604 lines
16 KiB
HTML
604 lines
16 KiB
HTML
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<!DOCTYPE html>
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<html>
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<head>
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<meta charset="utf-8" />
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<meta name="generator" content="pandoc" />
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<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
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<title>Indices, Primary Keys and Foreign Key Constraints</title>
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<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
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<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
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<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
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<style>h1 {font-size: 34px;}
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h1.title {font-size: 38px;}
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h2 {font-size: 30px;}
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h3 {font-size: 24px;}
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h4 {font-size: 18px;}
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h5 {font-size: 16px;}
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h6 {font-size: 12px;}
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code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
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pre:not([class]) { background-color: white }</style>
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<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
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<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
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<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
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<script src="site_libs/navigation-1.1/tabsets.js"></script>
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<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
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<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
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<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
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<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
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<style type="text/css">
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code{white-space: pre-wrap;}
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span.smallcaps{font-variant: small-caps;}
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span.underline{text-decoration: underline;}
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div.column{display: inline-block; vertical-align: top; width: 50%;}
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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ul.task-list{list-style: none;}
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</style>
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<style type="text/css">code{white-space: pre;}</style>
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<script type="text/javascript">
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if (window.hljs) {
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hljs.configure({languages: []});
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hljs.initHighlightingOnLoad();
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if (document.readyState && document.readyState === "complete") {
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window.setTimeout(function() { hljs.initHighlighting(); }, 0);
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}
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}
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</script>
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<link rel="stylesheet" href="style.css" type="text/css" />
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<style type = "text/css">
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.main-container {
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max-width: 940px;
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margin-left: auto;
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margin-right: auto;
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}
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img {
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max-width:100%;
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}
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.tabbed-pane {
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padding-top: 12px;
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}
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.html-widget {
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margin-bottom: 20px;
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}
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button.code-folding-btn:focus {
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outline: none;
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}
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summary {
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display: list-item;
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}
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pre code {
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padding: 0;
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}
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</style>
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<style type="text/css">
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.dropdown-submenu {
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position: relative;
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}
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.dropdown-submenu>.dropdown-menu {
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top: 0;
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left: 100%;
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margin-top: -6px;
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margin-left: -1px;
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border-radius: 0 6px 6px 6px;
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}
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.dropdown-submenu:hover>.dropdown-menu {
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display: block;
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}
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.dropdown-submenu>a:after {
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display: block;
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content: " ";
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float: right;
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width: 0;
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height: 0;
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border-color: transparent;
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border-style: solid;
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border-width: 5px 0 5px 5px;
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border-left-color: #cccccc;
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margin-top: 5px;
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margin-right: -10px;
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}
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.dropdown-submenu:hover>a:after {
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border-left-color: #adb5bd;
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}
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.dropdown-submenu.pull-left {
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float: none;
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}
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.dropdown-submenu.pull-left>.dropdown-menu {
