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Checking permissions before updating Flatpaks
AI IS FUCKING CRAZY

I wanted to make a script to check if flatpak update app permissions have changed before updating them. I decided to use ChatGPTs newest model, 01-preview for this task and holy crap am I impressed. I had to give it 14 commands to get to the final product and it seems to work great. That number could have been reduced quite a bit had I done things a bit differently.

I still had to find the problems, look up reference docs to correct it, and even debug in an IDE a little. But just telling it where the problems were, it got there in the end, and its user interaction output is way better than what I was planning on doing.

Anywho, here are the commands I gave it, followed by the code it gave me in the end. I have not throughly checked and tested the code, but it seems to work from a few quick trials. For demonstration purposes, I have left all of my original typos uncorrected below.


Write me a program in php that checks if there are any updates for my installed flatpaks. and then for each flatpak check and see if the permissions have changed between my current version and the new version. report to me the changes. then ask me if i want to continue with the updates.
your code doesnt work.
first $command = 'flatpak list --app --updates --columns=application,app,branch,origin,installation'; should be flatpak remote-ls --updates --columns=application,app,branch,origin (installation is an invalid column)
and then flatpak info --show-permissions doesnt give the original permissions. you have to get the original non-user-modified permissions from /var/lib/flatpak
the line if (empty($output)) { is incorrect, it should be if (count($output)) { as $output is an array, not a string
$columns = preg_split('/\s{2,}/', trim($line)); is incorrect. its tab delimited, so it just needs to be explode("\t", trim($line));
you also have a problem with the $metadataPath. its not always in /var/lib/flatpak/app/ . It may be in /var/lib/flatpak/runtime/. You can confirm which directory it should be in with the options column having "runtime" as an option.
in the --columns for your first command, "application" should be "name"
actually, you cant get the options from flatpak remote-ls --updates . you have to get the options from flatpak list
flatpak remote-info does not have an option --show-permissions
in your flatpak remote-info command, there is no --branch option.
there is no --assumeno option
there is no --dry-run permission. perhaps use --no-deploy?
you are incorrect. flatpak remote-info does not have an option --show-permissions . we already went over that. perhaps flatpak remote-info --show-metadata to get the permissions
flatpak remote-info does not have --branch
when checking the metadata, do not compare the info under [Application]
also, move the "Get architecture" line above its for loop
you have a problem with exec($remoteInfoCommand, $remoteOutput); you need to always empty $remoteOutput before running the exec. Otherwise, it appends the data to what is already there.


<?php
/**
 * This script checks for Flatpak updates and reports permission changes.
 */

// Function to parse permissions from Flatpak metadata
function parsePermissions($content) {
    $permissions = [];
    $lines = is_array($content) ? $content : explode("\n", $content);
    $currentSection = '';
    $skipSections = ['Application']; // Sections to skip

    foreach ($lines as $line) {
        $line = trim($line);

        if (empty($line)) {
            continue;
        }

        // Check for section headers
        if (preg_match('/^\[(.*)\]$/', $line, $matches)) {
            $currentSection = $matches[1];

            // Skip the [Application] section
            if (in_array($currentSection, $skipSections)) {
                $currentSection = '';
                continue;
            }

            $permissions[$currentSection] = [];
        } elseif ($currentSection !== '') {
            // Only process lines within non-skipped sections
            $parts = explode('=', $line, 2);
            if (count($parts) == 2) {
                $key = $parts[0];
                $values = explode(';', trim($parts[1], ';'));
                $permissions[$currentSection][$key] = $values;
            } else {
                // Handle keys without '=' (e.g., single permissions)
                $permissions[$currentSection][$line] = [];
            }
        }
    }

    return $permissions;
}

// Function to compare permissions
function comparePermissions($current, $new) {
    $differences = [];

    // Get all sections
    $sections = array_unique(array_merge(array_keys($current), array_keys($new)));

    foreach ($sections as $section) {
        $currentSection = isset($current[$section]) ? $current[$section] : [];
        $newSection = isset($new[$section]) ? $new[$section] : [];

        // Get all keys in this section
        $keys = array_unique(array_merge(array_keys($currentSection), array_keys($newSection)));

        foreach ($keys as $key) {
            $currentValues = isset($currentSection[$key]) ? $currentSection[$key] : [];
            $newValues = isset($newSection[$key]) ? $newSection[$key] : [];

