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Merge pull request #1 from fhdsl/week4
Week 4 lecture initial draft
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‎OTTR_Quarto.Rproj‎

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Version: 1.0
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ProjectId: 4325c7e5-7cad-438b-b62d-bd9b1dde5b7e
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RestoreWorkspace: Default
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SaveWorkspace: Default

‎_quarto.yml‎

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- index.qmd
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- concepts.qmd
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- week1.qmd
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- week4.qmd
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- miscellaneous.qmd
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- references.qmd
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‎data/GiBleed_5.3_1.1.duckdb‎

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‎docs/index.html‎

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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
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<meta charset="utf-8">
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<meta name="generator" content="quarto-1.6.40">
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<meta name="generator" content="quarto-1.5.57">
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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
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<script src="site_libs/quarto-html/tippy.umd.min.js"></script>
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<script src="site_libs/quarto-html/anchor.min.js"></script>
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<link href="site_libs/quarto-html/tippy.css" rel="stylesheet">
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<link href="site_libs/quarto-html/quarto-syntax-highlighting-549806ee2085284f45b00abea8c6df48.css" rel="stylesheet" id="quarto-text-highlighting-styles">
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<link href="site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
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<script src="site_libs/bootstrap/bootstrap.min.js"></script>
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<link href="site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
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<link href="site_libs/bootstrap/bootstrap-a1c1d0abbd8b67b8b47aad02bae1bfc9.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
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<link href="site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
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<script id="quarto-search-options" type="application/json">{
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"location": "sidebar",
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"copy-button": false,
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<a href="./week1.html" class="sidebar-item-text sidebar-link">
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<span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Week 1</span></span></a>
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</div>
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</li>
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<li class="sidebar-item">
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<div class="sidebar-item-container">
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<a href="./week4.html" class="sidebar-item-text sidebar-link">
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<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Week 4</span></span></a>
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</div>
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</li>
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<li class="sidebar-item">
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<div class="sidebar-item-container">
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<a href="./miscellaneous.html" class="sidebar-item-text sidebar-link">
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<span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Miscellaneous Grabbag</span></span></a>
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<span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Miscellaneous Grabbag</span></span></a>
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</div>
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</li>
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<li class="sidebar-item">
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<div class="sidebar-item-container">
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<a href="./references.html" class="sidebar-item-text sidebar-link">
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<span class="menu-text">References</span></a>
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</div>
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</li>
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</ul>
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<ul class="collapse">
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<li><a href="#course-description" id="toc-course-description" class="nav-link" data-scroll-target="#course-description">Course Description</a></li>
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<li><a href="#learning-objectives" id="toc-learning-objectives" class="nav-link" data-scroll-target="#learning-objectives">Learning Objectives</a></li>
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<li><a href="#instructors" id="toc-instructors" class="nav-link" data-scroll-target="#instructors">Instructors</a></li>
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<li><a href="#tentative-schedule" id="toc-tentative-schedule" class="nav-link" data-scroll-target="#tentative-schedule">Tentative Schedule</a></li>
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<li><a href="#format-of-class" id="toc-format-of-class" class="nav-link" data-scroll-target="#format-of-class">Format of Class</a></li>
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<li><a href="#posit-cloud-intro" id="toc-posit-cloud-intro" class="nav-link" data-scroll-target="#posit-cloud-intro">Posit Cloud Intro</a></li>
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<li><a href="#culture-of-the-course" id="toc-culture-of-the-course" class="nav-link" data-scroll-target="#culture-of-the-course">Culture of the course</a></li>
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<li><a href="#available-course-formats" id="toc-available-course-formats" class="nav-link" data-scroll-target="#available-course-formats">Available Course Formats</a></li>
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</ul></li>
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<li><strong>Explain</strong> data sources such as Databases and how to connect to them</li>
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<li><strong>Query</strong> data sources using database engines and Structured Query Language (SQL) to <strong>filter</strong>, <strong>join</strong>, and <strong>aggregate</strong> data</li>
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<li><strong>Construct</strong> and <strong>calculate</strong> new fields using <code>SELECT</code> or <code>CASE WHEN</code></li>
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<li>(optional) <strong>Read</strong> and <strong>explain</strong> a sample OMOP query: <a href="https://github.com/OHDSI/OMOP-Queries/tree/master" class="uri">https://github.com/OHDSI/OMOP-Queries/tree/master</a></li>
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</ul>
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</section>
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<section id="instructors" class="level2">
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<h2 class="anchored" data-anchor-id="instructors">Instructors</h2>
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<p>If you need to schedule some time to talk, please schedule with Ted.</p>
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<ul>
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<li><a href="https://laderast.github.io">Ted Laderas</a>, Office of the Chief Data Officer, Director of Training and Community</li>
