]*)?>/g, '');
}
export function renderCitationLinks(html, sources, options) {
var opts = options || {};
- return String(html || '').replace(/\[((?:\d+\s*,\s*)*\d+)\]/g, function (match, cluster) {
+ return String(html || '').replace(/<(pre|code|a)\b[^>]*>[\s\S]*?<\/\1>|<[^>]*>|\[((?:\d+\s*,\s*)*\d+)\]/gi, function (match, tag, cluster) {
+ if (!cluster) return match;
var nums = cluster.split(',').map(function (n) { return Number(n.trim()); }).filter(function (n) { return Number.isInteger(n) && n > 0; });
if (!nums.length || nums.some(function (n) { return !sources[n - 1]; })) return match;
return nums.map(function (n) {
@@ -51,7 +66,7 @@ export function renderCitationLinks(html, sources, options) {
var page = source && (source.page || source.page_number || source.pageNumber);
var label = 'Source ' + n + ': ' + title + (page ? ', page ' + page : '');
var text = opts.citationLabel === 'number' ? String(n) : 'src';
- return '' + text + '';
+ return '' + text + '';
}).join(' ');
});
}
@@ -93,9 +108,125 @@ function formatCitationCluster(nums) {
return '[' + nums.join(', ') + ']';
}
-export function normalizeMarkdownText(text) {
- return stripOrphanMarkdownMarkers(normalizeTableSourceCitationCells(String(text || '')
- .replace(/\r\n/g, '\n')
+// Keep Markdown structure and literal syntax out of prose cleanups. The installed
+// parser identifies complete blocks; the no-parser path only shields pipe lines.
+function textProtection(text, kind) {
+ var prefix = '\uE000' + (kind || 'markdown') + ':';
+ while (text.indexOf(prefix) !== -1) prefix += '\uE000';
+ var values = [];
+ var originals = [];
+ var pattern = new RegExp(prefix + '(\\d+)\uE001', 'g');
+ return {
+ hold: function(value, original) {
+ originals.push(typeof original === 'string' ? original : value);
+ return prefix + (values.push(value) - 1) + '\uE001';
+ },
+ restore: function(value, raw) {
+ var previous;
+ do {
+ previous = value;
+ value = value.replace(pattern, function(_, i) { return (raw ? originals : values)[Number(i)]; });
+ } while (value !== previous);
+ return value;
+ }
+ };
+}
+
+function protectBlocks(text, opts, hold, codeOnly) {
+ if (opts.marked && typeof opts.marked.lexer === 'function') {
+ return opts.marked.lexer(text, { gfm: true }).map(function(token) {
+ if (codeOnly) return token.type === 'code' ? hold(token.text, token.lang) + '\n\n' : token.raw;
+ if (['space', 'paragraph', 'heading'].includes(token.type)) return token.raw;
+ return hold(token.type === 'table' ? normalizeTableSourceCitationCells(stripTrailingMarkerLine(token.raw)) :
+ token.type === 'code' || token.type === 'html' ? token.raw : stripTrailingMarkerLine(token.raw)) + '\n\n';
+ }).join('');
+ }
+ if (opts.markdownIt && typeof opts.markdownIt.parse === 'function') {
+ var lines = text.split('\n');
+ var ranges = opts.markdownIt.parse(text, {}).filter(function(token) {
+ return token.map && (codeOnly ? ['fence', 'code_block'] :
+ ['table_open', 'fence', 'code_block', 'html_block', 'blockquote_open', 'bullet_list_open', 'ordered_list_open']).includes(token.type);
+ });
+ var end = 0;
+ ranges.forEach(function(token) {
+ if (token.map[0] < end) return;
+ end = token.map[1];
+ var raw = lines.slice(token.map[0], end).join('\n');
+ lines[token.map[0]] = codeOnly ? hold(token.content, token.info) : hold(token.type === 'table_open' ? normalizeTableSourceCitationCells(stripTrailingMarkerLine(raw)) :
+ ['fence', 'code_block', 'html_block'].includes(token.type) ? raw : stripTrailingMarkerLine(raw));
+ for (var i = token.map[0] + 1; i < end; i++) lines[i] = '';
+ });
+ return lines.join('\n');
+ }
+ text = text.replace(/^ {0,3}(`{3,}|~{3,})([^\n]*)\n([\s\S]*?)(?:^ {0,3}\1[^\n]*(?:\n|$)|(?![\s\S]))/gm, function(raw, fence, lang, code) {
+ return codeOnly ? hold(code, lang.trim()) : hold(raw);
+ });
+ return text.replace(/(?:^(?: {4}|\t)[^\n]*(?:\n|$))+/gm, function(raw) {
+ return codeOnly ? hold(raw.replace(/^(?: {4}|\t)/gm, ''), '') : hold(raw);
+ });
+}
+
+function stripTrailingMarkerLine(text) {
+ return text.replace(/\n[ \t]*(?:\*\*|__|\*|_)[ \t]*\n?$/, '\n');
+}
+
+export function normalizeMarkdownText(text, options) {
+ var opts = options || {};
+ text = String(text || '').replace(/\r\n/g, '\n');
+ var protectedText = textProtection(text);
+ text = protectBlocks(text, opts, protectedText.hold);
+ // These spans must not become headings/lists or apparent legacy row boundaries.
+ text = text.replace(/(`+)[\s\S]*?\1|\$\$[\s\S]*?\$\$|\\\[[\s\S]*?\\\]|\\\([\s\S]*?\\\)|\$[^$\n]+\$|!?\[[^\]\n]*\]\([^\n]*?\)|https?:\/\/[^\s<>]+|\\\|/g, protectedText.hold);
+ text = text.split('\n').map(function(line) {
+ if (!/\|[ \t]*:?-{2,}:?[ \t]*\|/.test(line)) return line;
+ var recovered = recoverLegacyTableLine(line);
+ if (recovered !== null) return recovered;
+ // A standalone delimiter row belongs to existing multiline Markdown.
+ if (/^[ \t]*\|?[ :|\t-]+$/.test(line)) return line;
+ var start = line.indexOf('|');
+ var raw = protectedText.restore(line.slice(start));
+ var literal = typeof opts.onUnrecoverable === 'function' ? opts.onUnrecoverable(raw) : raw;
+ return line.slice(0, start) + '\n\n' + protectedText.hold(literal);
+ }).join('\n');
+ text = protectBlocks(text, opts, protectedText.hold);
+ // Also leave incomplete/non-GFM pipe structures alone, rather than guessing.
