Many small pre-update fixes

classes/config.template.php

@@ -55,15 +55,15 @@ ENV::setPub('DEV', true);
 ENV::setPub(
     'SITE_NAME',
     (!$ENV->DEV
-        ? 'BioTorrents.de' # Production
-        : '[Dev] BioTorrents.de') # Development
+        ? 'torrents.bio' # Production
+        : 'dev.torrents.bio') # Development
 );
 
 # Meta description
 ENV::setPub('DESCRIPTION', 'A platform to share biological sequence and medical imaging data');
 
 # Navigation glyphs
-ENV::setPub('SEP', '⸬'); # e.g., News ⸬ BioTorrents.de
+ENV::setPub('SEP', '-'); # e.g., News ⸬ BioTorrents.de
 ENV::setPub('CRUMB', '›'); # e.g., Forums › Board › Thread
 
 # The FQDN of your site, e.g., dev.biotorrents.de
@@ -80,6 +80,15 @@ ENV::setPub(
         : 'dev.biotorrents.de') # Development
 );
 
+# Old domain, to handle the biotorrents.de => torrents.bio migration
+# If not needed, simply set to the same values as $ENV->SITE_DOMAIN
+ENV::setPub(
+    'OLD_SITE_DOMAIN',
+    (!$ENV->DEV
+        ? 'biotorrents.de' # Production
+        : 'dev.biotorrents.de') # Development
+);
+
 # The FQDN of your image host, e.g., pics.biotorrents.de
 ENV::setPub('IMAGE_DOMAIN', 'pics.biotorrents.de');
 

classes/security.class.php

@@ -21,7 +21,8 @@ class Security
     {
         foreach ($IDs as $ID) {
             if (!ID || !is_int($ID) || $ID < 1) {
-                error("Expected an integer > 1, got $ID in Security::checkInt.");
+                return "Expected an integer > 1, got $ID in Security::checkInt.";
+                #error("Expected an integer > 1, got $ID in Security::checkInt.");
             }
         }
 

classes/text.class.php

@@ -137,7 +137,7 @@ class Text
     public function fix_links($Parsed) {
             # Replace links to $ENV->SITE_DOMAIN
             $Parsed = preg_replace(
-                "/<a href=\"$ENV->RESOURCE_REGEX$ENV->SITE_DOMAIN\//",
+                "/<a href=\"$ENV->RESOURCE_REGEX($ENV->SITE_DOMAIN|$ENV->OLD_SITE_DOMAIN)\//",
                 '<a href="/',
                 $Parsed
             );

classes/util.php

@@ -508,7 +508,12 @@ function json_print($Status, $Message)
         $response = ['status' => $Status, 'response' => []];
     }
 
-    print(json_encode(add_json_info($response)));
+    print(
+        json_encode(
+            add_json_info($response),
+            JSON_UNESCAPED_SLASHES
+        )
+    );
 }
 
 /**

design/privateheader.php

@@ -333,11 +333,13 @@ if (isset(G::$LoggedUser['SearchType']) && G::$LoggedUser['SearchType']) { // Ad
             size="17">
         </form>
 
+        <!--
         <form class="search_form" name="artists" action="artist.php" method="get">
-          <input id="artistsearch" <?=Users::has_autocomplete_enabled('search')?>
+          <input id="artistsearch" <?=null#Users::has_autocomplete_enabled('search')?>
           aria-label="Search authors" accesskey="a" spellcheck="false" autocomplete="off" placeholder="Authors"
           type="text" name="artistname" size="17">
         </form>
+          -->
 
         <form class="search_form" name="requests" action="requests.php" method="get">
           <input id="requestssearch" aria-label="Search requests" spellcheck="false" autocomplete="off"

readme.md

@@ -25,7 +25,7 @@ BioTorrents.de supports an array of
 with the appropriate bold/italic glyphs and monospace.
 These options are available to every theme.
 Font Awesome 5 is also universally available.
-[Download the fonts](https://docs.biotorrents.de/dl/fonts.tgz).
+[Download the fonts](https://torrents.bio/fonts.tgz).
 
