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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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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<meta name="author" content="Norwin Roosen" />
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<meta name="date" content="2023-02-23" />
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<title>Caching openSenseMap Data for Reproducibility</title>
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<script>// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
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// be compatible with the behavior of Pandoc < 2.8).
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document.addEventListener('DOMContentLoaded', function(e) {
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var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
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var i, h, a;
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for (i = 0; i < hs.length; i++) {
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h = hs[i];
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if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
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a = h.attributes;
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while (a.length > 0) h.removeAttribute(a[0].name);
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}
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});
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</script>
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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">
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code {
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white-space: pre;
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}
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.sourceCode {
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overflow: visible;
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}
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</style>
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<style type="text/css" data-origin="pandoc">
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pre > code.sourceCode { white-space: pre; position: relative; }
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pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
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pre > code.sourceCode > span:empty { height: 1.2em; }
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.sourceCode { overflow: visible; }
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code.sourceCode > span { color: inherit; text-decoration: inherit; }
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div.sourceCode { margin: 1em 0; }
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pre.sourceCode { margin: 0; }
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@media screen {
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div.sourceCode { overflow: auto; }
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}
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@media print {
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pre > code.sourceCode { white-space: pre-wrap; }
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pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
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}
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pre.numberSource code
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{ counter-reset: source-line 0; }
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pre.numberSource code > span
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{ position: relative; left: -4em; counter-increment: source-line; }
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pre.numberSource code > span > a:first-child::before
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{ content: counter(source-line);
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position: relative; left: -1em; text-align: right; vertical-align: baseline;
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border: none; display: inline-block;
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-webkit-touch-callout: none; -webkit-user-select: none;
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-khtml-user-select: none; -moz-user-select: none;
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-ms-user-select: none; user-select: none;
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padding: 0 4px; width: 4em;
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color: #aaaaaa;
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}
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pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
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div.sourceCode
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{ }
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@media screen {
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pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
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}
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code span.al { color: #ff0000; font-weight: bold; }
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code span.an { color: #60a0b0; font-weight: bold; font-style: italic; }
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code span.at { color: #7d9029; }
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code span.bn { color: #40a070; }
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code span.bu { color: #008000; }
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code span.cf { color: #007020; font-weight: bold; }
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code span.ch { color: #4070a0; }
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code span.cn { color: #880000; }
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code span.co { color: #60a0b0; font-style: italic; }
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code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; }
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code span.do { color: #ba2121; font-style: italic; }
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code span.dt { color: #902000; }
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code span.dv { color: #40a070; }
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code span.er { color: #ff0000; font-weight: bold; }
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code span.ex { }
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code span.fl { color: #40a070; }
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code span.fu { color: #06287e; }
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code span.im { color: #008000; font-weight: bold; }
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code span.in { color: #60a0b0; font-weight: bold; font-style: italic; }
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code span.kw { color: #007020; font-weight: bold; }
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code span.op { color: #666666; }
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code span.ot { color: #007020; }
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code span.pp { color: #bc7a00; }
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code span.sc { color: #4070a0; }
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code span.ss { color: #bb6688; }
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code span.st { color: #4070a0; }
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code span.va { color: #19177c; }
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code span.vs { color: #4070a0; }
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code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; }