+ text = text.replace(/^[^\n]*\|[^\n]*(?:\n[^\n]*\|[^\n]*)*/gm, function(block) {
+ return protectedText.hold(normalizeTableSourceCitationCells(block));
+ });
+ return protectedText.restore(normalizeProse(text));
+}
+
+// Only outer-pipe rows separated by "| |", with a header + alignment row and
+// identical nonempty cell counts, survive whitespace collapse unambiguously.
+// Empty cells, trailing prose, partial rows and mixed separators are not guessed.
+function recoverLegacyTableLine(line) {
+ var start = line.indexOf('|');
+ var prefix = line.slice(0, start);
+ var candidate = line.slice(start).trimEnd();
+ if (start < 0 || !candidate.endsWith('|')) return null;
+ var rows = candidate.split(/(?<=\|)[ \t]+(?=\|)/);
+ if (rows.length < 3) return null;
+ var cells = rows.map(tableCells);
+ if (cells.some(function(row) { return row.length < 2 || row.some(function(cell) { return !cell; }); })) return null;
+ function separator(row) { return row.every(function(cell) { return /^:?-{2,}:?$/.test(cell); }); }
+ var output = [];
+ for (var i = 0; i < rows.length;) {
+ if (!cells[i + 1] || !separator(cells[i + 1]) || cells[i].length !== cells[i + 1].length || separator(cells[i])) return null;
+ var width = cells[i].length;
+ var end = i + 2;
+ while (end < rows.length && !(cells[end + 1] && separator(cells[end + 1]))) {
+ if (cells[end].length !== width || separator(cells[end])) return null;
+ end++;
+ }
+ if (end === i + 2) return null;
+ output.push(rows.slice(i, end).join('\n'));
+ i = end;
+ }
+ return (prefix.trim() ? prefix + '\n\n' : '') + output.join('\n\n');
+}
+
+function normalizeProse(text) {
+ return stripOrphanMarkdownMarkers(String(text || '')
.replace(/([^\n])\n+\s*(\[(?:\d+\s*,\s*)*\d+\])\s*(?:\n+\s*([.,;:]))?(?=\s*(?:\n|$))/g, '$1 $2$3')
.replace(/([.!?])\s*[-–—]\s+(\*\*)?/g, '$1\n- $2')
.replace(/(:)\s*[-–—]\s+(\*\*)?/g, '$1\n- $2')
@@ -104,8 +235,7 @@ export function normalizeMarkdownText(text) {
.replace(/(#{1,4}\s+[^\n]+?)\s+(-\s+)/g, '$1\n\n$2')
.replace(/(#{1,4}\s+[^\n]+)\n(-\s+)/g, '$1\n\n$2')
.replace(/([^\n])\s+(-\s+(?:Mainstay|Medications|Hospitalization|Other therapies|Prevention|Short-acting|Anticholinergics|Systemic|Adjuncts|Long-term|Infants|Differentiating|Persistent|Severe|Need for|Inadequate)\b)/g, '$1\n$2')
- .replace(/([^\n])\s+(-\s+[^\n])/g, '$1\n$2')
- .trim()));
+ .trim());
}
export function normalizeTableSourceCitationCells(text) {
@@ -222,16 +352,19 @@ function renderFallbackTable(lines) {
}
function tableCells(line) {
- return String(line || '').trim().replace(/^\|/, '').replace(/\|$/, '').split('|').map(function(cell) { return cell.trim(); });
+ return String(line || '').trim().replace(/^\|/, '').replace(/\|$/, '').split(/(?' +
'' + escapeHtml(heading) + '
' +
'Question: ' + escapeHtml(item.question || '') + '
' +
- (summary ? 'Summary
' + renderMarkdown(summary, sources, { citationLabel: 'number' }) + '
' : '') +
- 'Full Generated Answer
' + renderMarkdown(answer, sources, { citationLabel: 'number' }) + '
' +
+ (summary ? 'Summary
' + renderMarkdown(summary, sources, renderOptions) + '
' : '') +
+ 'Full Generated Answer
' + answerHtml + '
' +
(refs ? 'References
' + refs + '
' : '') +
'';
}).join('');
@@ -202,10 +205,10 @@ function inlineExportCss() {
}
function exportTableScrollCss() {
- return '.assistant-table-scroll{max-width:100%;overflow-x:auto;overflow-y:hidden;-webkit-overflow-scrolling:touch;margin:12px 0 18px;border:1px solid #e5e7eb;border-radius:10px;background:white}.answer .assistant-table-scroll table,#assistant-export-modal .answer .assistant-table-scroll table{width:max-content;min-width:100%;max-width:none;margin:0;border:0;border-radius:0}.answer .assistant-table-scroll th,.answer .assistant-table-scroll td,#assistant-export-modal .answer .assistant-table-scroll th,#assistant-export-modal .answer .assistant-table-scroll td{min-width:120px;overflow-wrap:normal;word-break:normal}.assistant-table-scroll::after{content:"Swipe table";display:block;position:sticky;left:0;bottom:0;padding:3px 9px;font-size:10px;font-weight:700;color:#6b7280;background:linear-gradient(90deg,rgba(255,255,255,.95),rgba(255,255,255,0));pointer-events:none}@media print{.assistant-table-scroll{overflow:visible;border:0}.assistant-table-scroll::after{display:none}.answer .assistant-table-scroll table,#assistant-export-modal .answer .assistant-table-scroll table{width:100%;max-width:100%}}';
+ return '.answer [align=right],#assistant-export-modal .answer [align=right]{text-align:right}.answer [align=center],#assistant-export-modal .answer [align=center]{text-align:center}.assistant-table-scroll{max-width:100%;overflow-x:auto;overflow-y:hidden;-webkit-overflow-scrolling:touch;margin:12px 0 18px;border:1px solid #e5e7eb;border-radius:10px;background:white}.answer .assistant-table-scroll table,#assistant-export-modal .answer .assistant-table-scroll table{width:max-content;min-width:100%;max-width:none;margin:0;border:0;border-radius:0}.answer .assistant-table-scroll th,.answer .assistant-table-scroll td,#assistant-export-modal .answer .assistant-table-scroll th,#assistant-export-modal .answer .assistant-table-scroll td{min-width:120px;overflow-wrap:normal;word-break:normal}.assistant-table-scroll::after{content:"Swipe table";display:block;position:sticky;left:0;bottom:0;padding:3px 9px;font-size:10px;font-weight:700;color:#6b7280;background:linear-gradient(90deg,rgba(255,255,255,.95),rgba(255,255,255,0));pointer-events:none}@media print{.assistant-table-scroll{overflow:visible;border:0}.assistant-table-scroll::after{display:none}.answer .assistant-table-scroll table,#assistant-export-modal .answer .assistant-table-scroll table{width:100%;max-width:100%}}';