 ## Markdown support
 

sections/api/torrents/group.php

@@ -81,15 +81,15 @@ $JsonTorrentDetails = [
     'id'            => (int) $TorrentDetails['id'],
     'identifier'    => $TorrentDetails['identifier'],
 
-    'category_id'   => (int) $TorrentDetails['category_id'],
-    'category_name' => $CategoryName,
+    'categoryId'   => (int) $TorrentDetails['category_id'],
+    'categoryName' => $CategoryName,
 
     'title'         => $TorrentDetails['title'],
     'subject'       => $TorrentDetails['subject'],
     'object'        => $TorrentDetails['object'],
 
     'authors'       => $Artists,
-    'published'     => (int) $TorrentDetails['published'],
+    'year'          => (int) $TorrentDetails['year'],
     'workgroup'     => $TorrentDetails['workgroup'],
     'location'      => $TorrentDetails['location'],
 
@@ -99,7 +99,7 @@ $JsonTorrentDetails = [
     'description'   => $TorrentDetails['description'],
    #'description'   => Text::full_format($TorrentDetails['description']),
     'picture'       => $TorrentDetails['picture'],
-    'tag_list'      => $TagList,
+    'tagList'      => $TagList,
 
     'bookmarked'    => Bookmarks::has_bookmarked('torrent', $GroupID),
     'timestamp'     => $TorrentDetails['timestamp'],
@@ -128,7 +128,7 @@ foreach ($TorrentList as $Torrent) {
     # todo: Update DB schema
     $JsonTorrentList[] = [
         'id'           => (int) $Torrent['ID'],
-        'info_hash'    => $Torrent['InfoHash'],
+        'infoHash'    => $Torrent['InfoHash'],
         'description'  => $Torrent['Description'],
 
         'platform'     => $Torrent['Media'],
@@ -139,19 +139,19 @@ foreach ($TorrentList as $Torrent) {
 
         'size'         => (int) $Torrent['Size'],
         'archive'      => $Torrent['Archive'],
-        'file_count'   => (int) $Torrent['FileCount'],
-        'file_path'    => $Torrent['FilePath'],
-        'file_list'    => $FileList,
+        'fileCount'   => (int) $Torrent['FileCount'],
+        'filePath'    => $Torrent['FilePath'],
+        'fileList'    => $FileList,
 
         'seeders'      => (int) $Torrent['Seeders'],
         'leechers'     => (int) $Torrent['Leechers'],
         'snatched'     => (int) $Torrent['Snatched'],
-        'free_torrent' => ($Torrent['FreeTorrent'] === 1),
+        'freeTorrent' => ($Torrent['FreeTorrent'] === 1),
 
         'reported'     => (bool) $Torrent['Reported'],
         'time'         => $Torrent['Time'],
 
-        'user_id'      => (int) ($Torrent['Anonymous'] ? 0 : $Torrent['UserID']),
+        'userId'      => (int) ($Torrent['Anonymous'] ? 0 : $Torrent['UserID']),
         'username'     => ($Torrent['Anonymous'] ? 'Anonymous' : $Userinfo['Username']),
     ];
 }

sections/api/torrents/torrent.php

@@ -1,5 +1,5 @@
 <?php
-declare(strict_types=1);
+#declare(strict_types=1);
 
 require_once SERVER_ROOT.'/sections/torrents/functions.php';
 
@@ -54,13 +54,13 @@ $JsonTorrentDetails = [
   'subject'     => $TorrentDetails['subject'],
   'object'       => $TorrentDetails['object'],
   'authors'      => $Artists,
-  'published'         => (int) $TorrentDetails['published'],
+  'year'         => (int) $TorrentDetails['published'],
   'identifier'    => $TorrentDetails['identifier'],
-  'category_id'   => (int) $TorrentDetails['category_id'],
-  'icategory_name' => $CategoryName,
+  'categoryId'   => (int) $TorrentDetails['category_id'],
+  'icategoryName' => $CategoryName,
   'timestamp'         => $TorrentDetails['timestamp'],
   'bookmarked' => Bookmarks::has_bookmarked('torrent', $GroupID),
-  'tag_list'         => $TagList
+  'tagList'         => $TagList
 ];
 
