Lots to do!

_packages/extension-parser/classes/config.php

@@ -0,0 +1,84 @@
+<?php
+
+# Sequencing Formats
+# https://www.ncbi.nlm.nih.gov/sra/docs/submitformats/
+$Containers = [
+  'BAM'        => ['bam'],
+  'CRAM'       => ['cram'],
+  'EMBL'       => ['embl'],
+  'FASTA'      => ['fa', 'fasta', 'fsa'],
+  'FASTA+QUAL' => ['qual'],
+  'CSFASTA'    => ['csfa', 'csfasta', 'csfsa'],
+  'FASTQ'      => ['fastq', 'fq', 'sanfastq'],
+  'GFF'        => ['gff', 'gff2', 'gff3'],
+  'GTF'        => ['gtf'],
+  'GenBank'    => ['gb', 'gbk', 'genbank'],
+  'HDF5'       => ['bash5', 'baxh5', 'fast5', 'hdf5'],
+  'PIR'        => ['pir'],
+  'QSeq'       => ['qseq'],
+  'SAM'        => ['sam'],
+  'SFF'        => ['sff'],
+  'SRF'        => ['srf'],
+  'SnapGene'   => ['dna', 'seq'],
+  'SwissProt'  => ['dat'],
+  'VCF'        => ['vcf'],
+  'Plain'      => ['csv', 'txt'],
+];
+
+# Imaging Formats
+# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3948928/
+$ContainersGames = [
+  'Analyze'   => ['hdr', 'img'],
+  'Interfile' => ['h33'],
+  'Dicom'     => ['dcm', 'dicom'],
+  'Nifti'     => ['nii', 'nifti'],
+  'Minc'      => ['minc', 'mnc'],
+  'JPEG'      => ['jfif', 'jpeg', 'jpg'],
+  'JPEG 2000' => ['j2k', 'jp2', 'jpf', 'jpm', 'jpx', 'mj2'],
+  'PNG'       => ['png'],
+  'TIFF'      => ['tif', 'tiff'],
+  'WebP'      => ['webp'],
+  'Other'     => [''],
+];
+
+# Protein Formats
+# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518119/
+# DO NOT PARSE RAW FILES. TOO MANY COMPETING VENDORS
+$ContainersProt = [
+  'ABI/Sciex'      => ['t2d', 'wiff'],
+  'APML'           => ['apml'],
+  'ASF'            => ['asf'],
+  'Agilent/Bruker' => ['baf', 'd', 'fid', 'tdf', 'yep'],
+  'BlibBuild'      => ['blib'],
+  'Bruker/Varian'  => ['sms', 'xms'],
+  'Finnigan'       => ['dat', 'ms'],
+  'ION-TOF'        => ['ita', 'itm'],
+  'JCAMP-DX'       => ['jdx'],
+  'MGF'            => ['mgf'],
+  'MS2'            => ['ms2'],
+  'MSF'            => ['msf'],
+  'OMSSA'          => ['omssa', 'omx'],
+  'PEFF'           => ['peff'],
+  'Shimadzu'       => ['lcd', 'qgd', 'spc'],
+  'Skyline'        => ['sky', 'skyd'],
+  'TPP/SPC'        => ['dta'],
+  'Tandem'         => ['tandem'],
+  'TraML'          => ['traml'],
+  'ULVAC-PHI'      => ['tdc'],
+  'mzML'           => ['mzml'],
+  'mzXML'          => ['mzxml'],
+  'mzData'         => ['mzdata'],
+  'pepXML'         => ['pepxml'],
+  'protXML'        => ['protxml'],
+  'Plain'          => ['csv', 'txt'],
+];
+
+$Archives = [
+  '7z' => ['7z'],
+  'bzip2' => ['bz2', 'bzip2'],
+  'gzip' => ['gz', 'gzip', 'tgz', 'tpz'],
+  'Pickle' => ['pickle', 'pkl'],
+  'RAR' => ['rar', 'rev'],
+  'ZIP' => ['zip', 'zipx'],
+  'None' => [''],
+];

_packages/extension-parser/classes/torrent_form.class.php

@@ -0,0 +1,55 @@
+<?php ?>
+
+<!-- Three container fields -->
+<tr id="container_tr">
+  <td class="label">
+    Format
+    <strong class="important_text">*</strong>
+  </td>
+  <td>
+    <select name="container">
+      <option value="Autofill">Autofill</option>
+      <?php
+          foreach ($this->Containers as $Name => $Container) {
+              echo "<option value='$Name'>$Name</option>\n";
+          } ?>
+    </select><br />
+    Data file format, or detect from file list
+  </td>
+</tr>
+
+<!-- 2 -->
+<tr id="container_games_tr">
+  <td class="label">
+    Format
+    <strong class="important_text">*</strong>
+  </td>
+  <td>
+    <select id="container" name="container">
+      <option value="Autofill">Autofill</option>
+      <?php
+          foreach ($this->ContainersGames as $Name => $Container) {
+              echo "<option value='$Name'>$Name</option>\n";
+          } ?>
+    </select><br />
+    Data file format, or detect from file list
+  </td>
+</tr>
+
+<!-- 3 -->
+<tr id="container_prot_tr">
+  <td class="label">
+    Format
+    <strong class="important_text">*</strong>
+  </td>
+  <td>
+    <select id="container" name="container">
+      <option value="Autofill">Autofill</option>
+      <?php
+          foreach ($this->ContainersProt as $Name => $Container) {
+              echo "<option value='$Name'>$Name</option>\n";
+          } ?>
+    </select><br />
+    Data file format, or detect from file list
+  </td>
+</tr>

_packages/extension-parser/readme.md

@@ -0,0 +1,11 @@
+## Detect and autofill file types by extension
+
+One of the challenges of tracking biology data is the overwhelming number of file formats.
+If a user leaves the container or archive dropdown blank, this tool:
+  * Adds the file sizes of each extension
+  * Sorts the torrent file list by size
+  * Returns the first matching extension value
+
+## In this repo
+Please find all the snippets you need to implement a similar feature on your own tracker.
+The file and folder structure mirrors what Oppaitime Gazelle uses.

classes/artists.class.php

@@ -83,7 +83,7 @@ class Artists
 
     /**
      * Format an array of artists for display.
-     * TODO: Revisit the logic of this, see if we can helper-function the copypasta.
+     * todo: Revisit the logic of this, see if we can helper-function the copypasta.
      *
      * @param array Artists an array of the form output by get_artists
      * @param boolean $MakeLink if true, the artists will be links, if false, they will be text.
@@ -199,7 +199,7 @@ class Artists
     /**
      * Remove LRM (left-right-marker) and trims, because people copypaste carelessly.
      * If we don't do this, we get seemingly duplicate artist names.
-     * TODO: make stricter, e.g. on all whitespace characters or Unicode normalisation
+     * todo: make stricter, e.g. on all whitespace characters or Unicode normalisation
      *
      * @param string $ArtistName
      */

classes/autoenable.class.php

@@ -307,7 +307,7 @@ class AutoEnable {
         }
 
         if (!empty($IP)) {
-            // TODO: make this work with encrypted IPs
+            // todo: Make this work with encrypted IPs
             $Where[] = "uer.IP = '$IP'";
         }
 