}
-function collectExportItems(messages, lastAnswer, lastSources) {
+function collectExportItems(messages, lastAnswer, lastSources, presentMessage) {
var items = [];
var pendingQuestion = '';
(messages || []).forEach(function (m) {
@@ -215,11 +218,13 @@ function collectExportItems(messages, lastAnswer, lastSources) {
}
if (m.role !== 'assistant' || !m.content) return;
if (isUtilityAssistantMessage(m.content)) return;
+ var display = typeof presentMessage === 'function' ? presentMessage(m) : { answer: m.content };
items.push({
question: pendingQuestion || 'Clinical question',
heading: deriveExportHeading(pendingQuestion, items.length),
summary: '',
- answer: m.content,
+ answer: display.answer,
+ notice: display.notice,
sources: Array.isArray(m.sources) && m.sources.length ? m.sources : lastSources
});
pendingQuestion = '';
@@ -230,31 +235,16 @@ function collectExportItems(messages, lastAnswer, lastSources) {
return items;
}
-function renderExportRefs(sources, sectionNumber, citedNumbers) {
- var cited = citedNumbers && citedNumbers.length ? new Set(citedNumbers.map(String)) : null;
- return (sources || []).filter(function (s, idx) {
- var n = s.number || idx + 1;
- return !cited || cited.has(String(n));
- }).map(function (s, idx) {
+function renderExportRefs(sources, sectionNumber, cited) {
+ return (sources || []).map(function (s, idx) {
var n = s.number || idx + 1;
+ if (cited.length && !cited.includes(String(n))) return '';
var title = s.title || s.resource || 'Untitled source';
var page = s.page || s.page_number || s.pageNumber;
- return '[' + n + '] ' + escapeHtml(title) + (page ? ', page ' + escapeHtml(page) : '') + '.';
+ return '[' + escapeHtml(n) + '] ' + escapeHtml(title) + (page ? ', page ' + escapeHtml(page) : '') + '.';
}).join('');
}
-function extractCitedSourceNumbers(text) {
- var found = new Set();
- String(text || '').replace(/\[(\d+(?:\s*,\s*\d+)*)\]/g, function (_, nums) {
- nums.split(',').forEach(function (n) {
- n = String(n || '').trim();
- if (n) found.add(n);
- });
- return _;
- });
- return Array.from(found).sort(function (a, b) { return Number(a) - Number(b); });
-}
-
function deriveExportHeading(question, idx) {
var text = String(question || '').replace(/\s+/g, ' ').trim();
if (!text || /^(what|which|when|why|how|and|also|what dose\??|dose\??)$/i.test(text)) return 'Clinical Question ' + (idx + 1);
@@ -267,6 +257,6 @@ function isUtilityAssistantMessage(content) {
export function buildExportCacheKey(items, imageSrc) {
return JSON.stringify({ items: (items || []).map(function (item) {
- return { q: item.question, a: item.answer, s: (item.sources || []).map(function (s) { return [s.number, s.title, s.page]; }) };
+ return { q: item.question, a: item.answer, notice: item.notice, s: (item.sources || []).map(function (s) { return [s.number, s.title, s.page]; }) };
}), image: imageSrc ? '1' : '' });
}
diff --git a/public/js/clinicalAssistant.js b/public/js/clinicalAssistant.js
index e3b403d..0386eb0 100644
--- a/public/js/clinicalAssistant.js
+++ b/public/js/clinicalAssistant.js
@@ -33,7 +33,7 @@ import {
var activeAssistantRequest = null;
var conversationChars = null;
var STREAM_MARKDOWN_LIMIT = 3500;
- var exporter = createAssistantExporter({ renderMarkdown: renderMarkdown, showToast: window.showToast });
+ var exporter = createAssistantExporter({ renderMarkdown: renderMarkdown, presentMessage: savedMessagePresentation, showToast: window.showToast });
var imageStore = createAssistantImageStore();
document.addEventListener('tabChanged', function (e) {
@@ -195,20 +195,6 @@ import {
};
}
- async function fetchAssistantResponse(payload, loading) {
- updateLoadingMessage(loading, 'Looking up sources...');
- var data = await fetchAssistantFallback(payload);
- setBusy(false, 'Ready');
- lastAnswer = data.answer || '';
- lastSources = data.sources || [];
- replaceLoadingMessage(loading, lastAnswer, lastSources, data.suggestions || []);
- renderSources(lastSources);
- if (data.model) {
- var label = document.getElementById('assistant-model-label');
- if (label) label.textContent = 'Chat: ' + data.model;
- }
- }
-
async function streamAssistantResponse(payload, loading, request) {
var response = await openAssistantStream(payload, { signal: request ? request.signal : undefined });
if (!response.ok || !response.body) {
@@ -232,6 +218,7 @@ import {
if (!bubble) return;
loading.classList.remove('assistant-loading-msg');
bubble.classList.remove('assistant-thinking');
+ bubble.assistantSources = streamSources;
bubble.innerHTML = partial ? renderStreamingAnswerHtml(partial, streamSources) : 'Generating answer...
