Code Style and documentation

libs/Config.php

@@ -2,11 +2,18 @@
 
 use ArrayObject;
 
-class Config extends ArrayObject {
+class Config extends ArrayObject
-
+{
-    public function merge($newValues, $override = true) {
+    /**
+     * Merge an array into the object
+     *
+     * @param array $newValues
+     * @param bool $override
+     */
+    public function merge($newValues, $override = true)
+    {
         foreach ($newValues as $key => $value) {
-            if (array_key_exists($key, $this) && $override == false) {
+            if ($override === false && array_key_exists($key, $this)) {
                 continue;
             }
 
@@ -14,7 +21,13 @@ class Config extends ArrayObject {
         }
     }
 
-    public function conservativeMerge($newValues) {
+    /**
+     * Merge an array into the object, ignore already added keys.
+     *
+     * @param $newValues
+     */
+    public function conservativeMerge($newValues)
+    {
         $this->merge($newValues, false);
     }
 }

libs/Daux.php

@@ -19,9 +19,10 @@ class Daux
     protected $processor;
 
     /**
-     * @var Tree\Entry
+     * @var Tree\Directory
      */
     public $tree;
+
     /**
      * @var Config
      */
@@ -84,6 +85,14 @@ class Daux
         $this->options->merge($default_config);
     }
 
+    /**
+     * Load the configuration files, first, "config.json"
+     * in the documentation and then the file specified
+     * when running the configuration
+     *
+     * @param string $override_file
+     * @throws Exception
+     */
     private function loadConfigOverrides($override_file)
     {
         // Read documentation overrides

libs/DauxHelper.php

@@ -4,6 +4,11 @@ use Todaymade\Daux\Tree\Directory;
 
 class DauxHelper
 {
+    /**
+     * @param Config $params
+     * @param string $current_url
+     * @return array
+     */
     public static function getTheme($params, $current_url)
     {
         $theme_folder = $params['local_base'] . DS . 'resources' . DS . 'themes' . DS . $params['theme-name'];
@@ -39,21 +44,19 @@ class DauxHelper
         $theme['templates'] = strtr($theme['templates'], $substitutions);
         $theme['favicon'] = utf8_encode(strtr($theme['favicon'], $substitutions));
 
-        foreach ($theme['css'] as $key => $css) {
+        foreach (['css', 'js', 'fonts'] as $element) {
-            $theme['css'][$key] = utf8_encode(strtr($css, $substitutions));
+            foreach ($theme[$element] as $key => $value) {
+                $theme[$element][$key] = utf8_encode(strtr($value, $substitutions));
             }
-
-        foreach ($theme['fonts'] as $key => $font) {
-            $theme['fonts'][$key] = utf8_encode(strtr($font, $substitutions));
-        }
-
-        foreach ($theme['js'] as $key => $js) {
-            $theme['js'][$key] = utf8_encode(strtr($js, $substitutions));
         }
 
         return $theme;
     }
 
+    /**
+     * @param string $path
+     * @return string
+     */
     public static function getCleanPath($path)
     {
         $path = str_replace(array('/', '\\'), DIRECTORY_SEPARATOR, $path);
@@ -72,24 +75,31 @@ class DauxHelper
         return implode(DIRECTORY_SEPARATOR, $absolutes);
     }
 
+    /**
+     * Get pathinfo for a file
+     *
+     * @param string $path
+     * @return array
+     */
     public static function pathinfo($path)
     {
         preg_match('%^(.*?)[\\\\/]*(([^/\\\\]*?)(\.([^\.\\\\/]+?)|))[\\\\/\.]*$%im', $path, $m);
-        if (isset($m[1])) {
+        $ret = [];
-            $ret['dir']=$m[1];
+        foreach (['dir' => 1, 'basename' => 2, 'filename' => 3, 'extension' => 5] as $key => $group) {
+            if (isset($m[$group])) {
+                $ret[$key] = $m[$group];
             }
-        if (isset($m[2])) {
-            $ret['basename']=$m[2];
-        }
-        if (isset($m[5])) {
-            $ret['extension']=$m[5];
-        }
-        if (isset($m[3])) {
-            $ret['filename']=$m[3];
         }
         return $ret;
     }
 
