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1486 lines (1382 loc) · 60.9 KB
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Publications – Cyril Pernet</title>
<style>
/* ── Base ─────────────────────────────────────────────── */
*, *::before, *::after { box-sizing: border-box; }
body {
margin: 0;
font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto,
"Helvetica Neue", Arial, sans-serif;
font-size: 1rem;
line-height: 1.65;
color: #222;
background: #fff;
}
a { color: #2b6cb0; }
h1 { margin: 0 0 0.25rem; font-size: 1.9rem; letter-spacing: -0.03em; }
/* ── Layout ───────────────────────────────────────────── */
.container { max-width: 1100px; margin: 0 auto; padding: 0 1.5rem; }
header.page-header {
border-bottom: 1px solid #e8e8e8;
padding: 1.5rem 0 1rem;
margin-bottom: 1.5rem;
}
header.page-header p { color: #555; margin: 0.25rem 0 0; font-size: 0.92rem; }
/* ── Search / controls bar ────────────────────────────── */
.controls {
display: flex;
flex-wrap: wrap;
gap: 0.6rem 1rem;
align-items: center;
margin-bottom: 1.25rem;
}
.controls label { font-size: 0.85rem; color: #555; }
.controls input[type="text"] {
padding: 0.35rem 0.65rem;
border: 1px solid #ccc;
border-radius: 4px;
font-size: 0.9rem;
min-width: 180px;
}
.controls select {
padding: 0.35rem 0.55rem;
border: 1px solid #ccc;
border-radius: 4px;
font-size: 0.9rem;
background: #fff;
}
.btn {
padding: 0.38rem 0.9rem;
border: none;
border-radius: 4px;
font-size: 0.88rem;
cursor: pointer;
transition: background 0.15s;
}
.btn-primary { background: #2b6cb0; color: #fff; }
.btn-primary:hover { background: #2558a3; }
.btn-secondary { background: #e2e8f0; color: #2d3748; }
.btn-secondary:hover { background: #cbd5e0; }
.btn-danger { background: #fc8181; color: #fff; font-size: 0.8rem; padding: 0.2rem 0.55rem; }
.btn-danger:hover { background: #f56565; }
.btn-edit { background: #f6e05e; color: #2d3748; font-size: 0.8rem; padding: 0.2rem 0.55rem; }
.btn-edit:hover { background: #ecc94b; }
/* ── Status / loader ──────────────────────────────────── */
#status {
font-size: 0.9rem; color: #555; margin-bottom: 0.75rem;
min-height: 1.4rem;
}
.spinner {
display: inline-block; width: 14px; height: 14px;
border: 2px solid #ccc; border-top-color: #2b6cb0;
border-radius: 50%; animation: spin 0.7s linear infinite;
vertical-align: middle; margin-right: 6px;
}
@keyframes spin { to { transform: rotate(360deg); } }
/* ── Stats strip ──────────────────────────────────────── */
#stats-bar {
display: flex; flex-wrap: wrap; gap: 1rem;
margin-bottom: 1rem; font-size: 0.88rem; color: #4a5568;
}
#stats-bar span strong { color: #1a202c; }
/* ── Filter chips ─────────────────────────────────────── */
.filter-chips { display: flex; flex-wrap: wrap; gap: 0.4rem; margin-bottom: 1rem; }
.chip {
padding: 0.2rem 0.65rem; border-radius: 99px; font-size: 0.8rem;
cursor: pointer; border: 1px solid #ccc; background: #f7fafc; color: #2d3748;
transition: background 0.12s, border-color 0.12s;
}
.chip.active { background: #2b6cb0; color: #fff; border-color: #2b6cb0; }
.chip:hover:not(.active) { background: #ebf4ff; border-color: #90cdf4; }
/* ── Table ────────────────────────────────────────────── */
.table-wrap { overflow-x: auto; }
table {
width: 100%;
border-collapse: collapse;
font-size: 0.88rem;
}
thead th {
background: #f7fafc;
border-bottom: 2px solid #e2e8f0;
padding: 0.55rem 0.65rem;
text-align: left;
font-weight: 600;
white-space: nowrap;
cursor: pointer;
user-select: none;
}
thead th:hover { background: #ebf4ff; }
thead th .sort-icon { font-size: 0.7rem; margin-left: 3px; opacity: 0.5; }
thead th.sorted .sort-icon { opacity: 1; color: #2b6cb0; }
tbody tr { border-bottom: 1px solid #edf2f7; }
tbody tr:hover { background: #f7fafc; }
tbody td { padding: 0.5rem 0.65rem; vertical-align: top; }
.td-num { width: 2.5rem; text-align: center; color: #718096; }
.td-topic { width: 7rem; }
.td-year { width: 3.5rem; text-align: center; }
