Line-by-line torrent form overhaul

classes/torrent_form.class.php

     public function head()
     {
         G::$DB->query("
-      SELECT COUNT(ID)
-      FROM torrents
-      WHERE UserID = ?", G::$LoggedUser['ID']);
+          SELECT COUNT(ID)
+          FROM torrents
+          WHERE UserID = ?", G::$LoggedUser['ID']);
         list($Uploads) = G::$DB->next_record(); ?>
 
+<!-- Everything until the catalogue number field-->
 <div class="thin">
-  <?php    if ($this->NewTorrent) { ?>
+  <?php if ($this->NewTorrent) { ?>
   <p style="text-align: center;">
-    If you would like to use your own torrent file, add the following to it:<br />
-    <?php      $Announces = call_user_func_array('array_merge', ANNOUNCE_URLS);
+    If you would like to use your own torrent file, add the following to it.
+    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>.
+  </p>
+
+  <p style="text-align: center;">
+    <?php
+      $Announces = call_user_func_array('array_merge', ANNOUNCE_URLS);
         foreach ($Announces as $Announce) {
-            ?>
-    Announce: <input type="text"
-      value="<?=$Announce . '/' . G::$LoggedUser['torrent_pass'] . '/announce'?>"
+            # Loop through tracker URLs
+    ?>
+    <strong>Announce</strong>
+    <input type="text" value="<?= $Announce . '/' . G::$LoggedUser['torrent_pass'] . '/announce' ?>"
       size="74" onclick="this.select();" readonly="readonly" /> <br />
     <?php
         } ?>
-    Source: <input type="text"
-      value="<?=Users::get_upload_sources()[0]?>" size="20"
+
+    <strong>Source</strong>
+    <input type="text" value="<?= Users::get_upload_sources()[0] ?>" size="20"
       onclick="this.select();" readonly="readonly" />
-    <p style="text-align: center;">
-      Otherwise, add none of it and simply redownload the torrent file after uploading it. All of the above data will be
-      added to it by the site.<br /><br />
-      <strong<?=((!$Uploads)?' class="important_text"':'')?>>
-        If you never have before, be sure to read this list of <a
-          href="wiki.php?action=article&name=uploadingpitfalls">uploading pitfalls</a>
-        </strong>
-    </p>
   </p>
-  <?php    }
+
+  <!-- Error display -->
+  <p style="text-align: center;">
+    <?php
+      }
         if ($this->Error) {
-            echo "\t".'<p style="color: red; text-align: center;">'.$this->Error."</p>\n";
+            echo "\t".'<p style="color: red; text-align: center;">' . $this->Error . "</p>\n";
         } ?>
+  </p>
+  
+  <!-- Torrent form hidden values -->
   <form class="create_form box pad" name="torrent" action="" enctype="multipart/form-data" method="post"
     onsubmit="$('#post').raw().disabled = 'disabled';">
     <div>
       <input type="hidden" name="submit" value="true" />
       <input type="hidden" name="auth"
         value="<?=G::$LoggedUser['AuthKey']?>" />
-      <?php    if (!$this->NewTorrent) { ?>
+      <?php if (!$this->NewTorrent) { ?>
       <input type="hidden" name="action" value="takeedit" />
       <input type="hidden" name="torrentid"
         value="<?=display_str($this->TorrentID)?>" />
       <input type="hidden" name="type"
         value="<?=display_str($this->Torrent['CategoryID']-1)?>" />
       <?php
-    } else {
-        if ($this->Torrent && $this->Torrent['GroupID']) {
-            ?>
+        } else {
+            if ($this->Torrent && $this->Torrent['GroupID']) {
+                # Find groups and requests
+      ?>
       <input type="hidden" name="groupid"
-        value="<?=display_str($this->Torrent['GroupID'])?>" />
+        value="<?= display_str($this->Torrent['GroupID']) ?>" />
       <input type="hidden" name="type"
-        value="<?=display_str($this->Torrent['CategoryID']-1)?>" />
+        value="<?= display_str($this->Torrent['CategoryID']-1) ?>" />
       <?php
-        }
-        if ($this->Torrent && ($this->Torrent['RequestID'] ?? false)) {
-            ?>
+            }