 $Torrent = $TorrentList[$TorrentID];

sections/forums/search.php

@@ -229,7 +229,7 @@ if (empty($ThreadID)) {
     </tr>
     <tr>
       <td colspan="2" class="center">
-        <input type="submit" value="Search" />
+        <input type="submit" class="button-primary" value="Search" />
       </td>
     </tr>
     </table>

sections/torrents/functions.php

@@ -81,7 +81,7 @@ function get_group_info($GroupID, $Return = true, $RevisionID = 0, $PersonalProp
           `id`,
           `user_id`,
           `timestamp`,
-          `resource`
+          `uri`
         FROM
           `torrents_mirrors`
         WHERE

sections/upload/upload_handle.php

@@ -710,7 +710,7 @@ if (!empty($T['Mirrors'])) {
     foreach ($Mirrors as $Mirror) {
         $DB->query(
             "
-        INSERT INTO torrents_mirrors
+        INSERT INTO `torrents_mirrors`
           (`torrent_id`, `user_id`, `timestamp`, `uri`)
         VALUES (?, ?, NOW(), ?)",
             $TorrentID,

sections/user/edit.php

@@ -156,7 +156,7 @@ $ProfileRewards = Donations::get_profile_rewards($UserID);
           </li>
 
           <li>
-            <input type="submit" id="submit" value="Save profile" />
+            <input type="submit" id="submit" class="button-primary" value="Save profile" />
           </li>
 
         </ul>
@@ -313,7 +313,7 @@ HTML;
           <td>
             <label>
               <input type="checkbox" name="autoload_comm_stats" <?Format::selected(
-              'AutoloadCommStats' ,
+              'AutoloadCommStats',
               1,
               'checked',
               $SiteOptions

static/styles/beluga/scss/beluga.scss

@@ -3,107 +3,6 @@
     padding: 0;
 }
 
-.cats_sequences,
-.cats_graphs,
-.cats_systems,
-.cats_geometric,
-.cats_scalars\/vectors,
-.cats_patterns,
-.cats_constraints,
-.cats_images,
-.cats_spatial,
-.cats_models,
-.cats_documents,
-.cats_machinedata {
-    width: 38px !important;
-    height: 38px !important;
-    line-height: 38px;
-}
-
-.cats_sequences:after {
-    content: "SEQ";
-    color: #3eaca7;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_graphs:after {
-    content: "GRF";
-    color: #1d818e;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_systems:after {
-    content: "SYS";
-    color: #88c796;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_geometric:after {
-    content: "GEO";
-    color: #4dc593;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_scalars\/vectors:after {
-    content: "MC2";
-    color: #77c5d4;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_patterns:after {
-    content: "PAT";
-    color: #0d5968;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_constraints:after {
-    content: "CNST";
-    color: #3eaca7;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_images:after {
-    content: "IMG";
-    color: #1d818e;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_spatial:after {
-    content: "SPTL";
-    color: #88c796;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_models:after {
-    content: "MOD";
-    color: #4dc593;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_documents:after {
-    content: "DOC";
-    color: #77c5d4;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
-.cats_machinedata:after {
-    content: "RAW";
-    color: #0d5968;
-    font-size: 18px;
-    letter-spacing: -2px;
-}
-
 body {
     width: 100%;
     font-family: "Open Sans", Helvetica, Arial, Tahoma, sans-serif;
@@ -197,6 +96,33 @@ input {
     color: #fff;
 }
 
+/* Buttons */
+button:not(.editor-toolbar button),
+input[type="button"],
+input[type="submit"] {
+    background: change-color(whitesmoke, $alpha: 0.75);
+    color: black;
+    border: 1px solid #bbb;
+
+    &.button-primary {
+        background: #50aca7;
+        border: 1px solid #bbb;
+        color: black;
+    }
+
+    &:hover {
+        background: #317f8e;
+        /* Primary hover default blue */
+        border: 1px solid #bbb !important;
+        color: black !important;
+    }
+
+    &:focus {
+        background: #2f707c;
+    }
+}
+
+/*
 button,
 input[type="button"],
 input[type="submit"] {
@@ -216,6 +142,7 @@ input[type="button"]:focus,
 input[type="submit"]:focus {
     background-color: #2f707c;
 }
+*/
 