.td-title { min-width: 220px; }
.td-journal { min-width: 120px; color: #4a5568; }
.td-authors { min-width: 150px; }
.td-actions { width: 6rem; white-space: nowrap; }
.topic-badge {
display: inline-block; padding: 0.1rem 0.5rem; border-radius: 99px;
font-size: 0.75rem; font-weight: 600; text-transform: uppercase;
letter-spacing: 0.04em;
cursor: pointer;
}
.topic-badge:hover { opacity: 0.78; }
/* inline topic picker shown when badge is clicked */
.topic-picker {
font-size: 0.82rem; border: 1px solid #90cdf4; border-radius: 4px;
padding: 0.15rem 0.3rem; background: #fff; cursor: pointer;
outline: none;
}
.topic-method { background: #7fc97f; color: #1a4731; }
.topic-stats { background: #beaed4; color: #44337a; }
.topic-data { background: #fdc086; color: #7b341e; }
.topic-clinical { background: #ffff99; color: #744210; }
.topic-cog-neuro { background: #386cb0; color: #fff; }
.topic-book { background: #f0027f; color: #fff; }
.topic-other { background: #bf5b17; color: #fff; }
/* ── Export dropdown ─────────────────────────────────── */
.export-wrap { position: relative; align-self: flex-end; }
.export-menu {
display: none; position: absolute; top: calc(100% + 4px); left: 0;
background: #fff; border: 1px solid #e2e8f0; border-radius: 6px;
box-shadow: 0 8px 24px rgba(0,0,0,0.12); z-index: 50;
min-width: 170px; overflow: hidden;
}
.export-menu.open { display: block; }
.export-menu button {
display: block; width: 100%; text-align: left;
padding: 0.5rem 1rem; border: none; background: none;
font-size: 0.88rem; cursor: pointer; color: #2d3748;
}
.export-menu button:hover { background: #ebf4ff; }
.export-menu hr { margin: 0.25rem 0; border: none; border-top: 1px solid #e2e8f0; }
/* ── Print / PDF styles ──────────────────────────────── */
@media print {
.controls, .filter-chips, #status, #stats-bar,
.td-actions, header.page-header p, footer { display: none !important; }
body { font-size: 10pt; color: #000; }
h1 { font-size: 16pt; margin-bottom: 0.5rem; }
table { font-size: 9pt; border-collapse: collapse; width: 100%; }
thead th { background: #f0f0f0 !important; border-bottom: 1.5pt solid #000; }
tbody tr { border-bottom: 0.5pt solid #ccc; }
tbody td { padding: 3pt 5pt; }
.topic-badge { border: 0.5pt solid #888; background: none !important;
color: #000 !important; padding: 0 3pt; }
a { color: #000; text-decoration: none; }
}
/* ── Add / edit modal ─────────────────────────────────── */
.modal-overlay {
display: none; position: fixed; inset: 0;
background: rgba(0,0,0,0.45); z-index: 100;
align-items: center; justify-content: center;
}
.modal-overlay.open { display: flex; }
.modal {
background: #fff; border-radius: 8px; padding: 1.5rem;
width: min(95vw, 580px); max-height: 90vh; overflow-y: auto;
box-shadow: 0 20px 60px rgba(0,0,0,0.2);
}
.modal h2 { margin: 0 0 1rem; font-size: 1.15rem; }
.form-grid {
display: grid; grid-template-columns: 1fr 1fr; gap: 0.75rem 1rem;
}
.form-grid .full { grid-column: 1 / -1; }
.form-group { display: flex; flex-direction: column; gap: 0.25rem; }
.form-group label { font-size: 0.82rem; font-weight: 600; color: #4a5568; }
.form-group input, .form-group select, .form-group textarea {
padding: 0.38rem 0.6rem; border: 1px solid #cbd5e0;
border-radius: 4px; font-size: 0.9rem; font-family: inherit;
}
.form-group textarea { resize: vertical; min-height: 60px; }
.modal-actions { display: flex; gap: 0.5rem; justify-content: flex-end; margin-top: 1rem; }
/* ── Footer ───────────────────────────────────────────── */
footer {
margin-top: 3rem; padding: 1rem 0;
border-top: 1px solid #e8e8e8;
font-size: 0.82rem; color: #718096; text-align: center;
}
</style>
</head>
<body>
<div class="container">
<header class="page-header">
<h1>Publications</h1>
<p>
Load your saved list, then fetch updates from <strong>PubMed</strong> and <strong>Semantic Scholar</strong>.
You can filter, sort, and manually add, edit, or remove entries.