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</style>
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<script>
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// apply pandoc div.sourceCode style to pre.sourceCode instead
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(function() {
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var sheets = document.styleSheets;
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for (var i = 0; i < sheets.length; i++) {
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if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
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try { var rules = sheets[i].cssRules; } catch (e) { continue; }
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var j = 0;
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while (j < rules.length) {
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var rule = rules[j];
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// check if there is a div.sourceCode rule
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if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") {
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j++;
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continue;
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}
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var style = rule.style.cssText;
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// check if color or background-color is set
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if (rule.style.color === '' && rule.style.backgroundColor === '') {
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j++;
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continue;
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}
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// replace div.sourceCode by a pre.sourceCode rule
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sheets[i].deleteRule(j);
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sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
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}
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}
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})();
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</script>
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<style type="text/css">body {
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background-color: #fff;
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margin: 1em auto;
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max-width: 700px;
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overflow: visible;
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padding-left: 2em;
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padding-right: 2em;
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font-family: "Open Sans", "Helvetica Neue", Helvetica, Arial, sans-serif;
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font-size: 14px;
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line-height: 1.35;
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}
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#TOC {
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clear: both;
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margin: 0 0 10px 10px;
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padding: 4px;
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width: 400px;
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border: 1px solid #CCCCCC;
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border-radius: 5px;
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background-color: #f6f6f6;
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font-size: 13px;
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line-height: 1.3;
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}
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#TOC .toctitle {
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font-weight: bold;
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font-size: 15px;
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margin-left: 5px;
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}
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#TOC ul {
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padding-left: 40px;
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margin-left: -1.5em;
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margin-top: 5px;
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margin-bottom: 5px;
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}
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#TOC ul ul {
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margin-left: -2em;
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}
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#TOC li {
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line-height: 16px;
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}
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table {
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margin: 1em auto;
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border-width: 1px;
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border-color: #DDDDDD;
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border-style: outset;
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border-collapse: collapse;
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}
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table th {
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border-width: 2px;
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padding: 5px;
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border-style: inset;
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}
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table td {
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border-width: 1px;
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border-style: inset;
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line-height: 18px;
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padding: 5px 5px;
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}
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table, table th, table td {
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border-left-style: none;
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border-right-style: none;
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}
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table thead, table tr.even {
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background-color: #f7f7f7;
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}
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p {
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margin: 0.5em 0;
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}
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blockquote {
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background-color: #f6f6f6;
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padding: 0.25em 0.75em;
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}
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hr {
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border-style: solid;
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border: none;
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border-top: 1px solid #777;
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margin: 28px 0;
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}
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dl {
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margin-left: 0;
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}
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dl dd {
