Bring the Extension Parser package up to speed

_packages/extension-parser/classes/config.php

 <?php
 
-# Line 224
+# Line 222
 # Sequencing Formats
 #
 # https://www.ncbi.nlm.nih.gov/sra/docs/submitformats/
   'SwissProt'  => ['dat'],
   'VCF'        => ['vcf'],
   'Plain'      => ['csv', 'txt'],
+  'Other'      => [],
 ];
 
 # Imaging Formats
   'PNG'       => ['png'],
   'TIFF'      => ['tif', 'tiff'],
   'WebP'      => ['webp'],
-  'Other'     => [''],
+  'Other'     => [],
 ];
 
 # Protein Formats
   'TraML'          => ['traml'],
   'ULVAC-PHI'      => ['tdc'],
   'Plain'          => ['csv', 'txt'],
+  'Other'          => [],
 ];
 
 # Extra Formats
   'Excel'            => ['xls', 'xlt', 'xlm', 'xlsx', 'xlsm', 'xltx', 'xltm', 'xlsb', 'xla', 'xlam', 'xll', 'xlw'],
   'PowerPoint'       => ['ppt', 'pot', 'pps', 'pptx', 'pptm', 'potx', 'potm', 'ppam', 'ppsx', 'ppsm', 'sldx', 'sldm'],
   'PDF'              => ['pdf', 'fdf', 'xfdf'],
-  'Other'            => [''],
+  'Plain'            => ['csv', 'txt'],
+  'Other'            => [],
 ];
 
 $Archives = [
   'Pickle'   => ['pickle', 'pkl'],
   'RAR'      => ['rar', 'rev'],
   'ZIP'      => ['zip', 'zipx'],
-  'None'     => [''],
+  'None'     => [],
 ];
-# Line 330
+# Line 331

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

-<?php ?>
+<?php
 
-<!-- Three container fields -->
+class TorrentForm
+{
+    # Line 13
+    public $Containers = [];
+    public $ContainersGames = [];
+    public $ContainersProt = [];
+    public $ContainersExtra = [];
+    # Line 16
+
+    public function __construct($Torrent = false, $Error = false, $NewTorrent = true)
+    {
+        # Line 45
+        $this->Containers = $Containers;
+        $this->ContainersGames = $ContainersGames;
+        $this->ContainersProt = $ContainersProt;
+        $this->ContainersExtra = $ContainersExtra;
+        # Line 48
+?>
+
+<!-- Line 510 -->
+<!-- Multiple container fields -->
 <tr id="container_tr">
   <td class="label">
     Format
   </td>
   <td>
     <select name="container">
+      <option value="">---</option>
       <option value="Autofill">Autofill</option>
       <?php
-          foreach ($this->Containers as $Name => $Container) {
-              echo "<option value='$Name'>$Name</option>\n";
-          } ?>
+        foreach ($this->Containers as $Name => $Container) {
+            echo "<option value='$Name'>$Name</option>\n";
+        } ?>
     </select><br />
     Data file format, or detect from file list
   </td>
   </td>
   <td>
     <select id="container" name="container">
+      <option value="">---</option>
       <option value="Autofill">Autofill</option>
       <?php
-          foreach ($this->ContainersGames as $Name => $Container) {
-              echo "<option value='$Name'>$Name</option>\n";
-          } ?>
+        foreach ($this->ContainersGames as $Name => $Container) {
+            echo "<option value='$Name'>$Name</option>\n";
+        } ?>
     </select><br />
     Data file format, or detect from file list
   </td>
   </td>
   <td>
     <select id="container" name="container">
+      <option value="">---</option>
+      <option value="Autofill">Autofill</option>
+      <?php
+        foreach ($this->ContainersProt as $Name => $Container) {
+            echo "<option value='$Name'>$Name</option>\n";
+        } ?>
+    </select><br />
+    Data file format, or detect from file list
+  </td>
+</tr>
+
+<!-- 4 -->
+<tr id="container_extra_tr">
+  <td class="label">
+    Format
+    <strong class="important_text">*</strong>
+  </td>
+  <td>
+    <select id="container" name="container">
+      <option value="">---</option>
       <option value="Autofill">Autofill</option>
       <?php
-          foreach ($this->ContainersProt as $Name => $Container) {
-              echo "<option value='$Name'>$Name</option>\n";
-          } ?>
+        foreach ($this->ContainersExtra as $Name => $Container) {
+            echo "<option value='$Name'>$Name</option>\n";
+        } ?>
     </select><br />
     Data file format, or detect from file list
   </td>
-</tr>
+</tr>
+
+<!-- Compression -->
+<tr id="archive_tr">
+  <td class="label">
+    Archive
+    <strong class="important_text">*</strong>
+  </td>
+  <td>
+    <select name='archive'>
+      <option value="">---</option>
+      <option value="Autofill">Autofill</option>
+      <?php
+        foreach ($this->Archives as $Name => $Archive) {
+            echo "\t\t\t\t\t\t<option value=\"$Name\"";
+            if ($Archive === ($Torrent['Archive'] ?? false)) {
+                echo ' selected';
+            }
+            echo ">$Name</option>\n";
+        } ?>
+    </select><br />
+    Compression algorithm, or detect from file list
+  </td>
+</tr>
+<!-- Line 607 -->