+    /**
+     * Locate a file in the tree. Returns the file if found or false
+     *
+     * @param Directory $tree
+     * @param string $request
+     * @return Tree\Entry|false
+     */
     public static function getFile($tree, $request)
     {
         $request = explode('/', $request);
@@ -149,10 +159,13 @@ class DauxHelper
         $separator = '_';
         // Convert all dashes into underscores
         $title = preg_replace('![' . preg_quote("-") . ']+!u', $separator, $title);
+
         // Remove all characters that are not the separator, letters, numbers, or whitespace.
         $title = preg_replace('![^' . preg_quote($separator) . '\pL\pN\s]+!u', '', $title);
+
         // Replace all separator characters and whitespace by a single separator
         $title = preg_replace('![' . preg_quote($separator) . '\s]+!u', $separator, $title);
+
         return trim($title, $separator);
     }
 
@@ -167,7 +180,9 @@ class DauxHelper
     {
         static $charsArray;
 
-        if (isset($charsArray)) return $charsArray;
+        if (isset($charsArray)) {
+            return $charsArray;
+        }
 
         return $charsArray = array(
             'a'    => array(

libs/Format/Base/CommonMark/LinkRenderer.php

@@ -22,12 +22,12 @@ class LinkRenderer extends \League\CommonMark\Inline\Renderer\LinkRenderer
     }
 
     /**
-     * @param $url
+     * @param string $url
      * @return Entry
      * @throws Exception
      */
-    protected function resolveInternalFile($url) {
+    protected function resolveInternalFile($url)
-
+    {
         $file = DauxHelper::getFile($this->daux['tree'], $url);
         if ($file) {
             return $file;

libs/Format/Confluence/Api.php

@@ -3,11 +3,9 @@
 use GuzzleHttp\Client;
 use GuzzleHttp\Exception\BadResponseException;
 use GuzzleHttp\Exception\ParseException;
-use GuzzleHttp\Exception\TransferException;
 
 class Api
 {
-
     protected $base_url;
     protected $user;
     protected $pass;
@@ -75,60 +73,23 @@ class Api
     }
 
     /**
-     * /rest/api/content/{id}/child/{type}
+     * Get a list of pages
      *
-     * @param $rootPage
+     * @param integer $rootPage
-     * @return mixed
+     * @param bool $recursive
+     * @return array
      */
-    public function getList($rootPage)
+    public function getList($rootPage, $recursive = false)
-    {
-        //We do a limit of 15 as it appears that confluence has
-        //a bug when retrieving more than 20 entries with "body.storage"
-        $url = "content/$rootPage/child/page?expand=version,body.storage&limit=15";
-
-        $pages = [];
-
-        do {
-            try {
-                $list = $this->getClient()->get($url)->json();
-            } catch (BadResponseException $e) {
-                throw $this->handleError($e);
-            }
-
-            foreach ($list['results'] as $result) {
-                $pages[$result['title']] = [
-                    "id" => $result['id'],
-                    "title" => $result['title'],
-                    "version" => $result['version']['number'],
-                    "content" => $result['body']['storage']['value'],
-                ];
-            }
-
-            if (array_key_exists('next', $list['_links'])) {
-                $url = $list['_links']['next'];
-            }
-
-        } while (array_key_exists('next', $list['_links']));
-
-        return $pages;
-    }
-
-    /**
-     * /rest/api/content/{id}/child/{type}
-     *
-     * @param $rootPage
-     * @return mixed
-     */
-    public function getHierarchy($rootPage)
     {
         $increment = 15;
 
-        //We do a limit of 15 as it appears that confluence has
+        // We set a limit of 15 as it appears that
-        //a bug when retrieving more than 20 entries with "body.storage"
+        // Confluence fails silently when retrieving
+        // more than 20 entries with "body.storage"
         $base_url = $url = "content/$rootPage/child/page?expand=version,body.storage&limit=$increment";
         $start = 0;
 