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margin-bottom: 13px;
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margin-left: 13px;
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}
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dl dt {
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font-weight: bold;
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}
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ul {
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margin-top: 0;
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}
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ul li {
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list-style: circle outside;
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}
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ul ul {
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margin-bottom: 0;
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}
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pre, code {
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background-color: #f7f7f7;
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border-radius: 3px;
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color: #333;
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white-space: pre-wrap;
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}
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pre {
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border-radius: 3px;
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margin: 5px 0px 10px 0px;
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padding: 10px;
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}
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pre:not([class]) {
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background-color: #f7f7f7;
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}
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code {
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font-family: Consolas, Monaco, 'Courier New', monospace;
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font-size: 85%;
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}
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p > code, li > code {
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padding: 2px 0px;
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}
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div.figure {
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text-align: center;
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}
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img {
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background-color: #FFFFFF;
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padding: 2px;
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border: 1px solid #DDDDDD;
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border-radius: 3px;
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border: 1px solid #CCCCCC;
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margin: 0 5px;
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}
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h1 {
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margin-top: 0;
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font-size: 35px;
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line-height: 40px;
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}
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h2 {
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border-bottom: 4px solid #f7f7f7;
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padding-top: 10px;
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padding-bottom: 2px;
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font-size: 145%;
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}
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h3 {
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border-bottom: 2px solid #f7f7f7;
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padding-top: 10px;
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font-size: 120%;
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}
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a {
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color: #800080; }
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a:visited:hover {
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color: #BB00BB; }
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a[href^="http:"] {
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text-decoration: underline; }
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a[href^="https:"] {
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text-decoration: underline; }
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code > span.kw { color: #555; font-weight: bold; }
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code > span.dt { color: #902000; }
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code > span.dv { color: #40a070; }
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code > span.bn { color: #d14; }
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code > span.st { color: #d14; }
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code > span.co { color: #888888; font-style: italic; }
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code > span.ot { color: #007020; }
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code > span.al { color: #ff0000; font-weight: bold; }
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code > span.fu { color: #900; font-weight: bold; }
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code > span.er { color: #a61717; background-color: #e3d2d2; }
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</style>
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</head>
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<body>
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<h1 class="title toc-ignore">Caching openSenseMap Data for
|
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Reproducibility</h1>
|
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|
|
<h4 class="author">Norwin Roosen</h4>
|
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<h4 class="date">2023-02-23</h4>
|
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<p>It may be useful to download data from openSenseMap only once. For
|
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reproducible results, the data should be saved to disk, and reloaded at
|
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a later point.</p>
|
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<p>This avoids..</p>
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<ul>
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<li>changed results for queries without date parameters,</li>
|
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<li>unnecessary wait times,</li>
|
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<li>risk of API changes / API unavailability,</li>
|
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|
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<li>stress on the openSenseMap-server.</li>
|
|
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|
|
|
</ul>
|
|
|
|
|
|
<p>This vignette shows how to use this built in
|
|
|
|
|
|
<code>opensensmapr</code> feature, and how to do it yourself in case you
|
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|
|
|
want to save to other data formats.</p>
|
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|
|
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># this vignette requires:</span></span>
|
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|
|
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(opensensmapr)</span>
|
|
|
|
|
|
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(jsonlite)</span>