After editing, <strong>Export → JSON</strong> and place <code>publications.json</code> next to this page — it will be loaded automatically on the next visit.
</p>
</header>
<!-- ── Author search ──────────────────────────────────── -->
<div class="controls">
<div>
<label for="author-input">Author name</label><br>
<input type="text" id="author-input" value="Cyril Pernet" placeholder="First Last" />
</div>
<button class="btn btn-primary" id="fetch-btn" style="align-self:flex-end">Fetch publications</button>
<button class="btn btn-secondary" id="add-btn" style="align-self:flex-end">＋ Add manually</button>
<div class="export-wrap">
<button class="btn btn-secondary" id="export-toggle" style="align-self:flex-end">⬇ Export ▾</button>
<div class="export-menu" id="export-menu">
<button data-fmt="apa">APA (.txt)</button>
<button data-fmt="bibtex">BibTeX (.bib)</button>
<button data-fmt="ris">RIS (.ris)</button>
<hr>
<button data-fmt="csv">CSV (.csv)</button>
<button data-fmt="json">JSON (.json)</button>
<hr>
<button data-fmt="pdf">Print / Save as PDF</button>
</div>
</div>
<button class="btn btn-secondary" id="import-btn" style="align-self:flex-end">⬆ Import JSON</button>
<input type="file" id="import-file" accept=".json" style="display:none" />
</div>
<!-- ── Sort controls ──────────────────────────────────── -->
<div class="controls">
<label>Sort by:</label>
<select id="sort-col">
<option value="year">Year</option>
<option value="topic">Topic</option>
<option value="firstAuthor">First author</option>
<option value="lastAuthor">Last author</option>
<option value="title">Title</option>
</select>
<select id="sort-dir">
<option value="desc">Descending</option>
<option value="asc">Ascending</option>
</select>
<button class="btn btn-secondary" id="sort-btn">Apply sort</button>
</div>
<!-- ── Topic filter chips ─────────────────────────────── -->
<div class="filter-chips" id="topic-chips">
<span class="chip active" data-topic="all">All</span>
<!-- chips are populated dynamically from TOPICS config -->
</div>
<!-- ── Status line ────────────────────────────────────── -->
<div id="status"></div>
<!-- ── Stats ──────────────────────────────────────────── -->
<div id="stats-bar"></div>
<!-- ── Table ──────────────────────────────────────────── -->
<div class="table-wrap">
<table id="pub-table">
<thead>
<tr>
<th class="td-num" data-col="num" title="Click to sort">#<span class="sort-icon">↕</span></th>
<th class="td-topic" data-col="topic" title="Click to sort">Topic<span class="sort-icon">↕</span></th>
<th class="td-authors" data-col="firstAuthor" title="Click to sort">Authors<span class="sort-icon">↕</span></th>
<th class="td-year" data-col="year" title="Click to sort">Year<span class="sort-icon">↕</span></th>
<th class="td-title" data-col="title" title="Click to sort">Title<span class="sort-icon">↕</span></th>
<th class="td-journal" data-col="journal" title="Click to sort">Journal<span class="sort-icon">↕</span></th>
<th class="td-actions">Actions</th>
</tr>
</thead>
<tbody id="pub-tbody"></tbody>
</table>
</div>
</div><!-- /container -->
<!-- ── Add / Edit modal ───────────────────────────────── -->
<div class="modal-overlay" id="modal-overlay" role="dialog" aria-modal="true" aria-labelledby="modal-title">
<div class="modal">
<h2 id="modal-title">Add publication</h2>
<div class="form-grid">
<div class="form-group full">
<label for="m-title">Title *</label>
<textarea id="m-title" rows="2"></textarea>
</div>
<div class="form-group full">
<label for="m-authors">Authors (comma-separated, Last FM format)</label>
<input type="text" id="m-authors" placeholder="Pernet C, Smith A, …" />
</div>
<div class="form-group">
<label for="m-year">Year *</label>
<input type="text" id="m-year" placeholder="2024" />
</div>
<div class="form-group">
<label for="m-journal">Journal</label>
<input type="text" id="m-journal" />
</div>
<div class="form-group">
<label for="m-volume">Volume</label>
<input type="text" id="m-volume" placeholder="12" />
</div>
<div class="form-group">
<label for="m-issue">Issue</label>
<input type="text" id="m-issue" placeholder="3" />
</div>
<div class="form-group">
<label for="m-pages">Pages</label>
<input type="text" id="m-pages" placeholder="45-67" />
</div>
<div class="form-group">
<label for="m-topic">Topic *</label>
<select id="m-topic"><!-- populated from TOPICS --></select>
</div>
<div class="form-group">
<label for="m-doi">DOI / URL</label>
<input type="text" id="m-doi" placeholder="10.xxxx/…" />
</div>
<div class="form-group">
<label for="m-pmid">PubMed ID</label>
<input type="text" id="m-pmid" />
</div>
<div class="form-group">
<label for="m-source">Source</label>
<input type="text" id="m-source" value="manual" />
</div>
</div>
<div class="modal-actions">
<button class="btn btn-secondary" id="modal-cancel">Cancel</button>
<button class="btn btn-primary" id="modal-save">Save</button>
</div>
</div>
</div>
<div class="modal-overlay" id="review-overlay" role="dialog" aria-modal="true" aria-labelledby="review-title">
<div class="modal" style="width:min(95vw,900px)">
<h2 id="review-title">Review fetched changes</h2>
<p id="review-summary"></p>
<p>New publications and empty-field additions are selected by default. Conflicting values stay unchanged unless selected. Topics and manual records are preserved.</p>
<div id="review-items"></div>
<div class="modal-actions">
<button class="btn btn-secondary" id="review-cancel">Discard fetched changes</button>
<button class="btn btn-primary" id="review-apply">Apply selected changes</button>
</div>
</div>
</div>
<footer>
<div class="container">
Publications fetched live from PubMed E-utilities & Semantic Scholar APIs.