            // Compare values
            $added = array_diff($newValues, $currentValues);
            $removed = array_diff($currentValues, $newValues);

            if (!empty($added) || !empty($removed)) {
                $differences[$section][$key] = [
                    'added' => $added,
                    'removed' => $removed,
                ];
            }
        }
    }

    return $differences;
}

//Dakusan: Added this function and wrapped other echo statements into it after the fact
//Function to output a line with appId (if given), colored red (IsError=true) or green (IsError=false)
function outputColor($appId, $str, $isError=true)
{
    //Determine if coloring should be used
    static $hasColors=null;
    if(!isset($hasColors)) {
        $hasColors=stream_isatty(STDOUT) && (!trim(`command -v tput`) || intval(`tput colors`)>=16);
    }

    echo
        (!$hasColors ? '' : ($isError ? "\e[31m" : "\e[32m")).
        ($appId ? "$appId: " : '').
        $str.
        (!$hasColors ? '' : "\e[0m").
	"\n";
}

// Function to display permission differences
function displayDifferences($appId, $differences) {
    outputColor($appId, 'Permission changes:');
    foreach ($differences as $section => $keys) {
        outputColor(null, "  [$section]");
        foreach ($keys as $key => $changes) {
            if (!empty($changes['added'])) {
                outputColor(null, "    + $key = " . implode(';', $changes['added']));
            }
            if (!empty($changes['removed'])) {
                outputColor(null, "    - $key = " . implode(';', $changes['removed']));
            }
        }
    }
    echo "\n";
}

// Get architecture (moved above the loop)
$archCommand = 'flatpak --default-arch';
exec($archCommand, $archOutput);
$arch = trim(implode('', $archOutput));

// Step 1: Get the list of installed Flatpaks
$installedCommand = 'flatpak list -a --columns=application,branch,origin,options'; //Dakusan: Added -a after the fact
exec($installedCommand, $installedOutput);

// Remove header line if present
if (!empty($installedOutput) && strpos($installedOutput[0], 'Application ID') !== false) {
    array_shift($installedOutput);
}

// Build an associative array of installed applications
$installedApps = [];

foreach ($installedOutput as $line) {
    // The output is tab-delimited
    $columns = explode("\t", trim($line));
    if (count($columns) >= 4) {
        $appId = $columns[0];
        $branch = $columns[1];
        $origin = $columns[2];
        $options = $columns[3];

        $installedApps[$appId] = [
            'appId' => $appId,
            'branch' => $branch,
            'origin' => $origin,
            'options' => $options,
        ];
    }
}

// Get the list of available updates
$updatesCommand = 'flatpak remote-ls --updates --columns=application';
exec($updatesCommand, $updatesOutput);

// Remove header line if present
if (!empty($updatesOutput) && strpos($updatesOutput[0], 'Application ID') !== false) {
    array_shift($updatesOutput);
}

// Build a list of applications that have updates
$updatesAvailable = array_map('trim', $updatesOutput);

if (empty($updatesAvailable)) {
    echo "No updates available for installed Flatpaks.\n";
    exit(0);
}

$permissionChanges = [];

foreach ($updatesAvailable as $appId) {
    if (!isset($installedApps[$appId])) {
        outputColor($appId, 'Installed app not found. Skipping.'); //Dakusan: Added this line after the fact
        continue;
    }

    $app = $installedApps[$appId];
    $branch = $app['branch'];
    $origin = $app['origin'];
    $options = $app['options'];

    // Determine if it's an app or runtime
    $isRuntime = strpos($options, 'runtime') !== false;

    // Paths to the metadata files
    if ($isRuntime) {
        $metadataPath = "/var/lib/flatpak/runtime/$appId/$arch/$branch/active/metadata";
    } else {
        $metadataPath = "/var/lib/flatpak/app/$appId/$arch/$branch/active/metadata";
    }

    // Check if the metadata file exists
    if (!file_exists($metadataPath)) {
        outputColor($appId, 'Metadata file not found. Skipping.');
        continue;
    }

    // Read current permissions from the metadata file
    $metadataContent = file_get_contents($metadataPath);
    $currentPermissions = parsePermissions($metadataContent);

    // Get new metadata from remote
    $ref = $appId . '/' . $arch . '/' . $branch;
    $remoteInfoCommand = 'flatpak remote-info --show-metadata ' . escapeshellarg($origin) . ' ' . escapeshellarg($ref);

    // Clear $remoteOutput before exec()
    $remoteOutput = [];
    exec($remoteInfoCommand, $remoteOutput);

    if (empty($remoteOutput)) {
        outputColor($appId, 'Failed to retrieve remote metadata. Skipping.');
        continue;
    }

    // Parse new permissions from the remote metadata
    $newPermissions = parsePermissions($remoteOutput);

