### Set Database Password via Helm Install Argument

Source: https://docs.posit.co/helm/charts/rstudio-workbench/README.html

This example demonstrates how to set the database password directly during `helm install` using the `--set` argument. This method allows for dynamic configuration without modifying the `values.yaml` file.

```bash
`helm install ... --set config.secret.'database\.conf'.password="<YOUR_PASSWORD_HERE>"`
```

--------------------------------

### Inline Configuration File Example

Source: https://docs.posit.co/helm/charts/rstudio-workbench/README.html

This snippet illustrates how to provide configuration file content directly within the `values.yaml` file using a multi-line string. This is useful for in-lining configuration files or mounting them verbatim.

```yaml
config:
  server:
    rserver.conf: |
      verbatim-file=format
```

--------------------------------

### Initialize UI components and clipboard functionality

Source: https://docs.posit.co/chronicle

This script initializes the documentation page UI, including the color scheme toggle and clipboard copy functionality for code blocks. It ensures that interactive elements are injected into the DOM and event listeners are attached for user interactions.

```javascript
window.document.addEventListener("DOMContentLoaded", function (event) {
  if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
    const a = window.document.createElement('a');
    a.classList.add('top-right');
    a.classList.add('quarto-color-scheme-toggle');
    a.href = "";
    a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
    const i = window.document.createElement("i");
    i.classList.add('bi');
    a.appendChild(i);
    window.document.body.appendChild(a);
  }
  setColorSchemeToggle(hasAlternateSentinel());
  const icon = "\ue9cb";
  const anchorJS = new window.AnchorJS();
  anchorJS.options = { placement: 'right', icon: icon };
  anchorJS.add('.anchored');

  const onCopySuccess = function(e) {
    const button = e.trigger;
    button.blur();
    button.classList.add('code-copy-button-checked');
    var currentTitle = button.getAttribute("title");
    button.setAttribute("title", "Copied!");
    setTimeout(function() {
      button.setAttribute("title", currentTitle);
      button.classList.remove('code-copy-button-checked');
    }, 1000);
    e.clearSelection();
  };

  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
    text: function(trigger) {
      const outerScaffold = trigger.parentElement.cloneNode(true);
      const codeEl = outerScaffold.querySelector('code');
      return codeEl.innerText;
    }
  });
  clipboard.on('success', onCopySuccess);
});
```

--------------------------------

### Configure License via Helm Install Argument

Source: https://docs.posit.co/helm/charts/rstudio-pm/README.html

Command-line argument to inject the license file contents directly during the Helm installation process.

```bash
--set-file license.file.contents=licenses/rstudio-pm.lic
```

--------------------------------

### Initialize Tippy.js Tooltips for Elements

Source: https://docs.posit.co/chronicle

Configures and attaches a Tippy.js instance to a DOM element. It supports custom content functions and trigger/untrigger callbacks, specifically tailored for the Quarto theme.

```javascript
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
  const config = {
    allowHTML: true,
    maxWidth: 500,
    delay: 100,
    arrow: false,
    appendTo: function(el) { return el.parentElement; },
    interactive: true,
    interactiveBorder: 10,
    theme: 'quarto',
    placement: 'bottom-start',
  };
  if (contentFn) { config.content = contentFn; }
  if (onTriggerFn) { config.onTrigger = onTriggerFn; }
  if (onUntriggerFn) { config.onUntrigger = onUntriggerFn; }
  window.tippy(el, config);
}
```

--------------------------------

### Deploy Example Shiny Server Configuration

Source: https://docs.posit.co/shiny-server

Copies an example Shiny Server configuration file and installs example applications. It requires root privileges and backs up the existing configuration first. The default configuration hosts applications in /srv/shiny-server/.

```bash
sudo /opt/shiny-server/bin/deploy-example default
```

--------------------------------

### Configure Custom Startup Files via Helm

Source: https://docs.posit.co/helm/charts/rstudio-workbench/README.html

Demonstrates how to mount custom configuration files into the /startup/custom directory using Helm values. The content is provided as a verbatim string.

```yaml
config:
  startupCustom:
    myfile.conf: |
      file-used-verbatim
```