';
renderEmbeddedBlocks(bubble);
var wrap = document.getElementById('assistant-messages');
@@ -371,48 +358,28 @@ import {
if (!bubble) return;
row.classList.remove('assistant-loading-msg');
bubble.classList.remove('assistant-thinking');
- bubble.innerHTML = renderAssistantBubbleHtml(content, sources || [], rawHtml);
- if (suggestions && suggestions.length) bubble.appendChild(renderSuggestionButtons(suggestions));
- renderEmbeddedBlocks(bubble);
+ fillMessageBubble(bubble, 'assistant', content, sources, suggestions, rawHtml);
var wrap = document.getElementById('assistant-messages');
if (wrap) wrap.scrollTop = wrap.scrollHeight;
messages.push({ role: 'assistant', content: content, sources: sources || [] });
updateConversationBudget();
}
- function renderAssistantBubbleHtml(content, sources, rawHtml) {
- if (rawHtml) return sanitize(String(content || ''));
- try {
- return renderMarkdown(content, sources || []);
- } catch (e) {
- console.warn('[clinical-assistant] markdown render failed:', e && e.message ? e.message : e);
- return '' + escapeHtml(String(content || '')).replace(/\n/g, '
') + '
';
- }
+ function renderAssistantBubbleHtml(content, sources, rawHtml, options) {
+ return rawHtml ? sanitize(String(content || '')) : renderMarkdown(content, sources || [], options);
+ }
+
+ function fillMessageBubble(bubble, role, content, sources, suggestions, rawHtml, options) {
+ bubble.assistantSources = role === 'assistant' && Array.isArray(sources) ? sources : [];
+ bubble.innerHTML = role === 'assistant' ? renderAssistantBubbleHtml(content, sources, rawHtml, options) : escapeHtml(content);
+ if (role !== 'assistant' && options && options.notice) bubble.innerHTML += '' + escapeHtml(options.notice) + '
';
+ if (role === 'assistant' && suggestions && suggestions.length) bubble.appendChild(renderSuggestionButtons(suggestions));
+ renderEmbeddedBlocks(bubble);
}
function appendMessage(role, content, sources, suggestions, rawHtml) {
- var wrap = document.getElementById('assistant-messages');
- if (!wrap) return;
- var empty = wrap.querySelector('.assistant-empty');
- if (empty) empty.remove();
-
- messages.push({ role: role, content: content, sources: role === 'assistant' ? (sources || []) : [] });
- var row = document.createElement('div');
- row.className = 'assistant-msg ' + role;
- var label = document.createElement('div');
- label.className = 'assistant-msg-label';
- label.textContent = role === 'user' ? 'You' : 'Assistant';
- var bubble = document.createElement('div');
- bubble.className = 'assistant-bubble';
- bubble.innerHTML = rawHtml ? sanitize(String(content || '')) : (role === 'assistant' ? renderMarkdown(content, sources || []) : escapeHtml(content));
- if (role === 'assistant' && suggestions && suggestions.length) {
- bubble.appendChild(renderSuggestionButtons(suggestions));
- }
- row.appendChild(label);
- row.appendChild(bubble);
- wrap.appendChild(row);
- renderEmbeddedBlocks(bubble);
- wrap.scrollTop = wrap.scrollHeight;
+ var row = appendMessageNode(role, content, sources, suggestions, rawHtml);
+ if (row) messages.push({ role: role, content: content, sources: role === 'assistant' ? (sources || []) : [] });
return row;
}
@@ -435,14 +402,22 @@ import {
function renderMarkdown(md, sources, options) {
var opts = options || {};
- return renderAssistantMarkdown(md, sources || [], {
- marked: window.marked,
- markdownIt: getMarkdownRenderer(),
- katex: window.katex,
- mathJax: window.MathJax,
- sanitize: sanitize,
- citationLabel: opts.citationLabel
- });
+ try {
+ return renderAssistantMarkdown(md, sources || [], {
+ marked: window.marked,
+ markdownIt: getMarkdownRenderer(),
+ katex: window.katex,
+ sanitize: sanitize,
+ citationLabel: opts.citationLabel,
+ citationTargetPrefix: opts.citationTargetPrefix,
+ notice: opts.notice
+ });
+ } catch (e) {
+ console.warn('[clinical-assistant] markdown render failed:', e && e.message ? e.message : e);
+ return '' + escapeHtml(String(md || '')) + '
' +
+ 'Formatting unavailable; retained text is shown unchanged.
' +
+ (opts.notice ? '' + escapeHtml(opts.notice) + '
' : '');
+ }
}
function getMarkdownRenderer() {
@@ -569,6 +544,12 @@ import {
}
function onAssistantDocumentClick(e) {
+ var citation = e.target.closest('#assistant-messages .assistant-cite');
+ if (citation) {
+ var bubble = citation.closest('.assistant-bubble');
+ if (bubble && Array.isArray(bubble.assistantSources)) renderSources(bubble.assistantSources);
+ return; // The native anchor navigates to the matching source in the refreshed panel.
+ }
var loadBtn = e.target.closest('[data-assistant-load-chat]');
if (loadBtn) {
e.preventDefault();
@@ -803,15 +784,27 @@ import {
function restoreSavedChat(payload) {
messages = Array.isArray(payload.messages) ? payload.messages.map(function (m) {
- return { role: m.role === 'assistant' ? 'assistant' : 'user', content: String(m.content || ''), sources: Array.isArray(m.sources) ? m.sources : [] };
+ var message = { role: m.role === 'assistant' ? 'assistant' : 'user', content: String(m.content || ''), sources: Array.isArray(m.sources) ? m.sources : [] };
+ if ((payload.version !== 2 || m.legacyClipped === true) && message.content.length === 12000 && !/[\r\n]/.test(message.content)) {
+ message.legacyClipped = true;
+ if (message.role === 'assistant' && isRetainedLegacyAnswer(message.content, m.retainedAnswer)) message.retainedAnswer = m.retainedAnswer;
+ }
+ return message;
}) : [];
lastSources = Array.isArray(payload.sources) ? payload.sources : [];
lastAnswer = String(payload.lastAnswer || lastAssistantMessage(messages) || '');
+ var finalMessage = messages[messages.length - 1];
+ if (finalMessage && finalMessage.role === 'assistant' && finalMessage.legacyClipped &&
+ (!finalMessage.sources.length || JSON.stringify(finalMessage.sources) === JSON.stringify(lastSources)) &&
+ isRetainedLegacyAnswer(finalMessage.content, lastAnswer)) finalMessage.retainedAnswer = lastAnswer;
lastGeneratedImageSrc = String(payload.generatedImage || '');
var wrap = document.getElementById('assistant-messages');
if (wrap) {
wrap.innerHTML = '';
- messages.forEach(function (m) { appendMessageNode(m.role, m.content, m.sources && m.sources.length ? m.sources : lastSources); });
+ messages.forEach(function (m) {
+ var display = savedMessagePresentation(m);
+ appendMessageNode(m.role, display.answer, m.sources && m.sources.length ? m.sources : lastSources, null, false, display);
+ });
wrap.scrollTop = wrap.scrollHeight;
}
renderSources(lastSources);
@@ -823,9 +816,27 @@ import {
updateConversationBudget();
}
- function appendMessageNode(role, content, sources) {
+ function isRetainedLegacyAnswer(content, retained) {
+ return typeof retained === 'string' && retained.length > content.length && retained.length <= 30000 &&
+ !/[\r\n]/.test(retained) && retained.startsWith(content);
+ }
+
+ function savedMessagePresentation(message) {
+ if (!message.legacyClipped) return { answer: message.content, notice: '' };
+ return {
+ answer: message.retainedAnswer || message.content,
+ notice: message.retainedAnswer ?