-        $children = [];
+        $pages = [];
 
         do {
             try {
@@ -138,24 +99,35 @@ class Api
             }
 
             foreach ($hierarchy['results'] as $result) {
-                $children[$result['title']] = [
+                $pages[$result['title']] = [
                     "id" => $result['id'],
                     "title" => $result['title'],
                     "version" => $result['version']['number'],
                     "content" => $result['body']['storage']['value'],
-                    "children" => $this->getHierarchy($result['id'])
                 ];
+
+                if ($recursive) {
+                    $pages[$result['title']]['children'] = $this->getList($result['id'], true);
+                }
             }
 
-			//We don't use _links->next as after ~30 elements it doesn't show any new elements
+            // We don't use _links->next as after ~30 elements
+            // it doesn't show any new elements. This seems
+            // to be a bug in Confluence
             $start += $increment;
             $url = "$base_url&start=$start";
 
         } while (!empty($hierarchy['results']));
 
-        return $children;
+        return $pages;
     }
 
+    /**
+     * @param integer $parent_id
+     * @param string $title
+     * @param string $content
+     * @return integer
+     */
     public function createPage($parent_id, $title, $content)
     {
         $body = [
@@ -175,6 +147,13 @@ class Api
         return $response['id'];
     }
 
+    /**
+     * @param integer $parent_id
+     * @param integer $page_id
+     * @param integer $newVersion
+     * @param string $title
+     * @param string $content
+     */
     public function updatePage($parent_id, $page_id, $newVersion, $title, $content)
     {
         $body = [
@@ -193,6 +172,12 @@ class Api
         }
     }
 
+    /**
+     * Delete a page
+     *
+     * @param integer $page_id
+     * @return mixed
+     */
     public function deletePage($page_id)
     {
         try {
@@ -202,6 +187,10 @@ class Api
         }
     }
 
+    /**
+     * @param integer $id
+     * @param array $attachment
+     */
     public function uploadAttachment($id, $attachment)
     {
         //get if attachment is uploaded
@@ -211,7 +200,7 @@ class Api
             throw $this->handleError($e);
         }
 
-        $url = "content/$id/child/attachment" . (count($result['results'])? "/{$result['results'][0]['id']}/data" : "");
+        $url = "content/$id/child/attachment" . count($result['results']) ? "/{$result['results'][0]['id']}/data" : "";
 
         try {
             $this->getClient()->post(

libs/Format/Confluence/Publisher.php

@@ -45,7 +45,8 @@ class Publisher
         $this->client->setSpace($confluence['space_id']);
     }
 
-    public function run($title, $closure) {
+    public function run($title, $closure)
+    {
         try {
             return $this->runAction($title, $this->output, $this->width, $closure);
         } catch (BadResponseException $e) {
@@ -69,7 +70,7 @@ class Publisher
             "Getting already published pages...",
             function() use (&$published) {
                 if ($published != null) {
-                    $published['children'] = $this->client->getHierarchy($published['id']);
+                    $published['children'] = $this->client->getList($published['id'], true);
                 }
             }
         );

libs/Format/HTML/Generator.php

@@ -32,6 +32,17 @@ class Generator
         $this->generateRecursive($daux->tree, $destination, $params, $output, $width);
     }
 
+    /**
+     * Recursively generate the documentation
+     *
+     * @param \Todaymade\Daux\Tree\Entry $tree
+     * @param string $output_dir
+     * @param \Todaymade\Daux\Config $params
+     * @param OutputInterface $output
+     * @param integer $width
+     * @param string $base_url
+     * @throws \Exception
+     */
     private function generateRecursive($tree, $output_dir, $params, $output, $width, $base_url = '')
     {
         $params['base_url'] = $params['base_page'] = $base_url;
@@ -46,7 +57,7 @@ class Generator
         foreach ($tree->value as $key => $node) {
             if ($node instanceof Directory) {
                 $new_output_dir = $output_dir . DS . $key;
-                @mkdir($new_output_dir);
+                mkdir($new_output_dir);
                 $this->generateRecursive($node, $new_output_dir, $params, $output, $width, '../' . $base_url);
             } elseif ($node instanceof Content) {
                 $this->runAction(

libs/Format/HTML/Template.php

@@ -7,6 +7,10 @@ class Template
 {
     protected $engine;
 