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

+<?php
+
+class Validate
+{
+    # Line 171
+    /**
+     * Extension Parser
+     *
+     * Takes an associative array of file types and extension, e.g.,
+     * $Archives = [
+     *   '7z'     => ['7z'],
+     *   'bzip2'  => ['bz2', 'bzip2'],
+     *   'gzip'   => ['gz', 'gzip', 'tgz', 'tpz'],
+     *   ...
+     * ];
+     *
+     * Then it finds all the extensions in a torrent file list,
+     * organizes them by file size, and returns the "heaviest" match.
+     *
+     * That way, you can have, e.g., 5 GiB FASTQ sequence data in one file,
+     * and 100 other small files, and get the format of the actual data.
+     *
+     * todo: Incorporate into the main function (remove if statements first)
+     */
+    public function ParseExtensions($FileList, $Category, $FileTypes)
+    {
+        # Make $Tor->file_list() output manageable
+        $UnNested = array_values($FileList[1]);
+        $Sorted = (usort($UnNested, function ($a, $b) {
+            return $b <=> $a; # Workaround because ↑ returns true
+        }) === true) ? array_values($UnNested) : null;
+        
+        # Harvest the wheat
+        $TopTen = array_slice($Sorted, 0, 10);
+        $Result = [];
+
+        foreach ($TopTen as $TopTen) {
+            # How many extensions to keep
+            $Extensions = array_slice(explode('.', strtolower($TopTen[1])), -2, 2);
+    
+            print_r('<pre>');
+            var_dump($FileTypes);
+            print_r('</pre>');
+
+            $Result = array_filter($Extensions, function ($a) {
+                foreach ($FileTypes as $FileType) {
+                    in_array($a, $FileType);
+                }
+            });
+
+            /*
+            foreach ($FileTypes as $k => $FileType) {
+                var_dump(array_intersect($Extensions, $FileTypes));
+            }
+            */
+        }
+
+        print_r('<pre>');
+        print_r('===== RESULTS =====');
+        print_r($Result);
+        print_r('</pre>');
+
+        # To be continued
+    }
+    # Line 229