+            if ($this->Torrent && ($this->Torrent['RequestID'] ?? false)) {
+                ?>
       <input type="hidden" name="requestid"
         value="<?=display_str($this->Torrent['RequestID'])?>" />
       <?php
-        }
-    } ?>
+            }
+        } ?>
     </div>
-    <?php    if ($this->NewTorrent) { ?>
+
+    <!-- New torrent options: file and category -->
+    <?php if ($this->NewTorrent) { ?>
     <table cellpadding="3" cellspacing="1" border="0" class="layout" width="100%">
       <tr>
-        <td class="label tooltip" title="Use the above announce URL and set the private flag in your BitTorrent client">
-          Torrent File</td>
-        <td><input id="file" type="file" name="file_input" size="50" /></td>
+        <td class="label">Torrent File</td>
+        <td><input id="file" type="file" name="file_input" size="50" /><br />
+          Use the above announce URL and set the private flag in your BitTorrent client, e.g.,
+          <pre>mktorrent -p -a &lt;announce&gt; &lt;target folder&gt;</pre>
+        </td>
       </tr>
       <tr>
-        <td class="label tooltip" title="What alphabet the sequence uses, n.b., plasmids fit in the Other category">Type
-        </td>
+        <td class="label">Type</td>
         <td>
-          <select id="categories" name="type" onchange="Categories()" <?=($this->DisabledFlag) ? ' disabled="disabled"' : ''?>>
-            <?php
-      foreach (Misc::display_array($this->Categories) as $Index => $Cat) {
-          echo "\t\t\t\t\t\t<option value=\"$Index\"";
-          if ($Cat == $this->Torrent['CategoryName']) {
-              echo ' selected="selected"';
-          }
-          echo ">$Cat</option>\n";
-      }
-?>
-          </select>
+          <select id="categories" name="type" onchange="Categories()"
+            <?= ($this->DisabledFlag) ? ' disabled="disabled"' : '' ?>>
+          <?php
+            foreach (Misc::display_array($this->Categories) as $Index => $Cat) {
+                echo "\t\t\t\t\t\t<option value=\"$Index\"";
+                if ($Cat == $this->Torrent['CategoryName']) {
+                    echo ' selected="selected"';
+                }
+                echo ">$Cat</option>\n";
+            }
+          ?>
+          </select><br />
+          What alphabet the sequence uses, n.b., plasmids fit in the Other category
         </td>
       </tr>
     </table>
-    <?php    }//if?>
+
+    <!-- Start the dynamic form -->
+    <?php } # if?>
     <div id="dynamic_form">
       <?php
     }
     {
         $Torrent = $this->Torrent; ?>
     </div>
+
+    <!-- Freeleech type -->
     <table cellpadding="3" cellspacing="1" border="0" class="layout slice" width="100%">
       <?php
-    if (!$this->NewTorrent) {
-        if (check_perms('torrents_freeleech')) {
-            ?>
+        if (!$this->NewTorrent) {
+            if (check_perms('torrents_freeleech')) {
+                ?>
       <tr id="freetorrent">
         <td class="label">Freeleech</td>
         <td>
           <select name="freeleech">
             <?php
-        $FL = array("Normal", "Free", "Neutral");
-            foreach ($FL as $Key => $Name) {
-                ?>
-            <option value="<?=$Key?>" <?=($Key == $Torrent['FreeTorrent'] ? ' selected="selected"' : '')?>><?=$Name?>
+              $FL = array("Normal", "Free", "Neutral");
+                foreach ($FL as $Key => $Name) {
+                    # Cycle types
+            ?>
+            <option value="<?= $Key ?>" <?= ($Key === $Torrent['FreeTorrent'] ? ' selected="selected"' : '') ?>><?= $Name ?>
             </option>
             <?php
-            } ?>
+                } ?>
           </select>
           because
           <select name="freeleechtype">
             <?php
-        $FL = array("N/A", "Staff Pick", "Perma-FL", "Freeleechizer", "Site-Wide FL");
-            foreach ($FL as $Key => $Name) {
-                ?>
-            <option value="<?=$Key?>" <?=($Key == $Torrent['FreeLeechType'] ? ' selected="selected"' : '')?>><?=$Name?>