+    /**
+     * @param string $base
+     * @param string $theme
+     */
     public function __construct($base, $theme)
     {
         // Create new Plates instance
@@ -19,6 +23,11 @@ class Template
         $this->registerFunctions();
     }
 
+    /**
+     * @param string $name
+     * @param array $data
+     * @return string
+     */
     public function render($name, array $data = array())
     {
         $this->engine->addData([
@@ -123,6 +132,10 @@ class Template
         return $nav;
     }
 
+    /**
+     * @param string $separator
+     * @return string
+     */
     private function getSeparator($separator)
     {
         switch ($separator) {

libs/Generator/Command.php

@@ -4,7 +4,6 @@ use Symfony\Component\Console\Command\Command as SymfonyCommand;
 use Symfony\Component\Console\Input\InputArgument;
 use Symfony\Component\Console\Input\InputInterface;
 use Symfony\Component\Console\Output\OutputInterface;
-
 use Todaymade\Daux\Daux;
 use Todaymade\Daux\Format\HTML\Generator as HTMLGenerator;
 use Todaymade\Daux\Format\Confluence\Generator as ConfluenceGenerator;

libs/Generator/Helper.php

@@ -2,15 +2,26 @@
 
 class Helper
 {
+    /**
+     * Copy all files from $path to $local_base
+     *
+     * @param string $path
+     * @param string $local_base
+     */
     public static function copyAssets($path, $local_base)
     {
-        @mkdir($path);
+        mkdir($path);
         static::rmdir($path);
 
-        @mkdir($path . DS . 'resources');
+        mkdir($path . DS . 'resources');
         static::copyRecursive($local_base . DS . 'resources', $path . DS . 'resources');
     }
 
+    /**
+     * Remove a directory recursively
+     *
+     * @param string $dir
+     */
     private static function rmdir($dir)
     {
         $it = new \RecursiveDirectoryIterator($dir);
@@ -27,16 +38,22 @@ class Helper
         }
     }
 
-    private static function copyRecursive($src, $dst)
+    /**
+     * Copy files recursively
+     *
+     * @param string $source
+     * @param string $destination
+     */
+    private static function copyRecursive($source, $destination)
     {
-        $dir = opendir($src);
+        $dir = opendir($source);
-        @mkdir($dst);
+        mkdir($destination);
         while (false !== ($file = readdir($dir))) {
-            if (( $file != '.' ) && ( $file != '..' )) {
+            if ($file != '.' && $file != '..') {
-                if (is_dir($src . '/' . $file)) {
+                if (is_dir($source . '/' . $file)) {
-                    static::copyRecursive($src . '/' . $file, $dst . '/' . $file);
+                    static::copyRecursive($source . '/' . $file, $destination . '/' . $file);
                 } else {
-                    copy($src . '/' . $file, $dst . '/' . $file);
+                    copy($source . '/' . $file, $destination . '/' . $file);
                 }
             }
         }

libs/Processor.php

@@ -21,6 +21,11 @@ class Processor
      */
     protected $width;
 
+    /**
+     * @param Daux $daux
+     * @param OutputInterface $output
+     * @param integer $width
+     */
     public function __construct(Daux $daux, OutputInterface $output, $width)
     {
         $this->daux = $daux;
@@ -28,10 +33,24 @@ class Processor
         $this->width = $width;
     }
 
+    /**
+     * With this connection point, you can transform
+     * the tree as you want, move pages, modify
+     * pages and even add new ones.
+     *
+     * @param Directory $root
+     */
     public function manipulateTree(Directory $root)
     {
     }
 
+    /**
+     * This connection point provides
+     * a way to extend the Markdown
+     * parser and renderer.
+     *
+     * @param Environment $environment
+     */
     public function extendCommonMarkEnvironment(Environment $environment)
     {
     }

libs/Server/ErrorPage.php

@@ -9,19 +9,32 @@ class ErrorPage extends SimplePage
     const MISSING_PAGE_ERROR_TYPE = 'MISSING_PAGE_ERROR';
     const FATAL_ERROR_TYPE = 'FATAL_ERROR';
 