 .spoilerButton {
     max-width: 604px;
@@ -351,11 +278,13 @@ ul.thin li {
     padding-top: 0;
 }
 
+/*
 .sidebar {
     float: right;
     width: 244px;
     height: 100%;
 }
+*/
 
 .sidebar .box .pad form {
     padding-bottom: 20px;
@@ -366,10 +295,12 @@ ul.thin li {
     padding: 5px 10px 10px 10px;
 }
 
+/*
 .main_column {
     width: 646px;
     float: left;
 }
+*/
 
 #logo {
     width: 900px;
@@ -386,7 +317,7 @@ ul.thin li {
 }
 
 #logo a::before {
-    content: "BioTorrents.de";
+    content: "torrents.bio";
     font-size: 40px;
     line-height: 56px;
     font-weight: 100;
@@ -1433,11 +1364,6 @@ blockquote {
     padding: 10px;
 }
 
-blockquote,
-pre {
-    background-color: #23252a !important;
-}
-
 .signature {
     border-top: 1px dotted #666;
     margin: 2em 0 0;
@@ -1534,11 +1460,17 @@ ul .invitetree {
 
 pre {
     color: #fff;
-    border: 1px dashed #55585f;
+    background: black;
+    border: 1px dashed #55585f !important;
     margin: 10px;
     padding: 10px;
 }
 
+code {
+    background: black;
+    border: none;
+}
+
 #donation {
     position: absolute;
     display: inline;
@@ -1901,6 +1833,7 @@ div#gift {
     z-index: 999;
 }
 
+/*
 .button {
     border: 0 solid #131313;
     color: #eee;
@@ -1911,6 +1844,7 @@ div#gift {
     text-transform: uppercase;
     padding: 5px 12px;
 }
+*/
 
 #store #content {
     position: relative;
@@ -2312,6 +2246,32 @@ body.style_pink ::-moz-selection {
     background: #8b518e;
 }
 
+/* Buttons */
+body.style_pink button:not(.editor-toolbar button),
+body.style_pink input[type="button"],
+body.style_pink input[type="submit"] {
+    color: black;
+    border: 1px solid #bbb;
+
+    &.button-primary {
+        background: #8b518e;
+        border: 1px solid #bbb;
+        color: black;
+    }
+
+    &:hover {
+        background: #643c72;
+        /* Primary hover default blue */
+        border: 1px solid #bbb !important;
+        color: black !important;
+    }
+
+    &:focus {
+        background: #78467f;
+    }
+}
+
+/*
 body.style_pink button,
 body.style_pink input[type="button"],
 body.style_pink input[type="submit"] {
@@ -2329,6 +2289,7 @@ body.style_pink input[type="button"]:focus,
 body.style_pink input[type="submit"]:focus {
     background-color: #78467f;
 }
+*/
 
 body.style_pink #userinfo_stats {
     color: #db7bc7;

static/styles/bookish/matcha/matcha.scss

@@ -45,7 +45,6 @@ body.style_matcha {
         width: 100%;
         z-index: 99999;
         margin-top: 2.4em;
-        /* margin-top: 32px; */
         left: 0;
     }
 
@@ -172,59 +171,26 @@ body.style_matcha {
         z-index: 100;
     }
 
-    /* Alerts, Toolbox, etc. */
-    .alertbar {
-        background-color: #fff9c7;
-        text-align: center;
-        color: black;
-        font-weight: bold;
-        width: 320px;
-        margin: 2em auto;
-        padding: 1em;
-
-        a {
-            color: black;
-            text-decoration: none;
-
-            &:hover {
-                color: black;
-                text-decoration: underline;
-            }
-        }
-
-        .warning {
-            background-color: #ffe68a;
-        }
-
-        .error {
-            background-color: #ff8a8a;
-        }
-    }
-
     /* Column heads */
-    .head {
-        background: #9fedd7;
-        color: black;
-        padding: 0.5em 1em;
-    }
-
-    .colhead {
-        background: #9fedd7;
-        font-weight: bold;
-        color: black;
-    }
-
+    .head,
+    .colhead,
     .colhead_dark {
         background: #9fedd7;
+        border-bottom: 2px solid change-color(black, $alpha: 0.25);
         color: black;
+        padding: 0.5em 1em;
     }
 