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left: -100%;
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margin-left: 10px;
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border-radius: 6px 0 6px 6px;
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}
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</style>
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<script type="text/javascript">
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// manage active state of menu based on current page
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$(document).ready(function () {
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// active menu anchor
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href = window.location.pathname
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href = href.substr(href.lastIndexOf('/') + 1)
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if (href === "")
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href = "index.html";
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var menuAnchor = $('a[href="' + href + '"]');
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// mark it active
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menuAnchor.tab('show');
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// if it's got a parent navbar menu mark it active as well
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menuAnchor.closest('li.dropdown').addClass('active');
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// Navbar adjustments
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var navHeight = $(".navbar").first().height() + 15;
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var style = document.createElement('style');
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var pt = "padding-top: " + navHeight + "px; ";
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var mt = "margin-top: -" + navHeight + "px; ";
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var css = "";
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// offset scroll position for anchor links (for fixed navbar)
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for (var i = 1; i <= 6; i++) {
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css += ".section h" + i + "{ " + pt + mt + "}\n";
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}
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style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
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document.head.appendChild(style);
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});
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</script>
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<!-- tabsets -->
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<style type="text/css">
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.tabset-dropdown > .nav-tabs {
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display: inline-table;
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max-height: 500px;
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min-height: 44px;
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overflow-y: auto;
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border: 1px solid #ddd;
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border-radius: 4px;
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}
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.tabset-dropdown > .nav-tabs > li.active:before {
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content: "";
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font-family: 'Glyphicons Halflings';
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display: inline-block;
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padding: 10px;
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border-right: 1px solid #ddd;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
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content: "";
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border: none;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
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content: "";
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font-family: 'Glyphicons Halflings';
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display: inline-block;
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padding: 10px;
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border-right: 1px solid #ddd;
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}
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.tabset-dropdown > .nav-tabs > li.active {
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display: block;
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}
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.tabset-dropdown > .nav-tabs > li > a,
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.tabset-dropdown > .nav-tabs > li > a:focus,
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.tabset-dropdown > .nav-tabs > li > a:hover {
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border: none;
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display: inline-block;
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border-radius: 4px;
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background-color: transparent;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
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display: block;
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float: none;
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}
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.tabset-dropdown > .nav-tabs > li {
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display: none;
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}
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</style>
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<!-- code folding -->
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<style type="text/css">
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#TOC {
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margin: 25px 0px 20px 0px;
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}
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@media (max-width: 768px) {
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#TOC {
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position: relative;
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width: 100%;
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}
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}
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@media print {
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.toc-content {
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/* see https://github.com/w3c/csswg-drafts/issues/4434 */
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float: right;
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}
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}
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.toc-content {
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padding-left: 30px;
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padding-right: 40px;
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}
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div.main-container {
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max-width: 1200px;
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}
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div.tocify {
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width: 20%;
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max-width: 260px;
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max-height: 85%;
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}
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@media (min-width: 768px) and (max-width: 991px) {
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div.tocify {
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width: 25%;
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}
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}