classes/charts.class.php

@@ -144,7 +144,7 @@ class PIE_CHART extends GOOGLE_CHARTS {
 
 
 class LOG_BAR_GRAPH extends GOOGLE_CHARTS {
-  //TODO: Finish.
+  // todo: Finish
   public function __construct ($Base, $Width, $Height, $Options = []) {
     parent::__construct('lc', $Width, $Height, $Options);
   }

classes/classloader.php

@@ -7,7 +7,7 @@
 spl_autoload_register(function ($ClassName) {
   $FilePath = SERVER_ROOT . '/classes/' . strtolower($ClassName) . '.class.php';
   if (!file_exists($FilePath)) {
-    // TODO: Rename the following classes to conform with the code guidelines
+    // todo: Rename the following classes to conform with the code guidelines
     switch ($ClassName) {
       case 'MASS_USER_BOOKMARKS_EDITOR':
         $FileName = 'mass_user_bookmarks_editor.class';

classes/collages.class.php

@@ -33,7 +33,7 @@ class Collages
         list($CollageCount) = G::$DB->next_record();
 
         if ($CollageCount >= G::$LoggedUser['Permissions']['MaxCollages']) {
-            // @todo Fix this, the query was for COUNT(ID), so I highly doubt that this works... - Y
+            // todo: Fix this, the query was for COUNT(ID), so I highly doubt that this works... - Y
             list($CollageID) = G::$DB->next_record();
             header('Location: collage.php?id='.$CollageID);
             die();

classes/comments.class.php

@@ -49,7 +49,8 @@ class Comments {
    * @param int $PostID
    * @param string $NewBody
    * @param bool $SendPM If true, send a PM to the author of the comment informing him about the edit
-   * @todo Move permission check out of here/remove hardcoded error(404)
+   * 
+   * todo: Move permission check out of here/remove hardcoded error(404)
    */
   public static function edit($PostID, $NewBody, $SendPM = false) {
     $QueryID = G::$DB->get_query_id();
@@ -113,7 +114,7 @@ class Comments {
       Misc::send_pm($AuthorID, 0, $PMSubject, $PMBody);
     }
 
-    return true; // TODO: this should reflect whether or not the update was actually successful, e.g. by checking G::$DB->affected_rows after the UPDATE query
+    return true; // todo: This should reflect whether or not the update was actually successful, e.g., by checking G::$DB->affected_rows after the UPDATE query
   }
 
   /**

classes/commentsview.class.php

@@ -24,7 +24,8 @@ class CommentsView {
    * @param string $Link The link to the post elsewhere on the site
    * @param string $Header The header used in the post
    * @param bool $Tools Whether or not to show [Edit], [Report] etc.
-   * @todo Find a better way to pass the page (artist, collages, requests, torrents) to this function than extracting it from $Link
+   * 
+   * todo: Find a better way to pass the page (artist, collages, requests, torrents) to this function than extracting it from $Link
    */
   static function render_comment($AuthorID, $PostID, $Body, $AddedTime, $EditedUserID, $EditedTime, $Link, $Unread = false, $Header = '', $Tools = true) {
     $UserInfo = Users::user_info($AuthorID);

classes/config.template

@@ -102,8 +102,8 @@ define('FLS_TEAM',       '33');
 define('FORUM_MOD',      '9001');
 
 // Forums
-define('STAFF_FORUM',           0); # @todo
-define('DONOR_FORUM',           0); # @todo
+define('STAFF_FORUM',           0); # todo
+define('DONOR_FORUM',           0); # todo
 define('TRASH_FORUM_ID',        8);
 define('ANNOUNCEMENT_FORUM_ID', 1);
 

classes/file_checker.class.php

@@ -32,7 +32,7 @@ function check_name($Name) {
    * These characters are invalid in NTFS on Windows systems:
    *    : ? / < > \ * | "
    *
-   * TODO: Add "/" to the blacklist. Adding "/" to the blacklist causes problems with nested dirs, apparently.
+   * todo: Add "/" to the blacklist. Adding "/" to the blacklist causes problems with nested dirs, apparently
    *
    * Only the following characters need to be escaped (see the link below):
    *    \ - ^ ]

classes/mysql.class.php

@@ -143,7 +143,7 @@ function db_array($Array, $DontEscape = [], $Quote = false) {
   return $Array;
 }
 
-// @todo Revisit access levels once Drone is replaced by ZeRobot
+// todo: Revisit access levels once Drone is replaced by ZeRobot
 class DB_MYSQL {
   public $LinkID = false;
   protected $QueryID = false;

classes/notificationsmanager.class.php

@@ -599,7 +599,8 @@ class NotificationsManager {
   }
 
 /*
-  // TODO: Figure out what these functions are supposed to do and fix them
+  // todo: Figure out what these functions are supposed to do and fix them
+  
   public static function send_notification($UserID, $ID, $Type, $Message, $URL, $Importance = 'alert', $AutoExpire = false) {
     $Notifications = G::$Cache->get_value("user_cache_notifications_$UserID");
     if (empty($Notifications)) {

classes/script_start.php

@@ -37,7 +37,8 @@ if (!empty($_SERVER['HTTP_X_FORWARDED_FOR'])
 
 if (!isset($argv) && !empty($_SERVER['HTTP_HOST'])) {
   // Skip this block if running from cli or if the browser is old and shitty
-  // This should really be done in nginx config TODO: Remove
+  // This should really be done in nginx config
+  // todo: Remove
   if ($_SERVER['HTTP_HOST'] == 'www.'.SITE_DOMAIN) {
     header('Location: https://'.SITE_DOMAIN.$_SERVER['REQUEST_URI']); die();
   }
@@ -73,7 +74,7 @@ require(SERVER_ROOT.'/classes/classloader.php');
 
 // Note: G::initialize is called twice.
 // This is necessary as the code inbetween (initialization of $LoggedUser) makes use of G::$DB and G::$Cache.
-// TODO: remove one of the calls once we're moving everything into that class
+// todo: Remove one of the calls once we're moving everything into that class
 G::initialize();
 
 //Begin browser identification
@@ -84,7 +85,7 @@ $OperatingSystem = UserAgent::operating_system($_SERVER['HTTP_USER_AGENT']);
 $Debug->set_flag('start user handling');
 
 // Get classes
-// TODO: Remove these globals, replace by calls into Users
+// todo: Remove these globals, replace by calls into Users
 list($Classes, $ClassLevels) = Users::get_classes();
 
 //-- Load user information
@@ -100,7 +101,7 @@ if (isset($_COOKIE['session']) && isset($_COOKIE['userid'])) {
   $SessionID = $_COOKIE['session'];
   $LoggedUser['ID'] = (int)$_COOKIE['userid'];
 
-  $UserID = $LoggedUser['ID']; //TODO: UserID should not be LoggedUser
+  $UserID = $LoggedUser['ID']; //todo: UserID should not be LoggedUser
 
   if (!$LoggedUser['ID'] || !$SessionID) {
     logout();
@@ -292,7 +293,7 @@ if (isset($_COOKIE['session']) && isset($_COOKIE['userid'])) {
     $Cache->cache_value('stylesheets', $Stylesheets, 0);
   }
 