--------------------------------

### Initialize Quarto UI and Interaction Features

Source: https://docs.posit.co/connect

This initialization script sets up the Quarto environment by injecting a color scheme toggle if missing, configuring clipboard copy buttons for code blocks, and applying external link attributes. It also initializes tooltip behavior for cross-references and footnotes using the Tippy.js library.

```javascript
window.document.addEventListener("DOMContentLoaded", function (event) {
  if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
    const a = window.document.createElement('a');
    a.classList.add('top-right', 'quarto-color-scheme-toggle');
    a.href = "";
    a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
    const i = window.document.createElement("i");
    i.classList.add('bi');
    a.appendChild(i);
    window.document.body.appendChild(a);
  }
  
  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
    text: function(trigger) {
      const outerScaffold = trigger.parentElement.cloneNode(true);
      const codeEl = outerScaffold.querySelector('code');
      return codeEl.innerText;
    }
  });

  function tippyHover(el, contentFn) {
    const config = { allowHTML: true, maxWidth: 500, theme: 'quarto' };
    if (contentFn) config.content = contentFn;
    window.tippy(el, config);
  }
});
```

--------------------------------

### Initialize UI Theme Toggle and Clipboard Utilities

Source: https://docs.posit.co/connect/admin/reference-architectures/overview

This script initializes the color scheme toggle button if missing and configures clipboard copy functionality for code blocks. It ensures a consistent user experience by dynamically injecting UI elements and managing copy-to-clipboard events.

```javascript
window.document.addEventListener("DOMContentLoaded", function (event) {
  if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
    const a = window.document.createElement('a');
    a.classList.add('top-right');
    a.classList.add('quarto-color-scheme-toggle');
    a.href = "";
    a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
    const i = window.document.createElement("i");
    i.classList.add('bi');
    a.appendChild(i);
    window.document.body.appendChild(a);
  }
  setColorSchemeToggle(hasAlternateSentinel());
  const icon = "\ue9cb";
  const anchorJS = new window.AnchorJS();
  anchorJS.options = { placement: 'right', icon: icon };
  anchorJS.add('.anchored');

  const onCopySuccess = function(e) {
    const button = e.trigger;
    button.blur();
    button.classList.add('code-copy-button-checked');
    var currentTitle = button.getAttribute("title");
    button.setAttribute("title", "Copied!");
    e.clearSelection();
    setTimeout(function() {
      button.setAttribute("title", currentTitle);
      button.classList.remove('code-copy-button-checked');
    }, 1000);
  };

  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
    text: function(trigger) {
      const outerScaffold = trigger.parentElement.cloneNode(true);
      const codeEl = outerScaffold.querySelector('code');
      return codeEl.innerText;
    }
  });
  clipboard.on('success', onCopySuccess);
});
```

--------------------------------

### Deploy Example SSL Configuration for Shiny Server

Source: https://docs.posit.co/shiny-server

Uses a provided script to configure Shiny Server to use an example SSL configuration file and install sample applications. It's recommended to back up your current configuration before running this command.

```bash
sudo /opt/shiny-server/bin/deploy-example ssl
```

--------------------------------

### Install Shiny Server on Ubuntu

Source: https://docs.posit.co/shiny-server

Installs Shiny Server on Ubuntu systems after R and the Shiny R package are installed. It uses apt to install the downloaded .deb package. The installation places Shiny Server in /opt/shiny-server/.

```bash
wget <link_to_shiny-server.deb>
sudo apt install ./shiny-server-<version>.deb
```

--------------------------------

### Install Shiny Server on RedHat/CentOS

Source: https://docs.posit.co/shiny-server

Installs Shiny Server on RedHat/CentOS systems after R and the Shiny R package are installed. It uses yum to install the RPM package, which includes Shiny Server and its dependencies (excluding R and Shiny). The installation places Shiny Server in /opt/shiny-server/.

```bash
wget <link_to_shiny-server.rpm>
sudo yum install --nogpgcheck shiny-server-<version>.rpm
```

--------------------------------

### Initialize Biblioreference Tooltips

Source: https://docs.posit.co/connect/admin/reference-architectures/azure/single-server

