@yeyuan98/opencode-bioresearcher-plugin 1.7.1-alpha.0 → 1.7.2

package/dist/tools/misc/markdown-to-html.js

@@ -25,6 +25,228 @@ th { background: #f6f8fa; font-weight: 600; }
 tr:nth-child(even) { background: #f6f8fa; }
 hr { border: none; border-top: 1px solid #d0d7de; margin: 2em 0; }
 img { max-width: 100%; border-radius: 6px; }
+.cite-ref { font-size: 0.75em; vertical-align: super; line-height: 0; }
+.cite-ref a { color: #0969da; cursor: pointer; text-decoration: none; font-weight: 600; padding: 0 0.1em; }
+.cite-ref a:hover { text-decoration: underline; }
+.cite-tooltip { position: absolute; z-index: 9999; max-width: 420px; min-width: 260px; padding: 12px 16px; background: #fff; border: 1px solid #d0d7de; border-radius: 8px; box-shadow: 0 8px 24px rgba(0,0,0,0.12); font-size: 13px; line-height: 1.5; color: #24292f; display: none; opacity: 0; transition: opacity 0.15s ease-in-out; }
+.cite-tooltip.visible { display: block; }
+.cite-tooltip.fade-in { opacity: 1; }
+.cite-tooltip.fade-out { opacity: 0; }
+.cite-tooltip .cite-label { font-size: 11px; color: #656d76; margin-bottom: 6px; text-transform: uppercase; letter-spacing: 0.05em; }
+.cite-tail { position: absolute; top: -6px; left: 50%; transform: translateX(-50%); width: 0; height: 0; border-left: 6px solid transparent; border-right: 6px solid transparent; border-bottom: 6px solid #d0d7de; }
+.cite-tail::after { content: ''; position: absolute; top: 1px; left: -5px; width: 0; height: 0; border-left: 5px solid transparent; border-right: 5px solid transparent; border-bottom: 5px solid #fff; }
+.cite-tail.flip { top: auto; bottom: -6px; border-bottom: none; border-top: 6px solid #d0d7de; }
+.cite-tail.flip::after { top: auto; bottom: 1px; border-bottom: none; border-top: 5px solid #fff; }
+.cite-tooltip a.ref-link { color: #0969da; text-decoration: none; }
+.cite-tooltip a.ref-link:hover { text-decoration: underline; }
+`.trim();
+const CITATION_POSTPROCESS_JS = `
+(function() {
+  var c = document.getElementById('content');
+  if (!c) return;
+  var hs = c.querySelectorAll('h1,h2,h3,h4,h5,h6');
+  var rh = null;
+  for (var i = 0; i < hs.length; i++) {
+    if (/^references?$/i.test(hs[i].textContent.trim())) { rh = hs[i]; break; }
+  }
+  if (!rh) return;
+  var re = new Set();
+  re.add(rh);
+  var el = rh.nextElementSibling;
+  while (el) {
+    if (/^H[1-6]$/i.test(el.tagName)) break;
+    re.add(el);
+    el = el.nextElementSibling;
+  }
+  var refs = new Map();
+  function extractRefs(node) {
+    var items = (node.tagName === 'OL' || node.tagName === 'UL')
+      ? node.querySelectorAll('li') : [node];
+    for (var i = 0; i < items.length; i++) {
+      var t = items[i].textContent.trim();
+      var m = t.match(/^\\[(\\d+)\\]\\s*([\\s\\S]*)/);
+      if (m) refs.set(parseInt(m[1]), m[2].trim());
+    }
+  }
+  re.forEach(function(e) { if (e !== rh) extractRefs(e); });
+  if (refs.size === 0) return;
+  function inRef(n) {
+    var p = n.parentElement;
+    while (p && p !== c) { if (re.has(p)) return true; p = p.parentElement; }
+    return false;
+  }
+  function inCode(n) {
+    var p = n.parentElement;
+    while (p && p !== c) {
+      if (p.tagName === 'CODE' || p.tagName === 'PRE') return true;
+      p = p.parentElement;
+    }
+    return false;
+  }
+  var w = document.createTreeWalker(c, NodeFilter.SHOW_TEXT);
