User:Udays108/common.js: Difference between revisions

Latest revision as of 17:46, 21 May 2026

/**
 * BioMicro Center Wiki — Full DOM Replacement
 * Paste into: User:USERNAME/common.js
 *
 * Strategy:
 * 1. Extract wiki article content from MediaWiki's DOM
 * 2. Inject the complete shell structure
 * 3. Place article content inside the shell
 * MediaWiki still runs underneath for editing, search, login, etc.
 */

( function () {
  'use strict';

  /* ── Extract nav from MediaWiki's sidebar DOM ─────────────── */
  function extractNavFromDom() {
    var SKIP_IDS = {
      'p-tb': 1, 'p-personal': 1, 'p-search': 1,
      'p-logo': 1, 'p-cactions': 1, 'p-views': 1,
      'p-lang': 1, 'p-namespaces': 1
    };

    var portlets = Array.prototype.slice.call(
      document.querySelectorAll( '[id^="p-"]' )
    );

    var nav = [];
    var currentUrl = window.location.href.split( '?' )[0];

    portlets.forEach( function ( portlet ) {
      if ( SKIP_IDS[ portlet.id ] ) return;

      var links = Array.prototype.slice.call(
        portlet.querySelectorAll( 'li a' )
      ).map( function ( a ) {
        return { label: a.textContent.trim(), href: a.href };
      } ).filter( function ( item ) { return item.label && item.href; } );

      if ( !links.length ) return;

      var headingEl = portlet.querySelector( '[id$="-label"], h3, h2' );
      var sectionLabel = headingEl ? headingEl.textContent.trim() : '';

      var isActive = links.some( function ( link ) {
        return link.href.split( '?' )[0] === currentUrl;
      } );

      if ( links.length === 1 ) {
        nav.push( {
          label:    links[0].label,
          href:     links[0].href,
          isActive: links[0].href.split( '?' )[0] === currentUrl
        } );
      } else {
        nav.push( {
          label:    sectionLabel || links[0].label,
          href:     links[0].href,
          items:    links,
          isActive: isActive
        } );
      }
    } );

    return nav;
  }

  /* ── Build topbar HTML ─────────────────────────────────────── */
  function buildTopbar() {
    var d = document.createElement( 'div' );
    d.className = 'bmc-topbar';
    d.innerHTML =
      '<div class="inner">' +
        '<a href="mailto:biomicro@mit.edu">biomicro@mit.edu</a>' +
        '<span>|</span>' +
        '617-715-4533' +
        '<span>|</span>' +
        'Building 68-322' +
      '</div>';
    return d;
  }

  /* ── Build nav dropdown item ───────────────────────────────── */
  function buildDropdownMenu( items ) {
    var menu = document.createElement( 'div' );
    menu.className = 'bmc-dropdown-menu';
    items.forEach( function ( item ) {
      if ( item.divider ) {
        var div = document.createElement( 'div' );
        div.className = 'bmc-divider';
        menu.appendChild( div );
      } else if ( item.groupLabel ) {
        var gl = document.createElement( 'div' );
        gl.className = 'bmc-group-label';
        gl.textContent = item.groupLabel;
        menu.appendChild( gl );
      } else {
        var a = document.createElement( 'a' );
        a.href = item.page ? mw.util.getUrl( item.page ) : item.href;
        a.textContent = item.label;
        if ( item.ext ) a.target = '_blank';
        menu.appendChild( a );
      }
    } );
    return menu;
  }

  /* ── Build full header ─────────────────────────────────────── */
  function buildHeader( currentPage, nav ) {
    /* Logo */
    var logo = document.createElement( 'a' );
    logo.href = mw.util.getUrl( 'BioMicroCenter' );
    logo.className = 'bmc-logo';
    logo.innerHTML =
      '<img class="bmc-logo-img" src="https://bmcwiki.mit.edu/images/c/c9/Logo.png" alt="MIT BioMicro Center" />';

    /* Nav */
    var ul = document.createElement( 'ul' );
    nav.forEach( function ( item ) {
      var li = document.createElement( 'li' );
      if ( item.isActive ) li.classList.add( 'bmc-active' );
      if ( item.items ) li.classList.add( 'bmc-dropdown' );

      var a = document.createElement( 'a' );
      a.href = item.page ? mw.util.getUrl( item.page ) : ( item.href || '#' );
      a.textContent = item.label;
      li.appendChild( a );

      if ( item.items ) {
        li.appendChild( buildDropdownMenu( item.items ) );
      }
      ul.appendChild( li );
    } );

    var navEl = document.createElement( 'nav' );
    navEl.className = 'bmc-nav';
    navEl.appendChild( ul );