Iterates through all bibliographical reference links (`a[role="doc-biblioref"]`) in the document. For each reference, it finds associated citation keys using `findCites` and then uses `tippyHover` to create tooltips that display the full citation content fetched from elements with IDs like 'ref-citekey'.

```javascript
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
    const ref = bibliorefs[i];
    const citeInfo = findCites(ref);
    if (citeInfo) {
        tippyHover(citeInfo.el, function() {
            var popup = window.document.createElement('div');
            citeInfo.cites.forEach(function(cite) {
                var citeDiv = window.document.createElement('div');
                citeDiv.classList.add('hanging-indent');
                citeDiv.classList.add('csl-entry');
                var biblioDiv = window.document.getElementById('ref-' + cite);
                if (biblioDiv) {
                    citeDiv.innerHTML = biblioDiv.innerHTML;
                }
                popup.appendChild(citeDiv);
            });
            return popup.innerHTML;
        });
    }
}
```

--------------------------------

### Install R on Ubuntu

Source: https://docs.posit.co/shiny-server

Installs R version 3.0 or higher on Ubuntu systems by adding the CRAN repository and then using apt to install the r-base package. It's recommended to add the CRAN repository to ensure the latest R version is installed.

```bash
sudo apt update
# Add CRAN repository as described in the Debian/Ubuntu documentation
sudo apt install r-base
```

--------------------------------

### Manage Shiny Server Legacy Installations

Source: https://docs.posit.co/shiny-server

Commands for removing legacy node.js-based installations and verifying the installed version of the Shiny R package.

```bash
sudo npm uninstall -g shiny-server
```

```bash
sudo su - -c "R -e \"packageVersion('shiny')\""
```

--------------------------------

### Bundle and Deploy Application to Connect

Source: https://docs.posit.co/how-to-guides/guides/migrate-shiny-server-pro-to-connect.html

Uses the connectapi package to create a client connection, bundle the application directory, and deploy it to the Posit Connect server.

```R
install.packages("connectapi")
library(connectapi)
client <- connect()
bund <- bundle_dir("<path-to-application>")
dep <- deploy(client, bund, "<application-name>")
poll_task(dep)
```

--------------------------------

### Install R on RedHat/CentOS

Source: https://docs.posit.co/shiny-server

Installs R version 3.0 or higher on RedHat/CentOS systems by first enabling the EPEL repository and then using yum to install the R package. This ensures that the necessary R version and its dependencies are available.

```bash
# Enable EPEL repository as described in the EPEL documentation
sudo yum install R
```