Last fetch: <span id="last-fetch">—</span>
</div>
</footer>
<script>
/* ════════════════════════════════════════════════════════════════
██ USER-EDITABLE CONFIGURATION — safe to change these values ██
════════════════════════════════════════════════════════════════
TOPICS
──────
Each entry: { id, label, keywords }
• id : used internally and as a CSS class suffix (no spaces).
• label : displayed in the UI.
• keywords: array of lowercase strings used to auto-classify a
publication by matching against its title/journal.
Add / remove words freely.
The FIRST topic whose keywords match wins; "other"
is the fallback.
Order matters — put the most specific topics first.
AUTHOR_VARIANTS
───────────────
All name forms PubMed might return for the target author.
Used to detect 1st-author and last-author status.
PUBMED_RETMAX
─────────────
Maximum number of PubMed records to fetch (hard cap: 9999).
*/
const CONFIG = {
TOPICS: [
{
id: "method",
label: "Method",
keywords: [
"artifact", "preprocessing", "pipeline", "toolbox", "standards",
"software", "algorithm", "open source", "reliability", "bids"
]
},
{
id: "stats",
label: "Stats",
keywords: [
"statistic", "statistical", "glm", "effect size",
"false discovery", "correction", "power", "cluster",
"robust", "univariate", "multivariate"
]
},
{
id: "data",
label: "Data",
keywords: [
"dataset", "data", "database", "repository", "open data"
]
},
{
id: "clinical",
label: "Clinical",
keywords: [
"patient", "disorder", "disease", "clinical", "schizophrenia",
"depression", "bipolar", "epilepsy", "autism", "adhd",
"stroke", "dementia", "alzheimer", "therapy", "treatment",
"diagnosis"
]
},
{
id: "cog-neuro",
label: "Cog Neuro",
keywords: [
"cognitive", "perception", "attention", "memory", "language",
"face", "emotion", "decision", "learning", "working memory",
"executive", "motor", "sensory", "cortex", "brain", "neural",
"neuroscience", "connectivity"
]
},
{
id: "book",
label: "Book",
keywords: [
"book", "chapter", "editor", "publisher"
]
}
/* ── ADD MORE TOPICS HERE following the same structure ── */
],
AUTHOR_VARIANTS: [
"Pernet C",
"Pernet CR",
"Pernet Cyril"
],
PUBMED_RETMAX: 500
}; /* ── END OF USER-EDITABLE CONFIG ── */
/* ════════════════════════════════════════════════════════════════
Application code — edit with care
════════════════════════════════════════════════════════════════ */
// ── State ──────────────────────────────────────────────────────
let publications = []; // master array
let filtered = []; // currently visible (after topic filter)
let sortState = { col: "year", dir: "desc" };
let activeFilter = "all";
let editingId = null; // null = new entry, string = existing id
let tombstones = new Set(); // normalised titles the user deleted
let cachedAuthor = ""; // author name currently in cache
let pendingReview = null;
let fetching = false;
let initializing = true;
// ── localStorage helpers ─────────────────────────────────────────
function storageKey(name) {
return "pubs_v1_" + name.toLowerCase().replace(/\s+/g, "_");
}
function tombstoneKey(name) {
return "pubs_tombs_v1_" + name.toLowerCase().replace(/\s+/g, "_");
}
function normTitle(t) {
return String(t).toLowerCase().replace(/[^a-z0-9]/g, "").slice(0, 60);
}
/** Persist current list + tombstones to localStorage for `name`. */
function saveToCache(name) {
if (!name) return;
try {
localStorage.setItem(storageKey(name), JSON.stringify(publications));
localStorage.setItem(tombstoneKey(name), JSON.stringify([...tombstones]));
localStorage.setItem(storageKey(name) + "_fetchdate",
document.getElementById("last-fetch").textContent);
} catch(e) { /* storage full – silently skip */ }
}
/** Load list + tombstones from localStorage for `name`. Returns true if found. */
function loadFromCache(name) {
if (!name) return false;
try {
const raw = localStorage.getItem(storageKey(name));
if (!raw) return false;
const tombs = localStorage.getItem(tombstoneKey(name));
const fd = localStorage.getItem(storageKey(name) + "_fetchdate");
return applyImportedData({ author: name, publications: JSON.parse(raw),
tombstones: tombs ? JSON.parse(tombs) : [], lastFetch: fd || '—' });
} catch(e) { return false; }
}
/**
* Commit all mutations: save to cache then re-render.