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@media (max-width: 767px) {
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div.tocify {
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width: 100%;
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max-width: none;
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}
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}
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.tocify ul, .tocify li {
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line-height: 20px;
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}
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.tocify-subheader .tocify-item {
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font-size: 0.90em;
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}
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.tocify .list-group-item {
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border-radius: 0px;
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}
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</style>
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</head>
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<body>
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<div class="container-fluid main-container">
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<!-- setup 3col/9col grid for toc_float and main content -->
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<div class="row">
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<div class="col-xs-12 col-sm-4 col-md-3">
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<div id="TOC" class="tocify">
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</div>
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</div>
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<div class="toc-content col-xs-12 col-sm-8 col-md-9">
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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<div class="container">
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<div class="navbar-header">
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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</button>
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<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
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</div>
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<div id="navbar" class="navbar-collapse collapse">
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<ul class="nav navbar-nav">
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<li>
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<a href="index.html">
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<span class="fa fa-home"></span>
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</a>
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fa fa-landmark"></span>
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Background
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="background.html">Model Background</a>
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</li>
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<li>
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<a href="vocabulary.html">How the Vocabulary is Built</a>
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</li>
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</ul>
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</li>
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<li>
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<a href="dataModelConventions.html">
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|||
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<span class="fa fa-list-alt"></span>
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Conventions
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|||
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</a>
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|||
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</li>
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|||
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<li class="dropdown">
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|||
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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|||
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<span class="fa fa-history"></span>
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|||
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CDM Versions
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<span class="caret"></span>
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|||
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</a>
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|||
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<ul class="dropdown-menu" role="menu">
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|||
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<li>
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|||
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<a href="cdm30.html">CDM v3.0</a>
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|||
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</li>
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|||
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<li>
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|||
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<a href="cdm531.html">CDM v5.3.1</a>
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|||
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</li>
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|||
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<li>
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|||
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<a href="cdm531.html">CDM v5.4</a>
|
|||
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</li>
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|||
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<li>
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|||
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<a href="cdm60.html">CDM v6.0</a>
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|||
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</li>
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|||
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</ul>
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|||
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</li>
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<li class="dropdown">
|
|||
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
|||
|
|
<span class="fa fa-plus-square"></span>
|
|||
|
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|
|||
|
|
Proposals
|
|||
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|
|||
|
|
<span class="caret"></span>
|
|||
|
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</a>
|
|||
|
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<ul class="dropdown-menu" role="menu">
|
|||
|
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<li>
|
|||
|
|
<a href="reviewProposals.html">Under Review</a>
|
|||
|
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</li>
|
|||
|
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<li class="dropdown-submenu">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="oncology.html">Oncology CDM Proposal</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
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</li>
|
|||
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</ul>
|
|||
|
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</li>
|
|||
|
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<li class="dropdown">
|
|||
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
|||
|
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<span class="fa fa-question"></span>
|
|||
|
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|
|||
|
|
Help
|
|||
|
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|
|||
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|
<span class="caret"></span>
|
|||
|