    /* Search */
    var searchForm = document.createElement( 'form' );
    searchForm.className = 'bmc-search-form';
    searchForm.method = 'get';
    searchForm.action = '/index.php';
    searchForm.innerHTML =
      '<input type="hidden" name="title" value="Special:Search">' +
      '<input type="search" name="search" placeholder="Search wiki…" aria-label="Search">' +
      '<button type="submit" aria-label="Search"><svg xmlns="http://www.w3.org/2000/svg" width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2.5" stroke-linecap="round" stroke-linejoin="round"><circle cx="11" cy="11" r="8"/><line x1="21" y1="21" x2="16.65" y2="16.65"/></svg></button>';

    var right = document.createElement( 'div' );
    right.className = 'bmc-header-right';
    right.appendChild( navEl );
    right.appendChild( searchForm );

    /* Inner wrapper */
    var inner = document.createElement( 'div' );
    inner.className = 'bmc-header-inner';
    inner.appendChild( logo );
    inner.appendChild( right );

    var header = document.createElement( 'header' );
    header.className = 'bmc-header';
    header.appendChild( inner );
    return header;
  }

  /* ── Build page hero ───────────────────────────────────────── */
  function buildHero( titleText ) {
    var crumb = document.createElement( 'div' );
    crumb.className = 'bmc-breadcrumb';
    crumb.innerHTML =
      '<a href="' + mw.util.getUrl( 'BioMicroCenter' ) + '">Home</a>' +
      '<span class="sep">›</span>' +
      document.createTextNode( titleText ).textContent; // plain text, no XSS

    var h1 = document.createElement( 'h1' );
    h1.textContent = titleText;

    var inner = document.createElement( 'div' );
    inner.className = 'inner';
    inner.appendChild( crumb );
    inner.appendChild( h1 );

    var hero = document.createElement( 'div' );
    hero.className = 'bmc-page-hero';
    hero.appendChild( inner );
    return hero;
  }

  /* ── Build sidebar TOC from MediaWiki #toc or heading scan ─── */
  function buildSidebarToc( mwToc, contentEl ) {
    var toc = document.createElement( 'div' );
    toc.className = 'bmc-toc';

    var h3 = document.createElement( 'h3' );
    h3.textContent = 'On this page';
    toc.appendChild( h3 );

    var list;

    if ( mwToc ) {
      /* Clone only the list from the MediaWiki TOC */
      var mwList = mwToc.querySelector( 'ul' );
      if ( mwList ) {
        list = mwList.cloneNode( true );
        /* Mark sub-items */
        list.querySelectorAll( 'li li' ).forEach( function ( li ) {
          li.classList.add( 'bmc-sub' );
        } );
      }
    } else if ( contentEl ) {
      /* Fall back to scanning h2/h3 headings directly */
      var headings = Array.prototype.slice.call(
        contentEl.querySelectorAll( 'h2, h3' )
      );
      if ( headings.length > 0 ) {
        list = document.createElement( 'ul' );
        headings.forEach( function ( heading ) {
          var anchor = heading.querySelector( '.mw-headline' );
          if ( !anchor || !anchor.id ) return;
          var li = document.createElement( 'li' );
          if ( heading.tagName === 'H3' ) li.classList.add( 'bmc-sub' );
          var a = document.createElement( 'a' );
          a.href = '#' + anchor.id;
          a.textContent = anchor.textContent.trim();
          li.appendChild( a );
          list.appendChild( li );
        } );
      }
    }

    if ( !list || list.childNodes.length === 0 ) return null;

    toc.appendChild( list );

    var aside = document.createElement( 'aside' );
    aside.className = 'bmc-sidebar';
    aside.appendChild( toc );
    return aside;
  }