+  var nodes = [];
+  while (w.nextNode()) nodes.push(w.currentNode);
+  var regex = /\\[(\\d+(?:\\s*[,，]\\s*\\d+)*(?:\\s*[-–]\\s*\\d+)?)\\]/g;
+  for (var i = 0; i < nodes.length; i++) {
+    var node = nodes[i];
+    if (inRef(node) || inCode(node)) continue;
+    var text = node.textContent;
+    if (!regex.test(text)) continue;
+    regex.lastIndex = 0;
+    var frag = document.createDocumentFragment();
+    var li = 0, m;
+    while ((m = regex.exec(text)) !== null) {
+      if (m.index > li)
+        frag.appendChild(document.createTextNode(text.slice(li, m.index)));
+      var nums = [];
+      m[1].split(/[,，]/).forEach(function(p) {
+        p = p.trim();
+        var rm = p.match(/^(\\d+)\\s*[-–]\\s*(\\d+)$/);
+        if (rm) {
+          for (var j = parseInt(rm[1]); j <= parseInt(rm[2]); j++) nums.push(j);
+        } else {
+          var n = parseInt(p);
+          if (!isNaN(n)) nums.push(n);
+        }
+      });
+      var sup = document.createElement('sup');
+      sup.className = 'cite-ref';
+      nums.forEach(function(num, idx) {
+        if (idx > 0) sup.appendChild(document.createTextNode(', '));
+        var a = document.createElement('a');
+        a.textContent = num;
+        a.setAttribute('data-ref', num);
+        a.href = '#ref-' + num;
+        sup.appendChild(a);
+      });
+      frag.appendChild(sup);
+      li = regex.lastIndex;
+    }
+    if (li < text.length)
+      frag.appendChild(document.createTextNode(text.slice(li)));
+    node.parentNode.replaceChild(frag, node);
+  }
+  re.forEach(function(e) {
+    if (e === rh) return;
+    var items = (e.tagName === 'OL' || e.tagName === 'UL')
+      ? e.querySelectorAll('li') : [e];
+    for (var i = 0; i < items.length; i++) {
+      var t = items[i].textContent.trim();
+      var m = t.match(/^\\[(\\d+)\\]/);
+      if (m) items[i].id = 'ref-' + m[1];
+    }
+  });
+  function esc(s) {
+    return s.replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;');
+  }
+  function linkify(s) {
+    var ph = [];
+    function phPush(html) { var i = ph.length; ph.push(html); return '%%PH' + i + '%%'; }
+    s = s.replace(/\\bdoi:\\s*(10\\.\\d{4,9}\\/\\S*[^\\s.,;:])/gi, function(_, doi) {
+      return phPush('<a class="ref-link" href="https://doi.org/' + esc(doi) + '" target="_blank" rel="noopener">doi:' + esc(doi) + '<\\/a>');
+    });
+    s = s.replace(/\\bPMID:\\s*(\\d+)/gi, function(_, id) {
+      return phPush('<a class="ref-link" href="https://pubmed.ncbi.nlm.nih.gov/' + id + '/" target="_blank" rel="noopener">PMID: ' + id + '<\\/a>');
+    });
+    var parts = s.split(/(https?:\\/\\/[^\\s<>"]+)/g);
+    return parts.map(function(p, i) {
+      if (i % 2 === 1) return '<a class="ref-link" href="' + esc(p) + '" target="_blank" rel="noopener">' + esc(p) + '<\\/a>';
+      return esc(p).replace(/%%PH(\\d+)%%/g, function(_, idx) { return ph[parseInt(idx)]; });
+    }).join('');
+  }
+  refs.forEach(function(text, num) {
+    var tt = document.createElement('div');
+    tt.className = 'cite-tooltip';
+    tt.id = 'cite-tooltip-' + num;
+    tt.innerHTML = '<div class="cite-tail"><\\/div><div class="cite-label">Reference [' + num + ']<\\/div><div>' + linkify(text) + '<\\/div>';
+    document.body.appendChild(tt);
+  });
+  var active = null, st = null, ht = null, hat = null;
+  function showTooltip(a) {