* Call this instead of bare applyFilterAndRender() after any change.
*/
function commitAndRender() {
saveToCache(cachedAuthor || document.getElementById("author-input").value.trim());
applyFilterAndRender();
}
// ── Helpers ────────────────────────────────────────────────────
function uid() {
return Math.random().toString(36).slice(2) + Date.now().toString(36);
}
function setStatus(html) {
document.getElementById("status").innerHTML = html;
}
function classifyTopic(title = "", journal = "") {
const haystack = (title + " " + journal).toLowerCase();
for (const t of CONFIG.TOPICS) {
if (t.keywords.some(kw => haystack.includes(kw))) return t.id;
}
return "other";
}
function parseAuthors(authorStr = "") {
// handles "A B, C D" or array of objects from APIs
if (Array.isArray(authorStr)) {
return authorStr.map(a => a.name || a.authname || "").filter(Boolean);
}
return authorStr.split(/[;,]/).map(s => s.trim()).filter(Boolean);
}
function isTargetAuthor(name) {
const n = name.toLowerCase().replace(/\s+/g, " ");
return CONFIG.AUTHOR_VARIANTS.some(v => {
const vl = v.toLowerCase().replace(/\s+/g, " ");
return n === vl || n.startsWith(vl.split(" ")[0]) && n.includes(vl.split(" ")[1] || "");
});
}
function computeAuthorFlags(authors) {
const isFirst = authors.length > 0 && isTargetAuthor(authors[0]);
const isLast = authors.length > 0 && isTargetAuthor(authors[authors.length - 1]);
return { isFirst, isLast };
}
function topicBadge(pubId, topicId) {
const topic = CONFIG.TOPICS.find(t => t.id === topicId);
const label = topic ? topic.label : "Other";
const cls = topic ? `topic-${topicId}` : "topic-other";
// title attribute hints the user they can click to change topic
return `<span class="topic-badge ${cls}" data-pubid="${pubId}" title="Click to change topic">${label}</span>`;
}
function formatAuthors(authors) {
if (!authors || authors.length === 0) return "—";
if (authors.length <= 4) return authors.join(", ");
return authors.slice(0, 3).join(", ") + " … " + authors[authors.length - 1];
}
// ── Build topic chips ──────────────────────────────────────────
function buildChips() {
const container = document.getElementById("topic-chips");
container.innerHTML = `<span class="chip active" data-topic="all">All</span>`;
for (const t of CONFIG.TOPICS) {
const chip = document.createElement("span");
chip.className = "chip";
chip.dataset.topic = t.id;
chip.textContent = t.label;
container.appendChild(chip);
}
// "Other" chip
const other = document.createElement("span");
other.className = "chip";
other.dataset.topic = "other";
other.textContent = "Other";
container.appendChild(other);
container.addEventListener("click", e => {
if (!e.target.classList.contains("chip")) return;
container.querySelectorAll(".chip").forEach(c => c.classList.remove("active"));
e.target.classList.add("active");
activeFilter = e.target.dataset.topic;
applyFilterAndRender();
});
}
// ── Populate modal topic select ────────────────────────────────
function buildTopicSelect() {
const sel = document.getElementById("m-topic");
sel.innerHTML = "";
for (const t of CONFIG.TOPICS) {
const opt = document.createElement("option");
opt.value = t.id;
opt.textContent = t.label;
sel.appendChild(opt);
}
const other = document.createElement("option");
other.value = "other";
other.textContent = "Other";
sel.appendChild(other);
}
// ── Stats bar ──────────────────────────────────────────────────