  /* ── Build footer ──────────────────────────────────────────── */
  function buildFooter() {
    var u = mw.util.getUrl;
    var inner = document.createElement( 'div' );
    inner.className = 'bmc-footer-inner';
    inner.innerHTML =
      '<div>' +
        '<h4>MIT BioMicro Center</h4>' +
        '<ul>' +
          '<li>Building 68-322</li>' +
          '<li>Cambridge, MA 02139</li>' +
          '<li><a href="mailto:biomicro@mit.edu">biomicro@mit.edu</a></li>' +
          '<li>617-715-4533</li>' +
        '</ul>' +
      '</div>' +
      '<div>' +
        '<h4>Services</h4>' +
        '<ul>' +
          '<li><a href="' + u( 'BioMicroCenter:Sequencing' ) + '">Bulk Sequencing</a></li>' +
          '<li><a href="' + u( 'BioMicroCenter:SingleCell' ) + '">Single Cell</a></li>' +
          '<li><a href="' + u( 'BioMicroCenter:SpTx' ) + '">Spatial Genomics</a></li>' +
          '<li><a href="https://igb.mit.edu/" target="_blank">Informatics</a></li>' +
        '</ul>' +
      '</div>' +
      '<div>' +
        '<h4>Resources</h4>' +
        '<ul>' +
          '<li><a href="' + u( 'BioMicroCenter:FAQ' ) + '">FAQs</a></li>' +
          '<li><a href="' + u( 'BioMicroCenter:Consulting' ) + '">Consulting</a></li>' +
          '<li><a href="' + u( 'BioMicroCenter:Pricing' ) + '">Grant Support &amp; Pricing</a></li>' +
          '<li><a href="' + u( 'BioMicroCenter:Acknowledgement' ) + '">Acknowledgements</a></li>' +
        '</ul>' +
      '</div>';

    var bottom = document.createElement( 'div' );
    bottom.className = 'bmc-footer-bottom';
    bottom.innerHTML =
      '<span>&copy; ' + new Date().getFullYear() + ' MIT BioMicro Center</span>' +
      '<span>' +
        '<a href="' + u( 'Special:UserLogin' ) + '">Log in</a>' +
        ' &nbsp;|&nbsp; ' +
        '<a href="https://accessibility.mit.edu" target="_blank">Accessibility</a>' +
      '</span>';

    var footer = document.createElement( 'footer' );
    footer.className = 'bmc-footer';
    footer.appendChild( inner );
    footer.appendChild( bottom );
    return footer;
  }

  /* ── Smooth scroll for anchor links ───────────────────────── */
  function initSmoothScroll( container ) {
    container.addEventListener( 'click', function ( e ) {
      var a = e.target.closest( 'a[href^="#"]' );
      if ( !a ) return;
      var id = decodeURIComponent( a.getAttribute( 'href' ).slice( 1 ) );
      var target = document.getElementById( id );
      if ( target ) {
        e.preventDefault();
        target.scrollIntoView( { behavior: 'smooth', block: 'start' } );
        history.pushState( null, '', '#' + id );
      }
    } );
  }

  /* ── Fix row separators on tables with rowspan cells ──────── */
  function fixRowspanSeparators( container ) {
    container.querySelectorAll( '.wikitable' ).forEach( function ( table ) {
      var tbody = table.querySelector( 'tbody' ) || table;
      var rows = Array.from( tbody.querySelectorAll( 'tr' ) );
      if ( !rows.length ) return;

      rows.forEach( function ( row, rowIdx ) {
        row.querySelectorAll( 'td[rowspan], th[rowspan]' ).forEach( function ( cell ) {
          var span = parseInt( cell.getAttribute( 'rowspan' ), 10 );
          if ( !span || span <= 1 ) return;

          cell.style.position = 'relative';

          for ( var i = 1; i < span; i++ ) {
            var targetRow = rows[ rowIdx + i ];
            if ( !targetRow ) break;

            var cellRect  = cell.getBoundingClientRect();
            var rowRect   = targetRow.getBoundingClientRect();
            var offsetTop = rowRect.top - cellRect.top;

            var sep = document.createElement( 'div' );
            sep.style.cssText =
              'position:absolute;left:0;right:0;' +
              'top:' + offsetTop + 'px;' +
              'height:1px;background:#e0e0e0;' +
              'pointer-events:none;z-index:1;';
            cell.appendChild( sep );
          }
        } );
      } );
    } );
  }

  /* ── Edit bar for logged-in users ─────────────────────────── */
  function buildEditBar( currentPage ) {
    if ( !mw.config.get( 'wgUserId' ) ) return null;
    var bar = document.createElement( 'div' );
    bar.className = 'bmc-edit-bar';
    var editHref = mw.util.getUrl( currentPage, { action: 'edit' } );
    var histHref = mw.util.getUrl( currentPage, { action: 'history' } );
    var talkHref = mw.util.getUrl( 'Talk:' + currentPage );
    bar.innerHTML =
      '<a href="' + editHref + '">Edit</a>' +
      '<a href="' + histHref + '">History</a>' +
      '<a href="' + talkHref + '">Talk</a>';
    return bar;
  }