|
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|
|
|
|
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(readr)</span></code></pre></div>
|
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|
|
|
<div id="using-the-opensensmapr-caching-feature" class="section level2">
|
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<h2>Using the opensensmapr Caching Feature</h2>
|
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|
|
<p>All data retrieval functions of <code>opensensmapr</code> have a
|
|
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|
|
|
built in caching feature, which serializes an API response to disk.
|
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|
|
Subsequent identical requests will then return the serialized data
|
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|
|
instead of making another request.</p>
|
|
|
|
|
|
<p>To use this feature, just add a path to a directory to the
|
|
|
|
|
|
<code>cache</code> parameter:</p>
|
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|
|
|
|
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>b <span class="ot">=</span> <span class="fu">osem_boxes</span>(<span class="at">grouptag =</span> <span class="st">'ifgi'</span>, <span class="at">cache =</span> <span class="fu">tempdir</span>())</span>
|
|
|
|
|
|
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
|
|
|
|
|
|
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="co"># the next identical request will hit the cache only!</span></span>
|
|
|
|
|
|
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>b <span class="ot">=</span> <span class="fu">osem_boxes</span>(<span class="at">grouptag =</span> <span class="st">'ifgi'</span>, <span class="at">cache =</span> <span class="fu">tempdir</span>())</span>
|
|
|
|
|
|
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a></span>
|
|
|
|
|
|
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="co"># requests without the cache parameter will still be performed normally</span></span>
|
|
|
|
|
|
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>b <span class="ot">=</span> <span class="fu">osem_boxes</span>(<span class="at">grouptag =</span> <span class="st">'ifgi'</span>)</span></code></pre></div>
|
|
|
|
|
|
<p>Looking at the cache directory we can see one file for each request,
|
|
|
|
|
|
which is identified through a hash of the request URL:</p>
|
|
|
|
|
|
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">list.files</span>(<span class="fu">tempdir</span>(), <span class="at">pattern =</span> <span class="st">'osemcache</span><span class="sc">\\</span><span class="st">..*</span><span class="sc">\\</span><span class="st">.rds'</span>)</span></code></pre></div>
|
|
|
|
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|
<pre><code>## [1] "osemcache.17db5c57fc6fca4d836fa2cf30345ce8767cd61a.rds"</code></pre>
|
|
|
|
|
|
<p>You can maintain multiple caches simultaneously which allows to only
|
|
|
|
|
|
store data related to a script in the same directory:</p>
|
|
|
|
|
|
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>cacheDir <span class="ot">=</span> <span class="fu">getwd</span>() <span class="co"># current working directory</span></span>
|
|
|
|
|
|
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>b <span class="ot">=</span> <span class="fu">osem_boxes</span>(<span class="at">grouptag =</span> <span class="st">'ifgi'</span>, <span class="at">cache =</span> cacheDir)</span>
|
|
|
|
|
|
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a></span>
|
|
|
|
|
|
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a><span class="co"># the next identical request will hit the cache only!</span></span>
|
|
|
|
|
|
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>b <span class="ot">=</span> <span class="fu">osem_boxes</span>(<span class="at">grouptag =</span> <span class="st">'ifgi'</span>, <span class="at">cache =</span> cacheDir)</span></code></pre></div>
|
|
|
|
|
|
<p>To get fresh results again, just call <code>osem_clear_cache()</code>
|
|
|
|
|
|
for the respective cache:</p>
|
|
|
|
|
|
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu">osem_clear_cache</span>() <span class="co"># clears default cache</span></span>
|
|
|
|
|
|
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="fu">osem_clear_cache</span>(<span class="fu">getwd</span>()) <span class="co"># clears a custom cache</span></span></code></pre></div>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
<div id="custom-de--serialization" class="section level2">
|
|
|
|
|
|
<h2>Custom (De-) Serialization</h2>
|
|
|
|
|
|
<p>If you want to roll your own serialization method to support custom
|
|
|
|
|
|
data formats, here’s how:</p>
|
|
|
|
|
|
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co"># first get our example data:</span></span>
|
|
|
|
|
|
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>measurements <span class="ot">=</span> <span class="fu">osem_measurements</span>(<span class="st">'Windgeschwindigkeit'</span>)</span></code></pre></div>
|
|
|
|
|
|
<p>If you are paranoid and worry about <code>.rds</code> files not being
|
|
|
|
|
|
decodable anymore in the (distant) future, you could serialize to a
|
|
|
|
|
|
plain text format such as JSON. This of course comes at the cost of
|
|
|
|
|
|
storage space and performance.</p>
|
|
|
|
|
|
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co"># serializing senseBoxes to JSON, and loading from file again:</span></span>
|
|
|
|
|
|
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="fu">write</span>(jsonlite<span class="sc">::</span><span class="fu">serializeJSON</span>(measurements), <span class="st">'measurements.json'</span>)</span>
|
|
|
|
|
|
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>measurements_from_file <span class="ot">=</span> jsonlite<span class="sc">::</span><span class="fu">unserializeJSON</span>(readr<span class="sc">::</span><span class="fu">read_file</span>(<span class="st">'measurements.json'</span>))</span>
|
|
|
|
|
|
<span id="cb8-4"><a href="#cb8-4" aria-hidden="true" tabindex="-1"></a><span class="fu">class</span>(measurements_from_file)</span></code></pre></div>
|
|
|
|
|
|
<pre><code>## [1] "osem_measurements" "tbl_df" "tbl"
|
|
|
|
|
|
## [4] "data.frame"</code></pre>
|
|
|
|
|
|
<p>This method also persists the R object metadata (classes,
|
|
|
|
|
|
attributes). If you were to use a serialization method that can’t
|
|
|
|
|
|
persist object metadata, you could re-apply it with the following
|
|
|
|
|
|
functions:</p>
|
|
|
|
|
|
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="co"># note the toJSON call instead of serializeJSON</span></span>
|
|
|
|
|
|
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="fu">write</span>(jsonlite<span class="sc">::</span><span class="fu">toJSON</span>(measurements), <span class="st">'measurements_bad.json'</span>)</span>
|
|
|
|
|
|
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a>measurements_without_attrs <span class="ot">=</span> jsonlite<span class="sc">::</span><span class="fu">fromJSON</span>(<span class="st">'measurements_bad.json'</span>)</span>
|
|
|
|
|
|
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a><span class="fu">class</span>(measurements_without_attrs)</span></code></pre></div>
|
|
|
|
|
|
<pre><code>## [1] "data.frame"</code></pre>
|
|
|
|
|
|
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a>measurements_with_attrs <span class="ot">=</span> <span class="fu">osem_as_measurements</span>(measurements_without_attrs)</span>
|
|
|
|
|
|
<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a><span class="fu">class</span>(measurements_with_attrs)</span></code></pre></div>
|
|
|
|
|
|
<pre><code>## [1] "osem_measurements" "tbl_df" "tbl"
|
|
|
|
|
|
## [4] "data.frame"</code></pre>
|
|
|
|
|
|
<p>The same goes for boxes via <code>osem_as_sensebox()</code>.</p>
|
|
|
|
|
|
</div>
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