-  //A9 TODO: Clean up this messy solution
+  // todo: Clean up this messy solution
   $LoggedUser['StyleName'] = $Stylesheets[$LoggedUser['StyleID']]['Name'];
 
   if (empty($LoggedUser['Username'])) {

classes/text.class.php

@@ -868,7 +868,7 @@ class Text {
           if (!self::valid_url($Block['Val'], '\.(mp3|ogg|wav)')) {
             $Str .= '[aud]'.$Block['Val'].'[/aud]';
           } else {
-            //TODO: Proxy this for staff?
+            // todo: Proxy this for staff?
             $Str .= '<audio controls="controls" src="'.$Block['Val'].'"><a rel="noreferrer" target="_blank" href="'.$Block['Val'].'">'.$Block['Val'].'</a></audio>';
           }
           break;

classes/time.class.php

@@ -116,7 +116,7 @@ function time_minus($Offset, $Fuzzy = false) {
 }
 
 // This is never used anywhere with $timestamp set
-// TODO: Why don't we just use NOW() in the sql queries?
+// todo: Why don't we just use NOW() in the sql queries?
 function sqltime($timestamp = NULL) {
   return date('Y-m-d H:i:s', ($timestamp ?? time()));
 }

classes/tools.class.php

@@ -129,7 +129,7 @@ class Tools {
    * @return string the host.
    */
   public static function lookup_ip($IP) {
-    //TODO: use the G::$Cache
+    // todo: Use the G::$Cache
     $Output = explode(' ',shell_exec('host -W 1 '.escapeshellarg($IP)));
     if (count($Output) == 1 && empty($Output[0]))  { return ''; }
     if (count($Output) != 5)                       { return false; }

classes/torrent_form.class.php

@@ -357,8 +357,8 @@ class TorrentForm
         if (!empty($Torrent['Artists'])) {
             foreach ($Torrent['Artists'] as $Num => $Artist) {
                 ?>
-      <input type="text" id="idols_<?= $Num ?>"
-        name="idols[]" size="45"
+      <input type="text" id="idols_<?= $Num ?>" name="idols[]"
+        size="45"
         value="<?= display_str($Artist['name']) ?>"
         <?= $this->Disabled ?>/>
       <?php if ($Num === 0) { ?>
@@ -417,8 +417,8 @@ class TorrentForm
   </tr>
   <?php } # Ends if NewTorrent line 256?>
 
-    <!-- Encoding -->
-    <tr id="codec_tr">
+  <!-- Encoding -->
+  <tr id="codec_tr">
     <td class="label">
       License
       <strong class="important_text">*</strong>
@@ -483,8 +483,8 @@ class TorrentForm
     </td>
   </tr>
 
-    <!-- Resolution -->
-    <tr id="resolution_tr">
+  <!-- Resolution -->
+  <tr id="resolution_tr">
     <td class="label">
       Assembly Level
       <strong class="important_text">*</strong>
@@ -519,7 +519,7 @@ class TorrentForm
     </td>
   </tr>
 
-  <!-- Container -->
+  <!-- Three container fields -->
   <tr id="container_tr">
     <td class="label">
       Format
@@ -529,19 +529,15 @@ class TorrentForm
       <select name="container">
         <option value="Autofill">Autofill</option>
         <?php
-          foreach ($this->Containers as $Cont) {
-              echo "\t\t\t\t\t\t<option value=\"$Cont\"";
-              if ($Cont === ($Torrent['Container'] ?? false)) {
-                  echo " selected";
-              }
-              echo ">$Cont</option>\n";
+          foreach ($this->Containers as $Name => $Container) {
+              echo "<option value='$Name'>$Name</option>\n";
           } ?>
       </select><br />
       Data file format, or detect from file list
     </td>
   </tr>
 
-  <!-- Alternate container 1 -->
+  <!-- 2 -->
   <tr id="container_games_tr">
     <td class="label">
       Format
@@ -551,20 +547,16 @@ class TorrentForm
       <select id="container" name="container">
         <option value="Autofill">Autofill</option>
         <?php
-          foreach ($this->ContainersGames as $Container) {
-              echo "\t\t\t\t\t\t<option value=\"$Container\"";
-              if ($Container === ($Torrent['Container'] ?? false)) {
-                  echo " selected";
-              }
-              echo ">$Container</option>\n";
+          foreach ($this->ContainersGames as $Name => $Container) {
+              echo "<option value='$Name'>$Name</option>\n";
           } ?>
       </select><br />
       Data file format, or detect from file list
     </td>
   </tr>
 
-    <!-- Alternate container 2 -->
-    <tr id="container_prot_tr">
+  <!-- 3 -->
+  <tr id="container_prot_tr">
     <td class="label">
       Format
       <strong class="important_text">*</strong>
@@ -573,12 +565,8 @@ class TorrentForm
       <select id="container" name="container">
         <option value="Autofill">Autofill</option>
         <?php
-          foreach ($this->ContainersProt as $Container) {
-              echo "\t\t\t\t\t\t<option value=\"$Container\"";
-              if ($Container === ($Torrent['Container'] ?? false)) {
-                  echo " selected";
-              }
-              echo ">$Container</option>\n";
+          foreach ($this->ContainersProt as $Name => $Container) {
+              echo "<option value='$Name'>$Name</option>\n";
           } ?>
       </select><br />
       Data file format, or detect from file list
@@ -595,12 +583,12 @@ class TorrentForm
       <select name='archive'>
         <option value="Autofill">Autofill</option>
         <?php
-          foreach ($this->Archives as $Archive) {
-              echo "\t\t\t\t\t\t<option value=\"$Archive\"";
+          foreach ($this->Archives as $Name => $Archive) {
+              echo "\t\t\t\t\t\t<option value=\"$Name\"";
               if ($Archive === ($Torrent['Archive'] ?? false)) {
                   echo ' selected';
               }
-              echo ">$Archive</option>\n";
+              echo ">$Name</option>\n";
           } ?>
       </select><br />
       Compression algorithm, or detect from file list

classes/torrents.class.php

@@ -229,7 +229,9 @@ class Torrents {
    * @param int $TorrentID
    * @param int $UserID
    * @param string $Message
-   * @param boolean $Hidden Currently does fuck all. TODO: Fix that.
+   * @param boolean $Hidden Currently does fuck all.
+   * 
+   * todo: Fix that
    */
   public static function write_group_log($GroupID, $TorrentID, $UserID, $Message, $Hidden) {
     global $Time;

classes/tracker.class.php

@@ -1,5 +1,5 @@
 <?
-// TODO: Turn this into a class with nice functions like update_user, delete_torrent, etc.
+// todo: Turn this into a class with nice functions like update_user, delete_torrent, etc.
 class Tracker {
   const STATS_MAIN = 0;
   const STATS_USER = 1;

classes/u2f.class.php

@@ -299,7 +299,7 @@ class U2F {
     if (openssl_verify($dataToVerify, $signature, $pemKey, 'sha256') === 1) {
       $ctr = unpack("Nctr", substr($signData, 1, 4));
       $counter = $ctr['ctr'];
-      /* TODO: wrap-around should be handled somehow.. */
+      /* todo: wrap-around should be handled somehow... */
       if ($counter > $reg->counter) {
         $reg->counter = $counter;
         return $reg;

classes/validate.class.php

@@ -1,6 +1,6 @@
 <?php
 
-/*-- TODO ---------------------------//
+/*-- todo ---------------------------//
 Writeup how to use the Validate class, add in support for form id checks
 Complete the number and date validation
 //-----------------------------------*/
@@ -44,7 +44,7 @@ class Validate
         foreach ($this->Fields as $FieldKey => $Field) {
             $ValidateVar = $ValidateArray[$FieldKey];
 