+    /**
+     * @var \Todaymade\Daux\Config
+     */
     private $params;
 
+    /**
+     * @param string $title
+     * @param string $content
+     * @param \Todaymade\Daux\Config $params
+     */
     public function __construct($title, $content, $params)
     {
         parent::__construct($title, $content);
         $this->params = $params;
     }
 
+    /**
+     * @return string
+     */
     protected function generatePage()
     {
         $params = $this->params;
-        $page['title'] = $this->title;
+        $page = [
-        $page['content'] = $this->content;
+            'title' => $this->title,
+            'content' => $this->content,
+        ];
 
         $template = new Template($params['templates'], $params['theme']['templates']);
         return $template->render('error', ['page' => $page, 'params' => $params]);

libs/Server/Server.php

@@ -6,7 +6,6 @@ use Todaymade\Daux\Exception;
 use Todaymade\Daux\Format\HTML\MarkdownPage;
 use Todaymade\Daux\Format\HTML\RawPage;
 use Todaymade\Daux\Format\HTML\SimplePage;
-use Todaymade\Daux\Tree\Directory;
 use Todaymade\Daux\Tree\Raw;
 
 class Server
@@ -16,6 +15,11 @@ class Server
     private $host;
     private $base_url;
 
+    /**
+     * Serve the documentation
+     *
+     * @throws Exception
+     */
     public static function serve()
     {
         $daux = new Daux(Daux::LIVE_MODE);
@@ -63,6 +67,9 @@ class Server
         }
     }
 
+    /**
+     * @return \Todaymade\Daux\Config
+     */
     public function getParams()
     {
         $params = $this->daux->getParams();
@@ -83,6 +90,14 @@ class Server
         return $params;
     }
 
+    /**
+     * Handle an incoming request
+     *
+     * @param array $query
+     * @return \Todaymade\Daux\Tree\Entry
+     * @throws Exception
+     * @throws NotFoundException
+     */
     public function handle($query = [])
     {
         $this->params = $this->getParams();
@@ -108,6 +123,14 @@ class Server
         }
     }
 
+    /**
+     * @param string $request
+     * @param string $content
+     * @return SimplePage
+     *
+     * @throws Exception
+     * @throws NotFoundException
+     */
     private function saveFile($request, $content)
     {
         $file = $this->getFile($request);
@@ -123,6 +146,11 @@ class Server
         return new SimplePage('Success', 'Successfully Edited');
     }
 
+    /**
+     * @param string $request
+     * @return \Todaymade\Daux\Tree\Entry
+     * @throws NotFoundException
+     */
     private function getPage($request)
     {
         $file = DauxHelper::getFile($this->daux->tree, $request);

libs/Tree/Builder.php

@@ -5,6 +5,15 @@ use Todaymade\Daux\DauxHelper;
 
 class Builder
 {
+    /**
+     * Build the initial tree
+     *
+     * @param string $dir
+     * @param array $ignore
+     * @param \Todaymade\Daux\Config $params
+     * @param array $parents
+     * @return Directory|void
+     */
     public static function build($dir, $ignore, $params, $parents = null)
     {
         if (!$dh = opendir($dir)) {
@@ -62,7 +71,13 @@ class Builder
         return $node;
     }
 
-    public static function getOrCreateDir($parent, $title) {
+    /**
+     * @param Entry $parent
+     * @param String $title
+     * @return Directory
+     */
+    public static function getOrCreateDir($parent, $title)
+    {
         $slug = DauxHelper::slug($title);
 
         if (array_key_exists($slug, $parent->value)) {
@@ -77,7 +92,13 @@ class Builder
         return $dir;
     }
 
-    public static function getOrCreatePage($parents, $title) {
+    /**
+     * @param array $parents
+     * @param string $title
+     * @return Content
+     */
+    public static function getOrCreatePage($parents, $title)
+    {
         $slug = DauxHelper::slug($title);
         $uri = $slug . ".html";
 

libs/Tree/Content.php

@@ -4,6 +4,9 @@ use Todaymade\Daux\DauxHelper;
 
 class Content extends Entry
 {
+    /**
+     * @var string
+     */
     protected $content;
 
     public function __construct($path = '', $parents = array())
@@ -13,6 +16,9 @@ class Content extends Entry
         $this->value = $this->uri;
     }
 