_packages/extension-parser/sections/upload/upload_handle.php

+<?php
+
+# Line 44
+# todo: Associate containers with categories beforehand
+# It may have to happen structurally in config.php, e.g.,
+# $Categories = [
+#   'GazelleName' => [$Name, $Icon, $Description, $Containers],
+#    ...
+#  ];
+$Properties['Archives'] = $Archives;
+$Properties['Containers'] = [
+    'DNA'      => $Containers,
+    'RNA'      => $Containers,
+    'Proteins' => $ContainersProt,
+    'Imaging'  => $ContainersGames,
+    'Extras'   => $ContainersExtra
+];
+# Line 57
+
+# Line 421
+//******************************************************************************//
+//--------------- Autofill format and archive ----------------------------------//
+
+if ($T['Container'] === 'Autofill') {
+    # torrents.Container
+    $Validate->ParseExtensions(
+        # $FileList
+        $Tor->file_list(),
+
+        # $Category
+        $T['CategoryName'],
+
+        # $FileTypes
+        $T['FileTypes'],
+    );
+}
+
+if ($T['Archive'] === 'Autofill') {
+    /*
+    # torrents.Archive
+    $Validate->ParseExtensions(
+        # $FileList
+        $Tor->file_list(),
+
+        # $Category
+        $T['CategoryName'],
+
+        # $FileTypes
+        $T['FileTypes'],
+    );
+    */
+}
+# Line 452

_packages/extension-parser/static/functions/upload.js

 // Line 11
 function Categories() {
     let def = [
-        'javdb', // Accession Number
-        'audio', // Version
-        'title', // Torrent Title
-        'title_rj', // Organism
-        'title_jp', // Strain/Variety
-        'idols', // Authors(s)
-        'studio', // Department/Lab
-        'series', // Location
-        'year', // Year
-        'codec', // License
-        // Platform changes below
-        'resolution', // Assembly Level
-        // Format changes below
-        'archive', // Archive
-        'tags', // Tags
-        'cover', // Picture
-        'mirrors', // Mirrors
-        'screenshots', // Publications
-        'group_desc', // Torrent Group Description
-        'release_desc', // Torrent Description
-        'censored', // Aligned/Annotated
-        'anon', // Upload Anonymously
+      'javdb', // Accession Number
+      'audio', // Version
+      'title', // Torrent Title
+      'title_rj', // Organism
+      'title_jp', // Strain/Variety
+      'idols', // Authors(s)
+      'studio', // Department/Lab
+      'series', // Location
+      'year', // Year
+      'codec', // License
+      // Platform changes below
+      'resolution', // Assembly Level
+      // Format changes below
+      'archive', // Archive
+      'tags', // Tags
+      'cover', // Picture
+      'mirrors', // Mirrors
+      'screenshots', // Publications
+      'group_desc', // Torrent Group Description
+      'release_desc', // Torrent Description
+      'censored', // Aligned/Annotated
+      'anon', // Upload Anonymously
     ]
   
     let cats = [
-        { // DNA
-            'media': {}, // Platform
-            'container': {}, // Format
-        },
-        { // RNA
-            'media': {}, // Platform
-            'container': {}, // Format
-        },
-        { // Proteins
-            'media': {}, // Platform
-            'container_prot': {}, // Format
-        },
-        { // Imaging
-            'media_manga': {}, // Platform
-            'container_games': {}, // Format
-        },
-        { // Extras
-            'media': {}, // Platform
-            'container_extra': {}, // Format
-        }
+      { // DNA
+        'media': {}, // Platform
+        'container': {}, // Format
+      },
+      { // RNA
+        'media': {}, // Platform
+        'container': {}, // Format
+      },
+      { // Proteins
+        'media': {}, // Platform
+        'container_prot': {}, // Format
+      },
+      { // Imaging
+        'media_manga': {}, // Platform
+        'container_games': {}, // Format
+      },
+      { // Extras
+        'media': {}, // Platform
+        'container_extra': {}, // Format
+      }
     ]
   
     let active = {}
     active = Object.assign(active, cats[category])
   
     let hide = el => {
-        Array.from($(`#${el.id} input, #${el.id} select, #${el.id} textarea`)).forEach(inp => inp.disabled = true)
-        $(el).ghide()
+      Array.from($(`#${el.id} input, #${el.id} select, #${el.id} textarea`)).forEach(inp => inp.disabled = true)
+      $(el).ghide()
     }
   