-            # @todo Change this to a switch statement
+            # todo: Change this to a switch statement
             if ($ValidateVar !== '' || !empty($Field['Required']) || $Field['Type'] === 'date') {
                 if ($Field['Type'] === 'string') {
                     if (isset($Field['MaxLength'])) {
@@ -63,6 +63,7 @@ class Validate
                     } elseif (strlen($ValidateVar) < $MinLength) {
                         return $Field['ErrorMessage'];
                     }
+
                 } elseif ($Field['Type'] === 'number') {
                     if (isset($Field['MaxLength'])) {
                         $MaxLength = $Field['MaxLength'];
@@ -90,6 +91,7 @@ class Validate
                     } elseif ($ValidateVar < $MinLength) {
                         return $Field['ErrorMessage']."$MinLength";
                     }
+
                 } elseif ($Field['Type'] === 'email') {
                     if (isset($Field['MaxLength'])) {
                         $MaxLength = $Field['MaxLength'];
@@ -109,6 +111,7 @@ class Validate
                     } elseif (strlen($ValidateVar) < $MinLength) {
                         return $Field['ErrorMessage'];
                     }
+
                 } elseif ($Field['Type'] === 'link') {
                     if (isset($Field['MaxLength'])) {
                         $MaxLength = $Field['MaxLength'];
@@ -128,6 +131,7 @@ class Validate
                     } elseif (strlen($ValidateVar) < $MinLength) {
                         return $Field['ErrorMessage'];
                     }
+
                 } elseif ($Field['Type'] === 'username') {
                     if (isset($Field['MaxLength'])) {
                         $MaxLength = $Field['MaxLength'];
@@ -147,18 +151,22 @@ class Validate
                     } elseif (strlen($ValidateVar) < $MinLength) {
                         return $Field['ErrorMessage'];
                     }
+
                 } elseif ($Field['Type'] === 'checkbox') {
                     if (!isset($ValidateArray[$FieldKey])) {
                         return $Field['ErrorMessage'];
                     }
+
                 } elseif ($Field['Type'] === 'compare') {
                     if ($ValidateArray[$Field['CompareField']] !== $ValidateVar) {
                         return $Field['ErrorMessage'];
                     }
+
                 } elseif ($Field['Type'] === 'inarray') {
                     if (array_search($ValidateVar, $Field['InArray']) === false) {
                         return $Field['ErrorMessage'];
                     }
+
                 } elseif ($Field['Type'] === 'regex') {
                     if (!preg_match($Field['Regex'], $ValidateVar)) {
                         return $Field['ErrorMessage'];

download.php

@@ -3,7 +3,7 @@
 /*
  * Force file downloads
  * Currently used to download BibTeX citations
- * @todo Make this work with POST and display Show/Hide and Download buttons on the same line
+ * todo: Make this work with POST and display Show/Hide and Download buttons on the same line
  *
 
 if (isset($_POST['file']) && isset($_POST['content'])) {

gazelle.sql

@@ -7,7 +7,7 @@
 --   * Ocelot tokens:      char(32)
 --   * Tag lists:          varchar(500)
 --
+-- todo: Finish explaining the schema
 
 SET FOREIGN_KEY_CHECKS = 0;
 

sections/ajax/autofill/jav.php

@@ -19,9 +19,9 @@ if (!$debug && $Cache->get_value('jav_fill_json_'.$cn)) {
 } else {
 
   # Query the API
-  # @todo Valida to change $db
+  # todo: Validate to change $db
 
-/* @todo
+/* todo
  * switch $category:
  *   case 'DNA' || 'RNA':
  *     if $number = refseq_regex:

sections/ajax/collage.php

@@ -32,7 +32,7 @@ if ($CollageData) {
   $SetCache = true;
 }
 
-// TODO: Cache this
+// todo: Cache this
 $DB->query("
   SELECT GroupID
   FROM collages_torrents

sections/ajax/forum/thread.php

@@ -1,5 +1,5 @@
 <?php
-//TODO: Normalize thread_*_info don't need to waste all that ram on things that are already in other caches
+// todo: Normalize thread_*_info don't need to waste all that ram on things that are already in other caches
 /**********|| Page to show individual threads || ********************************\
 
 Things to expect in $_GET:

sections/ajax/torrentgroupalbumart.php

@@ -3,15 +3,18 @@ require(SERVER_ROOT.'/sections/torrents/functions.php');
 
 $GroupID = (int)$_GET['id'];
 if ($GroupID === 0) {
-  error('bad id parameter', true);
+  error('Bad ID parameter', true);
 }
 
 $TorrentDetails = get_group_info($GroupID, true, 0, false);
 $TorrentDetails = $TorrentDetails[0];
 $Image = $TorrentDetails['WikiImage'];
+
+/*
 if (!$Image) { // handle no artwork
   $Image = STATIC_SERVER.'common/noartwork/'.$CategoryIcons[$TorrentDetails['CategoryID'] - 1];
 }
+*/
 
 json_die("success", array(
   'wikiImage' => $Image

sections/artist/download.php

@@ -1,5 +1,5 @@
 <?
-//TODO: freeleech in ratio hit calculations, in addition to a warning of whats freeleech in the Summary.txt
+// todo: Freeleech in ratio hit calculations, in addition to a warning of whats freeleech in the Summary.txt
 /*
 This page is something of a hack so those
 easily scared off by funky solutions, don't

sections/better/transcode_beta.php

@@ -302,7 +302,7 @@ if ($ResultCount == 0) {
     $TorrentTags = new Tags($Group['TagList']);
 
     foreach ($Group['Editions'] as $RemIdent => $Edition) {
-      // TODO: point to the correct FLAC (?)
+      // todo: Point to the correct FLAC (?)
       $FlacID = array_search(true, $Edition['FlacIDs']);
       $DisplayName = $ArtistNames . "<a href=\"torrents.php?id=$GroupID&amp;torrentid=$FlacID#torrent$FlacID\" class=\"tooltip\" title=\"View torrent\" dir=\"ltr\">$GroupName</a>";
       if ($GroupYear > 0) {

sections/bookmarks/edit_torrents.php

@@ -26,7 +26,7 @@ View::show_header('Organize Bookmarks', 'browse,jquery-ui,jquery.tablesorter,sor
 
 $EditType = isset($_GET['type']) ? $_GET['type'] : 'torrents';
 
-list(, $CollageDataList, $TorrentList) = Users::get_bookmarks($UserID); // TODO: $TorrentList might not have the correct order, use the $GroupIDs instead
+list(, $CollageDataList, $TorrentList) = Users::get_bookmarks($UserID); // todo: $TorrentList might not have the correct order, use the $GroupIDs instead
 
 $TT = new MASS_USER_TORRENTS_TABLE_VIEW($TorrentList, $CollageDataList, $EditType, 'Organize Torrent Bookmarks');
 $TT->render_all();

sections/collages/artist_collage.php

@@ -1,5 +1,5 @@
 <?
-// TODO: Cache this
+// todo: Cache this
 $DB->query("
   SELECT
     ca.ArtistID,

sections/collages/torrent_collage.php

@@ -4,7 +4,7 @@ function compare($X, $Y) {
 }
 
 // Build the data for the collage and the torrent list
-// TODO: Cache this
+// todo: Cache this
 $DB->query("
   SELECT
     ct.GroupID,

sections/donate/donate_gpal.php

@@ -1,8 +1,8 @@
 <?
-//TODO: Developer, add resend last donation when available AND add missing headers to Test IPN
+// todo: Developer, add resend last donation when available AND add missing headers to Test IPN
 enforce_login();
 