+    /**
+     * @return string
+     */
     public function getContent()
     {
         if (!$this->content) {
@@ -22,11 +28,18 @@ class Content extends Entry
         return $this->content;
     }
 
+    /**
+     * @param string $content
+     */
     public function setContent($content)
     {
         $this->content = $content;
     }
 
+    /**
+     * @param string $file
+     * @return string
+     */
     protected function getFilename($file)
     {
         return DauxHelper::pathinfo($file)['filename'];

libs/Tree/Entry.php

@@ -4,53 +4,90 @@ use Todaymade\Daux\DauxHelper;
 
 abstract class Entry
 {
+    /** @var string */
     protected $title;
+
+    /** @var string */
     protected $name;
+
+    /** @var Content */
     protected $index_page;
+
+    /** @var Content */
     protected $first_page;
+
+    /** @var string */
     protected $uri;
+
+    /** @var string */
     protected $local_path;
+
+    /** @var integer */
     protected $last_modified;
+
+    /** @var array */
     protected $parents;
 
+    /**
+     * @param string $path
+     * @param array $parents
+     */
     public function __construct($path = '', $parents = array())
     {
         $this->setPath($path);
         $this->setParents($parents);
     }
 
+    /**
+     * @return string
+     */
     public function getName()
     {
         return $this->name;
     }
 
+    /**
+     * @param string $name
+     */
     public function setName($name)
     {
         $this->name = $name;
     }
 
+    /**
+     * @return string
+     */
     public function getUri()
     {
         return $this->uri;
     }
 
+    /**
+     * @param string $uri
+     */
     public function setUri($uri)
     {
         $this->uri = $uri;
     }
 
+    /**
+     * @return Content
+     */
     public function getIndexPage()
     {
         return $this->index_page;
     }
 
+    /**
+     * @param Content $index_page
+     */
     public function setIndexPage($index_page)
     {
         $this->index_page = $index_page;
     }
 
     /**
-     * @return Entry
+     * @return Content
      */
     public function getFirstPage()
     {
@@ -80,36 +117,57 @@ abstract class Entry
         return false;
     }
 
+    /**
+     * @param Content $first_page
+     */
     public function setFirstPage($first_page)
     {
         $this->first_page = $first_page;
     }
 
+    /**
+     * @return string
+     */
     public function getTitle()
     {
         return $this->title;
     }
 
+    /**
+     * @param string $title
+     */
     public function setTitle($title)
     {
         $this->title = $title;
     }
 
+    /**
+     * @return array
+     */
     public function getParents()
     {
         return $this->parents;
     }
 
+    /**
+     * @param array $parents
+     */
     public function setParents($parents)
     {
         $this->parents = $parents;
     }
 
+    /**
+     * @return string
+     */
     public function getPath()
     {
         return $this->local_path;
     }
 
+    /**
+     * @param string $path
+     */
     public function setPath($path)
     {
         if (!isset($path) || $path == '' || !file_exists($path)) {
@@ -123,6 +181,10 @@ abstract class Entry
         $this->index_page = false;
     }
 
+    /**
+     * @param string $content
+     * @return bool
+     */
     public function write($content)
     {
         if (!is_writable($this->local_path)) {
@@ -133,6 +195,9 @@ abstract class Entry
         return true;
     }
 
+    /**
+     * @return string
+     */
     public function getUrl()
     {
         $url = '';
@@ -143,12 +208,20 @@ abstract class Entry
         return $url;
     }
 
+    /**
+     * @param string $file
+     * @return string
+     */
     protected function getFilename($file)
     {
         $parts = explode('/', $file);
         return end($parts);
     }
 
+    /**
+     * @param string $filename
+     * @return string
+     */
     protected function getTitleInternal($filename)
     {
         $filename = explode('_', $filename);
@@ -164,6 +237,10 @@ abstract class Entry
         return $filename;
     }
 
+    /**
+     * @param string $filename
+     * @return string
+     */
     protected function getUrlInternal($filename)
     {
         $filename = explode('_', $filename);