+    clearTimeout(hat); hat = null;
+    var n = a.getAttribute('data-ref');
+    var tt = document.getElementById('cite-tooltip-' + n);
+    if (!tt) return;
+    hideCurrent();
+    var r = a.getBoundingClientRect();
+    var sy = window.scrollY || document.documentElement.scrollTop;
+    var sx = window.scrollX || document.documentElement.scrollLeft;
+    tt.style.left = '0px';
+    tt.style.top = '0px';
+    tt.classList.add('visible');
+    tt.classList.remove('fade-out');
+    var tr = tt.getBoundingClientRect();
+    var l = r.left + sx + r.width / 2 - tr.width / 2;
+    var t = r.bottom + sy + 6;
+    if (l < 8) l = 8;
+    if (l + tr.width > window.innerWidth - 8) l = window.innerWidth - tr.width - 8;
+    if (t + tr.height > window.innerHeight + sy - 8) t = r.top + sy - tr.height - 6;
+    var above = t < r.top + sy;
+    var tail = tt.querySelector('.cite-tail');
+    if (tail) {
+      var tailL = (r.left + sx + r.width / 2) - l;
+      tail.style.left = tailL + 'px';
+      tail.style.transform = 'none';
+      if (above) tail.classList.add('flip'); else tail.classList.remove('flip');
+    }
+    tt.style.left = l + 'px';
+    tt.style.top = t + 'px';
+    requestAnimationFrame(function() { tt.classList.add('fade-in'); });
+    active = tt;
+  }
+  function hideCurrent() {
+    if (!active) return;
+    var prev = active;
+    prev.classList.remove('fade-in');
+    prev.classList.add('fade-out');
+    hat = setTimeout(function() {
+      prev.classList.remove('visible', 'fade-out');
+    }, 150);
+    if (active === prev) active = null;
+  }
+  function scheduleHide() {
+    ht = setTimeout(function() { hideCurrent(); }, 200);
+  }
+  function cancelHide() {
+    clearTimeout(ht);
+    ht = null;
+    clearTimeout(hat);
+    hat = null;
+  }
+  document.addEventListener('mouseenter', function(e) {
+    var a = e.target.closest('.cite-ref a');
+    if (!a) return;
+    cancelHide();
+    clearTimeout(st);
+    st = setTimeout(function() { showTooltip(a); }, 300);
+  }, true);
+  document.addEventListener('mouseleave', function(e) {
+    var a = e.target.closest('.cite-ref a');
+    if (!a) return;
+    clearTimeout(st);
+    scheduleHide();
+  }, true);
+  document.addEventListener('mouseenter', function(e) {
+    if (e.target.closest('.cite-tooltip')) cancelHide();
+  }, true);
+  document.addEventListener('mouseleave', function(e) {
+    if (e.target.closest('.cite-tooltip')) scheduleHide();
+  }, true);
+  document.addEventListener('click', function(e) {
+    var a = e.target.closest('.cite-ref a');
+    if (!a) return;
+    e.preventDefault();
+    var n = a.getAttribute('data-ref');
+    var tt = document.getElementById('cite-tooltip-' + n);
+    if (!tt) return;
+    if (active === tt && tt.classList.contains('fade-in')) {
+      hideCurrent();
+    } else {
+      clearTimeout(st);
+      showTooltip(a);
+    }
+  });
+})();
 `.trim();
 function buildHtml(markdown, title, extraCss) {
     const escapedMarkdown = JSON.stringify(markdown).replace(/<\//g, String.raw `<\/`);
@@ -42,6 +264,7 @@ function buildHtml(markdown, title, extraCss) {
 <div id="content"></div>
 <script>${MARKED_BUNDLE}</script>
 <script>document.getElementById('content').innerHTML = marked.parse(${escapedMarkdown});</script>
+<script>${CITATION_POSTPROCESS_JS}</script>
 </body>
 </html>`;
 }