--------------------------------

### JavaScript: Color Scheme and Giscus Theme Toggling

Source: https://docs.posit.co/chronicle

This JavaScript code handles toggling between light and dark color schemes, managing local storage for theme preferences, and updating the Giscus comment theme based on user preferences and system settings. It includes functions to manage the 'no-transition' class, check for file URLs, set and get color scheme preferences from local storage, and toggle the Giscus theme if the iframe is loaded.

```javascript
const toggleNoTransition = (el, enabled) => {
  const shouldRemove = !enabled;
  if (shouldRemove) {
    el.classList.remove('notransition');
  } else {
    el.classList.add('notransition');
  }
}

const isFileUrl = () => {
  return window.location.protocol === 'file:';
}

const hasAlternateSentinel = () => {
  let styleSentinel = getColorSchemeSentinel();
  if (styleSentinel !== null) {
    return styleSentinel === "alternate";
  } else {
    return false;
  }
}

const setStyleSentinel = (alternate) => {
  const value = alternate ? "alternate" : "default";
  if (!isFileUrl()) {
    window.localStorage.setItem("quarto-color-scheme", value);
  } else {
    localAlternateSentinel = value;
  }
}

const getColorSchemeSentinel = () => {
  if (!isFileUrl()) {
    const storageValue = window.localStorage.getItem("quarto-color-scheme");
    return storageValue != null ? storageValue : localAlternateSentinel;
  } else {
    return localAlternateSentinel;
  }
}

const toggleGiscusIfUsed = (isAlternate, darkModeDefault) => {
  const baseTheme = document.querySelector('#giscus-base-theme')?.value ?? 'light';
  const alternateTheme = document.querySelector('#giscus-alt-theme')?.value ?? 'dark';
  let newTheme = '';
  if(authorPrefersDark) {
    newTheme = isAlternate ? baseTheme : alternateTheme;
  } else {
    newTheme = isAlternate ? alternateTheme : baseTheme;
  }

  const changeGiscusTheme = () => {
    // From: https://github.com/giscus/giscus/issues/336
    const sendMessage = (message) => {
      const iframe = document.querySelector('iframe.giscus-frame');
      if (!iframe) return;
      iframe.contentWindow.postMessage({ giscus: message }, 'https://giscus.app');
    }
    sendMessage({ setConfig: { theme: newTheme } });
  }

  const isGiscussLoaded = window.document.querySelector('iframe.giscus-frame') !== null;
  if (isGiscussLoaded) {
    changeGiscusTheme();
  }
};

const authorPrefersDark = false;
const darkModeDefault = authorPrefersDark;

document.querySelector('link#quarto-text-highlighting-styles.quarto-color-scheme-extra').rel = 'disabled-stylesheet';
document.querySelector('link#quarto-bootstrap.quarto-color-scheme-extra').rel = 'disabled-stylesheet';

let localAlternateSentinel = darkModeDefault ? 'alternate' : 'default';

// Dark / light mode switch
window.quartoToggleColorScheme = () => {
  // Read the current dark / light value
  let toAlternate = !hasAlternateSentinel();
  toggleColorMode(toAlternate);
  setStyleSentinel(toAlternate);
  toggleGiscusIfUsed(toAlternate, darkModeDefault);
  window.dispatchEvent(new Event('resize'));
};

// Switch to dark mode if need be
if (hasAlternateSentinel()) {
  toggleColorMode(true);
} else {
  toggleColorMode(false);
}
```

--------------------------------

### Initialize Quarto UI and Clipboard Utilities

Source: https://docs.posit.co/cloud-products

This script initializes the color scheme toggle, configures ClipboardJS for code block copying, and sets up external link behavior. It ensures that code snippets are copyable and that external links open in new tabs with appropriate security attributes.

```javascript
window.document.addEventListener("DOMContentLoaded", function (event) {
  if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
    const a = window.document.createElement('a');
    a.classList.add('top-right');
    a.classList.add('quarto-color-scheme-toggle');
    a.href = "";
    a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
    const i = window.document.createElement("i");
    i.classList.add('bi');
    a.appendChild(i);
    window.document.body.appendChild(a);
  }
  setColorSchemeToggle(hasAlternateSentinel());
  
  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
    text: function(trigger) {
      const codeEl = trigger.previousElementSibling.cloneNode(true);
      return codeEl.innerText;
    }
  });
});
```

--------------------------------

### Install Shiny Package

Source: https://docs.posit.co/shiny-server

Executes the R command to download and install the Shiny package into the system library with root privileges.

```bash
sudo su - -c "R -e \"install.packages('shiny')\""
```

--------------------------------

### Initialize Quarto UI and Interaction Features

Source: https://docs.posit.co/connect/admin/reference-architectures/aws/load-balanced

Initializes the DOM environment for Quarto pages by injecting color scheme toggles, configuring clipboard copy buttons for code blocks, and setting up external link behavior. It relies on external libraries like ClipboardJS, Tippy.js, and Bootstrap for interactive components.

```javascript
window.document.addEventListener("DOMContentLoaded", function (event) {
  if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
    const a = window.document.createElement('a');
    a.classList.add('top-right');
    a.classList.add('quarto-color-scheme-toggle');
    a.href = "";
    a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
    const i = window.document.createElement("i");
    i.classList.add('bi');
    a.appendChild(i);
    window.document.body.appendChild(a);
  }
  setColorSchemeToggle(hasAlternateSentinel());

  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
    text: getTextToCopy
  });
  clipboard.on('success', onCopySuccess);
});
```