     let show = el => {
-        Array.from($(`#${el.id} input, #${el.id} select, #${el.id} textarea`)).forEach(inp => inp.disabled = false)
-        $(el).gshow()
+      Array.from($(`#${el.id} input, #${el.id} select, #${el.id} textarea`)).forEach(inp => inp.disabled = false)
+      $(el).gshow()
     }
   
     let trs = $('#dynamic_form tr')
     for (let tr of trs) {
-        let field = tr.id.slice(0, -3)
-        if (active[field]) {
-            if (active[field].name) {
-                tr.children[0].innerHTML = active[field].name
-            }
-            let notes = $(`#${tr.id} p.notes`).raw()
-            if (notes) notes.innerHTML = active[field].notes || ''
-            show(tr)
-        } else {
-            hide(tr)
+      let field = tr.id.slice(0, -3)
+      if (active[field]) {
+        if (active[field].name) {
+          tr.children[0].innerHTML = active[field].name
         }
+        let notes = $(`#${tr.id} p.notes`).raw()
+        if (notes) notes.innerHTML = active[field].notes || ''
+        show(tr)
+      } else {
+        hide(tr)
+      }
     }
-}
+  }
 // Line 91

classes/torrent_form.class.php

     Otherwise, add none of it and redownload the torrent file after uploading it.
     All of the above data will be added to it by the site.
     <strong>If you never have before, be sure to read this list of
-      <a href="wiki.php?action=article&name=uploadingpitfalls">uploading pitfalls</a></strong>.
+      <a href="wiki.php?action=article&name=uploadingpitfalls">uploading pitfalls</a>.</strong>
   </p>
 
   <!--

classes/validate.class.php

      * and 100 other small files, and get the format of the actual data.
      *
      * todo: Incorporate into the main function (remove if statements first)
-     * todo: Make this work with a more robust object than $Tor->file_list()
      */
-    public function ParseExtensions($FileList, $FileTypes)
+    public function ParseExtensions($FileList, $Category, $FileTypes)
     {
         # Make $Tor->file_list() output manageable
         $UnNested = array_values($FileList[1]);
-        $Sorted = usort($UnNested, function ($a, $b) {
-            return $b[0] > $a[0];
-        });
-        $TopTen = array_slice($Sorted, 0, 10); # Good
+        $Sorted = (usort($UnNested, function ($a, $b) {
+            return $b <=> $a; # Workaround because ↑ returns true
+        }) === true) ? array_values($UnNested) : null;
+        
+        # Harvest the wheat
+        $TopTen = array_slice($Sorted, 0, 10);
         $Result = [];
 
-        print_r('<pre>');
-        var_dump($Sorted);
-        print_r('</pre>');
-
-
         foreach ($TopTen as $TopTen) {
-            $Extensions = explode('.', strtolower($TopTen[1]));
+            # How many extensions to keep
+            $Extensions = array_slice(explode('.', strtolower($TopTen[1])), -2, 2);
+    
+            print_r('<pre>');
+            var_dump($FileTypes);
+            print_r('</pre>');
+
             $Result = array_filter($Extensions, function ($a) {
                 foreach ($FileTypes as $FileType) {
                     in_array($a, $FileType);
                 }
             });
-            /*
-            foreach ($FileTypes as $Key => $FileTypes) {
-                print_r('<pre>');
 