+              $FL = array("N/A", "Staff Pick", "Perma-FL", "Freeleechizer", "Site-Wide FL");
+                foreach ($FL as $Key => $Name) {
+                    # Cycle reasons
+            ?>
+            <option value="<?=$Key?>" <?= ($Key === $Torrent['FreeLeechType'] ? ' selected="selected"' : '') ?>><?= $Name ?>
             </option>
             <?php
-            } ?>
+                } ?>
           </select>
         </td>
       </tr>
       <?php
-        }
-    } ?>
+            }
+        } ?>
+
+      <!-- Rules notice (displays just before submit) -->
       <tr>
         <td colspan="2" style="text-align: center;">
-          <p>Be sure that your torrent is approved by the <a href="rules.php?p=upload" target="_blank">rules</a>. Not
-            doing this will result in a <strong class="important_text">warning</strong> or <strong
-              class="important_text">worse</strong>.</p>
-          <?php    if ($this->NewTorrent) { ?>
-          <p>After uploading the torrent, you will have a one hour grace period during which no one other than you can
-            fill requests with this torrent. Make use of this time wisely, and <a href="requests.php">search the list of
-              requests</a>.</p>
-          <?php    } ?>
-          <input id="post" type="submit" <?php if ($this->NewTorrent) {
-        echo ' value="Upload torrent"';
-    } else {
-        echo ' value="Edit torrent"';
-    } ?>
+          <p>Be sure that your torrent is approved by the <a href="rules.php?p=upload" target="_blank">rules</a>.
+          Not doing this will result in a <strong class="important_text">warning</strong> or <strong class="important_text">worse</strong>.</p>
+          <?php if ($this->NewTorrent) { ?>
+          <p>
+            After uploading the torrent, you will have a one hour grace period during which no one other than you can fill requests with this torrent.
+            Make use of this time wisely, and <a href="requests.php">search the list of requests</a>.
+          </p>
+          <?php } ?>
+          <input id="post" type="submit"
+          <?php
+            if ($this->NewTorrent) {
+                echo ' value="Upload torrent"';
+            } else {
+                echo ' value="Edit torrent"';
+            } ?>
           />
         </td>
       </tr>
     </table>
   </form>
 </div>
+
+<!-- Okay, finally the real form -->
 <?php
-    }
+    } # End
 
     public function upload_form()
     {
         $QueryID = G::$DB->get_query_id();
         $this->head();
         $Torrent = $this->Torrent; ?>
+
+<!-- Catalogue number field -->
 <table cellpadding="3" cellspacing="1" border="0" class="layout slice" width="100%">
   <?php if ($this->NewTorrent) { ?>
   <tr id="javdb_tr">
-    <td class="label tooltip" title="RefSeq accession number, e.g., NM_001183340.1">Accession Number</td>
+    <td class="label tooltip" title="">Accession Number</td>
     <td>
       <input type="text" id="catalogue" name="catalogue" size="10"
-        value="<?=display_str($Torrent['CatalogueNumber']) ?>"
-        <?=$this->Disabled?>/>
+        value="<?= display_str($Torrent['CatalogueNumber']) ?>"
+        <?= $this->Disabled ?>/>
       <?php if (!$this->DisabledFlag) { ?>
-      <input type="button" autofill="jav" value="Autofill" style="background: lightgrey; pointer-events: none;"></input>
+        <input type="button" autofill="jav" value="Autofill"
+          style="background: lightgrey; pointer-events: none;">
+        </input>
+        Coming Soon!<br />
+        RefSeq accession number, e.g., NM_001183340.1
       <?php } ?>
     </td>
   </tr>
+
+  <!-- Other autofill options -->
   <tr id="anidb_tr" class="hidden">
     <td class="label">AniDB Autofill (optional)</td>
     <td>
-      <input type="text" id="anidb" size="10" <?=$this->Disabled?>/>
+      <input type="text" id="anidb" size="10" <?= $this->Disabled ?>/>
       <?php if (!$this->DisabledFlag) { ?>