    // Compare permissions
    $differences = comparePermissions($currentPermissions, $newPermissions);

    if (!empty($differences)) {
        $permissionChanges[$appId] = $differences;
        displayDifferences($appId, $differences);
    } else { //Dakusan: Added this condition after the fact
        outputColor($appId, 'No permission changes found.', false);
    }
}

// If there are no permission changes, inform the user
if (empty($permissionChanges)) {
    echo "No permission changes detected in the available updates.\n";
}

// Ask user if they want to proceed
echo "Do you want to proceed with the updates? (y/N): ";
$handle = fopen("php://stdin", "r");
$line = fgets($handle);
$answer = trim(strtolower($line));

if ($answer == 'y' || $answer == 'yes') {
    // Proceed with updates
    echo "Updating Flatpaks...\n";
    passthru('flatpak update -y');
} else {
    echo "Updates canceled.\n";
}

fclose($handle);
?>
Installing KeePassXC & a Flatpak sandboxed browser

Since I have been moving my primary workstation to Linux, I have been in need of finding a new password manager after Roboform failed me. I decided to try out KeePassXC but was having trouble since my Ungoogled Chromium browser was sandboxed in Flatpak. The instructions for this on Unix Stack Exchange were no longer working so I had to dig into it myself.


The 2 primary problems were that:
1) The browsers’ sandboxes did not have the QT libs.
2) The interprocess communication pipe socket had been renamed from kpxc_server to org.keepassxc.KeePassXC.BrowserServer.


The following are the instructions to get KeePassXC running in Flatpak versions of both Chrome and Firefox. This was tested on Linux Mint 21.3 with both Ungoogled Chromium and Firefox. You will need to change the KP_FLATPAK_PACKAGE if you use other versions of Chrome.


  1. Run the relevant below environment variables in your command shell before running the commands in the following steps:
    #Shared environment variables:
    KP_CUSTOM=/home/$USER/keepass-browser
    KP_JSON_NAME=org.keepassxc.keepassxc_browser.json
    
    #Chrome environment variables:
    KP_FLATPAK_PACKAGE=io.github.ungoogled_software.ungoogled_chromium
    KP_JSON_START=~/.config/chromium/NativeMessagingHosts
    KP_JSON_END=~/.var/app/$KP_FLATPAK_PACKAGE/config/chromium/NativeMessagingHosts
    
    #Firefox environment variables:
    KP_FLATPAK_PACKAGE=org.mozilla.firefox
    KP_JSON_START=~/.mozilla/native-messaging-hosts
    KP_JSON_END=~/.var/app/$KP_FLATPAK_PACKAGE/.mozilla/native-messaging-hosts
    		
  2. Install and enable the browser extension:
    KeePassXD > Tools > Settings > Browser Integration:
    • Check “Enable Browser Integration”
    • Check “Chromium” and/or “Firefox”
    • Download the plugin listed on this screen in your browser
    • Click "OK"
    Note: This creates $KP_JSON_START/$KP_JSON_NAME

  3. Set up the needed files in the sandbox:
    #Put KeePass proxy and needed library files in user directory
    mkdir -p $KP_CUSTOM/lib
    mkdir -p $KP_JSON_END #Needed for firefox
    cp /usr/bin/keepassxc-proxy $KP_CUSTOM/
    rsync -a /usr/lib/x86_64-linux-gnu/libicudata* /usr/lib/x86_64-linux-gnu/libicuuc* /usr/lib/x86_64-linux-gnu/libicui* /usr/lib/x86_64-linux-gnu/libdouble* /usr/lib/x86_64-linux-gnu/libsodium* /usr/lib/x86_64-linux-gnu/libQt5* $KP_CUSTOM/lib
    
    #Copy the JSON file to the Flatpak app directory and change the executable path in the file
    cp $KP_JSON_START/$KP_JSON_NAME $KP_JSON_END/
    sed -i "s/\/usr\/bin\//"$(echo $KP_CUSTOM | sed 's_/_\\/_g')"\//" $KP_JSON_END/$KP_JSON_NAME
    		
  4. Add permissions to the Flatpak:
    flatpak override --user --filesystem=$KP_CUSTOM:ro $KP_FLATPAK_PACKAGE #Only required if home directory is not shared to the Flatpak
    flatpak override --user --filesystem=xdg-run/org.keepassxc.KeePassXC.BrowserServer:ro $KP_FLATPAK_PACKAGE
    flatpak override --user --env=LD_LIBRARY_PATH=$(flatpak info --show-permissions $KP_FLATPAK_PACKAGE | grep -oP '(?<=LD_LIBRARY_PATH=).*')";$KP_CUSTOM/lib" $KP_FLATPAK_PACKAGE