function updateStats() {
const bar = document.getElementById("stats-bar");
const total = publications.length;
const first = publications.filter(p => p.isFirst).length;
const last = publications.filter(p => p.isLast).length;
const topicCounts = {};
for (const p of publications) {
topicCounts[p.topic] = (topicCounts[p.topic] || 0) + 1;
}
let html = `<span>Total: <strong>${total}</strong></span>
<span>1st author: <strong>${first}</strong></span>
<span>Last author: <strong>${last}</strong></span>`;
for (const t of CONFIG.TOPICS) {
if (topicCounts[t.id]) {
html += `<span>${t.label}: <strong>${topicCounts[t.id]}</strong></span>`;
}
}
bar.innerHTML = html;
}
// ── Render table ───────────────────────────────────────────────
function applyFilterAndRender() {
filtered = activeFilter === "all"
? [...publications]
: publications.filter(p => p.topic === activeFilter);
// apply sort
const col = sortState.col;
const dir = sortState.dir === "asc" ? 1 : -1;
filtered.sort((a, b) => {
let va = a[col] || "", vb = b[col] || "";
if (col === "year") { va = parseInt(va) || 0; vb = parseInt(vb) || 0; }
else { va = String(va).toLowerCase(); vb = String(vb).toLowerCase(); }
return va < vb ? -dir : va > vb ? dir : 0;
});
renderTable();
updateStats();
updateSortHeaders();
}
function renderTable() {
const tbody = document.getElementById("pub-tbody");
if (filtered.length === 0) {
tbody.innerHTML = `<tr><td colspan="7" style="text-align:center;padding:2rem;color:#718096">No publications to display.</td></tr>`;
return;
}
tbody.innerHTML = filtered.map((p, i) => {
const firstFlag = p.isFirst ? ' title="First author"' : "";
const lastFlag = p.isLast ? ' title="Last author"' : "";
const authorsHtml = (() => {
if (!p.authors || p.authors.length === 0) return "—";
let parts;
if (p.authors.length <= 4) {
parts = p.authors.map((a, idx) => {
const isF = idx === 0 && p.isFirst;
const isL = idx === p.authors.length - 1 && p.isLast;
const style = (isF || isL) ? " style=\"font-weight:600\"" : "";
return `<span${style}>${a}</span>`;
});
return parts.join(", ");
} else {
const first3 = p.authors.slice(0, 3).map((a, idx) => {
const isF = idx === 0 && p.isFirst;
const style = isF ? " style=\"font-weight:600\"" : "";
return `<span${style}>${a}</span>`;
}).join(", ");
const lastA = p.authors[p.authors.length - 1];
const isL = p.isLast;
const lastStyle = isL ? " style=\"font-weight:600\"" : "";
return first3 + ` … <span${lastStyle}>${lastA}</span>`;
}
})();
const titleHtml = p.doi
? `<a href="${p.doi.startsWith("http") ? p.doi : "https://doi.org/" + p.doi}" target="_blank" rel="noopener">${escHtml(p.title)}</a>`
: escHtml(p.title);
return `<tr data-id="${p.id}">
<td class="td-num">${i + 1}</td>
<td class="td-topic">${topicBadge(p.id, p.topic)}</td>
<td class="td-authors">${authorsHtml}</td>
<td class="td-year">${p.year || "—"}</td>
<td class="td-title">${titleHtml}</td>
<td class="td-journal">${formatJournal(p)}</td>
<td class="td-actions">
<button class="btn btn-edit" onclick="openEdit('${p.id}')" title="Edit">✏</button>
<button class="btn btn-danger" onclick="removeEntry('${p.id}')" title="Remove">✕</button>
</td>
</tr>`;
}).join("");
}
// ── Inline topic picker ───────────────────────────────────────
// Clicking a topic badge replaces it with a <select>; choosing a
// value saves immediately and re-renders just that badge.