+ 'Showing the retained lastAnswer that exactly extends this legacy clipped message; the stored transcript is unchanged.' +
+ (message.retainedAnswer.length === 30000 ? ' That retained answer may also have been clipped at 30,000 characters; absent content cannot be recovered.' : '') :
+ 'This legacy message may have been clipped at 12,000 characters. Missing content cannot be recovered from the saved text.'
+ };
+ }
+
+ function appendMessageNode(role, content, sources, suggestions, rawHtml, options) {
var wrap = document.getElementById('assistant-messages');
if (!wrap) return;
+ var empty = wrap.querySelector('.assistant-empty');
+ if (empty) empty.remove();
var row = document.createElement('div');
row.className = 'assistant-msg ' + role;
var label = document.createElement('div');
@@ -833,11 +844,12 @@ import {
label.textContent = role === 'user' ? 'You' : 'Assistant';
var bubble = document.createElement('div');
bubble.className = 'assistant-bubble';
- bubble.innerHTML = role === 'assistant' ? renderMarkdown(content, sources || []) : escapeHtml(content);
row.appendChild(label);
row.appendChild(bubble);
wrap.appendChild(row);
- renderEmbeddedBlocks(bubble);
+ fillMessageBubble(bubble, role, content, sources, suggestions, rawHtml, options);
+ wrap.scrollTop = wrap.scrollHeight;
+ return row;
}
function deriveChatTitle() {
diff --git a/src/utils/clinicalConversation.js b/src/utils/clinicalConversation.js
index 60c4a86..2511d79 100644
--- a/src/utils/clinicalConversation.js
+++ b/src/utils/clinicalConversation.js
@@ -87,7 +87,17 @@ function savedImage(image) {
function savedChatPayload(body) {
const messages = validateMessages(body.messages).map(function(message, index) {
- return { ...message, sources: savedSources(body.messages[index].sources) };
+ const original = body.messages[index];
+ const copy = { ...message, sources: savedSources(original.sources) };
+ // Preserve legacy loss provenance and an existing retained raw field across
+ // a v2 re-save/follow-up; neither is inference history or replacement text.
+ if (original.legacyClipped === true && message.content.length === 12000 && !/[\r\n]/.test(message.content)) {
+ copy.legacyClipped = true;
+ if (message.role === 'assistant' && typeof original.retainedAnswer === 'string' && original.retainedAnswer.length > 12000 &&
+ original.retainedAnswer.length <= 30000 && !/[\r\n]/.test(original.retainedAnswer) &&
+ original.retainedAnswer.startsWith(message.content)) copy.retainedAnswer = original.retainedAnswer;
+ }
+ return copy;
});
if (body.lastAnswer !== undefined && typeof body.lastAnswer !== 'string') {
throw failure('Invalid saved answer.', 400, 'INVALID_SAVED_CHAT');
diff --git a/test/assistant-saved-tables.test.js b/test/assistant-saved-tables.test.js
new file mode 100644
index 0000000..bf9ed8d
--- /dev/null
+++ b/test/assistant-saved-tables.test.js
@@ -0,0 +1,287 @@
+const test = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('node:fs');
+const path = require('node:path');
+const vm = require('node:vm');
+const { JSDOM } = require('jsdom');
+const { marked } = require('marked');
+const MarkdownIt = require('markdown-it');
+const { savedChatPayload } = require('../src/utils/clinicalConversation');
+const read = file => fs.readFileSync(path.join(__dirname, '..', file), 'utf8');
+const sources = [{ title: 'Synthetic A', page: 7 }, { title: 'Synthetic B', page_number: 19 }];
+const table = '| Item | Value (mg/kg) | Notes | Sources |\n| :--- | ---: | :---: | --- |\n| Alpha | 1.25 | A - B | 2 |\n| Beta | 2-4 | unchanged | [1] |';
+const collapse = text => text.replace(/\s+/g, ' ').trim();
+
+function ui(t, parser = marked) {
+ const dom = new JSDOM('' + read('public/components/assistant.html') + '
', { url: 'https://example.test' });
+ const window = dom.window;
+ const style = window.document.createElement('style');
+ style.textContent = read('public/css/assistant.css');
+ window.document.head.appendChild(style);
+ window.marked = parser;
+ window.DOMPurify = require('dompurify')(window);
+ window.matchMedia = () => ({ matches: true });
+ const saves = [];
+ const context = { window, document: window.document, console, URL, Blob, TextDecoder, AbortController,
+ setTimeout() {}, showToast() {}, EMPTY_PROMPT_SETS: [[]],
+ createAssistantImageStore: () => ({ clear() {}, renderGeneratedImage: () => '' }),
+ fetchSavedAssistantChats: async () => ({ success: true, chats: [] }),
+ saveAssistantChat: async body => { saves.push(JSON.parse(JSON.stringify(savedChatPayload(body)))); return { success: true }; }
+ };
+ vm.createContext(context);
+ for (const file of ['assistant/citations.js', 'assistant/sources.js', 'assistant/export.js', 'clinicalAssistant.js']) {
+ vm.runInContext(read('public/js/' + file).replace(/^import[\s\S]*?from ['"][^'"]+['"];\s*/gm, '').replace(/^export /gm, ''), context);
+ }
+ t.after(() => window.close());
+ return { context, document: window.document, saves, window };
+}
+function rows(element) { return [...element.querySelectorAll('tbody tr')].map(row => [...row.cells].map(cell => cell.textContent.trim())); }
+function bubble(app) { return app.document.querySelector('.assistant-msg.assistant .assistant-bubble'); }
+function reopen(app, content, version = 2, lastAnswer = content) {