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</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
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<li>
|
|||
|
|
<a href="faq.html">FAQ</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="contribute.html">Ask a Question</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
<li class="dropdown">
|
|||
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
|||
|
|
<span class="fa fa-wrench"></span>
|
|||
|
|
|
|||
|
|
How to
|
|||
|
|
|
|||
|
|
<span class="caret"></span>
|
|||
|
|
</a>
|
|||
|
|
<ul class="dropdown-menu" role="menu">
|
|||
|
|
<li>
|
|||
|
|
<a href="sqlScripts.html">SQL Scripts</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="download.html">Download the DDL</a>
|
|||
|
|
</li>
|
|||
|
|
<li>
|
|||
|
|
<a href="drug_dose.html">Calculate Drug Dose</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
<ul class="nav navbar-nav navbar-right">
|
|||
|
|
<li>
|
|||
|
|
<a href="https://github.com/OHDSI/CommonDataModel">
|
|||
|
|
<span class="fa fa-github fa-lg"></span>
|
|||
|
|
|
|||
|
|
</a>
|
|||
|
|
</li>
|
|||
|
|
</ul>
|
|||
|
|
</div><!--/.nav-collapse -->
|
|||
|
|
</div><!--/.container -->
|
|||
|
|
</div><!--/.navbar -->
|
|||
|
|
|
|||
|
|
<div id="header">
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
<h1 class="title toc-ignore">Indices, Primary Keys and Foreign Key Constraints</h1>
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
|
|||
|
|
<div id="to-do" class="section level3">
|
|||
|
|
<h3>To Do</h3>
|
|||
|
|
<ul>
|
|||
|
|
<li>Need something for hashing</li>
|
|||
|
|
<li>What about constraints that aren’t foreign keys</li>
|
|||
|
|
</ul>
|
|||
|
|
</div>
|
|||
|
|
<div id="overview" class="section level2">
|
|||
|
|
<h2>Overview</h2>
|
|||
|
|
<p>Database indices improve the performance of queries against a database by organizing the data in a way that increase query execution.</p>
|
|||
|
|
<p>This article was written to provide guidance on the setting of indices, primary and foreign keys for data that has been transformed into the Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM). The community that supports the design and development of the OHDSI/CommonDataModel Github repository is a diverse collaborative of healthcare and technical profesisonals whom have limited data base adminstrative (DBA) experience. As a result, the comments below should be interpreted as suggestions and recommendations to help increase performance. Your teams needs may call for a modified configuration.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="general-recommendations" class="section level2">
|
|||
|
|
<h2>General Recommendations</h2>
|
|||
|
|
<p>Should your database of choice support indexing, the OMOP CDM Working Group recommends</p>
|
|||
|
|
<ul>
|
|||
|
|
<li>Indexing on all columns containing an "_id" (e.g. condition_occurrence_id, drug_exposure_id, measurement_id, procedure_occurrence_id, etc.)</li>
|
|||
|
|
<li>Indexing on primary and foreign keys</li>
|
|||
|
|
</ul>
|
|||
|
|
<p>For all databases, regardless of custom indice support, primary and foreign keys should be set. This is a step towards ensuring data integrity.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="database-support" class="section level2">
|
|||
|
|
<h2>Database support</h2>
|
|||
|
|
<p>The OHDSI/CommonDataModel package leverages OHDSI/SQLRender and as a result is only capable of supporting sources that are supported by OHDSI/SQLRender. The following databases are currently supported.</p>
|
|||
|
|
<div id="microsoft-sql-server" class="section level3">
|
|||
|
|
<h3>Microsoft SQL Server</h3>
|
|||
|
|
</div>
|
|||
|
|
<div id="oracle" class="section level3">
|
|||
|
|
<h3>Oracle</h3>
|
|||
|
|
</div>
|
|||
|
|
<div id="postgresql" class="section level3">
|
|||
|
|
<h3>PostgreSQL</h3>
|
|||
|
|
</div>
|
|||
|
|
<div id="amazon-redshift" class="section level3">
|
|||
|
|
<h3>Amazon Redshift</h3>
|
|||
|
|
<p>On AWS Redshift it is important to ensure that your data is properly distributed and sorted across nodes. Compression on certain columns may also help. The designed DDL does set DISTKEYS in an effort to optimize performance. This configuration can be seen within the <a href="https://github.com/OHDSI/CommonDataModel/blob/v5.4/ddl/5.4/redshift/OMOPCDM_redshift_5.4_ddl.sql">Redshift-specific DDL</a>.</p>
|
|||
|
|
</div>
|
|||
|
|
<div id="impala" class="section level3">
|
|||
|
|
<h3>Impala</h3>
|
|||
|
|
</div>
|
|||
|
|
<div id="ibm-netezza" class="section level3">
|
|||
|
|
<h3>IBM Netezza</h3>
|
|||
|
|
</div>
|
|||
|
|
<div id="google-bigquery" class="section level3">
|
|||
|
|
<h3>Google BigQuery</h3>
|
|||
|
|
<p>Google BigQuery does not require manual optimization and/or sizing. Google BigQuery does massive parallel full table scans and intensive caching, all under the hood. <a href="https://forums.ohdsi.org/t/iso-best-practices-of-cdm-indexing/10939/2">Reference</a></p>
|
|||
|
|
</div>
|
|||
|
|
<div id="microsoft-parallel-data-warehouse-pdw" class="section level3">
|
|||
|
|
<h3>Microsoft Parallel Data Warehouse (PDW)</h3>
|
|||
|
|
</div>
|
|||
|
|
<div id="sqlite" class="section level3">
|
|||
|
|
<h3>SQLite</h3>
|
|||
|
|
</div>
|
|||
|
|
<div id="databricks" class="section level3">
|
|||
|
|
<h3>Databricks</h3>
|
|||
|
|
<p>This database type is not yet supported but is actively being worked on by a number of collaborators. For more informtion, please contact Ajit Londhe of Amgen.</p>
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
<div id="references" class="section level2">
|
|||
|
|
<h2>References</h2>
|
|||
|
|
<p><a href="https://forums.ohdsi.org/t/iso-best-practices-of-cdm-indexing/10939/2">ISO Best Practices of CDM Indexing</a></p>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
</div>
|
|||
|
|
|
|||
|
|
<script>
|
|||
|
|
|
|||
|
|
// add bootstrap table styles to pandoc tables
|
|||
|
|
function bootstrapStylePandocTables() {
|
|||
|
|
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
|
|||
|
|
}
|
|||
|
|
$(document).ready(function () {
|
|||
|
|
bootstrapStylePandocTables();
|
|||
|
|
});
|
|||
|
|
|
|||
|
|
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
<!-- tabsets -->
|
|||
|
|
|
|||
|
|
<script>
|
|||
|
|
$(document).ready(function () {
|
|||
|
|
window.buildTabsets("TOC");
|
|||
|
|
});
|
|||
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|
|
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|
|
$(document).ready(function () {
|
|||
|
|
$('.tabset-dropdown > .nav-tabs > li').click(function () {
|
|||
|
|
$(this).parent().toggleClass('nav-tabs-open');
|
|||
|
|
});
|
|||
|
|
});
|
|||
|
|
</script>
|
|||
|
|
|
|||
|
|
<!-- code folding -->
|
|||
|
|
|
|||
|
|
<script>
|
|||
|
|
$(document).ready(function () {
|
|||
|
|
|
|||
|
|
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
|
|||
|
|
$('.unlisted.unnumbered').addClass('toc-ignore')
|
|||
|
|
|
|||
|
|
// move toc-ignore selectors from section div to header
|
|||
|
|
$('div.section.toc-ignore')
|
|||
|
|
.removeClass('toc-ignore')
|
|||
|
|
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
|
|||
|
|
|
|||
|
|
// establish options
|
|||
|
|
var options = {
|
|||
|
|
selectors: "h1,h2,h3,h4,h5",
|
|||
|
|
theme: "bootstrap3",
|
|||
|
|
context: '.toc-content',
|
|||
|
|
hashGenerator: function (text) {
|
|||
|
|
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
|
|||
|
|
},
|
|||
|
|
ignoreSelector: ".toc-ignore",
|
|||
|
|
scrollTo: 0
|
|||
|
|
};
|
|||
|
|
options.showAndHide = true;
|
|||
|
|
options.smoothScroll = true;
|
|||
|
|
|
|||
|
|
// tocify
|
|||
|
|
var toc = $("#TOC").tocify(options).data("toc-tocify");
|
|||
|
|
});
|
|||
|
|
</script>
|
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|
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|
<!-- dynamically load mathjax for compatibility with self-contained -->
|
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|
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<script>
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|
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</body>
|
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|
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</html>
|