Resume feature by tekrajchhetri · Pull Request #105 · sensein/brainkb-ui

tekrajchhetri · 2026-06-26T14:56:24Z

This PR adds the resume feature from the experiment UI and fixes the bug with resume for failed task.

gemini-code-assist

Code Review

This pull request enhances the SynthScholar literature review tool by introducing markdown rendering via react-markdown and remark-gfm, adding animated provenance timelines for both public and owner views, implementing search, status filtering, and sorting for the reviews list, and providing a full-page protocol creation experience with inline field guides. The code review feedback identifies several critical issues and improvement opportunities, including a potential crash due to a missing null guard in certaintyClass, a missing import for resolveOpenRouterKey causing a runtime error, React console warnings from spreading the node prop onto DOM elements in MarkdownContent, broken back navigation when clearing the active review selection, performance issues from frequent re-renders in ReviewDetail, and a side-effect inside a React state updater in useProgressStream.

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gemini-code-assist · 2026-06-26T14:59:08Z

+function certaintyClass(c: string) {
+  const v = c.toLowerCase();


If c is null or undefined, calling c.toLowerCase() will throw a TypeError and crash the public page. Guard against falsy values by fallback-defaulting to an empty string, matching the implementation of certaintyStyle in ProvenanceTimelineOwner.tsx.

Suggested change

function certaintyClass(c: string) {

const v = c.toLowerCase();

function certaintyClass(c: string) {

const v = (c || "").toLowerCase();

gemini-code-assist · 2026-06-26T14:59:08Z

+                // the retry body. Without this, the pipeline aborts with the
+                // exact "No OpenRouter API key available" 400 the user has
+                // been hitting.
+                const { key } = await resolveOpenRouterKey();


The function resolveOpenRouterKey is called here but is not imported in this file. This will cause a ReferenceError at runtime when a user attempts to retry or resume a review. Please import resolveOpenRouterKey from its defining module.

gemini-code-assist · 2026-06-26T14:59:08Z

+        components={{
+          // Headings: keep the visual hierarchy distinct without huge fonts —
+          // these often appear inside cards that already have their own h2.
+          h1: ({ ...p }) => <h2 style={{ fontSize: "1.4em", fontWeight: 600, margin: "0.8em 0 0.4em" }} {...p} />,
+          h2: ({ ...p }) => <h3 style={{ fontSize: "1.2em", fontWeight: 600, margin: "0.8em 0 0.3em" }} {...p} />,
+          h3: ({ ...p }) => <h4 style={{ fontSize: "1.05em", fontWeight: 600, margin: "0.7em 0 0.25em" }} {...p} />,
+          h4: ({ ...p }) => <h5 style={{ fontSize: "1em",    fontWeight: 600, margin: "0.6em 0 0.2em"  }} {...p} />,
+          // Paragraphs + lists with breathing room
+          p:  ({ ...p }) => <p  style={{ margin: "0.6em 0" }} {...p} />,
+          ul: ({ ...p }) => <ul style={{ margin: "0.5em 0", paddingLeft: "1.5em" }} {...p} />,
+          ol: ({ ...p }) => <ol style={{ margin: "0.5em 0", paddingLeft: "1.5em" }} {...p} />,
+          li: ({ ...p }) => <li style={{ margin: "0.2em 0" }} {...p} />,
+          // Blockquote
+          blockquote: ({ ...p }) => (
+            <blockquote
+              style={{
+                margin: "0.8em 0",
+                padding: "0.4em 0.9em",
+                borderLeft: "3px solid var(--bkb-accent, #4a4a4a)",
+                background: "var(--bkb-surfaceAlt, #f5f5f0)",
+                color: "var(--bkb-textMuted, #4a4a4a)",
+                borderRadius: "0 4px 4px 0",
+              }}
+              {...p}
+            />
+          ),
+          // Inline + block code
+          code: ({ ...p }) => (
+            <code
+              style={{
+                fontFamily: "ui-monospace, SFMono-Regular, Menlo, monospace",
+                fontSize: "0.9em",
+                background: "var(--bkb-surfaceAlt, #f0f0eb)",
+                padding: "0.1em 0.35em",
+                borderRadius: 3,
+              }}
+              {...p}
+            />
+          ),
+          pre: ({ ...p }) => (
+            <pre
+              style={{
+                margin: "0.8em 0",
+                padding: "0.8em 1em",
+                background: "var(--bkb-surfaceAlt, #f5f5f0)",
+                border: "1px solid var(--bkb-border, #e5e5e0)",
+                borderRadius: 6,
+                fontSize: "0.85em",
+                lineHeight: 1.5,
+                overflowX: "auto",
+              }}
+              {...p}
+            />
+          ),
+          // GFM tables — give them visible borders and a touch of padding
+          // so the cells don't run together.
+          table: ({ ...p }) => (
+            <div style={{ overflowX: "auto", margin: "0.8em 0" }}>
+              <table
+                style={{
+                  borderCollapse: "collapse",
+                  width: "100%",
+                  fontSize: "0.95em",
+                }}
+                {...p}
+              />
+            </div>
+          ),
+          th: ({ ...p }) => (
+            <th
+              style={{
+                textAlign: "left",
+                padding: "8px 10px",
+                borderBottom: "2px solid var(--bkb-border, #e5e5e0)",
+                background: "var(--bkb-surfaceAlt, #f5f5f0)",
+                fontWeight: 600,
+              }}
+              {...p}
+            />
+          ),
+          td: ({ ...p }) => (
+            <td
+              style={{
+                padding: "6px 10px",
+                borderBottom: "1px solid var(--bkb-border, #e5e5e0)",
+                verticalAlign: "top",
+              }}
+              {...p}
+            />
+          ),
+          // Horizontal rule — agent uses --- between sections
+          hr: () => (
+            <hr
+              style={{
+                margin: "1.4em 0",
+                border: "none",
+                borderTop: "1px solid var(--bkb-border, #e5e5e0)",
+              }}
+            />
+          ),
+          // Links open in a new tab; keep the visual subtle
+          a: ({ ...p }) => (
+            <a
+              target="_blank"
+              rel="noopener noreferrer"
+              style={{ color: "var(--bkb-accent, #1a73e8)", textDecoration: "underline" }}
+              {...p}
+            />
+          ),
+        }}