+ app.context.restoreSavedChat({ version, messages: [{ role: 'user', content: 'Synthetic question' }, { role: 'assistant', content, sources }], sources, lastAnswer });
+}
+
+test('raw v2 actual save/load and SSE/fallback/append/export share all table cells and source pages', async t => {
+ const app = ui(t);
+ const c = app.context;
+ for (const fallback of [false, true]) {
+ c.clearConversation();
+ c.openAssistantStream = async () => new Response(fallback ? '' : 'event: done\ndata: ' + JSON.stringify({ answer: table, sources }) + '\n\n');
+ c.fetchAssistantChat = async () => ({ success: true, answer: table, sources });
+ const loading = c.appendLoadingMessage();
+ await c.streamAssistantResponse({}, loading);
+ assert.deepEqual(rows(bubble(app)), [['Alpha', '1.25', 'A - B', 'src'], ['Beta', '2-4', 'unchanged', 'src']]);
+ assert.match(bubble(app).querySelector('.assistant-cite').title, /Source 2: Synthetic B, page 19/);
+ assert.equal(bubble(app).querySelectorAll('td')[1].getAttribute('align'), 'right');
+ assert.equal(app.window.getComputedStyle(bubble(app).querySelectorAll('td')[1]).textAlign, 'right');
+ assert.equal(bubble(app).querySelector('.assistant-table-scroll').getAttribute('tabindex'), '0');
+ await c.saveCurrentChat();
+ assert.equal(app.saves.at(-1).version, 2);
+ assert.equal(app.saves.at(-1).messages[0].content, table);
+ assert.equal(app.saves.at(-1).lastAnswer, table);
+ c.restoreSavedChat(app.saves.at(-1));
+ assert.equal(rows(bubble(app)).length, 2);
+ c.exportAnswerPdf();
+ const exported = app.document.querySelector('#assistant-export-modal');
+ assert.deepEqual(rows(exported), [['Alpha', '1.25', 'A - B', '2'], ['Beta', '2-4', 'unchanged', '1']]);
+ for (const cite of exported.querySelectorAll('.assistant-cite')) {
+ assert.ok(exported.querySelector(cite.getAttribute('href')), 'export citation resolves to its own reference');
+ }
+ c.clearConversation();
+ c.appendMessage('assistant', table, sources);
+ assert.equal(rows(bubble(app)).length, 2);
+ }
+});
+
+test('legacy collapsed complete tables recover for display only, including multiple tables', async t => {
+ const app = ui(t);
+ const raw = collapse(table + '\n\n' + table.replace(/Alpha/g, 'Gamma').replace(/Beta/g, 'Delta'));
+ reopen(app, raw, 1);
+ assert.equal(bubble(app).querySelectorAll('table').length, 2);
+ assert.deepEqual(rows(bubble(app)).map(row => row[0]), ['Alpha', 'Beta', 'Gamma', 'Delta']);
+ assert.equal(app.context.messages[1].content, raw);
+ await app.context.saveCurrentChat();
+ assert.equal(app.saves[0].messages[1].content, raw);
+ app.context.exportAnswerPdf();
+ assert.equal(app.document.querySelectorAll('#assistant-export-modal table').length, 2);
+});
+
+test('long new tables survive serialization and both installed parsers without losing tail, caption, notes or units', async t => {
+ for (const parser of [marked, null]) {
+ const app = ui(t, parser);
+ if (!parser) app.window.markdownit = MarkdownIt;
+ const long = 'Table 1. Synthetic dose comparison\n\n' + table + '\n' + Array.from({ length: 700 }, (_, n) => '| Row ' + n + ' | 0.25 | A - B, 5-10 mg/kg | [2] |').join('\n') + '\n\nNote: No real clinical data.\n\n† Synthetic footnote.';
+ const saved = JSON.parse(JSON.stringify(savedChatPayload({ messages: [{ role: 'assistant', content: long, sources }], lastAnswer: long, sources })));
+ app.context.restoreSavedChat(saved);
+ assert.equal(rows(bubble(app)).length, 702);
+ assert.equal(rows(bubble(app)).at(-1)[0], 'Row 699');
+ assert.match(bubble(app).textContent, /Table 1\. Synthetic dose comparison/);
+ assert.match(bubble(app).textContent, /† Synthetic footnote\./);
+ assert.equal(saved.messages[0].content, long);
+ }
+});
+
+test('code, math, escaped pipes and URLs cannot become lists or steal source-column cells', t => {
+ const app = ui(t);
+ const special = '| Item | Notes | Sources |\n| --- | --- | --- |\n| Alpha | `A - B [1]` and $x - y$ and \\(a - b\\) | 2 |\n| Beta | a\\|b and [URL](https://example.test/a-b?q=1%7C2) | [1] |';
+ reopen(app, special);
+ assert.equal(rows(bubble(app)).length, 2);
+ assert.equal(rows(bubble(app))[0][1], 'A - B [1] and $x - y$ and \\(a - b\\)');
+ assert.equal(rows(bubble(app))[1][1], 'a|b and URL');
+ assert.equal(rows(bubble(app))[1][2], 'src');
+ assert.equal(bubble(app).querySelector('code .assistant-cite'), null);
+ assert.equal(bubble(app).querySelector('a[href^="https:"]').getAttribute('href'), 'https://example.test/a-b?q=1%7C2');
+ for (const literal of ['`' + collapse(table) + '`', '~~~md\n' + collapse(table) + '\n~~~', ' ' + collapse(table), '$$' + collapse(table) + '$$', '\\[' + collapse(table) + '\\]', 'https://example.test/' + collapse(table).replace(/ /g, '%20')]) {
+ reopen(app, literal, 1);
+ assert.equal(bubble(app).querySelectorAll('table').length, 0, literal);
+ assert.equal(bubble(app).querySelectorAll('li').length, 0, literal);
+ }
+});
+
+test('ambiguous, empty-cell and truncated legacy tables are unchanged and honestly limited', t => {
+ const app = ui(t);
+ for (const raw of [collapse(table).slice(0, -3), '| A | B | | --- | --- | | x | |', '| A | B | | --- | --- | | x | y | extra |']) {
+ reopen(app, raw, 1);
+ assert.equal(bubble(app).querySelectorAll('table').length, 0);
