     if (!host) return;
+    // The headline used to be the WHOLE message, which meant every possible
+    // cause — a CORS block, a 404 on a stale model version, an aborted
+    // timeout, a Mol* parse failure — was reported to the user as "EBI is
+    // down". An audit found AlphaFold-DB up and serving 200s while this text
+    // was on screen, so the headline was simply wrong and there was no way to
+    // tell from the UI.
+    //
+    // Keep the friendly headline, but always carry the actual reason: one
+    // line under it for the user, the full error in the console for whoever
+    // is debugging. A retry button on a cause that retrying cannot fix is a
+    // loop, and the reason is what tells them which they are looking at.
+    if (reason) console.warn('[alphafold] ' + (transient ? 'transient' : 'absent') + ':', reason);
     const wrap = document.createElement('div');
     wrap.className = 'alphafold-loading';
-    wrap.textContent = transient
-        ? 'AlphaFold-DB is temporarily unreachable — this usually clears in a moment.'
+    const head = document.createElement('div');
+    head.textContent = transient
+        ? 'AlphaFold-DB did not return the model — this usually clears in a moment.'
         : 'No AlphaFold model is available for this protein entry.';
+    wrap.appendChild(head);
+    if (reason) {
+        const why = document.createElement('div');
+        why.textContent = String(reason).slice(0, 140);
+        why.style.cssText = 'margin-top:6px;font-size:12px;opacity:.7';
+        wrap.appendChild(why);
+    }
     if (transient && typeof retry === 'function') {
         const btn = document.createElement('button');
         btn.type = 'button';
@@ -4046,7 +4066,9 @@ async function mountAlphaFoldViewer(hit, host, extraOpts) {
 
     const molstar = await _afWaitMolstar();
     if (!molstar) {
-        _afShowError(host, true, () => mountAlphaFoldViewer(hit, host, extraOpts));   // CDN blip → retry, don't tell them to refresh
+        // The Mol* bundle itself never arrived — nothing to do with EBI.
+        _afShowError(host, true, () => mountAlphaFoldViewer(hit, host, extraOpts),
+                     'the 3-D viewer library did not load (CDN or network)');
         return;
     }
     try {
@@ -4063,14 +4085,21 @@ async function mountAlphaFoldViewer(hit, host, extraOpts) {
         if (!await _afTryLoad(viewer, candidates)) {
             // exists === false → genuinely no model; otherwise treat as a
             // transient EBI blip and offer a retry.
-            _afShowError(host, exists !== false, () => mountAlphaFoldViewer(hit, host, extraOpts));
+            _afShowError(host, exists !== false, () => mountAlphaFoldViewer(hit, host, extraOpts),
+                         exists === false
+                            ? 'the AlphaFold API has no entry for this accession'
+                            : 'every candidate model URL failed to load — tried '
+                              + (candidates || []).length + ' (newest version first)');
             return;
         }
         const overlay = host.querySelector('.alphafold-loading');
         if (overlay) overlay.remove();
         return viewer;   // hand the instance back so the caller can spin/pin/resize it
     } catch (err) {
-        _afShowError(host, true, () => mountAlphaFoldViewer(hit, host, extraOpts));
+        // Usually a Mol* parse/render failure, not a network one. Saying "EBI
+        // is unreachable" here sends people to check a service that is fine.
+        _afShowError(host, true, () => mountAlphaFoldViewer(hit, host, extraOpts),
+                     (err && err.message) || String(err));
     }
 }
 