In react-markdown v9+, custom renderer components receive the node object as a prop. Spreading ...p directly onto standard HTML elements passes the node prop to the DOM, which triggers React console warnings about unrecognized non-HTML attributes. Destructure node out of the props before spreading the rest onto the DOM elements.

components={{ // Headings: keep the visual hierarchy distinct without huge fonts — // these often appear inside cards that already have their own h2. h1: ({ node, ...p }) => <h2 style={{ fontSize: "1.4em", fontWeight: 600, margin: "0.8em 0 0.4em" }} {...p} />, h2: ({ node, ...p }) => <h3 style={{ fontSize: "1.2em", fontWeight: 600, margin: "0.8em 0 0.3em" }} {...p} />, h3: ({ node, ...p }) => <h4 style={{ fontSize: "1.05em", fontWeight: 600, margin: "0.7em 0 0.25em" }} {...p} />, h4: ({ node, ...p }) => <h5 style={{ fontSize: "1em", fontWeight: 600, margin: "0.6em 0 0.2em" }} {...p} />, // Paragraphs + lists with breathing room p: ({ node, ...p }) => <p style={{ margin: "0.6em 0" }} {...p} />, ul: ({ node, ...p }) => <ul style={{ margin: "0.5em 0", paddingLeft: "1.5em" }} {...p} />, ol: ({ node, ...p }) => <ol style={{ margin: "0.5em 0", paddingLeft: "1.5em" }} {...p} />, li: ({ node, ...p }) => <li style={{ margin: "0.2em 0" }} {...p} />, // Blockquote blockquote: ({ node, ...p }) => ( <blockquote style={{ margin: "0.8em 0", padding: "0.4em 0.9em", borderLeft: "3px solid var(--bkb-accent, #4a4a4a)", background: "var(--bkb-surfaceAlt, #f5f5f0)", color: "var(--bkb-textMuted, #4a4a4a)", borderRadius: "0 4px 4px 0", }} {...p} /> ), // Inline + block code code: ({ node, ...p }) => ( <code style={{ fontFamily: "ui-monospace, SFMono-Regular, Menlo, monospace", fontSize: "0.9em", background: "var(--bkb-surfaceAlt, #f0f0eb)", padding: "0.1em 0.35em", borderRadius: 3, }} {...p} /> ), pre: ({ node, ...p }) => ( <pre style={{ margin: "0.8em 0", padding: "0.8em 1em", background: "var(--bkb-surfaceAlt, #f5f5f0)", border: "1px solid var(--bkb-border, #e5e5e0)", borderRadius: 6, fontSize: "0.85em", lineHeight: 1.5, overflowX: "auto", }} {...p} /> ), // GFM tables — give them visible borders and a touch of padding // so the cells don't run together. table: ({ node, ...p }) => ( <div style={{ overflowX: "auto", margin: "0.8em 0" }}> <table style={{ borderCollapse: "collapse", width: "100%", fontSize: "0.95em", }} {...p} /> </div> ), th: ({ node, ...p }) => ( <th style={{ textAlign: "left", padding: "8px 10px", borderBottom: "2px solid var(--bkb-border, #e5e5e0)", background: "var(--bkb-surfaceAlt, #f5f5f0)", fontWeight: 600, }} {...p} /> ), td: ({ node, ...p }) => ( <td style={{ padding: "6px 10px", borderBottom: "1px solid var(--bkb-border, #e5e5e0)", verticalAlign: "top", }} {...p} /> ), // Horizontal rule — agent uses --- between sections hr: () => ( <hr style={{ margin: "1.4em 0", border: "none", borderTop: "1px solid var(--bkb-border, #e5e5e0)", }} /> ), // Links open in a new tab; keep the visual subtle a: ({ node, ...p }) => ( <a target="_blank" rel="noopener noreferrer" style={{ color: "var(--bkb-accent, #1a73e8)", textDecoration: "underline" }} {...p} /> ), }}

gemini-code-assist · 2026-06-26T14:59:08Z

+  React.useEffect(() => {
+    const onPop = () => {
+      const params = new URLSearchParams(window.location.search);
+      setMode(params.get("mode") === "new" ? "new" : "list");
+      const id = params.get("review");
+      if (id) setSelectedId(id);
+    };


When navigating back to a state where no review is selected (i.e., the review URL parameter is absent), the id variable will be null. The current guard if (id) setSelectedId(id); prevents clearing the active selection, leaving the previous review's detail panel open. Pass id directly to setSelectedId to allow clearing the selection on back navigation.