-//Include the header
+// Include the header
 if ($LoggedUser['RatioWatch']) {
   error('Due to the high volume of payment disputes, we do not accept donations from users on ratio watch. Sorry.');
 }

sections/forums/get_post.php

@@ -1,5 +1,5 @@
 <?
-//TODO: make this use the cache version of the thread, save the db query
+// todo: make this use the cache version of the thread, save the db query
 /*********************************************************************\
 //--------------Get Post--------------------------------------------//
 

sections/forums/search.php

@@ -1,6 +1,6 @@
 <?php
 
-// @todo Clean up this fucking mess
+// todo: Clean up this fucking mess
 
 /*
 Forums search result page

sections/forums/take_reply.php

@@ -1,7 +1,7 @@
 <?
 authorize();
 
-//TODO: Remove all the stupid queries that could get their information just as easily from the cache
+// todo: Remove all the stupid queries that could get their information just as easily from the cache
 /*********************************************************************\
 //--------------Take Post--------------------------------------------//
 
@@ -242,7 +242,7 @@ if ($ThreadInfo['LastPostAuthorID'] == $LoggedUser['ID'] && ((!check_perms('site
     'Body'         => $Body,
     'EditedUserID' => 0,
     'EditedTime'   => NULL,
-    'Username'     => $LoggedUser['Username'] //TODO: Remove, it's never used?
+    'Username'     => $LoggedUser['Username'] // todo: Remove, it's never used?
   ]);
   $Cache->commit_transaction(0);
 

sections/forums/thread.php

@@ -1,5 +1,7 @@
 <?php
-//TODO: Normalize thread_*_info don't need to waste all that ram on things that are already in other caches
+
+// todo: Normalize thread_*_info don't need to waste all that ram on things that are already in other caches
+
 /**********|| Page to show individual threads || ********************************\
 
 Things to expect in $_GET:

sections/inbox/get_post.php

@@ -1,5 +1,7 @@
-<?
-//TODO: make this use the cache version of the thread, save the db query
+<?php
+
+// todo: make this use the cache version of the thread, save the db query
+
 /*********************************************************************\
 //--------------Get Post--------------------------------------------//
 
@@ -13,7 +15,7 @@ $_GET['post'], which is the ID of the post.
 
 // Quick SQL injection check
 if (!$_GET['post'] || !is_number($_GET['post'])) {
-  error(0);
+    error(0);
 }
 
 // Variables for database input
@@ -32,5 +34,3 @@ $Body = apcu_exists('DBKEY') ? Crypto::decrypt($Body) : '[Encrypted]';
 // This gets sent to the browser, which echoes it wherever
 
 echo trim($Body);
-
-?>

sections/index/index.php

@@ -1,17 +1,16 @@
-<?
+<?php
 if (isset($LoggedUser['ID'])) {
-  if (!isset($_REQUEST['action'])) {
-    include('private.php');
-  } else {
-    switch ($_REQUEST['action']) {
+    if (!isset($_REQUEST['action'])) {
+        include('private.php');
+    } else {
+        switch ($_REQUEST['action']) {
       case 'poll':
         include(SERVER_ROOT.'/sections/forums/poll_vote.php');
         break;
       default:
         error(0);
     }
-  }
+    }
 } else {
-  header('Location: login.php');
+    header('Location: login.php');
 }
-?>

sections/index/private.php

@@ -169,6 +169,8 @@ if (count($Freeleeches)) {
 <?
 }
 ?>
+
+<!-- Stats -->
     <div class="box">
       <div class="head colhead_dark"><strong>Stats</strong></div>
       <ul class="stats nobullet">
@@ -260,7 +262,7 @@ if (($ArtistCount = $Cache->get_value('stats_artist_count')) === false) {
         <li>Torrent Groups: <?=number_format($GroupCount)?></li>
         <li>Artists: <?=number_format($ArtistCount)?></li>
 <?
-//End Torrent Stats
+// End Torrent Stats
 
 if (($RequestStats = $Cache->get_value('stats_requests')) === false) {
   $DB->query("
@@ -277,7 +279,7 @@ if (($RequestStats = $Cache->get_value('stats_requests')) === false) {
   list($RequestCount, $FilledCount) = $RequestStats;
 }
 
-// do not divide by zero
+// Do not divide by zero
 if ($RequestCount > 0) {
   $RequestsFilledPercent = $FilledCount / $RequestCount * 100;
 } else {
@@ -295,7 +297,7 @@ if ($SnatchStats = $Cache->get_value('stats_snatches')) {
 }
 
 if (($PeerStats = $Cache->get_value('stats_peers')) === false) {
-  //Cache lock!
+  // Cache lock!
   $PeerStatsLocked = $Cache->get_value('stats_peers_lock');
   if (!$PeerStatsLocked) {
     $Cache->cache_value('stats_peers_lock', 1, 30);
@@ -330,6 +332,8 @@ if (!$PeerStatsLocked) {
         <li>Seeder/leecher ratio: <?=$Ratio?></li>
       </ul>
     </div>
+
+    <!-- Polls -->
 <?
 if (($TopicID = $Cache->get_value('polls_featured')) === false) {
   $DB->query("
@@ -388,6 +392,7 @@ if ($TopicID) {
   list($UserResponse) = $DB->next_record();
 
 ?>
+
     <div class="box">
       <div class="head colhead_dark"><strong>Poll<? if ($Closed) { echo ' [Closed]'; } ?></strong></div>
       <div class="pad">
@@ -430,7 +435,7 @@ if ($TopicID) {
     </div>
 <?
 }
-//polls();
+// polls();
 ?>
   </div>
   <div class="main_column">

sections/login/index.php

@@ -1,6 +1,6 @@
 <?php
 
-/*-- TODO ---------------------------//
+/*-- todo ---------------------------//
 Add the JavaScript validation into the display page using the class
 //-----------------------------------*/
 