--------------------------------

### Initialize Quarto UI Components and Event Listeners

Source: https://docs.posit.co/connect-cloud

Initializes the color scheme toggle, configures AnchorJS for headings, and sets up clipboard functionality for code blocks. It ensures that UI elements are dynamically injected or configured upon DOMContentLoaded.

```javascript
window.document.addEventListener("DOMContentLoaded", function (event) {
  if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
    const a = window.document.createElement('a');
    a.classList.add('top-right', 'quarto-color-scheme-toggle');
    a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
    window.document.body.appendChild(a);
  }
  const anchorJS = new window.AnchorJS();
  anchorJS.options = { placement: 'right', icon: '' };
  anchorJS.add('.anchored');
});
```

--------------------------------

### Install Shiny Server RPM

Source: https://docs.posit.co/shiny-server

Installs the Shiny Server RPM package using the zypper package manager, which sets up the service in /opt/shiny-server/.

```bash
sudo zypper --no-gpg-checks install shiny-server-<version>.rpm
```

--------------------------------

### Initialize GLightbox for Quarto

Source: https://docs.posit.co/connect/admin/reference-architectures/azure/single-server-robust

This script initializes GLightbox with specific zoom effects and hooks into slide loading events. It ensures that data-URI images are correctly resolved and that Quarto's mathematical typesetting is triggered after a slide loads.

```javascript
var lightboxQuarto = GLightbox({"closeEffect":"zoom","descPosition":"bottom","loop":false,"openEffect":"zoom","selector":".lightbox"});
(function() {
  let previousOnload = window.onload;
  window.onload = () => {
    if (previousOnload) { previousOnload(); }
    lightboxQuarto.on('slide_before_load', (data) => {
      const { slideIndex, slideNode, slideConfig, player, trigger } = data;
      const href = trigger.getAttribute('href');
      if (href !== null) {
        const imgEl = window.document.querySelector(`a[href="${href}"] img`);
        if (imgEl !== null) {
          const srcAttr = imgEl.getAttribute("src");
          if (srcAttr && srcAttr.startsWith("data:")) {
            slideConfig.href = srcAttr;
          }
        }
      }
    });
    lightboxQuarto.on('slide_after_load', (data) => {
      const { slideIndex, slideNode, slideConfig, player, trigger } = data;
      if (window.Quarto?.typesetMath) {
        window.Quarto.typesetMath(slideNode);
      }
    });
  };
})();
```

--------------------------------

### Initialize Lightbox Gallery (JavaScript)

Source: https://docs.posit.co/connect/admin/reference-architectures/aws/load-balanced

Initializes a GLightbox instance for handling image lightboxes. It includes custom event listeners for 'slide_before_load' and 'slide_after_load' to handle image sources and math typesetting within slides.

```javascript
var lightboxQuarto = GLightbox({"closeEffect":"zoom","descPosition":"bottom","loop":false,"openEffect":"zoom","selector":".lightbox"});
(function() {
    let previousOnload = window.onload;
    window.onload = () => {
        if (previousOnload) {
            previousOnload();
        }
        lightboxQuarto.on('slide_before_load', (data) => {
            const { slideIndex, slideNode, slideConfig, player, trigger } = data;
            const href = trigger.getAttribute('href');
            if (href !== null) {
                const imgEl = window.document.querySelector(`a[href="${href}"] img`);
                if (imgEl !== null) {
                    const srcAttr = imgEl.getAttribute("src");
                    if (srcAttr && srcAttr.startsWith("data:")) {
                        slideConfig.href = srcAttr;
                    }
                }
            }
        });
        lightboxQuarto.on('slide_after_load', (data) => {
            const { slideIndex, slideNode, slideConfig, player, trigger } = data;
            if (window.Quarto?.typesetMath) {
                window.Quarto.typesetMath(slideNode);
            }
        });
    };
})();
```

--------------------------------

### Install R and Dependencies on SLES

Source: https://docs.posit.co/shiny-server

Commands to add the R repository and install the base R environment along with the C++ compiler required for building R packages from source.

```bash
sudo zypper addrepo -f http://download.opensuse.org/repositories/devel:/languages:/R:/patched/SLE_12/ R-base
sudo zypper install R-base
sudo zypper install gcc-c++
```