       <input type="button" autofill="anime" value="Autofill" />
       <?php } ?>
   <tr id="ehentai_tr" class="hidden">
     <td class="label">e-hentai URL (optional)</td>
     <td>
-      <input type="text" id="catalogue" size="50" <?=$this->Disabled?> />
+      <input type="text" id="catalogue" size="50" <?= $this->Disabled ?> />
       <?php if (!$this->DisabledFlag) { ?>
       <input type="button" autofill="douj" value="Autofill" />
       <?php } ?>
     </td>
   </tr>
+
+  <!-- Three title fields -->
   <tr id="title_tr">
-    <td class="label tooltip" title="FASTA definition line, e.g., Alcohol dehydrogenase ADH1">Sequence Name</td>
-    <td><input type="text" id="title" name="title" size="60"
-        value="<?=display_str($Torrent['Title']) ?>"
-        <?=$this->Disabled?>/></td>
+    <td class="label">Sequence Name</td>
+    <td>
+      <input type="text" id="title" name="title" size="60"
+        value="<?= display_str($Torrent['Title']) ?>"
+        <?= $this->Disabled ?>/><br />
+      Definition line, e.g., Alcohol dehydrogenase ADH1
+    </td>
   </tr>
+
   <tr id="title_rj_tr">
-    <td class="label tooltip" title="FASTA organism line binomial nomenclature, e.g., Saccharomyces cerevisiae">Organism
+    <td class="label tooltip" title="">Organism
+    </td>
+    <td>
+      <input type="text" id="title_rj" name="title_rj" size="60"
+        value="<?= display_str($Torrent['TitleRJ']) ?>"
+        <?= $this->Disabled ?>/><br />
+      Organism line binomial nomenclature, e.g., <em>Saccharomyces cerevisiae</em>
     </td>
-    <td><input type="text" id="title_rj" name="title_rj" size="60"
-        value="<?=display_str($Torrent['TitleRJ']) ?>"
-        <?=$this->Disabled?>/></td>
   </tr>
+
   <tr id="title_jp_tr">
-    <td class="label tooltip" title="FASTA organism line if applicable, e.g., S288C">Strain/Variety</td>
-    <td><input type="text" id="title_jp" name="title_jp" size="60"
-        value="<?=display_str($Torrent['TitleJP']) ?>"
-        <?=$this->Disabled?>/></td>
+    <td class="label">Strain/Variety</td>
+    <td>
+      <input type="text" id="title_jp" name="title_jp" size="60"
+        value="<?= display_str($Torrent['TitleJP']) ?>"
+        <?= $this->Disabled ?>/><br />
+      Organism line if applicable, e.g., S288C
+    </td>
   </tr>
+
+  <!-- Multiple artists -->
   <tr id="idols_tr">
-    <td class="label tooltip" title="FASTA authors line, e.g., Robert K. Mortimer and David Schild">Collaborator(s)</td>
+    <td class="label tooltip" title="">Authors(s)</td>
     <td id="idolfields">
-      <?php      if (!empty($Torrent['Artists'])) {
-            foreach ($Torrent['Artists'] as $Num => $Artist) { ?>
-      <input type="text" id="idols_<?=$Num?>" name="idols[]"
-        size="45"
-        value="<?=display_str($Artist['name'])?>"
-        <?=$this->Disabled?>/>
+      One author per field, e.g., Robert K. Mortimer [+] David Schild<br />
+      <?php
+        if (!empty($Torrent['Artists'])) {
+          foreach ($Torrent['Artists'] as $Num => $Artist) {
+      ?>
+      <input type="text" id="idols_<?= $Num ?>" name="idols[]"
+        size="45" value="<?= display_str($Artist['name']) ?>"
+        <?= $this->Disabled ?>/>
       <?php if ($Num == 0) { ?>
-      <a class="add_artist_button brackets">+</a> <a class="remove_artist_button brackets">&minus;</a>
-      <?php }
+      <a class="add_artist_button brackets">+</a>
+      <a class="remove_artist_button brackets">&minus;</a>
+      <?php
             }
-        } else { ?>
-      <input type="text" id="idols_0" name="idols[]" size="45" value="" <?=$this->Disabled?> />
-      <a class="add_artist_button brackets">+</a> <a class="remove_artist_button brackets">&minus;</a>
-      <?php        } ?>
+          }
+        } else {
+      ?>
+      <input type="text" id="idols_0" name="idols[]" size="45" value="" <?= $this->Disabled ?> />
+      <a class="add_artist_button brackets">+</a>
+      <a class="remove_artist_button brackets">&minus;</a>