sections/login/login.php

@@ -1,30 +1,51 @@
-<? View::show_header('Login'); ?>
-  <span id="no-cookies" class="hidden warning">You appear to have cookies disabled.<br /><br /></span>
-<?
-if (!$Banned) {
+<?php
+View::show_header('Login');
 ?>
-  <form class="auth_form" name="login" id="loginform" method="post" action="login.php">
-<?
+
+<span id="no-cookies" class="hidden warning">You appear to have cookies disabled.<br /><br /></span>
+
+<?php
+if (!$Banned) {
+    ?>
+
+<form class="auth_form" name="login" id="loginform" method="post" action="login.php">
+
+  <?php
   if (isset($Err)) {
-?>
+      ?>
+
   <span class="warning"><?=$Err?><br /><br /></span>
-<?  } ?>
-<?  if ($Attempts > 0) { ?>
-  You have <span class="info"><?=(6 - $Attempts)?></span> attempts remaining.<br /><br />
+
+  <?php
+  } ?>
+
+  <?php if ($Attempts > 0) { ?>
+
+  You have <span class="info"><?=(6 - $Attempts)?></span> attempts
+  remaining.<br /><br />
   <strong>WARNING:</strong> You will be banned for 6 hours after your login attempts run out!<br /><br />
-<?  } ?>
+
+  <?php } ?>
+
   <table class="layout">
+
+    <!-- todo: Put index page stats here -->
+
     <tr>
       <td colspan="2">
-        <input type="text" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" name="username" id="username" class="inputtext" required="required" maxlength="20" pattern="[A-Za-z0-9_?]{1,20}" autofocus="autofocus" placeholder="Username" size="40" />
+        <input type="text" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" name="username"
+          id="username" class="inputtext" required="required" maxlength="20" pattern="[A-Za-z0-9_?]{1,20}"
+          autofocus="autofocus" placeholder="Username" size="40" />
       </td>
     </tr>
     <tr>
       <td>
-        <input type="password" name="password" id="password" class="inputtext" required="required" maxlength="307200" pattern=".{6,307200}" placeholder="Password" />
+        <input type="password" name="password" id="password" class="inputtext" required="required" maxlength="307200"
+          pattern=".{6,307200}" placeholder="Password" />
       </td>
       <td>
-        <input type="text" name="twofa" id="twofa" class="inputtext" maxlength="6" pattern="[0-9]{6}" inputmode="numeric" placeholder="2FA" size="6" title="Leave blank if you have not enabled 2FA" />
+        <input type="text" name="twofa" id="twofa" class="inputtext" maxlength="6" pattern="[0-9]{6}"
+          inputmode="numeric" placeholder="2FA" size="6" title="Leave blank if you have not enabled 2FA" />
       </td>
     </tr>
     <tr>
@@ -33,18 +54,22 @@ if (!$Banned) {
       </td>
     </tr>
   </table>
-  </form>
-<?
+</form>
+<?php
 } else {
-?>
-  <span class="warning">You are banned from logging in for a few hours.</span>
-<?
-}
+      ?>
+<span class="warning">You are banned from logging in for a few hours.</span>
+<?php
+  }
 
 if ($Attempts > 0) {
-?>
-  <br /><br />
-  Forgot your password? <a href="login.php?act=recover" class="tooltip" title="Recover your password" style="text-decoration: underline;">Reset it here!</a>
-<?
+    ?>
+
+<br /><br />
+Forgot your password? <a href="login.php?act=recover" class="tooltip" title="Recover your password"
+  style="text-decoration: underline;">Reset it here!</a>
+
+<?php
 }
-View::show_footer(); ?>
+
+View::show_footer();

sections/reportsv2/search.php

@@ -1,21 +1,22 @@
-<?
+<?php
+
 /*
- * TODO: I'm not writing documentation for this page until I write this page >.>
+ * todo: I'm not writing documentation for this page until I write this page >.>
  */
+
 if (!check_perms('admin_reports')) {
-  error(403);
+    error(403);
 }
 
 View::show_header('Reports V2!', 'reportsv2');
-
 ?>
+
 <div class="header">
   <h2>Search</h2>
-<? include('header.php'); ?>
+  <?php include('header.php'); ?>
 </div>
 <div class="thin box pad">
   On hold until someone fixes the main torrents search.
 </div>
-<?
+<?php
 View::show_footer();
-?>

sections/requests/new_edit.php

@@ -1,6 +1,6 @@
 <?php
 
-# @todo Fix multiple authors and bounty preview
+# todo: Fix multiple authors and bounty preview
 
 /*
  * Yeah, that's right, edit and new are the same place again.
@@ -350,7 +350,7 @@ View::show_header(($NewRequest ? 'Create Request' : 'Edit Request'), 'bbcode,req
             <input type="hidden" id="current_downloaded"
               value="<?= $LoggedUser['BytesDownloaded'] ?>" />
             <ul>
-              <!-- @todo Return this feature
+              <!-- todo: Return this feature
               <li><strong>Bounty:</strong> <span id="bounty_after_tax">90.00 MB</span></li> -->
               <li><strong>Uploaded:</strong> <span id="new_uploaded"><?= Format::get_size($LoggedUser['BytesUploaded']) ?></span>
               </li>

sections/requests/request.php

@@ -322,7 +322,7 @@ $encoded_artist = urlencode($encoded_artist);
             <input id="total_bounty" type="hidden" value="<?=$RequestVotes['TotalBounty']?>" />
 
             <ul>
-              <!-- @todo Return this feature
+              <!-- todo: Return this feature
               <li><strong>Bounty:</strong> <span id="bounty_after_tax">0.00 MiB</span></li> -->
               <li><strong>Uploaded:</strong> <span id="new_uploaded"><?= Format::get_size($LoggedUser['BytesUploaded']) ?></span></li>
               <li><strong>Ratio:</strong> <span id="new_ratio"><?= Format::get_ratio_html($LoggedUser['BytesUploaded'],$LoggedUser['BytesDownloaded']) ?></span></li>

sections/schedule/daily/ratio_reqs.php

@@ -1,4 +1,4 @@
-<?
+<?php
 //------------------- Ratio requirements -----------------------//
 
 // Clear old seed time history
@@ -63,26 +63,24 @@ $DB->query("
   WHERE s.NumSnatches > 0");
 
 
-// TODO: change from PHP_INT_MAX to INF when we get prepared statements working (because apparently that works)
+// todo: Change from PHP_INT_MAX to INF when we get prepared statements working (because apparently that works)
 $DownloadBarrier = PHP_INT_MAX;
 
 foreach (RATIO_REQUIREMENTS as $Requirement) {
-  list($Download, $Ratio, $MinRatio) = $Requirement;
+    list($Download, $Ratio, $MinRatio) = $Requirement;
 
-  $DB->query("
+    $DB->query("
     UPDATE users_main
     SET RequiredRatio = RequiredRatioWork * $Ratio
     WHERE Downloaded >= $Download
       AND Downloaded < $DownloadBarrier");
 
-  $DB->query("
+    $DB->query("
     UPDATE users_main
     SET RequiredRatio = $MinRatio
     WHERE Downloaded >= $Download
       AND Downloaded < $DownloadBarrier
       AND RequiredRatio < $MinRatio");
 
-  $DownloadBarrier = $Download;
+    $DownloadBarrier = $Download;
 }
-
-?>

sections/schedule/hourly/front_page_stats.php

@@ -1,14 +1,15 @@
-<?
+<?php
+
 //------------- Front page stats ----------------------------------------//
 
-//Love or hate, this makes things a hell of a lot faster
+// Love or hate, this makes things a hell of a lot faster
 
-if ($Hour % 2 == 0) {
-  $DB->query("
+if ($Hour % 2 === 0) {
+    $DB->query("
     SELECT COUNT(uid) AS Snatches
     FROM xbt_snatched");
-  list($SnatchStats) = $DB->next_record();
-  $Cache->cache_value('stats_snatches', $SnatchStats, 0);
+    list($SnatchStats) = $DB->next_record();
+    $Cache->cache_value('stats_snatches', $SnatchStats, 0);
 }
 
 $DB->query("
@@ -44,4 +45,3 @@ $DB->query("
 list($UserStats['Month']) = $DB->next_record();
 
 $Cache->cache_value('stats_users', $UserStats, 0);
-?>

sections/staffpm/get_post.php

@@ -1,5 +1,6 @@
-<?
-//TODO: make this use the cache version of the thread, save the db query
+<?php
+// todo: Make this use the cache version of the thread, save the db query
+
 /*********************************************************************\
 //--------------Get Post--------------------------------------------//
 
@@ -13,14 +14,13 @@ $_GET['post'], which is the ID of the post.
 