document.getElementById("pub-tbody").addEventListener("click", e => {
const badge = e.target.closest(".topic-badge");
if (!badge) return;
const pubId = badge.dataset.pubid;
if (!pubId) return;
// Build inline select
const sel = document.createElement("select");
sel.className = "topic-picker";
for (const t of CONFIG.TOPICS) {
const opt = document.createElement("option");
opt.value = t.id;
opt.textContent = t.label;
sel.appendChild(opt);
}
const other = document.createElement("option");
other.value = "other"; other.textContent = "Other";
sel.appendChild(other);
const pub = publications.find(p => p.id === pubId);
if (pub) sel.value = pub.topic;
// Replace badge with select
badge.replaceWith(sel);
sel.focus();
function commit() {
const newTopic = sel.value;
if (pub) pub.topic = newTopic;
// Re-render only this cell to avoid full table repaint
const newBadge = document.createElement("span");
newBadge.outerHTML; // placeholder
const td = sel.parentElement;
if (td) td.innerHTML = topicBadge(pubId, newTopic);
// persist the topic change without a full re-render
saveToCache(cachedAuthor || document.getElementById("author-input").value.trim());
updateStats();
}
sel.addEventListener("change", commit);
sel.addEventListener("blur", commit);
sel.addEventListener("keydown", e => {
if (e.key === "Escape") {
// restore original badge without saving
const td = sel.parentElement;
if (td && pub) td.innerHTML = topicBadge(pubId, pub.topic);
}
});
});
function formatJournal(p) {
let s = escHtml(p.journal || "");
if (p.volume) {
s += ", <em>" + escHtml(p.volume) + "</em>";
if (p.issue) s += "(" + escHtml(p.issue) + ")";
}
if (p.pages) s += ":" + escHtml(p.pages);
return s || "—";
}
function escHtml(str) {
return String(str)
.replace(/&/g, "&")
.replace(/</g, "<")
.replace(/>/g, ">")
.replace(/"/g, """);
}
// ── Sort header highlighting ───────────────────────────────────
function updateSortHeaders() {
document.querySelectorAll("thead th[data-col]").forEach(th => {
const col = th.dataset.col;
th.classList.toggle("sorted", col === sortState.col);
const icon = th.querySelector(".sort-icon");
if (icon) {
icon.textContent = col === sortState.col
? (sortState.dir === "asc" ? "↑" : "↓")
: "↕";
}
});
}
// click-to-sort on headers
document.querySelectorAll("thead th[data-col]").forEach(th => {
th.addEventListener("click", () => {
const col = th.dataset.col;
if (col === "num") return;
if (sortState.col === col) {
sortState.dir = sortState.dir === "asc" ? "desc" : "asc";
} else {
sortState.col = col;
sortState.dir = "asc";
}
applyFilterAndRender();
});
});
// sort dropdown
document.getElementById("sort-btn").addEventListener("click", () => {
sortState.col = document.getElementById("sort-col").value;
sortState.dir = document.getElementById("sort-dir").value;
applyFilterAndRender();
});
// ── Remove / Edit ──────────────────────────────────────────────
function removeEntry(id) {
if (!confirm("Remove this publication?\n\nThis entry will not come back on re-fetch.")) return;
const pub = publications.find(p => p.id === id);
if (pub) {
tombstones.add(normTitle(pub.title));
if (pub.doi) tombstones.add("doi:" + normDoi(pub.doi));
if (pub.pmid) tombstones.add("pmid:" + String(pub.pmid).trim());
} // remember so re-fetch skips it
publications = publications.filter(p => p.id !== id);
commitAndRender();
}
function openEdit(id) {
const p = publications.find(x => x.id === id);
if (!p) return;
editingId = id;
document.getElementById("modal-title").textContent = "Edit publication";
document.getElementById("m-title").value = p.title || "";
document.getElementById("m-authors").value = (p.authors || []).join(", ");
document.getElementById("m-year").value = p.year || "";
document.getElementById("m-journal").value = p.journal || "";
document.getElementById("m-volume").value = p.volume || "";
document.getElementById("m-issue").value = p.issue || "";
document.getElementById("m-pages").value = p.pages || "";
document.getElementById("m-topic").value = p.topic || "other";
document.getElementById("m-doi").value = p.doi || "";
document.getElementById("m-pmid").value = p.pmid || "";
document.getElementById("m-source").value = p.source || "manual";
openModal();
}
// ── Modal ──────────────────────────────────────────────────────
function openModal() {
document.getElementById("modal-overlay").classList.add("open");
}
function closeModal() {
document.getElementById("modal-overlay").classList.remove("open");
editingId = null;
}
document.getElementById("add-btn").addEventListener("click", () => {
editingId = null;
document.getElementById("modal-title").textContent = "Add publication";