+      <?php
+        } ?>
     </td>
   </tr>
+
+  <!-- Production studio -->
   <tr id="studio_tr">
-    <td class="label tooltip" title="Who produced the sequence, e.g., Lawrence Berkeley Laboratory">Department/Lab</td>
-    <td><input type="text" id="studio" name="studio" size="60"
-        value="<?=display_str($Torrent['Studio']) ?>"
-        <?=$this->Disabled?>/></td>
+    <td class="label">Department/Lab</td>
+    <td>
+      <input type="text" id="studio" name="studio" size="60"
+        value="<?= display_str($Torrent['Studio']) ?>"
+        <?= $this->Disabled ?>/><br />
+      First author's institution, e.g., Lawrence Berkeley Laboratory
+    </td>
   </tr>
+
+  <!-- Location -->
   <tr id="series_tr">
-    <td class="label tooltip" title="Their physical location, e.g., Berkeley, CA">Location</td>
-    <td><input type="text" id="series" name="series" size="60"
-        value="<?=display_str($Torrent['Series']) ?>"
-        <?=$this->Disabled?>/></td>
+    <td class="label">Location</td>
+    <td>
+      <input type="text" id="series" name="series" size="60"
+        value="<?= display_str($Torrent['Series']) ?>"
+        <?= $this->Disabled ?>/><br />
+      Its physical location, e.g., Berkeley, CA
+    </td>
   </tr>
+
+  <!-- Year -->
   <tr id="year_tr">
-    <td class="label tooltip" title="What year they published the sequence in">Year</td>
-    <td><input type="text" id="year" name="year" maxlength="4" size="5"
-        value="<?=display_str($Torrent['Year']) ?>"
-        <?=$this->Disabled?>/></td>
+    <td class="label">Year</td>
+    <td>
+      <input type="text" id="year" name="year" maxlength="4" size="5"
+        value="<?= display_str($Torrent['Year']) ?>"
+        <?= $this->Disabled ?>/><br />
+      Original publication year
+    </td>
   </tr>
-  <?php } ?>
+
+  <!-- Media type -->
+  <?php } # Ends if NewTorrent line 256?>
   <tr id="media_tr">
-    <td class="label tooltip" title="What class of sequencing technology they used">Platform</td>
+    <td class="label">Platform</td>
     <td>
       <select name="media">
         <option>---</option>
         <?php
-    foreach ($this->Media as $Media) {
-        echo "\t\t\t\t\t\t<option value=\"$Media\"";
-        if ($Media == ($Torrent['Media'] ?? false)) {
-            echo " selected";
-        }
-        echo ">$Media</option>\n";
-    } ?>
-      </select>
-    </td>
-  </tr>
-  <tr id="archive_tr">
-    <td class="label tooltip" title="How the data is archived and compressed">Archive</td>
-    <td>
-      <select name='archive'>
-        <option>---</option>
-        <?php
-    foreach ($this->Archives as $Archive) {
-        echo "\t\t\t\t\t\t<option value=\"$Archive\"";
-        if ($Archive == ($Torrent['Archive'] ?? false)) {
-            echo ' selected';
-        }
-        echo ">$Archive</option>\n";
-    } ?>
-      </select>
+          foreach ($this->Media as $Media) {
+              echo "\t\t\t\t\t\t<option value=\"$Media\"";
+              if ($Media == ($Torrent['Media'] ?? false)) {
+                  echo " selected";
+              }
+              echo ">$Media</option>\n";
+          } ?>
+      </select><br />
+      Class of sequencing technology used
     </td>
   </tr>
+
+  <!-- Container -->
   <tr id="container_tr">
-    <td class="label tooltip" title="What file format the sequence is in">Format</td>
+    <td class="label">Format</td>
     <td>
       <select name="container">
         <option>---</option>
         <?php
-    foreach ($this->Containers as $Cont) {
-        echo "\t\t\t\t\t\t<option value=\"$Cont\"";
-        if ($Cont == ($Torrent['Container'] ?? false)) {
-            echo " selected";
-        }
-        echo ">$Cont</option>\n";
-    } ?>
-      </select>
-    </td>
-  </tr>
-  <tr id="codec_tr">
-    <td class="label tooltip" title="What license the collaborators released the data under">License</td>
-    <td>
-      <select name="codec">
-        <option>---</option>