 // Quick SQL injection check
 if (!$_GET['post'] || !is_number($_GET['post'])) {
-  error(0);
+    error(0);
 }
 
 // Variables for database input
 $PostID = $_GET['post'];
 
-// Message is selected providing the user quoting is the guy who opened the PM or has
-// the right level
+// Message is selected providing the user quoting is the guy who opened the PM or has the right level
 $DB->query("
   SELECT m.Message, c.Level, c.UserID
   FROM staff_pm_messages AS m
@@ -28,11 +28,9 @@ $DB->query("
   WHERE m.ID = '$PostID'");
 list($Message, $Level, $UserID) = $DB->next_record(MYSQLI_NUM);
 
-if (($LoggedUser['ID'] == $UserID) || ($IsFLS && $LoggedUser['Class'] >= $Level)) {
-  // This gets sent to the browser, which echoes it wherever
-  echo trim($Message);
+if (($LoggedUser['ID'] === $UserID) || ($IsFLS && $LoggedUser['Class'] >= $Level)) {
+    // This gets sent to the browser, which echoes it wherever
+    echo trim($Message);
 } else {
-  error(403);
+    error(403);
 }
-
-?>

sections/tools/index.php

@@ -351,7 +351,7 @@ switch ($_REQUEST['action']) {
     break;
 
   case 'ip_ban':
-    //TODO: Clean up DB table ip_bans.
+    // todo: Clean up DB table ip_bans
     include(SERVER_ROOT.'/sections/tools/managers/bans.php');
     break;
   case 'quick_ban':

sections/tools/managers/enable_requests.php

@@ -35,7 +35,7 @@ $OrderBy = "uer.Timestamp";
 $OrderWay = "DESC";
 
 // Build query for different views
-// TODO: Work with encrypted values
+// todo: Work with encrypted values
 if (!isset($_GET['view'])) {
   $_GET['view'] = 'main';
 }

sections/tools/managers/label_aliases.php

@@ -15,7 +15,7 @@ $OrderBy = $_GET['order'] === 'BadLabels' ? 'BadLabel' : 'AliasLabel';
 /*
 $LabelID = (int)$_GET['id'];
 $LabelNameSQL = '';
-//TODO join with labels table to get label name
+// todo: Join with labels table to get label name
 if (!empty($LabelID)) {
   $DB->query("
     SELECT name

sections/tools/misc/create_user.php

@@ -1,5 +1,5 @@
 <?
-//TODO: rewrite this, make it cleaner, make it work right, add it common stuff
+// todo: Rewrite this, make it cleaner, make it work right, add it common stuff
 if (!check_perms('admin_create_users')) {
   error(403);
 }

sections/torrents/browse.php

@@ -1,6 +1,6 @@
 <?php
 
-# @todo Go through line by line
+# todo: Go through line by line
 
 include(SERVER_ROOT.'/sections/torrents/functions.php');
 

sections/torrents/details.php

@@ -777,7 +777,7 @@ $filename = "BioTorrents.de-$TorrentID";
   note    = {Online; accessed ".strftime('%Y-%m-%d')."},
 },"; ?>
 
-              <!-- @todo Download BibTeX citation feature
+              <!-- todo: Download BibTeX citation feature
 <form method="post" action="download.php">
 <input type="hidden" name="file" id="file" value="< ? = urlencode($filename) ? >"
               />
@@ -1000,7 +1000,7 @@ if (count($PersonalCollages) > 0) {
         $ThumbURL = ImageTools::process($Screenshot['Image'], 'thumb');
         */
 
-      /* @todo Bring this back
+      /* todo: Bring this back
       if (check_perms('users_mod')) {
         ?><img class='tooltip lightbox-init' title='<?=Users::format_username($Screenshot['UserID'], false, false, false)?> - <?=time_diff($Screenshot['Time'])?>' lightbox-img="<?=$SSURL?>" src="<?=$ThumbURL?>" /><?
       } else {

sections/torrents/takeedit.php

@@ -433,7 +433,7 @@ $DB->query("
   WHERE ID = $GroupID");
 list($Name) = $DB->next_record(MYSQLI_NUM, false);
 
-Misc::write_log("Torrent $TorrentID ($Name) in group $GroupID was edited by ".$LoggedUser['Username']." ($LogDetails)"); // TODO: this is probably broken
+Misc::write_log("Torrent $TorrentID ($Name) in group $GroupID was edited by ".$LoggedUser['Username']." ($LogDetails)"); // todo: This is probably broken
 Torrents::write_group_log($GroupID, $TorrentID, $LoggedUser['ID'], $LogDetails, 0);
 $Cache->delete_value("torrents_details_$GroupID");
 $Cache->delete_value("torrent_download_$TorrentID");

sections/upload/upload_handle.php

@@ -31,7 +31,7 @@ $Feed = new Feed;
 //--------------- Set $Properties array ---------------------------------------//
 // This is used if the form doesn't validate, and when the time comes to enter //
 // it into the database.                 
-// @todo Do something about this mess
+// todo: Do something about this mess
 //****************************************************************************//
 
 $Properties = [];
@@ -131,7 +131,7 @@ $Validate->SetFields(
     array('inarray' => array_keys($Categories))
 );
 
-# @todo Remove the switch statement
+# todo: Remove the switch statement
 switch ($Type) {
     /*
   case 'Imaging':
@@ -231,6 +231,16 @@ default:
             array('inarray' => array_merge($Media, $MediaManga, $Platform))
         );
 
+        # torrents.Container
+        $Validate->SetFields(
+            'container',
+            '1',
+            'inarray',
+            'Please select a valid format.',
+            array('inarray' => array_merge($Containers, $ContainersGames, ContainersProt))
+        );
+
+        /*
         # torrents.Container
         $Validate->SetFields(
             'container',
@@ -239,6 +249,7 @@ default:
             'Please select a valid format.',
             array('inarray' => array_merge($Containers, $ContainersGames))
         );
+        */
 
         # torrents_group.TagList
         $Validate->SetFields(
@@ -509,7 +520,7 @@ if (!isset($GroupID) || !$GroupID) {
     $Cache->increment('stats_group_count');
 
     // Add screenshots
-    // @todo Clear DB_MYSQL::exec_prepared_query() errors
+    // todo: Clear DB_MYSQL::exec_prepared_query() errors
     $Screenshots = explode("\n", $T['Screenshots']);
     $Screenshots = array_map('trim', $Screenshots);
 
@@ -661,7 +672,7 @@ $Debug->set_flag('upload: ocelot updated');
 $Cache->cache_value("torrent_{$TorrentID}_lock", true, 600);
 
 // Give BP if necessary
-// @todo Repurpose this
+// todo: Repurpose this
 if (($Type === "Movies" || $Type === "Anime") && ($T['Container'] === 'ISO' || $T['Container'] === 'M2TS' || $T['Container'] === 'VOB IFO')) {
     $BPAmt = (int) 2*($TotalSize / (1024*1024*1024))*1000;
 

sections/user/index.php

@@ -1,5 +1,5 @@
 <?
-//TODO
+// todo
 /*****************************************************************
 Finish removing the take[action] pages and utilize the index correctly
 Should the advanced search really only show if they match 3 perms?

sections/user/permissions.php

@@ -1,5 +1,5 @@
 <?
-//TODO: Redo HTML
+// todo: Redo HTML
 if (!check_perms('admin_manage_permissions')) {
   error(403);
 }

sections/user/sessions.php

@@ -1,6 +1,6 @@
 <?
 