     /* Box */
     .box,
-    section {
+    .pad,
+    section,
+    /* Exceptions, fixes, etc. */
+    table.user_options {
         background-color: white;
         border: none;
         margin-bottom: 1em;
+        padding: 0.5rem;
     }
 
     /* Shadows */
@@ -236,7 +202,7 @@ body.style_matcha {
     .forum_index,
     #userinfo_minor > li > ul,
     .permissions table {
-        box-shadow: 2px 2px 10px -2px slategray;
+        box-shadow: 0 5px 4px -4px slategray;
     }
 
     /* Links */
@@ -282,21 +248,24 @@ body.style_matcha {
     button:not(.editor-toolbar button),
     input[type="button"],
     input[type="submit"] {
-        background: #fbe180;
-        border-radius: 0.25rem;
+        color: black;
+        border: 1px solid #bbb;
         box-shadow: 2px 2px 10px -5px slategray;
-    }
 
-    button:hover,
-    input[type="button"]:hover,
-    input[type="submit"]:hover {
-        background: #fff9c7;
-    }
+        &.button-primary {
+            background: #fbe180;
+        }
 
-    button:focus,
-    input[type="button"]:focus,
-    input[type="submit"]:focus {
-        background: #fff9c7;
+        &:hover {
+            background: #fff9c7;
+            /* Primary hover default blue */
+            border: 1px solid #bbb;
+            color: black;
+        }
+
+        &:focus {
+            background: #fff9c7;
+        }
     }
 
     /* Text input */
@@ -363,9 +332,4 @@ body.style_matcha {
     .forum_post.sticky_post {
         border: 2px solid #fbe180;
     }
-
-    /* Inbox */
-    tr.unreadpm {
-        background-color: #fff9c7;
-    }
 } /* end body.style_matcha */

static/styles/bookish/scss/layout.scss

@@ -12,7 +12,6 @@
 #content {
     margin: auto;
     margin-top: 2rem;
-    /* min-width: 720px; */
     overflow: hidden;
     width: 90%;
 }
@@ -44,34 +43,6 @@
     }
 }
 
-/* Main column and sidebar */
-@mixin column-flex($width) {
-    display: flex;
-    flex-direction: column;
-    align-items: stretch;
-    max-width: $width;
-    min-height: 0;
-    padding: 0 0.25rem;
-}
-
-.main_column {
-    @include column-flex(64%);
-
-    table {
-        margin-bottom: 1rem;
-    }
-}
-
-.sidebar {
-    @include column-flex(34%);
-    float: right;
-}
-
-/* Box: soon to be <section> */
-.box {
-    margin-bottom: 1rem;
-}
-
 /* Links */
 div.linkbox {
     text-align: center;

static/styles/global/scss/layout.scss

@@ -7,6 +7,50 @@
     padding: 0;
 }
 
+/**
+ * Main column and sidebar
+ */
+
+/* Main column and sidebar */
+@mixin column-flex($width) {
+    display: flex;
+    flex-direction: column;
+    align-items: stretch;
+    max-width: $width;
+    min-height: 0;
+    padding: 0 0.25rem;
+}
+
+.main_column {
+    @include column-flex(64%);
+
+    table {
+        margin-bottom: 1rem;
+    }
+}
+
+.sidebar {
+    @include column-flex(34%);
+    width: 34%;
+    float: right;
+
+    &.fixed {
+        width: 34%;
+    }
+}
+
+.sidebar {
+    float: right;
+    width: 30%;
+    min-width: 20%;
+    margin-right: 1rem;
+}
+
+/* Box: soon to be <section> */
+.box {
+    margin-bottom: 1rem;
+}
+
 /*
  * Flex elements
  */

static/styles/global/scss/skeleton-fixes.scss

@@ -91,6 +91,7 @@ legend {
 /* forum lists */ table.forum_index,
 /* notif filters */ form[name="notification"],
 /* service stats */ div.permission_container,
+/* user settings */ table.user_options,
 /* GENERIC */ table.skeleton-fix {
     td {
         border-bottom: 0 !important;
@@ -130,7 +131,7 @@ code {
 }
 