--------------------------------

### Initialize Quarto UI and Clipboard Functionality

Source: https://docs.posit.co/ide/user

This script initializes the Quarto documentation interface, including the color scheme toggle, AnchorJS for section links, and clipboard integration for code blocks. It also automatically identifies and adorns external links with target attributes and CSS classes.

```javascript
window.document.addEventListener("DOMContentLoaded", function (event) {
  if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
    const a = window.document.createElement('a');
    a.classList.add('top-right', 'quarto-color-scheme-toggle');
    a.href = "";
    a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
    const i = window.document.createElement("i");
    i.classList.add('bi');
    a.appendChild(i);
    window.document.body.appendChild(a);
  }
  setColorSchemeToggle(hasAlternateSentinel());
  const icon = "\ue9cb";
  const anchorJS = new window.AnchorJS();
  anchorJS.options = { placement: 'right', icon: icon };
  anchorJS.add('.anchored');

  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
    text: getTextToCopy
  });
  clipboard.on('success', onCopySuccess);
});
```

--------------------------------

### Install R Markdown Package for Shiny Server

Source: https://docs.posit.co/shiny-server

This command installs the 'rmarkdown' R package system-wide, making it available for Shiny Server to host R Markdown documents. It requires superuser privileges.

```bash
sudo su - -c "R -e \"install.packages('rmarkdown')\""
```

--------------------------------

### Set Database Password via Helm Install Argument

Source: https://docs.posit.co/helm/charts/rstudio-pm/README.html

This command demonstrates how to set the database password directly during `helm install` using the `--set` argument. This is an alternative to managing secrets separately in `values.yaml`.

```bash
--set config.Postgres.Password="<YOUR_PASSWORD_HERE>"
```

--------------------------------

### Initialize Quarto UI and Clipboard Features

Source: https://docs.posit.co/connect/admin/reference-architectures/aws/k8s

Initializes the color scheme toggle, configures AnchorJS for headings, and sets up ClipboardJS for code block copying. It also handles UI feedback for successful copy operations.

```javascript
window.document.addEventListener("DOMContentLoaded", function (event) {
  if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
    const a = window.document.createElement('a');
    a.classList.add('top-right');
    a.classList.add('quarto-color-scheme-toggle');
    a.href = "";
    a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
    const i = window.document.createElement("i");
    i.classList.add('bi');
    a.appendChild(i);
    window.document.body.appendChild(a);
  }
  setColorSchemeToggle(hasAlternateSentinel());
  const icon = "\ue9cb";
  const anchorJS = new window.AnchorJS();
  anchorJS.options = { placement: 'right', icon: icon };
  anchorJS.add('.anchored');
});
```

--------------------------------

### Install Posit Chronicle Helm Chart

Source: https://docs.posit.co/helm/charts/posit-chronicle/README.html

Installs or upgrades the Posit Chronicle Helm chart to a specific version. It requires adding the RStudio Helm repository first. This command ensures you are using a stable, pinned version for production environments.

```bash
helm repo add rstudio https://helm.rstudio.com
helm upgrade --install my-release rstudio/posit-chronicle --version=0.4.6
```

--------------------------------

### Configure Environment and Generate Manifest

Source: https://docs.posit.co/how-to-guides/guides/migrate-shiny-server-pro-to-connect.html

Sets up the required environment variables for Posit Connect authentication and generates a manifest file necessary for the deployment process.

```bash
su - shiny
cd <path-to-your-application-directory>
vi .Renviron
# Add these lines:
CONNECT_SERVER  = https://<connect-URL>
CONNECT_API_KEY = <my-secret-api-key>
```

```R
readRenviron(".Renviron")
install.packages("rsconnect")
library(rsconnect)
rsconnect::writeManifest("<path-to-application>")
```

--------------------------------

### Restart Shiny Server using Upstart

Source: https://docs.posit.co/shiny-server

This command stops and then starts the Shiny Server service. It is recommended to use separate 'stop' and 'start' commands for a full restart to ensure all changes are detected. This action will interrupt active sessions.

```bash
sudo stop shiny-server
sudo start shiny-server
```

--------------------------------

### Configure Tippy Tooltips for References

Source: https://docs.posit.co/ide/server-pro/admin/job_launcher/job_launcher.html

Initializes Tippy.js tooltips for document references and cross-references. It dynamically fetches content from referenced elements to display in a floating popover.

```javascript
function tippyHover(el, contentFn) {
  const config = {
    allowHTML: true,
    interactive: true,
    theme: 'quarto',
    placement: 'bottom-start',
    content: contentFn
  };
  window.tippy(el, config);
}
```