@@ -6583,13 +6612,17 @@ if (_quitBtn) {
             _afApplyBg(viewer);
             const { candidates, exists } = await _afResolve(pdbUrl);
             if (!await _afTryLoad(viewer, candidates)) {
-                _afShowError(host, exists !== false, () => _mountCrisprStructure(host, pdbUrl, residue));
+                _afShowError(host, exists !== false, () => _mountCrisprStructure(host, pdbUrl, residue),
+                             exists === false
+                                ? 'the AlphaFold API has no entry for this accession'
+                                : 'every candidate model URL failed to load');
                 return;
             }
             const ov = host.querySelector('.alphafold-loading'); if (ov) ov.remove();
             _highlightResidue(molstar, viewer, residue);
         } catch (err) {
-            _afShowError(host, true, () => _mountCrisprStructure(host, pdbUrl, residue));
+            _afShowError(host, true, () => _mountCrisprStructure(host, pdbUrl, residue),
+                         (err && err.message) || String(err));
         }
     }
 

dee/static/index.html

@@ -112,7 +112,7 @@
     <!-- ?v= query bumps invalidate browser + iframe asset caches when app.css /
          app.js change. Bump these numbers whenever you ship a frontend update —
          without them, users keep getting the stale file for up to a week. -->
-    <link rel="stylesheet" href="/static/app.css?v=20260819-lineage" />
+    <link rel="stylesheet" href="/static/app.css?v=20260819-lineage2" />
     <!-- The work catalog + the draggable rail. Kept out of app.css so two new
          self-contained surfaces stay reviewable; every colour is an app.css
          token, so both themes work with nothing added. -->
@@ -2907,9 +2907,9 @@
     <!-- Cloning reference data must load before app.js so the Designer
          can read VECTORS / ENZYMES / CLONING_METHODS / TAGS / LINKERS. -->
     <script src="/static/cloning_db.js?v=20260530-ui-polish" defer></script>
-    <script src="/static/context.js?v=20260819-lineage" defer></script>
-    <script src="/static/lineage.js?v=20260819-lineage" defer></script>
-    <script src="/static/app.js?v=20260819-lineage" defer></script>
+    <script src="/static/context.js?v=20260819-lineage2" defer></script>
+    <script src="/static/lineage.js?v=20260819-lineage2" defer></script>
+    <script src="/static/app.js?v=20260819-lineage2" defer></script>
     <!-- The decision trace, BEFORE cockpit.js: applyEvent calls TDTrace.push
          on the very first event, and both are `defer`, so document order is
          load order. Loading it after would drop the opening events of a

tests/test_fold_structure_tool.py

@@ -79,3 +79,44 @@ def test_fold_structure_surfaces_lookup_failure_honestly(monkeypatch):
     out = t._tool_fold_structure({"gene_symbol": "ZZZ", "organism": "human"})
     assert out["ok"] is False
     assert "ZZZ" in out["error"]
+
+
+# --------------------------------------------------------------------------- #
+# The failure UI must name the actual cause
+# --------------------------------------------------------------------------- #
+# An audit found AlphaFold-DB up and serving 200s (v6, ~0.3s) while the viewer
+# was telling a user "AlphaFold-DB is temporarily unreachable". The headline
+# was the WHOLE message, so every possible cause — a Mol* bundle that never
+# loaded, a stale model version 404, an aborted timeout, a parse failure —
+# was reported as an EBI outage, and nothing on screen could distinguish them.
+def _app_js():
+    with open("dee/static/app.js", encoding="utf-8") as fh:
+        return fh.read()
+
+
+def test_the_error_ui_accepts_and_shows_a_reason():
+    src = _app_js()
+    assert "function _afShowError(host, transient, retry, reason)" in src
+    # Shown to the user, and logged in full for whoever is debugging.
+    assert "console.warn('[alphafold] '" in src
+
+
+def test_the_headline_no_longer_asserts_that_ebi_is_down():
+    """'did not return the model' describes what we observed. 'is temporarily
+    unreachable' is a claim about a third party's uptime that we were making
+    without evidence — and that the audit showed was often false."""
+    src = _app_js()
+    assert "AlphaFold-DB is temporarily unreachable" not in src
+    assert "AlphaFold-DB did not return the model" in src
+
+
+def test_every_failure_path_passes_a_reason():
+    """A reason parameter nothing populates is decoration. Each call site must
+    say which failure it is reporting."""
+    src = _app_js()
+    for reason in (
+        "the 3-D viewer library did not load (CDN or network)",
+        "the AlphaFold API has no entry for this accession",
+        "every candidate model URL failed to load",
+    ):
+        assert reason in src, f"missing reason: {reason}"