-        <?php
-    foreach ($this->Codecs as $Codec) {
-        echo "\t\t\t\t\t\t<option value=\"$Codec\"";
-        if ($Codec == ($Torrent['Codec'] ?? false)) {
-            echo " selected";
-        }
-        echo ">$Codec</option>\n";
-    } ?>
-      </select>
+          foreach ($this->Containers as $Cont) {
+              echo "\t\t\t\t\t\t<option value=\"$Cont\"";
+              if ($Cont === ($Torrent['Container'] ?? false)) {
+                  echo " selected";
+              }
+              echo ">$Cont</option>\n";
+          } ?>
+      </select><br />
+      The data's file format
     </td>
   </tr>
+
+  <!-- Resolution -->
   <tr id="resolution_tr">
-    <td class="label tooltip" title="How complete the sequence data is">Assembly Level</td>
+    <td class="label">Assembly Level</td>
     <td>
       <select id="ressel" name="ressel" onchange="SetResolution()">
         <option value="">---</option>
         <?php
-    foreach ($this->Resolutions as $Res) {
-        echo "\t\t\t\t\t\t<option value=\"$Res\"";
-        if ($Res == ($Torrent['Resolution'] ?? false) || (!isset($FoundRes) && ($Torrent['Resolution'] ?? false) && $Res == "Other")) {
-            echo " selected";
-            $FoundRes = true;
-        }
-        echo ">$Res</option>\n";
-    } ?>
+          foreach ($this->Resolutions as $Res) {
+              echo "\t\t\t\t\t\t<option value=\"$Res\"";
+              if ($Res === ($Torrent['Resolution'] ?? false)
+              || (!isset($FoundRes) && ($Torrent['Resolution'] ?? false)
+              && $Res === 'Other')) {
+                  echo " selected";
+                  $FoundRes = true;
+              }
+              echo ">$Res</option>\n";
+          } ?>
       </select>
-      <input type="text" id="resolution" name="resolution" size="10" class="hidden tooltip" pattern="[0-9]+x[0-9]+"
-        title='Enter "Other" resolutions in the form ###x###'
-        value="<?=($Torrent['Resolution']??'')?>"
-        readonly></input>
+
+      <input type="text" id="resolution" name="resolution" size="10" class="hidden"
+        value="<?= ($Torrent['Resolution']??'') ?>"
+        readonly>
+      </input>
       <script>
         if ($('#ressel').raw().value == "Other") {
           $('#resolution').raw().readOnly = false
           $('#resolution').gshow()
         }
-      </script>
+      </script><br />
+      How complete the sequence is
     </td>
   </tr>
-  <?php    if ($this->NewTorrent) { ?>
-  <tr id="tags_tr">
-    <td class="label tooltip" title="Comma-seperated list of tags, n.b., use vanity.house for data you produced">Tags
+
+  <!-- Compression -->
+  <tr id="archive_tr">
+    <td class="label">Archive</td>
+    <td>
+      <select name='archive'>
+        <option>---</option>
+        <?php
+          foreach ($this->Archives as $Archive) {
+              echo "\t\t\t\t\t\t<option value=\"$Archive\"";
+              if ($Archive === ($Torrent['Archive'] ?? false)) {
+                  echo ' selected';
+              }
+              echo ">$Archive</option>\n";
+          } ?>
+      </select><br />
+      Its compression algorithm
     </td>
+  </tr>
+
+  <!-- Encoding -->
+  <tr id="codec_tr">
+    <td class="label">License</td>
+    <td>
+      <select name="codec">
+        <option>---</option>
+        <?php
+          foreach ($this->Codecs as $Codec) {
+              echo "\t\t\t\t\t\t<option value=\"$Codec\"";
+              if ($Codec === ($Torrent['Codec'] ?? false)) {
+                  echo " selected";
+              }
+              echo ">$Codec</option>\n";
+          } ?>
+      </select><br />
+      Please see <a href="http://www.dcc.ac.uk/resources/how-guides/license-research-data" target="_blank">How to License Research Data</a>
+    </td>
+  </tr>
+
+  <!-- Tags -->
+  <?php if ($this->NewTorrent) { ?>
+  <tr id="tags_tr">
+    <td class="label">Tags</td>
     <td>
       <?php
-  $GenreTags = G::$Cache->get_value('genre_tags');