 /* Unordered lists */
-ul {
+ul:not(.nobullet) {
     list-style: circle outside !important;
 }
 

static/styles/oppai/scss/oppai.scss

@@ -35,6 +35,33 @@ a:hover {
     color: #555;
 }
 
+/* Buttons */
+button:not(.editor-toolbar button),
+input[type="button"],
+input[type="submit"] {
+    color: black;
+    border: 1px solid #bbb;
+    box-shadow: 0 1px 1px 0 rgba(0, 0, 0, 0.14), 0 3px 1px -2px rgba(0, 0, 0, 0.2), 0 1px 5px 0 rgba(0, 0, 0, 0.12);
+
+    &.button-primary {
+        background: #eaabed;
+        border: 1px solid #bbb;
+        color: black;
+    }
+
+    &:hover {
+        background: #e197e5 !important;
+        /* Primary hover default blue */
+        border: 1px solid #bbb !important;
+        color: black !important;
+    }
+
+    &:focus {
+        background: #d48dd8;
+    }
+}
+
+/*
 button,
 input[type="button"],
 input[type="submit"] {
@@ -53,6 +80,7 @@ input[type="button"]:focus,
 input[type="submit"]:focus {
     background: #d48dd8;
 }
+*/
 
 .spoilerButton {
     max-width: 540px;
@@ -546,11 +574,6 @@ div.linkbox {
     padding-top: 0px;
 }
 
-.sidebar {
-    float: right;
-    width: 245px;
-}
-
 .head {
     padding: 4px;
     /* border-bottom: 1px solid #666; */
@@ -563,8 +586,8 @@ div.linkbox {
     padding: 3px 10px 10px 10px;
 }
 
-.main_column {
-    width: 592px;
+#content {
+    max-width: 67%;
 }
 
 .main_column table {

templates/legal/about.html

@@ -3,6 +3,8 @@
 <section class="tldr">
   <p>
     BioTorrents.de is a functional experiment in comfy data distribution.
+    The tagline is "What.cd for genome sequences."
+    The scope is multidisciplinary and social science friendly.
   </p>
 
   <p>
@@ -12,9 +14,10 @@
   </p>
 
   <p>
-    BioTorrents.de provides an open platform for disadvantaged researchers to host their data.
+    BioTorrents.de is an open platform for disadvantaged researchers to host their data.
     More importantly, it provides the necessary tools for others to find and cite it later.
     It's a place for the Google Drives, FTP folders, and network shares that may not be accepted elsewhere.
+    It also plays well with institutional repositories and can efficiently mirror their data.
   </p>
 
   <p>
@@ -27,7 +30,7 @@
       Email
     </strong>
     <br />
-    help at biotorrents dot de
+    hello at torrents dot bio 
   </p>
 
   <p>

templates/legal/dmca.html

@@ -3,8 +3,8 @@
 <section class="tldr">
   <p>
     <em>If</em> you're a copyright owner or an agent of one,
-    <em>and</em> you believe that user-generated content on the domain
-    https://biotorrents.de infringes your copyrights:
+    <em>and</em> you reasonably believe that user-generated content on the domains
+    torrents.bio or biotorrents.de infringes your copyrights:
     <em>then</em> you may notify our Digital Millennium Copyright Act (DMCA) agent in writing.
   </p>
 
@@ -69,7 +69,7 @@
       Email
     </strong>
     <br />
-    dmca at biotorrents dot de
+    dmca at torrents dot bio 
   </p>
 
   <p>

templates/legal/privacy.html

@@ -188,7 +188,7 @@
   </h3>
 
   <p>
-    We last updated this policy on 2021-07-14.
+    We last updated this policy on 2021-07-28.
   </p>
 
 
@@ -220,7 +220,7 @@
       Email
     </strong>
     <br />
-    privacy at biotorrents dot de
+    privacy at torrents dot bio 
   </p>
 
   <p>