+ assert.ok(bubble(app).textContent.includes(raw));
+ assert.match(bubble(app).textContent, /could not.*recover|cannot.*recover/i);
+ assert.equal(app.context.messages[1].content, raw);
+ }
+ const withLiterals = '| A | B | | --- | --- | | `x - y` and $a - b$ | [URL](https://example.test/) | incomplete';
+ reopen(app, withLiterals, 1);
+ assert.ok(bubble(app).textContent.includes(withLiterals));
+});
+
+test('legacy exact-limit prefix may display only retained lastAnswer, never manufacture missing content', async t => {
+ const app = ui(t);
+ const full = collapse(table + '\n' + Array.from({ length: 450 }, (_, n) => '| Row ' + n + ' | 2 | complete | [1] |').join('\n'));
+ assert.ok(full.length > 12000 && full.length < 30000);
+ const clipped = full.slice(0, 12000);
+ reopen(app, clipped, 1, full);
+ assert.equal(rows(bubble(app)).length, 452);
+ assert.match(bubble(app).textContent, /retained.*lastAnswer/i);
+ assert.equal(app.context.messages[1].content, clipped);
+ await app.context.saveCurrentChat();
+ assert.equal(app.saves[0].messages[1].content, clipped);
+ assert.equal(app.saves[0].lastAnswer, full);
+ app.context.exportAnswerPdf();
+ assert.equal(app.document.querySelectorAll('#assistant-export-modal tbody tr').length, 452);
+ for (const retained of [clipped, 'different ' + full]) {
+ reopen(app, clipped, 1, retained);
+ assert.match(bubble(app).textContent, /clipped|truncat/i);
+ assert.doesNotMatch(bubble(app).textContent, /Row 449/);
+ }
+ reopen(app, clipped, 2, full);
+ assert.doesNotMatch(bubble(app).textContent, /Row 449/, 'v2 does not infer truncation from an ordinary 12,000-character message');
+});
+
+test('all render entrypoints fail closed on missing sanitizer, malicious HTML or parser errors', t => {
+ const app = ui(t);
+ const malicious = table + '\n\n
bad';
+ for (const mode of ['normal', 'no-sanitizer', 'throw']) {
+ if (mode === 'no-sanitizer') delete app.window.DOMPurify;
+ if (mode === 'throw') app.window.marked = { lexer: marked.lexer, parse() { throw new Error('Synthetic parser failure'); } };
+ reopen(app, malicious);
+ app.context.exportAnswerPdf();
+ assert.equal(app.document.querySelector('script, [onerror], a[href^="javascript:"]'), null);
+ assert.ok(bubble(app).textContent.includes('Alpha'));
+ assert.ok(app.document.querySelector('#assistant-export-modal').textContent.includes('Beta'));
+ }
+});
+
+test('legacy recovery refuses missing boundaries; supports independent lines and literal syntax inside complete rows', t => {
+ const app = ui(t);
+ const escaped = '| Name | Notes | Source |\n| :--- | ---: | --- |\n| A | a\\|b and `x\\|y` and $x - y$ | 2 |\n| B | https://example.test/a?b=1%7C2 | 1 |';
+ reopen(app, collapse(escaped), 1);
+ assert.equal(rows(bubble(app)).length, 2);
+ assert.equal(rows(bubble(app))[0][1], 'a|b and x|y and $x - y$');
+ assert.equal(rows(bubble(app))[0][2], 'src');
+ reopen(app, collapse(table) + '\n\nCaption two\n\n' + collapse(table), 1);
+ assert.equal(bubble(app).querySelectorAll('table').length, 2);
+ for (const raw of ['| A | B | --- | --- | x | y |', '| A | B | | --- | --- | | x | y', '| A | B | | --- | --- | | x | y | trailing prose']) {
+ reopen(app, raw, 1);
+ assert.equal(bubble(app).querySelectorAll('table').length, 0);
+ assert.ok(bubble(app).textContent.includes(raw));
+ assert.match(bubble(app).textContent, /could not safely recover/i);
+ }
+});
+
+test('math/code literals and sentinel-shaped input survive postprocessing without citation or HTML interpretation', t => {
+ const app = ui(t);
+ const expressions = [];
+ app.window.katex = { renderToString(expression) { expressions.push(expression); return '' + expression.replace(/&/g, '&').replace(/'; } };
+ const raw = '| Item | Value | Sources |\n| --- | --- | --- |\n| Alpha | `a\\|b [2][1] $notmath$` and $x \\mid y [1]$ | 2 |\n| Beta | \\(a - b\\) | 1 |';
+ reopen(app, raw);
+ assert.equal(rows(bubble(app)).length, 2);
+ assert.equal(bubble(app).querySelector('code').textContent, 'a|b [2][1] $notmath$');
+ assert.equal(bubble(app).querySelector('code .katex, .katex .assistant-cite'), null);
+ assert.deepEqual(expressions, ['x \\mid y [1]', 'a - b']);
+ assert.equal(rows(bubble(app))[1][2], 'src');
+ for (const raw of ['$$\n' + table + '\n$$', '~~~md\n' + table + '\n[1][2] $code$\n~~~', '\uE000html:0\uE001 and `\uE000markdown:0\uE001 [2][1]`']) {
+ reopen(app, raw);
+ assert.equal(bubble(app).querySelectorAll('table, .assistant-cite').length, 0);
+ }
+ reopen(app, '[URL](https://example.test/[1][2]) and A - B and 5-10 mg/kg');
+ assert.equal(decodeURIComponent(bubble(app).querySelector('a').getAttribute('href')), 'https://example.test/[1][2]');
+ assert.match(bubble(app).textContent, /A - B and 5-10 mg\/kg/);
+ reopen(app, '[URL](https://example.test/$notmath$)');
+ assert.equal(bubble(app).querySelector('a').getAttribute('href'), 'https://example.test/$notmath$');
+ assert.ok(!expressions.includes('notmath'));
+});
+
+test('legacy loss provenance and retained raw extension survive v2 re-save and follow-up with strict guards', async t => {
+ const app = ui(t);
+ const full = collapse(table + '\n' + Array.from({ length: 450 }, (_, n) => '| Row ' + n + ' | 2 | retained | [1] |').join('\n'));
+ const clipped = full.slice(0, 12000);