--------------------------------

### Install Posit Connect Helm Chart

Source: https://docs.posit.co/helm/charts/rstudio-connect/README.html

Installs the Posit Connect Helm chart with a specific release name and version. It first adds the RStudio Helm repository if it's not already added. This command ensures a reproducible deployment by pinning the chart version.

```bash
helm repo add rstudio https://helm.rstudio.com
helm upgrade --install my-release rstudio/rstudio-connect --version=0.8.30
```

--------------------------------

### Initialize Kapa AI Widget

Source: https://docs.posit.co/connect/admin/reference-architectures/azure/k8s

Dynamically injects the Kapa AI chat widget script into the document head if the current page is part of the Posit documentation domain.

```javascript
(() => {
  const url = window.location.href;
  const scriptId = "posit-docs-kapa-widget";
  if (url.includes("docs.posit.co") && !document.getElementById(scriptId)) {
    const kapa = document.createElement("script");
    kapa.async = true;
    kapa.id = scriptId;
    kapa.src = "https://widget.kapa.ai/kapa-widget.bundle.js";
    kapa.setAttribute("data-button-text-color", "#447099");
    document.head.appendChild(kapa);
  }
})();
```

--------------------------------

### Initialize Citation Hover Tooltips

Source: https://docs.posit.co/connect/admin/reference-architectures/aws/single-server

Iterates through all elements with the role `doc-biblioref` (citation references). For each reference, it finds associated citation information using `findCites`. If found, it uses `tippyHover` to attach a tooltip that displays the content of the corresponding bibliography entries.

```javascript
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
  const ref = bibliorefs[i];
  const citeInfo = findCites(ref);
  if (citeInfo) {
    tippyHover(citeInfo.el, function() {
      var popup = window.document.createElement('div');
      citeInfo.cites.forEach(function(cite) {
        var citeDiv = window.document.createElement('div');
        citeDiv.classList.add('hanging-indent');
        citeDiv.classList.add('csl-entry');
        var biblioDiv = window.document.getElementById('ref-' + cite);
        if (biblioDiv) {
          citeDiv.innerHTML = biblioDiv.innerHTML;
        }
        popup.appendChild(citeDiv);
      });
      return popup.innerHTML;
    });
  }
});
```

--------------------------------

### Process Bibliographic Citations

Source: https://docs.posit.co/chronicle

Traverses the DOM to find citation references and attaches hover events to display bibliographic information in popups.

```javascript
const findCites = (el) => {
  const parentEl = el.parentElement;
  if (parentEl) {
    const cites = parentEl.dataset.cites;
    if (cites) return { el, cites: cites.split(' ') };
    else return findCites(el.parentElement);
  }
  return undefined;
};

var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
  const ref = bibliorefs[i];
  const citeInfo = findCites(ref);
  if (citeInfo) {
    tippyHover(citeInfo.el, function() {
      // Popup creation logic
    });
  }
}
```

--------------------------------

### Configure R Package Download Methods

Source: https://docs.posit.co/shiny-server

Sets the download method for R packages in Rprofile.site or ~/.Rprofile to ensure secure connections during installation.

```r
# For R 3.2
options(download.file.method = "libcurl")

# For R 3.1 and earlier
options(download.file.method = "wget")
```