Suggested change

React.useEffect(() => {

const onPop = () => {

const params = new URLSearchParams(window.location.search);

setMode(params.get("mode") === "new" ? "new" : "list");

const id = params.get("review");

if (id) setSelectedId(id);

};

// Listen for browser back/forward navigation between list and new modes.

React.useEffect(() => {

const onPop = () => {

const params = new URLSearchParams(window.location.search);

setMode(params.get("mode") === "new" ? "new" : "list");

const id = params.get("review");

setSelectedId(id);

};

gemini-code-assist · 2026-06-26T14:59:08Z

+  // 1-second tick used by the progress card to render "last update Ns ago".
+  // Without it the seconds-since-last-event display would only refresh when
+  // a new event arrives — defeating the whole point of a stuck-detector.
+  const [nowTick, setNowTick] = React.useState(() => Date.now());
+  React.useEffect(() => {
+    if (!isLive) return;
+    const id = setInterval(() => setNowTick(Date.now()), 1000);
+    return () => clearInterval(id);
+  }, [isLive]);


Updating the nowTick state every second at the ReviewDetail level triggers a full re-render of the entire detail panel (including headers, action buttons, and logs) when a review is live. To optimize performance and avoid high CPU usage, consider extracting the progress card or the freshness counter into a dedicated sub-component with its own local timer state.

gemini-code-assist · 2026-06-26T14:59:08Z

+        // Seed both the rendered list and the dedup window so the live SSE
+        // doesn't re-add events we already loaded from /reviews/{id}/log.
+        setEvents((prev) => {
+          if (prev.length > 0) return prev;
+          for (const e of seedEvents) seenSigsRef.current.add(_eventSignature(e));
+          return seedEvents;
+        });


Mutating seenSigsRef.current inside the setEvents state updater function is a side-effect. React state updater functions should be pure and free of side-effects, as they can run multiple times (e.g., in Strict Mode or during concurrent rendering). Populate seenSigsRef.current directly in the .then block before calling setEvents.

Suggested change

// Seed both the rendered list and the dedup window so the live SSE

// doesn't re-add events we already loaded from /reviews/{id}/log.

setEvents((prev) => {

if (prev.length > 0) return prev;

for (const e of seedEvents) seenSigsRef.current.add(_eventSignature(e));

return seedEvents;

});

for (const e of seedEvents) seenSigsRef.current.add(_eventSignature(e));

setEvents((prev) => (prev.length === 0 ? seedEvents : prev));

…ScR)

added Vocal biomarkers: depression & anxiety example

Update UI with tools info + Landing page design

tekrajchhetri added 4 commits May 5, 2026 18:22

added resume feature

cdf9764

resume feature from experiment ui added

5f51ad3

resume + cancel bug fixed + added markdown->html

bd3dbdf

provenance display added

d59da3c

tekrajchhetri mentioned this pull request Jun 26, 2026

Improvement design #104

Open

gemini-code-assist Bot reviewed Jun 26, 2026

View reviewed changes

tekrajchhetri and others added 22 commits June 26, 2026 11:13

added default example Vocal biomarkers: depression & anxiety (PRISMA-…

ab12480

…ScR)

Merge pull request #106 from sensein/add-voice-biomarkers-example

8cf6524

added Vocal biomarkers: depression & anxiety example

logo added for synthscholar and meetgraph

190f426

semantic concept mapper logo added

41ebfcd

updated page with editorial design direction

17d03a3

updated footer color

cad744b

updated logo of tools and libraries

6608376

added tools and use cases information

48887bc

made design consistent with home page

7a559cd

AbstractAtlas https://abstractatlas.brainkb.org/ added to brainkb

46fc469

AbstractAtlas added in menu

7576abf

re-ordered sections for story telling

5c051ab

made design consistent

bb36a52

updated video section to keep title fixed in case of multiple videos

ac925f5

added missing tools information

f286108

updated descriptions + added video

67e2857

updated hero message

7a7e4f6

enable youtube thumbnail

6c77e6b

updated description

eb5e8a7

meet-graph information added

0f078ef

updated description of tools

b8a58da

Merge pull request #107 from sensein/update-ui-with-tools-info

2ea1cf5

Update UI with tools info + Landing page design

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Resume feature#105

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		function certaintyClass(c: string) {
		const v = c.toLowerCase();

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