-  if (!$GenreTags) {
-      $DB->query("
-      SELECT Name
-      FROM tags
-      WHERE TagType = 'genre'
-      ORDER BY Name");
-      $GenreTags = $DB->collect('Name');
-      G::$Cache->cache_value('genre_tags', $GenreTags, 3600*6);
-  }
-?>
-      <select id="genre_tags" name="genre_tags" onchange="add_tag(); return false;" <?=($this->DisabledFlag) ? ' disabled="disabled"' : ''?>>
+        $GenreTags = G::$Cache->get_value('genre_tags');
+        if (!$GenreTags) {
+            $DB->query("
+            SELECT Name
+            FROM tags
+            WHERE TagType = 'genre'
+            ORDER BY Name");
+            $GenreTags = $DB->collect('Name');
+            G::$Cache->cache_value('genre_tags', $GenreTags, 3600*6);
+        }
+      ?>
+      <select id="genre_tags" name="genre_tags" onchange="add_tag(); return false;" <?= ($this->DisabledFlag) ? ' disabled="disabled"' : '' ?>>
         <option>---</option>
         <?php foreach (Misc::display_array($GenreTags) as $Genre) { ?>
-        <option value="<?=$Genre?>"><?=$Genre?>
+        <option value="<?= $Genre ?>"><?= $Genre ?>
         </option>
         <?php } ?>
       </select>
       <input type="text" id="tags" name="tags" size="60"
-        value="<?=display_str(implode(', ', explode(',', $Torrent['TagList']))) ?>"
-        <?php Users::has_autocomplete_enabled('other'); ?> />
-      <p class="min_padding notes"></p>
+        value="<?= display_str(implode(', ', explode(',', $Torrent['TagList']))) ?>"
+        <?php Users::has_autocomplete_enabled('other'); ?> /><br />
+      Comma-seperated list of tags, n.b., use <strong class="important_text_alt">vanity.house</strong> for data you produced
     </td>
   </tr>
+
+  <!-- Picture -->
   <tr id="cover_tr">
-    <td class="label tooltip" title="A meaningful picture, e.g., of the specimen">Picture</td>
-    <td><input type="text" id="image" name="image" size="60"
-        value="<?=display_str($Torrent['Image']) ?>"
-        <?=$this->Disabled?> /></td>
+    <td class="label">Picture</td>
+    <td>
+      <input type="text" id="image" name="image" size="60"
+        value="<?= display_str($Torrent['Image']) ?>"
+        <?= $this->Disabled ?> /><br />
+      A meaningful picture, e.g., of the specimen
+    </td>
   </tr>
+
+  <!-- Sample pictures/links -->
   <?php if (!$this->DisabledFlag && $this->NewTorrent) { ?>
   <tr id="screenshots_tr">
-    <td class="label tooltip" title="Relevant publications that use the data">Publications</td>
+    <td class="label">Publications</td>
     <td>
       <textarea rows="8" cols="60" name="screenshots"
-        id="screenshots"><?=display_str($Torrent['Screenshots'])?></textarea>
-      <p>Enter up to 10 links to studies for the torrent, one per line. The system will automatically remove malformed
-        or invalid links, as well as any links after the 10th. Remember to consult the <a
-          href="/rules.php?p=upload#h1.4">rules for adding publications</a>.</p>
-      <p class="min_padding notes"></p>
-  </tr>
+        id="screenshots"><?= display_str($Torrent['Screenshots'])?></textarea>
+      Up to ten DOI numbers relevant to the torrent, one per line
+    </tr>
   <?php } ?>
+
+  <!-- Artist description -->
   <tr id="group_desc_tr">
-    <td class="label tooltip" title="General info about the gene or protein's function or significance">Torrent Group
-      Description</td>
+    <td class="label">Torrent Group Description</td>
     <td>
-      <p class="min_padding notes"></p>
-      <?php new TEXTAREA_PREVIEW('album_desc', 'album_desc', display_str($Torrent['GroupDescription']), 60, 8, !$this->DisabledFlag, !$this->DisabledFlag, false, array($this->Disabled)); ?>
+      <?php
+        new TEXTAREA_PREVIEW(
+          'album_desc',
+          'album_desc',
+          display_str($Torrent['GroupDescription']),
+          60,
+          8,
+          !$this->DisabledFlag,
+          !$this->DisabledFlag,
+          false,
+          array($this->Disabled)