-            var_dump($UnNested);
-            var_dump( $FileTypes[$Key]);
-            print_r('</pre>');
-
-        }
-        */
-        }
-        /*
-        foreach ($TopTen as $TopTen) {
-            $Extensions = explode('.', strtolower($TopTen[1]));
-            #foreach ($FileTypes as $Key => $FileTypes) {
-                print_r('<pre>');
-                #$Result = (in_array($Extensions, $FileTypes)) ? $FileTypes[$Key] : false;
-                var_dump($Extensions);
+            /*
+            foreach ($FileTypes as $k => $FileType) {
                 var_dump(array_intersect($Extensions, $FileTypes));
-                print_r('</pre>');
-
-            #}
-            print_r('<pre>');
-            //var_dump(array_intersect($Extensions, $FileTypes));
-            //var_dump($Extensions);
-            print_r('</pre>');
-
+            }
+            */
         }
-        */
+
         print_r('<pre>');
-        #var_dump(array_intersect($UnNested, $FileTypes));
-        #print_r($Sorted);
+        print_r('===== RESULTS =====');
         print_r($Result);
         print_r('</pre>');
- 
-        /*
-        while ($Result === false) {
-           foreach ($UnNested as $Key => $UnNested) {
-               $Exploded = explode('.', strtolower($UnNested[1]));
-               foreach ($Needles as $Key => $Needle) {
-                   $ID = array_search($Exploded, $Needle);
-                   var_dump($Needle[$ID]);
-               }
-               $dump = array_filter($Exploded, function($s){
-                   foreach ($Needles as $Type => $Extension) {
-                       return array_search($s, $Extension);
-                   }
-               });
-               #var_dump($dump);
-               /*
-               if (array_search($Needle, $Exploded, true)) {
-                   $Result = $Needles;
-               #break;
-               }
-           }
-
-         }
-        */
-#var_dump($Result);
-        /*
-#do {
-    foreach ($UnNested as $UnNested) {
-        $Exploded = explode('.', strtolower($UnNested[1]));
-            #var_dump(in_array(vals($names), $Explode));
-
-        }
-/*
-        if (array_intersect($names, $Exploded)) {
-            $result = array_search($Exploded, $names);
-
-        }
-        *
-    }
-#} while ($result !== false);
-print_r($result);
-
 
-*/
+        # To be continued
     }
 
     public function GenerateJS($FormID)

sections/upload/upload_handle.php

 
 $Properties['CategoryID'] = $TypeID;
 $Properties['CategoryName'] = $Type;
+
+# todo: Associate containers with categories beforehand
+# It may have to happen structurally in config.php, e.g.,
+# $Categories = [
+#   'GazelleName' => [$Name, $Icon, $Description, $Containers],
+#    ...
+#  ];
+$Properties['ArchiveTypes'] = $Archives;
+$Properties['FileTypes'] = [
+    'DNA'      => $Containers,
+    'RNA'      => $Containers,
+    'Proteins' => $ContainersProt,
+    'Imaging'  => $ContainersGames,
+    'Extras'   => $ContainersExtra
+];
+
 $Properties['Title'] = $_POST['title'];
 $Properties['TitleRJ'] = $_POST['title_rj'];
 $Properties['TitleJP'] = $_POST['title_jp'];
+
 $Properties['Year'] = $_POST['year'];
 $Properties['Studio'] = isset($_POST['studio']) ? $_POST['studio'] : '';
 $Properties['Series'] = isset($_POST['series']) ? $_POST['series'] : '';
 //******************************************************************************//
 //--------------- Autofill format and archive ----------------------------------//
 
-if ($T['Container'] === 'Autofill' || $T['Archive'] === 'Autofill') {
+if ($T['Container'] === 'Autofill') {
     # torrents.Container
     $Validate->ParseExtensions(
+        # $FileList
         $Tor->file_list(),
-        array_merge($Containers, $ContainersGames, $ContainersProt)
+
+        # $Category
+        $T['CategoryName'],
+
+        # $FileTypes
+        $T['FileTypes'],
     );
+}
+
+if ($T['Archive'] === 'Autofill') {
     /*
     # torrents.Archive
     $Validate->ParseExtensions(
+        # $FileList
         $Tor->file_list(),
-        array_merge($Containers, $ContainersGames, $ContainersProt)
+
+        # $Category
+        $T['CategoryName'],
+
+        # $FileTypes
+        $T['FileTypes'],
     );
     */
 }