  /* ── Main: build and inject the shell ─────────────────────── */
  function buildShell( nav ) {
    var currentPage = mw.config.get( 'wgPageName' ) || '';

    /* 1. Extract wiki content BEFORE any DOM manipulation */
    var mwContentText = document.getElementById( 'mw-content-text' );
    if ( !mwContentText ) return; /* not a content page, bail */

    var contentClone = mwContentText.cloneNode( true );

    /* 2. Extract page title */
    var titleEl = document.getElementById( 'firstHeading' ) ||
      document.querySelector( '.mw-first-heading' );
    var titleText = titleEl
      ? titleEl.textContent.trim()
      : ( mw.config.get( 'wgTitle' ) || 'BioMicro Center' );

    /* 3. Extract MediaWiki TOC from the cloned content */
    var mwToc = contentClone.querySelector( '#toc, .toc' );
    if ( mwToc ) mwToc.parentNode.removeChild( mwToc ); /* remove from content body */

    /* 3b. Hide the BMC logo/header sticker by exact image filename.
           The sticker is BMC_Header_2020_3.png (from the {{BioMicroCenter}} template)
           and bmc_logo_square.png. Target the nearest meaningful container so the
           surrounding content (nav links, table structure) is preserved. */
    contentClone.querySelectorAll( 'img' ).forEach( function ( img ) {
      var src = img.getAttribute( 'src' ) || '';
      if ( /BMC_Header|bmc_logo_square|Bmc_logo|\/Logo\.png/i.test( src ) ) {
        var container = img.closest( '.thumb' ) || img.closest( 'figure' ) || img.closest( 'td' );
        if ( container ) {
          container.style.display = 'none';
        } else {
          img.style.display = 'none';
        }
      }
    } );

    /* 4. Build shell elements */
    var topbar = buildTopbar();
    var header = buildHeader( currentPage, nav );
    var hero   = buildHero( titleText );

    /* Page layout grid */
    var layout = document.createElement( 'div' );
    layout.className = 'bmc-page-layout';

    /* Sidebar — skip on the home page */
    var isHome = ( currentPage === 'BioMicroCenter' ||
                   currentPage === 'Main_Page' );
    var sidebar = isHome ? null : buildSidebarToc( mwToc, contentClone );
    if ( sidebar ) {
      layout.appendChild( sidebar );
    } else {
      /* No TOC — collapse to single-column via inline style */
      layout.style.gridTemplateColumns = '1fr';
    }

    /* Main content area */
    var main = document.createElement( 'main' );
    main.className = 'bmc-content';
    var editBar = buildEditBar( currentPage );
    if ( editBar ) { main.appendChild( editBar ); }
    main.appendChild( contentClone );
    layout.appendChild( main );

    var footer = buildFooter();

    /* 5. Build wrapper */
    var wrapper = document.createElement( 'div' );
    wrapper.id = 'bmc-wrapper';
    wrapper.appendChild( topbar );
    wrapper.appendChild( header );
    wrapper.appendChild( hero );
    wrapper.appendChild( layout );
    wrapper.appendChild( footer );

    /* 6. Inject into body (prepend so it appears first) */
    document.body.insertBefore( wrapper, document.body.firstChild );

    /* 7. Add class immediately so the CSS rule kicks in and hides
          all original MW elements (works for any skin version) */
    document.body.classList.add( 'bmc-active' );

    /* 8. Smooth scroll */
    initSmoothScroll( main );
    initSmoothScroll( sidebar || main );

    /* 9. Auto-style plain tables in content */
    main.querySelectorAll(
      '.mw-parser-output table:not(.wikitable):not(.infobox):not(.navbox)'
    ).forEach( function ( t ) {
      t.classList.add( 'wikitable' );
    } );

    /* 10. Fix row separators on rowspan tables */
    requestAnimationFrame( function () {
      fixRowspanSeparators( main );
    } );


  }

  /* ── Entry point ───────────────────────────────────────────── */
  mw.hook( 'wikipage.content' ).add( function () {
    /* Skip special pages (edit forms, history, etc.) to not break them */
    var ns     = mw.config.get( 'wgNamespaceNumber' );
    var action = mw.config.get( 'wgAction' );
    if ( action !== 'view' ) return;
    if ( ns < 0 ) return; /* Special: pages */

    var nav = extractNavFromDom();
    buildShell( nav );
  } );

} )();