+ reopen(app, clipped, 1, full);
+ app.context.appendMessage('user', 'Follow-up');
+ app.context.appendMessage('assistant', 'New answer', sources);
+ app.context.lastAnswer = 'New answer';
+ await app.context.saveCurrentChat();
+ const saved = app.saves[0];
+ assert.equal(saved.version, 2);
+ assert.equal(saved.messages[1].content, clipped);
+ assert.equal(saved.messages[1].retainedAnswer, full);
+ assert.equal(saved.messages[1].legacyClipped, true);
+ app.context.restoreSavedChat(saved);
+ assert.equal(rows(bubble(app)).length, 452);
+ assert.equal(app.context.messages[1].content, clipped);
+ assert.equal(app.context.conversationSize(''), saved.messages.reduce((n, m) => n + m.content.length, 0), 'display-only extension is not silently sent as inference history');
+ for (const extension of [clipped, 'not a prefix ' + full, full + 'x'.repeat(30000), full + '\n', undefined]) {
+ const result = savedChatPayload({ messages: [{ role: 'assistant', content: clipped, legacyClipped: true, retainedAnswer: extension }] });
+ assert.equal(result.messages[0].retainedAnswer, undefined);
+ assert.equal(result.messages[0].content, clipped);
+ }
+ const differentSources = { version: 1, messages: [{ role: 'assistant', content: clipped, sources: [{ title: 'Other', page: 99 }] }], sources, lastAnswer: full };
+ app.context.restoreSavedChat(differentSources);
+ assert.doesNotMatch(bubble(app).textContent, /Row 449/);
+ reopen(app, clipped, 1, clipped + 'x'.repeat(30000 - clipped.length));
+ assert.match(bubble(app).textContent, /30,000 characters.*absent content cannot be recovered/);
+});
+
+test('parser-unavailable literals stay inert, and embedded chart initialization retains an attached bubble', t => {
+ const app = ui(t, null);
+ for (const raw of [' ' + collapse(table), '~~~md\n' + table + '\n~~~', '$$' + table + '$$']) {
+ reopen(app, raw, 1);
+ assert.equal(bubble(app).querySelectorAll('table, .assistant-cite').length, 0);
+ assert.match(bubble(app).textContent, /Alpha/);
+ }
+ let rendered = 0;
+ app.window.HTMLCanvasElement.prototype.getContext = function() {
+ assert.equal(this.isConnected, true);
+ return { canvas: this };
+ };
+ app.window.Chart = function(context, config) {
+ assert.equal(context.canvas.isConnected, true);
+ assert.equal(config.type, 'bar');
+ rendered++;
+ };
+ app.context.appendMessage('assistant', '```chart\n{"type":"bar","data":{"labels":["[1]"],"datasets":[]}}\n```');
+ assert.equal(rendered, 1);
+});
+
+test('clicking reused citation numbers selects the original turn source without changing saved history', async t => {
+ const app = ui(t);
+ const first = [{ number: 1, title: 'First turn reference', page: 11, excerpt: 'First turn context.' }];
+ const second = [{ number: 1, title: 'Second turn reference', page: 23, excerpt: 'Second turn context.' }];
+ app.context.restoreSavedChat({ version: 2, messages: [
+ { role: 'user', content: 'First question' },
+ { role: 'assistant', content: 'First answer. [1]', sources: first },
+ { role: 'user', content: 'Second question' },
+ { role: 'assistant', content: 'Second answer. [1]', sources: second }
+ ], lastAnswer: 'Second answer. [1]', sources: second });
+ app.document.addEventListener('click', app.context.onAssistantDocumentClick);
+ const citations = app.document.querySelectorAll('#assistant-messages .assistant-cite');
+ assert.equal(citations.length, 2);
+ citations[0].click();
+ assert.match(app.document.querySelector('#assistant-source-1').textContent, /First turn reference.*page 11/is);
+ assert.doesNotMatch(app.document.querySelector('#assistant-source-1').textContent, /Second turn reference/);
+ citations[1].click();
+ assert.match(app.document.querySelector('#assistant-source-1').textContent, /Second turn reference.*page 23/is);
+ citations[0].click();
+ await app.context.saveCurrentChat();
+ assert.deepEqual(app.saves[0].messages[1].sources, first);
+ assert.deepEqual(app.saves[0].messages[3].sources, second);
+ assert.deepEqual(app.saves[0].sources, second, 'viewing an older source does not replace the latest retrieval map');
+ assert.equal(app.saves[0].messages[1].content, 'First answer. [1]');
+});
diff --git a/test/clinical-release-integration.test.js b/test/clinical-release-integration.test.js
index 065d30a..f97c4da 100644
--- a/test/clinical-release-integration.test.js
+++ b/test/clinical-release-integration.test.js
@@ -97,7 +97,9 @@ test('native admin and assistant modules retain budget, table/source identity an
assert.equal(element.querySelector('script, [onerror], [onload], a[href^="javascript:"]'), null);
if (purified) {
assert.equal(element.querySelectorAll('.assistant-table-scroll table tbody tr').length, 1);
- assert.equal(element.querySelector('.assistant-cite').getAttribute('href'), '#assistant-source-1');
+ const target = element.id === 'assistant-export-modal' ? '#ref-1-1' : '#assistant-source-1';
+ assert.equal(element.querySelector('.assistant-cite').getAttribute('href'), target);
+ assert.ok(document.querySelector(target), 'citation target exists in the displayed chat/export');
assert.match(element.querySelector('td').textContent, /Synthetic/);
} else {
assert.equal(element.querySelector('table, a, img, svg'), null, 'fallback is escaped text, not raw HTML');