-//TODO: restrict to viewing below class, username in h2
+//todo: restrict to viewing below class, username in h2
 if (isset($_GET['userid']) && check_perms('users_view_ips') && check_perms('users_logout')) {
   if (!is_number($_GET['userid'])) {
     error(404);

sections/user/take_edit.php

@@ -236,7 +236,7 @@ if (check_perms('site_advanced_search')) {
   unset($Options['SearchType']);
 }
 
-//TODO: Remove the following after a significant amount of time
+// todo: Remove the following after a significant amount of time
 unset($Options['ArtistNoRedirect']);
 unset($Options['ShowQueryList']);
 unset($Options['ShowCacheList']);

sections/userhistory/email_history2.php

@@ -29,7 +29,7 @@ if (!check_perms('users_view_email', $Class)) {
   error(403);
 }
 
-// TODO: Is this even used?
+// todo: Is this even used?
 $UsersOnly = $_GET['usersonly'] ?? false;
 
 $DB->query("

static/functions/ajax.class.js

@@ -1,5 +1,5 @@
 /*
-  TODO: Further optimize serialize function
+  todo: Further optimize serialize function
 
   UPDATE: We were forced to create an individual XHR for each request
   to avoid race conditions on slower browsers where the request would
@@ -18,7 +18,6 @@
     $('#quickpost').raw().value = "[quote="+username+"]" + ajax.response + "[/quote]";
   }
   ajax.get("?action=get_post&post=" + postid);
-
 */
 "use strict";
 var ajax = {
@@ -96,13 +95,14 @@ var ajax = {
     return query.substr(0, query.length - 1);
   }
 };
-//Bookmarks
+
+// Bookmarks
 function Bookmark(type, id, newName) {
   var bmLinks = $('#bookmarklink_' + type + '_' + id + ', .bookmarklink_' + type + '_' + id);
   var oldName = bmLinks.html();
-  ajax.get("bookmarks.php?action=add&type=" + type + "&auth=" + authkey + "&id=" + id, function() {
+  ajax.get("bookmarks.php?action=add&type=" + type + "&auth=" + authkey + "&id=" + id, function () {
     bmLinks.parent('.remove_bookmark, .add_bookmark').toggleClass('add_bookmark remove_bookmark');
-    bmLinks.html(newName).attr('title', 'Remove bookmark').removeAttr('onclick').off('click').click(function() {
+    bmLinks.html(newName).attr('title', 'Remove bookmark').removeAttr('onclick').off('click').click(function () {
       Unbookmark(type, id, oldName);
       return false;
     });
@@ -111,7 +111,7 @@ function Bookmark(type, id, newName) {
 
 function Unbookmark(type, id, newName) {
   if (window.location.pathname.indexOf('bookmarks.php') != -1) {
-    ajax.get("bookmarks.php?action=remove&type=" + type + "&auth=" + authkey + "&id=" + id, function() {
+    ajax.get("bookmarks.php?action=remove&type=" + type + "&auth=" + authkey + "&id=" + id, function () {
       $('#group_' + id).remove();
       $('.image_group_' + id).remove();
       $('.groupid_' + id).remove();
@@ -121,9 +121,9 @@ function Unbookmark(type, id, newName) {
   } else {
     var bmLinks = $('#bookmarklink_' + type + '_' + id + ', .bookmarklink_' + type + '_' + id);
     var oldName = bmLinks.html();
-    ajax.get("bookmarks.php?action=remove&type=" + type + "&auth=" + authkey + "&id=" + id, function() {
+    ajax.get("bookmarks.php?action=remove&type=" + type + "&auth=" + authkey + "&id=" + id, function () {
       bmLinks.parent('.remove_bookmark, .add_bookmark').toggleClass('add_bookmark remove_bookmark');
-      bmLinks.html(newName).attr('title', 'Add bookmark').removeAttr('onclick').off('click').click(function() {
+      bmLinks.html(newName).attr('title', 'Add bookmark').removeAttr('onclick').off('click').click(function () {
         Bookmark(type, id, oldName);
         return false;
       });

static/functions/bbcode.js

@@ -61,7 +61,7 @@ function EmojiBox(box) {
 }
 
 function BBEditor(box) {
-  // @todo Integrate BioJS functions here
+  // todo: Integrate BioJS functions here
   if (box.previousSibling && box.previousSibling.className == 'bbcode_bar') return
   let buttons = [
     {short:'B', name:'Bold', wrap:['[b]','[/b]']},

static/functions/cookie.class.js

@@ -1,6 +1,7 @@
 /*
-  TODO: Document.
+  todo: Document
 */
+
 "use strict";
 var cookie = {
   get: function (cookie_name) {

static/functions/countdown.class.js

@@ -1,5 +1,5 @@
 /*
-  TODO: Move to more efficient structure used in ajax.class.
+  todo: Move to more efficient structure used in ajax.class
 
   Example Usage:
   <script type="text/javascript">
@@ -12,6 +12,7 @@
     }
   </script>
 */
+
 "use strict";
 var count = {
   update: function (Offset) {

static/functions/storage.class.js

@@ -1,6 +1,7 @@
 /*
-  TODO: Document.
+  todo: Document
 */
+
 "use strict";
 
 var cookie = {

templates/filemap.csv

@@ -1,83 +0,0 @@
-# Containers
-# https://www.ncbi.nlm.nih.gov/sra/docs/submitformats/
-
-BAM		bam
-CRAM		cram
-EMBL		embl
-FASTA		fasta || fa || fsa
-FASTA+QUAL	fasta && qual
-CSFASTA+QUAL	csfasta && qual
-FASTQ		fastq || sanfastq || fq
-GFF		gff2 || gff3 || gff
-GTF		gtf
-GenBank		gb || gbk
-HDF5		hdf5 || (bash5 && baxh5) || fast5
-PIR		pir
-QSeq		qseq
-SAM		sam
-SFF		sff
-SRF		srf
-SnapGene	dna seq
-SwissProt	dat
-VCF		vcf
-Plain		txt csv
-
-
-# ContainersProt
-# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518119/
-# DO NOT PARSE RAW FILES. TOO MANY COMPETING VENDORS
-
-ABI/Sciex	wiff t2d
-APML		apml
-ASF		asf
-Agilent/Bruker	d yep baf tdf fid
-BlibBuild	blib
-Bruker/Varian	sms xms
-Finnigan	dat ms
-ION-TOF		itm ita
-JCAMP-DX	jdx
-MGF		mgf
-MS2		ms2
-MSF		msf
-OMSSA		omx
-PEFF		peff
-Pickle		pkl pickle
-Shimadzu	qgd lcd spc
-Skyline		sky skyd
-TPP/SPC		dta
-Tandem		tandem
-TraML		traml
-ULVAC-PHI	tdc
-mzML		mzml
-mzXML		mzxml
-mzData		mzdata
-pepXML		pepxml
-protXML		protxml
-Plain		csv txt
-
-
-# ContainersGames
-# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3948928/
-
-Analyze		img || hdr
-#Interfile	img || hdr &| h33
-Dicom		dcm
-JPEG		jpg jpeg jfif
-JPEG 2000	jp2 j2k jpf jpx jpm mj2
-Minc		mnc
-Nifti		nii
-PNG		png
-TIFF		tiff tif
-WebP		webp
-Other		''
-
-
-# Archives
-
-7z		7z
-bzip2		bz2 bzip2
-gzip		gz gzip
-Pickle		pkl pickle
-RAR		rar rev
-ZIP		zip zipx
-None		''