package/dist/tools/parser/pubmed/utils.js

@@ -1,4 +1,6 @@
+import * as fs from 'fs';
 import * as XLSX from '../../../vendor/xlsx.mjs';
+XLSX.set_fs(fs);
 export function getText(obj) {
     if (obj === null || obj === undefined)
         return null;

package/dist/tools/table/backends/base.d.ts

@@ -0,0 +1,8 @@
+export declare abstract class BaseTableBackend {
+    protected resolvedPath: string;
+    protected force: boolean;
+    constructor(resolvedPath: string, force: boolean);
+    abstract readonly type: string;
+    protected ensureSheetIndex(sheetIndex: number): void;
+    protected resolveSheetName(sheetName: string | undefined, availableNames: string[]): string;
+}

package/dist/tools/table/backends/base.js

@@ -0,0 +1,23 @@
+import { checkFileSize } from '../utils';
+export class BaseTableBackend {
+    resolvedPath;
+    force;
+    constructor(resolvedPath, force) {
+        this.resolvedPath = resolvedPath;
+        this.force = force;
+        checkFileSize(resolvedPath, force);
+    }
+    ensureSheetIndex(sheetIndex) {
+        if (sheetIndex !== 0) {
+            throw new Error('This file format only supports a single sheet (index 0)');
+        }
+    }
+    resolveSheetName(sheetName, availableNames) {
+        if (!sheetName)
+            return availableNames[0];
+        if (!availableNames.includes(sheetName)) {
+            throw new Error(`Sheet "${sheetName}" not found`);
+        }
+        return sheetName;
+    }
+}

package/dist/tools/table/backends/csv/index.d.ts

@@ -0,0 +1,64 @@
+import { BaseTableBackend } from '../base';
+import type { IWritableTableBackend, SheetInfo } from '../interface';
+export declare class CSVBackend extends BaseTableBackend implements IWritableTableBackend {
+    readonly type = "csv";
+    private delimiter;
+    private _headers;
+    private _totalDataRows;
+    constructor(resolvedPath: string, force: boolean);
+    private readHeaders;
+    private countDataRows;
+    listSheets(): SheetInfo[];
+    getHeaders(sheetIndex: number): {
+        headers: string[];
+        columnCount: number;
+    };
+    getTotalDataRows(sheetIndex: number): number;
+    getCell(sheetIndex: number, cellAddress: string): {
+        value: any;
+        type: string;
+    };
+    getRange(sheetIndex: number, range: string): any;
+    getPreview(sheetIndex: number, maxRows: number): {
+        rows: any[][];
+        totalRows: number;
+    };
+    search(sheetIndex: number, searchTerm: string, options: {
+        column?: string;
+        maxResults: number;
+        maxRowsScan: number;
+    }): {
+        results: any[];
+        totalMatchesFound: number;
+        rowsScanned: number;
+    };
+    filterRows(sheetIndex: number, column: string, operator: string, value: any, options: {
+        maxResults: number;
+        maxRowsScan: number;
+    }): {
+        matchedRows: Record<string, any>[];
+        totalMatchesFound: number;
+        totalDataRows: number;
+    };
+    summarize(sheetIndex: number, columns: string[] | undefined, options: {
+        maxRowsScan: number;
+    }): {
+        summaries: Record<string, any>;
+        rowCount: number;
+    };
+    groupBy(sheetIndex: number, groupColumn: string, aggColumn: string, aggType: string, options: {
+        maxRowsScan: number;
+    }): {
+        groups: Record<string, number>;
+    };
+    pivotSummary(sheetIndex: number, rowField: string, colField: string, valueField: string, agg: string, options: {
+        maxRowsScan: number;
+    }): {
+        columns: string[];
+        pivot: Record<string, Record<string, number>>;
+    };
+    appendRows(sheetIndex: number, rows: any[]): void;
+    updateCell(sheetIndex: number, cellAddress: string, value: any): void;
+    createFile(sheetName: string, data: any): void;
+    dispose(): void;
+}