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<li><a href="https://viveksriram.com/">Vivek Sriram</a>, Data Scientist, Office of the Chief Data Officer</li>
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<li><strong>Read</strong> and <strong>explain</strong> a sample OMOP query: <a href="https://github.com/OHDSI/OMOP-Queries/tree/master" class="uri">https://github.com/OHDSI/OMOP-Queries/tree/master</a></li>
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</ul>
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</section>
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<section id="tentative-schedule" class="level2">
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<h2 class="anchored" data-anchor-id="tentative-schedule">Tentative Schedule</h2>
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<p>All classes are on Fridays from 12:00-1:30 PM PST. Connection details will be provided. Office hours related to each class day are posted below, and the invite will be sent to you.</p>
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<p>All classes with be Fridays from 12:00-1:30 PM PST. Connection details will be provided.</p>
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<p>In class we will be going through the Quarto Notebooks that are hosted on Posit.cloud. No knowledge of R is necessary, we’ll show you what you need to know in class.</p>
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<p>Classes will be recorded, and those recordings will be sent to you after each class.</p>
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<table class="caption-top table">
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<thead>
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<tr class="header">
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<th>Week</th>
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<th>Date</th>
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<th>Subject</th>
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<th>Office Hours</th>
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</tr>
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</thead>
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<tbody>
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<tr class="odd">
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<td>Pre-class</td>
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<td>—-</td>
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<td><a href="concepts.html">Concepts of Databases</a></td>
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<td></td>
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</tr>
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<tr class="even">
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<td>1</td>
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<td>Feb 7</td>
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<td><a href="week1.html">Intro to SQL; <code>SHOW TABLES</code>, <code>DESCRIBE</code>, <code>SELECT</code>, <code>WHERE</code></a></td>
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<td>Feb 11</td>
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</tr>
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<tr class="odd">
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<td>2</td>
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<td>Feb 14</td>
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<td><code>JOIN</code>ing tables, more <code>WHERE</code></td>
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<td>Feb 25</td>
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</tr>
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<tr class="even">
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<td>-</td>
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<td>Feb 21</td>
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<td>No class (school break week)</td>
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<td>No office hours</td>
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</tr>
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<tr class="odd">
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<td>3</td>
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<td>Feb 28</td>
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<td>Calculating new fields, <code>GROUP BY</code>, <code>CASE WHEN</code>, <code>HAVING</code></td>
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<td>Mar 4</td>
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</tr>
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<tr class="even">
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<td>4</td>
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<td>Mar 7</td>
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<td>Subqueries/Views, Recap of course / review OMOP queries</td>
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<td>No office hours</td>
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</tr>
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</tbody>
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</table>
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</section>
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<section id="format-of-class" class="level2">
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<h2 class="anchored" data-anchor-id="format-of-class">Format of Class</h2>
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<p>I will teach online only, though you have the option of attending in the DaSL Lounge (Arnold M1-B406), which will have snacks and drinks available. Either Chris Lo or Vivek Sriram will host in person.</p>
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<p>We will spend the first 20-25 minutes of each class on catching up on last week’s exercises if you haven’t had the opportunity to work on them. Followed by that, we will have a short lecture/lab, where we will go through the notebooks for the week.</p>
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</section>
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<section id="posit-cloud-intro" class="level2">
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<h2 class="anchored" data-anchor-id="posit-cloud-intro">Posit Cloud Intro</h2>
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<p>Here is a short video introducing you to the Posit Cloud interface.</p>
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<div class="quarto-video ratio ratio-16x9"><iframe data-external="1" src="https://www.youtube.com/embed/tHHhVeQgYOU?si=qphKLor9wQdBB6VX&amp;t=46" title="" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen=""></iframe></div>
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</section>
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<section id="culture-of-the-course" class="level2">
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<h2 class="anchored" data-anchor-id="culture-of-the-course">Culture of the course</h2>
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<ul>
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});
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clipboard.on('success', onCopySuccess);
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if (window.document.getElementById('quarto-embedded-source-code-modal')) {
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// For code content inside modals, clipBoardJS needs to be initialized with a container option
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// TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
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const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
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text: getTextToCopy,
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container: window.document.getElementById('quarto-embedded-source-code-modal')
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if (window.Quarto?.typesetMath) {
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window.Quarto.typesetMath(note);
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}
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// TODO in 1.5, we should make sure this works without a callout special case
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if (note.classList.contains("callout")) {
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return note.outerHTML;
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} else {

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