--------------------------------

### Implement Cross-Reference Tooltips with Tippy.js

Source: https://docs.posit.co/connect/admin/reference-architectures/overview

This script enhances cross-references (xrefs) by using Tippy.js to display linked content in a tooltip. It handles both local and remote cross-references, fetching content dynamically when needed.

```javascript
const processXRef = (id, note) => {
  const stripColumnClz = (el) => {
    el.classList.remove("page-full", "page-columns");
    if (el.children) {
      for (const child of el.children) {
        stripColumnClz(child);
      }
    }
  }
  stripColumnClz(note)
  if (id === null || id.startsWith('sec-')) {
    const container = document.createElement("div");
    if (note.children && note.children.length > 2) {
      container.appendChild(note.children[0].cloneNode(true));
      for (let i = 1; i < note.children.length; i++) {
        const child = note.children[i];
        if (child.tagName === "P" && child.innerText === "") {
          continue;
        } else {
          container.appendChild(child.cloneNode(true));
          break;
        }
      }
      if (window.Quarto?.typesetMath) {
        window.Quarto.typesetMath(container);
      }
      return container.innerHTML
    } else {
      if (window.Quarto?.typesetMath) {
        window.Quarto.typesetMath(note);
      }
      return note.innerHTML;
    }
  } else {
    const anchorLink = note.querySelector('a.anchorjs-link');
    if (anchorLink) {
      anchorLink.remove();
    }
    if (window.Quarto?.typesetMath) {
      window.Quarto.typesetMath(note);
    }
    if (note.classList.contains("callout")) {
      return note.outerHTML;
    } else {
      return note.innerHTML;
    }
  }
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
for (var i=0; i<xrefs.length; i++) {
  const xref = xrefs[i];
  tippyHover(xref, undefined, function(instance) {
    instance.disable();
    let url = xref.getAttribute('href');
    let hash = undefined;
    if (url.startsWith('#')) {
      hash = url;
    } else {
      try {
        hash = new URL(url).hash;
      } catch {}
    }
    if (hash) {
      const id = hash.replace(/^#\/?/, "");
      const note = window.document.getElementById(id);
      if (note !== null) {
        try {
          const html = processXRef(id, note.cloneNode(true));
          instance.setContent(html);
        } finally {
          instance.enable();
          instance.show();
        }
      } else {
        fetch(url.split('#')[0])
          .then(res => res.text())
          .then(html => {
            const parser = new DOMParser();
            const htmlDoc = parser.parseFromString(html, "text/html");
            const note = htmlDoc.getElementById(id);
            if (note !== null) {
              const html = processXRef(id, note);
              instance.setContent(html);
            }
          }).finally(() => {
            instance.enable();
            instance.show();
          });
      }
    } else {
      fetch(url)
        .then(res => res.text())
        .then(html => {
          const parser = new DOMParser();
          const htmlDoc = parser.parseFromString(html, "text/html");
          const note = htmlDoc.querySelector('main.content');
          if (note !== null) {
            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
              note.children[0].remove();
            }
            const html = processXRef(null, note);
            instance.setContent(html);
          }
        }).finally(() => {
          instance.enable();
          instance.show();
        });
    }
  }, function(instance) {
  });
}
```

--------------------------------

### Code Annotation Check Function

Source: https://docs.posit.co/cloud

Defines a helper function `isCodeAnnotation` that checks if an HTML element has a class starting with 'code-annotation-'. This is used to identify and potentially remove annotation elements before copying code.

```javascript
const isCodeAnnotation = (el) => {
  for (const clz of el.classList) {
    if (clz.startsWith('code-annotation-')) {
      return true;
    }
  }
  return false;
}
```

--------------------------------

### Initialize Kapa.ai Documentation Widget

Source: https://docs.posit.co/connect/admin/reference-architectures/aws/load-balanced

Injects the Kapa.ai script into the document head to provide an AI-powered search and question-answering interface for Posit documentation.

```javascript
const url = window.location.href;
const scriptId = "posit-docs-kapa-widget";
if (url.includes("docs.posit.co") && !document.getElementById(scriptId)) {
  const kapa = document.createElement("script");
  kapa.async = true;
  kapa.id = scriptId;
  kapa.src = "https://widget.kapa.ai/kapa-widget.bundle.js";
  kapa.setAttribute("data-button-text-color", "#447099");
  document.head.appendChild(kapa);
}
```

--------------------------------

### Throttle Event Execution

Source: https://docs.posit.co/chronicle

A utility function to limit the frequency of function execution, commonly used for performance optimization during window resize events.

```javascript
function throttle(fn, ms) {
  let throttle = false;
  let timer;
  return (...args) => {
    if(!throttle) {
      fn.apply(this, args);
      throttle = true;
    } else {
      if(timer) clearTimeout(timer);
      timer = setTimeout(() => {
        fn.apply(this, args);
        timer = throttle = false;
      }, ms);
    }
  };
}
```