["m-title","m-authors","m-year","m-journal","m-volume","m-issue","m-pages","m-doi","m-pmid"].forEach(id =>
document.getElementById(id).value = "");
document.getElementById("m-topic").value = CONFIG.TOPICS[0]?.id || "other";
document.getElementById("m-source").value = "manual";
openModal();
});
document.getElementById("modal-cancel").addEventListener("click", closeModal);
document.getElementById("modal-overlay").addEventListener("click", e => {
if (e.target === e.currentTarget) closeModal();
});
document.getElementById("modal-save").addEventListener("click", () => {
const title = document.getElementById("m-title").value.trim();
if (!title) { alert("Title is required."); return; }
const authors = parseAuthors(document.getElementById("m-authors").value);
const { isFirst, isLast } = computeAuthorFlags(authors);
const entry = {
id: editingId || uid(),
title,
authors,
firstAuthor: authors[0] || "",
lastAuthor: authors[authors.length - 1] || "",
year: document.getElementById("m-year").value.trim(),
journal: document.getElementById("m-journal").value.trim(),
volume: document.getElementById("m-volume").value.trim(),
issue: document.getElementById("m-issue").value.trim(),
pages: document.getElementById("m-pages").value.trim(),
topic: document.getElementById("m-topic").value,
doi: document.getElementById("m-doi").value.trim(),
pmid: document.getElementById("m-pmid").value.trim(),
source: document.getElementById("m-source").value.trim(),
isFirst, isLast
};
if (editingId) {
const idx = publications.findIndex(p => p.id === editingId);
if (idx !== -1) publications[idx] = entry;
} else {
publications.push(entry);
}
closeModal();
commitAndRender();
});
// ── Export / Import ────────────────────────────────────────────
// APA
function formatAPA(p) {
const authors = (p.authors || []).join(", ");
const year = p.year ? `(${p.year})` : "(n.d.)";
const doi = p.doi
? "https://doi.org/" + p.doi.replace(/^https?:\/\/doi\.org\//, "")
: "";
let journalRef = p.journal || "";
if (p.volume) { journalRef += ", " + p.volume; if (p.issue) journalRef += "(" + p.issue + ")"; }
if (p.pages) journalRef += ", " + p.pages;
return [authors, year, (p.title || "Untitled") + ".", journalRef, doi]
.filter(Boolean).join(" ");
}
// BibTeX
function formatBibTeX(p, idx) {
const key = (p.authors?.[0] || "Unknown").replace(/\s+/g, "") + (p.year || "0000") + idx;
const author = (p.authors || []).join(" and ");
const doiLine = p.doi ? `\n doi = {${p.doi}},` : "";
const volumeLine = p.volume ? `\n volume = {${p.volume}},` : "";
const numberLine = p.issue ? `\n number = {${p.issue}},` : "";
const pagesLine = p.pages ? `\n pages = {${p.pages}},` : "";
return `@article{${key},\n author = {${author}},\n title = {${p.title || ""}},\n journal = {${p.journal || ""}},\n year = {${p.year || ""}},${volumeLine}${numberLine}${pagesLine}${doiLine}\n}`;
}
// RIS
function formatRIS(p) {
const lines = ["TY - JOUR"];
(p.authors || []).forEach(a => lines.push(`AU - ${a}`));
if (p.year) lines.push(`PY - ${p.year}`);
if (p.title) lines.push(`TI - ${p.title}`);
if (p.journal) lines.push(`JO - ${p.journal}`);
if (p.volume) lines.push(`VL - ${p.volume}`);
if (p.issue) lines.push(`IS - ${p.issue}`);
if (p.pages) lines.push(`SP - ${p.pages}`);
if (p.doi) lines.push(`DO - ${p.doi}`);
if (p.pmid) lines.push(`AN - ${p.pmid}`);
lines.push("ER - ");
return lines.join("\n");
}
// Download helper
function triggerDownload(content, filename, mime) {
const blob = new Blob([content], { type: mime });
const a = document.createElement("a");
a.href = URL.createObjectURL(blob);
a.download = filename;
a.click();
setTimeout(() => URL.revokeObjectURL(a.href), 10000);
}
// Export menu toggle
const exportToggle = document.getElementById("export-toggle");
const exportMenu = document.getElementById("export-menu");
exportToggle.addEventListener("click", e => {
e.stopPropagation();
exportMenu.classList.toggle("open");
});
document.addEventListener("click", () => exportMenu.classList.remove("open"));
exportMenu.addEventListener("click", e => {
const btn = e.target.closest("button[data-fmt]");
if (!btn) return;
exportMenu.classList.remove("open");
const fmt = btn.dataset.fmt;
// export what is currently visible (filtered), fall back to all
const list = filtered.length ? filtered : publications;
if (fmt === "json") {
// Always export the full dataset (all publications) + tombstones so the
// file can serve as a complete restore point when placed next to the page.
triggerDownload(JSON.stringify(buildExportObject(), null, 2), "publications.json", "application/json");
} else if (fmt === "apa") {
const text = list.map((p, i) => `${i + 1}. ${formatAPA(p)}`).join("\n\n");
triggerDownload(text, "publications_apa.txt", "text/plain");