+      );
+      ?><br />
+      General info about the gene or protein's function or significance
     </td>
   </tr>
-  <?php    } ?>
+  <?php } # Ends if NewTorrent line 499?>
+
+  <!-- Torrent description -->
   <tr id="release_desc_tr">
-    <td class="label tooltip" title="Specific info about what protocols and equipment helped generate the data">Torrent
-      Description (optional)</td>
+    <td class="label">Torrent Description</td>
     <td>
-      <p class="min_padding notes"></p>
-      <?php new TEXTAREA_PREVIEW('release_desc', 'release_desc', display_str($Torrent['TorrentDescription']??''), 60, 8); ?>
+      <?php
+        new TEXTAREA_PREVIEW(
+          'release_desc',
+          'release_desc',
+          display_str($Torrent['TorrentDescription'] ?? ''),
+          60,
+      ); ?><br />
+      Specific info about the protocols and equipment relevant to this data
     </td>
   </tr>
+
+  <!-- Boolean options -->
   <tr id="censored_tr">
-    <td class="label tooltip" title="Whether the torrent contains raw reads or alignment data">Aligned Sequence?</td>
+    <td class="label">Aligned Sequence?</td>
     <td>
-      <input type="checkbox" name="censored" value="1" <?=(($Torrent['Censored'] ?? 0) ? 'checked ' : '')?>/>
+      <input type="checkbox" name="censored" value="1"
+        <?= (($Torrent['Censored'] ?? 0) ? 'checked ' : '') ?>/>
+      Whether the torrent contains raw reads or alignment data
     </td>
   </tr>
+
   <tr id="anon_tr">
-    <td class="label tooltip" title="Hide your username from other users on the torrent details page">Upload
-      Anonymously?</td>
-    <td><input type="checkbox" name="anonymous" value="1" <?=(($Torrent['Anonymous'] ?? false) ? 'checked ' : '')?>/>
+    <td class="label">Upload Anonymously?</td>
+    <td>
+      <input type="checkbox" name="anonymous" value="1"
+        <?= (($Torrent['Anonymous'] ?? false) ? 'checked ' : '') ?>/>
+      Hide your username from other users on the torrent details page
     </td>
   </tr>
 </table>
 
 <?php
-    $this->foot();
+  # Phew
+  $this->foot();
         G::$DB->set_query_id($QueryID);
     }
 }

sections/torrents/details.php

 
 $DisplayName = "<span dir=\"ltr\">$GroupName</span><br />";
 $AltName = $GroupName; // Goes in the alt text of the image
-$Title = $GroupName; // goes in <title>
+$Title = $GroupName; // Goes in <title>
 $WikiBody = Text::full_format($WikiBody);
 
 $Artists = Artists::get_artist($GroupID);

sections/upload/upload_handle.php

 <?php
+
 //****************************************************************************//
 //--------------- Take upload ------------------------------------------------//
 // This pages handles the backend of the torrent upload function. It checks   //
 // the data to the database and the torrent to the disk.                      //
 //****************************************************************************//
 
-// Maximum allowed size for uploaded files.
-// http://php.net/upload-max-filesize
-ini_set('upload_max_filesize', 2097152); // 2 Mebibytes
-
+// Maximum allowed size for uploaded files
+// https://php.net/upload-max-filesize
+ini_set('upload_max_filesize', 2097152); // 2 MiB
 ini_set('max_file_uploads', 100);
 define('MAX_FILENAME_LENGTH', 180);
+
 include(SERVER_ROOT.'/classes/validate.class.php');
 include(SERVER_ROOT.'/classes/feed.class.php');
 include(SERVER_ROOT.'/sections/torrents/functions.php');
 $Validate = new VALIDATE;
 $Feed = new FEED;
 
-define('QUERY_EXCEPTION', true); // Shut up debugging
-
 //*****************************************************************************//
 //--------------- Set $Properties array ---------------------------------------//
 // This is used if the form doesn't validate, and when the time comes to enter //
 $Properties = [];
 $Type = $Categories[(int)$_POST['type']];
 $TypeID = $_POST['type'] + 1;
+
 $Properties['CategoryID'] = $TypeID;
 $Properties['CategoryName'] = $Type;
 $Properties['Title'] = $_POST['title'];